In Cancer – If It Seems Too Good to Be True, It Probably Is

The panoply of genomic tests that have become available for the selection of chemotherapy drugs and targeted agents continues to grow. Laboratories across the United States are using gene platforms to assess what they believe to be driver mutations and then identify potential treatments.

Among the earliest entrants into the field and one of the largest groups, offers a service that examines patient’s tumors for both traditional chemotherapy and targeted agents. This lab service was aggressively marketed under the claim that it was “evidence-based.” A closer examination of the “evidence” however, revealed tangential references and cell-line data but little if any prospective clinical outcomes and positive and negative predictive accuracies.

I have observed this group over the last several years and have been underwhelmed by the predictive validity of their methodologies. Dazzled by the science however, clinical oncologists began sending samples in droves, incurring high costs for these laboratory services of questionable utility.

In an earlier blog, I had described some of the problems associated with these broad brush genomic analyses. Among the greatest shortcomings are Type 1 errors.  These are the identification of the signals (or analytes) that may not predict a given outcome. They occur as signal-to-noise ratios become increasingly unfavorable when large unsupervised data sets are distilled down to recommendations, without anyone taking the time to prospectively correlate those predictions with patient outcomes.

Few of these companies have actually conducted trials to prove their predictive values. This did not prevent these laboratories from offering their “evidence-based” results.

In April of 2013, the federal government indicted the largest purveyor of these techniques.  While the court case goes forward, it is not surprising that aggressively marketed, yet clinically unsubstantiated methodologies ran afoul of legal standards.

A friend and former professor at Harvard Business School once told me that there are two reasons why start-ups fail.  The first are those companies that “can do it, but can’t sell it.”  The other types are companies that “can sell it, but can’t do it.”  It seems that in the field of cancer molecular biology, companies that can sell it, but can’t do it, are on the march.

Cancer as a Metabolic Disorder

I received an inquiry via Twitter “Has anyone thought about using a sugar medium (similar to PET scans) to deliver chemo drugs?”

Although no one would use PET scans nor the PET reagents as therapy, the question is actually profound. There is a growing recognition that cancer is not a genetic disease but instead a metabolic disorder. One could not attend a lecture at the American Association of Cancer Research without there being reference to Otto Warburg’s 1956 paper “On the Origin of Cancer Cells” that described the metabolic basis of human malignancy.

Despite our myopic focus on cancer genomics, there is a growing recognition that cancer represents dysregulated energy metabolism. The high utilization of glucose, a hallmark of malignantly transformed cells, (and the target of PET scan diagnostics), in part reflects the process of aerobic glycolysis, whereby cells provided ample oxygen nonetheless eschew the efficiency of mitochondrial oxidative phosphorylation in favor of seemingly inefficient lactate production.

Into this new realm of biochemically driven developments, a growing number of therapeutic agents that target glucose metabolism are finding their way into the clinic. To the dismay of some, the mutations that our molecular biologists identify are increasingly found to represent intermediates of cellular metabolism, forcing many to go back to relearn biochemistry. Thus, the avidity for glucose represented by uptake of the PET scan reagent F18 fluorodeoxyglucose by tumor cells, is a diagnostic application of what, in the future, may provide meaningful therapeutic opportunities.

Cancer Medicine – A Humbling Experience

In his brilliant 1998 book, Consilience, Edward O. Wilson, notes: “The cost of scientific advance is the humbling recognition that reality was not constructed to be easily grasped by the human mind.”

This sententious point has remained a guiding principle in my thinking about human cancer. It is critically important for scientific investigators to be humble. We are explorers in a field more complex than any man-made system. We must be instructed by biology – as biological events will always find a way to outsmart our best efforts to explain them.

