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Item Autoantibodies neutralizing type I IFNs are present in similar to 4\% of uninfected individuals over 70 years old and account for similar to 20\% of COVID-19 deaths(AMER ASSOC ADVANCEMENT SCIENCE, 2021-01-01) Bastard, Paul; Gervais, Adrian; Le Voyer, Tom; Rosain, Jeremie; Philippot, Quentin; Manry, Jeremy; Michailidis, Eleftherios; Hoffmann, Hans-Heinrich; Eto, Shohei; Garcia-Prat, Marina; Bizien, Lucy; Parra-Martinez, Alba; Yang, Rui; Haljasmagi, Liis; Migaud, Melanie; Sarekannu, Karita; Maslovskaja, Julia; de Prost, Nicolas; Tandjaoui-Lambiotte, Yacine; Luyt, Charles-Edouard; Amador-Borrero, Blanca; Gaudet, Alexandre; Poissy, Julien; Morel, Pascal; Richard, Pascale; Cognasse, Fabrice; Troya, Jesus; Trouillet-Assant, Sophie; Belot, Alexandre; Saker, Kahina; Garcon, Pierre; Riviere, Jacques G.; Lagier, Jean-Christophe; Gentile, Stephanie; Rosen, Lindsey B.; Shaw, Elana; Morio, Tomohiro; Tanaka, Junko; Dalmau, David; Tharaux, Pierre-Louis; Sene, Damien; Stepanian, Alain; Megarbane, Bruno; Triantafyllia, Vasiliki; Fekkar, Arnaud; Heath, James R.; Franco, Jose Luis; Anaya, Juan-Manuel; Sole-Violan, Jordi; Imberti, Luisa; Biondi, Andrea; Bonfanti, Paolo; Castagnoli, Riccardo; Delmonte, Ottavia M.; Zhang, Yu; Snow, Andrew L.; Holland, Steven M.; Biggs, Catherine M.; Moncada-Velez, Marcela; Arias, Andres Augusto; Lorenzo, Lazaro; Boucherit, Soraya; Coulibaly, Boubacar; Anglicheau, Dany; Planas, Anna M.; Haerynck, Filomeen; Duvlis, Sotirija; Nussbaum, Robert L.; Ozcelik, Tayfun; Keles, Sevgi; Bousfiha, Ahmed A.; El Bakkouri, Jalila; Ramirez-Santana, Carolina; Paul, Stephane; Pan-Hammarstrom, Qiang; Hammarstrom, Lennart; Dupont, Annabelle; Kurolap, Alina; Metz, Christine N.; Aiuti, Alessandro; Casari, Giorgio; Lampasona, Vito; Ciceri, Fabio; Barreiros, Lucila A.; Dominguez-Garrido, Elena; Vidigal, Mateus; Zatz, Mayana; van de Beek, Diederik; Sahanic, Sabina; Tancevski, Ivan; Stepanovskyy, Yurii; Boyarchuk, Oksana; Nukui, Yoko; Tsumura, Miyuki; Vidaur, Loreto; Tangye, Stuart G.; Burrel, Sonia; Duffy, Darragh; Quintana-Murci, Lluis; Klocperk, Adam; Kann, Nelli Y.; Shcherbina, Anna; Lau, Yu-Lung; Leung, Daniel; Coulongeat, Matthieu; Marlet, Julien; Koning, Rutger; Reyes, Luis Felipe; Chauvineau-Grenier, Angelique; Venet, Fabienne; Monneret, Guillaume; Nussenzweig, Michel C.; Arrestier, Romain; Boudhabhay, Idris; Baris-Feldman, Hagit; Hagin, David; Wauters, Joost; Meyts, Isabelle; Dyer, Adam H.; Kennelly, Sean P.; Bourke, Nollaig M.; Halwani, Rabih; Sharif-Askari, Narjes Saheb; Dorgham, Karim; Sallette, Jerome; Sedkaoui, Souad Mehlal; AlKhater, Suzan; Rigo-Bonnin, Raul; Morandeira, Francisco; Roussel, Lucie; Vinh, Donald C.; Ostrowski, Sisse Rye; Condino-Neto, Antonio; Prando, Carolina; Bondarenko, Anastasiia; Spaan, Andras N.; Gilardin, Laurent; Fellay, Jacques; Lyonnet, Stanislas; Bilguvar, Kaya; Lifton, Richard P.; Mane, Shrikant; Anderson, Mark S.; Boisson, Bertrand; Beziat, Vivien; Zhang, Shen-Ying; Andreakos, Evangelos; Hermine, Olivier; Pujol, Aurora; Peterson, Part; Mogensen, Trine H.; Rowen, Lee; Mond, James; Debette, Stephanie; de Lamballerie, Xavier; Duval, Xavier; Mentre, France; Zins, Marie; Soler-Palacin, Pere; Colobran, Roger; Gorochov, Guy; Solanich, Xavier; Susen, Sophie; Martinez-Picado, Javier; Raoult, Didier; Vasse, Marc; Gregersen, Peter K.; Piemonti, Lorenzo; Rodriguez-Gallego, Carlos; Notarangelo, Luigi D.; Su, Helen C.; Kisand, Kai; Okada, Satoshi; Puel, Anne; Jouanguy, Emmanuelle; Rice, Charles M.; Tiberghien, Pierre; Zhang, Qian; Cobat, Aurelie; Abel, Laurent; Casanova, Jean-Laurent; Lab, H. G. I. D.; Clinicians, C. O. V. I. D.; Clinicians, C. O. V. I. D.