Browsing by Author "Chinn, Ivan K."
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Item Absent B cells, agammaglobulinemia, and hypertrophic cardiomyopathy in folliculin-interacting protein 1 deficiency(2020) Saettini, Francesco; Poli, Cecilia; Vengoechea, Jaime; Bonanomi, Sonia; Orellana, Julio C.; Fazio, Grazia; Rodriguez, Fred H.; Noguera, Loreani; Booth, Claire; Jarur-Chamy, Valentina; Shams, Marissa; Iascone, María; Vukic, Maja; Gasperini, Serena; Quadri, Manuel; Barroeta Seijas, Amairelys; Rivers, Elizabeth; Mauri, Mario; Badolato, Raffaele; Cazzaniga, Gianni; Bugarin, Cristina; Gaipa, Giuseppe; Kroes, Wilma G. M.; Moratto, Daniele; Oostaijen-Ten Dam, Monique M. van; Baas, Frank; Maarel, Silvère van der; Piazza, Rocco; Coban-Akdemir, Zeynep H.; Lupski, James R.; Yuan, Boi; Daxinger, Lucia; Biondi, Andrea; Chinn, Ivan K.Agammaglobulinemia is the most profound primary antibody deficiency that can occur due to an early termination of B-cell development. We here investigated three novel patients, including the first known adult, from unrelated families with agammaglobulinemia, recurrent infections, and hypertrophic cardiomyopathy (HCM). Two of them also presented with intermittent or severe chronic neutropenia. We identified homozygous or compound heterozygous variants in the gene for Folliculin interacting protein 1 (FNIP1), leading to loss of the FNIP1 protein. B-cell metabolism, including mitochondrial numbers and activity and PI3K/AKT pathway, was impaired. These defects recapitulated the Fnip1 -/- animal model. Moreover, we identified either uniparental disomy or copy number variants [CNV] in two patients, expanding the variant spectrum of this novel inborn error of immunity. The results indicate that FNIP1 deficiency can be caused by complex genetic mechanisms and support the clinical utility of exome sequencing and CNV analysis in patients with broad phenotypes, including agammaglobulinemia and HCM. FNIP1 deficiency is a novel inborn error of immunity characterized by early and severe B-cell development defect, agammaglobulinemia, variable neutropenia, and HCM. Our findings elucidate a functional and relevant role of FNIP1 in B-cell development and metabolism and potentially neutrophil activity.Item Genetic and mechanistic diversity in pediatric hemophagocytic lymphohistiocytosis(2018) Chinn, Ivan K.; Eckstein, Olive S.; Peckham-Gregory, Erin C.; Goldberg, Baruch R.; Forbes, Lisa R.; Nicholas, Sarah K.; Mace, Emily M.; Vogel, Tiphanie P.; Abhyankar, Harshal A.; Diaz, Maria I.; Heslop, Helen E.; Krance, Robert A.; Martinez, Caridad A.; Nguyen, Trung C.; Bashir, Dalia A.; Goldman, Jordana R.; Stray-Pedersen, Asbjørg; Pedroza, Luis A.; Poli, Cecilia; Aldave-Becerra, Juan C.; McGhee, Sean A.; Al-Herz, Waleed; Chamdin, Aghiad; Coban-Akdemir, Zeynep H.; Jhangiani, Shalini N.; Muzny, Donna M.; Cao, Tram N.; Hong, Diana N.; Gibbs, Richard A.; Lupski, James R.; Orange, Jordan S.; McClain, Kenneth L.; Allen, Carl E.The HLH-2004 criteria are used to diagnose hemophagocytic lymphohistiocytosis (HLH), yet concern exists for their misapplication, resulting in suboptimal treatment of some patients. We sought to define the genomic spectrum and associated outcomes of a diverse cohort of children who met the HLH-2004 criteria. Genetic testing was performed clinically or through research-based whole-exome sequencing. Clinical metrics were analyzed with respect to genomic results. Of 122 subjects enrolled over the course of 17 years, 101 subjects received genetic testing. Biallelic familial HLH (fHLH) gene defects were identified in only 19 (19%) and correlated with presentation at younger than 1 year of age (P < .0001). Digenic fHLH variants were observed but lacked statistical support for disease