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1. Selenoprotein deficiency disorder predisposes to aortic aneurysm formation.

Author

Schoenmakers, Erik, Marelli, Federica, Jørgensen, Helle, Visser, W, Moran, Carla, Groeneweg, Stefan, Avalos, Carolina, Jurgens, Sean, Figg, Nichola, Finigan, Alison, Wali, Neha, Agostini, Maura, Wardle-Jones, Hannah, Lyons, Greta, Rusk, Rosemary, Gopalan, Deepa, Twiss, Philip, Visser, Jacob, Goddard, Martin, Nashef, Samer, Heijmen, Robin, Clift, Paul, Sinha, Sanjay, Pirruccello, James, Ellinor, Patrick, Busch-Nentwich, Elisabeth, Ramirez-Solis, Ramiro, Murphy, Michael, Persani, Luca, Bennett, Martin, and Chatterjee, Krishna

Subjects
Humans, Male, Mice, Animals, Zebrafish, Selenocysteine, Muscle, Smooth, Vascular, Aortic Aneurysm, Selenoproteins, Myocytes, Smooth Muscle
Abstract

Aortic aneurysms, which may dissect or rupture acutely and be lethal, can be a part of multisystem disorders that have a heritable basis. We report four patients with deficiency of selenocysteine-containing proteins due to selenocysteine Insertion Sequence Binding Protein 2 (SECISBP2) mutations who show early-onset, progressive, aneurysmal dilatation of the ascending aorta due to cystic medial necrosis. Zebrafish and male mice with global or vascular smooth muscle cell (VSMC)-targeted disruption of Secisbp2 respectively show similar aortopathy. Aortas from patients and animal models exhibit raised cellular reactive oxygen species, oxidative DNA damage and VSMC apoptosis. Antioxidant exposure or chelation of iron prevents oxidative damage in patients cells and aortopathy in the zebrafish model. Our observations suggest a key role for oxidative stress and cell death, including via ferroptosis, in mediating aortic degeneration.

Published
2023

2. Digenic inheritance involving a muscle-specific protein kinase and the giant titin protein causes a skeletal muscle myopathy

Author

Töpf, Ana, Cox, Dan, Zaharieva, Irina T., Di Leo, Valeria, Sarparanta, Jaakko, Jonson, Per Harald, Sealy, Ian M., Smolnikov, Andrei, White, Richard J., Vihola, Anna, Savarese, Marco, Merteroglu, Munise, Wali, Neha, Laricchia, Kristen M., Venturini, Cristina, Vroling, Bas, Stenton, Sarah L., Cummings, Beryl B., Harris, Elizabeth, Marini-Bettolo, Chiara, Diaz-Manera, Jordi, Henderson, Matt, Barresi, Rita, Duff, Jennifer, England, Eleina M., Patrick, Jane, Al-Husayni, Sundos, Biancalana, Valerie, Beggs, Alan H., Bodi, Istvan, Bommireddipalli, Shobhana, Bönnemann, Carsten G., Cairns, Anita, Chiew, Mei-Ting, Claeys, Kristl G., Cooper, Sandra T., Davis, Mark R., Donkervoort, Sandra, Erasmus, Corrie E., Fassad, Mahmoud R., Genetti, Casie A., Grosmann, Carla, Jungbluth, Heinz, Kamsteeg, Erik-Jan, Lornage, Xavière, Löscher, Wolfgang N., Malfatti, Edoardo, Manzur, Adnan, Martí, Pilar, Mongini, Tiziana E., Muelas, Nuria, Nishikawa, Atsuko, O’Donnell-Luria, Anne, Ogonuki, Narumi, O’Grady, Gina L., O’Heir, Emily, Paquay, Stéphanie, Phadke, Rahul, Pletcher, Beth A., Romero, Norma B., Schouten, Meyke, Shah, Snehal, Smuts, Izelle, Sznajer, Yves, Tasca, Giorgio, Taylor, Robert W., Tuite, Allysa, Van den Bergh, Peter, VanNoy, Grace, Voermans, Nicol C., Wanschitz, Julia V., Wraige, Elizabeth, Yoshimura, Kimihiko, Oates, Emily C., Nakagawa, Osamu, Nishino, Ichizo, Laporte, Jocelyn, Vilchez, Juan J., MacArthur, Daniel G., Sarkozy, Anna, Cordell, Heather J., Udd, Bjarne, Busch-Nentwich, Elisabeth M., Muntoni, Francesco, and Straub, Volker