-S. T. O. R. M.; Grp, N.I.A.I.D. Immune Response Covid; Grp, N. H.-C.O.V.A.I.R. Study; Danish, C. H. G. E.; Study, Danish Blood Donor; Interest, St Jamess Hosp Sars CoV2; Grp, French C.O.V.I.D. Cohort Study; COVID-Grp, Imagine; Consortium, Milieu Interieur; Cohort, CoV-Contact; Inv, Amsterdam Umc Covid-19 Biobank; Efft, C.O.V.I.D. Human Genetic; Cohort, C. O. N. S. T. A. N. C. E. S.; Study, 3C.-Dijon; HealthCare, Cerba; Grp, Etab Sang StudyCirculating autoantibodies (auto-Abs) neutralizing high concentrations (10 ng/mlItem The risk of COVID-19 death is much greater and age dependent with type I IFN autoantibodies(NATL ACAD SCIENCES, 2022-01-01) Manry, Jeremy; Bastard, Paul; Gervais, Adrian; Le Voyer, Tom; Rosain, Jeremie; Philippot, Quentin; Michailidis, Eleftherios; Hoffmann, Hans-Heinrich; Eto, Shohei; Garcia-Prat, Marina; Bizien, Lucy; Parra-Martinez, Alba; Yang, Rui; Haljasmagi, Liis; Migaud, Melanie; Sarekannu, Karita; Maslovskaja, Julia; de Prost, Nicolas; Tandjaoui-Lambiotte, Yacine; Luyt, Charles-Edouard; Amador-Borrero, Blanca; Gaudet, Alexandre; Poissy, Julien; Morel, Pascal; Richard, Pascale; Cognasse, Fabrice; Troya, Jesus; Trouillet-Assant, Sophie; Belot, Alexandre; Saker, Kahina; Garcon, Pierre; Riviere, Jacques G.; Lagier, Jean-Christophe; Gentile, Stephanie; Rosen, Lindsey B.; Shaw, Elana; Morio, Tomohiro; Tanaka, Junko; Dalmau, David; Tharaux, Pierre-Louis; Sene, Damien; Stepanian, Alain; Megarbane, Bruno; Triantafyllia, Vasiliki; Fekkar, Arnaud; Heath, James R.; Franco, Jose Luis; Anaya, Juan-Manuel; Sole-Violan, Jordi; Imberti, Luisa; Biondi, Andrea; Bonfanti, Paolo; Castagnoli, Riccardo; Delmonte, Ottavia M.; Zhang, Yu; Snow, Andrew L.; Holland, Steven M.; Biggs, Catherine M.; Moncada-Velez, Marcela; Arias, Andres Augusto; Lorenzo, Lazaro; Boucherit, Soraya; Anglicheau, Dany; Planas, Anna M.; Haerynck, Filomeen; Duvlis, Sotirija; Ozcelik, Tayfun; Keles, Sevgi; Bousfiha, Ahmed A.; El Bakkouri, Jalila; Ramirez-Santana, Carolina; Paul, Stephane; Pan-Hammarstrom, Qiang; Hammarstrom, Lennart; Dupont, Annabelle; Kurolap, Alina; Metz, Christine N.; Aiuti, Alessandro; Casari, Giorgio; Lampasona, Vito; Ciceri, Fabio; Barreiros, Lucila A.; Dominguez-Garrido, Elena; Vidigal, Mateus; Zatz, Mayana; van de Beek, Diederik; Sahanic, Sabina; Tancevski, Ivan; Stepanovskyy, Yurii; Boyarchuk, Oksana; Nukui, Yoko; Tsumura, Miyuki; Vidaur, Loreto; Tangye, Stuart G.; Burrel, Sonia; Duffy, Darragh; Quintana-Murci, Lluis; Klocperk, Adam; Kann, Nelli Y.; Shcherbina, Anna; Lau, Yu-Lung; Leung, Daniel; Coulongeat, Matthieu; Marlet, Julien; Koning, Rutger; Reyes, Luis Felipe; Chauvineau-Grenier, Angelique; Venet, Fabienne; Monneret, Guillaume; Nussenzweig, Michel C.; Arrestier, Romain; Boudhabhay, Idris; Baris-Feldman, Hagit; Hagin, David; Wauters, Joost; Meyts, Isabelle; Dyer, Adam H.; Kennelly, Sean; Bourkeh, Nollaig M.; Halwan, Rabih; Sharif-Askar, Fatemeh Saheb; Dorgham, Karim; Sallette, Jerome; Sedkaoui, Souad Mehlal; AlKhater, Suzan; Rigo-Bonnin, Raul; Morandeira, Francisco; Roussel, Lucie; Vinh, Donald C.; Erikstrup, Christian; Condino-Neto, Antonio; Prando, Carolina; Bondarenko, Anastasiia; Spaan, Andras