Sequence and Copy Number Analyses of HEXB Gene in Patients Affected by Sandhoff Disease: Functional Characterization of 9 Novel Sequence Variants
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{"title"=>"Sequence and copy number analyses of HEXB gene in patients affected by sandhoff disease: Functional characterization of 9 novel sequence variants", "type"=>"journal", "authors"=>[{"first_name"=>"Stefania", "last_name"=>"Zampieri", "scopus_author_id"=>"14040966000"}, {"first_name"=>"Silvia", "last_name"=>"Cattarossi", "scopus_author_id"=>"55324344000"}, {"first_name"=>"Ana Maria", "last_name"=>"Ramirez", "scopus_author_id"=>"57198233822"}, {"first_name"=>"Camillo", "last_name"=>"Rosano", "scopus_author_id"=>"7004092715"}, {"first_name"=>"Charles Marques", "last_name"=>"Lourenco", "scopus_author_id"=>"22934659700"}, {"first_name"=>"Nadia", "last_name"=>"Passon", "scopus_author_id"=>"26029964400"}, {"first_name"=>"Isabella", "last_name"=>"Moroni", "scopus_author_id"=>"6602137148"}, {"first_name"=>"Graziella", "last_name"=>"Uziel", "scopus_author_id"=>"7005521533"}, {"first_name"=>"Antonella", "last_name"=>"Pettinari", "scopus_author_id"=>"57195731389"}, {"first_name"=>"Franco", "last_name"=>"Stanzial", "scopus_author_id"=>"6506477301"}, {"first_name"=>"Raquel Dodelson", "last_name"=>"de Kremer", "scopus_author_id"=>"6602479925"}, {"first_name"=>"Nydia Beatriz", "last_name"=>"Azar", "scopus_author_id"=>"55302952400"}, {"first_name"=>"Filiz", "last_name"=>"Hazan", "scopus_author_id"=>"35200763900"}, {"first_name"=>"Mirella", "last_name"=>"Filocamo", "scopus_author_id"=>"7004257534"}, {"first_name"=>"Bruno", "last_name"=>"Bembi", "scopus_author_id"=>"7003606384"}, {"first_name"=>"Andrea", "last_name"=>"Dardis", "scopus_author_id"=>"6602396626"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"pmid"=>"22848519", "sgr"=>"84864417054", "doi"=>"10.1371/journal.pone.0041516", "scopus"=>"2-s2.0-84864417054", "pui"=>"365338911", "issn"=>"19326203"}, "id"=>"88df04ee-457f-332f-b570-6b7a59bc904b", "abstract"=>"Sandhoff disease (SD) is a lysosomal disorder caused by mutations in the HEXB gene. To date, 43 mutations of HEXB have been described, including 3 large deletions. Here, we have characterized 14 unrelated SD patients and developed a Multiplex Ligation-dependent Probe Amplification (MLPA) assay to investigate the presence of large HEXB deletions. Overall, we identified 16 alleles, 9 of which were novel, including 4 sequence variation leading to aminoacid changes [c.626C>T (p.T209I), c.634C>A (p.H212N), c.926G>T (p.C309F), c.1451G>A (p.G484E)] 3 intronic mutations (c.1082+5G>A, c.1242+1G>A, c.1169+5G>A), 1 nonsense mutation c.146C>A (p.S49X) and 1 small in-frame deletion c.1260_1265delAGTTGA (p.V421_E422del). Using the new MLPA assay, 2 previously described deletions were identified. In vitro expression studies showed that proteins bearing aminoacid changes p.T209I and p.G484E presented a very low or absent activity, while proteins bearing the p.H212N and p.C309F changes retained a significant residual activity. The detrimental effect of the 3 novel intronic mutations on the HEXB mRNA processing was demonstrated using a minigene assay. Unprecedentedly, minigene studies revealed the presence of a novel alternative spliced HEXB mRNA variant also present in normal cells. In conclusion, we provided new insights into the molecular basis of SD and validated an MLPA assay for detecting large HEXB deletions.", "link"=>"http://www.mendeley.com/research/sequence-copy-number-analyses-hexb-gene-patients-affected-sandhoff-disease-functional-characterizati", "reader_count"=>10, "reader_count_by_academic_status"=>{"Unspecified"=>2, "Researcher"=>1, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>2, "Other"=>2}, "reader_count_by_user_role"=>{"Unspecified"=>2, "Researcher"=>1, "Student > Doctoral Student"=>1, "Student > Ph. D. Student"=>2, "Student > Postgraduate"=>2, "Other"=>2}, "reader_count_by_subject_area"=>{"Unspecified"=>3, "Agricultural and Biological Sciences"=>2, "Medicine and Dentistry"=>3, "Neuroscience"=>1, "Psychology"=>1}, "reader_count_by_subdiscipline"=>{"Medicine and Dentistry"=>{"Medicine and Dentistry"=>3}, "Neuroscience"=>{"Neuroscience"=>1}, "Psychology"=>{"Psychology"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>2}, "Unspecified"=>{"Unspecified"=>3}}, "group_count"=>0}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/601012"], "description"=>"<p>Chains A and B are drawn as orange and blue ribbons respectively. Positions of mutations are indicated by arrows and the residues represented by spaced-filled spheres.</p>", "links"=>[], "tags"=>["hexb", "mutations", "3d"], "article_id"=>271493, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.g003", "stats"=>{"downloads"=>2, "page_views"=>35, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Location_of_HEXB_mutations_on_the_3D_structural_model_/271493", "title"=>"Location of HEXB mutations on the 3D structural model.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:24:53"}
