Implementation of the patient-derived explant (PDE) platform for evaluating tumour responses to novel immunotherapies and BRAF inhibitors

Melanoma is a leading cause of skin cancer deaths, often progressing to metastasis and treatment resistance after surgery. Many oncology drugs fail in clinical trials due to inadequate preclinical models predictive of patient outcome, especially for immune checkpoint inhibitors (ICIs), necessitating accurate predictive models. We have established a metastatic melanoma (MM) PDE pre-clinical model, which represents the “live” culture of MM tumour fragments and retains tumour architecture intact. These cultures were used to test and predict the responses to ICIs. BRAF is the most common mutation in melanoma and BRAF inhibitors have been known to be effective.

Tumours obtained from surgery were sectioned into explants and cultured for 16-24 h. PDEs were transferred into fresh media containing ICIs and BRAF inhibitors for 24h and then fixed, and formalin fixed paraffin embedded (FFPE) blocks generated. Multi-immunofluorescence (mIF) staining coupled to digital pathology tools was used to segment tumour and stroma areas, followed by quantitation of proliferation (Ki67) and cell death (cPARP) response to the drugs. Key immunological subsets (CD4, CD8, FOXP3) were evaluated using mIF to investigate the density of key immune cells in response to treatments.

Differential apoptotic responses to ICIs as well as BRAF inhibitors (i) across the MM-PDEs were observed which matched clinical outcomes, with the highest response rate to α-PD1 inhibition and combination treatment (αPD1+ α-CTLA4) and (BARFi + MEKi). Differential levels of CD4+FOXP3+ regulatory T cells and CD8+ Cytotoxic T Lymphocytes (CTLs) infiltration into stroma and tumour areas of the MM-PDEs was observed. This allowed us to distinguish immune “hot” and “cold” tumours and correlate this status with cell death induction by ICIs and patient outcomes in the clinic.

Positive correlations of intrinsic CTL densities with positive patient outcomes and negative correlation of intrinsic CTL density with ICI treated PDEs and cell death were found. Further analysis of these data with clinical comparisons, will allow us to understand the extent to which the MM-PDEs are predictive of patient outcomes in the preclinical testing of ICIs.