N.; Gilardin, Laurent; Fellay, Jacques; Lyonnet, Stanislas; Bilguvar, Kaya; Lifton, Richard P.; Mane, Shrikant; Anderson, Mark S.; Boisson, Bertrand; Beziat, Vivien; Zhang, Shen-Ying; Andreakos, Evangelos; Hermine, Olivier; Pujol, Aurora; Peterson, Part; Mogensen, Trine H.; Rowen, Lee; Mond, James; Debette, Stephanie; de Lamballerie, Xavier; Burdet, Charles; Bouadma, Lila; Zins, Marie; Soler-Palacin, Pere; Colobran, Roger; Gorochov, Guy; Solanich, Xavier; Susen, Sophie; Martinez-Picado, Javier; Raoult, Didier; Vasse, Marc; Gregersen, Peter K.; Piemonti, Lorenzo; Rodriguez-Gallego, Carlos; D Notarangelo, Luigi; Su, Helen C.; Kisand, Kai; Okada, Satoshi; Puel, Anne; Jouanguy, Emmanuelle; Rice, Charles M.; Tiberghien, Pierre; Zhang, Qian; Casanova, Jean-Laurent; Abel, Laurent; Cobat, Aurelie; Lab, H. G. I. D.; Clinicians, C. O. V. I. D.; Clinicians, C. O. V. I. D.-S. T. O. R. M.; Grp, N.I.A.I.D. Immune Response C. O. V. I. D.; Grp, N. H.-C.O.V.A.I.R. Study; Danish, C. H. G. E.; Study, Danish Blood Donor; Hosp, St Jamess; Grp, French C.O.V.I.D. Cohort Study; COVID-Grp, Imagine; Consortium, Milieu Interieur; Cohort, CoV-Contact; Biobank, Amsterdam U.M.C. Covid-19; Effort, C.O.V.I.D. Human Genetic; Grp, C. P.-C. O. V. I. D.-19; Cohort, C. O. N. S. T. A. N. C. E. S.; Study, 3C.-Dijon; Hlth-Care, Cerba; Grp, Etab Francais Sang StudySevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection fatality rate (IFR) doubles with every 5 y of age from childhood onward. Circulating autoantibodies neutralizing IFN-alpha, IFN-omega, and/or IFN-beta are found in similar to 20\% of deceased patients across age groups, and in similar to 1\% of individuals aged <70 y and in >4\% of those >70 y old in the general population. With a sample of 1,261 unvaccinated deceased patients and 34,159 individuals of the general population sampled before the pandemic, we estimated both IFR and relative risk of death (RRD) across age groups for individuals carrying autoantibodies neutralizing type I IFNs, relative to noncarriers. The RRD associated with any combination of autoantibodies was higher in subjects under 70 y old. For autoantibodies neutralizing IFN-alpha 2 or IFN-omega, the RRDs were 17.0 (95\% CI: 11.7 to 24.7) and 5.8 (4.5 to 7.4) for individuals <70 y and >= 70 y old, respectively, whereas, for autoantibodies neutralizing both molecules, the RRDs were 188.3 (44.8 to 774.4) and 7.2 (5.0 to 10.3), respectively. In contrast, IFRs increased with age, ranging from 0.17\% (0.12 to 0.31) for individuals <40 y old to 26.7\% (20.3 to 35.2) for those >= 80 y old for autoantibodies neutralizing IFN-alpha 2 or IFN-omega, and from 0.84\% (0.31 to 8.28) to 40.5\% (27.82 to 61.20) for autoantibodies neutralizing both. Autoantibodies against type I IFNs increase IFRs, and are associated with high RRDs, especially when neutralizing both IFN-alpha 2 and IFN-omega. Remarkably, IFRs increase with age, whereas RRDs decrease with age. Autoimmunity to type I IFNs is a strong and common predictor of COVID-19 death.Item Biallelic loss of human CTNNA2, encoding alpha N-catenin, leads to ARP2/3 complex overactivity and disordered cortical neuronal migration(NATURE PUBLISHING GROUP, 2018-01-01) Schaffer, Ashleigh E.; Breuss, Martin W.; Caglayan, Ahmet Okay; Al-Sanaa, Nouriya; Al-Abdulwahed, Hind Y.; Kaymakcalan, Hande; Yilmaz, Cahide; Zaki, Maha S.; Rosti, Rasim O.; Copeland, Brett; Baek, Seung