GLB1 Research Articles

A GM1 gangliosidosis mutant mouse model exhibits activated microglia and disturbed autophagy.

GM1 gangliosidosis is a rare lysosomal storage disease caused by a deficiency of β-galactosidase due to mutations in the GLB1 gene. We established a C57BL/6 mouse model with Glb1G455R mutation using CRISPR/Cas9 genome editing. The β-galactosidase enzyme activity of Glb1G455R mice measured by fluorometric assay was negligible throughout the whole body. Mutant mice displayed no marked phenotype at eight weeks. After 16 weeks, GM1 ganglioside accumulation in the brain of mutant mice was observed by immunohistochemical staining. Meanwhile, a declining performance in behavioral tests was observed among mutant mice from 16 to 32 weeks. As the disease progressed, the neurological symptoms of mutant mice worsened, and they then succumbed to the disease by 47 weeks of age. We also observed microglia activation and proliferation in the cerebral cortex of mutant mice at 16 and 32 weeks. In these activated microglia, the level of autophagy regulator LC3 was up-regulated but the mRNA level of LC3 was normal. In conclusion, we developed a novel murine model that mimicked the chronic phenotype of human GM1. This Glb1G455R murine model is a practical in vivo model for studying the pathogenesis of GM1 gangliosidosis and exploring potential therapies.

Morquio B disease: From pathophysiology towards diagnosis

Morquio B disease is an attenuated phenotype within the spectrum of beta galactosidase (GLB1) deficiencies. It is characterised by dysostosis multiplex, ligament laxity, mildly coarse facies and heart valve defects due to keratan sulphate accumulation, predominantly in the cartilage. Morquio B patients have normal neurological development, setting them apart from those with the more severe GM1 gangliosidosis.Morquio B disease, with an incidence of 1:250.000 to 1:1.000.000 live births, is very rare. Here we report the clinical-biochemical data of nine patients. High amounts of keratan sulfate were detected using LC-MS/MS in the patients' urinary samples, while electrophoresis, the standard procedure of qualitative glycosaminoglycans analysis, failed to identify this metabolite in any of the patients' samples.We performed molecular analyses at gene, gene expression and protein expression levels, for both isoforms of the GLB1 gene, lysosomal GLB1, and the cell-surface expressed Elastin Binding Protein. We characterised three novel GLB1 mutations [c.75 + 2 T > G, c.575A > G (p.Tyr192Cys) and c.2030 T > G (p.Val677Gly)] identified in three heterozygous patients. We also set up a copy number variation assay by quantitative PCR to evaluate the presence of deletions/ insertions in the GLB1 gene.We propose a diagnostic plan, setting out the specific clinical- biochemical and molecular features of Morquio B, in order to avoid misdiagnoses and improve patients' management.

Clinical Features of Infantile GM1 Gangliosidosis: Report of an Iranian Patient

Background: GM1 gangliosidosis is an autosomal recessive lysosomal storage disease due to a lack of β-galactosidase activity, exactly because of mutations in the GLB1 gene. GM1 gangliosidosis is a rare disease that could occur either during infancy (infantile type 1), as a juvenile (type 2), or in adulthood (type 3) in both nervous and skeletal systems. Type 1 is characterized by premature psychomotor deterioration, visceromegaly, macular cherry-red spot, skeletal deformities, and death in the first 2 years of life. Case Presentation: We reported an Iranian infant who, on initial check-up, had coarse face, visceromegaly, dystonia, and hepatosplenomegaly that increased at 15 months of age. At the initial check-up, a genetic test was performed and GM1 gangliosidosis type 1 was diagnosed. Conclusion: infant form is characterized by early-onset before the age of 6 months and rapidly progressive psychomotor deterioration, facial abnormalities, and visceromegaly.

