Genetic and epigenetic study of uveal melanoma
Characterization of genetic heterogeneity
M Rodrigues and MH Stern
Background: Institut Curie is a pioneer center for surgical treatment of uveal melanoma metastases. A significant metastatic tissue bank has been created.
Institut Curie is also an expert center for single cell analysis. This technique is particularly important for the exploration of tumor heterogeneity.
Hypothesis: Tumor heterogeneity could explain treatment resistance. Should a number of resistant clones not have been destroyed during primary treatment they could be responsible for recurrent lesions.
Objectives: Carry out a comparison of a primary tumor and metastases (complete genome and RNA) or of the different metastases as well as a heterogeneity analysis within each sample with the aim to identify new therapeutic targets.
Characterization of epigenetic alterations
Background: BAP1 inactivation is the second most common mutation observed in uveal melanoma. BAP1 is a coding gene for an enzyme involved in chromatin regulation (epigenetic regulation).
Thanks to a collection of frozen samples, cell lines, and PDXs (patient-derived xenografts) Institut Curie is in a unique position to study epigenetic consequences of BAP1 inactivation.
Hypothesis: Understanding how BAP1 inactivation remodels chromatin and promotes tumor progression and studying the possibility of counteracting this mechanism to identify sensitive biomarkers and develop new therapeutic approaches.
Objectives: Identify mechanisms that could compensate for the loss of BAP1.
Identification of new therapeutic strategies
Background: Synthetic lethality is a cell death resulting from the combination of two mutations, each of these mutations being viable when present alone in the cell. A therapeutic strategy would consist of inducing a second mutation within a cell that already has a known mutation. This approach could be interesting in the case of metastatic uveal melanoma for which there is no efficient therapeutic approach.
Hypothesis: Use the fragility induced by the BAP1 mutation to develop a synthetic lethality approach allowing the treatment of mutated tumors for BAP1. In particular BAP1 mutations illustrate the importance of chromatin regulation in uveal melanoma. Targeting chromatin regulation could constitute a new therapeutic approach.
- Carry out a genetic screen on cell lines to identify one or more synthetic lethality events
- Test the efficacy of epidrugs in models then evaluate the efficacy of these drugs in combination with targeted therapies (PKC, MEK and MDM2 inhibitors) or in combination with drugs identified in the genetic screen described above
- Study pharmacodynamics markers for resistant and respondent models for different drugs/combinations
Epigenetic circulating biomarkers for disease diagnosis and monitoring
Background: DNA aberrant methylation (hyper or hypo methylation) is a characteristic of tumor cells. New approaches now allow us to study tumor DNA methylation using tumor DNA circulating in blood.
Hypothesis: Detect specific methylation changes of uveal melanoma in the blood which would inform the diagnosis and follow the treatment in a non-invasive way.
Objectives: Develop a highly sensitive new approach enabling the monitoring of multiple regions and DNA copy sequences extracted by patient blood samples.
This approach is based on bisulfite multiplex sequencing tests for the detection of specific hyper methylated regions identified using TCGA (The Cancer Genome Atlas) data as well as hypo methylations targeting repetitions recognized as hypo methylated in multiple cancers.