  • {"files"=>["https://ndownloader.figshare.com/files/314807", "https://ndownloader.figshare.com/files/314880"], "description"=>"<div><p>Sandhoff disease (SD) is a lysosomal disorder caused by mutations in the <em>HEXB</em> gene. To date, 43 mutations of <em>HEXB</em> have been described, including 3 large deletions. Here, we have characterized 14 unrelated SD patients and developed a Multiplex Ligation-dependent Probe Amplification (MLPA) assay to investigate the presence of large <em>HEXB</em> deletions. Overall, we identified 16 alleles, 9 of which were novel, including 4 sequence variation leading to aminoacid changes [c.626C>T (p.T209I), c.634C>A (p.H212N), c.926G>T (p.C309F), c.1451G>A (p.G484E)] 3 intronic mutations (c.1082+5G>A, c.1242+1G>A, c.1169+5G>A), 1 nonsense mutation c.146C>A (p.S49X) and 1 small in-frame deletion c.1260_1265delAGTTGA (p.V421_E422del). Using the new MLPA assay, 2 previously described deletions were identified. <em>In vitro</em> expression studies showed that proteins bearing aminoacid changes p.T209I and p.G484E presented a very low or absent activity, while proteins bearing the p.H212N and p.C309F changes retained a significant residual activity. The detrimental effect of the 3 novel intronic mutations on the <em>HEXB</em> mRNA processing was demonstrated using a minigene assay. Unprecedentedly, minigene studies revealed the presence of a novel alternative spliced <em>HEXB</em> mRNA variant also present in normal cells. In conclusion, we provided new insights into the molecular basis of SD and validated an MLPA assay for detecting large <em>HEXB</em> deletions.</p> </div>", "links"=>[], "tags"=>["analyses", "patients", "affected", "sandhoff", "characterization", "variants"], "article_id"=>122087, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0041516.s001", "https://dx.doi.org/10.1371/journal.pone.0041516.s002"], "stats"=>{"downloads"=>19, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Sequence_and_Copy_Number_Analyses_of_HEXB_Gene_in_Patients_Affected_by_Sandhoff_Disease_Functional_Characterization_of_9_Novel_Sequence_Variants/122087", "title"=>"Sequence and Copy Number Analyses of <em>HEXB</em> Gene in Patients Affected by Sandhoff Disease: Functional Characterization of 9 Novel Sequence Variants", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-07-27 00:34:47"}
  • {"files"=>["https://ndownloader.figshare.com/files/601111"], "description"=>"<p>RT-PCR analysis of the <i>HEXB</i> mRNA in cells transfected with normal (pcDNA3HEXBN) and minigenes containing mutations c.1082+5G>A (pcDNA3HEX1082) and c.1169+5G>A (pcDNA3HEX1169) (panels A and C, respectively). MW: 1 kb Plus DNA Ladder. Schematic representation of the effect of the novel mutations on the splicing process (panels B and D). Sequencing analysis of RT-PCR products showed that the c.1082+5G>A mutation determines the skipping of 178 nt of exon 8 (panel B), whereas the presence of c.1169+5G>A mutation determines the retention of 87 nt of exon 9 (panel D).</p>", "links"=>[], "tags"=>["mutations"], "article_id"=>271592, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.g004", "stats"=>{"downloads"=>1, "page_views"=>21, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vitro_functional_analysis_of_mutations_c_1082_5G_A_and_c_1169_5G_A_/271592", "title"=>"<i>In vitro</i> functional analysis of mutations c.1082+5G>A and c.1169+5G>A.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:26:32"}
  • {"files"=>["https://ndownloader.figshare.com/files/601217"], "description"=>"<p>Panel A: RT-PCR analysis of the <i>HEXB</i> mRNA in cells transfected with normal (pcDNA3HEXBN) and a minigene containing mutation c.1242+1G>A (pcDNA3HEX1242) MW: 1 kb Plus DNA Ladder. Panel B: Schematic representation of the effect of the novel mutations on the splicing process. Sequencing analysis of RT-PCR products showed that the presence of c.1242+1G>A mutation determines the skipping of 73 nt of exon 10. In addition the presence of a 3′ cryptic splice site (present in both normal and mutant minigenes) determines the skipping of 112 nt in exon 11(denoted as red box) in cells transfected with both normal and mutant minigenes. Panel C: RT-PCR analysis of the <i>HEXB</i> mRNA in normal fibroblasts. MW: 1 kb Plus DNA Ladder.</p>", "links"=>[], "tags"=>["mutation", "exon", "11", "splicing"], "article_id"=>271692, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.g005", "stats"=>{"downloads"=>0, "page_views"=>12, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vitro_functional_analysis_of_mutation_c_1242_1G_A_and_exon_11_splicing_analysis_in_normal_fibroblasts_/271692", "title"=>"<i>In vitro</i> functional analysis of mutation c.1242+1G>A and exon 11 splicing analysis in normal fibroblasts.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:28:12"}
