Even when a cancer diagnosis has cutting edge treatments available, the threat of resistance lingers. Around 90 percent of cancer-related deaths are estimated to be related to cancer drug resistance, whereby tumor cells carry genetic mutations that allow them to resist the drug from the start, or they acquire them during treatment. Unfortunately, it remains difficult for physicians and researchers to identify which genes cause resistance.
Now, researchers led by Marco Herold at the Olivia Newton-John Cancer Research Institute have created a new tool that could make it much easier to identify target genes. The team developed Partita, a whole-genome library for murine models that the research team used to examine blood cancers, including resistance against the commonly prescribed drug venetoclax, a B-cell lymphoma-2 (BCL-2) protein inhibitor.
The platform rests on CRISPR activation — which activates genes rather than deleting them. Partita gives researchers the inside view on what happens when every gene in the mouse genome is activated in both in vivo and in vitro models when a specific cancer treatment is given.
“We were able to find unexpected resistance factors in our venetoclax screens, and were also surprised by the high efficiency of Partita,” Herold told DDN.
If the new gain-of-function platform allows researchers to identify novel gene targets underlying treatment resistance, it could pave the way for new therapies to silence these genes and vastly improve drug resistance-related deaths.
Validating the platform
Partita offers several advantages over other CRISPR activation libraries, including increasing the amount of sgRNAs (single-guide RNAs) available to 10 per gene and improving the sgRNA scaffold that allows the genes to be activated. The platform is also organized into five sublibraries, such that researchers can use smaller subsets in a screen if needed.
“The tools for CRISPR activation were not ideal for use in more complex systems such as primary cells in vitro or in vivo, partly due to sgRNA efficiencies but also markers on the vectors carrying the sgRNAs,” said Herold.
Using Partita, the researchers identified that the Irx5 (Iroquois homeobox 5) gene allows blood cancer cells to survive against venetoclax. Large-scale screens also showed that the Runx2 and 3 (runt-related transcription factor) and Csf1r (colony stimulating factor 1 receptor) genes promote tumor growth in MYC-driven lymphoma.
These validations of the new library show the tool’s promise in studying cancer resistance, but also highlight their applicability to broader scientific contexts in the study of gene functions and their role in pathobiology.
The future of Partita
Moving forward, Herold noted that the team will continue to optimize Partita for use as a gain-of-function screening library for drug resistance.
“We are currently using it to explore factors that determine haematopoietic lineages in vivo, as well as looking at genes driving resistance to a number of other promising drugs and therapies,” he said.
But its potential to help guide cancer treatment may not stop there. In the future, Herold said the platform could be used to uncover genes that, when upregulated, could enhance cancer treatment as well.
