Despite clear successes, only a small number of tumor patients currently benefit from molecular profiling. Read here how the CRISPR procedure could change this.
Using the CRISPR method, two research teams (sources 1 and 2) have succeeded in inactivating about 18,000 genes - one after the other - in hundreds of cancer cell lines. In this way, they identified specific genes that certain types of cancer need to survive. These genes or the proteins encoded by them are now potential targets for targeted therapies (source 3).
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) are repeating segments in the genome of many prokaryotes. These serve a mechanism that protects against the intrusion of foreign DNA (such as harmful viruses) - an archaic form of the immune system. During infection, CRISPR-associated (Cas) proteins break down the genome of the invading viruses into short fragments, which are then inserted into the CRISPR section. On renewed contact with the virus, these CRISPR fragments are rewritten into RNA. This "controls" the viral DNA. If the DNA matches the stored section, it is cut by the Cas proteins (source 4).
This system allows DNA strands - not only in bacteria, but in principle in all organisms - to be specifically cut through and, in the course of the subsequent repair, individual DNA building blocks can be cut out, exchanged or inserted. This happens in the same way as with a natural mutation - with the difference that this takes place randomly, while the CRISPR/Cas system enables precise, selective changes to the DNA (genome editing). The method is already used in animal and plant breeding. Compared to other genome editing methods, it is simpler, more precise, cheaper and faster (e.g. several genome changes can be made simultaneously).
The current issues of Nature (sources 1 and 2) and the New England Journal of Medicine (source 3) report on the great potential for oncology. Some challenges have so far prevented the widespread use of molecular investigations for the selection of effective therapies: in addition to the limited access to such procedures for many patients in the world, it is not possible to find a mutant oncogene for most tumors by means of sequencing, which would be suitable as the target of a "targeted therapy" and even for very well-validated oncogenes we lack active substances.
The two research teams mentioned above took advantage of the progress made in genome engineering and used the CRISPR/Cas system to test how the deletion of every single human gene from 324 (source 2) or 517 (source 1) cancer cell lines affects their survival and proliferation. This enabled them to identify genes that are necessary for the survival of certain but not all cancer cell lines and, taking into account the (known or suspected) function of the gene products and their suitability as therapy targets ("druggability"), and to identify classes of potential therapeutic targets, the majority of which were not the focus of conventional tumour therapies.
A promising potential target discovered in this way is WRN helicase activity. In order to understand its importance for a therapeutic concept, we must first explain what "synthetic lethality" means. If the joint occurrence of two genetic alterations leads to cell death, each of which cannot be used as a therapeutic target, this is referred to as synthetic lethality. DNA repair processes are attractive synthetic lethal targets, as many neoplasms have disorders of a DNA repair pathway, which can lead to dependence on specific repair proteins.
One example is the success of PARP-1 inhibitors. PARP is a DNA repair enzyme whose inhibition means that single-strand breaks can only be repaired by homologous recombination. Tumors with a frequent defect of the homologous recombination could, therefore, be destroyed by PARP inhibitors.
The researchers used CRISPR knockout to search for such "lethal chains" and found the WRN helicase. For tumors with a second defect, the elimination of the WRN helicase has a lethal effect, i.e. in the case of a disturbed base mismatch repair. This leads to microsatellite instability (MSI). Selectively in these cell lines (i.e. not in cancer cells that are microsatellite-stable), loss of the WRN helicase leads to double-strand breaks, apoptosis and cell cycle arrest. WRN thus represents a synthetic lethal weak point and a possible therapeutic starting point for MSI tumors.
That was some basic research today, but we hope you found it interesting. The application of the CRISPR/Cas system could allow more effective prioritization of therapy targets and better selection of drugs suitable for the specific tumor, thus protecting patients from exposure to therapeutics that are unlikely to provide benefit.
Sources:
1. Chan, E. M. et al. WRN helicase is a synthetic lethal target in microsatellite unstable cancers. Nature 568, 551-556 (2019).
2. Behan, F. M. et al. Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens. Nature 568, 511-516 (2019).
3. Hahn, W. C. A CRISPR Way to Identify Cancer Targets. New England Journal of Medicine 380, 2475-2477 (2019).
4. CRISPR/Cas system. transGEN Available at: https://www.transgen.de/lexikon/1845.crispr-cas.html. (Accessed: 14th July 2019)