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Fruit Fly Model Provides Personalized Cancer Therapy Recommendation

NEW YORK (GenomeWeb) – A group led by researchers at the Icahn School of Medicine at Mount Sinai has built a fruit fly model to develop a personalized therapy for a patient with treatment-resistant metastatic KRAS-mutation colorectal cancer (CRC).

Specifically, the team altered orthologs of nine key driver genes identified through genomic analysis of a patient's tumor and conducted a robotic screen of the fruit fly models to find that a combination of trametinib and zoledronate could act as a cancer treatment option.

The team has partnered with London-based startup My Personal Therapeutics to commercialize a targeted therapeutic recommendation tool based on the whole-exosome sequencing (WES) and fruit fly "avatar"-based approach, first reported by GenomeWeb earlier this month.

The researchers described their work in a proof-of-concept paper published today in Science Advances.

In order to perform a comprehensive analysis of the patient's tumor genomic landscape, the team extracted DNA from the primary tumor specimen and patient's blood. They then performed WES, copy number analysis (CNA), and Ion AmpliSeq Cancer Hotspot Panel (Thermo Fisher Scientific) assays on the sample, revealing 132 somatic and 965 rare germline variants in the tumor.

The group then focused on mutations in recurrently mutational cancer driver genes and genes that regulate cancer-relevant signaling pathways and cellular processes. WES found the oncogenic KRAS (G13A) mutation, CRC drivers APC, TP53, and FBXW7, and germline missense mutation TBFBR2. The group also identified somatic mutations in SMARCA4, FAT4, and MAPK13 and a heterozygous germline mutation in CDH1.  

The investigators then altered Drosophila orthologs of the nine genes identified in the genomic analysis in the fruit fly's hindgut using the GAL4/UAS expression system. Specifically, they cloned transgenes downstream of UAS, a yeast-derived promoter that is responsive specifically to the yeast GAL4 transcription factor. To target transgenes to the hindgut, they then crossed together transgenic flies containing a stable genomic insertion of UAS-transgenes with flies directing GAL4 expression in the hindgut. They also included a UAS-GFP reporter to visualize transformed tissue.

For drug screening, the researchers built a custom library of US Food and Drug Administration-approved drugs containing 121 drugs for cancer, non-cancer indications with reported antitumor effects, and noncancer indications with any cancer-relevant targets. Applying a robotics-based screen using the platform in the Drosophila, the researchers identified trametinib and zoledronate as a potential candidate treatment combination for the patient.

The team then started treatment on the cancer patient, prescribing oral trametinib twice per day and intravenous zoledronate every four weeks. They found target and nontarget lesions showed a strong partial response, with a 45 percent reduction in tumor burden over 11 months.

Examining the patient's mutational profile of treatment-resistant peripancreatic and periportal nodes extracted from a tissue biopsy, the group did not identify any new mutations on the panel, ruling out the majority of drug targets as well as mutations that promote resistance.

The study authors noted that they "focused on variants in genes identified as currently mutated drivers of cancer and those with clear cancer-relevant functions; however, our exclusion criteria are necessarily incomplete, and a large number of candidate variants remained."

The team therefore believes that future studies will potentially improve the technology's ability to generate more refined models to capture the genomic complexity of tumor genomic landscapes.

In contrast to other animal models, the study authors argued that using Drosophila models could be used for any patients with isolated tumor tissue more quickly and cheaply.

"The advantage of Drosophila is the ability to alter a large number of genes in a single tissue and screen a large number of drugs and drug combinations in a whole-animal setting with a simple readout for efficacy and toxicity," the study authors noted. "Identifying an effective, unique drug combination … emphasize[s] the potential for moderately high-throughput screens that can be accomplished in a timeframe that is useful for treating a patient."

By focusing on each cancer's genomic complexity, the team believes the personalized approach could provide an alternative treatment option for diseases such as KRAS-mutant CRC.

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