The Human Micro Biome

There is a growing recognition that we as a species, humans that is, are not a single organism but a community of organisms living in synchrony. As scientists have recognized for many years, the human gut, skin, and digestive tract are colonized by trillions of bacteria, fungi and other microbes. What we did not realize until recently, was how important these organisms are to our health and well-being

The microenvironment of the human gastrointestinal tract reflects the interplay between bacteria, our diet, intestinal digestive enzymes, lipids, polysaccharides, amino acids, and the by-products of metabolism. The specific make-up of each individual reflects their environment, diet, and family heritage. Indeed, our bacterial flora are transmitted to us by our mothers, who prior to the advent of pasteurized baby-foods, pre-chewed their infant’s food.

More to the point, we now realize that bacterial infections and exposures to foreign antigens early in life protect and prepare us for a healthy adult life. Many modern maladies, such as asthma, diabetes, hypertension, even possibly autism and schizophrenia, may reflect infections, immune responses and the timing thereof. It has been suggested that infections with parasites modulate our immune response. In our increasingly clean environment, devoid of hookworms, tapeworms, and the like, our overactive immune system creates autoimmunity in the form of rheumatoid arthritis, systemic lupus and other maladies.

This reflects the growing recognition that human biology is in fact human ecology. The importance of this cannot be overstated when we examine human tumor biology. We are continually bombarded by the teachings of a cadre of scientists who believe whole heartedly that they can answer the puzzle of human cancer by examining the intricacies of individual human cancer cells, primarily at the level of DNA.  Nothing could be further from the truth.

Take for example just one of the myriad of signaling pathways. Beta catenin is among the most potent tumor promoters. The deranged function of beta-catenin has been identified in several human tumors including prostate, lung and colon. Its closest association being that with colon cancer, wherein the loss of the APC protein (adenomatous polyposis coli), results in a particularly aggressive form of the disease.  The APC protein normally combines with axin and glycogen synthase kinase 3 beta (GSK3B) which all together function to regulate beta-catenin. It is the loss of APC that releases Beta-catenin and drives polyps to become cancerous.

However, upstream of this triumvirate of regulatory proteins are the integrin-ca cadherin proteins that communicate across the cell membrane. By changing the environment of the colon itself, we can influence the integrins, which regulate the cadherins. This in turn regulates beta catenin.  Thus, colon cancer may not arise from changes in our genetic makeup but instead may be driven by micro-environmental changes in the colonic milieu that alter cellular behavior and drive malignant transformation.

Again and again, we are forced to recognize the complexity of human biology. Now we realize that it is not just the genome to the transcriptome to the proteome, but indeed the micro biome.

Tumor Ecology, Not Tumor Biology

During the first years of this millennium as the newly discovered field of anti-angiogenesis was reaching a fevered pitch, I had the opportunity to attend an AACR Special Symposium, held at Whistler Resort in British Columbia. While there I attended a symposium by Dr. Rakesh Jain. Dr. Jain a long-time colleague of Judah Folkman, MD,  at Harvard University presented his observations on tumor vascularity and its implications for therapy. Despite the prevailing belief that tumor angiogenesis was a linear phenomenon, from cessation of blood supply – and thereby nutrients and oxygen – to the death of cancer, Dr. Jain provided compelling evidence to the contrary.

Every so often I read an article, hear a lecture, or attend a symposium that changes the way I think. Dr. Jain’s presentation that year was just that type of lecture. In the span of an hour he described the dynamics of blood flow through the network of disorganized tumor blood vessels. He showed that anti-angiogenic factors actually “pruned” the blood supply and returned normal flow. He went on to point out that most of the experiments being reported at that time by other investigators had short windows of observation during which the effects of Bevacizumab could be captured, photomicrographed and published to great acclaim in the most prestigious journals. But there was a fly in the ointment. Bevacizumab by itself had a miniscule response rate. Indeed, in the absence of chemotherapy, it was single digits.

Jain, an engineer by training, developed a novel tissue “window” method that enabled him to explore the temporal sequence of cellular response to VEGF therapy. He found that it all wasn’t as simple or tidy as it had seemed. The short-term control of vasculature was followed by revascularization. Cells deprived of oxygen and nutrients devolved into more stem cell-like phenotypes. Therapies based on an incomplete understanding of angiogenesis might, in his opinion, be adding to the problem.