I was reminded of E.O. Wilson, when a colleague forwarded a recent publication from Molecular Cancer Therapy, “Molecular Profiling of Patient with Colorectal Cancer and Matched Targeted Therapy in Phase I Clinical Trials,” Dienstmann, R. et al MOL CANCER THER Sept 2012. The study conducted by the Molecular Therapeutics Research Unit at Vall d’Hebron Institute of Oncology in Barcelona, Spain, evaluated 254 patients for evidence of specific genetic aberrations. Their genomic analyses included, KRAS, BRAF, PIK3CA, PTEN, and pMET. Patients were then provided clinical therapy trials that matched the targeted agents (drugs with activity against the specific mutation) with their individual mutation profiles

In all, 68 patients received treatment constituting a total of 82 different molecularly targeted therapies. The clinical response rate for this population of patients who received molecularly selected therapy was 1.2%. No that isn’t a typo; it was really one point two percent.

While I applaud the scientific concept of this trial and must admit that I might have expected a somewhat higher response rate, I am not surprised by the result. In keeping with E. O. Wilson’s quote, human biology is not a puzzle designed to be solved by humans; it is instead the complex product of a billion years of evolution. Rather than demanding that cancer patients respond to those treatments we have selected for them based on genetic information, we should be instructed by the tumor’s behavior of each patient and use those insights to select amongst active drugs, whatever genetic elements they may have been originally designed to target. In my lectures, I describe this approach as the wisdom of whole cell experimental models.

I am continually humbled by the complexity of human tumor biology and delighted to have the insights that my patient’s cancer cells provide through the functional profile created by our EVA-PCD assay. Not only do I gain exciting scientific knowledge, but my patients have very good responses to the drugs we select. Not a bad day’s work.

Stalking Leukemia Genes One Whole Genome at a Time

An article by Gina Kolata on the front page of the July 8, Sunday New York Times, “In Leukemia Treatment, Glimpses of the Future,” tells the heartwarming story of a young physician afflicted with acute lymphoblastic leukemia. Diagnosed in medical school, the patient initially achieved a complete remission, only to suffer a recurrence that led him to undergo a bone marrow transplant. When the disease recurred a second time years later, his options were more limited.

As a researcher at Washington University himself, this young physician had access to the most sophisticated genomic analyses in the world. His colleagues and a team of investigators put all 26 of the University’s gene sequencing machines to work around the clock to complete a whole genome sequence, in search of a driver mutation. The results identified FLT3. This mutation had previously been described in acute leukemia and is known to be a target for several available small molecule tyrosine kinase inhibitors. After arranging to procure sunitinib (Sutent, Pfizer Pharmaceuticals), the patient began treatment and had a prompt and complete remission, one that he continues to enjoy to this day.

The story is one of triumph over adversity and exemplifies genomic analysis in the identification of targets for therapy. What it also represents is a labor-intensive, costly, and largely unavailable approach to cancer management. While good outcomes in leukemia have been the subject of many reports, imatinib for CML among them, this does not obtain for most of the common, solid tumors that lack targets for these new silver bullets. Indeed, the article itself describes unsuccessful efforts on the part of Steve Jobs and Christopher Hitchens, to probe their own genomes for effective treatments. More to the point, few patients have access to 26 gene-sequencing machines capable of identifying genomic targets. A professor of bioethics from the University of Washington, Wiley Burke, raised additional ethical questions surrounding the availability of these approaches only to the most connected and wealthiest of individuals.

While brute force sequencing of human genomes are becoming more popular, the approach lacks scientific elegance. Pattern recognition yielding clues, almost by accident, relegates scientists to the role of spectator and removes them from hypothesis-driven investigation that characterized centuries of successful research.

The drug sunitinib is known for its inhibitory effect upon VEGF 1, 2 and 3, PDGFr, c-kit and FLT3. Recognizing the attributes of this drug and being well aware of C-KIT and FLT3’s role in leukemias, we regularly add sunitinib into our leukemia tissue cultures to test for cytotoxic effects in malignantly transformed cells.  The insights gained enable us to simply and quickly gauge the likelihood of efficacy in patients for drugs like sunitinib.

