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  • 1
    Publication Date: 2015-07-25
    Description: Mutations in the LRBA gene (encoding the lipopolysaccharide-responsive and beige-like anchor protein) cause a syndrome of autoimmunity, lymphoproliferation, and humoral immune deficiency. The biological role of LRBA in immunologic disease is unknown. We found that patients with LRBA deficiency manifested a dramatic and sustained improvement in response to abatacept, a CTLA4 (cytotoxic T lymphocyte antigen-4)-immunoglobulin fusion drug. Clinical responses and homology of LRBA to proteins controlling intracellular trafficking led us to hypothesize that it regulates CTLA4, a potent inhibitory immune receptor. We found that LRBA colocalized with CTLA4 in endosomal vesicles and that LRBA deficiency or knockdown increased CTLA4 turnover, which resulted in reduced levels of CTLA4 protein in FoxP3(+) regulatory and activated conventional T cells. In LRBA-deficient cells, inhibition of lysosome degradation with chloroquine prevented CTLA4 loss. These findings elucidate a mechanism for CTLA4 trafficking and control of immune responses and suggest therapies for diseases involving the CTLA4 pathway.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Lo, Bernice -- Zhang, Kejian -- Lu, Wei -- Zheng, Lixin -- Zhang, Qian -- Kanellopoulou, Chrysi -- Zhang, Yu -- Liu, Zhiduo -- Fritz, Jill M -- Marsh, Rebecca -- Husami, Ammar -- Kissell, Diane -- Nortman, Shannon -- Chaturvedi, Vijaya -- Haines, Hilary -- Young, Lisa R -- Mo, Jun -- Filipovich, Alexandra H -- Bleesing, Jack J -- Mustillo, Peter -- Stephens, Michael -- Rueda, Cesar M -- Chougnet, Claire A -- Hoebe, Kasper -- McElwee, Joshua -- Hughes, Jason D -- Karakoc-Aydiner, Elif -- Matthews, Helen F -- Price, Susan -- Su, Helen C -- Rao, V Koneti -- Lenardo, Michael J -- Jordan, Michael B -- 1RC2 HG005608/HG/NHGRI NIH HHS/ -- 1ZIAAI000769-14/PHS HHS/ -- Intramural NIH HHS/ -- New York, N.Y. -- Science. 2015 Jul 24;349(6246):436-40. doi: 10.1126/science.aaa1663.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Molecular Development of the Immune System Section and Clinical and Molecular Genomics Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. michael.jordan@cchmc.org. ; Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA. michael.jordan@cchmc.org. ; Molecular Development of the Immune System Section and Clinical and Molecular Genomics Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. ; NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Human Immunological Diseases Unit, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. ; Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. ; Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA. ; Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA. ; Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA. ; Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, and Division of Allergy, Pulmonary, and Critical Care, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA. ; Departments of Pathology and Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, CA, USA. ; Section of Allergy and Immunology, Nationwide Children's Hospital, Columbus, OH, USA. ; Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA. ; Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center/ University of Cincinnati, Cincinnati, OH, USA. ; Merck Research Laboratories, Merck & Co, Boston, MA, USA. ; Molecular Development of the Immune System Section and Clinical and Molecular Genomics Unit, Laboratory of Immunology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. NIAID Clinical Genomics Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Division of Human Genetics, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA. Human Immunological Diseases Unit, Laboratory of Host Defenses, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Lymphocyte Biology Section, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA. Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA. Division of Pediatric Hematology and Oncology, Department of Pediatrics, University of Alabama at Birmingham, AL, USA. Division of Allergy, Immunology, and Pulmonary Medicine, Department of Pediatrics, and Division of Allergy, Pulmonary, and Critical Care, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA. Departments of Pathology and Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, CA, USA. Section of Allergy and Immunology, Nationwide Children's Hospital, Columbus, OH, USA. Department of Pediatrics and Adolescent Medicine, Mayo Clinic, Rochester, MN, USA. Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center/ University of Cincinnati, Cincinnati, OH, USA. Merck Research Laboratories, Merck & Co, Boston, MA, USA. Marmara University, Division of Pediatric Allergy and Immunology, Istanbul, Turkey. ; Division of Bone Marrow Transplantation and Immune Deficiency, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, OH, USA. Division of Immunobiology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center/ University of Cincinnati, Cincinnati, OH, USA. michael.jordan@cchmc.org.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26206937" target="_blank"〉PubMed〈/a〉
    Keywords: Abatacept ; Adaptor Proteins, Signal Transducing/genetics/*metabolism ; Adolescent ; Autoimmune Diseases/*drug therapy/metabolism ; CTLA-4 Antigen/*deficiency/genetics ; Child ; Chloroquine/pharmacology ; Common Variable Immunodeficiency/*drug therapy/metabolism ; Endosomes/metabolism ; Female ; Forkhead Transcription Factors/analysis ; Gene Knockdown Techniques ; HEK293 Cells ; Humans ; Immunoconjugates/*therapeutic use ; Lung Diseases, Interstitial/drug therapy/metabolism ; Lymphocyte Activation ; Lysosomes/metabolism ; Male ; Proteolysis ; T-Lymphocytes/drug effects/immunology ; Young Adult
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2014-08-21
    Description: Key Points Synergistic effects were observed in the granule mediated lymphocyte cytotoxicity. Digenic pathogenesis contributed to the development of hemophagocytic lymphohistiocytosis.