Published
2024
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3. Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, Smith, Kellie N, Forde, Patrick M, Niknafs, Noushin, Bhattacharya, Rohit, White, James, Zhang, Theresa, Adleff, Vilmos, Phallen, Jillian, Wali, Neha, Hruban, Carolyn, Guthrie, Violeta B, Rodgers, Kristen, Naidoo, Jarushka, Kang, Hyunseok, Sharfman, William, Georgiades, Christos, Verde, Franco, Illei, Peter, Li, Qing Kay, Gabrielson, Edward, Brock, Malcolm V, Zahnow, Cynthia A, Baylin, Stephen B, Scharpf, Robert B, Brahmer, Julie R, Karchin, Rachel, Pardoll, Drew M, and Velculescu, Victor E

Subjects
Prevention, Cancer, Immunization, Clinical Research, Lung, Lung Cancer, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Aetiology, 2.1 Biological and endogenous factors, Good Health and Well Being, Adult, Antibodies, Monoclonal, Antigens, Neoplasm, Antineoplastic Agents, Immunological, CTLA-4 Antigen, Carcinoma, Non-Small-Cell Lung, Cell Cycle Checkpoints, Cohort Studies, Drug Resistance, Neoplasm, Female, Humans, Immunotherapy, Ipilimumab, Janus Kinase 1, Janus Kinase 2, Lung Neoplasms, Male, Middle Aged, Mutation, Nivolumab, Programmed Cell Death 1 Receptor, Receptors, Antigen, T-Cell, Oncology and Carcinogenesis
Abstract

Immune checkpoint inhibitors have shown significant therapeutic responses against tumors containing increased mutation-associated neoantigen load. We have examined the evolving landscape of tumor neoantigens during the emergence of acquired resistance in patients with non-small cell lung cancer after initial response to immune checkpoint blockade with anti-PD-1 or anti-PD-1/anti-CTLA-4 antibodies. Analyses of matched pretreatment and resistant tumors identified genomic changes resulting in loss of 7 to 18 putative mutation-associated neoantigens in resistant clones. Peptides generated from the eliminated neoantigens elicited clonal T-cell expansion in autologous T-cell cultures, suggesting that they generated functional immune responses. Neoantigen loss occurred through elimination of tumor subclones or through deletion of chromosomal regions containing truncal alterations, and was associated with changes in T-cell receptor clonality. These analyses provide insight into the dynamics of mutational landscapes during immune checkpoint blockade and have implications for the development of immune therapies that target tumor neoantigens.Significance: Acquired resistance to immune checkpoint therapy is being recognized more commonly. This work demonstrates for the first time that acquired resistance to immune checkpoint blockade can arise in association with the evolving landscape of mutations, some of which encode tumor neoantigens recognizable by T cells. These observations imply that widening the breadth of neoantigen reactivity may mitigate the development of acquired resistance. Cancer Discov; 7(3); 264-76. ©2017 AACR.See related commentary by Yang, p. 250This article is highlighted in the In This Issue feature, p. 235.

Published
2017

5. Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma

Author

Schubert, Adrian D., Channah Broner, Esther, Agrawal, Nishant, London, Nyall, Pearson, Alexander, Gupta, Anuj, Wali, Neha, Seiwert, Tanguy Y., Wheelan, Sarah, Lingen, Mark, Macleod, Kay, Allen, Hailey, Chatterjee, Aditi, Vassiliki, Saloura, Gaykalova, Daria, Hoque, Mohammad O., Sidransky, David, Suresh, Karthik, and Izumchenko, Evgeny

Published
2020
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6. The next-generation oral selective estrogen receptor degrader camizestrant (AZD9833) suppresses ER+ breast cancer growth and overcomes endocrine and CDK4/6 inhibitor resistance

Author

Lawson, Mandy, primary, Cureton, Natalie, additional, Ros, Susana, additional, Cheraghchi-Bashi-Astaneh, Azadeh, additional, Urosevic, Jelena, additional, D'Arcy, Sophie, additional, Delpuech, Oona, additional, DuPont, Michelle, additional, Fisher, David I., additional, Gangl, Eric T., additional, Lewis, Hilary, additional, Trueman, Dawn, additional, Wali, Neha, additional, Williamson, Stuart Charles., additional, Moss, Jennifer, additional, Montaudon, Elodie, additional, Derrien, Héloïse, additional, Marangoni, Elisabetta, additional, Miragaia, Ricardo J., additional, Gagrica, Sladjana, additional, Morentin Gutierrez, Pablo, additional, Moss, Thomas, additional, Maglennon, Gareth A., additional, Sutton, Daniel, additional, Polanski, Radoslaw, additional, Rosen, Alan, additional, Cairns, Jonathan, additional, Zhang, Pei, additional, Sánchez-Guixé, Mònica, additional, Serra, Violeta, additional, Critchlow, Susan E., additional, Scott, James S., additional, Lindemann, Justin P.O., additional, Barry, Simon T., additional, Klinowska, Teresa, additional, Morrow, Christopher J., additional, and Carnevalli, Larissa S., additional