Once again we find that expensive, difficult tests seem preferable to inexpensive, simple ones. While the technocrats at the helm of oncology research promise to drive the price of these tests down to a level of affordability, everyday we wait 1,581 Americans die of cancer. Perhaps, while we await perfect tests that might work tomorrow, we should use good tests that work today.

What is Personalized Cancer Therapy?

Personalized therapy is the right treatment, at the right dose for the right patient. Like the weather, however, it seems that everyone’s talking about it, but no one is doing anything about it.

In its simplest form personalized care is treatment that is designed to meet an individual’s unique biological features. Like a key in a lock, the right drug or combination opens the door to a good outcome.

When over the years I lectured on the development of the cisplatin/gemcitabine doublet, my two boys were quite young. I would show a slide depicting a doorknob with a key in the keyhole. I likened our lab’s capacity to identify sensitivity to the cisplatin/gemcitabine combination as “unlocking” an individual’s response.

At the time my wife and I would leave the key in the inside of the front door enabling us to unlock it when going out. We reasoned at the time that our 2-year-old would not be strong enough, nor tall enough to turn the key and let himself outside.  We reasoned wrong, for one day our son Alex reached up, turned the key and opened the door right in front of us. Lesson learned: Given the right key, anyone can open a door.

I continued my analogy by saying that even Arnold Schwarzenegger would be unable to open a door given the wrong key, but might, if he continued trying, snap it off in the lock.

The right key is the right treatment, effortlessly unlocking a good response, while the wrong key is the wrong treatment more often than not too much, too late, akin to a solid tumor bone marrow transplant.

In recent years, personalized care has come to be considered synonymous with genomic profiling. While we applaud breakthroughs in human genomics today, there is no molecular platform that can match patients to treatments.  The objective response rate of just 10 percent, almost all in breast and ovarian cancer patients in one study (Von Hoff J Clin Oncol 2010 Nov 20:28(33): 4877-83), suggests that cancer biology is demonstrably more complex than an enumeration of its constituent DNA base pairs. The unilateral focus on this area of investigation over others might be described as “the triumph of hope over experience” (James Boswell, Life of Samuel Johnson, 1791).

But hope springs eternal and with it the very real possibility of improving our patients outcomes. By accepting, even embracing, the complexity of human tumor biology we are at the crossroads of a new future in cancer medicine.

William Withering (1741-1799) the English physician and botanist credited with discovering digitalis as the therapy for dropsy, e.g. congestive heart failure (An Account of the Foxglove and some of its Medical Uses, Withering W. 1785), had absolutely no idea what a membrane ATPase was, when he made his remarkable discovery. It didn’t matter. Cardiac glycosides provided lifesaving relief to those who suffered from this malady for fully two centuries before Danish scientist, Jens Christian Skou, identified these membrane bound enzymes, for which he was awarded a Nobel Prize in 1997.

Similarly, penicillin, aspirin, and morphine were in all use for decades, centuries, even millenia before their actual modes of action were unraveled. Medical doctors must use any and all resources at their disposal to meet the needs of their patients. They do not need to know “how” something works so much as they (and their patients) need to know “that” it works.

The guiding principle of personalized medicine is to match patients to therapies. Nowhere in this directive is there a prescription of the specific platform to be used. Where genomic signatures provide useful insights for drug selection, as they do in APL (ATRA, Arsenic trioxide); NSCLC (EGFr, ROS1, ALK); CML (Imatinib, Dasatanib) then they should be used.

However, in those disease where we haven’t the luxury of known targets or established pathways, i.e. most human malignancies, then more global assessments of human tumor biology should, indeed must, be used if we are to meet the needs of our patients.  Primary culture analyses like the EVA/PCD® provide a window onto human tumor biology. They are vehicles for therapy improvement and conduits for drug discovery.  Scientists and clinicians alike need to apply any and all available methodologies to advance their art. The dawn of personalized medicine will indeed be bright if we use all the arrows in our quiver to advance clinical therapeutics and basic research.

