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4. High-throughput discovery of novel developmental phenotypes

Author

McKay, Matthew, Urban, Barbara, Lund, Caroline, Froeter, Erin, LaCasse, Taylor, Mehalow, Adrienne, Gordon, Emily, Donahue, Leah Rae, Taft, Robert, Kutney, Peter, Dion, Stephanie, Goodwin, Leslie, Kales, Susan, Urban, Rachel, Palmer, Kristina, Pertuy, Fabien, Bitz, Deborah, Weber, Bruno, Goetz-Reiner, Patrice, Jacobs, Hughes, Le Marchand, Elise, El Amri, Amal, El Fertak, Leila, Ennah, Hamid, Ali-Hadji, Dalila, Ayadi, Abdel, Wattenhofer-Donze, Marie, Jacquot, Sylvie, André, Philippe, Birling, Marie-Christine, Pavlovic, Guillaume, Sorg, Tania, Morse, Iva, Benso, Frank, Stewart, Michelle E, Copley, Carol, Harrison, Jackie, Joynson, Samantha, Guo, Ruolin, Qu, Dawei, Spring, Shoshana, Yu, Lisa, Ellegood, Jacob, Morikawa, Lily, Shang, Xueyuan, Feugas, Pat, Creighton, Amie, Castellanos Penton, Patricia, Danisment, Ozge, Griggs, Nicola, Tudor, Catherine L, Green, Angela L, Icoresi Mazzeo, Cecilia, Siragher, Emma, Lillistone, Charlotte, Tuck, Elizabeth, Gleeson, Diane, Sethi, Debarati, Bayzetinova, Tanya, Burvill, Jonathan, Habib, Bishoy, Weavers, Lauren, Maswood, Ryea, Miklejewska, Evelina, Woods, Michael, Grau, Evelyn, Newman, Stuart, Sinclair, Caroline, Brown, Ellen, Ayabe, Shinya, Iwama, Mizuho, and Murakami, Ayumi

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Biomedical and Clinical Sciences, Genetics, Human Genome, Biotechnology, 2.1 Biological and endogenous factors, 1.1 Normal biological development and functioning, Animals, Conserved Sequence, Disease, Embryo, Mammalian, Genes, Essential, Genes, Lethal, Genome-Wide Association Study, High-Throughput Screening Assays, Humans, Imaging, Three-Dimensional, Mice, Mice, Inbred C57BL, Mice, Knockout, Mutation, Penetrance, Phenotype, Polymorphism, Single Nucleotide, Sequence Homology, International Mouse Phenotyping Consortium, Jackson Laboratory, Infrastructure Nationale PHENOMIN, Institut Clinique de la Souris, Charles River Laboratories, MRC Harwell, Toronto Centre for Phenogenomics, Wellcome Trust Sanger Institute, RIKEN BioResource Center, General Science & Technology
Abstract

Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.

Published
2016

6. Differentiation and Transplantation of Embryonic Stem Cell-Derived Cone Photoreceptors into a Mouse Model of End-Stage Retinal Degeneration

Author

Kruczek, Kamil, Gonzalez-Cordero, Anai, Goh, Debbie, Naeem, Arifa, Jonikas, Mindaugas, Blackford, Samuel J.I., Kloc, Magdalena, Duran, Yanai, Georgiadis, Anastasios, Sampson, Robert D., Maswood, Ryea N., Smith, Alexander J., Decembrini, Sarah, Arsenijevic, Yvan, Sowden, Jane C., Pearson, Rachael A., West, Emma L., and Ali, Robin R.