As the years have gone on I’ve carried the insights from that lecture with me. At a subsequent AACR presentation by Napoleon Ferrara, PhD, many years later, Dr. Ferrara, who developed Bevacizumab, reminded his audience that VEGF was originally known as VPF (vascular permeability factor). Perhaps this aspect of the VEGF effects were responsible for its minimal single agent activity, yet profound combinatorial effect.

With this as a backdrop, I sat among 15,000 medical oncologists at the plenary session lecture where Dr Jain presented his work and I delighted in the possibility (however slight) that his message of experimental analysis and systems biology would sink in.

Cancer is not a cell, it is a system. Tumor cells are but a small portion of the process. Carcinogenesis may represent a response to cellular stress, some of which, we as “therapists” may inflict. The indiscriminate use of cytotoxic agents and antivascular drugs may, in some circumstances, be more harmful than helpful to our patients.

What is the appropriate dose of Bevacizumab? How should it be given? In what sequence with radiation or chemotherapy? With what drugs or targeted agents? Are low doses better than high doses? Is the effect of VGEF inhibition a driver of response or an epiphenomenon? What about the fibroblast matrix, lymphatic vessels, infiltrating monocytes, T-cells, B-cells and neutrophils? Dr. Jain elegantly outlined the complexities of the human tumor microenvironment.

It was with more than a small amount of satisfaction, that I realized how quite correct our approach to this disease has been over the years. It is not just the cancer cell that is important, but the tumor as a whole. Cancer cells are just part of the problem. Using native state microspheroids replete with vasculature, cytokines, stromal elements and tumor cells; we feel that we are now poised to advance the growing use of effective targeted therapies in ever-expanding ways.

Venture Capital Goes Genomic

During the 1960s, 70s and into the 90s, a field of investigation arose that examined buyer’s practices when it came to the consumption of goods and services. Algorithms were developed to interrogate consumer choice. One such treatise was reported in 1994 (Carson, RT et al, Experimental Analysis of Choice, Marketing Letters 1994). What these researchers explored were the motivations and forces that drove consumption. When choices are offered, decisions are driven by such factors as complexity and utility. Complexity demands personal expertise or failing that, input from experts, while utility places a value on the good or service.

A recent report from a small biotechnology company called Foundation Medicine has brought this field of endeavor to mind. It seems that this group will be offering DNA sequencing to select chemotherapy drugs. This service, currently priced at $5,800, will focus upon a small cassette of genes that they described as “key” in tumor growth. Based on their technology they have already raised $33.5 million from the likes of Third Rock, Google and Kleiner Perkins Caulfield & Byers, venture capital sources. The CEO of Foundation substantiates the approach by pointing out that fully 150 people have already used their services. One hundred and fifty!

It seems from this report that our colleagues in the field of molecular profiling have studied the dictates of “Experimental Analysis of Choice” to a “T.” What we have is the perfect storm of medical marketing.

First, the technology is so complex as to be beyond the ken of both patients and physicians alike. Thus, expertise is required and that expertise is provided by those engaged in the field. Second, the utility of drug selection is beyond reproach. Who in their right mind wouldn’t want to receive a drug with a higher likelihood of a response when we consider the toxicities and costs, as well as the consequences of the wrong treatment? Dazzled by the prospect of curative outcomes, patients will, no doubt, be lining up around the block.

But, let’s deconstruct what this report is actually telling us. First, a scientifically interesting technology has been brought to the market. Second, it exists to meet an unmet need. So far, so good. What is lacking, however, is evidence. Not necessarily evidence in the rarefied Cochrane sense of idealized survival curves, nor even Level II evidence, but any evidence at all. Like whirling dervishes, patients and their physicians are drawn into a trancelike state, when terms like NextGen sequencing, SNP analysis and splice variants are bandied about.

Despite the enthusiastic reception by investors, I fear a lack of competent due diligence. To wit, a recent article in Biotechniques, “Will the Real Cancer Cell Please Stand Up,” comes to mind. It seems that cancer cells are not individual entities but networks. A harmonic oscillation develops between tumor, stroma, vasculature and cytokines. In this mix, the cancer cell is but one piece of the puzzle.