Genetic Assessment of Mucopolysaccharidosis Type IV and the First Pathological Mutation of c.313A>G in the Iranian Population

Aims Morquio syndrome is a mucopolysaccharidosis (type 4) that has autosomal recessive inheritance. Moreover, it is caused by defects in the two genes; GALNS (Murcio A) and GLB1 (Murcio B). The prevalence rate of this condition is estimated to be about 1 per 200000 live births globally. Besides, Middle Eastern cases shape the greatest ratio, due to higher rates of consanguineous marriages. The most frequent clinical manifestations of the disease include skeletal abnormalities, hearing and vision problems, decreased physical growth, and cardiac malformations. Methods & Materials This study investigated the pathogenic mutations in two Iranian individuals. Both cases were the result of consanguineous marriages with mucopolysaccharidosis type 4 (A or B types, each). Following of genomic DNA extraction, Whole Exome Sequencing was conducted for the study patients. Then, for the validation of observed pathogenic mutations, sanger sequencing was performed for the patients. Findings Two explored patients demonstrated homozygote mutations. Mutation analysis of the GLB1 gene revealed c.443G>A mutation in one patient and GALNS gene c.313A>G in the other. Conclusion Two pathogenic mutations in GLB1 and GALNS gene were found in 2 Iranian patients in this study. The NGS was a desirable and reliable technique for detecting these two mutations. The c.313A> G mutation in the GALNS gene was novel and had not been reported in the world.

In‐vivo synthesis of GM1 Ganglioside through CRISPR‐Cas9 mutation in CHO‐K1, Chinese hamster ovary cells (Cricetulus griseus)

GM1 ganglioside has been shown to have therapeutic properties against, Parkinson’s disease, Alzheimer’s, dementia and with dramatic results in Huntington’s Disease (Holler, et al., 2016). Studies also show recovery in CNS related injuries with GM1 therapy (Karpiak et al., 1986). New studies continue to confirm GM1 gangliosides therapeutic properties and may increase the need for GM1 ganglioside. Currently, large scale, synthesis of this ganglioside involves isolation from a natural product. New synthesis methods, such as chemical synthesis, yields an insignificant quantity for alternative large‐scale production (Aureli et al., 2015). Research presented here attempts to address a new method of large‐scale production by in vivo synthesis of GM1 ganglioside through a CRISPR‐Cas9 induced mutation in Chinese Hamster Ovary cells (CHO‐K1) by introducing the mutation of the GLB1 gene that causes a substantial accumulation of GM1 in cells known as GM1 gangliosidosis. In‐vivo synthesis provides relief from natural product isolation and may be cost effective to chloroform: methanol protocols while providing similar results.Support or Funding InformationThis material is based upon work supported by the National Science Foundation/EPSCoR Cooperative Agreement #OIA‐1849206 and by the State of South Dakota, SD‐GOED, NSF I‐Corps Team program and Dr. Larry and Sue Holler, GlycoScience Research Incorporated

Specific role of N-methyl-D-aspartate (NMDA) receptor in elastin-derived VGVAPG peptide-dependent calcium homeostasis in mouse cortical astrocytes in vitro

Under physiological and pathological conditions, elastin is degraded to produce elastin-derived peptides (EDPs). EDPs are detected in the healthy human brain, and its concentration significantly increases after ischemic stroke. Both elastin and EDPs contains replications of the soluble VGVAPG hexapeptide, which has a broad range of biological activities. Effects of VGVAPG action are mainly mediated by elastin-binding protein (EBP), which is alternatively spliced, enzymatically inactive form of the GLB1 gene. This study was conducted to elucidate the activation and role of the N-methyl-D-aspartate receptor (NMDAR) in elastin-derived VGVAPG peptide-dependent calcium homeostasis in mouse cortical astrocytes in vitro. Cells were exposed to 10 nM VGVAPG peptide and co-treated with MK-801, nifedipine, verapamil, or Src kinase inhibitor I. After cell stimulation, we measured Ca2+ level, ROS production, and mRNA expression. Moreover, the Glb1 and NMDAR subunits (GluN1, GluN2A, and GluN2B) siRNA gene knockdown were applied. We found the VGVAPG peptide causes Ca2+ influx through the NMDA receptor in mouse astrocytes in vitro. Silencing of the Glb1, GluN1, GluN2A, and GluN2B gene prevented VGVAPG peptide-induced increase in Ca2+. Nifedipine does not completely reduce VGVAPG peptide-activated ROS production, whereas MK-801, verapamil, and Src inhibitor reduce VGVAPG peptide-activated Ca2+ influx and ROS production. These data suggest the role of Src kinase signal transduction from EBP to NMDAR. Moreover, the VGVAPG peptide affects the expression of NMDA receptor subunits.

