scholarly journals Aberrant Splicing of SDHC in Families With Unexplained Succinate Dehydrogenase-Deficient Paragangliomas

2020 ◽  
Vol 4 (12) ◽  
Author(s):  
Sunita M C De Sousa ◽  
John Toubia ◽  
Tristan S E Hardy ◽  
Jinghua Feng ◽  
Paul Wang ◽  
...  
Keyword(s):  
Succinate Dehydrogenase ◽  
Transcriptome Analysis ◽  
Haplotype Analysis ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Chromosome 1 ◽  
Sequencing Analysis ◽  
Kit Mutation ◽  
Whole Exome ◽  
Genetic Test Results

Abstract Context Germline mutations in the succinate dehydrogenase genes (SDHA/B/C/D, SDHAF2—collectively, “SDHx”) have been implicated in paraganglioma (PGL), renal cell carcinoma (RCC), gastrointestinal stromal tumor (GIST), and pituitary adenoma (PA). Negative SDHB tumor staining is indicative of SDH-deficient tumors, usually reflecting an underlying germline SDHx mutation. However, approximately 20% of individuals with SDH-deficient tumors lack an identifiable germline SDHx mutation. Methods We performed whole-exome sequencing (WES) of germline and tumor DNA followed by Sanger sequencing validation, transcriptome analysis, metabolomic studies, and haplotype analysis in 2 Italian-Australian families with SDH-deficient PGLs and various neoplasms, including RCC, GIST, and PA. Results Germline WES revealed a novel SDHC intronic variant, which had been missed during previous routine testing, in 4 affected siblings of the index family. Transcriptome analysis demonstrated aberrant SDHC splicing, with the retained intronic segment introducing a premature stop codon. WES of available tumors in this family showed chromosome 1 deletion with loss of wild-type SDHC in a PGL and a somatic gain-of-function KIT mutation in a GIST. The SDHC intronic variant identified was subsequently detected in the second family, with haplotype analysis indicating a founder effect. Conclusions This is the deepest intronic variant to be reported among the SDHx genes. Intronic variants beyond the limits of standard gene sequencing analysis should be considered in patients with SDH-deficient tumors but negative genetic test results.

scholarly journals Attenuated Type of Asphyxiating Thoracic Dysplasia due to Mutations in DYNC2H1 Gene

2019 ◽  
Vol 120 (4) ◽  
pp. 124-130
Author(s):  
Anna Čechová ◽  
Alice Baxová ◽  
Jiří Zeman ◽  
Lukáš Lambert ◽  
Tomáš Honzík ◽  
...  
Keyword(s):  
Dna Analysis ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Chest Circumference ◽  
Anthropometric Parameters ◽  
Age Related ◽  
Whole Exome ◽  
Asphyxiating Thoracic Dysplasia ◽  
Health And Disease ◽  
Postnatal Adaptation

Asphyxiating thoracic dysplasia (ATD) represents a heterogeneous group of skeletal dysplasias with short ribs, narrow chest and reduced thoracic capacity. Mutations in several genes including IFT80, DYNC2H1, TTC21B and WDR19 have been found in patients with ATD. Both severe and milder course of the disease were described in correlation with secondary involvement of lung’s function. Two children with attenuated form of ATD are described. Their anthropometric parameters for birth weight, length and head circumference were normal but narrow thorax was observed in both of them in early infancy with chest circumference < –3 SD (standard deviation) in comparison to age related controls. The postnatal adaptation and development of both children was uneventful except for mild tachypnoea in one of them which persisted till the age of 6 months. In both children, radiographs revealed narrow upper half of the chest with shorter ribs and atypical configuration of pelvis with horizontally running acetabula and coarse internal edges typical for ATD. Molecular analyses using whole exome sequencing in one family revealed that the patient is compound heterozygote in DYNC2H1 gene for a frame-shift mutation c.4458delT resulting in premature stop-codon p.Phe1486Leufs*11 and a missense mutation c.9044A>G (p.Asp3015Gly). The second family refused the DNA analysis. Regular monitoring of anthropometric parameters during childhood is of big importance both in health and disease. In addition, measurement of the chest circumference should be included, at least at birth and during infancy.

