@article {771, title = {Defective glycosylation and multisystem abnormalities characterize the primary immunodeficiency XMEN disease.}, journal = {J Clin Invest}, volume = {130}, year = {2020}, month = {2020 01 02}, pages = {507-522}, abstract = {

X-linked immunodeficiency with magnesium defect, EBV infection, and neoplasia (XMEN) disease are caused by deficiency of the magnesium transporter 1 (MAGT1) gene. We studied 23 patients with XMEN, 8 of whom were EBV naive. We observed lymphadenopathy (LAD), cytopenias, liver disease, cavum septum pellucidum (CSP), and increased CD4-CD8-B220-TCRαβ+ T cells (αβDNTs), in addition to the previously described features of an inverted CD4/CD8 ratio, CD4+ T lymphocytopenia, increased B cells, dysgammaglobulinemia, and decreased expression of the natural killer group 2, member D (NKG2D) receptor. EBV-associated B cell malignancies occurred frequently in EBV-infected patients. We studied patients with XMEN and patients with autoimmune lymphoproliferative syndrome (ALPS) by deep immunophenotyping (32 immune markers) using time-of-flight mass cytometry (CyTOF). Our analysis revealed that the abundance of 2 populations of naive B cells (CD20+CD27-CD22+IgM+HLA-DR+CXCR5+CXCR4++CD10+CD38+ and CD20+CD27-CD22+IgM+HLA-DR+CXCR5+CXCR4+CD10-CD38-) could differentially classify XMEN, ALPS, and healthy individuals. We also performed glycoproteomics analysis on T lymphocytes and show that XMEN disease is a congenital disorder of glycosylation that affects a restricted subset of glycoproteins. Transfection of MAGT1 mRNA enabled us to rescue proteins with defective glycosylation. Together, these data provide new clinical and pathophysiological foundations with important ramifications for the diagnosis and treatment of XMEN disease.

}, keywords = {Antigens, CD, Autoimmune Lymphoproliferative Syndrome, Cation Transport Proteins, CD4-CD8 Ratio, Female, Glycosylation, Humans, Magnesium Deficiency, Male, X-Linked Combined Immunodeficiency Diseases}, issn = {1558-8238}, doi = {10.1172/JCI131116}, author = {Ravell, Juan C and Matsuda-Lennikov, Mami and Chauvin, Samuel D and Zou, Juan and Biancalana, Matthew and Deeb, Sally J and Price, Susan and Su, Helen C and Notarangelo, Giulia and Jiang, Ping and Morawski, Aaron and Kanellopoulou, Chrysi and Binder, Kyle and Mukherjee, Ratnadeep and Anibal, James T and Sellers, Brian and Zheng, Lixin and He, Tingyan and George, Alex B and Pittaluga, Stefania and Powers, Astin and Kleiner, David E and Kapuria, Devika and Ghany, Marc and Hunsberger, Sally and Cohen, Jeffrey I and Uzel, Gulbu and Bergerson, Jenna and Wolfe, Lynne and Toro, Camilo and Gahl, William and Folio, Les R and Matthews, Helen and Angelus, Pam and Chinn, Ivan K and Orange, Jordan S and Trujillo-Vargas, Claudia M and Franco, Jose Luis and Orrego-Arango, Julio and Guti{\'e}rrez-Hincapi{\'e}, Sebastian and Patel, Niraj Chandrakant and Raymond, Kimiyo and Patiroglu, Turkan and Unal, Ekrem and Karakukcu, Musa and Day, Alexandre Gr and Mehta, Pankaj and Masutani, Evan and De Ravin, Suk S and Malech, Harry L and Altan-Bonnet, Gr{\'e}goire and Rao, V Koneti and Mann, Matthias and Lenardo, Michael J} } @article {759, title = { Mutation Distribution and Type Suggests Genetic Differences between the Etiology of Orofacial Clefting and Gastric Cancer.}, journal = {Genes (Basel)}, volume = {11}, year = {2020}, month = {2020 04 03}, abstract = {

