Creation of cell lines modelling complex karyotype in B cell lymphomas using CRISPR/Cas9

Description

Chronic lymphocytic leukaemia (CLL) and diffuse large B cell lymphoma (DLBCL) make up more than half of all the newly diagnosed cases of non-Hodgkin’s lymphoma (NHL), the 6th most common cancer in the UK. Among these cases of CLL and DLBCL there will be some which harbour malignant cells bearing deletion of the short arm of chromosome 17p (del(17p)), marking the disease that these patients suffer as high-risk because the malignant cells can easily build resistance to therapy and behave in a clinically aggressive manner. Whilst therapy resistance can be explained by the functional loss of TP53, aggressive behaviour of the malignant cells cannot. In fact, we know very little about the impact of del(17p) on cells because there is a lack of cell models with which to study this deletion. Our preliminary work so far shows we are able to use CRISPR/Cas9 to remove large sections of genomic DNA, and we have successfully removed the TP53 gene from 17p in cells. This work therefore supports the aim of this project: to use CRISPR/Cas9 to create cell line models of CLL and DLBCL which bear deletion of chromosome 17p in order to study how such deletion impacts gene expression and cell behaviour as well as response to therapy. Gene dropout screens of the protein coding, lncRNA and microRNA genes that are present on 17p will provide insight into how these genes function to promote cell resistance to therapy as well as maintain cell survival, potentially identifying synthetic lethalities that can be exploited for therapeutic use. This project will use advanced technologies, such as mass cytometry and proximity ligand assay for RNA (PLAYR), to understand if gene expression associated with therapy resistance in our in-vitro models can be validated using primary CLL cells from patients with this disease.

 

Informal applications should be made directly to Professor Joseph Slupsky (email: jslupsky@liverpool.ac.uk) and should include your CV and a covering letter explaining your motivation for applying to this project.

 

Websites:

https://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/joseph-slupsky/

https://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/nagesh-kalakonda/

https://www.liverpool.ac.uk/systems-molecular-and-integrative-biology/staff/mark-glenn/

Availability

Open to students worldwide

Funding information

Self-funded project

Note: this position is unfunded, but support will be provided for suitably strong applicants that are eligible to apply for appropriate scholarships covering research costs, tuition fees and stipends.

For example: the Duncan Norman Research Fellowship (for non-University of Liverpool students and non-XJLTU) or the Douglas Endowment Studentship (for University of Liverpool Institute for Systems, Molecular & Integrative Biology MSc/MRes and 4th year MBiol students).

Other Scholarship Opportunities are listed here and for Commonwealth nationalities here.

Details of international tuition fee costs can be found on the University website: 

https://www.liverpool.ac.uk/study/postgraduate-research/fees-and-funding/fees-and-costs/

Supervisors

References

  1. Kipps TJ, Stevenson FK, Wu CJ, et al. Chronic lymphocytic leukaemia. Nat Rev Dis Primers. 2017;3:17008.
  2. Chapuy B, Stewart C, Dunford AJ, et al. Molecular subtypes of diffuse large B cell lymphoma are associated with distinct pathogenic mechanisms and outcomes. Nat Med. 2018;24(5):679-690.
  3. Duckworth AD, Gherardini PF, Sykorova M, Yasin F, Nolan GP, Slupsky JR, Kalakonda N. Multiplexed profiling of RNA and protein expression signatures in individual cells using flow or mass cytometry. Nat Protoc. 2019 Mar;14(3):901-920.