Tae; Musaev, Damir; Scott, Eric C.; Ben-Omran, Tawfeg; Kariminejad, Ariana; Kayserili, Hulya; Mojahedi, Faezeh; Kara, Majdi; Cai, Na; Silhavy, Jennifer L.; Elsharif, Seham; Fenercioglu, Elif; Barshop, Bruce A.; Kara, Bulent; Wang, Rengang; Stanley, Valentina; James, Kiely N.; Nachnani, Rahul; Kalur, Aneesha; Megahed, Hisham; Incecik, Faruk; Danda, Sumita; Alanay, Yasemin; Faqeih, Eissa; Melikishvili, Gia; Mansour, Lobna; Miller, Ian; Sukhudyan, Biayna; Chelly, Jamel; Dobyns, William B.; Bilguvar, Kaya; Abou Jamra, Rami; Gunel, Murat; Gleeson, Joseph G.Neuronal migration defects, including pachygyria, are among the most severe developmental brain defects in humans. Here, we identify biallelic truncating mutations in CTNNA2, encoding alpha N-catenin, in patients with a distinct recessive form of pachygyria. CTNNA2 was expressed in human cerebral cortex, and its loss in neurons led to defects in neurite stability and migration. The alpha N-catenin paralog, alpha E-catenin, acts as a switch regulating the balance between beta-catenin and Arp2/3 actin filament activities(1). Loss of alpha N-catenin did not affect beta-catenin signaling, but recombinant alpha N-catenin interacted with purified actin and repressed ARP2/3 actin-branching activity. The actin-binding domain of alpha N-catenin or ARP2/3 inhibitors rescued the neuronal phenotype associated with CTNNA2 loss, suggesting ARP2/3 de-repression as a potential disease mechanism. Our findings identify CTNNA2 as the first catenin family member with biallelic mutations in humans, causing a new pachygyria syndrome linked to actin regulation, and uncover a key factor involved in ARP2/3 repression in neurons.Item De Novo Mutation in Genes Regulating Neural Stem Cell Fate in Human Congenital Hydrocephalus(CELL PRESS, 2018-01-01) Furey, Charuta Gavankar; Choi, Jungmin; Jin, Sheng Chih; Zeng, Xue; Timberlake, Andrew T.; Nelson-Williams, Carol; Mansuri, M. Shahid; Lu, Qiongshi; Duran, Daniel; Panchagnula, Shreyas; Allocco, August; Karimy, Jason K.; Khanna, Arjun; Gaillard, Jonathan R.; DeSpenza, Tyrone; Antwi, Prince; Loring, Erin; Butler, William E.; Smith, Edward R.; Warf, Benjamin C.; Strahle, Jennifer M.; Limbrick, David D.; Storm, Phillip B.; Heuer, Gregory; Jackson, Eric M.; Iskandar, Bermans J.; Johnston, James M.; Tikhonova, Irina; Castaldi, Christopher; Lopez-Giraldez, Francesc; Bjornson, Robert D.; Knight, James R.; Bilguvar, Kaya; Mane, Shrikant; Alper, Seth L.; Haider, Shozeb; Guclu, Bulent; Bayri, Yasar; Sahin, Yener; Apuzzo, Michael L. J.; Duncan, Charles C.; DiLuna, Michael L.; Gunel, Murat; Lifton, Richard P.; Kahle, Kristopher T.Congenital hydrocephalus (CH), featuring markedly enlarged brain ventricles, is thought to arise from failed cerebrospinal fluid (CSF) homeostasis and is treated with lifelong surgical CSF shunting with substantial morbidity. CH pathogenesis is poorly understood. Exome sequencing of 125 CH trios and 52 additional probands identified three genes with significant burden of rare damaging de novo or transmitted mutations: TRIM71 (p = 2.15 x 10(-7)), SMARCC1 (p = 8.15 x 10(-10)), and PTCH1 (p = 1.06 x 10(-6)). Additionally, two de novo duplications were identified at the SHH locus, encoding the PTCH1 ligand (p = 1.2 x 10(-4)). Together, these probands account for similar to 10\% of studied cases. Strikingly, all four genes are required for neural tube development and regulate ventricular zone