Genomic Profiling for Lung Cancer: the Good, the Bad and the Ugly

Genomic profiling has gained popularity in medical oncology. Using NextGen platforms, protein coding regions of human tumors known as exomes can be examined for mutations, amplifications, deletions, splice variants and SNPs. In select tumors the results can be extremely helpful. Among the best examples are adenocarcinomas of the lung where EGFr, ALK and ROS-1 mutations, deletions and/or re-arrangements identified by DNA analysis can guide the selection of “targeted agents” like Erlotinib and Crizotinib.

An article published in May 2014 issue of JAMA reported results using probes for 10 “oncogenic driver” mutations in lung cancer patients. They screened for at least one gene in 1,007 patients and all 10 genes in 733. The most common was k-ras at 25%, followed by EGFR in 17% and ALK in 8%. The incidence then fell off with other EGFr mutations in 4%, B-raf mutations in 2%, with the remaining mutations each found in less than 1%.

Median survival at 3.5 vs 2.4 years was improved for patients who received treatments guided by the findings (Kris MG et al, Using multiplex assays of oncogenic drivers in lung cancers to select targeted drugs. JAMA, May 2014). Do these results indicate that genomic analyses should be used for treatment selection in all patients? Yes and no.

Noteworthy is the fact that 28% of the patients had driver mutations in one of three genes, EGFr, HER2 or ALK. All three of these mutations have commercially available chemotherapeutic agents in the form of Erlotinib, Afatinib and Crizotinib. Response rates of 50% or higher, with many patients enjoying durable benefits have been observed. Furthermore, patients with EGFr mutations are often younger, female and non-smokers whose tumors often respond better to both targeted and non-targeted therapies. These factors would explain in part the good survival numbers reported in the JAMA article. Today, a large number of commercial laboratories offer these tests as part of standard panels. And, like k-ras mutations in colon cancer or BCR-abl in CML (the target of Gleevec), the arguments in favor of the use of these analyses is strong.

Non-small cell lung cancer

Non-small cell lung cancer

But what of the NSCLC patients for whom no clear identifiable driver can be found? What of the 25% with k-ras mutations for whom no drug exists? What of those with complex mutational findings? And finally what of those patients whose tumors are driven by normal genes functioning abnormally? In these patients no mutations exists at all. How best do we manage these patients?

I was reminded of this question as I reviewed a genomic analysis reported to one of my colleagues. He had submitted a tissue block to an east coast commercial lab when one of his lung cancer patients relapsed. The results revealed mutations in EGFr L858R & T790M, ERBB4, HGF, JAK2, PTEN, STK11, CCNE1, CDKN2A/B, MYC, MLL2 W2006, NFKB1A, and NKX2-1. With a tumor literally bristling with potential targets, what is a clinician to do? How do we take over a dozen genetically identified targets and turn them into effective treatment strategies? In this instance, too much information can be every bit as paralyzing as too little.

Our preferred approach is to examine the small molecule inhibitors that target each of the identified aberrancies in our laboratory platform. We prefer to drill down to the next level of certainty e.g. cellular function. After all, the presence of a target does not a response make.

In this patient I would conduct a biopsy. This would enable us to examine the drugs and combinations that are active against the targets. A “hit” by the EVA-PCD assay would then isolate the “drivers” from the “passengers” and enable the clinician to intelligently select effective treatments. Combining genomic analyses with functional profiling (phenotypic analyses) provides the opportunity to turn speculative observations into actionable events.

This is the essence of Rational Therapeutics.

Functional Profiling Leads to Identification of Accurate Genomic Findings

The 2013 American Society of Clinical Oncology annual meeting, held May 31 – June 1, in Chicago, afforded the opportunity to report three studies.

Crizotinib (Xalkori) Mechanism of Action

Crizotinib (Xalkori)
Mechanism of Action

The first, “An examination of crizotinib activity in human tumor primary culture micro-spheroids isolated from patients with advanced non-small cell lung cancer,” reports our experience using the EVA-PCD platform to examine the drug crizotinib. This small molecule originally developed as an inhibitor of the oncogenic pathway MET, was later found to be highly active in a subset of cancer patients who carried a novel gene rearrangement for anaplastic lymphoma kinase (ALK). It was this observation that lead to the drug (sold under the name Xalkori) being approved for the treatment of advanced ALK positive lung cancer. The subsequent observation that this same drug inhibited yet another gene target known as ROS-1 found in a subset of lung cancer patients, has led to its use in this patient population.

Our exploration of crizotinib activity identified a series of patients who received the drug and responded dramatically. This included both ALK positive and ROS-1 positive patients. One patient however, appeared highly sensitive to the drug in our studies, but was found negative for the ALK gene rearrangement by genomic analysis. We repeated our functional analysis only to the find again, the same high degree of crizotinib sensitivity. I felt confident the patient should receive crizotinib, but at the time the drug was not yet commercially available and he didn’t qualify for the protocols, as he was ALK negative.