scholarly journals AIMP1 Mutation Long-Term Follow-Up, With Decreased Brain N-Acetylaspartic Acid and Secondary Mitochondrial Abnormalities

2019 ◽  
Vol 6 ◽  
pp. 2329048X1982952 ◽  
Author(s):  
Aneal Khan ◽  
Jennifer Bennett ◽  
Morris H. Scantlebury ◽  
Xing-Chang Wei ◽  
Marina Kerr
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Monozygotic Twins ◽  
Trna Synthetase ◽  
Resonance Spectroscopy ◽  
Multifunctional Protein ◽  
Whole Exome ◽  
Long Term Follow Up

Aminoacyl transfer RNA (tRNA) synthetase complex-interacting multifunctional protein I is a noncatalytic component of tRNA multi-synthetase complexes. Although important in joining tRNAs to their cognate amino acids, AIMP1 has several other functions including axonal growth, cytokine activity, and interactions with N-acetylaspartic acid in ribosomal tRNA synthetase complexes. Further, N-acetylaspartic acid donates an aspartate during myelination and is therefore important to axonal integrity. Mutations in AIMP1 can disrupt these functions, as demonstrated in this clinical case study of 2 monozygotic twins, who display congenital opisthotonus, microcephaly, severe developmental delay, and seizures. Whole exome sequencing was used to identify a premature stop codon in the AIMP1 gene (g. 107248613_c.115C>T; p.(Gln39). In the absence of whole exome sequencing, we propose that decreased N-acetylaspartic acid peaks on magnetic resonance spectroscopy could act as a biomarker for AIMP1 mutations.

scholarly journals Succinate Dehydrogenase (SDH) D Subunit (SDHD) Inactivation in a Growth-Hormone-Producing Pituitary Tumor: A New Association for SDH?

2012 ◽  
Vol 97 (3) ◽  
pp. E357-E366 ◽  
Author(s):  
Paraskevi Xekouki ◽  
Karel Pacak ◽  
Madson Almeida ◽  
Christopher A. Wassif ◽  
Pierre Rustin ◽  
...  
Keyword(s):  
Succinate Dehydrogenase ◽  
Loss Of Heterozygosity ◽  
Pituitary Tumor ◽  
Stop Codon ◽  
Genetic Locus ◽  
Premature Stop Codon ◽  
Pituitary Tumors ◽  
Tumor Formation ◽  
Protein Loss ◽  
Down Regulation

Background: Mutations in the subunits B, C, and D of succinate dehydrogenase (SDH) mitochondrial complex II have been associated with the development of paragangliomas (PGL), gastrointestinal stromal tumors, papillary thyroid and renal carcinoma (SDHB), and testicular seminoma (SDHD). Aim: Our aim was to examine the possible causative link between SDHD inactivation and somatotropinoma. Patients and Methods: A 37-yr-old male presented with acromegaly and hypertension. Other family members were found with PGL. Elevated plasma and urinary levels of catecholamines led to the identification of multiple PGL in the proband in the neck, thorax, and abdomen. Adrenalectomy was performed for bilateral pheochromocytomas (PHEO). A GH-secreting macroadenoma was also found and partially removed via transsphenoidal surgery (TTS). Genetic analysis revealed a novel SDHD mutation (c.298_301delACTC), leading to a frame shift and a premature stop codon at position 133 of the protein. Loss of heterozygosity for the SDHD genetic locus was shown in the GH-secreting adenoma. Down-regulation of SDHD protein in the GH-secreting adenoma by immunoblotting and immunohistochemistry was found. A literature search identified other cases of multiple PGL and/or PHEO in association with pituitary tumors. Conclusion: We describe the first kindred with a germline SDHD pathogenic mutation, inherited PGL, and acromegaly due to a GH-producing pituitary adenoma. SDHD loss of heterozygosity, down-regulation of protein in the GH-secreting adenoma, and decreased SDH enzymatic activity supports SDHD's involvement in the pituitary tumor formation in this patient. Older cases of multiple PGL and PHEO and pituitary tumors in the literature support a possible association between SDH defects and pituitary tumorigenesis.

