How a Cancer’s Genome Can Tell Us How to Treat it

By Gesa Junge, PhD


Any drug that is approved by the FDA has to have completed a series of clinical trials showing that the drug is safe to use and brings a therapeutic benefit, usually longer responses, better disease control, or fewer toxicities.

Generally, a phase I study of a potential cancer drug will include less than a hundred patients with advanced disease that have no more treatment options, and often includes many (or all) types of cancer. The focus in Phase I studies is on safety, and on finding the best dose of the drug to use in subsequent trials. Phase II studies involve larger patient groups (around 100 to 300) and the aim is to show that the treatment works and is safe in the target patient population, while Phase III trials can involve thousands of patients across several hospitals (or even countries) and aims to show a clinical benefit compared to existing therapies. Choosing the right patient population to test a drug in can make the difference between a successful and a failed drug. Traditionally, phase II and III trial populations are based on tumour site (e.g. lung or skin) and/or histology, i.e. the tissue where the cancer originates (e.g. carcinomas are cancer arising from epithelial tissues, while sarcomas develop in connective tissue).

However, as our understanding of cancer biology improves, it is becoming increasingly clear that the molecular basis of a tumour may be more relevant to therapy choice than where in the body it develops. For example, about half of all cutaneous melanoma cases (the most aggressive form of skin cancer) have a mutation in a signalling protein called B-Raf (BRAF V600). B-Raf is usually responsible for transmitting growth signals to cells, but while the normal, unmutated protein does this in a very controlled manner, the mutated version provides a constant growth signal, causing the cell to grow even when it shouldn’t, which leads to the formation of a tumour. A drug that specifically targets and inhibits the mutated version of B-Raf, Vemurafenib, was approved for the treatment of skin cancer in 2011, after trials showed it lead to longer survival and better response rates compared to the standard therapy at the time. It worked so well that patients in the comparator group were switched to the vemurafenib group halfway through the trial.

While B-Raf V600 mutations are especially common in skin cancer, they also occur in various other cancers, although at much lower percentages (often less than 5%), for example in lung and colorectal cancer. And since inhibition of B-Raf V600 works so well in B-Raf mutant skin cancer, should it not work just as well in lung or colon cancer with the same mutation? As the incidence of B-Raf V600 mutations is so low in most cancers, it would be difficult to find enough people to conduct a traditional trial and answer this question. However, a recently published study at Sloan Kettering Cancer Centre took a different approach: This study included 122 patients with non-melanoma cancers positive for B-Raf V600 and showed that lung cancer patients positive for B-Raf V600 mutations responded well to Vemurafenib, but colorectal cancer patients did not. This suggests that the importance of the mutated B-Raf protein for the survival of the tumour cells is not the same across cancer types, although at this point there is no explanation as to why.

Trials in which the patient population is chosen based on tumour genetics are called basket trials, and they are a great way to study the effect of a certain mutation on various different cancer types, even if only very few cases show this mutation. A major factor here is that DNA sequencing has come a long way and is now relatively cheap and quick to do. While the first genome that was sequenced as part of the Human Genome Project cost about $2.7bn and took over a decade to complete, a tumour genome can now be sequenced for around $1000 in a matter of days. This technological advance may make it possible to routinely determine a patient’s tumour’s DNA code and assign them to a therapy (or a study) based on this information.

The National Cancer Institute is currently running a trial which aims to evaluate this model of therapy. In the Molecular Analysis for Therapy Choice (MATCH) Trial, patients are assigned to a therapy based on their tumour genome. Initially, only ten treatments were included and the study is still ongoing, but an interim analysis after the 500th patient had been recruited in October 2015 showed that 9% of patients could be assigned to therapy based on mutations in their tumour, which is expected to increase as the trial is expanded to include more treatments.

This approach may be especially important for newer types of chemotherapy, which are targeted to a tumour-specific mutation that usually causes a healthy cell to become a cancer cell in the first place, as opposed to older generation chemotherapeutic drugs which target rapidly dividing cells and are a lot less selective. Targeted therapies may only work in a smaller number of patients, but are usually much better tolerated and often more effective, and molecular-based treatment decisions could be a way to allow more patients access to effective therapies faster.

