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.

Cancer Patients, Genetic Testing and Clinical Outcomes

Two years ago in this blog, I described a young man with an aggressive non-small cell lung cancer. Following his diagnosis he was screened for EGFR mutation (the target of Erlotinib [Tarceva]) and ALK gene rearrangement (the target of Crizotinib [Xalkori]). Found negative for both, his options were limited to chemotherapy.

When I met the patient, a PleurX catheter had already been inserted to remove fluid that was rapidly re-accumulating in his right chest. This provided access to cancer-laden fluid and offered an excellent opportunity for EVA-PCD® laboratory analysis.

The results showed the expected resistance to Erlotinib (for which no mutation was found) but very high activity for Crizotinib. When he returned for follow-up we repeated a second analysis. The results were identical. One possibility was that the patient carried a second mutation sensitive to this class of drugs, like ROS-1 or MET, both targets of Crizotinib. However, at the time, MET and ROS-1 gene testing was not readily available. I referred the patient to a colleague who was conducting Crizotinib trials. Fluid was re-aspirated and submitted to a different reference lab for genomic analysis. The finding: The original laboratory test had been erroneous. The patient was indeed, ALK gene rearranged.

After a course of chemotherapy, he qualified for and responded beautifully to single-agent Crizotinib. In my blog, I examined how our functional profile more closely approximated the patient’s biology (phenotype) over the genomic profile (genotype). However appealing these genomic tests may be, they can only identify potential targets for therapy that may or may not be relevant to a patient’s ultimate clinical response.

A year later, a female patient with a mucinous adenocarcinoma presented with brain metastases. An EVA-PCD analysis revealed relative chemotherapy resistance and no activity for Erlotinib (Tarceva). She was found EGFR non-mutated. Unfortunately, there was insufficient tissue for the EVA-PCD to test Crizotinib.

During subsequent Cyber-Knife treatment for her brain metastases, a specimen of tumor showed the ALK gene rearrangement and the patient started Crizotinib. She responded promptly.

At the one-year point, signs of progression appeared in the opposite lung, but while she continued to experience good response in the original sites, a repeat biopsy was performed. This time the EVA-PCD functional profile revealed no activity for Crizotinib, but identified activity for the combination of Platinum and Vinorelbine. We combined these two drugs with the Crizotinib and she remained in remission for an additional year. Low blood counts forced us to withhold chemotherapy and her disease progressed. She was referred to a clinical trial with a second-generation ALK inhibitor. By the second month, her disease had progressed rapidly.

Cancerous cells from a bronchoscopic biopsy were submitted for analysis. The finding: No ALK gene mutation. Instead her tumor carried a MET mutation. The patient now rapidly progressing will require immediate therapy, but what?  Fortunately, a small sample of fluid aspirated from the lung provided adequate cells for analysis. The results are striking since they confirm persistent activity for Crizotinib. The patient has now been re-challenged with Crizotinib and we await clinical follow-up.

Taken together, these cases offer interesting insights. The first reflects the medical community’s preternatural faith in genomics. We, as a society, have so completely accepted the accuracy and predictive validity of genetic tests, that no one seems willing to scrutinize the data for its ultimate accuracy. This may not be serving our patients well, as both these cases exemplify. An error that missed the ALK gene re-arrangement in the first patient almost cost this young man his life, despite our protestations. Then, an error in this woman’s analysis serendipitously led to her response to the right drug for the wrong reason, her gene results notwithstanding

We forget at our peril, that all tests are fallible. Clinicians must recognize that highly sophisticated analyses using the most advanced technologies still function within the infinitely complex confines of human biology. The crosstalk, redundancy and promiscuity of human cellular circuitry remain demonstrably more complex than our best artificial neural networks. Genomic analyses and companion diagnostics now dictate who can and who cannot receive drugs, but as can be seen here, these wonders of modern science are not perfect predictors. They have the potential to deprive patients of life-saving treatment while subjecting others to drugs with little chance of benefit. Physicians must remember to be artful as we apply the science of our trade.