neural stem cell fate. These results implicate impaired neurogenesis (rather than active CSF accumulation) in the pathogenesis of a subset of CH patients, with potential diagnostic, prognostic, and therapeutic ramifications.Item The genetic structure of the Turkish population reveals high levels of variation and admixture(NATL ACAD SCIENCES, 2021-01-01) Kars, M. Ece; Basak, A. Nazli; Onat, O. Emre; Bilguvar, Kaya; Choi, Jungmin; Itan, Yuval; Caglar, Caner; Palvadeau, Robin; Casanova, Jean-Laurent; Cooper, David N.; Stenson, Peter D.; Yavuz, Alper; Bulus, Hakan; Gunel, Murat; Friedman, Jeffrey M.; Ozcelik, TayfunThe construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50\% of TR individuals had high inbreeding coefficients (>= 0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28\% of exome and 49\% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.Item Associations of meningioma molecular subgroup and tumor recurrence(OXFORD UNIV PRESS INC, 2021-01-01) Youngblood, Mark W.; Miyagishima, Danielle F.; Jin, Lan; Gupte, Trisha; Li, Chang; Duran, Daniel; Montejo, Julio D.; Zhao, Amy; Sheth, Amar; Tyrtova, Evgeniya; Ozduman, Koray; Iacoangeli, Francesco; Peyre, Matthieu; Boetto, Julien; Pease, Matthew; Avsar, Timucin; Huttner, Anita; Bilguvar, Kaya; Kilic, Turker; Pamir, M. Necmettin; Amankulor, Nduka; Kalamarides, Michel; Erson-Omay, E. Zeynep; Gunel, Murat; Moliterno, JenniferBackground. We and others have identified mutually exclusive molecular subgroups of meningiomasItem Comparative transmissibility of SARS-CoV-2 variants Delta and Alpha in New England, USA(ELSEVIER, 2022-01-01) Earnest, Rebecca; Uddin, Rockib; Matluk, Nicholas; Renzette, Nicholas; Turbett, Sarah E.; Siddle, Katherine J.; Loreth, Christine; Adams, Gordon; Tomkins-Tinch, Christopher H.; Petrone, Mary E.; Rothman, Jessica E.; Breban I, Mallery; Koch, Robert Tobias; Billig, Kendall; Fauver, Joseph R.; Vogels, Chantal B. F.; Bilguvar, Kaya; De Kumar, Bony; Landry, Marie L.; Peaper, David R.; Kelly, Kevin; Omerza, Greg; Grieser, Heather; Meak, Sim; Martha, John; Dewey, Hannah B.; Kales, Susan; Berenzy, Daniel; Carpenter-Azevedo, Kristin; King, Ewa; Huard, Richard C.; Novitsky, Vlad; Howison, Mark; Darpolor, Josephine; Manne, Akarsh; Kantor, Rami; Smole, Sandra C.; Brown, Catherine M.; Fink, Timelia; Lang, Andrew S.; Gallagher, Glen R.; Pitzer, Virginia E.; Sabeti, Pardis C.; Gabriel, Stacey; MacInnis, Bronwyn L.; Tewhey, Ryan; Adams, Mark D.; Park, Daniel J.; Lemieux, Jacob E.; Grubaugh, Nathan D.; Team, New England Variant InvestThe SARS-CoV-2 Delta variant rose to dominance in mid-2021, likely propelled by an estimated 40\%???80\% increased transmissibility over Alpha. To investigate if this ostensible difference in transmissibility is uniform across populations, we partner with public health programs from all six states in New England in the United States. We compare logistic growth rates during each variant???s respective emergence period, finding that Delta emerged 1.37???2.63 times faster than Alpha (range across states). We compute variant-specific effective reproductive numbers, estimating that Delta is 63\%???167\% more transmissible than Alpha (range across states). Finally, we estimate that Delta infections generate on average 6.2 (95\% CI 3.1???10.9) times more viral RNA copies per milliliter than Alpha infections during their respective emergence. Overall, our evidence suggests