Published
2023
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7. Common and distinct transcriptional signatures of mammalian embryonic lethality

Author

Collins, John E., White, Richard J., Staudt, Nicole, Sealy, Ian M., Packham, Ian, Wali, Neha, Tudor, Catherine, Mazzeo, Cecilia, Green, Angela, Siragher, Emma, Ryder, Edward, White, Jacqueline K., Papatheodoru, Irene, Tang, Amy, Füllgrabe, Anja, Billis, Konstantinos, Geyer, Stefan H., Weninger, Wolfgang J., Galli, Antonella, Hemberger, Myriam, Stemple, Derek L., Robertson, Elizabeth, Smith, James C., Mohun, Timothy, Adams, David J., and Busch-Nentwich, Elisabeth M.

Published
2019
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8. Supplementary Materials and Methods and Supplementary Tables 1-2 from Macrophage Activation Status Rather than Repolarization Is Associated with Enhanced Checkpoint Activity in Combination with PI3Kγ Inhibition

Author

Carnevalli, Larissa S., primary, Taylor, Molly A., primary, King, Matthew, primary, Coenen-Stass, Anna M.L., primary, Hughes, Adina M., primary, Bell, Sigourney, primary, Proia, Theresa A., primary, Wang, Yanjun, primary, Ramos-Montoya, Antonio, primary, Wali, Neha, primary, Carroll, Danielle, primary, Singh, Maneesh, primary, Moschetta, Michele, primary, Gutierrez, Pablo Morentin, primary, Gardelli, Cristina, primary, Critchlow, Susan E., primary, Klinowska, Teresa, primary, Fawell, Stephen E., primary, and Barry, Simon T., primary

Published
2023
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9. Supplementary Figures 1-7 from Macrophage Activation Status Rather than Repolarization Is Associated with Enhanced Checkpoint Activity in Combination with PI3Kγ Inhibition

Author

Carnevalli, Larissa S., primary, Taylor, Molly A., primary, King, Matthew, primary, Coenen-Stass, Anna M.L., primary, Hughes, Adina M., primary, Bell, Sigourney, primary, Proia, Theresa A., primary, Wang, Yanjun, primary, Ramos-Montoya, Antonio, primary, Wali, Neha, primary, Carroll, Danielle, primary, Singh, Maneesh, primary, Moschetta, Michele, primary, Gutierrez, Pablo Morentin, primary, Gardelli, Cristina, primary, Critchlow, Susan E., primary, Klinowska, Teresa, primary, Fawell, Stephen E., primary, and Barry, Simon T., primary

Published
2023
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10. Data from Macrophage Activation Status Rather than Repolarization Is Associated with Enhanced Checkpoint Activity in Combination with PI3Kγ Inhibition

Author

Carnevalli, Larissa S., primary, Taylor, Molly A., primary, King, Matthew, primary, Coenen-Stass, Anna M.L., primary, Hughes, Adina M., primary, Bell, Sigourney, primary, Proia, Theresa A., primary, Wang, Yanjun, primary, Ramos-Montoya, Antonio, primary, Wali, Neha, primary, Carroll, Danielle, primary, Singh, Maneesh, primary, Moschetta, Michele, primary, Gutierrez, Pablo Morentin, primary, Gardelli, Cristina, primary, Critchlow, Susan E., primary, Klinowska, Teresa, primary, Fawell, Stephen E., primary, and Barry, Simon T., primary

Published
2023
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11. Supplementary Tables S1 - S18 from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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12. Supplementary Figures S1 - S16 from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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13. Data from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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14. Supplementary Figure Legends from Evolution of Neoantigen Landscape during Immune Checkpoint Blockade in Non–Small Cell Lung Cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., primary, Forde, Patrick M., primary, Niknafs, Noushin, primary, Bhattacharya, Rohit, primary, White, James, primary, Zhang, Theresa, primary, Adleff, Vilmos, primary, Phallen, Jillian, primary, Wali, Neha, primary, Hruban, Carolyn, primary, Guthrie, Violeta B., primary, Rodgers, Kristen, primary, Naidoo, Jarushka, primary, Kang, Hyunseok, primary, Sharfman, William, primary, Georgiades, Christos, primary, Verde, Franco, primary, Illei, Peter, primary, Li, Qing Kay, primary, Gabrielson, Edward, primary, Brock, Malcolm V., primary, Zahnow, Cynthia A., primary, Baylin, Stephen B., primary, Scharpf, Robert B., primary, Brahmer, Julie R., primary, Karchin, Rachel, primary, Pardoll, Drew M., primary, and Velculescu, Victor E., primary

