scholarly journals Whole-exome sequencing-based discovery of STIM1 deficiency in a child with fatal classic Kaposi sarcoma

2010 ◽  
Vol 207 (11) ◽  
pp. 2307-2312 ◽  
Author(s):  
Minji Byun ◽  
Avinash Abhyankar ◽  
Virginie Lelarge ◽  
Sabine Plancoulaine ◽  
Ayse Palanduz ◽  
...  

Classic Kaposi sarcoma (KS) is exceedingly rare in children from the Mediterranean Basin, despite the high prevalence of human herpesvirus-8 (HHV-8) infection in this region. We hypothesized that rare single-gene inborn errors of immunity to HHV-8 may underlie classic KS in childhood. We investigated a child with no other unusually severe infectious or tumoral phenotype who died from disseminated KS at two years of age. Whole-exome sequencing in the patient revealed a homozygous splice-site mutation in STIM1, the gene encoding stromal interaction molecule 1, which regulates store-operated Ca2+ entry. STIM1 mRNA splicing, protein production, and Ca2+ influx were completely abolished in EBV-transformed B cell lines from the patient, but were rescued by the expression of wild-type STIM1. Based on the previous discovery of STIM1 deficiency in a single family with a severe T cell immunodeficiency and the much higher risk of KS in individuals with acquired T cell deficiencies, we conclude that STIM1 T cell deficiency precipitated the development of lethal KS in this child upon infection with HHV-8. Our report provides the first evidence that isolated classic KS in childhood may result from single-gene defects and provides proof-of-principle that whole-exome sequencing in single patients can decipher the genetic basis of rare inborn errors.

2017 ◽  
Vol 3 (5) ◽  
pp. e177 ◽  
Author(s):  
Javier Ruiz-Martínez ◽  
Luis J. Azcona ◽  
Alberto Bergareche ◽  
Jose F. Martí-Massó ◽  
Coro Paisán-Ruiz

Objective:Despite the enormous advancements made in deciphering the genetic architecture of Parkinson disease (PD), the majority of PD is idiopathic, with single gene mutations explaining only a small proportion of the cases.Methods:In this study, we clinically evaluated 2 unrelated Spanish families diagnosed with PD, in which known PD genes were previously excluded, and performed whole-exome sequencing analyses in affected individuals for disease gene identification.Results:Patients were diagnosed with typical PD without relevant distinctive symptoms. Two different novel mutations were identified in the CSMD1 gene. The CSMD1 gene, which encodes a complement control protein that is known to participate in the complement activation and inflammation in the developing CNS, was previously shown to be associated with the risk of PD in a genome-wide association study.Conclusions:We conclude that the CSMD1 mutations identified in this study might be responsible for the PD phenotype observed in our examined patients. This, along with previous reported studies, may suggest the complement pathway as an important therapeutic target for PD and other neurodegenerative diseases.


2019 ◽  
Vol 33 (2) ◽  
pp. 319-319
Author(s):  
Maria Antonella Laginestra ◽  
Luciano Cascione ◽  
Giovanna Motta ◽  
Fabio Fuligni ◽  
Claudio Agostinelli ◽  
...  

An amendment to this paper has been published and can be accessed via a link at the top of the paper.


2020 ◽  
Vol 40 (5) ◽  
pp. 729-740 ◽  
Author(s):  
Tsubasa Okano ◽  
Kohsuke Imai ◽  
Takuya Naruto ◽  
Satoshi Okada ◽  
Motoi Yamashita ◽  
...  

2019 ◽  
Vol 33 (2) ◽  
pp. 179-187 ◽  
Author(s):  
Maria Antonella Laginestra ◽  
Luciano Cascione ◽  
Giovanna Motta ◽  
Fabio Fuligni ◽  
Claudio Agostinelli ◽  
...  

2019 ◽  
Vol 17 (1) ◽  
Author(s):  
Irit Tirosh ◽  
Shiri Spielman ◽  
Ortal Barel ◽  
Reut Ram ◽  
Tali Stauber ◽  
...  

