Chromatin binding patterns of SWI/SNF chromatin remodeling complex components and interaction partners in FET sarcoma
| dc.contributor.author | Grönqvist, Kajsa | |
| dc.contributor.department | Chalmers tekniska högskola / Institutionen för life sciences | sv |
| dc.contributor.department | Chalmers University of Technology / Department of Life Sciences | en |
| dc.contributor.examiner | Westerlund, Fredrik | |
| dc.contributor.supervisor | Lindén, Malin | |
| dc.contributor.supervisor | Ståhlberg, Anders | |
| dc.date.accessioned | 2024-10-01T13:18:10Z | |
| dc.date.available | 2024-10-01T13:18:10Z | |
| dc.date.issued | 2024 | |
| dc.date.submitted | ||
| dc.description.abstract | Sarcoma is a group of cancers originating in supportive tissues in the body, such as muscle, bone, and fat. FET sarcoma, often found in young patients, is a subgroup of sarcoma. Treatment plans for certain types of FET sarcomas, can leave patients at a high risk of developing a secondary cancer later in life. FET sarcomas are characterized by the presence of fusion genes consisting of a member from the FET family partnered with a transcription factor for example DDIT3, and these fusion genes encode FET fusion oncoproteins, also called FET-FOPs. The FET fusion oncogenes are in several cases the only mutation present in FET sarcomas, indicating that the mutation can induce oncogenesis. FET-FOPs have been found to interact with the SWI/SNF chromatin remodeling complex, which is a complex responsible for remodeling nucleosomes to enable access to DNA for processes such as transcription. This project aimed to determine the chromatin binding strength of SWI/SNF components and known interaction partners in the cell line HT1080 with stable expression of different FET fusion oncoproteins. This was done by using sequential salt extraction (SSE), a method used to solubilize nuclear proteins iteratively with increasing salinity. The salt concentration at which the proteins were extracted reflects their binding strength. The protocol for SSE was optimized to use on HT1080 as the nuclei in the cells were prone to rupturing, resulting in gel pellets that did not allow collection of the nuclear fractions. The change in the protocol that gave desirable results was to resuspend the cell pellet in a buffer with low salt concentration before adding a higher salt concentration buffer as this minimized the occurrence of local high salt concentration, which was believed to be the cause of the ruptured nuclei. Three antibodies targeting the SWI/SNF components BCL7A/B/C were also optimized to be used on Western blot to ensure that they targeted the correct proteins. The final extracts from SSE were then evaluated on Western blot with antibodies targeting SWI/SNF components and known interaction partners to assess if the expression of FET-FOPs alter the chromatin binding strength. SWI/SNF components displayed a unique salt extraction profile, different from most interaction partners but no patterns in regard to functional module or SWI/SNF subtype was observed. The results indicated that the expression of FET-FOPs could have an influence on the binding strength of SWI/SNF components and interaction partners as different expression profiles were detected for some proteins. However, more experiments are needed to confirm this conclusion. By discovering more about the cellular mechanisms between FET-FOPs and SWI/SNF, new targeted treatments for FET sarcomas may be explored. | |
| dc.identifier.coursecode | BBTX03 | |
| dc.identifier.uri | http://hdl.handle.net/20.500.12380/308836 | |
| dc.language.iso | eng | |
| dc.setspec.uppsok | LifeEarthScience | |
| dc.subject | FET sarcoma | |
| dc.subject | SWI/SNF (BAF) chromatin remodeling complex | |
| dc.subject | sequential salt extraction | |
| dc.subject | Western blot | |
| dc.subject | binding profiles | |
| dc.title | Chromatin binding patterns of SWI/SNF chromatin remodeling complex components and interaction partners in FET sarcoma | |
| dc.type.degree | Examensarbete för masterexamen | sv |
| dc.type.degree | Master's Thesis | en |
| dc.type.uppsok | H | |
| local.programme | Biotechnology (MPBIO), MSc |