Elastin-derived peptide VGVAPG affects the proliferation of mouse cortical astrocytes with the involvement of aryl hydrocarbon receptor (Ahr), peroxisome proliferator-activated receptor gamma (Pparγ), and elastin-binding protein (EBP)

During aging and ischemic and hemorrhagic stroke, elastin molecules are degraded and elastin-derived peptides are released into the brain microenvironment. Val-Gly-Val-Ala-Pro-Gly (VGVAPG) is a repeating hexapeptide in the elastin molecule. It is well documented that the peptide sequence binds with high affinity to elastin-binding protein (EBP) located on the cell surface, thereby transducing a molecular signal into the cell. The aim of our study was to investigate whether EBP, aryl hydrocarbon receptor (Ahr), and peroxisome proliferator-activated receptor gamma (Pparγ) are involved in VGVAPG-stimulated proliferation. Primary astrocytes were maintained in DMEM/F12 medium without phenol red, supplemented with 10 or 1% charcoal/dextran-treated fetal bovine serum (FBS). The cells were exposed to increasing concentrations of VGVAPG peptide, and resazurin reduction was measured. In addition, Glb1, Pparγ, and Ahr genes were silenced. After 48 h of exposure to 10 nM and 1 µM of VGVAPG peptide, the level of estradiol (E2) and the expression of Ki67 and S100B proteins were measured. The results showed that at a wide range of concentrations, VGVAPG peptide increased the metabolism of astrocytes depending on the concentration of FBS. After silencing of Glb1, Pparγ, and Ahr genes, VGVAPG peptide did not affect the cell metabolism which suggests the involvement of all the mentioned receptors in its mechanism of action. Interestingly, in the low-FBS medium, the silencing of Glb1 gene did not result in complete inhibition of VGVAPG-stimulated proliferation. On the other hand, in the medium with 10% FBS VGVAPG increased Ki67 expression after Pparγ silencing, whereas in the medium with 1% FBS VGVAPG decreased Ki67 expression. Following the application of Ahr siRNA, VGVAPG peptide decreased the production of E2 and increased the expression of Ki67 and S100B proteins.

Characterization of glycan substrates accumulating in GM1 Gangliosidosis

IntroductionGM1 gangliosidosis is a rare autosomal recessive genetic disorder caused by the disruption of the GLB1 gene that encodes β-galactosidase, a lysosomal hydrolase that removes β-linked galactose from the non-reducing end of glycans. Deficiency of this catabolic enzyme leads to the lysosomal accumulation of GM1 and its asialo derivative GA1 in β-galactosidase deficient patients and animal models. In addition to GM1 and GA1, there are other glycoconjugates that contain β-linked galactose whose metabolites are substrates for β-galactosidase. For example, a number of N-linked glycan structures that have galactose at their non-reducing end have been shown to accumulate in GM1 gangliosidosis patient tissues and biological fluids. ObjectiveIn this study, we attempt to fully characterize the broad array of GLB1 substrates that require GLB1 for their lysosomal turnover. ResultsUsing tandem mass spectrometry and glycan reductive isotope labeling with data-dependent mass spectrometry, we have confirmed the accumulation of glycolipids (GM1 and GA1) and N-linked glycans with terminal beta-linked galactose. We have also discovered a novel set of core 1 and 2 O-linked glycan metabolites, many of which are part of structurally-related isobaric series that accumulate in disease. In the brain of GLB1 null mice, the levels of these glycan metabolites increased along with those of both GM1 and GA1 as a function of age. In addition to brain tissue, we found elevated levels of both N-linked and O-linked glycan metabolites in a number of peripheral tissues and in urine. Both brain and urine samples from human GM1 gangliosidosis patients exhibited large increases in steady state levels for the same glycan metabolites, demonstrating their correlation with this disease in humans as well. ConclusionsOur studies illustrate that GLB1 deficiency is not purely a ganglioside accumulation disorder, but instead a broad oligosaccharidosis that include representatives of many β-linked galactose containing glycans and glycoconjugates including glycolipids, N-linked glycans, and various O-linked glycans. Accounting for all β-galactosidase substrates that accumulate when this enzyme is deficient increases our understanding of this severe disorder by identifying metabolites that may drive certain aspects of the disease and may also serve as informative disease biomarkers to fully evaluate the efficacy of future therapies.