I scoured the country looking for a way to get the patient treated with crizotinib. From Sloan Kettering to UCLA, no one could help. And then, in collaboration with my abstract co-author Ignatius Ou from UC Irvine, we decided to repeat the ALK analysis. That proved to be a very good idea. For the patient was indeed positive for ALK gene rearrangement by second analysis and subsequently responded beautifully to a treatment for which he would not otherwise qualify. Once again, phenotype trumped genotype. (The complete story of this patient can be found in Chapter 19 of Outliving Cancer.)

A final patient in the series represented a particularly interesting application of functional analysis. The patient, a young woman with an extremely rare pediatric sarcoma, had failed to respond to multiple courses of intensive chemotherapy and her family was desperate. As she approached the end of her third year in high school, it looked unlikely that she would reach her senior year. A portion of her tumor was submitted for analysis. The results confirmed relative resistance to chemotherapeutics, many of which she had already received and failed, but showed exquisite sensitivity to crizotinib. Indeed, our inclusion of crizotinib in the analysis reflected our intense effort to identify any activity for this previously refractory patient.

We reported our findings to the pediatric oncologist and encouraged them to consider an ALK rearrangement analysis, despite this particular pathway not being on anyone’s radar prior to our study. The result – a positive gene rearrangement. This led to a successful petition to the drug company for the use of this agent for an off-label indication. The response was prompt and dramatic, and remains durable to this day, nearly a year later. Again, the phenotypic analysis guided us to the correct genomic finding.

Our other presentations at this year’s meetings will be reported in future blogs.

The Molecular Origins of Lung Cancer

I had the luxury of attending the AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer; Biology, Therapy and Personalized Medicine held in San Diego earlier this month. I say luxury, for as my schedule closes in on me and I sometimes find myself working 13-hour days, it can be difficult to take even a couple of days away to attend meetings. But this conference was too good to pass up (hats off to Marge Foti and all the AACR staff for all their great work).

This symposium organized by David Carbone and Roy Herbst, brought together a broad spectrum of sophisticated scientists and international investigators, as well as community members and fundraising organizations who had the opportunity to present a special session on patient advocacy.

The meeting began with a keynote address examining microRNAs and lung cancer presented by Frank Slack from Yale University. He examined the growing recognition that lung cancer arises not only from gene mutations but also from small fragments of RNA that can up- or down-regulate normal genes in abnormal ways. This was the topic of discussion for many subsequent presentations.

As an aside, many of the readers will know that I am generally underwhelmed by genomic analyses for the prediction of cancer response. The fact that normal genes can function abnormally under the control of these small RNA sequences is just one more example of the genotype–phenotype dichotomy that cannot be adequately examined on static contemporary genomic platforms.

Many presentations examined the molecular biology of lung cancer with important distinctions being drawn between adenocarcinoma and squamous cell carcinomas. While adenocarcinomas reveal a growing number of targets – EGFR, ALK, ROS, RAS, and others – all the subject of small molecule inhibitors; squamous cell carcinomas provide fewer opportunities for the use of these classes of drugs.

One of the interesting discussions was the frequent mutation of LKB1 in lung cancers. Work going back several years by John Minna, a pioneer in this field, identified changes in this metabolic regulator as a common finding in lung malignancies.

Additional presentations examined chemoprevention, molecular pathology, new mechanisms to categorize lung cancer subtypes, and a very interesting discussion of field cancerization. In a particularly interesting analysis, Ignacio Wistuba from M.D. Anderson, showed that molecular changes in the surface epithelium of the lung bronchioles recapitulated the molecular biology of the final tumor in a step-wise manner, inversely related to the distance to the tumor. That is, starting at the main bronchi, one or two mutational changes were detected. Moving closer to the site of the tumor, additional mutations were accumulated. Finally arriving at the site of the established malignancy, all of the constituent mutations associated with this particular cancer became manifest; a saltatory slide into cancer presumably associated with exposure to carcinogens.

Among the other exciting presentations were updates on redox-based approaches to cancer presented by Kenneth Tew and Garth Powis.

Jeff Engelman presented an update on a new class of agents that target the RAS pathway. This is ongoing work that he and his group have reported on over the last several years. We have been engaged in related work using an MEK/ERK inhibitor similar to the compound that Dr. Englemen reported on at this meeting. It is exciting indeed to see early clinical results with this class of compounds, for we have identified many patients who might benefit from this pathways’ inhibition. We wait with great anticipation for FDA approval of these compounds so that our patients currently being identified as candidates in the laboratory may soon receive these treatments.