A team led by researchers at the Wellcome Sanger Institute has used genome-scale CRISPR screening to create a new resource of cancer dependencies and develop a framework to prioritize existing cancer drug targets and suggest new ones.
As they reported today in Nature, the researchers performed CRISPR-Cas9 screens in more than 300 human cancer cell lines from 30 cancer types. They integrated cell fitness effects with genomic biomarkers and target tractability for drug development to systematically prioritize new targets in defined tissues and for specific genotypes. Using this method, they were able to verify the Werner syndrome ATP-dependent helicase (WRN) as a synthetic lethal target in tumors from multiple cancer types with microsatellite instability.
“The principles described in this study can inform the initial stages of drug development by contributing to a new, diverse, and more effective portfolio of cancer drug targets,” the authors wrote.
To comprehensively catalogue genes that are required for cancer cell fitness, the team began by performing 941 CRISPR fitness screens in 339 cancer cell lines, targeting 18,009 genes. After quality controls, the final analysis set included 324 cell lines from 30 different cancer types across 19 different tissues, ranging from common cancers — such as lung, colon and breast cancer — to cancers of unmet clinical need — such as lung and pancreatic cancer.
The researchers also identified a median of 1,459 fitness genes in each cell line. In total, 41 percent of all targeted genes had a fitness effect in one or more cell lines and 83 percent of these genes induced a dependency in less than 50 percent of the tested cell lines.
In order to identify core fitness genes, they then developed a statistical method called the adaptive daisy model, or ADaM. Genes that were defined as core fitness in at least 12 out of 13 cancer types were classified as pan-cancer core fitness genes. This analysis yielded a median of 866 cancer-type-specific and 553 pan-cancer core fitness genes.
Of the pan-cancer core fitness genes the researchers identified using ADaM, 399 were previously defined as essential genes. They also found that 125 of these genes are involved in essential cellular processes. The remaining 132 genes were newly identified and are also significantly enriched in cellular housekeeping genes and pathways.
The team noted that blood cancer cell lines had the most distinctive profile of core fitness genes. It further found that cancer-type-specific core fitness genes were generally highly expressed in matched healthy tissues, consistent with their predicted role in fundamental cellular processes. This suggested that they could show potential toxicity if used as targets.
“Overall, using a statistical approach, we refined and expanded our current knowledge of core fitness genes in humans and identified genes that have a high likelihood of toxicity, which thus represent less favorable therapeutic targets,” the authors wrote. “Furthermore, owing to the large scale of our dataset, we could now define context-specific fitness genes, many of which had a loss-of-fitness effect that was similar to or stronger than core fitness genes.”
In order to winnow the list of context-specific fitness genes down to a list of promising therapeutic targets, the researchers developed a computational framework to assign each gene a target priority score — excluding genes that were likely to be poor targets because of potential toxicity, core fitness genes, and genes that were not expressed or homozygously deleted. For each gene, 70 percent of the priority score was derived from CRISPR experimental evidence and averaged across dependent cell lines on the basis of the fitness effect size, the significance of fitness deficiency, target gene expression, target mutational status, and evidence for other fitness genes in the same pathway. The remaining 30 percent of the priority score was based on evidence of a genetic biomarker that was associated with a target dependency and the frequency at which the target was somatically altered in patients’ tumors.
“In total, we identified 628 unique priority targets, including 92 pan-cancer and 617 cancer-type-specific targets. The number of priority targets varied approximately threefold across cancer types with a median of 88 targets,” the authors wrote. “The majority of cancer-type priority targets (74 percent) were identified in only one or two cancer types, underscoring their context specificity. Most priority pan-cancer targets (88 percent) were also identified in the cancer-type-specific analyses.”
The team then split these targets into three groups according to their tractability, with group 1 comprised of targets of approved anticancer drugs or compounds in clinical or preclinical development, group 2 containing targets without drugs in clinical development but with evidence that supports target tractability, and group 3 including targets that had no support or a lack of information that could inform tractability.
“Priority targets in tractability group 1 were enriched in protein kinases, highlighting a major focus of drug development against this class of targets, compared to groups 2 and 3, which included a more functionally diverse set of targets,” the team noted. “Targets in group 2 are most likely to be novel and tractable through conventional modalities and, therefore, represent good candidates for drug development.”
Importantly, the researchers added, this target prioritization strategy confirmed the WRN helicase as a promising target in MSI cancers. WRN has diverse roles in DNA repair, replication, transcription, and telomere maintenance. The team’s findings showed that the helicase is necessary to sustain in vivo growth of colorectal cancer cells with MSI.
“New approaches are needed to effectively prioritize candidate therapeutic targets for cancer treatments,” the authors concluded. “Confirmatory studies are necessary to further evaluate the priority targets that we identified. Even a modest improvement in drug-development success rates, and an expanded repertoire of targets, through approaches such as ours could provide benefits to patients with cancer.”
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