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1. Identification of evolutionarily conserved gene networks mediating neurodegenerative dementia

Author

Swarup, Vivek, Hinz, Flora I., Rexach, Jessica E., Noguchi, Ken-ichi, Toyoshiba, Hiroyoshi, Oda, Akira, Hirai, Keisuke, Sarkar, Arjun, Seyfried, Nicholas T., Cheng, Chialin, Haggarty, Stephen J., Ferrari, Raffaele, Rohrer, Jonathan D., Ramasamy, Adaikalavan, Hardy, John, Hernandez, Dena G., Nalls, Michael A., Singleton, Andrew B., Kwok, John B. J., Dobson-Stone, Carol, Brooks, William S., Schofield, Peter R., Halliday, Glenda M., Hodges, John R., Piguet, Olivier, Bartley, Lauren, Thompson, Elizabeth, Haan, Eric, Hernández, Isabel, Ruiz, Agustín, Boada, Mercè, Borroni, Barbara, Padovani, Alessandro, Cairns, Nigel J., Cruchaga, Carlos, Binetti, Giuliano, Ghidoni, Roberta, Benussi, Luisa, Forloni, Gianluigi, Albani, Diego, Galimberti, Daniela, Fenoglio, Chiara, Serpente, Maria, Scarpini, Elio, Clarimón, Jordi, Lleó, Alberto, Blesa, Rafael, Waldö, Maria Landqvist, Nilsson, Karin, Nilsson, Christer, Mackenzie, Ian R. A., Hsiung, Ging-Yuek R., Mann, David M. A., Grafman, Jordan, Morris, Christopher M., Attems, Johannes, Griffiths, Timothy D., McKeith, Ian G., Thomas, Alan J., Jaros, Evelyn, Pietrini, Pietro, Huey, Edward D., Wassermann, Eric M., Tierney, Michael C., Baborie, Atik, Pastor, Pau, Ortega-Cubero, Sara, Razquin, Cristina, Alonso, Elena, Perneczky, Robert, Diehl-Schmid, Janine, Alexopoulos, Panagiotis, Kurz, Alexander, Rainero, Innocenzo, Rubino, Elisa, Pinessi, Lorenzo, Rogaeva, Ekaterina, George-Hyslop, Peter St., Rossi, Giacomina, Tagliavini, Fabrizio, Giaccone, Giorgio, Rowe, James B., Schlachetzki, Johannes C. M., Uphill, James, Collinge, John, Mead, Simon, Danek, Adrian, Van Deerlin, Vivianna M., Grossman, Murray, Trojanowski, John Q., Pickering-Brown, Stuart, Momeni, Parastoo, van der Zee, Julie, Cruts, Marc, Van Broeckhoven, Christine, Cappa, Stefano F., Leber, Isabelle, Brice, Alexis, Hannequin, Didier, Golfier, Véronique, Vercelletto, Martine, Nacmias, Benedetta, Sorbi, Sandro, Bagnoli, Silvia, Piaceri, Irene, Nielsen, Jørgen E., Hjermind, Lena E., Riemenschneider, Matthias, Mayhaus, Manuel, Gasparoni, Gilles, Pichler, Sabrina, Ibach, Bernd, Rossor, Martin N., Fox, Nick C., Warren, Jason D., Spillantini, Maria Grazia, Morris, Huw R., Rizzu, Patrizia, Heutink, Peter, Snowden, Julie S., Rollinson, Sara, Gerhard, Alexander, Richardson, Anna, Bruni, Amalia C., Maletta, Raffaele, Frangipane, Francesca, Cupidi, Chiara, Bernardi, Livia, Anfossi, Maria, Gallo, Maura, Conidi, Maria Elena, Smirne, Nicoletta, Rademakers, Rosa, Baker, Matt, Dickson, Dennis W., Graff-Radford, Neill R., Petersen, Ronald C., Knopman, David, Josephs, Keith A., Boeve, Bradley F., Parisi, Joseph E., Miller, Bruce L., Karydas, Anna M., Rosen, Howard, Seeley, William W., van Swieten, John C., Dopper, Elise G. P., Seelaar, Harro, Pijnenburg, Yolande A. L., Scheltens, Philip, Logroscino, Giancarlo, Capozzo, Rosa, Novelli, Valeria, Puca, Annibale A., Franceschi, Massimo, Postiglione, Alfredo, Milan, Graziella, Sorrentino, Paolo, Kristiansen, Mark, Chiang, Huei-Hsin, Graff, Caroline, Pasquier, Florence, Rollin, Adeline, Deramecourt, Vincent, Lebouvier, Thibaud, Ferrucci, Luigi, Kapogiannis, Dimitrios, Lah, James J., Levey, Allan I., Kondou, Shinichi, Geschwind, Daniel H., Int Frontotemporal Dementia Gen, Swarup, Vivek, Hinz, Flora I., Rexach, Jessica E., Noguchi, Ken-ichi, Toyoshiba, Hiroyoshi, Oda, Akira, Hirai, Keisuke, Sarkar, Arjun, Seyfried, Nicholas T., Cheng, Chialin, Haggarty, Stephen J., Ferrari, Raffaele, Rohrer, Jonathan D., Ramasamy, Adaikalavan, Hardy, John, Hernandez, Dena G., Nalls, Michael A., Singleton, Andrew B., Kwok, John B. J., Dobson-Stone, Carol, Brooks, William S., Schofield, Peter R., Halliday, Glenda M., Hodges, John R., Piguet, Olivier, Bartley, Lauren, Thompson, Elizabeth, Haan, Eric, Hernández, Isabel, Ruiz, Agustín, Boada, Mercè, Borroni, Barbara, Padovani, Alessandro, Cairns, Nigel J., Cruchaga, Carlo, Binetti, Giuliano, Ghidoni, Roberta, Benussi, Luisa, Forloni, Gianluigi, Albani, Diego, Galimberti, Daniela, Fenoglio, Chiara, Serpente, Maria, Scarpini, Elio, Clarimón, Jordi, Lleó, Alberto, Blesa, Rafael, Waldö, Maria Landqvist, Nilsson, Karin, Nilsson, Christer, Mackenzie, Ian R. A., Hsiung, Ging-Yuek R., Mann, David M. A., Grafman, Jordan, Morris, Christopher M., Attems, Johanne, Griffiths, Timothy D., Mckeith, Ian G., Thomas, Alan J., Jaros, Evelyn, Pietrini, Pietro, Huey, Edward D., Wassermann, Eric M., Tierney, Michael C., Baborie, Atik, Pastor, Pau, Ortega-Cubero, Sara, Razquin, Cristina, Alonso, Elena, Perneczky, Robert, Diehl-Schmid, Janine, Alexopoulos, Panagioti, Kurz, Alexander, Rainero, Innocenzo, Rubino, Elisa, Pinessi, Lorenzo, Rogaeva, Ekaterina, George-Hyslop, Peter St., Rossi, Giacomina, Tagliavini, Fabrizio, Giaccone, Giorgio, Rowe, James B., Schlachetzki, Johannes C. M., Uphill, Jame, Collinge, John, Mead, Simon, Danek, Adrian, Van Deerlin, Vivianna M., Grossman, Murray, Trojanowski, John Q., Pickering-Brown, Stuart, Momeni, Parastoo, van der Zee, Julie, Cruts, Marc, Van Broeckhoven, Christine, Cappa, Stefano F., Leber, Isabelle, Brice, Alexi, Hannequin, Didier, Golfier, Véronique, Vercelletto, Martine, Nacmias, Benedetta, Sorbi, Sandro, Bagnoli, Silvia, Piaceri, Irene, Nielsen, Jørgen E., Hjermind, Lena E., Riemenschneider, Matthia, Mayhaus, Manuel, Gasparoni, Gille, Pichler, Sabrina, Ibach, Bernd, Rossor, Martin N., Fox, Nick C., Warren, Jason D., Spillantini, Maria Grazia, Morris, Huw R., Rizzu, Patrizia, Heutink, Peter, Snowden, Julie S., Rollinson, Sara, Gerhard, Alexander, Richardson, Anna, Bruni, Amalia C., Maletta, Raffaele, Frangipane, Francesca, Cupidi, Chiara, Bernardi, Livia, Anfossi, Maria, Gallo, Maura, Conidi, Maria Elena, Smirne, Nicoletta, Rademakers, Rosa, Baker, Matt, Dickson, Dennis W., Graff-Radford, Neill R., Petersen, Ronald C., Knopman, David, Josephs, Keith A., Boeve, Bradley F., Parisi, Joseph E., Miller, Bruce L., Karydas, Anna M., Rosen, Howard, Seeley, William W., van Swieten, John C., Dopper, Elise G. P., Seelaar, Harro, Pijnenburg, Yolande A. L., Scheltens, Philip, Logroscino, Giancarlo, Capozzo, Rosa, Novelli, Valeria, Puca, Annibale A., Franceschi, Massimo, Postiglione, Alfredo, Milan, Graziella, Sorrentino, Paolo, Kristiansen, Mark, Chiang, Huei-Hsin, Graff, Caroline, Pasquier, Florence, Rollin, Adeline, Deramecourt, Vincent, Lebouvier, Thibaud, Ferrucci, Luigi, Kapogiannis, Dimitrio, Lah, James J., Levey, Allan I., Kondou, Shinichi, and Geschwind, Daniel H.