Published
2023
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15. Supplementary figure 4 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients

Author

Khanna, Swati, primary, Graef, Suzanne, primary, Mussai, Francis, primary, Thomas, Anish, primary, Wali, Neha, primary, Yenidunya, Bahar Guliz, primary, Yuan, Constance, primary, Morrow, Betsy, primary, Zhang, Jingli, primary, Korangy, Firouzeh, primary, Greten, Tim F., primary, Steinberg, Seth M., primary, Stetler-Stevenson, Maryalice, primary, Middleton, Gary, primary, De Santo, Carmela, primary, and Hassan, Raffit, primary

Published
2023
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16. Supplementary figure 3 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients

Author

Khanna, Swati, primary, Graef, Suzanne, primary, Mussai, Francis, primary, Thomas, Anish, primary, Wali, Neha, primary, Yenidunya, Bahar Guliz, primary, Yuan, Constance, primary, Morrow, Betsy, primary, Zhang, Jingli, primary, Korangy, Firouzeh, primary, Greten, Tim F., primary, Steinberg, Seth M., primary, Stetler-Stevenson, Maryalice, primary, Middleton, Gary, primary, De Santo, Carmela, primary, and Hassan, Raffit, primary

Published
2023
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17. Supplementary Figs and Tables from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients

Author

Khanna, Swati, primary, Graef, Suzanne, primary, Mussai, Francis, primary, Thomas, Anish, primary, Wali, Neha, primary, Yenidunya, Bahar Guliz, primary, Yuan, Constance, primary, Morrow, Betsy, primary, Zhang, Jingli, primary, Korangy, Firouzeh, primary, Greten, Tim F., primary, Steinberg, Seth M., primary, Stetler-Stevenson, Maryalice, primary, Middleton, Gary, primary, De Santo, Carmela, primary, and Hassan, Raffit, primary

Published
2023
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18. Supplementary figure 1 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients

Author

Khanna, Swati, primary, Graef, Suzanne, primary, Mussai, Francis, primary, Thomas, Anish, primary, Wali, Neha, primary, Yenidunya, Bahar Guliz, primary, Yuan, Constance, primary, Morrow, Betsy, primary, Zhang, Jingli, primary, Korangy, Firouzeh, primary, Greten, Tim F., primary, Steinberg, Seth M., primary, Stetler-Stevenson, Maryalice, primary, Middleton, Gary, primary, De Santo, Carmela, primary, and Hassan, Raffit, primary

Published
2023
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19. Supplementary figure 2 from Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients

Author

Khanna, Swati, primary, Graef, Suzanne, primary, Mussai, Francis, primary, Thomas, Anish, primary, Wali, Neha, primary, Yenidunya, Bahar Guliz, primary, Yuan, Constance, primary, Morrow, Betsy, primary, Zhang, Jingli, primary, Korangy, Firouzeh, primary, Greten, Tim F., primary, Steinberg, Seth M., primary, Stetler-Stevenson, Maryalice, primary, Middleton, Gary, primary, De Santo, Carmela, primary, and Hassan, Raffit, primary

Published
2023
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20. Selenoprotein deficiency disorder predisposes to aortic aneurysm formation

Author

Schoenmakers, Erik, primary, Marelli, Federica, additional, Jorgensen, Helle, additional, Edward, Visser W., additional, Moran, Carla, additional, Groeneweg, Stefan, additional, Avalos, Carolina, additional, Figg, Nichola, additional, Finigan, Alison, additional, Wali, Neha, additional, Agostini, Maura, additional, Wardle-Jones, Hannah, additional, Lyons, Greta, additional, Rusk, Rosemary, additional, Gopalan, Deepa, additional, Johannes, Visser Jacob, additional, Goddard, Martin, additional, Nashef, Samer, additional, Heijmen, Robin, additional, Clift, Paul, additional, Sinha, Sanjay, additional, Busch-Nentwich, Elisabeth, additional, Ramirez-Solis, Ramiro, additional, Persani, Luca, additional, Bennett, Martin, additional, and Chatterjee, Krishna, additional

Published
2022
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21. Total Nucleic Acid Extraction from Single Zebrafish Embryos for Genotyping and RNA-seq

Author

Wali, Neha, Merteroglu, Munise, White, Richard J., and Busch-Nentwich, Elisabeth M.