Indeed, according to recent work from Baylor, some of the tumor promotion signals in the form of small interfering RNAs, may arise not from the cancer cells, but instead from the surrounding stroma. How then, will even the most punctiliously perfect genomic analyses of a cancer cells play out in the real world of human tumor biology and clinical response prediction? Not very well I fear. But then again such a discussion would require data on the predictive validity of the method, something that appears to be sorely lacking.

Will today’s gene profile companies prove to be the biotech Facebook IPOs of tomorrow?

No One is More Interested in Curing Your Cancer Than You

A diagnosis of cancer thrusts a, heretofore, healthy individual into the strange and unfamiliar territory of medical oncology. Many of my patients describe this transition as “entering the cancer bubble.” Suddenly, you are on the inside and everyone on the outside is talking at you about what to do, where to go, whom to see, and what treatments to receive.

From the inside of the bubble however, all of this has a hollow ring as you ponder many options, few good and some, positively frightening. Unfortunately, few patients have the time to complete a MD, or PhD, between diagnosis and the initiation of treatment. Lacking the requisite expertise, they turn to the “authorities” for advice.

Depending on which “authority” one consults, the recommendations may be colored by prejudices and biases. Some physicians adhere strictly to the National Comprehensive Cancer Network guidelines. Others insist upon accrual to Cooperative Group and Phase II trials. University-based investigators will often recommend developmental studies. And some physicians will follow the path of least resistance, examining such issues as cost, chair time and reimbursement, before considering what treatment to deliver.

It is in this milieu, that patients find themselves adrift. Who exactly should you trust? What is their motivation? To put it crassly, when they recommend a specific treatment, what’s in it for them: Cooperative Group points (provided to the most active accruers), academic accolades (the currency of junior faculty), cost containment (the purview of the managed care physicians), or finally, profit margins? Yes, there are a small number of physicians whose choices reflect their own pecuniary interests.

The antidote to all this uncertainty lies within each patient; answers to vexing questions crying out to be heard. These answers reflect the biologic features of each individual’s tumor. What pathway, what repair mechanism, what survival signal drives your tumor? No one has a perfect answer, not the genomic investigators (despite their protestations to the contrary), nor the immunohistochemists, despite the significant appeal of the platform. And not the immunologist (despite brilliant progress in this field over recent years). The closest approximation to human tumor biology is, well, human tumor biology. Using cellular constructs, in the form of native state microspheroids, we can today approximate the response profiles of patients undergoing systemic therapies. Using systems approaches to complex questions, the multitude of factors that contribute to objective response can be examined and elucidated.

No test is perfect. No patient is guaranteed a good outcome. Yet, doubling the objective response rate, and as we and others have documented, improving the time to progression and overall survival can be achieved with available methodologies that apply functional profiling to individual tumors.

No one would walk away from an investment formula that doubled the value of their portfolio. Few would turn down the opportunity to enhance their real estate positions predicated on reliable information from a realtor. Yet everyday, physicians convince patients to walk away from available, published, established methods that can improve response rates, diminish toxicities and avoid futile care. In this environment it is critical for patients to take charge of their own cancer management. Patients must not be dissuaded from seeking the best possible outcomes. Physicians, no matter how well intentioned, are human. Their opinions can be colored by misconceptions and an incomplete understanding of the questions at hand. Laboratory analysis empowers patients to make smart decisions.

In the game of cancer we need all the help we can get. After all, no one is more interested in saving your life than you.

Gee (G719X) Whiz: Novel Mutations and Response to Targeted Therapies

In a recent online forum a patient described her experience using Tarceva as a therapy for an EGFR mutation negative lung cancer. For those of you familiar with the literature you will know that Lynch and Paez both described the sensitizing mutations that allow patients with certain adenocarcinoma to respond beautifully to the small molecule inhibitors.  The majority of these mutations are found in Exon 19 and Exon 21, within the EGFR domain. Response rates for the EGFR-TKI (gefitinib and erlotinib) clearly favor mutation positive patients. Depending upon the study, mutation positive patients have response rates from 53 – 100 percent, generally around 70 percent, while mutation negative response patients have a response rate of 0 – 25 percent, generally about 10 percent.So why don’t all the mutation positive patients respond and conversely why do some mutation negative patients respond?