Subjects
Proteomics, Genetics and Molecular Biology (all), 0301 basic medicine, Messenger, Gene regulatory network, Inbred C57BL, Biochemistry, Transgenic, Mice, 0302 clinical medicine, Gene Regulatory Networks, Regulation of gene expression, Cell Death, Drug discovery, Neurodegeneration, Neurodegenerative Diseases, General Medicine, Chemistry, Frontotemporal Dementia, 030220 oncology & carcinogenesis, Frontotemporal dementia, Evolution, Systems biology, Genetic Vectors, Animals, Dementia, Disease Models, Animal, Gene Expression Regulation, Genetic Predisposition to Disease, Humans, Mice, Inbred C57BL, Mice, Transgenic, MicroRNAs, RNA, Messenger, Reproducibility of Results, Transcriptome, tau Proteins, Evolution, Molecular, Computational biology, Biology, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, microRNA, medicine, Biochemistry, Genetics and Molecular Biology (all), Animal, Molecular, medicine.disease, 030104 developmental biology, Disease Models, RNA, Human medicine
Abstract

Identifying the mechanisms through which genetic risk causes dementia is an imperative for new therapeutic development. Here, we apply a multistage, systems biology approach to elucidate the disease mechanisms in frontotemporal dementia. We identify two gene coexpression modules that are preserved in mice harboring mutations in MAPT, GRN and other dementia mutations on diverse genetic backgrounds. We bridge the species divide via integration with proteomic and transcriptomic data from the human brain to identify evolutionarily conserved, disease-relevant networks. We find that overexpression of miR-203, a hub of a putative regulatory microRNA (miRNA) module, recapitulates mRNA coexpression patterns associated with disease state and induces neuronal cell death, establishing this miRNA as a regulator of neurodegeneration. Using a database of drug-mediated gene expression changes, we identify small molecules that can normalize the disease-associated modules and validate this experimentally. Our results highlight the utility of an integrative, cross-species network approach to drug discovery.

Published
2018

2. Clinical spectrum of individuals with pathogenic NF1 missense variants affecting p.Met1149, p.Arg1276, and p.Lys1423: genotype-phenotype study in neurofibromatosis type 1

Author

Koczkowska, Magdalena, Callens, Tom, Chen, Yunjia, Gomes, Alicia, Hicks, Alesha D, Sharp, Angela, Johns, Eric, Uhas, Kim Armfield, Armstrong, Linlea, Bosanko, Katherine Armstrong, Babovic-Vuksanovic, Dusica, Baker, Laura, Basel, Donald G, Bengala, Mario, Bennett, James T, Chambers, Chelsea, Clarkson, Lola K, Clementi, Maurizio, Cortés, Fanny M, Cunningham, Mitch, D'Agostino, M Daniela, Delatycki, Martin B, Digilio, Maria C, Dosa, Laura, Esposito, Silvia, Fox, Stephanie, Freckmann, Mary-Louise, Fauth, Christine, Giugliano, Teresa, Giustini, Sandra, Goetsch, Allison, Goldberg, Yael, Greenwood, Robert S, Griffis, Cristin, Gripp, Karen W, Gupta, Punita, Haan, Eric, Hachen, Rachel K, Haygarth, Tamara L, Hernández-Chico, Concepción, Hodge, Katelyn, Hopkin, Robert J, Hudgins, Louanne, Janssens, Sandra, Keller, Kory, Kelly-Mancuso, Geraldine, Kochhar, Aaina, Korf, Bruce R, Lewis, Andrea M, Liebelt, Jan, Lichty, Angie, Listernick, Robert H, Lyons, Michael J, Maystadt, Isabelle, Ojeda, Mayra Martinez, McDougall, Carey, McGregor, Lesley K, Melis, Daniela, Mendelsohn, Nancy, Nowaczyk, Malgorzata J M, Ortenberg, June, Panzer, Karin, Pappas, John G, Pierpont, Mary Ella, Piluso, Giulio, Pinna, Valentina, Pivnick, Eniko K, Pond, Dinel A, Powell, Cynthia M, Rogers, Caleb, Shahar, Noa Ruhrman, Rutledge, S Lane, Saletti, Veronica, Sandaradura, Sarah A, Santoro, Claudia, Schatz, Ulrich A, Schreiber, Allison, Scott, Daryl A, Sellars, Elizabeth A, Sheffer, Ruth, Siqveland, Elizabeth, Slopis, John M, Smith, Rosemarie, Spalice, Alberto, Stockton, David W, Streff, Haley, Theos, Amy, Tomlinson, Gail E, Tran, Grace, Trapane, Pamela L, Trevisson, Eva, Ullrich, Nicole J, Van den Ende, Jenneke, Schrier Vergano, Samantha A, Wallace, Stephanie E, Wangler, Michael F, Weaver, David D, Yohay, Kaleb H, Zackai, Elaine, Zonana, Jonathan, Zurcher, Vickie, Claes, Kathleen B M, Eoli, Marica, Martin, Yolanda, Wimmer, Katharina, De Luca, Alessandro, Legius, Eric, Messiaen, Ludwine M, Koczkowska, Magdalena, Callens, Tom, Chen, Yunjia, Gomes, Alicia, Hicks, Alesha D, Sharp, Angela, Johns, Eric, Uhas, Kim Armfield, Armstrong, Linlea, Bosanko, Katherine Armstrong, Babovic-Vuksanovic, Dusica, Baker, Laura, Basel, Donald G, Bengala, Mario, Bennett, James T, Chambers, Chelsea, Clarkson, Lola K, Clementi, Maurizio, Cortés, Fanny M, Cunningham, Mitch, D'Agostino, M Daniela, Delatycki, Martin B, Digilio, Maria C, Dosa, Laura, Esposito, Silvia, Fox, Stephanie, Freckmann, Mary-Louise, Fauth, Christine, Giugliano, Teresa, Giustini, Sandra, Goetsch, Allison, Goldberg, Yael, Greenwood, Robert S, Griffis, Cristin, Gripp, Karen W, Gupta, Punita, Haan, Eric, Hachen, Rachel K, Haygarth, Tamara L, Hernández-Chico, Concepción, Hodge, Katelyn, Hopkin, Robert J, Hudgins, Louanne, Janssens, Sandra, Keller, Kory, Kelly-Mancuso, Geraldine, Kochhar, Aaina, Korf, Bruce R, Lewis, Andrea M, Liebelt, Jan, Lichty, Angie, Listernick, Robert H, Lyons, Michael J, Maystadt, Isabelle, Ojeda, Mayra Martinez, Mcdougall, Carey, Mcgregor, Lesley K, Melis, Daniela, Mendelsohn, Nancy, Nowaczyk, Malgorzata J M, Ortenberg, June, Panzer, Karin, Pappas, John G, Pierpont, Mary Ella, Piluso, Giulio, Pinna, Valentina, Pivnick, Eniko K, Pond, Dinel A, Powell, Cynthia M, Rogers, Caleb, Shahar, Noa Ruhrman, Rutledge, S Lane, Saletti, Veronica, Sandaradura, Sarah A, Santoro, Claudia, Schatz, Ulrich A, Schreiber, Allison, Scott, Daryl A, Sellars, Elizabeth A, Sheffer, Ruth, Siqveland, Elizabeth, Slopis, John M, Smith, Rosemarie, Spalice, Alberto, Stockton, David W, Streff, Haley, Theos, Amy, Tomlinson, Gail E, Tran, Grace, Trapane, Pamela L, Trevisson, Eva, Ullrich, Nicole J, Van den Ende, Jenneke, Schrier Vergano, Samantha A, Wallace, Stephanie E, Wangler, Michael F, Weaver, David D, Yohay, Kaleb H, Zackai, Elaine, Zonana, Jonathan, Zurcher, Vickie, Claes, Kathleen B M, Eoli, Marica, Martin, Yolanda, Wimmer, Katharina, De Luca, Alessandro, Legius, Eric, and Messiaen, Ludwine M

