Cancer mutations explored using organoids and CRISPR

Organoids and CRISPR/Cas9 have been combined in a novel method to study genetic mutations occurring in cancer.

Researchers applied the method to investigate the function of commonly mutated DNA repair genes in the development of colon and breast cancer.

'Within these organoids, we have disabled a single gene using CRISPR/Cas9. This gene normally prevents the accumulation of mutations in the DNA and thereby counteracts colon cancer development. We have eliminated this prevention,' Dr Ruben Van Boxtel, joint first author on the study, told Drug Target Review.

Applying techniques first developed by the researcher Professor Hans Clevers, scientists can grow organoids from a range of tissues, including guts, kidneys and brains, using stem cells. By combining this with the genome editing technique CRISPR/Cas9, which can be used to accurately introduce mutations into cells, the functional effect of genetic mutations found in cancer can be examined.

In a study published in Science by the Clevers group at the Hubrecht Institute in Utrecht, the Netherlands, this combination of techniques was used to investigate the role of DNA repair genes in generating cancer-causing mutations. By individually deleting two DNA repair genes (MLH1 and NTHL1) commonly found mutated in cancer, in human colon organoids, researchers accurately replicated the patterns of mutation accumulation usually observed in, respectively, certain types of colon cancer, and a specific kind of hereditary breast cancer.

'With the help of CRISPR/Cas9 in organoids, we can perfectly mimic this mutation accumulation seen in patients,' said Dr Jarno Drost, the other joint first author.

The processes by which cancer arises and progresses leaves specific patterns or 'mutational signatures' in the DNA. Currently, about 30 different signatures have been identified in different types of cancer. The type of signature can provide information about how the cancer arises and can be used to help predict whether patients will respond to specific treatments.

Removing the gene NTHL1 in organoids closely mimicked the previously identified 'mutational signature 30', whose origin had been unclear. By going back to a patient with hereditary breast cancer in which this mutational signature had been identified, the researchers in this study found a mutation in the NTHL1 gene. This confirmed that the method can replicate what is observed in real cancers, thus paving the way for a greater use of this technique in future studies.

Organoid technology is being increasingly used for a variety of purposes in biological research. Among other applications, novel drugs can now be tested in human tissue organoids instead of animal models or patients, and personalised patient or tumour-specific organoids can be grown.