Comprehensive molecular profiling: Expanding therapeutic options in advanced cancers

Dr. Alexander Drilon
19 Jul 2017
Comprehensive molecular profiling: Expanding therapeutic options in advanced cancers
With the dramatic evolution of sequencing technology and emergence of effective targeted therapies, using a comprehensive molecular approach to guide treatment decisions is becoming more accessible and applicable in the clinic. At the recent Foundation Medicine meeting in Hong Kong, Dr Alexander Drilon, clinical director of the Early Drug Development Service at Memorial Sloan Kettering Cancer Center (MSKCC), New York, US, discussed the current landscape and potential benefits of comprehensive molecular profiling in non-small cell lung cancer (NSCLC).

had been identified in 1999 as a driver mutation in NSCLC. However, driver mutations remained unknown in 75 percent of tumours. With recent advances in sequencing technology, the proportion of NSCLC for which no driver mutation can be identified is down to about 12 percent with comprehensive sequencing in 2017, using data generated at our institution, said Drilon.

Traditionally, tumour biopsies are subjected to a series of tests to look for specific genomic alterations. With broad, hybrid capture-based next-generation sequencing (NGS), select tests are able to analyse close to 500 cancer-related genes and detect a broad range of alterations. The utility of this approach was demonstrated in a study of 31 NSCLC patients who had prior testing and were deemed to be ‘driver negative’. In eight patients (26 percent), driver mutations that had been missed by prior testing were identified. In addition, for 12 patients (39 percent), alterations were detected that made them eligible for inclusion in clinical trials. [Clin Cancer Res 2015;21:3631-3639]

“The take-home message here is that with a comprehensive test, you’re not only able to pick up mutations that could be missed by ‘piecemeal testing’, but you can also broaden the menu of therapies that you can potentially offer to your patient,” said Drilon.

Many drivers identified by comprehensive sequencing are clinically actionable
The targeted therapy approval landscape is rapidly evolving (Figure 1) and because of the potential to match targeted therapies with mutational profile, many actionable mutations are now included in the NCCN guidelines. [Lancet Oncol 2016;17:e347-362; NCCN Guidelines NSCLC Version 2.2017]


The BRAF V600E mutation responds well to targeted therapy with B-Raf kinase inhibitors, and this response was substantially increased when the MEK inhibitor trametinib was added to dabrafenib. [Lancet Oncol 2016;17:984-993] Crizotinib is effective in patients with high-level MET amplifications, and these can be detected by FISH or by comprehensive genomic profiling (CGP), but the most notable advance in terms of MET in NSCLC was the discovery of MET exon 14 skipping mutations. [Clin Cancer Res 2016;22:2832-2834]

Exon 14 encodes an area of the protein that targets it for degradation, and the absence of this leads to reduced degradation and increased MET receptor on the tumour cell surface. These mutations occur in about 4 percent of NSCLCs, but they are very heterogeneous and there is no single gene test that can detect them. Patients with these alterations tend to be older and have a higher pack-year history of smoking. “This challenges the paradigm of only testing younger, never-smoking patients,” said Drilon. It is important to identify these patients because they can have clinically meaningful responses to crizotinib.

Fusions and rearrangements, such as RET rearrangements, which are conventionally detected by cytogenetics or FISH, can be picked up with a good NGS platform. Several RET inhibitors are available, but generally, responses with current RET inhibitors have been disappointing, partly due to dose reductions secondary to intolerability. It is hoped that new RET inhibitors in development will be more effective. [Lancet Oncol 2016;17:1653-1660]

Comprehensive NGS has extended the array of therapy options for patients with advanced NSCLC, and using molecular profiling to identify matched targeted therapies leads to measurable clinical benefit for patients. [Cancer Discov 2017;7:596-609]

Comprehensive profiling in the setting of acquired resistance to targeted therapy in NSCLC
At some point after treatment with a first-generation EGFR TKI, resistance in the form of a gatekeeper mutation, usually T790M, is acquired. Resistance mutations like T790M can now be detected by ‘liquid biopsies’ or assays (blood or urine), and this is particularly important for patients in whom it is not safe or feasible to do a biopsy of tumour.

“In ALK-rearranged NSCLC, there are specific drugs that are effective against certain acquired resistance mutations, so in these patients, molecular profiling can really help to inform the next treatment,” said Drilon.

Biomarkers of potential response to immunotherapy with comprehensive sequencing
Beyond PD-L1, there might be other reasons why some patients respond to immunotherapy. A recent study showed that patients with a higher tumour mutational burden (TMB) respond better to pembrolizumab than those with low TMB. [Science 2015;348:124-128] This might be because tumours with TMB will have a more highly complex profile of neoantigens expressed on the tumour cell surface, making them more visible to the immune system. In addition, patients with mismatch repair-deficient tumours have better progression-free survival (PFS) and overall survival (OS) responses to pembrolizumab. [N Engl J Med 2015;372:2509-2520] Comprehensive profiling reports now include mutational burden to give an indication of the potential for response to immunotherapy.

Comprehensive profiling drives early phase/basket trial investigations for advanced solid tumours
Traditionally, response rates in phase I trials have not been very good, but treatment outcomes are much better in trials where the therapy is matched with molecular profiling compared with unmatched therapy. However, 85 percent of all hotpot mutations occur in <5 percent of any cancer type in which they are found, a phenomenon known as the ‘long tail’ of hotspot mutations, and this exists at the gene, variant, and tumour level (Figure 2). [Nat Biotechnol 2016;34:155-163]


This phenomenon has led to phase I studies to introduce expansion cohorts, where patients with any tumour type can be included as long as they have the appropriate target alteration. Other novel study designs, such as basket studies, have also moved away from the traditional histological approach to a molecularly enriched approach. “The early phase clinical trials testing field has really advanced. Now we are able to help patients who have driver events found very rarely,” said Drilon. “If you include patients in a very enriched, focused, and unbiased manner, you can help the majority of them with an active drug.”

Relevance of comprehensive profiling in the Asian setting
Doing comprehensive NGS outside of the US remains very relevant, said Drilon. “The problem with single gene tests or focused gene panels is that when you do several of these you can quickly run out of tumour tissue, and you might have to ask the patient to undergo more than one biopsy, which brings with it the potential for morbidity for the patient. When feasible, therefore, performing NGS should be considered for patients in an attempt to match them to targeted therapy treatments. Beyond standard-of-care tyrosine kinase inhibitors, we have seen an increase in the number of targeted therapy clinical trials in Asia, and many of these are treatments that can result in very significant benefits for patients.”

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