Human GLB1 knockout cerebral organoids: A model system for testing AAV9-mediated GLB1 gene therapy for reducing GM1 ganglioside storage in GM1 gangliosidosis

GM1 gangliosidosis is an autosomal recessive neurodegenerative disorder caused by the deficiency of lysosomal β-galactosidase (β-gal) and resulting in accumulation of GM1 ganglioside. The disease spectrum ranges from infantile to late onset and is uniformly fatal, with no effective therapy currently available. Although animal models have been useful for understanding disease pathogenesis and exploring therapeutic targets, no relevant human central nervous system (CNS) model system has been available to study its early pathogenic events or test therapies. To develop a model of human GM1 gangliosidosis in the CNS, we employed CRISPR/Cas9 genome editing to target GLB1 exons 2 and 6, common sites for mutations in patients, to create isogenic induced pluripotent stem (iPS) cell lines with lysosomal β-gal deficiency. We screened for clones with <5% of parental cell line β-gal enzyme activity and confirmed GLB1 knockout clones using DNA sequencing. We then generated GLB1 knockout cerebral organoids from one of these GLB1 knockout iPS cell clones. Analysis of GLB1 knockout organoids in culture revealed progressive accumulation of GM1 ganglioside. GLB1 knockout organoids microinjected with AAV9-GLB1 vector showed a significant increase in β-gal activity and a significant reduction in GM1 ganglioside content compared with AAV9-GFP–injected organoids, demonstrating the efficacy of an AAV9 gene therapy-based approach in GM1 gangliosidosis. This proof-of-concept in a human cerebral organoid model completes the pre-clinical studies to advance to clinical trials using the AAV9-GLB1 vector.

Genotype-phenotype correlation of gangliosidosis mutations using in silico tools and homology modeling

Gangliosidoses, including GM1-gangliosidosis and GM2-gangliosidosis (Tay-Sachs disease and Sandhoff disease), are lysosomal disorders resulting from enzyme deficiencies and accumulation of gangliosides. Phenotypes of gangliosidoses range from infantile, late-infantile, juvenile, and to the adult form. The genotype-phenotype correlation is essential for prognosis and clinical care planning for patients with a gangliosidosis condition. Previously, we have developed a method to establish the genotype-phenotype correlation of another lysosomal disease, mucopolysaccharidosis type I, with in silico tools. This same method was applied to analyze the genotype and phenotype of 38 patients diagnosed with a gangliosidosis disease in the United States. Out of 40 mutations identified, 3 were novel, including p.Tyr192His and p.Phe556Ser of the GLB1 gene and p.Gly461Val of the HEXA gene. Furthermore, the mutant protein structure of all missense mutations was constructed by homology modeling. A systemic structural analysis of these models revealed the specific mechanisms of how each mutation may lead to the disease. In summary, the method developed in this study holds promise as a tool that can be broadly applicable to other lysosomal diseases and monogenic diseases.

Antiproliferative Effect of Elastin-Derived Peptide VGVAPG on SH-SY5Y Neuroblastoma Cells

Throughout the lifetime of humans, the amount of stem cells and the rate of cell proliferation continue to decrease. Reactive oxygen species (ROS) are one among the many factors that promote stem cell aging. Both a decrease in the level of stem cells and increase in ROS production can lead to the development of different neurodegenerative diseases. This study was conducted to determine how the VGVAPG peptide, liberated from elastin during the aging process and under pathological conditions, affects ROS production and activities of antioxidant enzymes in undifferentiated, proliferating SH-SY5Y cells. SH-SY5Y cells were maintained in Dulbecco’s modified Eagle’s medium/nutrient mixture F-12 supplemented with 10% heat-inactivated fetal bovine serum (FBS). After treating the SH-SY5Y cells with VGVAPG peptide, we measured ROS production; cell metabolism, proliferation, and expression; and activities of superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT). We demonstrated that the VGVAPG peptide increases GPx expression and activity, whereas it decreases CAT expression in SH-SY5Y cells. Silencing of the GLB1 gene prevents changes in GPx activity. Despite the fact that the VGVAPG peptide increases GPx expression, it increases the ROS level. Moreover, the VGVAPG peptide decreases SH-SY5Y proliferation, which is prevented by the ROS scavenger N-acetyl-L-cysteine. Our data suggest that ROS production and decreased proliferation of SH-SY5Y cells are the results of excitotoxicity meditated through close unrecognized molecular pathways. More research is needed to elucidate the unknown mechanism of action of VGVAPG peptide in the nervous system.

