Childhood Cancer

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Identification of Aberrantly Methylated Differentially Expressed Genes to Distinguish High- vs. Low-Risk Retinoblastoma

Children’s Hospital Los Angeles
Jesse Berry, MD
Grant Type: 
Reach Grants
Year Awarded: 
Type of Childhood Cancer: 
Project Description: 

Retinoblastoma (RB) is the most common eye cancer, affecting ~8000 children every year worldwide. This cancer can form in one or both eyes of babies and toddlers. Untreated, RB can lead to death of the child, however even with treatment the tumor may respond poorly and requiring the eye to be removed in 50% of advanced cases. There is a need to better understand the mechanisms behind treatment resistance and relapse for children with RB. For a long time we were limited in understanding this because RB tumors cannot be directly biopsied due to risk of cancer spread outside the eye. Thus, there was no access to tumor information to better understand these mechanisms of treatment resistance. However, 5 years ago we demonstrated that the aqueous humor, the clear fluid in the front of the eye, can be used as a liquid biopsy for this cancer. A liquid biopsy means that you can find information about the tumor in the liquid, without an actual tumor biopsy. This research on the aqueous humor as a liquid biopsy for RB started at CHLA and has now expanded around the world. It has allowed for identification of tumor DNA and other tumor molecules in the aqueous humor, in eyes with RB.

This research has allowed us to address the true clinical problems of: 1) our inability to directly biopsy the ocular tumor tissue in RB and 2) the lack of prognostic and precision biomarkers for RB that result from lack of tumor tissue in this childhood cancer.

The long-term objectives our laboratory are to establish the aqueous humor, the clear fluid in front of the eye, as a clinically utilized ocular liquid biopsy platform that can be used to direct care in future clinical trials. By using the aqueous humor liquid biopsy we can profile tumor information on molecular level even without access to tumor tissue. The success of this proposal will enable the use of methylation signature as part of this liquid biopsy platform. This will enable precision medicine-based approaches for treatment of these young cancer patients suffering from this rare malignancy, with promise to greatly improve the efficacy of their treatment, and thus, their quality of life.

Project Goal

It is well know that methylation of genes plays a role in the behavior of cancers. Methylation can turn good, anti-cancer genes off and bad, pro-cancer genes on. Methylation of genes plays a role in both initiation as well as progression of multiple pediatric cancers, including RB. However, the specific methylated genes that identify high and low risk disease, remains uncharted due to lack of tumor tissue in treated eyes. Thus, our established liquid biopsy approach can now facilitate access to this information. Importantly, identification of tumor-initiated DNA hypermethylation of RB1 or other gene promoters may help stratify patients not only as high- or low-risk for treatment failure, but in the future for epigenetic methylation treatment regimens in clinical trials.

Herein we propose the following aims:

  • Our first aim is to better understand the differing methylation signatures in the aqueous humor for high- and low-risk retinoblastoma in 50 patients with known clinical outcomes (i.e. 25 patients that were saved with therapy, and 25 patients that failed therapy). The goal is to further determine whether there are specific methylated genes identified in the liquid biopsy, that can help stratify children at risk of tumor recurrence and treatment failure (high-risk RB)
  • Once these genes are identified, our second aim is to better understand how these genes function in high-risk tumors which will be tested by knockdown (i.e. turning off) or overexpression (i.e. turning on) experiments. This will help us understand the genes that may be therapeutic targets in the future.
  • Finally, once our methylation signature has been established, our third aim is to establish a clinical test based on methylation analysis in the aqueous humor. This will be done as a final step to prepare for a future clinical trial based on stratification of children with high- and low-risk retinoblastoma.