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
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  • 3
    Publication Date: 2012-11-16
    Description: Abstract 976 Introduction: Erythrocyte cytoskeleton disorders, a common cause of hereditary hemolytic anemia, consist of a genetically and phenotypically variable group of diseases that include hereditary spherocytosis (HS), elliptocytosis (HE), pyropoikilocytosis (HPP), and stomatocytosis (HSt) syndromes. The diagnosis is most commonly based on the morphology of the red blood cells (RBCs) on the blood smear and on ektacytometry and osmotic fragility studies. However, in infants and children with transfusion-dependent hemolytic anemia these studies are challenging to obtain since the patient has mostly transfused RBCs. Molecular diagnosis has not been easily attainable so far due to the number and large size of the genes involved in pathogenesis and due to the fact that each kindred has frequently a private mutation in the responsible gene(s) (Gallagher, Hematology, 2005). Methods and Results: We have developed a high-throughput assay for the diagnosis of known and discovery of new genetic mutations causing erythrocyte cytoskeleton disorders. The complete exon sequences of 24 genes encoding cytoskeleton proteins (spectrin a-chain (SPTA1), spectrin b-chain (SPTB), ankyrin 1 (ANK1), band 3 (SLC4A1), protein 4.1 (EPB41), protein 4.2 (EPB42), adducins (ADD), dematin (EPB49), tropomyosins (TPM), tropomodulins (TMOD), Rh-associated glycoprotein (RhAG), erythrocyte protein p55 (MPP1), stomatin (EPB72), Glut1-glucose transporter (SLC2A1), and K-Cl-cotransporter (SLC12A4, SLC12A6, SLC12A7) were determined using a Next Generation Sequencing technology. Analysis was performed on eleven patients diagnosed with erythrocyte cytoskeleton disorder along with a negative control. Informed consent was obtained from all subjects under an Institutional Review Board-approved protocol. The RainDance Technologies RDT1000 instrument was used for target enrichment covering the exons, 20 bases of exon/intron junctions, and 500 bases up and downstream of the 24 genes of interest. The products were then sequenced on an Illumina HiSeq2000 system. Bioinformatic analysis was performed in a blinded fashion as to the disease characteristics and inheritance mode of the patient using the GATK software package from the Broad Institute (DePristo et al, Nature Genetics, 2011). Mutations predicted to have significant impact to the corresponding protein structure and therefore likely to cause disease were identified in 9 out of the 11 patients (Table 1). Shared pathogenic mutation(s) were identified blindly in family members, e.g. siblings HS-S1 and HS-S2, or parents sHS-M, sHS-F with child sHS. Two EPB49 mutations predicted to impair gene function were identified in an infant with clinical picture of HPP, implicating dematin in HPP pathogenesis. Immunoblotting of RBC membranes from this patient demonstrated decreased dematin. Conclusions: Next generation sequencing for the genetically variable erythrocyte cytoskeleton disorders can provide a cost-effective and faster patient diagnosis compared with a gene-by-gene approach and it is a feasible diagnostic method in a transfusion-dependent child. Moreover, a precise genetic diagnosis can facilitate natural history studies to understand genotype-phenotype correlations in the erythrocyte cytoskeleton disorders and offer valuable insights into the structure-function relationship of the erythrocyte cytoskeleton proteins. Disclosures: No relevant conflicts of interest to declare.