Subjects
Strategy and Management, Mechanical Engineering, Methods Article, Metals and Alloys, Industrial and Manufacturing Engineering
Abstract

RNA sequencing allows for the quantification of the transcriptome of embryos to investigate transcriptional responses to various perturbations (e.g., mutations, infections, drug treatments). Previous protocols either lack the option to genotype individual samples, or are laborious and therefore difficult to do at a large scale. We have developed a protocol to extract total nucleic acid from individual zebrafish embryos. Individual embryos are lysed in 96-well plates and nucleic acid is extracted using SPRI beads. The total nucleic acid can be genotyped and then DNase I treated to produce RNA samples for sequencing. This protocol allows for processing large numbers of individual samples, with the ability to genotype each sample, which makes it possible to undertake transcriptomic analysis on mutants at timepoints before the phenotype is visible. Graphic abstract: [Image: see text] Extraction of total nucleic acid from individual zebrafish embryos for genotyping and RNA-seq.

Published
2022
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22. Placentation defects are highly prevalent in embryonic lethal mouse mutants

Author

Perez-Garcia, Vicente, Fineberg, Elena, Wilson, Robert, Murray, Alexander, Mazzeo, Cecilia Icoresi, Tudor, Catherine, Sienerth, Arnold, White, Jacqueline K., Tuck, Elizabeth, Ryder, Edward J., Gleeson, Diane, Siragher, Emma, Wardle-Jones, Hannah, Staudt, Nicole, Wali, Neha, Collins, John, Geyer, Stefan, Busch-Nentwich, Elisabeth M., Galli, Antonella, Smith, James C., Robertson, Elizabeth, Adams, David J., Weninger, Wolfgang J., Mohun, Timothy, and Hemberger, Myriam

Subjects
Observations, Genetic aspects, Placenta -- Genetic aspects, Embryonic development -- Genetic aspects, Gene mutation -- Observations
Abstract

Author(s): Vicente Perez-Garcia [1, 2]; Elena Fineberg [1, 2]; Robert Wilson [3]; Alexander Murray [1, 2]; Cecilia Icoresi Mazzeo [4]; Catherine Tudor [4]; Arnold Sienerth [1, 2]; Jacqueline K. White [...], Large-scale phenotyping efforts have demonstrated that approximately 2530% of mouse gene knockouts cause intrauterine lethality. Analysis of these mutants has largely focused on the embryo and not the placenta, despite the crucial role of this extraembryonic organ for developmental progression. Here we screened 103 embryonic lethal and sub-viable mouse knockout lines from the Deciphering the Mechanisms of Developmental Disorders program for placental phenotypes. We found that 68% of knockout lines that are lethal at or after mid-gestation exhibited placental dysmorphologies. Early lethality (embryonic days 9.514.5) is almost always associated with severe placental malformations. Placental defects correlate strongly with abnormal brain, heart and vascular development. Analysis of mutant trophoblast stem cells and conditional knockouts suggests that a considerable number of factors that cause embryonic lethality when ablated have primary gene function in trophoblast cells. Our data highlight the hugely under-appreciated importance of placental defects in contributing to abnormal embryo development and suggest key molecular nodes that govern placenta formation.

Published
2018
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23. A systematic genome-wide analysis of zebrafish protein-coding gene function

Author

Kettleborough, Ross N.W., Busch-Nentwich, Elisabeth M., Harvey, Steven A., Dooley, Christopher M., de Bruijn, Ewart, van Eeden, Freek, Sealy, Ian, White, Richard J., Herd, Colin, Nijman, Isaac J., Fenyes, Fruzsina, Mehroke, Selina, Scahill, Catherine, Gibbons, Richard, Wali, Neha, Carruthers, Samantha, Hall, Amanda, Yen, Jennifer, Cuppen, Edwin, and Stemple, Derek L.

Subjects
Genetic aspects, Research, Zebrafish -- Genetic aspects -- Research, DNA sequencing -- Research, Nucleotide sequencing -- Research, Zebra fish -- Genetic aspects -- Research
Abstract

Since the publication of the human reference genome, the identities of specific genes associated with human diseases are being discovered at a rapid rate. A central problem is that the [...]

