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Applying functional genomic approaches to find vulnerabilities of cancers for therapeutic exploitation
The academic partners in the PERSIST-SEQ consortium represent the leading-edge of single-cell sequencing and cancer biology research. Prof. René Bernards’ laboratory at the Netherlands Cancer Institute is a crucial academic partner in PERSIST-SEQ with its integral role to find vulnerabilities of drug tolerant persister cells in cancer. Scientists at his lab use functional genomic approaches, or genetic screens, to find vulnerabilities of cancers and exploit these to prevent cancer recurrence. Targeting such vulnerabilities with selective drugs should result in clinical responses, causing death of only the drug-resistant tumour cells.
The Netherlands Cancer Institute (NKI)
PERSIST-SEQ principal investigator René Bernards is a professor of molecular carcinogenesis at the Netherlands Cancer Institute (NKI) – a globally acclaimed research institute and a cancer clinic in Amsterdam. The centre comprises about 60 research groups in basic and translational research, combined with a 220-bed cancer hospital. The NKI hospital has the second largest phase 1 clinical trials unit in the European Union. In fact, many proof of concept trials are performed based on the new insights gained by NKI’s basic researchers.
Prof. Bernards’ lab
Prof. Bernards’ laboratory uses functional genomic approaches or genetic screens to find vulnerabilities of cancers that can be exploited therapeutically. Moreover, René’s laboratory identified the now FDA approved combination of a BRAF inhibitor and an EGFR inhibitor as effective for the treatment of BRAF mutant colon cancer. He also developed the first clinically used gene expression test for early breast cancer prognosis - MammaPrint, which has helped over 250,000 women in making the right treatment decision.
Drug tolerant persister cells (DTPs)
In PERSIST-SEQ, Prof. Bernards will use the expertise of his group to help identify vulnerabilities of drug tolerant persister cells (DTPs) in cancer. The DTPs have developed an altered, or a “sleeping”, state that keeps them alive and enables them to survive cancer therapies. Moreover, DTPs don’t divide and are therefore insensitive to agents used to kill dividing cancer cells. However, “every disadvantage has an advantage”, prof. Bernards explains:
“Since they are different, DTPs have an advantage by surviving the chemotherapy or another therapy. Nonetheless, they must have acquired a new vulnerability precisely because they are different. If the cell is in a different state, it always comes with its own vulnerabilities. My task is to find the vulnerabilities of the DTPs that we can exploit to selectively kill them. If you have one therapy that kills the dividing cells and a second therapy that kills the non-dividing cells, then you should effectively kill all the cancer cells and prevent that cancer ever comes back.”
Functional genomic approaches
In order to find the vulnerabilities of these DTPs, scientist test all genes one by one to see whether an activation of a gene leads to death of the DTPs. Researchers now have the technologies necessary – by using genome scale CRISPR screens - to inactivate all 20,000 genes one by one. Then, they investigate which gene, when inactivated, kills the DTPs but does not kill the proliferating cancer cells. The goal of this process is to be selective for the DTPs.
Researchers at Prof. Bernards’ lab conduct two experiments. First, they explore which genes are essential for the survival of proliferating cancer cells. In the second experiment, they investigate the genes essential for the survival of DTPs. They look for the genes that only kill the DTPs and not the proliferating cancer cells. Scientists can apply the same approach by using the so-called “drug screens” which look into a collection of 5,000 drugs while treating the DTPs and the proliferating cancer cells. The key question here is whether there is any drug that only kills the DTPs and not the proliferating cancer cells.
Prof. Bernards shares: “Remarkably, we have already conducted all these experiments and, in an absolutely ideal world, the drug screen and the CRISPR screen would point toward the same gene. Then you are absolutely certain of your results. In the past, we have been in this very fortunate position to get exactly that result. The drug screen pointed to a family of epigenetic modulators and the CRISPR screen identified exactly one member of that family of epigenetic modulators for which there are already drugs available. They are called BRD (bromodomain) inhibitors. We have seen that BRD inhibitors are very effective in killing DTPs.”
How this approach helps explain therapy resistance in cancer
BRD inhibitors have no major effect on the proliferating cancer cells. If scientists test this drug on proliferating cancer cells, they would not see any effect. “In fact, DTPs comprise only about 0,1% of all cancer cells. Obviously, a drug that removes only 0,1% of the cancer cells is a terrible drug! However, if this drug kills exactly that 0,1% that persists after regular cancer therapy, then all cancer cells would have been removed.” – prof. Bernards elaborates. “The idea is that if you combine these BDR inhibitors with conventional cancer therapy, the chance that the tumour comes back is significantly reduced because of the removal of the DTPs.”
The most challenging aspect of PERSIST-SEQ’s goals
“I think the work we do is the most challenging but also the most relevant aspect of PERSIST-SEQ. We need to describe DTPs and understand how they are different, but the end goal is to kill these cells. Basically, we have already figured this out. In fact, all of our experiments so far are done in cell culture wherein we have identified vulnerabilities of DTPs and we have figured out how to kill them. Now, the question is how to apply this knowledge to animal models in cancer. It will take time to answer these questions as they require long-term experiments. One important question is how do you sequence these drugs. Do you give one first or the other, or both at the same time? We need to figure out what is the most optimal schedule for the cancer treatment.”, prof. Bernards explains.
How PERSIST-SEQ will help improve the wider field of cancer research
“This will depend on how relevant and important DTPs are in most cancer types”, prof. Bernards says. “It is integral to realize that DTPs have so far primary been described in cell culture. This means that the cells were grown under controlled conditions outside of their natural environment, the living tissue. The evidence that DTPs exists in tumours in patients is relatively thin. This does not mean that they are not there but that we have hardly ever seen proof thereof. Therefore, the key question is how relevant is this phenomenon for recurrent cancer since cancer often comes back after treatment. In fact, this phenomenon was described in lung cancer first, and later - in melanoma. We currently do not know whether other cancer types have the same frequency of DTPs. There is still a lot to learn but the PERSIST-SEQ consortium is well-equipped to do that!”
Public-private collaborations
“I think public-private collaborations between industry partners, academia and other stakeholders are increasingly important. We each have our own area of expertise - for instance, pharmaceutical companies have the essential expertise in making drugs. We academics have a different role – we need to figure out how fundamental mechanisms work which can then be used to develop novel drugs. Collaborations are necessary and inevitable. Of course, you cannot solve all the world’s problems in collaboration with Pharma only. The government needs to invest in fundamental research because it is the one that can discover new mechanisms that pharma can then tackle through the development of new drugs. It is not the task of the pharmaceutical industry to do basic research, that is the responsibility of academia. In addition to partnerships, we also need basic research to make progress in the battle against cancer”, prof. Bernards says.