scholarly journals Sequencing Analysis and Enzyme Activity Assay of SrUGT76G1 Revealed the Mechanism Toward on/off Production of Rebaudioside-A in Stevia Plants

2021 ◽  
Author(s):  
Simone Ribeiro Lucho ◽  
Marcelo do Amaral ◽  
Valmor Bianchi ◽  
Lorena Almagro ◽  
Maria Ferrer ◽  
...  
Keyword(s):  
Stop Codon ◽  
Premature Stop Codon ◽  
Binding Pocket ◽  
Structural Features ◽  
Steviol Glycosides ◽  
Sequencing Analysis ◽  
Structural Level ◽  
Rebaudioside A ◽  
Enzyme Activity Assay ◽  
Structure Activity

Abstract Stevia plants is known for its ability to synthesize steviol glycosides (SGs), a natural sweetener blend. Stevioside (STEV) and Rebaudioside-A (Reb-A) are the main SGs. However, Reb-A is more palatable than STEV and shows reduced bitter aftertaste. SrUGT76G1 catalyzes the conversion of STEV to Reb-A, improving their organoleptic properties. The better understanding of the structure/activity of SrUGT76G1 would allow shedding light up on on/off production of Reb-A in stevia plants. Thus, we analyzed the STEV and Reb-A content in stevia leaves of plants from Brazil and Spain and did not find detectable levels of Reb-A in Brazilian samples (off production). For this reason, we used a sequencing tool to study at the genetic and structural level the SrUGT76G1 gene. Changes in key amino acid residues in Brazilian samples were found, such as Leu204Phe, Thr284Leu and Leu126Ile. Leu204Phe mutants can narrow substrate-binding pocket to favor flavonoids recognition and decrease SGs synthesis, while Thr284 is considered key for 1,3-glucosylation of SGs, including Reb-A. These punctual mutations may partly explain the lack of functionality of UGT76G1 enzyme and off production of Reb-A in stevia plants from Brazil. Following this trend, Brazilian samples exhibited a T-to-A substitution, resulting in premature stop codon. As expected, the relative expression of SrUGT76G1 gene showed a higher level in Spanish samples than in Brazilian ones. Collectively, the results presented here show the structure-activity interplay of SrUGT76G1 enzyme and provide new insights on structural features and its role toward Reb-A synthesis.

scholarly journals First description of antimicrobial resistance in carbapenem-susceptible Klebsiella pneumoniae after imipenem treatment, driven by outer membrane remodeling

2020 ◽  
Author(s):  
Xuebin Tian ◽  
Qiongdan Wang ◽  
Laura Perlaza-Jiménez New ◽  
Xiangkuo Zheng ◽  
Yajie Zhao ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Outer Membrane ◽  
Gel Electrophoresis ◽  
Stop Codon ◽  
Polyacrylamide Gel Electrophoresis ◽  
Sodium Dodecyl ◽  
Premature Stop Codon ◽  
Sequencing Analysis ◽  
Membrane Remodeling ◽  
Carbapenem Resistant