Published
2017
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7. Intravitreal administration of recombinant human opticin protects against hyperoxia-induced pre-retinal neovascularization

Author

Klaska, Izabela P., primary, White, Anne, additional, Villacampa, Pilar, additional, Hoke, Justin, additional, Hervás, Laura A., additional, Maswood, Ryea N., additional, Ali, Robin R., additional, Bunce, Catey, additional, Unwin, Richard D., additional, Cooper, Garth J.S., additional, Bishop, Paul N., additional, and Bainbridge, James W., additional

Published
2021
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8. A resource of targeted mutant mouse lines for 5,061 genes

Author

Birling, Marie-Christine, Yoshiki, Atsushi, Chiani, Francesco, Kaloff, Cornelia, Hörlein, Andreas, Teichmann, Sandy, Tasdemir, Adriane, Krause, Heidi, German, Dorota, Könitzer, Anne, Weber, Sarah, Beig, Joachim, McKay, Matthew, Chin, Hsian-Jean Genie, Bedigian, Richard, Dion, Stephanie, Kutny, Peter, Kelmenson, Jennifer, Perry, Emily, Nguyen-Bresinsky, Dong, Seluke, Audrie, Leach, Timothy, Perkins, Sara, Slater, Amanda, Christou, Skevoulla, Petit, Michaela, Urban, Rachel, Kales, Susan, DaCosta, Michael, McFarland, Michael, Palazola, Rick, Peterson, Kevin A, Svenson, Karen, Braun, Robert E, Taft, Robert, Codner, Gemma F, Rhue, Mark, Garay, Jose, Clary, Dave, Araiza, Renee, Grimsrud, Kristin, Bower, Lynette, Anchell, Nicole L, Jager, Kayla M, Young, Diana L, Dao, Phuong T, DeMayo, Francesco J, Gardiner, Wendy, Bell, Toni, Kenyon, Janet, Stewart, Michelle E, Lynch, Denise, Loeffler, Jorik, Caulder, Adam, Hillier, Rosie, Quwailid, Mohamed M, Zaman, Rumana, Dickinson, Mary E, Santos, Luis, Obata, Yuichi, Iwama, Mizuho, Nakata, Hatsumi, Hashimoto, Tomomi, Kadota, Masayo, Masuya, Hiroshi, Tanaka, Nobuhiko, Miura, Ikuo, Yamada, Ikuko, Doe, Brendan, Furuse, Tamio, Selloum, Mohammed, Jacquot, Sylvie, Ayadi, Abdel, Ali-Hadji, Dalila, Charles, Philippe, Le Marchand, Elise, El Amri, Amal, Kujath, Christelle, Fougerolle, Jean-Victor, Donahue, Leah Rae, Mellul, Peggy, Legeay, Sandrine, Vasseur, Laurent, Moro, Anne-Isabelle, Lorentz, Romain, Schaeffer, Laurence, Dreyer, Dominique, Erbs, Valérie, Eisenmann, Benjamin, Rossi, Giovanni, Fray, Martin D, Luppi, Laurence, Mertz, Annelyse, Jeanblanc, Amélie, Grau, Evelyn, Sinclair, Caroline, Brown, Ellen, Kundi, Helen, Madich, Alla, Woods, Mike, Pearson, Laila, Gambadoro, Alessia, Mayhew, Danielle, Griggs, Nicola, Houghton, Richard, Bussell, James, Ingle, Catherine, Valentini, Sara, Gleeson, Diane, Sethi, Debarati, Bayzetinova, Tanya, Burvill, Jonathan, Adams, David