that Delta???s enhanced transmissibility can be attributed to its innate ability to increase infectiousness, but its epidemiological dynamics may vary depending on underlying population attributes and sequencing data availability.Item The Essential Role of Centrosomal NDE1 in Human Cerebral Cortex Neurogenesis(CELL PRESS, 2011-01-01) Bakircioglu, Mehmet; Carvalho, Ofelia P.; Khurshid, Maryam; Cox, James J.; Tuysuz, Beyhan; Barak, Tanyeri; Yilmaz, Saliha; Caglayan, Okay; Dincer, Alp; Nicholas, Adeline K.; Quarrell, Oliver; Springell, Kelly; Karbani, Gulshan; Malik, Saghira; Gannon, Caroline; Sheridan, Eamonn; Crosier, Moira; Lisgo, Steve N.; Lindsay, Susan; Bilguvar, Kaya; Gergely, Fanni; Gunel, Murat; Woods, C. GeoffreyWe investigated three families whose offspring had extreme microcephaly at birth and profound mental retardation. Brain scans and postmortem data showed that affected individuals had brains less than 10\% of expected size (<= 10 standard deviation) and that in addition to a massive reduction in neuron production they displayed partially deficient cortical lamination tinicrolissencephaly). Other body systems were apparently unaffected and overall growth was normal. We found two distinct homozygous mutations of NDE1, c.83+1G>T (p.Ala29GlnfsX114) in a Turkish family and c.684\_685del (p.Pro229TrpfsX85) in two families of Pakistani origin. Using patient cells, we found that c.83+1G>T led to the use of a novel splice site and to a frameshift after NDE1 exon 2. Transfection of tagged NDE1 constructs showed that the c.684\_685del mutation resulted in a NDE1 that was unable to localize to the centrosome. By staining a patient-derived cell line that carried the c.83+1G>T mutation, we found that this endogeneously expressed mutated protein equally failed to localize to the centrosome. By examining human and mouse embryonic brains, we determined that NDE1 is highly expressed in neuroepithelial cells of the developing cerebral cortex, particularly at the centrosome. We show that NDE1 accumulates on the mitotic spindle of apical neural precursors in early neurogenesis. Thus, NDE1 deficiency causes both a severe failure of neurogenesis and a deficiency in cortical lamination. Our data further highlight the importance of the centrosome in multiple aspects of neurodevelopment.Item Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations(NATURE PUBLISHING GROUP, 2010-01-01) Bilguvar, Kaya; Ozturk, Ali Kemal; Louvi, Angeliki; Kwan, Kenneth Y.; Choi, Murim; Tatli, Burak; Yalnizoglu, Dilek; Tuysuz, Beyhan; Caglayan, Ahmet Okay; Gokben, Sarenur; Kaymakcalan, Hande; Barak, Tanyeri; Bakircioglu, Mehmet; Yasuno, Katsuhito; Ho, Winson; Sanders, Stephan; Zhu, Ying; Yilmaz, Sanem; Dincer, Alp; Johnson, Michele H.; Bronen, Richard A.; Kocer, Naci; Per, Hueseyin; Mane, Shrikant; Pamir, Mehmet Necmettin; Yalcinkaya, Cengiz; Kumandas, Sefer; Topcu, Meral; Ozmen, Meral; Sestan, Nenad; Lifton, Richard P.; State, Matthew W.; Gunel, MuratThe development of the human cerebral cortex is an orchestrated process involving the generation of neural progenitors in the periventricular germinal zones, cell proliferation characterized by symmetric and asymmetric mitoses, followed by migration of post-mitotic neurons to their final destinations in six highly ordered, functionally specialized layers(1,2). An understanding of the molecular mechanisms guiding these intricate processes is in