Subjects
congenital, hereditary, and neonatal diseases and abnormalities, Heterozygote, VONRECKLINGHAUSEN NEUROFIBROMATOSIS, INDEPENDENT NF1, Neurofibromatosis 1, NF1, genotype-phenotype correlation, p.Arg1276, p.Lys1423, p.Met1149, NOONAN-SYNDROME, Mutation, Missense, PULMONARY STENOSIS, AU-LAIT SPOTS, Medicine and Health Sciences, Humans, Genetic Predisposition to Disease, Met1149, Alleles, Genetic Association Studies, Research Articles, Arg1276, Genetics & Heredity, SPINAL NEUROFIBROMATOSIS, Science & Technology, Neurofibromin 1, MUTATIONS, OPTIC PATHWAY TUMORS, NATURAL-HISTORY, genotype–phenotype correlation, SOUTH EAST WALES, nervous system diseases, Lys1423, Cross-Sectional Studies, Phenotype, Amino Acid Substitution, Human medicine, Life Sciences & Biomedicine, Research Article
Abstract

We report 281 individuals carrying a pathogenic recurrent NF1 missense variant at p.Met1149, p.Arg1276, or p.Lys1423, representing three nontruncating NF1 hotspots in the University of Alabama at Birmingham (UAB) cohort, together identified in 1.8% of unrelated NF1 individuals. About 25% (95% confidence interval: 20.5-31.2%) of individuals heterozygous for a pathogenic NF1 p.Met1149, p.Arg1276, or p.Lys1423 missense variant had a Noonan-like phenotype, which is significantly more compared with the "classic" NF1-affected cohorts (all p

Published
2019

3. Additional file 2: of Genetic variation affecting DNA methylation and the human imprinting disorder, Beckwith-Wiedemann syndrome

Author

Dagar, Vinod, Hutchison, Wendy, Muscat, Andrea, Krishnan, Anita, Hoke, David, Buckle, Ashley, Siswara, Priscillia, Amor, David, Mann, Jeffrey, Pinner, Jason, Colley, Alison, Wilson, Meredith, Sachdev, Rani, McGillivray, George, Edwards, Matthew, Kirk, Edwin, Collins, Felicity, Jones, Kristi, Taylor, Juliet, Hayes, Ian, Thompson, Elizabeth, Barnett, Christopher, Haan, Eric, Mary-Louise Freckmann, Turner, Anne, White, Susan, Kamien, Ben, Ma, Alan, Mackenzie, Fiona, Baynam, Gareth, Kiraly-Borri, Cathy, Field, Michael, Dudding-Byth, Tracey, and Algar, Elizabeth

Subjects
urogenital system, embryonic structures, environment and public health
Abstract

Figure S1. DNMT1 sequence variants identified in BWS patients. Figure S2. Sequence traces of DNMT1 variants generated by site-directed mutagenesis. Figure S3. Expression of GFP-tagged DNMT1 proteins in HeLa cells. Figure S4. Schematic of the trapping assay adapted from Frauer and Leonhardt (2009). (PPTX 1525Â kb)

Published
2018
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4. Additional file 1: of Genetic variation affecting DNA methylation and the human imprinting disorder, Beckwith-Wiedemann syndrome

Author

Dagar, Vinod, Hutchison, Wendy, Muscat, Andrea, Krishnan, Anita, Hoke, David, Buckle, Ashley, Siswara, Priscillia, Amor, David, Mann, Jeffrey, Pinner, Jason, Colley, Alison, Wilson, Meredith, Sachdev, Rani, McGillivray, George, Edwards, Matthew, Kirk, Edwin, Collins, Felicity, Jones, Kristi, Taylor, Juliet, Hayes, Ian, Thompson, Elizabeth, Barnett, Christopher, Haan, Eric, Mary-Louise Freckmann, Turner, Anne, White, Susan, Kamien, Ben, Ma, Alan, Mackenzie, Fiona, Baynam, Gareth, Kiraly-Borri, Cathy, Field, Michael, Dudding-Byth, Tracey, and Algar, Elizabeth

Abstract

Table S1. Methylation at non-11p15 imprinting centres in BWS cases with loss of methylation at KCNQ1OT1 TSS-DMR. Only samples with identified methylation changes are listed. Tables S2. aâ e Primers used for HRM of MTHFR, MTR, MTRR, MAT1A, CBS. Table S3. aâ e Primers used for sequencing MTHFR, MTR, MTRR, MAT1A, CBS. Table S4. aâ d. DNMT1 primers. Table S5 Pyrosequencing primers. (DOCX 226Â kb)

Published
2018
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5. Additional file 1: Table S1. of Novel missense mutation in the bZIP transcription factor, MAF, associated with congenital cataract, developmental delay, seizures and hearing loss (AymĂŠ-Gripp syndrome)

Author

Javadiyan, Shari, Craig, Jamie, Shiwani Sharma, Lower, Karen, Casey, Theresa, Haan, Eric, Souzeau, Emmanuelle, and Burdon, Kathryn

Subjects
genetic structures, sense organs, eye diseases
Abstract

List of reported paediatric cataract genes selected for sequencing in this study. (DOCX 39Â kb)

Published
2017
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6. Frontotemporal dementia and its subtypes: a genome-wide association study

