Next-level CRISPR screening: New method for identifying cancer’s Achilles’ heels
Cancer remains a leading cause of death worldwide, claiming approximately 10 million lives annually. In the last years, scientists have developed targeted cancer treatments that exploit cancer cells’ vulnerabilities: genes that are essential only in cancer cells and fuel their growth and survival, while not being essential in healthy cells. These "Achilles' heels" of cancer cells are potential drug targets for successfully and safely eliminating cancer cells, while not killing healthy cells of the patient. However, such targeted treatments are only available for 15% of cancer patients, as for many cancer types and subtypes, no such drug targets have been found so far.
Genetic vulnerabilities are typically identified in genetic screenings, whereby scientists perturb each gene one by one in cancer cell lines to observe the effect on the cells. However, these screens are typically done in cell culture, a condition that poorly mimics the complexity and heterogeneity of cancer. The complexity of cancer arises from its interactions with the patients’ cells, such as the immune system, and therefore, scientists have long strived to perform such genetic screens within more complex model systems, for example within tumors.
In the new publication, Elling and colleagues present a new CRISPR screening paradigm, allowing researchers to perform genetic screens in complex environments, including tumors.
In conventional CRISPR screens, cells are harvested upon genetic perturbation and their phenotype compared to the historic timepoint before genetic perturbation. In complex settings like tumors, this conventional paradigm of CRISPR screening largely failed for high-throughput approaches. This failure is due to the scale required for such experiments to overcome stochastic events: Random genetic drift, a well-documented phenomenon in population genetics, hampers obtaining robust results in cell population-based experiments. The patented new technology presented by Elling and colleagues overcomes these complexities by introducing a new CRISPR screening paradigm that leverages internal controls.
Ulrich Elling and colleagues developed a novel concept for high-throughput CRISPR screening that no longer compares the final cell population to the cell population before the experiment. Instead, comparisons are made with an internal control cell population that is born at the same place and time as the edited cell population, and derived from the same mother cell. The only difference between the two populations is the presence or absence of precisely one gene per population. This internal control population experiences all the same heterogeneity, and is exposed to the same cellular environment, as the edited population. This breakthrough was possible by a patented method developed by Elling and his team. The method enables them to activate the CRISPR system in precisely half of the cell population through an induced stochastic, mutually exclusive recombination event of the guide RNAs, producing either active or inactive guides. They called this method CRISPR-StAR for Stochastic Activation by Recombination.
As a proof-of-concept, the researchers used CRISPR-StAR to test all genes in the genome for their role in melanoma growth, identifying potential new target genes in Braf-resistant melanoma models. Such an experiment was previously unfeasible due to the required experimental scale. The team’s findings underscore the importance of using in vivo models for finding molecular drivers of cancer, as the genes identified to be required for the cancer to grow in vivo indeed differed from those identified in tissue culture models. CRISPR-StAR therefore empowers genetic screening in complex models. Apart from the study of tumors, the scientists envision its applicability to study gene function in 3D cultures and even directly in tissues. This breakthrough therefore opens the door to discovering therapies for many other diseases, that are only meaningfully modelled in vivo.