Biology subjects

Roura, A.-J.

Publications and source records attributed to Roura, A.-J..

2 recordsLinked to original sources

bioRxiv2020

Epigenetic regulation of differentially expressed genes between various glioma types

Gliomas are the most frequent primary tumors of the central nervous system (CNS) and encompass two major subgroups: diffuse, malignant gliomas and benign, well differentiated gliomas showing a more circumscribed growth. Genome-wide next generation sequencing studies have uncovered specific genetic alterations, transcriptomic patterns and epigenetic profiles associated with different types of gliomas improving tumor diagnosis and having important implications for future clinical trials and patient management. We have recently created a unique resource encompassing genome-wide profiles of open chromatin, histone H3K27ac and H3Kme3 modifications, DNA methylation and transcriptomes of 33 glioma samples of different grades. Here, we took advantage of a wealth of data from those high-throughput experiments, intersected those data with topologically associating domains (TADs) and demonstrated that the chromatin organization and epigenetic landscape of enhancers have a strong impact on genes differentially expressed in low grade versus high grade gliomas. We identified TADs enriched in glioma grade-specific genes and/or epigenetic marks. We found a set of transcription factors, including REST, E2F1 and NFKB1, that are most likely to regulate gene expression in multiple TADs, containing glioma-related genes. Moreover, many genes associated with the cell-matrix adhesion Gene Ontology group, in particular 14 PROTOCADHERINs, were found to be regulated by the long range contacts with enhancers. Overall, the results presented here demonstrate the existence of epigenetic differences associated with chromatin organization driving differential gene expression in gliomas of different malignancy. We demonstrated that integration of whole genome epigenetic data with Hi-C data and transcriptomic profiles described in this work, can segregate low and high grade gliomas and reveal new regulatory networks that could explain some of the functional differences between gliomas of different malignancies. HighlightsO_LIIntegration of ATAC-seq, ChIP-seq and RNA-seq reveals glioma malignancy-related gene regulatory networks. C_LIO_LITADs segmentation contributes to gene-epigenetically modified enhancer relationships. C_LIO_LIContacts of active enhancers in gliomas of different malignancies might affect expression of genes involved in cancerogenesis, such as PROTOCADHERINs or EGFR. C_LI

cancer biology↗

bioRxiv2020

TOP2A substitution enhances topoisomerase activity and causes transcriptional dysfunction in glioblastoma patients

BackgroundHigh grade gliomas (HGGs) are aggressive, primary brain tumors with poor clinical outcomes. We aim to better understand glioma pathobiology and find potential therapeutic susceptibilities. MethodsWe designed a custom panel of 664 cancer- and epigenetics-related genes, and employed targeted next generation sequencing to study the genomic landscape of somatic and germline variants in 182 gliomas of different malignancy grades. mRNA sequencing was performed to detect transcriptomic abnormalities. ResultsIn addition to known alterations in TP53, IDH1, ATRX, EGFR genes found in this cohort, we identified a novel, recurrent mutation in the TOP2A gene coding for Topoisomerase 2A occurring only in glioblastomas (GBM, WHO grade IV gliomas). Biochemical assays with recombinant proteins demonstrated stronger DNA binding and DNA supercoil relaxation activities of the variant proteins. GBM patients carrying the mutated TOP2A had shorter overall survival than those with the wild type TOP2A. Computational analyses of transcriptomic data showed that GBMs with the mutated TOP2A have different transcriptomic patterns suggesting higher transcriptomic activity. ConclusionWe identified a novel TOP2A E948Q variant that strongly binds to DNA and is more active than the wild type protein. Our findings suggest that the discovered TOP2A variant is gain-of-function mutation. Key pointsO_LIThe most frequent genetic alterations in high grade gliomas are reported. C_LIO_LIA new mutation in the TOP2A gene was found in 4 patients from Polish population. C_LIO_LIA E948Q substitution changes TOP2A activities towards DNA. C_LIO_LIThe recurrent TOP2A variant is a gain-of-function mutation. C_LI Importance of the studyGlioblastoma is a deadly disease. Despite recent advancements in genomics and innovative targeted therapies, glioblastoma therapy has not shown improvements. Insights into glioblastoma biology may improve diagnosis, prognosis, and treatment prediction, directing to a better outcome. We performed targeted sequencing of 664 cancer genes, and identified a new variant of the TOP2A gene encoding topoisomerase 2A in glioblastomas. The TOP2A protein variant shows a higher affinity towards DNA and causes transcriptional alterations, suggesting a higher de novo transcription rate.

cancer biology↗