Published
2013
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25. Macrophage Activation Status Rather than Repolarization Is Associated with Enhanced Checkpoint Activity in Combination with PI3Kγ Inhibition

Author

Carnevalli, Larissa S., primary, Taylor, Molly A., additional, King, Matthew, additional, Coenen-Stass, Anna M.L., additional, Hughes, Adina M., additional, Bell, Sigourney, additional, Proia, Theresa A., additional, Wang, Yanjun, additional, Ramos-Montoya, Antonio, additional, Wali, Neha, additional, Carroll, Danielle, additional, Singh, Maneesh, additional, Moschetta, Michele, additional, Gutierrez, Pablo Morentin, additional, Gardelli, Cristina, additional, Critchlow, Susan E., additional, Klinowska, Teresa, additional, Fawell, Stephen E., additional, and Barry, Simon T., additional

Published
2021
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27. Digenic Inheritance Involving a Muscle Specific Protein Kinase and the Giant Titin Protein Causes a Skeletal Muscle Myopathy

Author

Topf, Ana, primary, Zaharieva, Irina, additional, Di Leo, Valeria, additional, Vihola, Anna, additional, Wali, Neha, additional, Savarese, Marco, additional, Laricchia, Kristen, additional, Venturini, Cristina, additional, Vroling, Bas, additional, Cummings, Beryl, additional, Barresi, Rita, additional, Harris, Elizabeth, additional, Marini Bettolo, Chiara, additional, Cox, Dan, additional, Duff, Jennifer, additional, England, Eleina, additional, Patrick, Jane, additional, Biancalana, Valerie, additional, Bommireddipalli, Shobhana, additional, Bonnemann, Carsten, additional, Cairns, Anita, additional, Chiew, Mei, additional, Claeys, Kristl G., additional, Cooper, Sandra, additional, Davis, Mark R., additional, Donkervoort, Sandra, additional, Erasmus, Corrie E., additional, Grosmann, Carla, additional, Jungbluth, Heinz, additional, Kamsteeg, Erik-Jan, additional, Lornage, Xaviere, additional, Löscher, Wolfgang, additional, Malfatti, Edoardo, additional, Manzur, Adnan, additional, Marti, Pilar, additional, Mongini, Tiziana, additional, Muelas, Nuria, additional, Nishikawa, Atsuko, additional, Ogonuki, Narumi, additional, O'Grady, Gina, additional, Paquay, Stephanie, additional, Phadke, Rahul, additional, Pletcher, Beth, additional, Romero, Norma, additional, Schouten, Meyke, additional, Shah, Snehal, additional, Sznajer, Yves, additional, Tasca, Giorgio, additional, Tuite, Allysa, additional, van den Bergh, Peter, additional, Voermans, Nicol, additional, Wanschitz, Julia, additional, Wraige, Elizabeth, additional, Yoshimura, Kimihiko, additional, Oates, Emily, additional, Nakagawa, Osamu, additional, Nishino, Ichizo, additional, Laporte, Jocelyn, additional, Vilchez, Juan, additional, Macarthur, Daniel, additional, Sarkozy, Anna, additional, Udd, Bjarne, additional, Busch-Nentwich, Elisabeth, additional, Muntoni, Francesco, additional, and Straub, Volker, additional

Published
2021
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30. Tumor-Derived GM-CSF Promotes Granulocyte Immunosuppression in Mesothelioma Patients

Author

Khanna, Swati, primary, Graef, Suzanne, additional, Mussai, Francis, additional, Thomas, Anish, additional, Wali, Neha, additional, Yenidunya, Bahar Guliz, additional, Yuan, Constance, additional, Morrow, Betsy, additional, Zhang, Jingli, additional, Korangy, Firouzeh, additional, Greten, Tim F., additional, Steinberg, Seth M., additional, Stetler-Stevenson, Maryalice, additional, Middleton, Gary, additional, De Santo, Carmela, additional, and Hassan, Raffit, additional

Published
2018
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33. A high-resolution mRNA expression time course of embryonic development in zebrafish

Author

White, Richard J, primary, Collins, John E, additional, Sealy, Ian M, additional, Wali, Neha, additional, Dooley, Christopher M, additional, Digby, Zsofia, additional, Stemple, Derek L, additional, Murphy, Daniel N, additional, Billis, Konstantinos, additional, Hourlier, Thibaut, additional, Füllgrabe, Anja, additional, Davis, Matthew P, additional, Enright, Anton J, additional, and Busch-Nentwich, Elisabeth M, additional

Published
2017
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34. Author response: A high-resolution mRNA expression time course of embryonic development in zebrafish

Author

White, Richard J, primary, Collins, John E, additional, Sealy, Ian M, additional, Wali, Neha, additional, Dooley, Christopher M, additional, Digby, Zsofia, additional, Stemple, Derek L, additional, Murphy, Daniel N, additional, Billis, Konstantinos, additional, Hourlier, Thibaut, additional, Füllgrabe, Anja, additional, Davis, Matthew P, additional, Enright, Anton J, additional, and Busch-Nentwich, Elisabeth M, additional