Author

Ferrari, Raffaele, Hernandez, Dena G, Nalls, Michael A, Rohrer, Jonathan D, Ramasamy, Adaikalavan, Kwok, John BJ, Dobson-Stone, Carol, Brooks, William S, Schofield, Peter R, Halliday, Glenda M, Hodges, John R, Piguet, Olivier, Bartley, Lauren, Thompson, Elizabeth, Haan, Eric, Hernández, Isabel, Ruiz, Agustín, Boada, Mercè, Borroni, Barbara, Padovani, Alessandro, Cruchaga, Carlos, Cairns, Nigel J, Benussi, Luisa, Binetti, Giuliano, Ghidoni, Roberta, Forloni, Gianluigi, Galimberti, Daniela, Fenoglio, Chiara, Serpente, Maria, Scarpini, Elio, Clarimón, Jordi, Lleó, Alberto, Blesa, Rafael, Waldö, Maria Landqvist, Nilsson, Karin, Nilsson, Christer, Mackenzie, Ian RA, Hsiung, Ging-Yuek R, Mann, David MA, Grafman, Jordan, Morris, Christopher M, Attems, Johannes, Griffiths, Timothy D, McKeith, Ian G, Thomas, Alan J, Pietrini, P, Huey, Edward D, Wassermann, Eric M, Baborie, Atik, Jaros, Evelyn, Tierney, Michael C, Pastor, Pau, Razquin, Cristina, Ortega-Cubero, Sara, Alonso, Elena, Perneczky, Robert, Diehl-Schmid, Janine, Alexopoulos, Panagiotis, Kurz, Alexander, Rainero, Innocenzo, Rubino, Elisa, Pinessi, Lorenzo, Rogaeva, Ekaterina, St George-Hyslop, Peter, Rossi, Giacomina, Tagliavini, Fabrizio, Giaccone, Giorgio, Rowe, James B, Schlachetzki, Johannes CM, Uphill, James, Collinge, John, Mead, Simon, Danek, Adrian, Van Deerlin, Vivianna M, Grossman, Murray, Trojanowski, John Q, van der Zee, Julie, Deschamps, William, Van Langenhove, Tim, Cruts, Marc, Van Broeckhoven, Christine, Cappa, Stefano F, Le Ber, Isabelle, Hannequin, Didier, Golfier, Véronique, Vercelletto, Martine, Brice, Alexis, Nacmias, Benedetta, Sorbi, Sandro, Bagnoli, Silvia, Piaceri, Irene, Nielsen, Jørgen E, Hjermind, Lena E, Riemenschneider, Matthias, Mayhaus, Manuel, Ibach, Bernd, Gasparoni, Gilles, Pichler, Sabrina, Gu, Wei, and Rossor, Martin N

Subjects
Adult, Male, Aging, Genotype, Clinical Sciences, Neurodegenerative, Rare Diseases, Clinical Research, 80 and over, Genetics, Acquired Cognitive Impairment, Humans, 2.1 Biological and endogenous factors, Aetiology, Alzheimer's Disease Related Dementias (ADRD), Aged, Neurology & Neurosurgery, Human Genome, Neurosciences, Alzheimer's Disease including Alzheimer's Disease Related Dementias (AD/ADRD), Middle Aged, Brain Disorders, Frontotemporal Dementia (FTD), Frontotemporal Dementia, Neurological, Female, Dementia, Genome-Wide Association Study
Abstract

BackgroundFrontotemporal dementia (FTD) is a complex disorder characterised by a broad range of clinical manifestations, differential pathological signatures, and genetic variability. Mutations in three genes-MAPT, GRN, and C9orf72--have been associated with FTD. We sought to identify novel genetic risk loci associated with the disorder.MethodsWe did a two-stage genome-wide association study on clinical FTD, analysing samples from 3526 patients with FTD and 9402 healthy controls. To reduce genetic heterogeneity, all participants were of European ancestry. In the discovery phase (samples from 2154 patients with FTD and 4308 controls), we did separate association analyses for each FTD subtype (behavioural variant FTD, semantic dementia, progressive non-fluent aphasia, and FTD overlapping with motor neuron disease [FTD-MND]), followed by a meta-analysis of the entire dataset. We carried forward replication of the novel suggestive loci in an independent sample series (samples from 1372 patients and 5094 controls) and then did joint phase and brain expression and methylation quantitative trait loci analyses for the associated (p

Published
2014

7. Homologous recombination DNA repair defects in PALB2- associated breast cancers

Author

Li, Anqi, Geyer, Felipe C., Blecua, Pedro, Lee, Ju Youn, Selenica, Pier, Brown, David N., Pareja, Fresia, Lee, Simon S. K., Kumar, Rahul, Rivera, Barbara, Bi, Rui, Piscuoglio, Salvatore, Wen, Hannah Y., Lozada, John R., Gularte-Mérida, Rodrigo, Cavallone, Luca, Rezoug, Zoulikha, Nguyen-Dumont, Tu, Peterlongo, Paolo, Tondini, Carlo, Terkelsen, Thorkild, Rønlund, Karina, Boonen, Susanne E., Mannerma, Arto, Winqvist, Robert, Janatova, Marketa, Rajadurai, Pathmanathan, Xia, Bing, Norton, Larry, Robson, Mark E., Ng, Pei-Sze, Looi, Lai-Meng, Southey, Melissa C., Weigelt, Britta, Soo-Hwang, Teo, Tischkowitz, Marc, Foulkes, William D., Reis-Filho, Jorge S., Aghmesheh, Morteza, Amor, David, Andrews, Leslie, Antill, Yoland, Balleine, Rosemary, Beesley, Jonathan, Blackburn, Anneke, Bogwitz, Michael, Brown, Melissa, Burgess, Matthew, Burke, Jo, Butow, Phyllis, Caldon, Liz, Campbell, Ian, Christian, Alice, Clarke, Christine, Cohen, Paul, Crook, Ashley, Cui, James, Cummings, Margaret, Dawson, Sarah-Jane, De Fazio, Anna, Delatycki, Martin, Dobrovic, Alex, Dudding, Tracy, Duijf, Pascal, Edkins, Edward, Edwards, Stacey, Farshid, Gelareh, Fellows, Andrew, Field, Michael, Flanagan, James, Fong, Peter, Forbes, John, Forrest, Laura, Fox, Stephen, French, Juliet, Friedlander, Michael, Ortega, David Gallego, Gattas, Michael, Giles, Graham, Gill, Grantley, Gleeson, Margaret, Greening, Sian, Haan, Eric, Harris, Marion, Hayward, Nick, Hickie, Ian, Hopper, John, Hunt, Clare, James, Paul, Jenkins, Mark, Kefford, Rick, Kentwell, Maira, Kirk, Judy, Kollias, James, Lakhani, Sunil, Lindeman, Geoff, Lipton, Lara, Lobb, Lizz, Lok, Sheau, Macrea, Finlay, Mann, Graham, Marsh, Deb, McLachlan, Sue-Anne, Meiser, Bettina, Milne, Roger, Nightingale, Sophie, O’Connell, Shona, Pachter, Nick, Patterson, Briony, Phillips, Kelly, Saleh, Mona, Salisbury, Elizabeth, Saunders, Christobel, Saunus, Jodi, Scott, Clare, Scott, Rodney, Sexton, Adrienne, Shelling, Andrew, Simpson, Peter, Spigelman, Allan, Spurdle, Mandy, Stone, Jennifer, Taylor, Jessica, Thorne, Heather, Trainer, Alison, Trench, Georgia, Tucker, Kathy, Visvader, Jane, Walker, Logan, Wallis, Mathew, Williams, Rachael, Winship, Ingrid, Wu, Kathy, and Young, Mary Anne