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2018-11-29
    Description: CDAR (ClinicalTrials.gov Identifier: NCT02964494), a registry for patients with Congenital Dyserythropoietic Anemia (CDA) in North America, has been created with the goal to provide a longitudinal database and associated biorepository to facilitate natural history studies and research on the molecular pathways involved in the pathogenesis of CDAs. A 1 y.o. female patient with non-immune hemolytic anemia with suboptimal reticulocytosis, requiring frequent transfusions, and with the pathologic diagnosis of CDA was enrolled in CDAR. Her father had a similar phenotypical presentation in early childhood and underwent splenectomy at 3 years of age. Since then, he has rarely required transfusions but he continues to have a mild anemia at baseline with characteristics of hemolysis and with suboptimal reticulocytosis; at the time of enrollment, he had hemoglobin of 9.3 g/dL with absolute reticulocyte count of 115 x 106 cells/µl. Next Generation sequencing and deletion/duplication assay for the known CDA-associated genes (CDAN1, C15ORF41, SEC23B, KIF23, GATA1) identified no mutations. Whole-exome sequencing for the patient and her parents (family-trio design) revealed a novel PRDX2 missense variant (c.154C〉T; p.Pro52Ser) present in heterozygous state in both proband and her father; no mutation in this gene was present in the asymptomatic mother. In silico prediction programs suggest that this variant is probably damaging and deleterious, causing a non-conservative substitution of a phylogenetically highly-conserved amino acid (down to Baker's yeast), and located in an enzymatically active protein domain, adjacent to the active Cys51, with the potential to change its conformation. Peroxiredoxin II is highly expressed during terminal erythropoiesis and is one of the most abundant proteins after hemoglobin in erythroblasts and mature erythrocytes. It is an antioxidant enzyme that reduces the reactive oxygen species (ROS), like hydrogen peroxide and alkyl hydroperoxides readily produced within the erythroid cells due to the presence of heme iron and oxygen. In addition, PRDX2 has been implicated in intracellular signaling, cellular proliferation and differentiation, and as a regulator of iron homeostasis. PRDX2-/- mice were found to have hemolytic anemia with evidence of oxidative damage of the erythrocyte proteins resulting to decreased red blood cell (RBC) survival. The aim of this work is to validate the pathogenetic role of the PRDX2 variant found in this family as the molecular cause of this dominantly-inherited CDA and further investigate the role of PRDX2 in human terminal erythropoiesis. Central review of the patient's bone marrow aspirate and biopsy slides, according to the CDAR protocol, revealed erythroid hyperplasia with dyserythropoiesis, including megaloblastoid changes, nuclear lobation and fragmentation, and binucleated erythroblasts (less than 10%), compatible with atypical CDA. There were rare erythroids with cytoplasmic bridging but no nuclear bridges. Review of the peripheral blood smear showed significant poikilocytosis, mild polychromasia, and the presence of blister and ghost cells reminiscent of G6PD deficiency, pointing to RBC damage by oxidative stress. Induced pluripotent stem cells (iPSCs) and EBV-immortalized lymphocytes were generated from the patients' peripheral blood mononuclear cells after informed consent per CDAR protocol, to allow further in vitro studies of the peroxiredoxin II-deficiency. Flow cytometry confirmed significantly increased ROS in the patients' derived versus control EBV-immortalized lymphocytes as well as in the reticulocytes and mature erythrocytes of the proband and her father, indicating that their PRDX2 variant is causing loss-of-function of the enzyme and increased oxidative stress. Further work is ongoing to explore the mechanisms of pathogenicity of peroxiredoxin II deficiency towards human dyserythropoiesis and decreased erythrocyte lifespan. To our knowledge, this is the first case of anemia described in humans associated with PRDX2 mutation implicating this gene as a novel candidate gene for atypical, dominantly-inherited CDA. Disclosures No relevant conflicts of interest to declare.
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
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  • 5
  • 6
    Publication Date: 2013-11-15
    Description: Hereditary hemolytic anemia is caused by defects in hemoglobin, in the red blood cell (RBC) cytoskeleton proteins, or by deficiencies in RBC enzymes. RBC cytoskeletal disorders include hereditary spherocytosis (HS), elliptocytosis (HE), pyropoikilocytosis (HPP), and stomatocytosis (HSt), which are typically inherited as autosomal dominant disorders but can also present as recessive forms, frequently severe. The RBC enzymopathies, such as glucose-6-phosphate dehydrogenase (G6PD) and pyruvate kinase (PK) deficiency, are X-linked or recessively inherited disorders causing hemolytic anemia. Although rare, congenital dyserythropoietic anemias (CDA) are inherited red cell lineage disorders which occasionally, especially CDA-II, can be misdiagnosed as HS. Diagnosis of an inherited hemolytic anemia not due to a hemoglobin disorder is based upon morphology of the RBCs, functional analysis of the RBCs through ektacytometry or osmotic fragility, and enzymatic assays. The diagnosis of severely affected patients is complicated by transfusion dependence. Diagnosis based on genetic mutations is attractive, especially in transfused patients, and provides additional insight into the mechanisms of disease. Despite these advantages, genetic diagnoses have been limited by expense and long turn-around times for clinical results. To address these issues, we have developed a rapid comprehensive clinical next-generation sequencing-based assay that