Pathogenic variants in , encoding epithelial cadherin (E-cadherin), have been implicated in hereditary diffuse gastric cancer (HDGC), lobular breast cancer, and both syndromic and non-syndromic cleft lip/palate (CL/P). Despite the large number of mutations described, the nature of the phenotypic consequence of such mutations is currently not able to be predicted, creating significant challenges for genetic counselling. This study collates the phenotype and molecular data for available variants that have been classified, using the American College of Medical Genetics and Genomics criteria, as at least {\textquoteright}likely pathogenic{\textquoteright}, and correlates their molecular and structural characteristics to phenotype. We demonstrate that variant type and location differ between HDGC and CL/P, and that there is clustering of CL/P variants within linker regions between the extracellular domains of the cadherin protein. While these differences do not provide for exact prediction of the phenotype for a given mutation, they may contribute to more accurate assessments of risk for HDGC or CL/P for individuals with specific variants.

}, keywords = {Antigens, CD, Brain, Cadherins, Cleft Lip, Cleft Palate, Female, Genetic Counseling, Genetic Predisposition to Disease, Germ-Line Mutation, Humans, Male, Pedigree, Phenotype, Stomach Neoplasms}, issn = {2073-4425}, doi = {10.3390/genes11040391}, author = {Selvanathan, Arthavan and Nixon, Cheng Yee and Zhu, Ying and Scietti, Luigi and Forneris, Federico and Uribe, Lina M Moreno and Lidral, Andrew C and Jezewski, Peter A and Mulliken, John B and Murray, Jeffrey C and Buckley, Michael F and Cox, Timothy C and Roscioli, Tony} } @article {336, title = {Multilevel analyses of SCN5A mutations in arrhythmogenic right ventricular dysplasia/cardiomyopathy suggest non-canonical mechanisms for disease pathogenesis.}, journal = {Cardiovasc Res}, volume = {113}, year = {2017}, month = {2017 01}, pages = {102-111}, abstract = {

AIMS: Arrhythmogenic Right Ventricular Dysplasia/Cardiomyopathy (ARVD/C) is often associated with desmosomal mutations. Recent studies suggest an interaction between the desmosome and sodium channel protein Na1.5. We aimed to determine the prevalence and biophysical properties of mutations in SCN5A (the gene encoding Na1.5) in ARVD/C.

METHODS AND RESULTS: We performed whole-exome sequencing in six ARVD/C patients (33\% male, 38.2 {\textpm} 12.1 years) without a desmosomal mutation. We found a rare missense variant (p.Arg1898His; R1898H) in SCN5A in one patient. We generated induced pluripotent stem cell-derived cardiomyocytes (hIPSC-CMs) from the patient{\textquoteright}s peripheral blood mononuclear cells. The variant was then corrected (R1898R) using Clustered Regularly Interspaced Short Palindromic Repeats/Cas9 technology, allowing us to study the impact of the R1898H substitution in the same cellular background. Whole-cell patch clamping revealed a 36\% reduction in peak sodium current (P = 0.002); super-resolution fluorescence microscopy showed reduced abundance of Na1.5 (P = 0.005) and N-Cadherin (P = 0.026) clusters at the intercalated disc. Subsequently, we sequenced SCN5A in an additional 281 ARVD/C patients (60\% male, 34.8 {\textpm} 13.7 years, 52\% desmosomal mutation-carriers). Five (1.8\%) subjects harboured a putatively pathogenic SCN5A variant (p.Tyr416Cys, p.Leu729del, p.Arg1623Ter, p.Ser1787Asn, and p.Val2016Met). SCN5A variants were associated with prolonged QRS duration (119 {\textpm} 15 vs. 94 {\textpm} 14 ms, P < 0.01) and all SCN5A variant carriers had major structural abnormalities on cardiac imaging.