What Exactly are the Targets of Targeted Therapy?

The term “targeted therapy” has entered common parlance. Like personalized medicine, targeted therapy is a generic description of drugs and combinations that inhibit specific cancer-related pathways. I am impressed by how quickly esoteric phenomena like the downstream signal in the insulin factor pathway have entered the lexicon of medical oncologists. With the advent of temsirolimus and everolimus, both rapamycin derivatives that target mTOR, we now have at our disposal agents that are every bit a part of the therapy repertoire. Unlike erlotinib that targets a specific tyrosine kinase, mTOR is a complex and multifaceted target.

There are actually two separate forms of mTOR, TORC1 and TORC2, and they sit at a critical point in cellular determination. Stimulated by the insulin growth pathway, cells must decide whether they will grow in size or divide. The mTOR proteins participate in this process by regulating protein synthesis and glucose uptake among other functions. In turn, the mTOR pathway is regulated by numerous other factors like AMP kinase and AKT. The current crop of mTOR inhibitors all target TORC1.

New classes of compounds are being developed that inhibit both TORC1 and TORC2. More interesting are the compounds that influence upstream signaling, including phosphoinositol kinase (PI3K) and AKT. What we are coming to learn, however, is that these are not targets but collections of targets. Indeed, the PI3K inhibitors themselves have influence on one, two or all of the distinct classes of phosphoinositol kinases.

Most of the studies to date have used compounds that affect all the classes equally (pan-inhibitors). Pharmaceutical companies are now developing highly selective inhibitors of this fundamental pathway. In addition, duel inhibitors that target both PI3K and mTOR are in clinical trials. What we are coming to realize is the complexity of these pathways. What may prove more vexing still is their redundancy. One well-established by-product of successful inhibition of mTOR (principally TORC1) is the upstream activity of AKT via a feedback loop. This has the undesirable affect of redoubling mTOR stimulation through the very pharmacological manipulation that was designed to inhibit it. Again, an unintended consequence of a well laid plan.

To unravel the complexities and redundancies of these processes, we have utilized the primary culture platform. It enables us to examine the end result of signal inhibition and dissect disease specific profiles. Using this approach we can partner with collaborators to define the specific operative pathways in each disease entity.

Biological complexity is the hallmark of life. We ignore it at our peril.

Targeted Therapies for Cancer Confronts Hurdles

The September 1 issue of the ASCO Post, a periodical published by the American Society of Clinical Oncology, features an article entitled “Research in Combining Targeted Agents Faces Numerous Challenges.” Contributors to the article by Margo J. Fromer, participated in a conference sponsored by the Institute of Medicine. These scientists representing both public and private institutions examined the obstacles that confront researchers in their efforts to develop effective combinations of targeted agents.

One of the participants, Jane Perlmutter, PhD, of the Gemini Group, pointed out that advances in genomics have provided sophisticated target therapies, but noted, “cellular pathways contain redundancies that can be activated in response to inhibition of one or another pathway, thus promoting emergence of resistant cells and clinical relapse.”

James Doroshow, MD, deputy director for clinical and translational research at the NCI, said, “the mechanism of actions for a growing number of targeted agents that are available for trials, are not completely understood.” He went on to say that the “lack of the right assays or imaging tools means inability to assess the target effect of many agents.” He added that “we need to investigate the molecular effects . . .  in surrogate tissues,” and concluded “this is a huge undertaking.”

Michael T. Barrett, PhD, of TGen,  pointed out that “each patient’s cancer could require it’s own specific therapy.” This was followed by Kurt Bachman of GlaxoSmithKline, who opined, “the challenge is to identify the tumor types most likely to respond, to find biomarkers that predict response, and to define the relationship of the predictors to biology of the inhibitors.”

