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van Gerven MR, Schild L, van Arkel J, Koopmans B, Broeils LA, Meijs LAM, van Oosterhout R, van Noesel MM, Koster J, van Hooff SR, Molenaar JJ, van den Boogaard ML. Two opposing gene expression patterns within ATRX aberrant neuroblastoma. PLoS One 2023; 18:e0289084. [PMID: 37540673 PMCID: PMC10403137 DOI: 10.1371/journal.pone.0289084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/02/2023] [Indexed: 08/06/2023] Open
Abstract
Neuroblastoma is the most common extracranial solid tumor in children. A subgroup of high-risk patients is characterized by aberrations in the chromatin remodeller ATRX that is encoded by 35 exons. In contrast to other pediatric cancer where ATRX point mutations are most frequent, multi-exon deletions (MEDs) are the most frequent type of ATRX aberrations in neuroblastoma. 75% of these MEDs are predicted to produce in-frame fusion proteins, suggesting a potential gain-of-function effect compared to nonsense mutations. For neuroblastoma there are only a few patient-derived ATRX aberrant models. Therefore, we created isogenic ATRX aberrant models using CRISPR-Cas9 in several neuroblastoma cell lines and one tumoroid and performed total RNA-sequencing on these and the patient-derived models. Gene set enrichment analysis (GSEA) showed decreased expression of genes related to both ribosome biogenesis and several metabolic processes in our isogenic ATRX exon 2-10 MED model systems, the patient-derived MED models and in tumor data containing two patients with an ATRX exon 2-10 MED. In sharp contrast, these same processes showed an increased expression in our isogenic ATRX knock-out and exon 2-13 MED models. Our validations confirmed a role of ATRX in the regulation of ribosome homeostasis. The two distinct molecular expression patterns within ATRX aberrant neuroblastomas that we identified imply that there might be a need for distinct treatment regimens.
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Affiliation(s)
- Michael R van Gerven
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Linda Schild
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Jennemiek van Arkel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Bianca Koopmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Luuk A Broeils
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Loes A M Meijs
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Romy van Oosterhout
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Max M van Noesel
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
- Department of Cancer and Imaging, University Medical Center Utrecht, Utrecht, Utrecht, The Netherlands
| | - Jan Koster
- Department of Oncogenomics, University Medical Center Amsterdam, Amsterdam, North-Holland, The Netherlands
| | - Sander R van Hooff
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
| | - Jan J Molenaar
- Princess Máxima Center for Pediatric Oncology, Utrecht, Utrecht, The Netherlands
- Department of Pharmaceutical Sciences, Faculty of Science, Utrecht University, Utrecht, Utrecht, The Netherlands
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Brkljacic J, Wittler B, Lindsey BE, Ganeshan VD, Sovic MG, Niehaus J, Ajibola W, Bachle SM, Fehér T, Somers DE. Frequency, composition and mobility of Escherichia coli-derived transposable elements in holdings of plasmid repositories. Microb Biotechnol 2021; 15:455-468. [PMID: 34875147 PMCID: PMC8867978 DOI: 10.1111/1751-7915.13962] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 10/14/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022] Open
Abstract
By providing the scientific community with uniform and standardized resources of consistent quality, plasmid repositories play an important role in enabling scientific reproducibility. Plasmids containing insertion sequence elements (IS elements) represent a challenge from this perspective, as they can change the plasmid structure and function. In this study, we conducted a systematic analysis of a subset of plasmid stocks distributed by plasmid repositories (The Arabidopsis Biological Resource Center and Addgene) which carry unintended integrations of bacterial mobile genetic elements. The integration of insertion sequences was most often found in, but not limited to, pBR322‐derived vectors, and did not affect the function of the specific plasmids. In certain cases, the entire stock was affected, but the majority of the stocks tested contained a mixture of the wild‐type and the mutated plasmids, suggesting that the acquisition of IS elements likely occurred after the plasmids were acquired by the repositories. However, comparison of the sequencing results of the original samples revealed that some plasmids already carried insertion mutations at the time of donation. While an extensive BLAST analysis of 47 877 plasmids sequenced from the Addgene repository uncovered IS elements in only 1.12%, suggesting that IS contamination is not widespread, further tests showed that plasmid integration of IS elements can propagate in conventional Escherichia coli hosts over a few tens of generations. Use of IS‐free E. coli hosts prevented the emergence of IS insertions as well as that of small indels, suggesting that the use of IS‐free hosts by donors and repositories could help limit unexpected and unwanted IS integrations into plasmids.
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Affiliation(s)
| | | | | | | | - Michael G Sovic
- Center For Applied Plant Sciences, The Ohio State University, Columbus, OH, USA
| | | | - Walliyulahi Ajibola
- Systems and Synthetic Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, Szeged, Hungary.,Doctoral School in Biology, University of Szeged, Szeged, Hungary
| | | | - Tamás Fehér
- Systems and Synthetic Biology Unit, Institute of Biochemistry, Biological Research Centre of the Eötvös Lóránd Research Network, Szeged, Hungary
| | - David E Somers
- Arabidopsis Biological Resource Center, Columbus, OH, USA.,Center For Applied Plant Sciences, The Ohio State University, Columbus, OH, USA.,Department of Molecular Genetics, The Ohio State University, Columbus, OH, USA
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Atrx inactivation drives disease-defining phenotypes in glioma cells of origin through global epigenomic remodeling. Nat Commun 2018. [PMID: 29535300 PMCID: PMC5849741 DOI: 10.1038/s41467-018-03476-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Mutational inactivation of the SWI/SNF chromatin regulator ATRX occurs frequently in gliomas, the most common primary brain tumors. Whether and how ATRX deficiency promotes oncogenesis by epigenomic dysregulation remains unclear, despite its recent implication in both genomic instability and telomere dysfunction. Here we report that Atrx loss recapitulates characteristic disease phenotypes and molecular features in putative glioma cells of origin, inducing cellular motility although also shifting differentiation state and potential toward an astrocytic rather than neuronal histiogenic profile. Moreover, Atrx deficiency drives widespread shifts in chromatin accessibility, histone composition, and transcription in a distribution almost entirely restricted to genomic sites normally bound by the protein. Finally, direct gene targets of Atrx that mediate specific Atrx-deficient phenotypes in vitro exhibit similarly selective misexpression in ATRX-mutant human gliomas. These findings demonstrate that ATRX deficiency and its epigenomic sequelae are sufficient to induce disease-defining oncogenic phenotypes in appropriate cellular and molecular contexts. ATRX inactivation frequently occurs in glioma. Here, the authors explore the role of ATRX inactivation in oncogenesis, highlighting ATRX deficiency driven epigenomic changes that influence the expression of genes crucial to the oncogenic phenotype.
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