  • {"files"=>["https://ndownloader.figshare.com/files/600834"], "description"=>"<p>Panels A–C: Capillary electrophoresis profile of the MLPA analysis performed in a normal control (panel A) and patients SD4 (panel B) and SD1 (panel C). Each peak corresponds to the amplification of a probe specific for each exon of <i>HEXB</i> gene (numbered 1 to 14) and for 3 different reference genes (R1, R2, R3). Arrows indicate the peaks corresponding to the <i>HEXB</i> exons deleted in SD1 and SD4 patients. Panel D) Relative quantification of <i>HEXB</i> copy number was obtained by dividing the height of each gene-specific peak by the sum of the heights of 3 reference gene peaks. This ratio was then compared to the average ratio obtained from 8 control samples having each 2 <i>HEXB</i> gene copies. A ratio between 0.75 and 1.25 corresponds to 2 <i>HEXB</i> copy number while a ratio between 0.25 and 0.75 corresponds to 1 <i>HEXB</i> copy number.</p>", "links"=>[], "tags"=>["sd1", "sd4"], "article_id"=>271315, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.g001", "stats"=>{"downloads"=>1, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_MLPA_analysis_of_SD1_and_SD4_patients_/271315", "title"=>"MLPA analysis of SD1 and SD4 patients.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:21:55"}
  • {"files"=>["https://ndownloader.figshare.com/files/601347"], "description"=>"<p>ND: not detectable; NA: not available. Novel mutations are indicated in bold, *RefSeq cDNA:NM_000521. For cDNA numbering +1 corresponds to the A of the first ATG translation initiation codon. RefSeq protein: NP_000512.1. **indicates parents’ consanguinity. m: month; y: years; +deceased; §Owing to the use of different assay methods and tissue samples, total Hex activity values are expressed as a percentage of average control values.</p>", "links"=>[], "tags"=>["sd", "patients"], "article_id"=>271828, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.t001", "stats"=>{"downloads"=>1, "page_views"=>19, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Genotypes_of_SD_patients_analyzed_in_this_study_/271828", "title"=>"Genotypes of SD patients analyzed in this study.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:30:28"}
  • {"files"=>["https://ndownloader.figshare.com/files/600929"], "description"=>"<p>Total Hex activity after immunoprecipitation with anti-myc antibody of HEXB missense mutant proteins expressed in Hek293cells. Results are expressed as the percentage of total Hex activity detected after immunoprecipitation of myc-tagged normal HEXB expressed in Hek293cells (N). The data are shown as mean±SD of three different experiments, each performed in duplicate. <sup>*</sup>p<0.05.</p>", "links"=>[], "tags"=>["missense"], "article_id"=>271413, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.g002", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_vitro_functional_analysis_of_new_missense_sequence_variations_/271413", "title"=>"<i>In vitro</i> functional analysis of new missense sequence variations.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-07-27 00:23:33"}
  • {"files"=>["https://ndownloader.figshare.com/files/601395"], "description"=>"<p>ND: Not detected; ME: Maximum Entropy; NN: Neural Network.</p>", "links"=>[], "tags"=>["splicing"], "article_id"=>271877, "categories"=>["Biochemistry", "Genetics"], "users"=>["Stefania Zampieri", "Silvia Cattarossi", "Ana Maria Oller Ramirez", "Camillo Rosano", "Charles Marques Lourenco", "Nadia Passon", "Isabella Moroni", "Graziella Uziel", "Antonella Pettinari", "Franco Stanzial", "Raquel Dodelson de Kremer", "Nydia Beatriz Azar", "Filiz Hazan", "Mirella Filocamo", "Bruno Bembi", "Andrea Dardis"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0041516.t002", "stats"=>{"downloads"=>0, "page_views"=>13, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_In_silico_analysis_of_novel_splicing_mutations_/271877", "title"=>"<i>In silico</i> analysis of novel splicing mutations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-07-27 00:31:17"}

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Relative Metric

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