Subjects
631/67/68, article, 631/67/1347, 692/699/67/69, 3. Good health
Abstract

Mono-allelic germline pathogenic variants in the Partner And Localizer of BRCA2 (PALB2) gene predispose to a high-risk of breast cancer development, consistent with the role of PALB2 in homologous recombination (HR) DNA repair. Here, we sought to define the repertoire of somatic genetic alterations in PALB2-associated breast cancers (BCs), and whether PALB2-associated BCs display bi-allelic inactivation of PALB2 and/or genomic features of HR-deficiency (HRD). Twenty-four breast cancer patients with pathogenic PALB2 germline mutations were analyzed by whole-exome sequencing (WES, n = 16) or targeted capture massively parallel sequencing (410 cancer genes, n = 8). Somatic genetic alterations, loss of heterozygosity (LOH) of the PALB2 wild-type allele, large-scale state transitions (LSTs) and mutational signatures were defined. PALB2-associated BCs were found to be heterogeneous at the genetic level, with PIK3CA (29%), PALB2 (21%), TP53 (21%), and NOTCH3 (17%) being the genes most frequently affected by somatic mutations. Bi-allelic PALB2 inactivation was found in 16 of the 24 cases (67%), either through LOH (n = 11) or second somatic mutations (n = 5) of the wild-type allele. High LST scores were found in all 12 PALB2-associated BCs with bi-allelic PALB2 inactivation sequenced by WES, of which eight displayed the HRD-related mutational signature 3. In addition, bi-allelic inactivation of PALB2 was significantly associated with high LST scores. Our findings suggest that the identification of bi-allelic PALB2 inactivation in PALB2-associated BCs is required for the personalization of HR-directed therapies, such as platinum salts and/or PARP inhibitors, as the vast majority of PALB2-associated BCs without PALB2 bi-allelic inactivation lack genomic features of HRD.