When I read this article I dashed to my phone and waited breathlessly for these august investigators to contact me for guidance. It was obvious that they were describing precisely the work that my colleagues and I have been doing for the past two decades. Obviously, there had been an epiphany. The complexities and redundancies of human tumor biology had finally dawned on these investigators, who had previously clung unwaiveringly to their analyte-based molecular platforms.

Eureka! Our day of vindication was at hand. The molecular biologists humbled by the manifest complexity of human tumor biology had finally recognized that they were outgunned and would, no doubt, be contacting me presently. Whole-cell experimental models had gained the hegemony they so rightly deserved. The NCI and big pharma would be beating a path to my door.

But the call never came. Perhaps they lost my number. Yes, that must be it. So let me provide it: 562.989.6455. Remember I’m on Pacific Daylight Time.

Can PARP Inhibitors be Tested Using the EVA-PCD Assay?

Poly ADP ribose polymerase (PARP) is a nuclear enzyme associated with response to DNA damage. Following single strand DNA breaks, the enzyme attaches a backbone of ADP and ribose that serves to initiate DNA repair. Certain classes of chemotherapeutics, specifically alkylating agents, can induce injury that results in extensive poly ADP ribosylation resulting in the exhaustion of intercellular pools of NAD and ATP ultimately leading to cell death.

Although PARP inhibitors have recently entered the clinical cancer literature mostly relating to the treatment of BRCA+ and triple negative patients, neither PARP nor PARP inhibitors are new to the cancer researcher community.

Our group first became interested following a 1988 study by Distelhorst from Case Western Reserve (Distelhorst CW, Blood 1988 Oct;72(4):1305-09) that described a mechanism of cell death that correlated with our work in childhood leukemia. Previously, investigators at Scripps Clinic had described PARP’s role in response to 2CDA (Seto, S., et al. J Clin. Invest. 1985 Feb;75(2):377-83). We have studied small molecule inhibitors of PARP for many years, and more recently, we have expanded these investigations to include BSI201 (iniparib) and AZD2281 (olaparib). Both of which are undergoing clinical investigations. We will be reporting our findings with these PARP inhibitors at the 2011 ASCO meeting (Nagourney, R., et al Proceedings Amer Soc Clin Oncol. 2011).

PARP inhibitors are easily studied and provide interesting signals in the tissue studied. We see activity in BRCA+ patients and some triple negative breast cancers. We have also identified synergy with other classes of drugs. The compounds are a welcome addition to our cancer therapy armamentarium and continue to be actively studied in the EVA-PCD platform.

Of interest is the recent failure of the iniparib plus Carboplatin & gemcitabine Phase III trial to meet progression-free and overall survival goals in triple negative breast cancer patients (Zacks Investment Research on January 31, 2011). This failure may reflect the need to apply predictive methodologies to select candidates for these drugs, similar to our successful work with other classes of compounds.

American Association of Cancer Research (AACR) Meeting 2011

The Sunday, April 3, 2011, experimental and molecular therapeutics session at the AACR 102nd annual meeting included our presentation on signal transduction inhibitors. Using MEK/ERK and PI3K-MTOR inhibitors we explored the activities, synergies and possible clinical utilities of these novel compounds.

The findings were instructive. First, we saw a good signal for both compounds utilizing the Ex-vivo Analysis of Programmed Cell Death (EVA-PCD) platform. Second, we saw disease-specific activity for both compounds. For the MEK/ERK inhibitor, melanoma appeared to be a favored clinical target. This is highly consistent with our expectation. After all, many melanomas carry mutations in the BRAF gene, and BRAF signals downstream to MEK/ERK. By blocking MEK/ERK, it appeared that we blocked a pathway fundamental to melanoma progression. Indeed, MEK/ERK inhibitors are currently under investigation for melanoma.

