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8 results on '"Molenaar, Piet"'

1. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Abstract

Neuroblastomas are childhood tumors with frequent fatal relapses after induction treatment, which is related to tumor evolution with additional genomic events. Our whole-genome sequencing data analysis revealed a high frequency of somatic cytosine > adenine (C > A) substitutions in primary neuroblastoma tumors, which was associated with poor survival. We showed that increased levels of C > A substitutions correlate with copy number loss (CNL) of OGG1 or MUTYH Both genes encode DNA glycosylases that recognize 8-oxo-guanine (8-oxoG) lesions as a first step of 8-oxoG repair. Tumor organoid models with CNL of OGG1 or MUTYH show increased 8-oxoG levels compared to wild-type cells. We used CRISPR-Cas9 genome editing to create knockout clones of MUTYH and OGG1 in neuroblastoma cells. Whole-genome sequencing of single-cell OGG1 and MUTYH knockout clones identified an increased accumulation of C > A substitutions. Mutational signature analysis of these OGG1 and MUTYH knockout clones revealed enrichment for C > A signatures 18 and 36, respectively. Clustering analysis showed that the knockout clones group together with tumors containing OGG1 or MUTYH CNL. In conclusion, we demonstrate that defects in 8-oxoG repair cause accumulation of C > A substitutions in neuroblastoma, which contributes to mutagenesis and tumor evolution.

Published
2021

2. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Published
2021

3. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Published
2021

4. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Published
2021

5. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Published
2021

6. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Published
2021

7. Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma

Author

Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, Molenaar, Jan J, Afd Pharmaceutics, Pharmaceutics, van den Boogaard, Marlinde L, Oka, Rurika, Hakkert, Anne, Schild, Linda, Ebus, Marli E, van Gerven, Michael R, Zwijnenburg, Danny A, Molenaar, Piet, Hoyng, Lieke L, Dolman, M Emmy M, Essing, Anke H W, Koopmans, Bianca, Helleday, Thomas, Drost, Jarno, van Boxtel, Ruben, Versteeg, Rogier, Koster, Jan, and Molenaar, Jan J

Published
2021

8. The Cytoscape Automation app article collection.

Author

Demchak, Barry, Demchak, Barry, Otasek, David, Pico, Alexander R, Bader, Gary D, Ono, Keiichiro, Settle, Brett, Sage, Eric, Morris, John H, Longabaugh, William, Lopes, Christian, Kucera, Michael, Treister, Adam, Schwikowski, Benno, Molenaar, Piet, Ideker, Trey, Demchak, Barry, Demchak, Barry, Otasek, David, Pico, Alexander R, Bader, Gary D, Ono, Keiichiro, Settle, Brett, Sage, Eric, Morris, John H, Longabaugh, William, Lopes, Christian, Kucera, Michael, Treister, Adam, Schwikowski, Benno, Molenaar, Piet, and Ideker, Trey

Abstract

Cytoscape is the premiere platform for interactive analysis, integration and visualization of network data. While Cytoscape itself delivers much basic functionality, it relies on community-written apps to deliver specialized functions and analyses. To date, Cytoscape's CyREST feature has allowed researchers to write workflows that call basic Cytoscape functions, but provides no access to its high value app-based functions. With Cytoscape Automation, workflows can now call apps that have been upgraded to expose their functionality. This article collection is a resource to assist readers in quickly and economically leveraging such apps in reproducible workflows that scale independently to large data sets and production runs.

Published
2018

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