8. The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Author

Figlioli, Gisella, Bogliolo, Massimo, Catucci, Irene, Caleca, Laura, Lasheras, Sandra Viz, Pujol, Roser, Kiiski, Johanna I., Muranen, Taru A., Barnes, Daniel R., Dennis, Joe, Michailidou, Kyriaki, Bolla, Manjeet K., Leslie, Goska, Aalfs, Cora M., Adank, Muriel A., Adlard, Julian, Agata, Simona, Cadoo, Karen, Agnarsson, Bjarni A., Ahearn, Thomas, Aittomäki, Kristiina, Ambrosone, Christine B., Andrews, Lesley, Anton-Culver, Hoda, Antonenkova, Natalia N., Arndt, Volker, Arnold, Norbert, Aronson, Kristan J., Arun, Banu K., Asseryanis, Ella, Auber, Bernd, Auvinen, Päivi, Azzollini, Jacopo, Balmaña, Judith, Barkardottir, Rosa B., Barrowdale, Daniel, Barwell, Julian, Beane Freeman, Laura E., Beauparlant, Charles Joly, Beckmann, Matthias W., Behrens, Sabine, Benitez, Javier, Berger, Raanan, Bermisheva, Marina, Blanco, Amie M., Blomqvist, Carl, Bogdanova, Natalia V., Bojesen, Anders, Bojesen, Stig E., Bonanni, Bernardo, Borg, Ake, Brady, Angela F., Brauch, Hiltrud, Brenner, Hermann, Brüning, Thomas, Burwinkel, Barbara, Buys, Saundra S., Caldés, Trinidad, Caliebe, Almuth, Caligo, Maria A., Campa, Daniele, Campbell, Ian G., Canzian, Federico, Castelao, Jose E., Chang-Claude, Jenny, Chanock, Stephen J., Claes, Kathleen B. M., Clarke, Christine L., Collavoli, Anita, Conner, Thomas A., Cox, David G., Cybulski, Cezary, Czene, Kamila, Daly, Mary B., De La Hoya, Miguel, Devilee, Peter, Diez, Orland, Ding, Yuan Chun, Dite, Gillian S., Ditsch, Nina, Domchek, Susan M., Dorfling, Cecilia M., Dos-Santos-Silva, Isabel, Durda, Katarzyna, Dwek, Miriam, Eccles, Diana M., Ekici, Arif B., Eliassen, A. Heather, Ellberg, Carolina, Eriksson, Mikael, Evans, D. Gareth, Fasching, Peter A., Figueroa, Jonine, Flyger, Henrik, Foulkes, William D., Friebel, Tara M., Friedman, Eitan, Gabrielson, Marike, Gaddam, Pragna, Gago-Dominguez, Manuela, Gao, Chi, Gapstur, Susan M., Garber, Judy, García-Closas, Montserrat, García-Sáenz, José A., Gaudet, Mia M., Gayther, Simon A., Giles, Graham G., Glendon, Gord, Godwin, Andrew K., Goldberg, Mark S., Goldgar, David E., Guénel, Pascal, Gutierrez-Barrera, Angelica M., Haeberle, Lothar, Haiman, Christopher A., Håkansson, Niclas, Hall, Per, Hamann, Ute, Harrington, Patricia A., Hein, Alexander, Heyworth, Jane, Hillemanns, Peter, Hollestelle, Antoinette, Hopper, John L., Hosgood, H. Dean, Howell, Anthony, Hu, Chunling, Hulick, Peter J., Hunter, David J., Imyanitov, Evgeny N., Isaacs, Claudine, Jakimovska, Milena, Jakubowska, Anna, James, Paul, Janavicius, Ramunas, Janni, Wolfgang, John, Esther M., Jones, Michael E., Jung, Audrey, Kaaks, Rudolf, Karlan, Beth Y., Khusnutdinova, Elza, Kitahara, Cari M., Konstantopoulou, Irene, Koutros, Stella, Kraft, Peter, Lambrechts, Diether, Lazaro, Conxi, Le Marchand, Loic, Lester, Jenny, Lesueur, Fabienne, Lilyquist, Jenna, Loud, Jennifer T., Lu, Karen H., Luben, Robert N., Lubinski, Jan, Mannermaa, Arto, Manoochehri, Mehdi, Manoukian, Siranoush, Margolin, Sara, Martens, John W. M., Maurer, Tabea, Mavroudis, Dimitrios, Mebirouk, Noura, Meindl, Alfons, Menon, Usha, Miller, Austin, Montagna, Marco, Nathanson, Katherine L., Neuhausen, Susan L., Newman, William G., Nguyen-Dumont, Tu, Nielsen, Finn Cilius, Nielsen, Sarah, Nikitina-Zake, Liene, Offit, Kenneth, Olah, Edith, Olopade, Olufunmilayo I., Olshan, Andrew F., Olson, Janet E., Olsson, Håkan, Osorio, Ana, Ottini, Laura, Peissel, Bernard, Peixoto, Ana, Peto, Julian, Plaseska-Karanfilska, Dijana, Pocza, Timea, Presneau, Nadege, Pujana, Miquel Angel, Punie, Kevin, Rack, Brigitte, Rantala, Johanna, Rashid, Muhammad U., Rau-Murthy, Rohini, Rennert, Gad, Lejbkowicz, Flavio, Rhenius, Valerie, Romero, Atocha, Rookus, Matti A., Ross, Eric A., Rossing, Maria, Rudaitis, Vilius, Ruebner, Matthias, Saloustros, Emmanouil, Sanden, Kristin, Santamariña, Marta, Scheuner, Maren T., Schmutzler, Rita K., Schneider, Michael, Scott, Christopher, Senter, Leigha, Shah, Mitul, Sharma, Priyanka, Shu, Xiao-Ou, Simard, Jacques, Singer, Christian F., Sohn, Christof, Soucy, Penny, Southey, Melissa C., Spinelli, John J., Steele, Linda, Stoppa-Lyonnet, Dominique, Tapper, William J., Teixeira, Manuel R., Terry, Mary Beth, Thomassen, Mads, Thompson, Jennifer, Thull, Darcy L., Tischkowitz, Marc, Tollenaar, Rob A.E.M., Torres, Diana, Troester, Melissa A., Truong, Thérèse, Tung, Nadine, Untch, Michael, Vachon, Celine M., Van Rensburg, Elizabeth J., Van Veen, Elke M., Vega, Ana, Viel, Alessandra, Wappenschmidt, Barbara, Weitzel, Jeffrey N., Wendt, Camilla, Wieme, Greet, Wolk, Alicja, Yang, Xiaohong R., Zheng, Wei, Ziogas, Argyrios, Zorn, Kristin K., Dunning, Alison M., Lush, Michael, Wang, Qin, McGuffog, Lesley, Parsons, Michael T., Pharoah, Paul D. P., Fostira, Florentia, Toland, Amanda E., Andrulis, Irene L., Ramus, Susan J., Swerdlow, Anthony J., Greene, Mark H., Chung, Wendy K., Milne, Roger L., Chenevix-Trench, Georgia, Dörk, Thilo, Schmidt, Marjanka K., Easton, Douglas F., Radice, Paolo, Hahnen, Eric, Antoniou, Antonis C., Couch, Fergus J., Nevanlinna, Heli, Surrallés, Jordi, Peterlongo, Paolo, Balleine, Rosemary, Baxter, Robert, Braye, Stephen, Carpenter, Jane, Dahlstrom, Jane, Forbes, John, Lee, C. Soon, Marsh, Deborah, Morey, Adrienne, Pathmanathan, Nirmala, Scott, Rodney, Simpson, Peter, Spigelman, Allan, Wilcken, Nicholas, Yip, Desmond, Zeps, Nikolajs, Belotti, Muriel, Bertrand, Ophélie, Birot, Anne-Marie, Buecher, Bruno, Caputo, Sandrine, Dupré, Anaïs, Fourme, Emmanuelle, Gauthier-Villars, Marion, Golmard, Lisa, Le Mentec, Marine, Moncoutier, Virginie, De Pauw, Antoine, Saule, Claire, Boutry-Kryza, Nadia, Calender, Alain, Giraud, Sophie, Léone, Mélanie, Bressac-De-Paillerets, Brigitte, Caron, Olivier, Guillaud-Bataille, Marine, Bignon, Yves-Jean, Uhrhammer, Nancy, Bonadona, Valérie, Lasset, Christine, Berthet, Pascaline, Castera, Laurent, Vaur, Dominique, Bourdon, Violaine, Noguès, Catherine, Noguchi, Tetsuro, Popovici, Cornel, Remenieras, Audrey, Sobol, Hagay, Coupier, Isabelle, Pujol, Pascal, Adenis, Claude, Dumont, Aurélie, Révillion, Françoise, Muller, Danièle, Barouk-Simonet, Emmanuelle, Bonnet, Françoise, Bubien, Virginie, Longy, Michel, Sevenet, Nicolas, Gladieff, Laurence, Guimbaud, Rosine, Feillel, Viviane, Toulas, Christine, Dreyfus, Hélène, Leroux, Christine Dominique, Peysselon, Magalie, Rebischung, Christine, Legrand, Clémentine, Baurand, Amandine, Bertolone, Geoffrey, Coron, Fanny, Faivre, Laurence, Jacquot, Caroline, Lizard, Sarab, Kientz, Caroline, Lebrun, Marine, Prieur, Fabienne, Fert-Ferrer, Sandra, Mari, Véronique, Vénat-Bouvet, Laurence, Bézieau, Stéphane, Delnatte, Capucine, Mortemousque, Isabelle, Colas, Chrystelle, Coulet, Florence, Soubrier, Florent, Warcoin, Mathilde, Bronner, Myriam, Sokolowska, Johanna, Collonge-Rame, Marie-Agnès, Damette, Alexandre, Gesta, Paul, Lallaoui, Hakima, Chiesa, Jean, Molina-Gomes, Denise, Ingster, Olivier, Manouvrier-Hanu, Sylvie, Lejeune, Sophie, Aghmesheh, Morteza, Greening, Sian, Amor, David, Gattas, Mike, Botes, Leon, Buckley, Michael, Friedlander, Michael, Koehler, Jessica, Meiser, Bettina, Saleh, Mona, Salisbury, Elizabeth, Trainer, Alison, Tucker, Kathy, Antill, Yoland, Dobrovic, Alexander, Fellows, Andrew, Fox, Stephen, Harris, Marion, Nightingale, Sophie, Phillips, Kelly, Sambrook, Joe, Thorne, Heather, Armitage, Shane, Arnold, Leanne, Kefford, Rick, Kirk, Judy, Rickard, Edwina, Bastick, Patti, Beesley, Jonathan, Hayward, Nick, Spurdle, Amanda, Walker, Logan, Beilby, John, Saunders, Christobel, Bennett, Ian, Blackburn, Anneke, Bogwitz, Michael, Gaff, Clara, Lindeman, Geoff, Pachter, Nick, Scott, Clare, Sexton, Adrienne, Visvader, Jane, Taylor, Jessica, Winship, Ingrid, Brennan, Meagan, Brown, Melissa, French, Juliet, Edwards, Stacey, Burgess, Matthew, Burke, Jo, Patterson, Briony, Butow, Phyllis, Culling, Bronwyn, Caldon, Liz, Callen, David, Chauhan, Deepa, Eisenbruch, Maurice, Heiniger, Louise, Chauhan, Manisha, Christian, Alice, Dixon, Joanne, Kidd, Alexa, Cohen, Paul, Colley, Alison, Fenton, Georgina, Crook, Ashley, Dickson, Rebecca, Field, Michael, Cui, James, Cummings, Margaret, Dawson, Sarah-Jane, DeFazio, Anna, Delatycki, Martin, Dudding, Tracy, Edkins, Ted, Farshid, Gelareh, Flanagan, James, Fong, Peter, Forrest, Laura, Gallego-Ortega, David, George, Peter, Gill, Grantley, Kollias, James, Haan, Eric, Hart, Stewart, Jenkins, Mark, Hunt, Clare, Lakhani, Sunil, Lipton, Lara, Lobb, Liz, Mann, Graham, McLachlan, Sue Anne, O’Connell, Shona, O’Sullivan, Sarah, Pieper, Ellen, Robinson, Bridget, Saunus, Jodi, Scott, Elizabeth, Shelling, Andrew, Williams, Rachael, and Young, Mary Ann

Subjects
692/4028/67/68, 631/67/68, article, nutritional and metabolic diseases, 631/208/68, skin and connective tissue diseases, 3. Good health
Abstract

Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors.