Repair Gone Wrong: Targeting The DNA Damage Response To Treat Cancer

By Gesa Junge, PhD


Our cells are subject to damage every minute of every day, be it from endogenous factors such as reactive oxygen species generated as part of normal cell respiration, or exogenous factors such as UV radiation from the sun. Together, these factors can lead to as many as 60 000 damaged DNA bases per cell per day. Most of these are changes to the DNA bases or single strand breaks (SSBs), which only affect one strand of the double helix, and can usually be repaired before the DNA is replicated and the cell divides. However, about 1% of SSBs escape and become double stand breaks (DSBs) upon DNA replication. DSBs are highly toxic, and a single DSB can be lethal to a cell if not repaired.

Usually, cells are well-equipped to deal with DNA damage and have several pathways that can remove damaged DNA bases and restore the DNA sequence. Nucleotide excision repair (NER, e.g. for UV damage) and base excision repair (BER, for oxidative damage) are the main SSB repair pathways, and homologous recombination (HR) and non-homologous enjoining (NHEJ) repair most DSBs. HR is the more accurate pathways for DSB repair, as it relies on a homologous DNA sequence on the sister chromosome to restore the damaged bases, whereas NHEJ simply relegates the ends of the break, potentially losing genetic information. However, NHEJ can function at any time in the cell cycle whereas HR requires a template and is only active once the DNA is replicated (i.e. in G2 and S-phase).

Depending on the severity of the damage, cells can either stop the cell cycle to allow for repair to take place or, if the damage is too severe, undergo apoptosis and die, which in a multicellular organism is generally favourable to surviving with damaged DNA. If cells are allowed to replicate with unrepaired DNA damage, they pass this damage on to their daughter cells in mitosis, and mutations in the DNA accumulate. While mutations are essential to evolution, they can also be problematic. Genomic instability, and mutations in genes such as those that control the cell cycle and the DNA damage response can increase the risk of developing cancer. For example, germline mutations in ATM, a key protein in HR pathway of DSB repair, leads to Ataxia Telangiectasia (AT), a neurodegenerative disorder. AT sufferers are hypersensitive to DSB-inducing agents such as x-rays, and have a high risk of developing cancer. Deficiencies in NER proteins lead to conditions such as Xeroderma Pigmentosa or Cockayne Syndrome which are characterised by hypersensitivity to UV radiation and an increased risk of skin cancer, and mutations BRCA2, another key HR protein, increase a woman’s risk of developing breast cancer to 60-80% (compared to 13% on average).

Even though deficiencies in DNA repair can predispose to cancer, DNA repair is also emerging as a viable target for cancer therapy. For example, DNA repair inhibitors can be used to sensitise cancer cells to chemotherapy- or radiation-induced damage, making it possible to achieve more tumour cell kill with the same dose of radiation or chemotherapy. However, this approach is not yet used clinically and a major complication is that it often increases both the efficacy as well as the toxicity of treatment.

Another approach is the idea of “synthetic lethality”, which relies on a cancer cell being dependent on a specific DNA repair pathway because it is defective in another, such that deficiency of either one of two pathways is sustainable, but loss of both leads to cell death. This concept was first described by Calvin Bridges in 1922 in a study of fruit flies and is now used in the treatment of breast cancer in the form of an inhibitor of Poly-ADP ribose polymerase (PARP), a key enzyme in the repair of SSBs. Loss of PARP function leads to increased DSBs after cell division due to unrepaired SSBs, which in normal tissue are removed by the DSB repair system. However, BRCA2-deficient tumours are defective in HR and cannot repair the very toxic DSBs, leading to cell death. Therefore, BRCA2-deficient tumours are hypersensitive to PARP inhibitors, which are now an approved therapy for advanced BRCA2-deficient breast and ovarian cancer.

PARP inhibitors are a good example of a so-called “target therapy” for cancer, which is the concept of targeting the molecular characteristics that distinguish the tumour cell from healthy cells (in this case, BRCA2 deficiency), as opposed to most older, cytotoxic chemotherapies, which generally target rapidly dividing cells by inducing DNA damage, and can actually lead to second cancers. With an improved understanding of the molecular differences between normal and tumour cells, cancer therapy is slowly moving away from non-specific cytotoxic drugs towards more tolerable and effective treatments.