CRISPR-KOALA Reveals 81 Hidden Genetic Drivers of Triple-Negative Breast Cancer in Living Tumors
Key Insights
Toronto researchers developed CRISPR-KOALA, a dual-function gene-editing tool that can simultaneously silence and activate genes within living mouse models to mimic chromosomal chaos.
Screening over 3,700 genes identified 81 previously unrecognized cancer-driving genes in basal-like breast cancer (search), with 90% going undetected in standard cell culture experiments.
The gene PLGRKT (search) emerged as a potent driver, helping cancer cells survive in oxygen-deprived tumor regions by switching metabolic processes, making it a compelling therapeutic target.
A Toronto-based research team has cracked open a long-standing mystery in oncology: which genes, among the hundreds scrambled by chromosomal chaos in aggressive breast cancer, actually drive the disease? Using a newly developed gene-editing platform called CRISPR-KOALA, scientists identified 81 previously unrecognized cancer-driving genes in basal-like breast cancer (search) (BLBC), the most aggressive and hardest-to-treat form of the disease.
Published in Nature, the study was led by Dr. Daniel Schramek, Deputy Director of Discovery Research at Sinai Health (search) and Senior Investigator at the Lunenfeld-Tanenbaum Research Institute (search) (LTRI), along with Dr. Khalid Al-Zahrani, formerly a postdoctoral fellow at LTRI and now a faculty member at the Donnelly Centre for Cellular and Biomolecular Research at the University of Toronto.
The findings represent a significant leap forward for a cancer subtype that has stubbornly resisted precision medicine approaches. BLBC, also known as triple-negative breast cancer (search), lacks the three receptors — estrogen, progesterone, and HER2 — that clinicians routinely target in other breast cancers. Without these molecular handles, patients face limited treatment options and poorer outcomes.
"In many types of breast cancer that have been extensively researched, the five-year survival rate is around 95 percent. Most people survive because we were able to find the genes that drive the cancer," said Dr. Schramek, who holds the Canada Research Chair in Functional Cancer Genomics. "In this one subset, we don't know what the driver of the cancer is and therefore, it has some of the worst outcomes for patients."
The challenge of chromosomal chaos
BLBC disproportionately affects younger women of color and is characterized by aneuploidy — a state in which large regions of chromosomes are lost or duplicated many times over. While this chromosomal instability devastates healthy cells, it supercharges cancer cells, fueling their growth and spread.
The scale of the disruption has long confounded researchers. A single duplicated or deleted chromosomal region can contain hundreds of genes, making it nearly impossible to determine which specific genetic changes matter most for tumor development. Without knowing the key drivers, developing targeted therapies has remained out of reach.
CRISPR-KOALA: a dual-function breakthrough
To address this challenge, the team built on years of prior work adapting CRISPR genome editing for use in the mouse mammary gland, a well-established model for studying breast cancer. The existing platform could silence genes — simulating what happens when genetic material is lost — but it could not switch genes on to mimic the gene duplication events that also characterize aneuploidy.
Dr. Al-Zahrani developed CRISPR-KOALA (Knockout and Activation Linked Assay) during his postdoctoral training with Dr. Schramek and Dr. Jeff Wrana, also a senior investigator at LTRI. The tool can, within a single mouse, both silence genes and activate others, allowing researchers to systematically test what happens when individual genes are missing or multiplied as a result of chromosomal rearrangements.
Using this system, the team screened more than 3,700 genes residing on chromosomes commonly altered in BLBC and identified 81 previously unrecognized cancer-driving genes. Strikingly, 90 percent of these genes went entirely undetected in standard cell culture experiments.
"The reason we hadn't found many of these driving genes before is that we were working in cell culture models," said Dr. Schramek, who is also a professor in the Department of Molecular Genetics at the University of Toronto. "Now that we can study this cancer directly in a living system, we can observe the biological intricacies that only emerge in the context of a real tumor environment."
PLGRKT: a metabolic survival switch
Among the newly identified cancer-driving genes, PLGRKT (search) stood out as a particularly potent driver of BLBC. The researchers discovered that it helps cancer cells survive deep inside tumors where oxygen is scarce. Under these hypoxic conditions, PLGRKT enables cells to switch to an alternative metabolic process to generate energy without oxygen. That resilience actively promotes tumor growth, making PLGRKT a compelling candidate for future targeted therapy research.
"This work brought together computational analysis, biotechnology development and functional genomics experiments across a range of mouse and human breast cancer models," said Dr. Al-Zahrani, also an assistant professor in the University of Toronto's Department of Molecular Genetics. "Combining all of that enabled us to uncover roles for many genes that we did not know were driving breast cancer and to start thinking about how to tackle BLBC in a targeted way."
The study underscores the critical importance of studying cancer within living systems, where the tumor microenvironment — including immune cells, blood vessels, and varying oxygen levels — reveals genetic dependencies that cell culture models simply cannot replicate. By mapping the full genetic landscape of BLBC, the researchers have opened new avenues for therapeutic development against one of breast cancer's most formidable subtypes.