9. Mutations in ELAC2 associated with hypertrophic cardiomyopathy impair mitochondrial tRNA 3'-end processing

Author

Saoura, Makenzie, Powell, Christopher A, Kopajtich, Robert, Alahmad, Ahmad, Al-Balool, Haya H, Albash, Buthaina, Alfadhel, Majid, Alston, Charlotte L, Bertini, Enrico, Bonnen, Penelope E, Bratkovic, Drago, Carrozzo, Rosalba, Donati, Maria A, Di Nottia, Michela, Ghezzi, Daniele, Goldstein, Amy, Haan, Eric, Horvath, Rita, Hughes, Joanne, Invernizzi, Federica, Lamantea, Eleonora, Lucas, Benjamin, Pinnock, Kyla-Gaye, Pujantell, Maria, Rahman, Shamima, Rebelo-Guiomar, Pedro, Santra, Saikat, Verrigni, Daniela, McFarland, Robert, Prokisch, Holger, Taylor, Robert W, Levinger, Louis, and Minczuk, Michal

Subjects
Male, Genotype, Protein Conformation, Gene Expression, Substrate Specificity, Cohort Studies, Structure-Activity Relationship, RNA, Transfer, Humans, Genetic Predisposition to Disease, Protein Interaction Domains and Motifs, RNA Processing, Post-Transcriptional, Alleles, Genetic Association Studies, Infant, Cardiomyopathy, Hypertrophic, 3. Good health, Mitochondria, Neoplasm Proteins, Enzyme Activation, mitochondrial disease, Kinetics, Genes, Mitochondrial, Phenotype, Amino Acid Substitution, Mutation, RNA, Female, cardiomyopathy, Biomarkers, RNase Z
Abstract

Mutations in either the mitochondrial or nuclear genomes are associated with a diverse group of human disorders characterized by impaired mitochondrial respiration. Within this group, an increasing number of mutations have been identified in nuclear genes involved in mitochondrial RNA metabolism, including ELAC2. The ELAC2 gene codes for the mitochondrial RNase Z, responsible for endonucleolytic cleavage of the 3' ends of mitochondrial pre-tRNAs. Here, we report the identification of 16 novel ELAC2 variants in individuals presenting with mitochondrial respiratory chain deficiency, hypertrophic cardiomyopathy (HCM), and lactic acidosis. We provide evidence for the pathogenicity of the novel missense variants by studying the RNase Z activity in an in vitro system. We also modeled the residues affected by a missense mutation in solved RNase Z structures, providing insight into enzyme structure and function. Finally, we show that primary fibroblasts from the affected individuals have elevated levels of unprocessed mitochondrial RNA precursors. Our study thus broadly confirms the correlation of ELAC2 variants with severe infantile-onset forms of HCM and mitochondrial respiratory chain dysfunction. One rare missense variant associated with the occurrence of prostate cancer (p.Arg781His) impairs the mitochondrial RNase Z activity of ELAC2, suggesting a functional link between tumorigenesis and mitochondrial RNA metabolism.

10. Assessment of myocardial oxygenation, strain, and diastology in MYBPC3-related hypertrophic cardiomyopathy: a cardiovascular magnetic resonance and echocardiography study

Author

Rachael Lloyd, Eric Haan, Laura Yeates, Joseph B. Selvanayagam, Richard J. Woodman, John Atherton, Suchi Grover, Pey Wen Lou, Rebecca Perry, Christopher Semsarian, Grover, Suchi, Lloyd, Rachael, Perry, Rebecca, Lou, Pey Wen, Haan, Eric, Yeates, Laura, Woodman, Richard, Atherton, John J, Semsarian, Chris, and Selvanayagam, Joseph B

Subjects
Male, medicine.medical_specialty, Longitudinal strain, Cardiac-Gated Imaging Techniques, Diastole, Contrast Media, Magnetic Resonance Imaging, Cine, 030204 cardiovascular system & hematology, Left ventricular hypertrophy, 030218 nuclear medicine & medical imaging, diastolic function, speckle-tracking strain, 03 medical and health sciences, Oxygen Consumption, 0302 clinical medicine, Internal medicine, Image Interpretation, Computer-Assisted, Organometallic Compounds, medicine, Humans, Radiology, Nuclear Medicine and imaging, cardiovascular diseases, medicine.diagnostic_test, Strain (chemistry), business.industry, Myocardium, Myocardial oxygenation, Hypertrophic cardiomyopathy, Magnetic resonance imaging, General Medicine, Oxygenation, Cardiomyopathy, Hypertrophic, Middle Aged, hypertrophic cardiomyopathy, medicine.disease, left ventricular hypertrophy, Echocardiography, myocardial oxygenation, Case-Control Studies, Exercise Test, Cardiology, Female, Hypertrophy, Left Ventricular, Carrier Proteins, Cardiology and Cardiovascular Medicine, business
Abstract

Aims Myocardial oxygenation is impaired in hypertrophic cardiomyopathy (HCM) patients with left ventricular hypertrophy (LVH), and possibly also in HCM gene carriers without LVH. Whether these oxygenation changes are also associated with abnormalities in diastolic function or left ventricular (LV) strain are unknown. Methods and results We evaluated 60 subjects: 20 MYBPC3 gene positive patients with LVH (G+LVH+), 18 MYBPC3 gene positive without LVH (G+LVH−), 11 gene negative siblings (G−), and 11 normal controls (NC). All subjects underwent 2D transthoracic echocardiography and cardiovascular magnetic resonance imaging for assessment of ventricular volumes, mass, and myocardial oxygenation at rest and adenosine stress using the blood oxygen level dependent (BOLD) technique. Maximal septal thickness was 20 mm in the G+LVH+ group, vs. 9 mm for the G+LVH− group. As expected, the G+LVH+ group had a more blunted myocardial oxygenation response to stress when compared with the G+LVH− group (−5% ± 3% vs. 2% ± 4%, P Conclusion Myocardial deoxygenation during stress is observed in MYBPC3 HCM patients, even in the presence of normal LV diastolic function, LV global longitudinal strain, and LV wall thickness.

Published
2019

11. Targeted Next‐Generation Sequencing Analysis of 1,000 Individuals with Intellectual Disability

Author

Shoumo Bhattacharya, Olivera Spasic-Boskovic, Charles E. Schwartz, Catherine Cosgrove, Kathryn Friend, Keren J. Carss, F. Lucy Raymond, Roger E. Stevenson, Anna Hackett, Eric Haan, Zaamin B. Hussain, Matthew E. Hurles, Michael Field, Detelina Grozeva, James A B Floyd, Jozef Gecz, Maria-Isabel Tejada, Jamie Bentham, Mark A. Corbett, Bernard Keavney, Elizabeth Thompson, Marie Shaw, Alessandra Renieri, Cambridge Institute for Medical Research (CIMR), University of Cambridge [UK] (CAM), Department of Haematology, Hospital Universitario Cruces = Cruces University Hospital, University of Adelaide, Women’s and Children’s Hospital [Adelaide], Università degli Studi di Siena = University of Siena (UNISI), The Greenwood Genetic Center, Grozeva, Detelina, Carss, Keren, Spasic Boskovic, Olivera, Tejada, Maria Isabel, Gecz, Jozef, Shaw, Marie, Corbett, Mark, Haan, Eric, Thompson, Elizabeth, Friend, Kathryn, Hussain, Zaamin, Hackett, Anna, Field, Michael, Renieri, Alessandra, Stevenson, Roger, Schwartz, Charle, Floyd, James A. B., Bentham, Jamie, Cosgrove, Catherine, Keavney, Bernard, Bhattacharya, Shoumo, Hurles, Matthew, Raymond, F. Lucy, and Franco, Brunella

Subjects
Male, Proband, Developmental delay, Intellectual disability, Mendelian disease, Next-generation sequencing, Genetics, Genetics (clinical), Sequence analysis, Alleles, Cohort Studies, Computational Biology, Female, Humans, Inheritance Patterns, Intellectual Disability, Mutation, Polymorphism, Single Nucleotide, Genetic Association Studies, High-Throughput Nucleotide Sequencing, next‐generation sequencing, Biology, Bioinformatics, DNA sequencing, Genetic, medicine, Missense mutation, Polymorphism, Allele, developmental delay, intellectual disability, next-generation sequencing, Research Articles, ATRX, Single Nucleotide, medicine.disease, Settore MED/03 - Genetica Medica, [SDV.GEN.GH]Life Sciences [q-bio]/Genetics/Human genetics, CUL4B, Research Article
Abstract