association. In 28 (58%) of 48 subjects, research whole-exome sequencing analyses successfully identified likely molecular explanations, including underlying primary immunodeficiency diseases, dysregulated immune activation and proliferation disorders, and potentially novel genetic conditions. Two-thirds of patients identified by the HLH-2004 criteria had underlying etiologies for HLH, including genetic defects, autoimmunity, and malignancy. Overall survival was 45%, and increased mortality correlated with HLH triggered by infection or malignancy (P < .05). Differences in survival did not correlate with genetic profile or extent of therapy. HLH should be conceptualized as a phenotype of critical illness characterized by toxic activation of immune cells from different underlying mechanisms. In most patients with HLH, targeted sequencing of fHLH genes remains insufficient for identifying pathogenic mechanisms. Whole-exome sequencing, however, may identify specific therapeutic opportunities and affect hematopoietic stem cell transplantation options for these patients.Item Genetic errors of immunity distinguish pediatric nonmalignant lymphoproliferative disorders(2022) Forbes, Lisa R.; Eckstein, Olive S.; Gulati, Nitya; Peckham-Gregory, Erin C.; Ozuah, Nmazuo W.; Lubega, Joseph; El-Mallawany, Nader K.; Agrusa, Jennifer E.; Poli, Cecilia; Vogel, Tiphanie P.; Chaimowitz, Natalia S.; Rider, Nicholas L.; Mace, Emily M.; Orange, Jordan S.; Caldwell, Jason W.; Aldave-Becerra, Juan C.; Jolles, Stephen; Saettini, Francesco; Chong, Hey J.; Stray-Pedersen, Asbjorg; Heslop, Helen E.; Kamdar, Kala Y.; Rouce, R. Helen; Muzny, Donna M.; Jhangiani, Shalini N.; Gibbs, Richard A.; Coban-Akdemir, Zeynep H.; Lupski, James R.; McClain, Kenneth L.; Allen, Carl E.; Chinn, Ivan K.Background: Pediatric nonmalignant lymphoproliferative disorders (PLPDs) are clinically and genetically heterogeneous. Long-standing immune dysregulation and lymphoproliferation in children may be life-threatening, and a paucity of data exists to guide evaluation and treatment of children with PLPD. Objective: The primary objective of this study was to ascertain the spectrum of genomic immunologic defects in PLPD. Secondary objectives included characterization of clinical outcomes and associations between genetic diagnoses and those outcomes. Methods: PLPD was defined by persistent lymphadenopathy, lymph organ involvement, or lymphocytic infiltration for more than 3 months, with or without chronic or significant Epstein-Barr virus (EBV) infection. Fifty-one subjects from 47 different families with PLPD were analyzed using whole exome sequencing. Results: Whole exome sequencing identified likely genetic errors of immunity in 51% to 62% of families (53% to 65% of affected children). Presence of a genetic etiology was associated with younger age and hemophagocytic lymphohistiocytosis. Ten-year survival for the cohort was 72.4%, and patients with viable genetic diagnoses had a higher survival rate (82%) compared to children without a genetic explanation (48%, P = .03). Survival outcomes for individuals with EBV-associated disease and no genetic explanation were particularly worse than outcomes for subjects with EBV-associated disease and a genetic explanation (17% vs 90%; P = .002). Ascertainment of a molecular diagnosis provided targetable treatment options for up to 18 individuals and led to active management changes for 12 patients. Conclusions: PLPD defines children at high risk for mortality, and whole exome sequencing informs clinical risks and therapeutic opportunities for this diagnosis.Item Heterozygous Truncating Variants in POMP Escape Nonsense-Mediated Decay and Cause a Unique Immune Dysregulatory Syndrome(2018) Poli, Cecilia; Ebstein, Frédéric; Nicholas, Sarah