Tumor heterogeneity: a central foe in the war on cancer

Fueling resistance

Arguably, heterogeneity presents one of the most significant barriers to effective cancer therapy, and this has become increasingly true in the era of personalized medicine in which targeted therapies take aim at specific molecular abnormalities.

It is vital that drugs target the truncal alterations that are present in all cancer cells to ensure that the entire cancer is eradicated. However, it is not always possible to target these alterations, for example, at the present time tumor suppressor proteins like p53 are not druggable.

Even when truncal alterations have been targeted successfully, such as epidermal growth factor receptor (EGFR) mutations and anaplastic lymphoma kinase (ALK) chromosomal rearrangements in non–small-cell lung cancer (NSCLC) and BRAF mutations in melanoma, the long-term efficacy of these drugs is almost invariably limited by the development of resistance.

Tumor heterogeneity and the clonal evolution it fuels are central drivers of resistance. Because tumors are dynamic and continue to evolve, anticancer treatments can act as a strong selective pressure and drive the emergence of drug-resistant subclones that allow the tumor to persist. In fact, study findings have revealed that small populations of resistant cells may be present before treatment. Thus, resistance may also occur as a result of the outgrowth of preexisting treatment-resistant cells that suddenly find that they acquire a survival advantage in the presence of a drug.^1,6
 

Tackling heterogeneity

Despite extensive clinical documentation of the existence of heterogeneity and its underlying mechanisms across a range of tumor types, the development of novel clinical trial designs and therapeutic strategies that account for its effects have only recently begun to be explored.

For the most part, this was because of a lack of effective methods for evaluating intratumor heterogeneity. Multiregion biopsies, in which tissue derived from multiple different regions of a single tumor mass or from distinct cancerous lesions within the same patient, give a snapshot of tumor heterogeneity at a single point in time. The repeated longitudinal sampling required to gain a deeper appreciation of tumor heterogeneity over the course of tumor evolution is often not possible because of the morbidity associated with repeated surgical procedures.

Liquid biopsies, in which DNA sequencing can be performed on tumor components that are found circulating in the blood of cancer patients (including circulating tumor cells and cell-free circulating tumor DNA) have rapidly gained traction in the past several decades and offer an unprecedented opportunity for real-time assessment of evolving tumor heterogeneity.

They have proved to be highly sensitive and specific, with a high degree of concordance with tissue biopsy, they can identify both clonal and subclonal mutations, and they can detect resistance substantially earlier than radiographic imaging, which could permit earlier intervention.^10,11 The first liquid biopsy-based companion diagnostic test was approved by the US Food and Drug Administration in 2016, for the detection of EGFR mutations associated with NSCLC.

Yet, even liquid biopsy alone is not able to fully dissect the extent of tumor heterogeneity, especially because it is limited in its ability to assess spatial heterogeneity. Truly effective assessment of tumor heterogeneity is likely to require a combination of liquid biopsy, carefully selected tumor tissue biopsies, imaging diagnostics, and biomarkers.

The ongoing TRACERx (Tracking cancer evolution through therapy [Rx]) trials are evaluating a combination of approaches to follow tumor evolution across the course of treatment. The study in NSCLC began in 2014 with a target enrollment of 842 patients and will follow patients over 6 years. Preliminary data from the first 100 patients were recently published and demonstrated that increased intratumor heterogeneity correlated with increased risk of recurrence or death.¹²

If patients consent, the TRACERx trials also feed into the PEACE (Posthumous evaluation of advanced cancer environment) trials, which are collecting postmortem biopsies to further evaluate tumor heterogeneity and evolution. TRACERx trials in several other cancer types are now also underway.
 

Cutting off the source

The main therapeutic strategies for overcoming tumor heterogeneity are focused on the mechanisms of resistance that it drives. It is becoming increasingly apparent that rationally designed combinations of drugs are likely to be required and might need to be administered early in the course of disease to prevent resistance.

However, according to mathematical modeling studies, combinations of at least 3 drugs may be necessary.¹³ In many cases, this is unlikely to be feasible owing to the unavailability of drugs for certain targets and issues of toxicity, as well as the high cost.

An alternative strategy is to use immunotherapy, because a single treatment can target multiple neoantigens simultaneously. Although immunotherapy has proved to be a highly effective treatment paradigm in multiple tumor types, resistance still arises through varied mechanisms with tumor heterogeneity at their core.^14,15

A promising avenue for drug development is to cut off the source of tumor heterogeneity – genomic instability and the mutagenic processes that foster it (Table 2). This is exemplified by the success of poly(ADP-ribose) polymerase (PARP) inhibitors in patients with breast cancer susceptibility (BRCA1/2) gene mutations.

Both germline and somatic mutations in the BRCA1/2 genes are observed in 10% to 15% of patients with ovarian cancer and a substantial number of patients with other types of cancer, including breast, pancreatic, and prostate cancers.^16,17

These genes play a central role in the homologous recombination (HR) pathway of DNA repair, which repairs double-strand breaks in DNA. PARP inhibitors target a different DNA repair pathway, base excision repair, which repairs single-strand breaks. The use of PARP inhibitors in patients with BRCA1/2 mutations is designed to create irreparable damage to the DNA repair processes and drive an unsustainable level of genome instability that leads to cell death, whereas normal cells without HR deficiency can survive.¹⁸

A growing number of PARP inhibitors are now approved for use in the United States for the treatment of ovarian cancer. In January, olaparib became the first PARP inhibitor approved for patients with BRCA1/2-mutant breast cancer, based on data from the OlympiAD trial in which 302 patients were randomized to receive olaparib 300 mg twice daily or physician’s choice of chemotherapy. Olaparib improved progression-free survival from 4.2 months to 7.0 months (hazard ratio, 0.58; P = .0009), and the most common adverse events included anemia, nausea, fatigue, and vomiting.¹⁹

Tumors with other defects in HR have also shown susceptibility to PARP inhibition, shifting interest toward identifying and treating these tumors as a group, independent of histology – about a quarter of all tumors display HR deficiency.²⁰ This novel strategy of targeting mutational processes across a range of tumor types has also been exploited in the development of immunotherapies.

Patients with defects in the mismatch repair (MMR) pathway and microsatellite instability (MSI) – multiple alterations in the length of microsatellite markers within the DNA – are more sensitive to immunotherapy, likely because they are predisposed to a high level of somatic mutations that can serve as neoantigens to provoke a strong anti-tumor immune response.

In 2017, 2 immune checkpoint inhibitors were approved for use in patients with MSI-high or defective MMR (dMMR) cancers. The indication for pembrolizumab (Keytruda) was independent of tumor histology, the first approval of its kind. It was based on the results of 5 clinical trials in which 149 patients with MSI-H or dMMR cancers were given pembrolizumab 200 mg every 3 weeks or 10 mg/kg every 2 weeks for a maximum of 24 months. The overall response rate was 39.6%, including 11 complete responses and 48 partial responses.²¹