J, Gao, Xiang, Habib, Bishoy, Weavers, Lauren, Maswood, Ryea, Miklejewska, Evelina, Cook, Ross, Platte, Radka, Price, Stacey, Vyas, Sapna, Collinson, Adam, Hardy, Matt, Gertsenstein, Marina, Dalvi, Priya, Iyer, Vivek, West, Tony, Thomas, Mark, Mujica, Alejandro, Sins, Elodie, Barrett, Daniel, Dobbie, Michael, Grobler, Anne, Loots, Glaudina, Gomez-Segura, Alba, Hayeshi, Rose, Scholtz, Liezl-Marie, Bester, Cor, Pheiffer, Wihan, Venter, Kobus, Bosch, Fatima, Goodwin, Leslie O, Heaney, Jason D, Hérault, Yann, de Angelis, Martin Hrabě, Jiang, Si-Tse, Justice, Monica J, Kasparek, Petr, Ayabe, Shinya, King, Ruairidh E, Kühn, Ralf, Lee, Ho, Lee, Youngik, Liu, Zhiwei, Lloyd, K C Kent, Lorenzo, Isabel, Mallon, Ann-Marie, McKerlie, Colin, Meehan, Terrence F, Beaudet, Arthur L, Fuentes, Violeta Munoz, Newman, Stuart, Nutter, Lauryl M J, Oh, Goo Taeg, Pavlovic, Guillaume, Ramirez-Solis, Ramiro, Rosen, Barry, Ryder, Edward J, Santos, Luis A, Schick, Joel, Bottomley, Joanna, Seavitt, John R, Sedlacek, Radislav, Seisenberger, Claudia, Seong, Je Kyung, Skarnes, William C, Sorg, Tania, Steel, Karen P, Tamura, Masaru, Tocchini-Valentini, Glauco P, Wang, Chi-Kuang Leo, Bradley, Allan, Wardle-Jones, Hannah, Wattenhofer-Donzé, Marie, Wells, Sara, Wiles, Michael V, Willis, Brandon J, Wood, Joshua A, Wurst, Wolfgang, Xu, Ying, Consortium, International Mouse Phenotyping, Teboul, Lydia, Brown, Steve D M, Murray, Stephen A, Gallegos, Juan J, Green, Jennie R, Bohat, Ritu, Zimmel, Katie, Pereira, Monica, MacMaster, Suzanne, Tondat, Sandra, Wei, Linda, Carroll, Tracy, Bürger, Antje, Cabezas, Jorge, Fan-Lan, Qing, Jacob, Elsa, Creighton, Amie, Castellanos-Penton, Patricia, Danisment, Ozge, Clarke, Shannon, Joeng, Joanna, Kelly, Deborah, To, Christine, Bushell, Wendy, van Bruggen, Rebekah, Gailus-Durner, Valerie, Fuchs, Helmut, Marschall, Susan, Dunst, Stefanie, Romberger, Markus, Rey, Bernhard, Fessele, Sabine, Gormanns, Philipp, Friedel, Roland, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), and Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Cancer Research, Genotype, Knockout, International Cooperation, [SDV]Life Sciences [q-bio], Mutant, Mutagenesis (molecular biology technique), cytology [Mouse Embryonic Stem Cells], Mouse Mutant Strains, Biology, Genome, Medical and Health Sciences, Article, 03 medical and health sciences, Mice, 0302 clinical medicine, Research community, ddc:570, Genetics, Animals, Allele, Gene, Genetic Association Studies, 030304 developmental biology, Mice, Knockout, 0303 health sciences, Internet, metabolism [Mouse Embryonic Stem Cells], Information Dissemination, mutant mouse IMPC, Mouse Embryonic Stem Cells, Biological Sciences, Null allele, Embryonic stem cell, Phenotype, Mutagenesis, Montertondo Mouse Production, Technology Platforms, International Mouse Phenotyping Consortium, Function (biology), 030217 neurology & neurosurgery, Gene Deletion, Developmental Biology
Abstract