2021 ◽  
Author(s):  
Stephanie L Rouse ◽  
Michelle M Florentine ◽  
Emily Taketa ◽  
Dylan K Chan

Abstract Racial/ethnic disparities in the diagnostic efficacy of genetic testing for hearing loss has been described. These disparities may relate to differences in variant classification between different racial/ethnic groups, which may in turn derive from disparate representation of these groups in the published literature. We sought to quantify racial/ethnic disparities in the published literature on the human genetics of hearing loss. We conducted a search of PubMed for articles describing single-gene, multiple-gene, or whole-exome sequencing for individuals with sensorineural hearing loss. Data on the populations studied, including race/ethnicity and/or region of origin, subjects tested, and method of testing, were extracted. 1,355 unique populations representing 311,092 subjects from 1,165 studies were included. Overall, White and Asian populations and subjects were equivalently represented, but Latinx, Black, and Native American/Hawaiian groups were significantly underrepresented; over 96% of all subjects in the published literature were White or Asian. Within racial/ethnic groups, the majority of subjects derived from a small subset of countries. The observed racial/ethnic disparity was greater for multiple-gene and whole-exome sequencing than for single-gene sequencing. These findings illustrate the large disparity in published literature on the genetics of hearing loss, and demonstrate the need for increased representation of Latinx, Black, and Native American populations.


Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 936-936
Author(s):  
Hanna Koskela ◽  
Samuli Eldfors ◽  
Henrikki Almusa ◽  
Emma Andersson ◽  
Pekka Ellonen ◽  
...  

Abstract Abstract 936 BACKGROUND: T-cell large granular lymphocyte (LGL) leukemia is an uncommon lymphoproliferative disorder characterized in most cases by expansion of mature, clonal CD3+CD8+ cytotoxic T lymphocytes (CTLs). The pathogenesis of LGL-leukemia is unknown, and leukemic cells closely resemble normal terminally differentiated effector memory CTLs. While resistance to apoptotic pathways (Fas/Fas ligand, sphingolipid) and activation of survival signaling pathways (Ras) have been implicated in LGL leukemia, the underlying genetic defects have not yet been elucidated. We aimed to identify somatic mutations in LGL leukemia by whole exome sequencing of leukemic and matched healthy control cells. METHODS: Our index patient is a 70 year-old male with untreated CD8+ LGL leukemia diagnosed in 2009 with a clonal rearrangement in the T-cell receptor (TCR) delta and gamma gene. He has been asymptomatic with grade 2 neutropenia and an absolute lymphocyte count of 4–15 ×109/L. The patient had one large predominant T-cell clone: 94% of CD8+ cells consisted of a single Vβ16 clone, as assessed by flow cytometry. No clonal expansions were observed in the CD4+ fraction. DNA was extracted from FACS-sorted CD8+ (leukemic) and CD4+ (control) cells and sequenced by exome capture using an Agilent SureSelect All exon 50 MB capture kit and the Illumina GAII sequencing platform. Candidate somatic mutations were identified with a bioinformatics pipeline consisting of BWA for sequence alignment, Samtools for alignment filtering and Varscan for somatic mutation calling. Mutations were manually reviewed in IGV for alignment artifacts and validated by capillary sequencing. DNA samples from 8 additional untreated LGL-leukemia patients were used for further screening of confirmed somatic mutations by capillary sequencing. From six of these patients DNA was extracted from CD8 sorted cells and from two patients from whole blood. RESULTS: Whole exome sequencing of CD8+ leukemic DNA from the index patient identified a missense mutation in the STAT3 gene (D661V), which was subsequently confirmed by capillary sequencing. As STAT3 signaling has been associated with LGL leukemia pathogenesis previously, we next designed primers for the secondary screening of the six exomes of STAT3 SH2 region from the remaining patients. Another recurrent somatic missense mutation (STAT3 Y640F) was identified in two additional patients. Thus, three out of nine LGL patients (33%) showed evidence of mutations in the STAT3 SH2 region. Both missense mutations found (D661V and Y640F) were located in the area of the SH2 domain known to mediate STAT3 protein dimerization and activation. The Y640F mutation alters a conserved tyrosine residue leading to a hyperactivating STAT protein (Scarzello et al. Mol Biol Cell, 2007) and was recently found in a human inflammatory hepatocellular adenoma causing cytokine-independent tyrosine phosphorylation and activation as well as cytokine-dependent hyperactivation of STAT3 (Pitali et al., J Exp Med, 2011). The D661V mutation has not been described previously. CONCLUSIONS: Our data imply for the first time that STAT3 is a common mutational target in LGL leukemia, revealing insights to the molecular pathogenesis of this rare disease. Known structural and functional data on STAT biology imply that the mutations are leading to STAT3 hyperactivation and could also confer ligand-independent signaling. While confirmatory data from a larger series of patients are necessary, our results pinpoint STAT3 mutations and aberrations in the STAT3 pathway as key pathogenetic events in true clonal LGL leukemia. Detection of STAT3 mutations could therefore be applied in the diagnostic assessment, disease stratification and therapeutic monitoring of LGL patients. Disclosures: Koskela: Novartis: Honoraria. Kuittinen:Roche: Consultancy. Porkka:Novartis: Honoraria; Bristol-Myers Squibb: Honoraria. Mustjoki:Novartis: Honoraria; Bristol-Myers Squibb: Honoraria.


Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 258-258
Author(s):  
Johann Greil ◽  
Tobias Rausch ◽  
Thomas Giese ◽  
Obul Reddy Bandapalli ◽  
Volker Daniel ◽  
...  

Abstract Abstract 258 Primary immunodeficiencies represent model diseases for the mechanistic understanding of the human innate and the adaptive immune response and are per se clinically highly relevant, because in SCID patients infections by opportunistic pathogens are typically life-threatening early in life. We identified an infant of consanguineous parents suffering from a novel form of SCID, who presented with a life-threatening Pneumocystis jirovecii pneumonia. This entity was characterized by agammaglobulinemia and profoundly deficient T-cell function despite quantitatively normal T- and B-lymphocytes. Lymphocyte proliferation was strongly inhibited after stimulation of PBMCs with T-cell mitogens such as PHA, Con A, or anti-CD3 monoclonal antibody. The expression of several T-cell response associated cytokines upon stimulation with PMA/ionomycin was dramatically reduced in comparison to normal controls. By contrast, proliferation induced by the classical B-cell mitogen PWM was almost comparable to healthy controls. Immunophenotyping revealed a predominantly naïve phenotype (CD45RA+ CCR7+) in CD4+ and CD8+ T-lymphocytes, whereas central memory T-lymphocytes (CD45RA− CCR7+) were nearly absent. B-lymphocytes from peripheral blood were mainly naïve B-cells (CD27−) with a uniformly immature transitional B-lymphocyte phenotype (CD24++, CD38++). Patient B-lymphocytes retained the ability to proliferate and differentiate in response to BCR-independent stimuli, while their response to BCR activation was defective. Our findings thus revealed a combined defect of TCR-mediated T-lymphocyte functions and BCR-mediated B-lymphocyte functions but did not enable us to link the immunological phenotype with one of the known molecularly defined categories of SCID. Diagnostic whole-exome sequencing and systematic variant categorization revealed a single pathogenic homozygous nonsense mutation of the caspase recruitment domain 11 (CARD11) gene. CARD11 is a scaffold protein that is known to be required for the assembly and activation of the NF-kB complex. In reconstitution assays we demonstrated that the patient derived truncated CARD11 protein is defective in antigen receptor signaling and NF-kB activation. Several lines of evidence substantiate the involvement of the identified CARD11 mutation in the new form of SCID that we report here. First, PCR and Sanger re-sequencing validated the truncating CARD11 mutation to be homozygous in the patient and heterozygous in the parents, in agreement with the recessive transmission of the mutation through the healthy consanguineous parents. Second, CARD11 is a scaffold protein required for TCR- and BCR-induced NF-kB activation as well as lymphocyte activation and proliferation, which is specifically expressed in hematopoietic cells, consistent with a causative role of CARD11 mutations in the context of an immune disorder. Third, the GUK domain of CARD11, which is missing in the mutated form of CARD11 due to truncation, was previously reported to be necessary for NF-kB activation by PMA/ionomycin treatment, further supporting the presumed damaging nature of the homozygous CARD11 mutation observed in the female patient reported here. Finally, the immunological findings in this patient are compatible with the phenotype of a previously described Card11 −/− k.o. mouse, which shows a selective defect in NF-κB activation leading to diminished antigen receptor or PKC mediated proliferation and defective cytokine production in T-cells and B-cells. Thus, we have identified an inactivating CARD11 mutation linking defective NF-kB signaling with a novel cause of autosomal recessive SCID, which must be considered in the diagnostic assessment of patients with suspected SCID but with quantitatively normal T-cells. Disclosures: No relevant conflicts of interest to declare.


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