Studies

One of the main characteristics of BLM syndrome patients and BLM deficient cell lines is the enhanced occurence of sister chromatid exhange, detectable in metaphase chromosome spreads. Successful BLM depletion in our homozygous BLM-AID cell line was accompanied by a significant increase of sister chromatid exchange (SCE).

To study how mitotic functions of BLM helicase contribute to genome stability, we genereated chromosomally stable HCT116 cell lines, in which BLM protein can be rapidly degraded in a cell-cycle specific manner. Using the CRISPR/Cas9 technology, a homology donor encoding an auxin-inducible degron (AID), GFP and a selection marker was inserted at the last coding exon of the endogenous BLM gene. To generate the homology donor, a modular cloning system was set up using the Golden Gate assembly strategy. ...

FANCD2 ChIP-MS experiments in refined synchronized HCT116 cells with different types of replication stress are performed to identify additional proteins involved in the resolution of UFBs. Through reciprocal ChIP-MS and colocalization analysis by immunofluorescence experiments observed interactions will be validated. In collaboration with SP-Z promising candidates will be prioritized and subsequently tested for their contribution to the resolution of UFBs and chromosome segregation. In collaboration ...

In this study we can investigate the ability to pull down BLM in BLM-AID cells with its inserted GFP tag and use the BLM-depleted cell line as a control. The ChIP-MS analysis of BLM in synchronized cells can reveal new interaction partners invovled in the resolution of UFBs. On the other hand pulling down other UFB binding proteins in BLM depleted cells can help to understand the impact of cell-cycle specific BLM depletion on UFB resolution.

We implemented the pan-cancer chromosomal instability association studies pipeline using R-3.6. The source code and data are available at https://github.com/mcmzxx/pancan_cin

All statistical and machine learning analysis was done with R 3.6.3 and Python 3.6, the source code is available at https://github.com/mcmzxx/mfMap.py.