The story outlined in this online forum gives some insight. The individual in question carried a rare, and only recently recognized, Exon 18 mutation known as a G719X. This uncommon form of mutation had previously been unknown and few laboratories knew to test for it. Nonetheless, G719X positive patients respond to erlotinib and related agents. Indeed, there may be reason to believe that the more potent irreversible EGFR/HER2 dual inhibitor HKI-272, may be even more selective for this point mutation.

The excellent and durable response described by this individual, would not have been possible had the patient’s first physician followed the rules. That is, had her physician refused to give erlotinib to an (putatively) EGFR mutation negative patient she might well not be here to tell her story. More to the point, her good response (a clinical observation) led to the next level of investigation, namely the identification of this specific EGFR variant

The lessons from this experience are numerous. The first is that cancer biology is complex and, to paraphrase E.O. Wilson, was not put on earth for us to necessarily figure it out. The second, is that molecular biologists can only seek and identify that which they know about apriori.  To wit, if you don’t know about it (G719X) and you don’t have a test for it, and you don’t know to look for it, then it’s a virtual certainty that you aren’t going to find it.

The premise of our work at Rational Therapeutics is that the observation of a biological signal identifies a candidate for therapy whether we understand or recognize the target. Crizotinib was originally developed as a clinical therapy for patients who carried the CMET mutation. Serendipity led to the recognition that the responding subpopulation was actually carrying a heretofore-unrecognized ALK gene rearrangement. Sorafenib was originally evaluated for the treatment of BRAF mutation positive diseases. Yet it was the drug’s cross-reactivity with the VGEF tyrosine kinases that lead to its broad clinical applications. Each of these phenomena represents accidental successes. Were it not for the clinical observation of response in patients, the investigators conducting these trials would have been unlikely to make the discoveries that today provide such good clinical responses in others.

To put it quite simply, these patients and their disease entities educated the molecular biologists.

When we first identified lung cancer as a target for gefitinib, and began to administer the closely related erlotinib to lung cancer patients, neither Lynch nor Paez had identified the sensitizing EGFR mutations. That had absolutely no impact upon the excellent responses that we observed. It didn’t matter why it worked, but that it worked.  While the EGFR story has now been well-described, might we not use functional analytical platforms (functional profiling) to gain insights into the next, and the next generation of drugs and therapies that target pathways like MEK, ERK, SHH, FGFR, PI3K, etc., etc., etc. . . .

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.

Cancer Research Becomes “Curiouser and Curiouser”

Following the Gina Kolata New York Times article on July 8, 2011, which described the failure of the Duke University gene profile program in lung cancer, a second New York Times article popped up on the radar screen.  “Cancer’s Secrets Come into Sharper Focus” by George Johnson, examined the growing complexity of cancer research.

This article explored the growing realization that human biology is not linear. Included were references to work that we have previously described in this blog, including the groundbreaking work of Pier Paolo Pandolfi. It also described the interaction between the human body and its microbial flora. We have long recognized that human health is, in part, associated with our interaction with microbes in our environment. The gastrointestinal tract has numerous species that are increasingly believed to contribute to our health. The growing field of probiotics, wherein people consume “healthy organisms,” has gone from quackery to community standard in less than a decade.

What is interesting over the past years is the growing recognition that many cancers are related to infections. Viral infections are known to be oncogenic, with the Epstein-Barr virus, HPV and other viruses now known to be causative of lymphomas, cervical, head and neck, and other cancers. The association between helicobacter and ulcers, gastric lymphoma, and esophageal malignancies are of interest both epidemiologically and therapeutically.

What is most interesting of all is the growing recognition that the cancer cell is but a small component of the cancer.

Here at Rational Therapeutics we recognized the interplay between cells, stroma, vascular elements, cytokines, macrophages, lymphocytes and other environmental factors. This lead to our focus on the human tumor primary culture microspheroid, which contains all of these elements. In our earlier work, we endeavored to isolate tumor cells from their benign constituents so as to study “pure” tumor cells. As time went on, however, we found that these disaggregated cells were artificially sensitized to the effects of chemotherapy and provided false positive results in vitro.

Early work by Beverly Teicher and Robert Kerbel that examined cells alone and in 3-dimensional structures, lead to the realization that cancer cells inhabit a microenvironment. Our lab now studies cancer response to drugs within this microenvironment, enabling us to provide clinically relevant predictions to our patients.