The International Mouse Phenotyping Consortium reports the generation of new mouse mutant strains for over 5,000 genes from targeted embryonic stem cells on the C57BL/6N genetic background. This includes 2,850 null alleles for which no equivalent mutant mouse line exists, 2,987 novel conditional-ready alleles, and 4,433 novel reporter alleles. This nearly triples the number of genes with reporter alleles and almost doubles the number of conditional alleles available to the scientific community. When combined with more than 30 years of community effort, the total mutant allele mouse resource covers more than half of the genome. The extensively validated collection is archived and distributed through public repositories, facilitating availability to the worldwide biomedical research community, and expanding our understanding of gene function and human disease.

Published
2021
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11. High-throughput discovery of novel developmental phenotypes

Author

Dickinson, Mary E., Flenniken, Ann M., Ji, Xiao, Teboul, Lydia, Wong, Michael D., White, Jacqueline K., Meehan, Terrence F., Weninger, Wolfgang J., Westerberg, Henrik, Adissu, Hibret, Baker, Candice N., Bower, Lynette, Brown, James M., Caddle, L. Brianna, Chiani, Francesco, Clary, Dave, Cleak, James, Daly, Mark J., Denegre, James M., Doe, Brendan, Dolan, Mary E., Edie, Sarah M., Fuchs, Helmut, Gailus-Durner, Valerie, Galli, Antonella, Gambadoro, Alessia, Gallegos, Juan, Guo, Shiying, Horner, Neil R., Hsu, Chih-Wei, Johnson, Sara J., Kalaga, Sowmya, Keith, Lance C., Lanoue, Louise, Lawson, Thomas N., Lek, Monkol, Mark, Manuel, Marschall, Susan, Mason, Jeremy, McElwee, Melissa L., Newbigging, Susan, Nutter, Lauryl M. J., Peterson, Kevin A., Ramirez-Solis, Ramiro, Rowland, Douglas J., Ryder, Edward, Samocha, Kaitlin E., Seavitt, John R., Selloum, Mohammed, Szoke-Kovacs, Zsombor, Tamura, Masaru, Trainor, Amanda G., Tudose, Ilinca, Wakana, Shigeharu, Warren, Jonathan, Wendling, Olivia, West, David B., Wong, Leeyean, Yoshiki, Atsushi, McKay, Matthew, Urban, Barbara, Lund, Caroline, Froeter, Erin, LaCasse, Taylor, Mehalow, Adrienne, Gordon, Emily, Donahue, Leah Rae, Taft, Robert, Kutney, Peter, Dion, Stephanie, Goodwin, Leslie, Kales, Susan, Urban, Rachel, Palmer, Kristina, Pertuy, Fabien, Bitz, Deborah, Weber, Bruno, Goetz-Reiner, Patrice, Jacobs, Hughes, Le Marchand, Elise, El Amri, Amal, El Fertak, Leila, Ennah, Hamid, Ali-Hadji, Dalila, Ayadi, Abdel, Wattenhofer-Donze, Marie, Jacquot, Sylvie, Andr, Philippe, Birling, Marie-Christine, Pavlovic, Guillaume, Sorg, Tania, Morse, Iva, Benso, Frank, Stewart, Michelle E., Copley, Carol, Harrison, Jackie, Joynson, Samantha, Guo, Ruolin, Qu, Dawei, Spring, Shoshana, Yu, Lisa, Ellegood, Jacob, Morikawa, Lily, Shang, Xueyuan, Feugas, Pat, Creighton, Amie, Castellanos Penton, Patricia, Danisment, Ozge, Griggs, Nicola, Tudor, Catherine L., Green, Angela L., Icoresi Mazzeo, Cecilia, Siragher, Emma, Lillistone, Charlotte, Tuck, Elizabeth, Gleeson, Diane, Sethi, Debarati, Bayzetinova, Tanya, Burvill, Jonathan, Habib, Bishoy, Weavers, Lauren, Maswood, Ryea, Miklejewska, Evelina, Woods, Michael, Grau, Evelyn, Newman, Stuart, Sinclair, Caroline, Brown, Ellen, Ayabe, Shinya, Iwama, Mizuho, Murakami, Ayumi, MacArthur, Daniel G., Tocchini-Valentini, Glauco P., Gao, Xiang, Flicek, Paul, Bradley, Allan, Skarnes, William C., Justice, Monica J., Parkinson, Helen E., Moore, Mark, Wells, Sara, Braun, Robert E., Svenson, Karen L., de Angelis, Martin Hrabe, Herault, Yann, Mohun, Tim, Mallon, Ann-Marie, Henkelman, R. Mark, Brown, Steve D. M., Adams, David J., Lloyd, K. C. Kent, McKerlie, Colin, Beaudet, Arthur L., Buan, Maja, and Murray, Stephen A.

