Genetically modified organoids reveal cause of hereditary cancer

Researchers at Hubrecht Institute, UMC Utrecht and Princess Máxima Center have developed a method, based on CRISPR-Cas9 technology in organoids, to study the genetic cause of hereditary forms of cancer. This method can be of great significance for the diagnosis and treatment of multiple forms of cancer. Their study shows that by examining a tumour’s DNA, a familial cause of colon and breast cancer can be identified, for example, through a germline mutation in the NTHL1 gene. The publication was published in Science on September 14th.

CRISPR-Cas9 is a technique that can be used to introduce very precise changes in the DNA. In this project, the researchers used this technique to make changes to the DNA of healthy organoids: mini-colon cultures generated from human stem cells. Worldwide Cancer Research-funded scientist Dr Ruben van Boxtel: “Within these organoids we have disabled a single gene using CRISPR-Cas9. This gene normally prevents the build-up of mutations in the DNA, and thereby counteracts colon cancer development. We have eliminated this prevention.” In the DNA of these modified organoids, a mutation pattern appeared that also occurs in patients with an inheritable form of colon cancer: Lynch syndrome. Researcher Dr. Jarno Drost: “With the help of CRISPR-Cas9 in organoids, we can perfectly mimic this mutation accumulation seen in patients.”

Helping decide treatment choices
The use of CRISPR-Cas9 in organoids makes it possible to directly study processes that underlie the initiation and progression of cancer. These processes leave specific patterns in the DNA, so-called mutational signatures. Currently, there are about thirty different signatures identified in different types of cancer. These signatures can provide valuable information about the processes that cause these DNA mutations and consequently the cancer. The presence of a specific signature within the tumour’s DNA may point towards a genetic predisposition that underlies the cancer, and this can help guide the choice of treatment. The research on the organoids was carried out in the groups of prof. Hans Clevers (Hubrecht Institute / Princess Máxima Center) and prof. Edwin Cuppen (UMC Utrecht).

NTHL1 gene mutation
In the second part of the study, a relatively unknown form of hereditary cancer was copied in the organoids by turning off the NTHL1 gene using CRISPR-Cas9. Earlier genetic research, by among others dr. Roland Kuiper (Princess Máxima Center), had shown that patients of families with inherited NTHL1 mutations have an increased risk of developing colon cancer. In the DNA of the modified organoids, the researchers saw a very specific mutational signature. Previously, the same signature was identified in a patient with an unknown form of breast cancer. It turns out that this patient has a congenital mutation in the NTHL1 gene. Van Boxtel: “With this finding, we showed that the presence of this specific signature in the DNA of a tumour is a strong indication that an inherited NTHL1 mutation is the cause of the disease.” This observation also indicates that it is possible to directly detect an inheritable cause of cancer by sequencing the DNA of a tumour, which is important information for patients and their families.”

Prof. dr. Hans Clevers is group leader at the Hubrecht Institute (KNAW), Professor of Molecular Genetics at the University Medical Center Utrecht and Utrecht University and Scientific Director of the Princess Máxima Center for pediatric oncology.

Use of CRISPR-modified human stem cell organoids to study the origin of mutational signatures in cancer
Science 2017.