its infancy, substantially driven by the discovery of rare mutations that cause malformations of cortical development(3-6). Mapping of disease loci in putative Mendelian forms of malformations of cortical development has been hindered by marked locus heterogeneity, small kindred sizes and diagnostic classifications that may not reflect molecular pathogenesis. Here we demonstrate the use of whole-exome sequencing to overcome these obstacles by identifying recessive mutations in WD repeat domain 62 (WDR62) as the cause of a wide spectrum of severe cerebral cortical malformations including microcephaly, pachygyria with cortical thickening as well as hypoplasia of the corpus callosum. Some patients with mutations in WDR62 had evidence of additional abnormalities including lissencephaly, schizencephaly, polymicrogyria and, in one instance, cerebellar hypoplasia, all traits traditionally regarded as distinct entities. In mice and humans, WDR62 transcripts and protein are enriched in neural progenitors within the ventricular and subventricular zones. Expression of WDR62 in the neocortex is transient, spanning the period of embryonic neurogenesis. Unlike other known microcephaly genes, WDR62 does not apparently associate with centrosomes and is predominantly nuclear in localization. These findings unify previously disparate aspects of cerebral cortical development and highlight the use of whole-exome sequencing to identify disease loci in settings in which traditional methods have proved challenging.Item Integrated genomic characterization of IDH1-mutant glioma malignant progression(NATURE PUBLISHING GROUP, 2016-01-01) Bai, Hanwen; Harmanci, Akdes Serin; Erson-Omay, E. Zeynep; Li, Jie; Coskun, Sueleyman; Simon, Matthias; Krischek, Boris; Ozduman, Koray; Omay, S. Buelent; Sorensen, Eric A.; Turcan, Sevin; Bakirciglu, Mehmet; Carrion-Grant, Geneive; Murray, Phillip B.; Clark, Victoria E.; Ercan-Sencicek, A. Gulhan; Knight, James; Sencar, Leman; Altinok, Selin; Kaulen, Leon D.; Guelez, Burcu; Timmer, Marco; Schramm, Johannes; Mishra-Gorur, Ketu; Henegariu, Octavian; Moliterno, Jennifer; Louvi, Angeliki; Chan, Timothy A.; Tannheimer, Stacey L.; Pamir, M. Necmettin; Vortmeyer, Alexander O.; Bilguvar, Kaya; Yasuno, Katsuhito; Guenel, MuratGliomas represent approximately 30\% of all central nervous system tumors and 80\% of malignant brain tumors(1). To understand the molecular mechanisms underlying the malignant progression of low-grade gliomas with mutations in IDH1 (encoding isocitrate dehydrogenase 1), we studied paired tumor samples from 41 patients, comparing higher-grade, progressed samples to their lower-grade counterparts. Integrated genomic analyses, including whole-exome sequencing and copy number, gene expression and DNA methylation profiling, demonstrated nonlinear clonal expansion of the original tumors and identified oncogenic pathways driving progression. These include activation of the MYC and RTK-RAS-PI3K pathways and upregulation of the FOXM1- and E2F2-mediated cell cycle transitions, as well as epigenetic silencing of developmental transcription factor genes bound by Polycomb repressive complex 2 in human embryonic stem cells. Our results not only provide mechanistic insight into the genetic and epigenetic mechanisms driving glioma progression but also identify inhibition of the bromodomain and extraterminal (BET) family as a potential therapeutic approach.