Subjects
Research, Methods, Phenotypes -- Research, Genetic research, High-throughput screening (Biochemical assaying) -- Methods
Abstract

Author(s): Mary E. Dickinson [1]; Ann M. Flenniken [2, 3]; Xiao Ji [4]; Lydia Teboul [5]; Michael D. Wong [2, 6]; Jacqueline K. White [7]; Terrence F. Meehan [8]; Wolfgang [...], Approximately one-third of all mammalian genes are essential for life. Phenotypes resulting from knockouts of these genes in mice have provided tremendous insight into gene function and congenital disorders. As part of the International Mouse Phenotyping Consortium effort to generate and phenotypically characterize 5,000 knockout mouse lines, here we identify 410 lethal genes during the production of the first 1,751 unique gene knockouts. Using a standardized phenotyping platform that incorporates high-resolution 3D imaging, we identify phenotypes at multiple time points for previously uncharacterized genes and additional phenotypes for genes with previously reported mutant phenotypes. Unexpectedly, our analysis reveals that incomplete penetrance and variable expressivity are common even on a defined genetic background. In addition, we show that human disease genes are enriched for essential genes, thus providing a dataset that facilitates the prioritization and validation of mutations identified in clinical sequencing efforts.

Published
2016
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12. AAV-mediated ERdj5 overexpression protects against P23H rhodopsin toxicity

Author

Aguila, Monica, Bellingham, James, Athanasiou, Dimitra, Bevilacqua, Dalila, Duran, Yanai, Maswood, Ryea, Parfitt, David A., Iwawaki, Takao, Spyrou, Ioannis, Smith, Alexander J., Ali, Robin R., Cheetham, Michael E., Aguila, Monica, Bellingham, James, Athanasiou, Dimitra, Bevilacqua, Dalila, Duran, Yanai, Maswood, Ryea, Parfitt, David A., Iwawaki, Takao, Spyrou, Ioannis, Smith, Alexander J., Ali, Robin R., and Cheetham, Michael E.

Abstract

Rhodopsin misfolding caused by the P23H mutation is a major cause of autosomal dominant retinitis pigmentosa (adRP). To date, there are no effective treatments for adRP. The BiP co-chaperone and reductase ERdj5 (DNAJC10) is part of the endoplasmic reticulum (ER) quality control machinery, and previous studies have shown that overexpression of ERdj5 in vitro enhanced the degradation of P23H rhodopsin, whereas knockdown of ERdj5 increased P23H rhodopsin ER retention and aggregation. Here, we investigated the role of ERdj5 in photoreceptor homeostasis in vivo by using an Erdj5 knockout mouse crossed with the P23H knock-in mouse and by adeno-associated viral (AAV) vector-mediated gene augmentation of ERdj5 in P23H-3 rats. Electroretinogram (ERG) and optical coherence tomography of Erdj5(-/-) and P23H(+/-):Erdj5(-/-) mice showed no effect of ERdj5 ablation on retinal function or photoreceptor survival. Rhodopsin levels and localization were similar to those of control animals at a range of time points. By contrast, when AAV2/8-ERdj5-HA was subretinally injected into P23H-3 rats, analysis of the full-field ERG suggested that overexpression of ERdj5 reduced visual function loss 10 weeks post-injection (PI). This correlated with a significant preservation of photoreceptor cells at 4 and 10 weeks PI. Assessment of the outer nuclear layer (ONL) morphology showed preserved ONL thickness and reduced rhodopsin retention in the ONL in the injected superior retina. Overall, these data suggest that manipulation of the ER quality control and ER-associated degradation factors to promote mutant protein degradation could be beneficial for the treatment of adRP caused by mutant rhodopsin., Funding Agencies|Wellcome TrustWellcome Trust [092621, 205041, 099173]; Retina UK [GR576]; Fight for Sight; Foundation Fighting Blindness USA; UCL and Moorfields Eye Hospital NIHR Biomedical Research Centre

