A novel deep intronic "SERPING1" variant as a cause of hereditary angioedema due to C1-inhibitor deficiency

Background In about 5% of patients with hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE) no mutation in the SERPING1 gene is detected. Methods C1-INH-HAE cases with no mutation in the coding region of SERPING1 after conventional genotyping were examined for defects in the intronic or untranslated regions of the gene. Using a next-generation sequencing (NGS) platform targeting the entire SERPING1, 14 unrelated C1-INH-HAE patients with no detectable mutations in the coding region of the gene were sequenced. Detected variants with a global minor allele frequency lower than the frequency of C1-INH-HAE (0.002%), were submitted to in silico analysis using ten different bioinformatics tools. Pedigree analysis and examination of their pathogenic effect on the RNA level were performed for filtered in variants. Results In two unrelated patients, the novel mutation c.-22-155G > T was detected in intron 1 of the SERPING1 gene by the use NGS and confirmed by Sanger sequencing. All bioinformatics tools predicted that the variant causes a deleterious effect on the gene and pedigree analysis showed its co-segregation with the disease. Degradation of the mutated allele was demonstrated by the loss of heterozygosity on the cDNA level. According to the American College of Medical Genetics and Genomics 2015 guidelines the c.-22-155G > T was curated as pathogenic. Conclusions For the first time, a deep intronic mutation that was detected by NGS in the SERPING1 gene, was proven pathogenic for C1-INH-HAE. Therefore, advanced DNA sequencing methods should be performed in cases of C1-INH-HAE where standard approaches fail to uncover the genetic alteration

Deciphering the genetics of primary angioedema with normal levels of C1 inhibitor

The genetic alteration underlying the great majority of primary angioedema with normal C1 inhibitor (nl-C1-INH-HAE) cases remains unknown. To search for variants associated with nl-C1-INH-HAE, we genotyped 133 unrelated nl-C1-INH-HAE patients using a custom next-generation sequencing platform targeting 55 genes possibly involved in angioedema pathogenesis. Patients already diagnosed with F12 alterations as well as those with histaminergic acquired angioedema were excluded. A variant pathogenicity curation strategy was followed, including a comparison of the results with those of genotyping 169 patients with hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE), and only filtered-in variants were studied further. Among the examined nl-C1-INH-HAE patients, carriers of neither the ANGPT1 p.Ala119Ser nor the KNG1 p.Met379Lys variant were found, whereas the PLG p.Lys330Glu was detected in four (3%) unrelated probands (one homozygote). In total, 182 different variants were curated, 21 of which represented novel mutations. Although the frequency of variants per gene was comparable between nl-C1-INH-HAE and C1-INH-HAE, variants of the KNG1 and XPNPEP1 genes were detected only in nl-C1-INH-HAE patients (six and three, respectively). Twenty-seven filtered variants in 23 different genes were detected in nl-C1-INH-HAE more than once, whereas 69/133 nl-C1-INH-HAE patients had compound heterozygotes of filtered variants located in the same or different genes. Pedigree analysis was performed where feasible. Our results indicate the role that alterations in some genes, like KNG1, may play in disease pathogenesis, the complex trait that is possibly underlying in some cases, and the existence of hitherto unrecognized disease endotypes

Foxp3 expression in human cancer cells

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Hereditary angioedema with normal C1 Inhibitor associated with Carboxypeptidase N deficiency

International audienceBackground: Hereditary angioedema (HAE) is a potentially life-threatening disordercharacterized by recurrent episodes of subcutaneous or submucosal swelling. HAE withnormal C1 Inhibitor (HAE-nC1-INH) is an under-diagnosed condition. Although theassociation with genetic variants has been identified for some families, the genetic causes inmany patients with HAE-nC1-INH remain unknown. The role of genes associated withbradykinin catabolism is not fully understood.Objective: We investigated the biological parameters and the genes related to kallikrein-kininsystem (KKS) in families with a clinical phenotype of HAE-nC1-INH and presenting with acarboxypeptidase N (CPN) deficiency.Methods: This study includes four families presenting with HAE-nC1-INH and CPNdeficiency. Patients’ clinical records were examined, biological parameters of KKS measured,genetics was analyzed by next-generation sequencing and Sanger sequencing. Predictivealgorithms (HSF®, SIFT®, Polyphen-2®, MutationTaster®, ClinPred®) were used to classifyvariants as affecting splicing, as benign to deleterious, or as disease-causing.Results: Patients presented with angioedema and urticaria, mainly on face/lips, but also withabdominal pain or laryngeal symptoms. Affected patients displayed low CPN activity –30 to50% of median value in plasma. We identified three variants of the CPN1 gene encoding thecatalytic 55-kDa subunit of CPN at: c.533G>A, c.582A>G and c.734C>T. CPN deficiencyassociated with genetic variants segregated with HAE-nC1-INH symptoms in affected familymembers.Conclusions: CPN1 gene variants are associated with CPN deficiency and HAE-nC1-INHsymptoms in four unrelated families. Genetic CPN deficiency may contribute to bradykininand anaphylatoxins accumulation, with synergistic effects in angioedema and urticarialsymptoms