Abstract Background:The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a looming threat to human health. Although there are numerous studies regarding porin alteration in association with the production of ESBLs and/or AmpC β-lactamase, a systematic study on the treatment-emergence of porins alteration in antibiotic resistance does not yet exist. The aim of this study was to investigate the underlying mechanism and evolution of resistance of K. pneumoniae during carbapenem treatment. Results:Here, we report three strains (FK-2624, FK-2723 and FK-2820) isolated from one patient before and after imipenem treatment during hospitalization. Antibiotic susceptibility testing indicated that that the first isolate, FK-2624, was susceptible to almost all tested antimicrobials, being resistant only to fosfomycin. The subsequent isolates FK-2723 and FK-2820 were multidrug resistant (MDR). After imipenem therapy, FK-2820 had evolved to be carbapenem-resistant. PCR and Genome Sequencing analysis indicated that oqxA, and fosA5, were identified in all three strains. In addition, FK-2624 also harbored bla SHV-187 and blaTEM-116. The blaSHV-187 and blaTEM-116 genes were not detected in FK-2723 and FK-2820. blaDHA-1, qnrB4, aac (6’)-IIc, and blaSHV-12, EreA2, CatA2, SulI, and tetD , were identified in both FK-2723 and FK-2820. Moreover, the genes bla DHA -1, qnrB4, aac(6’)-IIc were co-harbored on a plasmid. Of the virulence factors found in this study, ybtA, ICEKp6, mrkD, entB, iroN, rmpA2-6, wzi16 and capsular serotype K57 were found in the three isolates. The results of pairwise comparisons, multi-locus sequencing typing (MLST) and pulsed-field gel electrophoresis (PFGE) revealed high homology among the isolates. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) results showed that isolate FK-2820 lacked OmpK36, with genome sequence data validating that there was a premature stop codon in the ompK36 gene and real-time RT-PCR suggesting high turnover of the ompK36 non-sense transcript in FK-2820, with the steady-state mRNA level 0.007 relative to the initial isolate. Conclusion:This study in China highlight that the alteration of outer membrane porins due to the 14-day use of imipenem play a potential role in leading to clinical presentation of carbapenem-resistance. This is the first description of increased resistance developing from a carbapenem-susceptible K. pneumoniae with imipenem treatment driven by outer membrane remodeling.

Identification of New CD177 Isoform in NB1 Deficient Individuals

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 1270-1270
Author(s):  
Behnaz Bayat ◽  
Karin Kissel ◽  
Silke Werth ◽  
Sentot Santoso
Keyword(s):  
Stop Codon ◽  
High Surface ◽  
Specific Antigen ◽  
Premature Stop Codon ◽  
Transcriptional Analysis ◽  
Sequencing Analysis ◽  
Short Transcript ◽  
Rabbit Polyclonal Antibody ◽  
Protein Isoform

Abstract Human neutrophil-specific antigen CD177 (NB1; HNA-2a) belongs to the member of the cyctein-rich LY-6 superfamily. Transcriptional analysis of this family revealed intron-retaining mechanism, which produce many spliced forms of gene. In some cases, this mis-spliced isoform was the most abundant form suggesting a control mechanism of gene expression. CD177 glycoprotein carries neutrophil antigen HNA-2a, and antibodies to HNA-2a frequently causes transfusion related acute lung injury (TRALI). Recently, CD177 has been found to be associated with the expression of proteinase-3 (PR3) which plays a role in autoantibody mediated Wegener’s granulomatosis. Neutrophils from some people lack CD177 (termed HNA-2a negative), however, the mechanism responsible for this deficiency is not fully understood. In this study, we investigated whether mis-spliced form of CD177 exist in neutrophils. Neutrophil from blood donors were phenotyped for the presence or absence of CD177 by flow cytometry using two mabs 7D8, MEM166 recognising different epitopes on CD177. HNA-2a positive individuals carrying high surface CD177 density and HNA-2a negative individuals were selected. mRNA was isolated from CD177 phenotyped individuals and were analyzed by PCR using different sets of primer set. Amplification of CD177 transcript (bases 98–1401) showed the expected ~1300 bp band encoding for the entire CD177 (isoform 1), and a smaller band (~417bp) with similar intensity in HNA-2a positive as well as in HNA-2a negative individuals. Sequencing analysis of the short transcript showed the presence of intronic sequence between exon 3 and 4, which produces premature stop codon. Transfection of insect cells with related transcript resulted in production of a ~23 kDa protein which is detectable in immunoblot using rabbit polyclonal antibody against synthetic CD177 peptide. This ~23 kDa protein (isoform 4) did not react with mabs 7D8 and MEM166. Furthermore, immunoblotting analysis of other blood cells showed that isoform 4 was exclusively found on neutrophils. In contrast to the isoform 1, isoform 4 was not upregulated on neutrophils of individuals receiving GCSF. Neutrophils treated with fMLP in vitro showed down-regulation of isoform 4 transcript. This phenomenon however, has not been observed in neutrophils treated with LPS and IL-8. In summary, we characterized a new CD177 isoform in neutrophils. The presence of this isoform in both HNA-2a positive and negative CD177 phenotyped individuals and its regulation with fMLP indicate the role of this protein in inflammatory process.