Published
2020
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13. Neonatal brain-directed gene therapy rescues a mouse model of neurodegenerative CLN6 Batten disease

Author

kleine Holthaus, Sophia-Martha, primary, Herranz-Martin, Saul, additional, Massaro, Giulia, additional, Aristorena, Mikel, additional, Hoke, Justin, additional, Hughes, Michael P, additional, Maswood, Ryea, additional, Semenyuk, Olha, additional, Basche, Mark, additional, Shah, Amna Z, additional, Klaska, Izabela P, additional, Smith, Alexander J, additional, Mole, Sara E, additional, Rahim, Ahad A, additional, and Ali, Robin R, additional

Published
2019
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14. Neonatal brain-directed gene therapy rescues a mouse model of neurodegenerative CLN6 Batten disease

Author

Holthaus, Sophia-Martha kleine, primary, Martin-Herranz, Saul, additional, Massaro, Giulia, additional, Aristorena, Mikel, additional, Hoke, Justin, additional, Hughes, Michael P., additional, Maswood, Ryea, additional, Semenyuk, Olha, additional, Basche, Mark, additional, Shah, Amna Z., additional, Klaska, Izabela P., additional, Smith, Alexander J., additional, Mole, Sara E., additional, Rahim, Ahad A, additional, and Ali, Robin R, additional

Published
2019
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15. Late neuroprogenitors contribute to normal retinal vascular development in a Hif2a-dependent manner

Author

Cristante, Enrico, primary, Liyanage, Sidath E., additional, Sampson, Robert D., additional, Kalargyrou, Aikaterini, additional, De Rossi, Giulia, additional, Rizzi, Matteo, additional, Hoke, Justin, additional, Ribeiro, Joana, additional, Maswood, Ryea N., additional, Duran, Yanai, additional, Matsuki, Takaaki, additional, Aghaizu, Nozie, additional, Luhmann, Ulrich F., additional, Smith, Alexander J., additional, Ali, Robin R., additional, and Bainbridge, James W. B., additional

Published
2018
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17. Prevention of Photoreceptor Cell Loss in a Cln6nclfMouse Model of Batten Disease Requires CLN6Gene Transfer to Bipolar Cells

Author

kleine Holthaus, Sophia-Martha, Ribeiro, Joana, Abelleira-Hervas, Laura, Pearson, Rachael A., Duran, Yanai, Georgiadis, Anastasios, Sampson, Robert D., Rizzi, Matteo, Hoke, Justin, Maswood, Ryea, Azam, Selina, Luhmann, Ulrich F.O., Smith, Alexander J., Mole, Sara E., and Ali, Robin R.

Abstract

The neuronal ceroid lipofuscinoses (NCLs) are inherited lysosomal storage disorders characterized by general neurodegeneration and premature death. Sight loss is also a major symptom in NCLs, severely affecting the quality of life of patients, but it is not targeted effectively by brain-directed therapies. Here we set out to explore the therapeutic potential of an ocular gene therapy to treat sight loss in NCL due to a deficiency in the transmembrane protein CLN6. We found that, although Cln6nclfmice presented mainly with photoreceptor degeneration, supplementation of CLN6 in photoreceptors was not beneficial. Because the level of CLN6is low in photoreceptors but high in bipolar cells (retinal interneurons that are only lost in Cln6-deficient mice at late disease stages), we explored the therapeutic effects of delivering CLN6to bipolar cells using adeno-associated virus (AAV) serotype 7m8. Bipolar cell-specific expression of CLN6slowed significantly the loss of photoreceptor function and photoreceptor cells. This study shows that the deficiency of a gene normally expressed in bipolar cells can cause the loss of photoreceptors and that this can be prevented by bipolar cell-directed treatment.

Published
2018
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