CONCLUSIONS: Almost 2\% of ARVD/C patients harbour rare SCN5A variants. For one of these variants, we demonstrated reduced sodium current, Na1.5 and N-Cadherin clusters at junctional sites. This suggests that Na1.5 is in a functional complex with adhesion molecules, and reveals potential non-canonical mechanisms by which Na1.5 dysfunction causes cardiomyopathy.

}, keywords = {Adult, Antigens, CD, Arrhythmogenic Right Ventricular Dysplasia, Cadherins, Cell Differentiation, CRISPR-Cas Systems, DNA Mutational Analysis, Electrocardiography, Exome, Female, Gene Editing, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, HEK293 Cells, Humans, Induced Pluripotent Stem Cells, Magnetic Resonance Imaging, Male, Membrane Potentials, Middle Aged, Multilevel Analysis, Mutation, Missense, Myocytes, Cardiac, NAV1.5 Voltage-Gated Sodium Channel, Netherlands, Phenotype, Sodium, Transfection, United States, Young Adult}, issn = {1755-3245}, doi = {10.1093/cvr/cvw234}, author = {Te Riele, Anneline S J M and Agullo-Pascual, Esperanza and James, Cynthia A and Leo-Macias, Alejandra and Cerrone, Marina and Zhang, Mingliang and Lin, Xianming and Lin, Bin and Sobreira, Nara L and Amat-Alarcon, Nuria and Marsman, Roos F and Murray, Brittney and Tichnell, Crystal and van der Heijden, Jeroen F and Dooijes, Dennis and van Veen, Toon A B and Tandri, Harikrishna and Fowler, Steven J and Hauer, Richard N W and Tomaselli, Gordon and van den Berg, Maarten P and Taylor, Matthew R G and Brun, Francesca and Sinagra, Gianfranco and Wilde, Arthur A M and Mestroni, Luisa and Bezzina, Connie R and Calkins, Hugh and Peter van Tintelen, J and Bu, Lei and Delmar, Mario and Judge, Daniel P} } @article {380, title = {Unraveling genetic predisposition to familial or early onset gastric cancer using germline whole-exome sequencing.}, journal = {Eur J Hum Genet}, volume = {25}, year = {2017}, month = {2017 11}, pages = {1246-1252}, abstract = {

Recognition of individuals with a genetic predisposition to gastric cancer (GC) enables preventive measures. However, the underlying cause of genetic susceptibility to gastric cancer remains largely unexplained. We performed germline whole-exome sequencing on leukocyte DNA of 54 patients from 53 families with genetically unexplained diffuse-type and intestinal-type GC to identify novel GC-predisposing candidate genes. As young age at diagnosis and familial clustering are hallmarks of genetic tumor susceptibility, we selected patients that were diagnosed below the age of 35, patients from families with two cases of GC at or below age 60 and patients from families with three GC cases at or below age 70. All included individuals were tested negative for germline CDH1 mutations before or during the study. Variants that were possibly deleterious according to in silico predictions were filtered using several independent approaches that were based on gene function and gene mutation burden in controls. Despite a rigorous search, no obvious candidate GC predisposition genes were identified. This negative result stresses the importance of future research studies in large, homogeneous cohorts.

