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.