It is our capacity to study human tumor microenvironments that distinguishes us from other platforms in the field. And, it is this capacity that enables us to conduct discovery work on the most sophisticated classes of compounds that influence cell signaling at the level of notch, hedgehog and WNT, among other (Gonsalves, F, et al. (2011). An RNAi-based chemical genetic screen identifies three small-molecule inhibitors of WNT/wingless signaling pathway. PNAS vol. 108, no. 15, pp. 5954-5963).  With this clinically validated platform we are now positioned to streamline drug development and advance experimental therapeutics.

The TEDx Experience

On Saturday July 16, I had the opportunity to present at the TEDxSoCal conference held here in Long Beach. The overall theme for this event was “thriving,” and appropriately, I presented in the afternoon session called, “well-being.” My lecture was entitled “The Future of Cancer Research Lies Behind Us.”

I chose this topic in light of the growing recognition that genomic analyses are not providing the therapeutic insights that our patients so desperately need. As I have written before in this blog, the Duke University lung cancer gene program, which has received much attention recently, is emblematic of the hubris associated with contemporary genomic analytic platforms.

I reviewed the contemporary experience in clinical trials, examined the potential pitfalls of gene-based analysis, and described the brilliant work conducted by biochemists and cell biologists, like Hans Krebs and Otto Warburg, who published their seminal observations decades before the discovery of the double helix structure of DNA.

I described insights gained using our ex-vivo analytic platform, that lead to treatments used today around the world, all of which were initially discovered using cell-based studies. More interesting still will be the opportunity to use these platforms to explore the next generation of cancer therapies – those treatments that influence the cell at its most fundamental level – its metabolism.

Many attendees stopped me after my lecture to thank and congratulate me for my presentation. Fearing that my topic might have been too esoteric, I was delighted by the reception and more convinced than ever that there are many enlightened individuals who thirst for new approaches to cancer treatment. It is these people who will forge the next generation of therapy.

Looking Forward to TEDxSoCal

I remember my first recollection of the TED (Technology Entertainment Design) conferences, which have been held annually for almost two decades. Drawing together innovators in a broad spectrum of disciplines, these programs have become an institution unto themselves. With invited speakers ranging from Harvard’s Edward O. Wilson to business leaders, like Microsoft’s Bill Gates, the lectures cover a panoply of interesting topics.

It was with a sense of delight that I received an invitation to speak at the TEDxSoCal conference on July 16 at the Long Beach Terrace Theater. As the date approaches, I am looking forward to the event with great anticipation. Since the event is sold out, I understand I’ll have 800 attendees in the audience.

What an interesting opportunity to engage this group in a discussion of cancer biology with our focus on biochemistry and metabolism. This is timely in the context of Gina Kolata’s recent article in the New York Times on the failures of genomics platforms in the field of functional profiling for cancer treatment.

I will report next week on this experience.

Disrupting Cancer’s Circuitry – an Electrician’s View of Oncology

In many ways, cancer can be viewed like an integrated circuit. On-off switches and back up switches constitute the controls. When one of these switches stops working and a cell “short circuits,” cancer is the result. As we become more sophisticated in our understanding of cancer biology, we begin to create drugs that specifically target these short circuits.

On April 3, 2011, I will be reporting our most recent findings on novel compounds that target two parallel circuits in cancer cells. These compounds, or small molecules, disrupt the signal that drives cancer cell survival and proliferation. While the profiles of each drug alone are of interest, the profiles of the drugs in combination are better still. The phenomenon of cross talk defines an escape mechanism whereby cancer cells blocked from one passage, find a second. When we as therapists have the capacity to block more than one pathway, the cancer cell is trapped and often dies. This is what we have observed with these duel inhibitor combinations.

What is interesting is the fact that the activities cut across tumor types. Melanomas, colon cancers and lung cancers seem to have similar propensities to drive along these paths. Once again, we find that cancer biology is non-linear. Moreover, cancers share pathways across tumor types, pathways that might not intuitively seem related. This is the beauty of our platform — for it allows us to explore drugs and combinations that most people wouldn’t think of. It is these counterintuitive explorations that will likely lead to meaningful advances.