Genome-wide CRISPR-Cas9 dropout and resistance screens in isogenic cells to identify cancer genetic vulnerabilities

Key information

Application close date
07 February 2023, 11:59 GMT
Hours per week
36 (full time)
Application guidance
Posted 22 December 2022

Research topics

Cell Biology Cell Cycle & Chromosomes Genetics & Genomics Genome Integrity & Repair
Background texture taken from the lab imagery.

This is a summer student position supervised by Sandra Segura-Bayona from Simon Boulton's lab. 

Introduction to the Science

Genomic instability is a characteristic of most cancer cells, where an increased tendency for genetic alterations occurs during cell division. This can result in subpopulations of cells with even more aggressive properties. Cancer cells must also maintain their telomeres, which protect the end of chromosomes, in order to divide indefinitely. Cancers solve this problem of telomere maintenance either by expressing the enzyme telomerase, or by the alternative lengthening of telomeres (ALT) mechanism, which is based on recombining and copying telomeres. Up to 15% of all cancers are ALT-dependent and these are highly associated with a deficiency in the ATRX gene. Currently, there are no targeted treatments specifically designed for treating ATRX-deficient tumours.

We conducted genome-wide CRISPR-Cas9 knockout screens in isogenic wild-type and ATRX-deficient cells, to identify factors that are essential/reduce the viability of cells lacking ATRX. We also identified factors whose loss confers resistance to specific drug treatments, specifically in cells lacking ATRX.

To understand this further, we will use a panel of patient-derived cells and additional isogenic models to screen the proteins identified in the above screen, to see which are essential for the survival of ATRX-deficient cancers but are dispensable in normal cells. We will use a range of cellular and molecular biology assays such as growth inhibition/toxicity assays, immunoblotting, high-content microscopy and foci analysis, flow cytometry and CRISPR cell line models.

About the Project

The proposed project will enable the student to provide mechanistic insights into potential novel concepts for synthetic lethality in a cancer-relevant setting. The student will help to design and perform the experiments to analyse the molecular mechanism of action of selected synthetic lethal and resistance interactions.

About You

The project would suit candidates with a keen interest in molecular and cellular biology, with a special focus on telomere biology and genome stability.

References

1.         Gao, J. and Pickett, H.A. (2022)

            Targeting telomeres: advances in telomere maintenance mechanism-specific cancer therapies.

            Nature Reviews Cancer 22: 515-532. PubMed abstract

2.         Panier, S., Maric, M., Hewitt, G., Mason-Osann, E., Gali, H., Dai, A., . . . Boulton, S.J. (2019)

            SLX4IP antagonizes promiscuous BLM activity during ALT maintenance.

            Molecular Cell 76: 27-43.e11. PubMed abstract