Published
2017
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36. Abstract NG01: Evolution of neoantigen landscape during immune checkpoint blockade in non-small cell lung cancer

Author

Anagnostou, Valsamo, primary, Smith, Kellie N., additional, Forde, Patrick M., additional, Niknafs, Noushin, additional, Bhattacharya, Rohit, additional, White, James, additional, Adleff, Vilmos, additional, Phallen, Jillian, additional, Wali, Neha, additional, Hruban, Carolyn, additional, Guthrie, Violeta B., additional, Rodgers, Kristen, additional, Naidoo, Jarushka, additional, Kang, Hyunseok, additional, Sharfman, William, additional, Georgiades, Christos, additional, Verde, Franco, additional, Illei, Peter, additional, Li, Qing Ka, additional, Gabrielson, Edward, additional, Brock, Malcolm, additional, Zahnow, Cynthia, additional, Baylin, Stephen B., additional, Scharpf, Rob, additional, Brahmer, Julie R., additional, Karchin, Rachel, additional, Pardoll, Drew M., additional, and Velculescu, Victor E., additional

Published
2017
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37. A high-resolution mRNA expression time course of embryonic development in zebrafish

Author

White, Richard J., primary, Collins, John E., additional, Sealy, Ian M., additional, Wali, Neha, additional, Dooley, Christopher M., additional, Digby, Zsofia, additional, Stemple, Derek L., additional, Murphy, Daniel N., additional, Hourlier, Thibaut, additional, Füllgrabe, Anja, additional, Davis, Matthew P., additional, Enright, Anton J., additional, and Busch-Nentwich, Elisabeth M., additional

Published
2017
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39. The Ribosome Biogenesis Protein Nol9 Is Essential for Definitive Hematopoiesis and Pancreas Morphogenesis in Zebrafish

Author

Bielczyk-Maczyńska, Ewa, primary, Lam Hung, Laure, additional, Ferreira, Lauren, additional, Fleischmann, Tobias, additional, Weis, Félix, additional, Fernández-Pevida, Antonio, additional, Harvey, Steven A., additional, Wali, Neha, additional, Warren, Alan J., additional, Barroso, Inês, additional, Stemple, Derek L., additional, and Cvejic, Ana, additional

Published
2015
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40. High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

Author

Collins, John E., primary, Wali, Neha, additional, Sealy, Ian M., additional, Morris, James A., additional, White, Richard J., additional, Leonard, Steven R., additional, Jackson, David K., additional, Jones, Matthew C., additional, Smerdon, Nathalie C., additional, Zamora, Jorge, additional, Dooley, Christopher M., additional, Carruthers, Samantha N., additional, Barrett, Jeffrey C., additional, Stemple, Derek L., additional, and Busch-Nentwich, Elisabeth M., additional

Published
2015
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41. Common and distinct transcriptional signatures of mammalian embryonic lethality

Author

Collins, John E, White, Richard J, Staudt, Nicole, Sealy, Ian M, Packham, Ian, Wali, Neha, Tudor, Catherine, Mazzeo, Cecilia, Green, Angela, Siragher, Emma, Ryder, Edward, White, Jacqueline K, Papatheodoru, Irene, Tang, Amy, Füllgrabe, Anja, Billis, Konstantinos, Geyer, Stefan H, Weninger, Wolfgang J, Galli, Antonella, Hemberger, Myriam, Stemple, Derek L, Robertson, Elizabeth, Smith, James C, Mohun, Timothy, Adams, David J, and Busch-Nentwich, Elisabeth M

Subjects
Mice, Transcription, Genetic, Sequence Analysis, RNA, Mutation, Animals, Gene Expression Regulation, Developmental, Embryo, Mammalian, Transcriptome, 3. Good health
Abstract

The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.

42. Common and distinct transcriptional signatures of mammalian embryonic lethality

Author

Collins, John E, White, Richard J, Staudt, Nicole, Sealy, Ian M, Packham, Ian, Wali, Neha, Tudor, Catherine, Mazzeo, Cecilia, Green, Angela, Siragher, Emma, Ryder, Edward, White, Jacqueline K, Papatheodoru, Irene, Tang, Amy, Füllgrabe, Anja, Billis, Konstantinos, Geyer, Stefan H, Weninger, Wolfgang J, Galli, Antonella, Hemberger, Myriam, Stemple, Derek L, Robertson, Elizabeth, Smith, James C, Mohun, Timothy, Adams, David J, and Busch-Nentwich, Elisabeth M

Subjects
Model organisms, Signalling & Oncogenes, Stem Cells, Gene Expression, 3. Good health, Imaging, Developmental Biology, Computational & Systems Biology
Abstract

The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.