K.; Guzman, Marietta M. de; Forbes, Lisa R.; Chinn, Ivan K.; Mace, Emily M.; Vogel, Tiphanie P.; Carisey, Alexandre F.; Benavides, Felipe; Coban-Akdemir, Zeynep H.; Gibbs, Richard A.; Jhangiani, Shalini N.; Muzny, Donna M.; Carvalho, Claudia M. B.; Schady, Deborah A.; Jain, Mahim; Rosenfeld, Jill A .; Emrick, Lisa; Lewis, Richard A.; Lee, Brendan; Undiagnosed Diseases Network members; Zieba, Barbara A.; Küry, Sébastien; Krüger, Elke; Lupski, James R.; Bostwick, Bret L.; Orange, Jordan S.The proteasome processes proteins to facilitate immune recognition and host defense. When inherently defective, it can lead to aberrant immunity resulting in a dysregulated response that can cause autoimmunity and/or autoinflammation. Biallelic or digenic loss-of-function variants in some of the proteasome subunits have been described as causing a primary immunodeficiency disease that manifests as a severe dysregulatory syndrome: chronic atypical neutrophilic dermatosis with lipodystrophy and elevated temperature (CANDLE). Proteasome maturation protein (POMP) is a chaperone for proteasome assembly and is critical for the incorporation of catalytic subunits into the proteasome. Here, we characterize and describe POMP-related autoinflammation and immune dysregulation disease (PRAID) discovered in two unrelated individuals with a unique constellation of early-onset combined immunodeficiency, inflammatory neutrophilic dermatosis, and autoimmunity. We also begin to delineate a complex genetic mechanism whereby de novo heterozygous frameshift variants in the penultimate exon of POMP escape nonsense-mediated mRNA decay (NMD) and result in a truncated protein that perturbs proteasome assembly by a dominant-negative mechanism. To our knowledge, this mechanism has not been reported in any primary immunodeficiencies, autoinflammatory syndromes, or autoimmune diseases. Here, we define a unique hypo- and hyper-immune phenotype and report an immune dysregulation syndrome caused by frameshift mutations that escape NMD.Item Hypomorphic caspase activation and recruitment domain 11 (CARD11) mutations associated with diverse immunologic phenotypes with or without atopic disease(2019) Dorjbal, Batsukh; Stinson, Jeffrey R.; Ma, Chi A.; Weinreich, Michael A.; Miraghazadeh, Bahar; Hartberger, Julia M.; Frey-Jakobs, Stefanie; Weidinger, Stephan; Moebus, Lena; Franke, Andre; Schäffer, Alejandro; Bulashevska, Alla; Fuchs, Sebastian; Ehl, Stephan; Limaye, Sandhya; Arkwright, Peter D.; Briggs, Tracy A.; Langley, Claire; Bethune, Claire; Whyte, Andrew F; Alachkar, Hana; Nejentsev, Sergey; DiMaggio, Thomas; Nelson, Celeste G.; Stone, Kelly D.; Nason, Martha; Brittain, Erica H.; Oler, Andrew J.; Veltri, Daniel P.; Leahy, T Ronan; Conlon, Niall; Poli, Cecilia; Borzutzky, Arturo; Cohen, Jeffrey I.; Davis, Joie; Lambert, Michele P.; Romberg, Neil; Sullivan, Kathleen E.; Paris, Kenneth; Freeman, Alexandra F.; Lucas, Laura; Chandrakasan, Shanmuganathan; Savic, Sinisa; Hambleton, Sophie; Patel, Smita Y.; Jordan, Michael B.; Theos, Amy; Lebensburger, Jeffrey; Atkinson, Prescott; Torgerson, Troy R.; Chinn, Ivan K.; Milner, Joshua D.; Grimbacher, Bodo; Cook, Matthew C.; Snow, Andrew L.Background: Caspase activation and recruitment domain 11 (CARD11) encodes a scaffold protein in lymphocytes that links antigen receptor engagement with downstream signaling to nuclear factor κB, c-Jun N-terminal kinase, and mechanistic target of rapamycin complex 1. Germline CARD11 mutations cause several distinct primary immune disorders in human subjects, including severe combined immune deficiency (biallelic null mutations), B-cell expansion with nuclear factor κB and T-cell anergy (heterozygous, gain-of-function mutations), and severe atopic disease (loss-of-function, heterozygous, dominant interfering mutations), which has focused attention on CARD11 mutations discovered by using whole-exome sequencing. Objectives: We sought to determine the molecular actions of an extended allelic series of CARD11 and to characterize the expanding range of clinical phenotypes associated with heterozygous CARD11 loss-of-function alleles. Methods: Cell transfections and primary T-cell assays were used to evaluate signaling and function of CARD11 variants. Results: Here we report on an expanded cohort of patients harboring novel heterozygous CARD11 mutations that extend beyond atopy to include other immunologic phenotypes not previously associated with CARD11 mutations. In addition to (and sometimes excluding) severe atopy, heterozygous missense and indel mutations in CARD11 presented with immunologic phenotypes similar to those observed in signal transducer and activator of transcription 3 loss of function, dedicator of cytokinesis 8 deficiency, common variable immunodeficiency, neutropenia, and immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like syndrome. Pathogenic variants exhibited dominant negative activity and were largely confined to the CARD or coiled-coil domains of the CARD11 protein. Conclusion: These results illuminate a broader phenotypic spectrum associated with CARD11 mutations in human subjects and underscore the need for functional studies to demonstrate that rare gene variants encountered in expected and unexpected phenotypes must nonetheless be validated for pathogenic activity.Item Identifying Genes Whose Mutant Transcripts Cause Dominant Disease Traits by Potential Gain-of-Function Alleles(2018) Coban-Akdemir, Zeynep; White, Janson J.; Song, Xiaofei; Jhangiani, Shalini N.; Fatih, Jawid M.; Gambin, Tomasz; Bayram, Yavuz; Chinn, Ivan K.; Karaca, Ender; Punetha, Jaya; Poli, Cecilia; Baylor-Hopkins Center for Mendelian Genomics; Boerwinkle, Eric; Shaw, Chad A.; Orange, Jordan S.; Gibbs, Richard A.; Lappalainen, Tuuli; Lupski, James R.; Carvalho, Claudia M.B.Premature termination codon (PTC)-bearing transcripts are often degraded by nonsense-mediated decay (NMD) resulting in loss-of-function (LoF) alleles. However, not all PTCs result in LoF mutations, i.e., some such transcripts escape NMD and are translated to truncated peptide products that result in disease due to gain-of-function (GoF) effects. Since the location of the PTC is a major factor determining transcript fate, we hypothesized that depletion of protein-truncating variants (PTVs) within the gene region predicted to escape NMD in control databases could provide a rank for genic susceptibility for disease through GoF versus LoF. We developed an NMD escape intolerance score to rank genes based on the depletion of PTVs that would render them able to escape NMD using the Atherosclerosis Risk in Communities Study (ARIC) and the Exome Aggregation Consortium (ExAC) control databases, which was further used to screen the Baylor-Center for Mendelian Genomics disease database. This analysis revealed 1,996 genes significantly depleted for PTVs that are predicted to escape from NMD, i.e., PTVesc; further studies provided evidence that revealed a subset as candidate genes underlying Mendelian phenotypes. Importantly, these genes have characteristically low pLI scores, which can cause them to be overlooked as candidates for dominant diseases. Collectively, we demonstrate that this NMD escape intolerance score is an effective and efficient tool for gene discovery in Mendelian diseases due to production of truncated or altered proteins. More importantly, we provide a complementary analytical tool to aid identification of genes associated with dominant traits through a mechanism distinct from LoF.