scholarly journals A novel spontaneous mutation of Irs1 in mice results in hyperinsulinemia, reduced growth, low bone mass and impaired adipogenesis

2009 ◽  
Vol 204 (3) ◽  
pp. 241-253 ◽  
Author(s):  
Victoria E DeMambro ◽  
Masanobu Kawai ◽  
Thomas L Clemens ◽  
Keertik Fulzele ◽  
Jane A Maynard ◽  
...  
Keyword(s):  
Stop Codon ◽  
Spontaneous Mutation ◽  
Premature Stop Codon ◽  
Chromosome 1 ◽  
Tartrate Resistant Acid Phosphatase ◽  
Mrna Levels ◽  
Normal Numbers ◽  
Mineral Density ◽  
Insulin Resistant

A spontaneous mouse mutant, designated ‘small’ (sml), was recognized by reduced body size suggesting a defect in the IGF1/GH axis. The mutation was mapped to the chromosome 1 region containing Irs1, a viable candidate gene whose sequence revealed a single nucleotide deletion resulting in a premature stop codon. Despite normal mRNA levels in mutant and control littermate livers, western blot analysis revealed no detectable protein in mutant liver lysates. When compared with the control littermates, Irs1sml/Irs1sml (Irs1sml/sml) mice were small, lean, hearing impaired; had 20% less serum IGF1; were hyperinsulinemic; and were mildly insulin resistant. Irs1sml/sml mice had low bone mineral density, reduced trabecular and cortical thicknesses, and low bone formation rates, while osteoblast and osteoclast numbers were increased in the females but not different in the males compared with the Irs1+/+ controls. In vitro, Irs1sml/sml bone marrow stromal cell cultures showed decreased alkaline phosphatase-positive colony forming units (pre-osteoblasts; CFU-AP+) and normal numbers of tartrate-resistant acid phosphatase-positive osteoclasts. Irs1sml/sml stromal cells treated with IGF1 exhibited a 50% decrease in AKT phosphorylation, indicative of defective downstream signaling. Similarities between engineered knockouts and the spontaneous mutation of Irs1sml were identified as well as significant differences with respect to heterozygosity and gender. In sum, we have identified a spontaneous mutation in the Irs1 gene associated with a major skeletal phenotype. Changes in the heterozygous Irs1+/sml mice raise the possibility that similar mutations in humans are associated with short stature or osteoporosis.

scholarly journals A Novel Mutation in theCYP11B1Gene Causes Steroid 11β-Hydroxylase Deficient Congenital Adrenal Hyperplasia with Reversible Cardiomyopathy

2015 ◽  
Vol 2015 ◽  
pp. 1-5 ◽  
Author(s):  
Mohammad A. Alqahtani ◽  
Ayed A. Shati ◽  
Minjing Zou ◽  
Ali M. Alsuheel ◽  
Abdullah A. Alhayani ◽  
...  
Keyword(s):  
Congenital Adrenal Hyperplasia ◽  
Stop Codon ◽  
Novel Mutation ◽  
Skin Pigmentation ◽  
Premature Stop Codon ◽  
Molecular Defect ◽  
Sequencing Analysis ◽  
Adrenal Hyperplasia ◽  
Biallelic Mutation ◽  
Hydroxylase Deficiency