International audience; To identify genetic causes of intellectual disability (ID), we screened a cohort of 986 individuals with moderate to severe ID for variants in 565 known or candidate ID-associated genes using targeted next-generation sequencing. Likely pathogenic rare variants were found in ß11% of the cases (113 variants in 107/986 individuals: ß8% of the individuals had a likely pathogenic loss-of-function [LoF] variant, whereas ß3% had a known pathogenic missense variant). Variants in SETD5, ATRX, CUL4B, MECP2, and ARID1B were the most common causes of ID. This study assessed the value of sequencing a cohort of probands to provide a molecular diagnosis of ID, without the availability of DNA from both parents for de novo sequence analysis. This modeling is clinically relevant as 28% of all UK families with dependent children are single parent households. In conclusion, to diagnose patients with ID in the absence of parental DNA, we recommend investigation of all LoF variants in known genes that cause ID and assessment of a limited list of proven pathogenic missense variants in these genes. This will provide 11% additional diagnostic yield beyond the 10%–15% yield from array CGH alone.

Published
2015

12. Mutations in USP9X Are Associated with X-Linked Intellectual Disability and Disrupt Neuronal Cell Migration and Growth

Author

Lachlan A. Jolly, F. Lucy Raymond, Eric Haan, Lam Son Nguyen, Raman Kumar, Claire C. Homan, Jozef Gecz, Fatima Abidi, Martine Raynaud, Charles E. Schwartz, Stephen A. Wood, Homan, Claire C, Kumar, Raman, Nguyen, Lam Son, Haan, Eric, Raymond, F Lucy, Abidi, Fatima, Raynaud, Martine, Schwartz, Charles E, Wood, Stephen A, Gecz, Jozef, and Jolly, Lachlan A

Subjects
Male, Proband, Time Factors, X-linked intellectual disability, Neurogenesis, Mutation, Missense, USP9X, Biology, medicine.disease_cause, Mice, 03 medical and health sciences, 0302 clinical medicine, Cell Movement, Genes, X-Linked, Report, Intellectual Disability, Genetics, medicine, Animals, Humans, Genetics(clinical), Gene, Cytoskeleton, Genetics (clinical), X chromosome, Loss function, Cell Proliferation, 030304 developmental biology, Family Health, Mice, Knockout, Neurons, Chromosomes, Human, X, 0303 health sciences, Mutation, disease-associated DNA variants, Genetic Variation, medicine.disease, Phenotype, DNA-Binding Proteins, intellectual disability, Knockout mouse, Female, Ubiquitin Thiolesterase, 030217 neurology & neurosurgery, Transcription Factors
Abstract

With a wealth of disease-associated DNA variants being recently reported, the challenges of providing their functional characterization are mounting. Previously, as part of a large systematic resequencing of the X chromosome in 208 unrelated families with nonsyndromic X-linked intellectual disability, we identified three unique variants (two missense and one protein truncating) in USP9X. To assess the functional significance of these variants, we took advantage of the Usp9x knockout mouse we generated. Loss of Usp9x causes reduction in both axonal growth and neuronal cell migration. Although overexpression of wild-type human USP9X rescued these defects, all three USP9X variants failed to rescue axonal growth, caused reduced USP9X protein localization in axonal growth cones, and (in 2/3 variants) failed to rescue neuronal cell migration. Interestingly, in one of these families, the proband was subsequently identified to have a microdeletion encompassing ARID1B, a known ID gene. Given our findings it is plausible that loss of function of both genes contributes to the individual's phenotype. This case highlights the complexity of the interpretations of genetic findings from genome-wide investigations. We also performed proteomics analysis of neurons from both the wild-type and Usp9x knockout embryos and identified disruption of the cytoskeleton as the main underlying consequence of the loss of Usp9x. Detailed clinical assessment of all three families with USP9X variants identified hypotonia and behavioral and morphological defects as common features in addition to ID. Together our data support involvement of all three USP9X variants in ID in these families and provide likely cellular and molecular mechanisms involved. Refereed/Peer-reviewed

Published
2014

13. Epilepsy and mental retardation limited to females with PCDH19 mutations can present de novo or in single generation families

Author

Samuel F. Berkovic, Raffaella Smith, Samantha J. Turner, Michael R. Stratton, Gillian Turner, Eric Haan, Natasha J Brown, Jozef Gecz, Tarishi Desai, Ingrid E. Scheffer, Kim Hynes, John Christodoulou, Leanne M. Dibbens, Marta A. Bayly, Zahyia Al Raisi, Helen Leonard, Patrick S. Tarpey, Deepak Gill, Hynes, Kim, Tarpey, Patrick, Dibbens, Leanne M, Bayly, Marta A, Berkovic, Samuel F, Smith, Raffaella, Al Raisi, Zahyia, Turner, Samantha J, Brown, Natasha J, Desai, Tarishi D, Haan, Eric, Turner, Gillian, Christodoulou, John, Leonard, Helen, Gill, Deepak, Stratton, Michael R, Gecz, Jozef, and Scheffer, Ingrid E

Subjects
Adult, infantile onset seizures, seizure, Molecular Sequence Data, CDKL5, autism, Rett syndrome, protocadherin 19, mental retardation, MECP2, Epilepsy, Intellectual disability, Genetics, medicine, Humans, Missense mutation, Family, Amino Acid Sequence, Family history, Child, Genetics (clinical), Family Characteristics, Base Sequence, Sequence Homology, Amino Acid, business.industry, Cadherins, medicine.disease, Protocadherins, Pedigree, Child Development Disorders, Pervasive, intellectual disability, Mutation, Mental Retardation, X-Linked, epilepsy, Autism, Female, mutation, business, EFMR
Abstract

Background: Epilepsy and mental retardation limited to females (EFMR) is an intriguing X-linked disorder affecting heterozygous females and sparing hemizygous males. Mutations in the protocadherin 19 (PCDH19) gene have been identified in seven unrelated families with EFMR. Methods and results: Here, we assessed the frequency of PCDH19 mutations in individuals with clinical features which overlap those of EFMR. We analysed 185 females from three cohorts: 42 with Rett syndrome who were negative for MECP2 and CDKL5 mutations, 57 with autism spectrum disorders, and 86 with epilepsy with or without intellectual disability. No mutations were identified in the Rett syndrome and autism spectrum disorders cohorts suggesting that despite sharing similar clinical characteristics with EFMR, PCDH19 mutations are not generally associated with these disorders. Among the 86 females with epilepsy (of whom 51 had seizure onset before 3 years), with or without intellectual disability, we identified two (2.3%) missense changes. One (c.1671C-G, p.N557K), reported previously without clinical data, was found in two affected sisters, the first EFMR family without a multigenerational family history of affected females. The second, reported here, is a novel de novo missense change identified in a sporadic female. The change, p.S276P, is predicted to result in functional disturbance of PCDH19 as it affects a highly conserved residue adjacent to the adhesion interface of EC3 of PCDH19. those with the characteristic family history of EFMR. Conclusions: This de novo PCDH19 mutation in a sporadic female highlights that mutational analysis should be considered in isolated instances of girls with infantile onset seizures and developmental delay, in addition to Refereed/Peer-reviewed

Published
2009

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