The Good, the Bad and the Good

Two years ago, almost to the day, I met a charming gentleman who had been diagnosed the preceding month with metastatic non small cell lung cancer.

The work-up that confirmed his diagnosis also identified an EGFR mutation. This mutation enabled him to receive the targeted agent erlotinib (Tarceva®) as first line therapy and it provided immediate benefit. An incidental finding in his work-up was a meningioma (a benign brain tumor that often arises in the midline of the brain, in an area known as the falx).

Follow up MRI showed no growth of the meningioma. The patient remained on the same therapy for three months at which time his treating physician decided to consolidate him with chemotherapy. The patient’s tolerance could not have been worse: nausea, malaise, fatigue and a 30 pound weight loss. He requested that I assume his care. After careful consideration, I put him right back on what worked in the first place – erlotinib.

With the exception of a few minor toxicities the patient did beautifully. As we approached his restaging with PET/CT and MRI of the brain, scheduled for August 2012 (his two-year point), he presented to a university medical center with disturbing neurological symptoms. An MRI revealed the meningioma to be much larger than originally found two years earlier. Surgery was scheduled for the following day.

The patient and I discussed his situation by phone as he sat in his hospital room awaiting the surgery. If this were a meningioma, it could be removed. However, if this was related to his lung cancer, then there was an opportunity at hand to determine (using the EVA-PCD® platform) whether the cancer was still responsive to erlotinib or had developed mutations that might confer resistance (e.g., T790M). On the one hand, high dose pulse erlotinib can be effective for CNS disease, so long as resistance has not developed. On the other hand, newer classes of drugs that target T7090M might be required.

We needed tissue for testing, so we could create a functional profile of the tumor, and the surgery was 12 hours away. The patient wanted us to do the study. I wanted to do the study. The problem was that I needed to arrange to get tissue to the lab and time was running short.

With an admirable degree of sleuth work, we identified the surgical resident on duty that evening. We explained our need and he proceeded to explain in great detail that this would never happen. Above and beyond the protocols and standards by which he delivered care, he had 45 other patients to cover, as well as consults to conduct. I hung up disappointed that this opportunity would be missed.

The next morning as I finished hospital rounds I noticed a 6:40 a.m missed call on my cell phone. It was from the hospital where the patient was undergoing surgery. I then received a second call from the same number. It was the attending senior surgeon. He was about to scrub in for the scheduled surgery and offered to assist me in any way he could. He explained that they hoped and believed that this was a benign meningioma. If it was, he would remove it and there would be no need for our involvement. An hour later, communicating via speakerphone in the OR, the surgeon explained that this was indeed adenocarcinoma consistent with the patient’s lung cancer diagnosis. He promised to process the tissue carefully, and then provided his cell phone number so we could communicate. I felt a sense of great relief.

While I cannot say what our laboratory tests will find, the story is both educational and inspirational. The patient is an example of a breakthrough in medical science that provided him an excellent and durable response with comparatively little toxicity. That was the good.

The bad reflected the overworked resident’s insouciance. He was busy, it was late and it appeared that we had confused him with someone who cared. After all, there is no payback to perform above-and-beyond-the-call-of-duty medicine. That was sad, for we are now training physicians who are technicians and not healers. They play by the rules and never extend themselves. No one can ding them for doing their job and no one applauds them for doing more.

The really good news was the response of the attending physician. This individual whom I have never met, evidenced an admirable degree of patient advocacy, commitment and compassion. This patient’s good outcome mattered to him and if there was something that I could bring to the table to help this person in need, then he was all there.

We are at a crossroads in medicine. Will we sponsor the healers or promote the technicians? In our laboratory we do everything in our power to provide all the science that we can bring to bear for every patient. The one component that we cannot offer as a service is the art of medicine. That is up to each individual physician.