Congenital adrenal hyperplasia (CAH) due to steroid 11β-hydroxylase deficiency is the second most common form of CAH, resulting from a mutation in theCYP11B1gene. Steroid 11β-hydroxylase deficiency results in excessive mineralcorticoids and androgen production leading to hypertension, precocious puberty with acne, enlarged penis, and hyperpigmentation of scrotum of genetically male infants. In the present study, we reported 3 male cases from a Saudi family who presented with penile enlargement, progressive darkness of skin, hypertension, and cardiomyopathy. The elder patient died due to heart failure and his younger brothers were treated with hydrocortisone and antihypertensive medications. Six months following treatment, cardiomyopathy disappeared with normal blood pressure and improvement in the skin pigmentation. The underlying molecular defect was investigated by PCR-sequencing analysis of all coding exons and intron-exon boundary of theCYP11B1gene. A novel biallelic mutation c.780 G>A in exon 4 of theCYP11B1gene was found in the patients. The mutation created a premature stop codon at amino acid 260 (p.W260∗), resulting in a truncated protein devoid of 11β-hydroxylase activity. Interestingly, a somatic mutation at the same codon (c.779 G>A,p.W260∗) was reported in a patient with papillary thyroid cancer (COSMIC database). In conclusion, we have identified a novel nonsense mutation in theCYP11B1gene that causes classic steroid 11β-hydroxylase deficient CAH. Cardiomyopathy and cardiac failure can be reversed by early diagnosis and treatment.

scholarly journals Neuroacanthocytosis diagnózisa új generációs exom-szekvenálással

2017 ◽  
Vol 158 (42) ◽  
pp. 1681-1684 ◽  
Author(s):  
Kinga Hadzsiev ◽  
Mónika Szőts ◽  
Anett Fekete ◽  
László Balikó ◽  
Kim Boycott ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
International Collaboration ◽  
Huntington Disease ◽  
Stop Codon ◽  
Neurological Diseases ◽  
Premature Stop Codon ◽  
Pathogenic Mutation ◽  
Normal Result ◽  
Whole Exome ◽  
Specific Symptoms

Abstract: In a patient with marked symptoms of Huntington disease after the huntingtin testing, which gave normal result, a whole exome sequencing (WES) has been performed based on an international collaboration. A homozygous G>A nucleotid change in the exon 34 of the VPS13A gene has been detected with WES, a mutation resulting in a premature stop codon at the position 1301. This change is a known pathogenic mutation. The aim of this article is to draw attention on the importance of the WES in the diagnosis of rare neurological diseases without any specific symptoms. Orv Hetil. 2017; 158(42): 1681–1684.

A New Germline Stop Codon Mutation in Exon 15 of the APC Gene Predisposing to Familial Adenomatous Polyposis

2013 ◽  
Vol 28 (4) ◽  
pp. 405-408 ◽  
Author(s):  
Laura Schirosi ◽  
Marcello Pellegrino ◽  
Paolo Tarantino ◽  
Salvatore Mauro ◽  
Andrea Tinelli ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Familial Adenomatous Polyposis ◽  
Germline Mutation ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Colorectal Tumor ◽  
Apc Gene ◽  
Sequencing Analysis ◽  
Adenomatous Polyposis ◽  
Truncated Protein

Familial adenomatous polyposis (FAP) is an autosomal dominant disorder related to germline mutations of the adenomatous polyposis coli ( APC) gene. It is characterized by the detection of numerous adenomatous polyps that, if untreated, develop into colorectal cancer. We studied an Italian family with FAP history and the related colorectal tumor sample of the proband. Sequencing analysis of blood samples revealed the presence of a never-reported germline mutation in the APC gene (exon 15): an heterozygous G deletion at position c.2126 resulting in a premature stop codon (p.Gly721GlufsX6) and in a truncated protein. This mutation was also identified in the colorectal tumor tissue, together with a second known pathogenic heterozygotic somatic mutation, c.4348C>T (p.Arg1450X), which generates a premature truncated protein. The novel identified germline mutation is therefore related to FAP and, in accordance with Knudson's “two hit” hypothesis, can be considered the first event predisposing to the insurgence of colorectal cancer in these patients. The somatic hit inactivating the second allele of the APC gene is located in the mutation cluster region of the gene; this is not a random event since it depends on the position of the germline mutation. The inactivation of APC generates the neoplastic growth advantage to the cell.

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