Colorectal cancer (CRC) is the 4th most common cancer in the UK and kills >53,000 people per year worldwide. CRC is characterised by a high inter-patient variability and high intra-tumour genetic heterogeneity. In addition to genetic heterogeneity, increased stromal heterocellularity correlates with poorer survival in CRC. The stroma plays an important role in tumour progression, with cancer-associated fibroblasts (CAFs) being one of the most abundant cell-types in the tumour microenvironment (TME). Cancer cells interact with CAFs during all stages of CRC progression and can even protect cancer cells from therapy.
Patient-derived tumour organoids (PDOs) are self-organising heterocellular cancer models generated from tumour biopsies that are capable of recapitulating physiologically relevant phenotypes of their tissue of origin. There is increasing evidence that PDOs mimic their parent tumours’ physiology as well as response to chemotherapy and targeted therapy. However, given the dominant role of the TME in cancer progression, the PDO monocultures used in current studies cannot recapitulate the complex TME therapies must navigate in vivo.
The Cell Communication Lab at UCL Cancer Institute have recently developed a new Thiol-reactive Organoid Barcoding in situ (TOBis) mass cytometry (MC) platform to study post-translational modification (PTM) cell-signalling networks in organoid models of the CRC TME (Qin et al., Nature Methods, 2020). This method can generate single-cell data for >30 PTMs from millions of cells across 126 organoid co-cultures in a single MC run (Sufi & Qin et al., Nature Protocols, 2021).
We are now using TOBis MC to study how stromal CAFs regulate human CRC PDOs response to clinical therapies. Preliminary experiments have revealed CAFs can protect PDOs from traditional anti-CRC chemotherapies – albeit through unknown mechanisms. By understanding this process in molecular detail, it could be possible to provide novel anti-stromal therapeutic options to CRC patients.
In this PhD project, we will systematically CRISPR-knock out kinases and growth factor ligands in CAFs, then co-culture CAFs with PDOs, treated with or without clinical therapies (e.g. SN-38). Cell-type-specific drug responses in both PDOs and CAFs will be measured using TOBis MC. This will be performed over the following aims:
- Aim 1 – Establish a panel of human CRC CAFs from UCLH expressing Cas9.
- Aim 2 – Perform a CRISPR-screen of kinase and growth factor ligand knockouts in CAFs co-cultured with a panel of CRC PDOs +/- SN-38 treatment and measure cell-type-specific signalling using TOBis MC.
- Aim 3 – Validate key signalling nodes in CAFs that protect CRC PDOs from therapy.
Unlike traditional CRISPR screens that focus on knocking out genes in cancer cells, this project will explore how genes in stromal fibroblasts can regulate how cancer cells respond to chemotherapy. By treating tumours as an integrated network of heterotypic cells rather just tumour cells alone, this project will reveal how stromal cells can be targeted to improve treatments for CRC patients.
For more information, please contact Dr. Chris Tape ([Email Address Removed]) (www.tape-lab.com).
Person Specification Essential Criteria:
- Minimum upper second-class Honours Degree in an associated discipline, or an overseas qualification of an equivalent standard.
- Knowledge of cell signalling, cell culture, CRISPR, and single-cell analysis.
- Evidence of motivation for and understanding cell-signalling in cancer.
- Ability to develop understanding of complex problems and apply in-depth knowledge to address them.
- Potential to develop expertise in new areas of the subject.
- Potential for innovation and initiative, and evidence of an ability to work independently.
- Effective communication skills in both written and spoken English.
Person Specification Desirable Criteria:
- Experience of flow/mass cytometry.
- Experience of 3D cell culture (ideally organoids).
- Experience of CRISPR technology (ideally screening).
- Experience of large-scale biological data analysis using R, Python, and/or other appropriate programming languages.
Predicted start: September 2022.
Duration: 3-years (in first instance).
Stipend: £21,000 p.a.
Funding: Constance Travis Charitable Trust
For more information, please contact Dr. Chris Tape ([Email Address Removed]) (www.tape-lab.com).
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