Institutional creator:

Instytut Biologii Doświadczalnej im. Marcelego Nenckiego PAN

Contributor:

Wojtaś, Bartosz (1983– ) : Supervisor ; Kamińska-Kaczmarek, Bożena (1961– ) : Supervisor

Publisher:

Nencki Institute of Experimental Biology PAS

Place of publishing:

Warsaw

Description:

160 pages : illustrations ; 30 cm ; Bibliography ; Summary in Polish

Degree name:

PhD in Biological Sciences

Degree discipline :

Biological Sciences

Degree grantor:

Nencki Institute of Experimental Biology PAS ; degree obtained: 27.04.2022

Type of object:

Thesis

Abstract:

High-grade gliomas (HGGs), the most frequent and severe primary brain tumours in adults, invariably recur due to incomplete surgery or therapeutic resistance. The major checkpoint in regulation of gene expression is the initiation of transcription, which is mostly regulated by a class of DNA-binding proteins known as transcription factors (TFs). The expression of essential TFs is required by cancer cells to carry on a variety of biological processes in cancer cells such as cellular transformation, oncogenesis and progression, cell proliferation, metastasis, and chemo-resistance. In HGGs, several interconnected biological components such as somatic mutations, transcriptomic and TF dysregulations, as well as alterations in histone modifications, DNA methylation and chromatin remodelling contribute to the disease aggressiveness. Transcriptomic profiles of HGGs at recurrence have not been thoroughly investigated yet. Moreover, despite significant efforts, the specific regulation of genes overexpressed in HGGs by TFs remains largely unknown. A better understanding of events occurring in open chromatin regions in HGGs is crucial to comprehend routes of brain cancer progression. We employed targeted DNA- and RNA-sequencing to identify single nucleotide variants, small insertions and deletions, copy number aberrations (CNAs), gene expression alterations and pathway dysregulations in 16 matched pairs of primary and recurrent HGGs. The majority of somatic mutations found in primary HGGs were not found in relapsed tumours, implying a sub-clone substitution during tumour progression. A novel frame-shift insertion in the ZNF384 gene was discovered, which may play a role in extracellular matrix remodelling. The presence of focal CNAs in the EGFR and PTEN genes was found to be inversely correlated. In silico analysis of the tumour microenvironment demonstrated that tumour supportive (M2) macrophages and immature dendritic cells are enriched in recurrent HGGs indicating a prominent immunosuppressive signature in those tumours. Immunohistochemistry staining of tumour sections confirmed the accumulation of immunosuppressive cells in recurrent HGGs. We identified glioma grade-specific TFs binding sites in glioblastoma tissues as well as in human LN18 and LN229 glioma cells, using ATAC-seq data and confirmed their roles in controlling gene regulatory networks in HGGs. We explored different datasets that comprise DNA methylation profiles, histone acetylation profiles, GBM cell line RNA-seq and TCGA (the Cancer Genome Atlas) datasets (RNA-seq and lllumina 450K array DNA methylation). The comparative analyses of those profiles in gliomas of different malignancy grades revealed the importance of the c-Jun TF for the disease progression. c-Jun may play a role in the regulation of genes overexpressed in glioblastoma by binding to the gene promoters. Furthermore, we found that in the majority of c-Jun gene targets, DNA methylation plays an important role in the c-Jun dependent regulation. The bioinformatic predictions have been validated experimentally by testing c-Jun binding to various probes in the electrophoretic mobility shift assay (EMSA). Chromatin remodelling proteins SMARCA2 and SMARCA4 are frequently mutated in high-grade gliomas. To determine the role of those proteins, we performed knockdown of genes coding them in human LN18 glioma cells and tested the impact of SMARCA2 and SMARCA4 deficiencies on chromatin accessibility using the Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq). We discovered an increase in chromatin openness in SMARCA2/4 deficient cells, which affected expression of genes critical for signal transduction, including those from the transforming growth factor beta pathway: SMAD1, SMAD3, BMPR1A, and TGFBR2, implying the interdependence of chromatin remodellers and specific signalling pathways

Detailed Resource Type:

PhD Dissertations

Resource Identifier:

oai:rcin.org.pl:234693

Source:

IBD PAN, call no. 19936

Language:

eng

Language of abstract:

pol

Rights:

Rights Reserved - Free Access

Terms of use:

Copyright-protected material. May be used within the limits of statutory user freedoms

Copyright holder:

Publication made available with the written permission of the author

Digitizing institution:

Nencki Institute of Experimental Biology of the Polish Academy of Sciences

Original in:

Library of the Nencki Institute of Experimental Biology PAS

Access:

Open