}, keywords = {Adult, Aged, Antigens, CD, Cadherins, Early Detection of Cancer, Exome, Female, Genetic Predisposition to Disease, Genetic Testing, Germ-Line Mutation, Humans, Male, Middle Aged, Sequence Analysis, DNA, Stomach Neoplasms}, issn = {1476-5438}, doi = {10.1038/ejhg.2017.138}, author = {Vogelaar, Ingrid P and van der Post, Rachel S and van Krieken, J Han Jm and Spruijt, Liesbeth and van Zelst-Stams, Wendy Ag and Kets, C Marleen and Lubinski, Jan and Jakubowska, Anna and Teodorczyk, Urszula and Aalfs, Cora M and van Hest, Liselotte P and Pinheiro, Hugo and Oliveira, Carla and Jhangiani, Shalini N and Muzny, Donna M and Gibbs, Richard A and Lupski, James R and de Ligt, Joep and Vissers, Lisenka E L M and Hoischen, Alexander and Gilissen, Christian and van de Vorst, Maartje and Goeman, Jelle J and Schackert, Hans K and Ranzani, Guglielmina N and Molinaro, Valeria and G{\'o}mez Garc{\'\i}a, Encarna B and Hes, Frederik J and Holinski-Feder, Elke and Genuardi, Maurizio and Ausems, Margreet G E M and Sijmons, Rolf H and Wagner, Anja and van der Kolk, Lizet E and Bj{\o}rnevoll, Inga and H{\o}berg-Vetti, Hildegunn and van Kessel, Ad Geurts and Kuiper, Roland P and Ligtenberg, Marjolijn J L and Hoogerbrugge, Nicoline} } @article {72, title = {Loss of B Cells in Patients with Heterozygous Mutations in IKAROS.}, journal = {N Engl J Med}, volume = {374}, year = {2016}, month = {2016 Mar 17}, pages = {1032-1043}, abstract = {

BACKGROUND: Common variable immunodeficiency (CVID) is characterized by late-onset hypogammaglobulinemia in the absence of predisposing factors. The genetic cause is unknown in the majority of cases, and less than 10\% of patients have a family history of the disease. Most patients have normal numbers of B cells but lack plasma cells.

METHODS: We used whole-exome sequencing and array-based comparative genomic hybridization to evaluate a subset of patients with CVID and low B-cell numbers. Mutant proteins were analyzed for DNA binding with the use of an electrophoretic mobility-shift assay (EMSA) and confocal microscopy. Flow cytometry was used to analyze peripheral-blood lymphocytes and bone marrow aspirates.

RESULTS: Six different heterozygous mutations in IKZF1, the gene encoding the transcription factor IKAROS, were identified in 29 persons from six families. In two families, the mutation was a de novo event in the proband. All the mutations, four amino acid substitutions, an intragenic deletion, and a 4.7-Mb multigene deletion involved the DNA-binding domain of IKAROS. The proteins bearing missense mutations failed to bind target DNA sequences on EMSA and confocal microscopy; however, they did not inhibit the binding of wild-type IKAROS. Studies in family members showed progressive loss of B cells and serum immunoglobulins. Bone marrow aspirates in two patients had markedly decreased early B-cell precursors, but plasma cells were present. Acute lymphoblastic leukemia developed in 2 of the 29 patients.

CONCLUSIONS: Heterozygous mutations in the transcription factor IKAROS caused an autosomal dominant form of CVID that is associated with a striking decrease in B-cell numbers. (Funded by the National Institutes of Health and others.).

}, keywords = {Adolescent, Adult, Antigens, CD, B-Lymphocytes, Bone Marrow, Bone Marrow Examination, Child, Child, Preschool, Chromosomes, Human, Pair 7, Common Variable Immunodeficiency, Exome, Female, Heterozygote, Humans, Ikaros Transcription Factor, Immunoglobulin G, Lymphocyte Count, Male, Mutation, Pedigree, Sequence Analysis, DNA}, issn = {1533-4406}, doi = {10.1056/NEJMoa1512234}, author = {Kuehn, H S and Boisson, B and Cunningham-Rundles, C and Reichenbach, J and Stray-Pedersen, A and Gelfand, E W and Maffucci, P and Pierce, K R and Abbott, J K and Voelkerding, K V and South, S T and Augustine, N H and Bush, J S and Dolen, W K and Wray, B B and Itan, Y and Cobat, A and Sorte, H S and Ganesan, S and Prader, S and Martins, T B and Lawrence, M G and Orange, J S and Calvo, K R and Niemela, J E and Casanova, J-L and Fleisher, T A and Hill, H R and Kum{\'a}novics, A and Conley, M E and Rosenzweig, S D} }