43. Common and distinct transcriptional signatures of mammalian embryonic lethality

Author

Collins, John E., White, Richard J., Staudt, Nicole, Sealy, Ian M., Packham, Ian, Wali, Neha, Tudor, Catherine, Mazzeo, Cecilia, Green, Angela, Siragher, Emma, Ryder, Edward, White, Jacqueline K., Papatheodoru, Irene, Tang, Amy, Füllgrabe, Anja, Billis, Konstantinos, Geyer, Stefan H., Weninger, Wolfgang J., Galli, Antonella, Hemberger, Myriam, Stemple, Derek L., Robertson, Elizabeth, Smith, James C., Mohun, Timothy, Adams, David J., and Busch-Nentwich, Elisabeth M.

Subjects
631/208/199, 631/208/135, 14/63, article, 631/1647/514/1949, 14, 3. Good health, 38, 38/91
Abstract

The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4–36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.

44. Common and distinct transcriptional signatures of mammalian embryonic lethality

Author

Collins, John E, White, Richard J, Staudt, Nicole, Sealy, Ian M, Packham, Ian, Wali, Neha, Tudor, Catherine, Mazzeo, Cecilia, Green, Angela, Siragher, Emma, Ryder, Edward, White, Jacqueline K, Papatheodoru, Irene, Tang, Amy, Füllgrabe, Anja, Billis, Konstantinos, Geyer, Stefan H, Weninger, Wolfgang J, Galli, Antonella, Hemberger, Myriam, Stemple, Derek L, Robertson, Elizabeth, Smith, James C, Mohun, Timothy, Adams, David J, and Busch-Nentwich, Elisabeth M

Subjects
Model organisms, Signalling & Oncogenes, Stem Cells, Gene Expression, 3. Good health, Imaging, Developmental Biology, Computational & Systems Biology
Abstract

The Deciphering the Mechanisms of Developmental Disorders programme has analysed the morphological and molecular phenotypes of embryonic and perinatal lethal mouse mutant lines in order to investigate the causes of embryonic lethality. Here we show that individual whole-embryo RNA-seq of 73 mouse mutant lines (>1000 transcriptomes) identifies transcriptional events underlying embryonic lethality and associates previously uncharacterised genes with specific pathways and tissues. For example, our data suggest that Hmgxb3 is involved in DNA-damage repair and cell-cycle regulation. Further, we separate embryonic delay signatures from mutant line-specific transcriptional changes by developing a baseline mRNA expression catalogue of wild-type mice during early embryogenesis (4-36 somites). Analysis of transcription outside coding sequence identifies deregulation of repetitive elements in Morc2a mutants and a gene involved in gene-specific splicing. Collectively, this work provides a large scale resource to further our understanding of early embryonic developmental disorders.

45. The age of heterozygous telomerase mutant parents influences the adult phenotype of their offspring irrespective of genotype in zebrafish.

Author

Scahill CM, Digby Z, Sealy IM, White RJ, Wali N, Collins JE, Stemple DL, and Busch-Nentwich EM

Abstract

Background: Mutations in proteins involved in telomere maintenance lead to a range of human diseases, including dyskeratosis congenita, idiopathic pulmonary fibrosis and cancer. Telomerase functions to add telomeric repeats back onto the ends of chromosomes, however non-canonical roles of components of telomerase have recently been suggested., Methods: Here we use a zebrafish telomerase mutant which harbours a nonsense mutation in tert to investigate the adult phenotypes of fish derived from heterozygous parents of different ages. Furthermore we use whole genome sequencing data to estimate average telomere lengths., Results: We show that homozygous offspring from older heterozygotes exhibit signs of body wasting at a younger age than those of younger parents, and that offspring of older heterozygous parents weigh less irrespective of genotype. We also demonstrate that tert homozygous mutant fish have a male sex bias, and that clutches from older parents also have a male sex bias in the heterozygous and wild-type populations. Telomere length analysis reveals that the telomeres of younger heterozygous parents are shorter than those of older heterozygous parents., Conclusions: These data indicate that the phenotypes observed in offspring from older parents cannot be explained by telomere length. Instead we propose that Tert functions outside of telomere length maintenance in an age-dependent manner to influence the adult phenotypes of the next generation., Competing Interests: Competing interests: No competing interests were disclosed.

Published
2017
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