CRISPR/Cas9 mediated gene knockout of Glb1 gene in mouse embryonic fibroblasts

BackgroundThe occurrence of mutations at different locations in the Glb1 gene in nerve cells can lead to the deficient activity of a hydrolase enzyme called β-galactosidase 1 in the lysosomal organelle. Therefore, the substrates of this enzyme (gangliosides) aggregate in the cells at toxic levels, leading to the progressive degeneration of nerve cells. Since humans are incapable of repairing the damaged nerve cells, this in itself causes a rare genetic disorder called GM1 gangliosidosis. Doctors are only able to reduce the signs of this disease, and technically, no effective treatment exists capable of eliminating its cause. Recently, using methods based on genome editing, aiming to achieve a more accurate understanding of the basic cellular and molecular mechanisms leading to this disease and find new therapeutic solutions. MethodsIn the current study, specific guide RNAs was designed for exons 2 and 6 of the Glb1 gene, and entered these gRNAs into lenticrispr expression vector containing CRISPR elements. Then, mouse embryonic fibroblast (MEF) cells transferred with recombinant vectors containing our gRNAs. Finally, the generated mutations were investigated via the polymerase chain reaction (PCR) test. ResultsOur results confirmed correct transformation process through colony PCR and Sanger sequencing. Then, by performing PCR test on genomic DNA of puromycin resistant MEF cells, a product band of 824 bp was observed that indicated successful knockout of the Glb1 gene. ConclusionsThe current study was designed as a proof of concept to show possibility of knocking out the Glb1 gene, using designed sgRNAs.

The VGVAPG Peptide Regulates the Production of Nitric Oxide Synthases and Reactive Oxygen Species in Mouse Astrocyte Cells In Vitro

The products of elastin degradation, namely elastin-derived peptides (EDPs), are detectable in the cerebrospinal fluid of healthy individuals and in patients after ischemic stroke, and their number increases with age. Depending on their concentrations, both nitric oxide (NO) and reactive oxygen species (ROS) take part either in myocardial ischemia reperfusion injury or in neurovascular protection after ischemic stroke. The aim of our study was to determine the impact of VGVAPG peptide on ROS and NO production and expression of endothelial nitric oxide synthase (eNos), inducible nitric oxide synthase (iNos) and neuronal nitric oxide synthase (nNos) in mouse cortical astrocytes in vitro. Primary astrocytes were maintained in DMEM/F12 without phenol red supplemented with 10% fetal bovine serum. The cells were exposed to rising VGVAPG peptide concentrations, and ROS and NO production was measured. After 6 h (for mRNA) and 24 (for the protein) of exposure to 10 nM and 1 µM of the peptide, expression of nNos, iNos and eNos was measured. Moreover, the Glb1 siRNA gene knockdown method and Pioglitazone, a peroxisome proliferator-activated receptor gamma (Pparγ) agonist, were applied. Our study shows that the VGVAPG peptide decreased eNos, iNos and nNos mRNA and protein expression in mouse astrocytes in vitro. The VGVAPG peptide also decreased NO production while increasing ROS production in the cells. Furthermore, silencing of the Glb1 gene reversed all effects caused by the VGVAPG peptide. However, due to the lack of sufficient data explaining the molecular mechanism of action of the VGVAPG peptide in the nervous system, more studies in this area are necessary.

Infantile GM1-Gangliosidosis Revealed by Slate-Grey Mongolian Spots

Introduction: GM1-gangliosidosis is an inherited metabolic disease caused by mutations in the GLB1 gene resulting in deficiency of β-galactosidase. Three forms have been identified: Infantile, juvenile, and adult. The infantile type progresses rapidly and aggressively and a delayed diagnosis hampers the prevention of many neurological deficits. This delay in diagnosis may be due to the variability of clinical expression of the disorder. Hypothesis: Extensive Mongolian or slate-grey spots deserve special attention as possible indications of associated inborn errors of metabolism, especially GM1-gangliosidosis and mucopolysaccharidosis. Only symptomatic treatments are available for GM1-gangliosidosis; research is underway. Observation: In this article, we report a case of infantile GM1-gangliosidosis revealed by slate-grey Mongolian spots, a rare condition in Morocco, and a review of the literature. Conclusion: The finding of persistent and extensive slate-grey mongolian spots in infant could lead to early detection of GM1-gangliosidosis before irreversible organ damage occurs.