Searching for genetic biomarkers for hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE)

Existing evidence indicates that modifier genes could change the phenotypic outcome of the causal SERPING1 variant and thus explain the expression variability of hereditary angioedema due to C1-inhibitor deficiency (C1-INH-HAE). To further examine this hypothesis, we investigated the presence or absence of 18 functional variants of genes encoding proteins involved in the metabolism and function of bradykinin, the main mediator of C1-INH-HAE attacks, in relation to three distinct phenotypic traits of patients with C1-INH-HAE, i.e., the age at disease onset, the need for long-term prophylaxis (LTP), and the severity of the disease. Genetic analyses were performed by a validated next-generation sequencing platform. In total, 233 patients with C1-INH-HAE from 144 unrelated families from five European countries were enrolled in the study. Already described correlations between five common functional variants [F12-rs1801020, KLKB1-rs3733402, CPN1-rs61751507, and two in SERPING1 (rs4926 and rs28362944)] and C1-INH-HAE severity were confirmed. Furthermore, significant correlations were found between either the age at disease onset, the LTP, or the severity score of the disease and a series of other functional variants (F13B-rs6003, PLAU-rs2227564, SERPINA1-rs28929474, SERPINA1-rs17580, KLK1-rs5515, SERPINE1-rs6092, and F2-rs1799963). Interestingly, correlations uncovered in the entire cohort of patients were different from those discovered in the cohort of patients carrying missense causal SERPING1 variants. Our findings indicate that variants other than the SERPING1 causal variants act as independent modifiers of C1-INH-HAE severity and could be tested as possible prognostic biomarkers

Wybrane aspekty genotypowania wrodzonego obrzęku naczynioruchowego w erze NGS: gen F12

Objective. To screen a cohort of patients diagnosed with non-FXII angioedema for carriage of variants of F12 gene. Material and methods. DNA samples from 191 patients suffering from primary angioedema with normal C1-INH, 54 samples from non- -affected family members, and 161 samples from C1-INH-HAE (154 type I, 7 type II) patients were included in the study. The F12 gene was genotyped by targeted NGS (100% coverage of translated regions). Sanger sequencing was performed for the verification of all identified variants and family segregation studies. Results. The pathogenic F12 variant c.983C>A was detected in three patients from two unrelated families initially diagnosed as U-HAE. Six additional mutations were identified, four of which were characterized as benign (c.41T>C, c.418C>G, c.1025C>T, c.530C>T) and two of uncertain significance (c.1530G>C, c.1768T>G). Two synonymous variants (c.756C>T and c.711C>T), the common polymorphism c.619G>C, and the functional polymorphism c.-4T>C were detected in allele frequencies similar to those presented in the ExAC database for the European population. One more not yet reported synonymous variant (c. 1599A>G) was also found. Conclusion. Analyzing the entire translated region of F12 gene is important in order to identify new variants that possibly affect HAE expressivity. Interestingly, genetic analysis of F12 supports not only the diagnosis of FXII-HAE but also the correct exclusion diagnosis of U-HAE.Cel. Przesiewowe badanie kohorty pacjentów z rozpoznanym obrzę- kiem naczynioruchowym innym niż zależny od FXII w kierunku nosicielstwa wariantów genu F12. Materiał i metody. Do badania włączono próbki DNA 191 pacjentów cierpiących na pierwotny obrzęk naczynioruchowy z prawidłowym C1-INH, 54 zdrowych członków rodzin oraz 161 pacjentów z C1-INH-HAE (154 typ I, 7 typ II). Gen F12 był genotypowany metodą NGS (obejmującą cały rejon poddany translacji). Sekwencjonowanie metodą Sangera zostało wykonane celem weryfikacji wszystkich zidentyfikowanych wariantów i badań segregacyjnych rodzin. Wyniki. U trzech pacjentów z dwóch niespokrewnionych rodzin pierwotnie zdiagnozowanych jako U-HAE wykryto patogenny wariant F12: c.983C>A. Zidentyfikowano sześć dodatkowych mutacji, z których cztery zostały określone jako łagodne (c.41T>C, c.418C>G, c.1025C>T, c.530C>T), a dwie jako mutacje o niepewnym znaczeniu (c.1530G>C, c.1768T>G). Stwierdzono dwa warianty synonimiczne (c.756C>T oraz c.711C>T), pospolity polimorfizm (c.619G>C) oraz czynnościowy polimorfizm c.-4T>C z częstością alleliczną podobną do podawanej w bazie ExAC dla populacji europejskiej. Wykryto również jeden nie raportowany dotychczas wariant synonimiczny (c. 1599A>G). Wnioski. Analiza całego rejonu genu F12 poddawanego translacji jest ważna dla identyfikowania nowych wariantów, które mogą oddziaływać na ekspresję HAE. Ponadto, analiza genetyczna F12 pozwala nie tylko na potwierdzenie rozpoznania FXII-HAE, ale również prawidłowe wykluczenie rozpoznania U-HAE