For PI3K inhibitors, the highest activity was observed in uterine cancers. This is interest, because uterine carcinomas are often associated with a mutation in the PTEN gene. PTEN is a phosphatase tumor suppressor that functions to block activation of the PI3K pathway. Thus, mutations in the tumor suppressor unleash PI3K signaling, driving tumors to grow and metastasize. Blocking PI3K provided a strong signal, indicating that this approach may be very active in tumors associated with these oncogenic events.

The third point of interest in our report was, perhaps, its most important. Specifically, that we can explore those diseases where MEK-ERK, PI3K and mTOR signaling are less established targets. Cancers of the lung, ovary, colon or breast all manifested profiles of interest. When we combined both pathway inhibitors in a process we call horizontal inhibition, renal cell carcinoma popped up as the best target. These results, though exploratory, suggest a superior approach for drug development, allowing us to identify important leads much faster than the clinical trial process.

Are New Cancer Drugs Always Better?

Few cancers instill a greater sense of fear in the medical oncologist that metastatic renal cell carcinoma, the most common form of which is known as clear cell cancer. This type of kidney cancer — driven by a mutation in a gene know as VHL — spreads rapidly, metastasizes to almost any and all organs and historically responded to almost no therapies. The development of Interleukin-2 (IL-2) in the 1980s offered a glimmer of hope. Yet, even this breakthrough ultimately yielded complete and durable responses in a mere 10 percent of patients.

By focusing on the hyper-vascular nature of this disease, investigators then developed a second line of defense that attacked the blood supply of these cancers. Following the introduction of Avastin, a number of small molecule VEGF inhibitors were introduced. Most recently, a class of drugs known as mTOR inhibitors gained popularity by providing objective responses and showing evidence of improved survival.

But what happens when all the really “hot new drugs” fail to provide benefit?

This was a question I confronted in a charming, 68-year-old neurologist who traveled to visit me from Stanford University where he received highly appropriate, yet unfortunately ineffective therapy. The patient presented in July 2010 with rapidly progressive kidney cancer that had overtaken his lungs. He was started on oral Sutent (the treatment of choice). His management was complicated by a hemolytic anemia. When I met the patient in October, I was concerned that he could not survive long enough to take on another treatment, no matter how effective it might ultimately prove to be.

As a physician, he beseeched me to study his tumor in the hope of finding any therapy to salvage him from his rapidly deteriorating course. A small biopsy was obtained with the help of one of our surgical colleagues. The results were striking — no evidence of activity for sorafenib, sunitinib (Sutent), nor the Rapalogs (Rapamycin derivatives). In one fell swoop, all of the newest therapies were swept aside with little likelihood of benefit. Despite the established literature, this patient was clearly sensitive to chemotherapeutics. It was evident to me that the treatment outline, a combination of three drugs, could provide meaningful clinical benefit if the patient could tolerate even the most modest associated side effects. With the kind cooperation of the treating physician in Northern California, our recipe was followed to a T.

The treating oncologist pulled no punches in his description of this patient’s prognosis. Nonetheless, he kindly assisted in the management of the treatment we described. While the cancer-related hemolytic anemia raged, and the patient fought for air, the treatments were delivered. Too ill to leave the hospital, his entire first course of therapy was delivered on an inpatient basis.

For several weeks, we anticipated the worst. And then, a phone call from a chipper-sounding patient. Breathing comfortable, his chest x-ray had cleared, his anemia had resolved and he was being readied for discharge. A short time later, an abdominal ultrasound revealed measurable improvement in the kidney cancer, further confirming objective response.

The patient, now home, could not be happier. The excellent outcome is as gratifying as it is unexpected. There is no question that no one else would have given this treatment. And there is further no question that the patient would not be alive today had he not received it. There are many lessons to be learned from this experience. Among them, that every patient deserves the opportunity to get better; that laboratory analyses can identify unexpected options for patients, even with the worst malignancies; that new drugs aren’t always better drugs; and finally, that nothing succeeds like success.