Dual positive and negative control of Chlamydomonas PII signal transduction protein expression by nitrate/nitrite and NO via the components of nitric oxide cycle

BackgroundThe PII proteins constitute a large superfamily, present in all domains of life. Until now, PII proteins research in Chloroplastida (green algae and land plants) has mainly focused on post-translation regulation of these signal transductors. Emerging evidence suggests that PII level is tightly controlled with regard to the nitrogen source and the physiological state of cells.ResultHere we identify that a balance of positive (nitrate and nitrite) and negative (nitric oxide) signals regulates Chlamydomonas GLB1. We found that PII expression is downregulated by ammonium through a nitric oxide (NO)-dependent mechanism. We show that nitrate reductase (NR) and its partner, truncated hemoglobin 1 (THB1), participate in a signaling pathway for dual control of GLB1 expression. Moreover, NO dependent guanilate cyclase appeared to be involved in the negative control of GLB1 transcription.ConclusionThis study has revealed the existence of the complex GLB1 control at transcription level, which is dependent on nitrogen source. Importantly, we found that GLB1 gene expression pattern is very similar to that observed for nitrate assimilation genes, suggesting interconnecting/coordinating PII-dependent and nitrate assimilation pathways.

Comprehensive behavioral and biochemical outcomes of novel murine models of GM1-gangliosidosis and Morquio syndrome type B

Deficiencies in the lysosomal hydrolase β-galactosidase (β-gal) lead to two distinct diseases: the skeletal disease Morquio syndrome type B, and the neurodegenerative disease GM1-gangliosidosis. Utilizing CRISPR-Cas9 genome editing, the mouse β-gal encoding gene, Glb1, was targeted to generate both models of β-gal deficiency in a single experiment. For Morquio syndrome type B, the common human missense mutation W273L (position 274 in mice) was introduced into the Glb1 gene (Glb1W274L), while for GM1-gangliosidosis, a 20 bp mutation was generated to remove the catalytic nucleophile of β-gal (β-gal−/−). Glb1W274L mice showed a significant reduction in β-gal enzyme activity (8.4–13.3% of wildtype), but displayed no marked phenotype after one year. In contrast, β-gal−/− mice were devoid of β-gal enzyme activity (≤1% of wildtype), resulting in ganglioside accumulation and severe cellular vacuolation throughout the central nervous system (CNS). β-gal−/− mice also displayed severe neuromotor and neurocognitive dysfunction, and as the disease progressed, the mice became emaciated and succumbed to the disease by 10 months of age. Overall, in addition to generating a novel murine model that phenotypically resembles GM1-gangliosidosis, the first model of β-galactosidase deficiency with residual enzyme activity has been developed.

Clinical and molecular characteristics of 11 Chinese probands with GM1 gangliosidosis.

GM1 gangliosidosis is an autosomal recessive lysosomal storage disease caused by the deficiency of β-galactosidase activity, precisely due to mutations in the GLB1 gene. To explore the clinical and molecular characteristics of GM1 gangliosidosis patients from China, GLB1 gene were analyzed in 11 probands with GM1 gangliosidosis by exploiting direct Sanger-sequencing. Among them, five patients were classified as the infantile type and the remaining six as the late-infantile or juvenile type. In these probands, eight novel mutations p.Y50N, p.Y237C, p.S267F, p.G453R, p.K578N, c.618delC, c.475_478delGACA and c.1979_1980insG have been identified. Among them, three novel missense mutations p.Y50N, p.S267F and p.G453R were transiently transfected in COS-7 cells by plasmid system for functional verification. In vitro GLB1 activities carrying the aforesaid missense mutants p.Y50N, p.S267F and p.G453R were 0.11%, 0 and 0.55% of wild-type, respectively. Mutation c.495_497delTCT and p.S149F accounted for 22.7 and 13.6% of the mutant alleles, respectively. Our results expand the spectrum of GLB1 gene, provide new insights into the clinical and molecular characteristics of GM1 gangliosidosis in China.

SAAMP 2.0: An algorithm to predict genotype-phenotype correlation of lysosomal storage diseases.