evaluates 27 genes with published disease-causing mutations for RBC cytoskeletal disorders, enzymopathies, and CDAs. The protein-coding exons plus 25 bases of exon/intron junction as well as promoter sequences with known relationship to clinical phenotypes were included in the design. Genomic DNA was digested with a panel of 8 restriction enzymes and oligonucleotide probes were used to enrich the target regions. Enriched samples were then sequenced on an Illumina MiSeq benchtop sequencer with 150 base pair, paired-end reads. Enrichment and sequencing were completed within 48 hours. Sequencing reads were aligned to the human genome reference sequence and analysis of coverage and variants was completed using NextGENe software. Initial validation included 5 affected probands, 1 affected sibling of a proband, 4 parental samples, and 2 unrelated control individuals with no history of hemolytic anemia. Overall, 〉 99% of all nucleotides in the regions of interest had at least 20X sequencing coverage. Our assay confirmed a previously identified maternally inherited nonsense mutation, Y1089X, and a paternally inherited A970D missense variant in SPTA1 in a patient (SPCA) with severe HS. The A970D SPTA1 missense change was also seen in two unaffected parents and an unaffected control, further validating that this missense variant alone does not cause dominant HS. The common SPTA1 allele, αLELY was seen in the clinically unaffected mother of SPCA, but was not found in the affected child, suggesting that this allele must be inherited in trans with a pathologic SPTA1 mutation to have clinical effect. Analysis of additional probands revealed both dominant and recessive forms of HS due to mutations in ANK1. Patient AAHS2 presented with typical dominant HS, and was found to have a novel ANK1 frameshift mutation, c.3464delG. Patient HEEM presented with severe transfusion-dependent anemia and was found to have one reported ANK1 missense mutation, T1075I (ankyrin Tubarao) in the spectrin-binding domain, and one novel nonsense mutation, Y735X. In addition, we identified novel amino acid changes in the newly identified dehydrated HSt gene PIEZO1. HEGR, a patient with hemolytic anemia, splenomegaly and portal vein thrombosis in infancy was found to have a novel 6 base pair insertion at R1462 in PIEZO1. Thal1 was previously diagnosed with dominant β-thalassemia, however had a more severe presentation than expected. We found a PIEZO1missense mutation R2302H in Thal1 that likely explains the severe phenotype. The initial validation of this comprehensive sequencing assay has demonstrated that this is a robust and rapid diagnostic tool for patients with severe hereditary hemolytic anemia. Simultaneous investigation of the key protein-coding genes involved in proper RBC function and survival, provides new insight into the variable phenotypes of patients with hemolytic anemia and ultimately will improve the management of patients with severe disease. Disclosures: No relevant conflicts of interest to declare.
    Print ISSN: 0006-4971
    Electronic ISSN: 1528-0020
    Topics: Biology , Medicine
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  • 7
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  • 9
    Publication Date: 2021-03-02
    Description: Background VCF formatted files are the lingua franca of next-generation sequencing, whereas HL7 FHIR is emerging as a standard language for electronic health record interoperability. A growing number of FHIR-based clinical genomics applications are emerging. Here, we describe an open source utility for converting variants from VCF format into HL7 FHIR format. Results vcf2fhir converts VCF variants into a FHIR Genomics Diagnostic Report. Conversion translates each VCF row into a corresponding FHIR-formatted variant in the generated report. In scope are simple variants (SNVs, MNVs, Indels), along with zygosity and phase relationships, for autosomes, sex chromosomes, and mitochondrial DNA. Input parameters include VCF file and genome build (‘GRCh37’ or ‘GRCh38’); and optionally a conversion region that indicates the region(s) to convert, a studied region that lists genomic regions studied by the lab, and a non-callable region that lists studied regions deemed uncallable by the lab. Conversion can be limited to a subset of VCF by supplying genomic coordinates of the conversion region(s). If studied and non-callable regions are also supplied, the output FHIR report will include ‘region-studied’ observations that detail which portions of the conversion region were studied, and of those studied regions, which portions were deemed uncallable. We illustrate the vcf2fhir utility via two case studies. The first, 'SMART Cancer Navigator', is a web application that offers clinical decision support by linking patient EHR information to cancerous gene variants. The second, 'Precision Genomics Integration Platform', intersects a patient's FHIR-formatted clinical and genomic data with knowledge bases in order to provide on-demand delivery of contextually relevant genomic findings and recommendations to the EHR. Conclusions Experience to date shows that the vcf2fhir utility can be effectively woven into clinically useful genomic-EHR integration pipelines. Additional testing will be a critical step towards the clinical validation of this utility, enabling it to be integrated in a variety of real world data flow scenarios. For now, we propose the use of this utility primarily to accelerate FHIR Genomics understanding and to facilitate experimentation with further integration of genomics data into the EHR.
    Electronic ISSN: 1471-2105
    Topics: Biology , Computer Science
    Published by BioMed Central
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  • 10
    Publication Date: 2015-07-24
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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