Lysosomal storage diseases (LSDs) are a group of genetic disorders, resulting from deficiencies of lysosomal enzyme. Genotype-phenotype correlation is essential for timely and proper treatment allocation. Recently, by integrating prediction outcomes of 7 bioinformatics tools, we developed a SAAMP algorithm to predict the impact of individual amino-acid substitution. To optimize this approach, we evaluated the performance of these bioinformatics tools in a broad array of genes. PolyPhen and PROVEAN had the best performances, while SNP&GOs, PANTHER and I-Mutant had the worst performances. Therefore, SAAMP 2.0 was developed by excluding 3 tools with worst performance, yielding a sensitivity of 94% and a specificity of 90%. To generalize the guideline to proteins without known structures, we built the three-dimensional model of iduronate-2-sulfatase by homology modeling. Further, we investigated the phenotype severity of known disease-causing mutations of the GLB1 gene, which lead to 2 LSDs (GM1 gangliosidosis and Morquio disease type B). Based on the previous literature and structural analysis, we associated these mutations with disease subtypes and proposed a theory to explain the complicated genotype-phenotype correlation. Collectively, an updated guideline for phenotype prediction with SAAMP 2.0 was proposed, which will provide essential information for early diagnosis and proper treatment allocation, and they may be generalized to many monogenic diseases.

Genotype, phenotype and in silico pathogenicity analysis of HEXB mutations: Panel based sequencing for differential diagnosis of gangliosidosis

ObjectivesGangliosidosis is an inherited metabolic disorder causing neurodegeneration and motor regression. Preventive diagnosis is the first choice for the affected families due to lack of straightforward therapy. Genetic studies could confirm the diagnosis and help families for carrier screening and prenatal diagnosis. An update of HEXB gene variants concerning genotype, phenotype and in silico analysis are presented. Patients and MethodsPanel based next generation sequencing and direct sequencing of four cases were performed to confirm the clinical diagnosis and for reproductive planning. Bioinformatic analyses of the HEXB mutation database were also performed. ResultsDirect sequencing of HEXA and HEXB genes showed recurrent homozygous variants at c.509G>A (p.Arg170Gln) and c.850C>T (p.Arg284Ter), respectively. A novel variant at c.416T>A (p.Leu139Gln) was identified in the GLB1 gene. Panel based next generation sequencing was performed for an undiagnosed patient which showed a novel mutation at c.1602C>A (p.Cys534Ter) of HEXB gene. Bioinformatic analysis of the HEXB mutation database showed 97% consistency of in silico genotype analysis with the phenotype. Bioinformatic analysis of the novel variants predicted to be disease causing. In silico structural and functional analysis of the novel variants showed structural effect of HEXB and functional effect of GLB1 variants which would provide fast analysis of novel variants. ConclusionsPanel based studies could be performed for overlapping symptomatic patients. Consequently, genetic testing would help affected families for patients’ management, carrier detection, and family planning’s.

Rapid Targeted Genomics in Critically Ill Newborns

Rapid diagnostic whole-genome sequencing has been explored in critically ill newborns, hoping to improve their clinical care and replace time-consuming and/or invasive diagnostic testing. A previous retrospective study in a research setting showed promising results with diagnoses in 57%, but patients were highly selected for known and likely Mendelian disorders. The aim of our prospective study was to assess the speed and yield of rapid targeted genomic diagnostics for clinical application. We included 23 critically ill children younger than 12 months in ICUs over a period of 2 years. A quick diagnosis could not be made after routine clinical evaluation and diagnostics. Targeted analysis of 3426 known disease genes was performed by using whole-genome sequencing data. We measured diagnostic yield, turnaround times, and clinical consequences. A genetic diagnosis was obtained in 7 patients (30%), with a median turnaround time of 12 days (ranging from 5 to 23 days). We identified compound heterozygous mutations in the EPG5 gene (Vici syndrome), the RMND1 gene (combined oxidative phosphorylation deficiency-11), and the EIF2B5 gene (vanishing white matter), and homozygous mutations in the KLHL41 gene (nemaline myopathy), the GFER gene (progressive mitochondrial myopathy), and the GLB1 gene (GM1-gangliosidosis). In addition, a 1p36.33p36.32 microdeletion was detected in a child with cardiomyopathy. Rapid targeted genomics combined with copy number variant detection adds important value in the neonatal and pediatric intensive care setting. It led to a fast diagnosis in 30% of critically ill children for whom the routine clinical workup was unsuccessful.