Archive for the ‘Oncology’ Category

Time to Rethink Cancer Therapy?

Wednesday, November 28th, 2012

In an earlier post, I wondered a bit about the ultimately causes of cancer.  For the last several decades cancer has been labeled as a genetic disease, an idea which we have chased with great fervor.  Yet, It feels to me sometimes as though the evolving story of the causes of cancer is like a hall of mirrors in an amusement park in that there seems to be an ever receding chain of causal genetic alterations fueling cancer’s inexorable progression.

The most visible of these alterations are in the growth modulating molecules of the cell.  Over expressed growth factor receptors or transcription factors, mutant signaling molecules, etc.  How did these components come to be broken?  Genetic insults of various kinds have been discovered, studied, and labeled as causes of cancer.  We are actually getting pretty good at intervening in some of these malfunctioning growth pathways that have been co-opted by cancer.  For example, antibodies that block the activity of HER2, the human epidermal growth factor receptor that seems in some cases to drive breast cancer proliferation are quite effective.

Yet, even when we do intervene with seeming effective tools, such as trastuzumab for HER2 over-expressing breast cancer, the cancer seems in most cases to rebound by activating still other pathways of growth.  It has come to be reminiscent of the proverbial leaky dike and us with not enough fingers to plug the leaks.

The genomic instability that is so characteristic of most cancers seems to be the driver of genetic diversity that provides resistant variants.  It appears that cancers “evolve” to a state of significant heterogeneity and the genomic instability seems to be a player in that process.  But, where does the genomic instability come from?  We can then propose a change in cells that causes genetic instability.  But, where then does that come from?  See what I mean?

This genetic, linear causation idea is the foundation on which our cancer therapy strategy is built.  Naturally, our combat strategy is direct.  Cut it out.  If you can’t cut it out, hammer it with chemicals or radiation.  If a little doesn’t work, then try a lot.  Too much cell division and DNA replication? Inhibit DNA replication.  Too much RAF signaling? Inhibit RAF signaling.  Battle this problem where it occurs: inside the cancer cell itself.  This strategy has produced some remarkable results; however, for most cancers, the fact remains that some cells inevitably escape destruction to arise as an even more fulminant tumor later.

The feeling of frustration in chasing cancer up the path only to have it resurrect out of seemingly nowhere still further upstream is a signal to me.  I have sensed in this frustration a signal to think about cancer pathogenesis and treatment in new ways, like I’m sure others have.  Recently I have been gratified to hear a number of researchers propose new views of what cancer is and new strategies for treating it.

I have been a member of a tumor microenvironment interest group for a while, mostly to keep an ear to the ground in that area.  Having spent many years trying to grow cancer cells in various ways, it is clear to me that they depend heavily on their microenvironment to survive.

Over the summer I noticed a few publications (see this news story in Nature Medicine for more details) suggesting that resistance to chemical therapy may be mediated by more than just the response of the tumor cells.  These studies suggest that the tumor microenvironment may provide protection from anti-cancer agents by secreting of growth factors from stromal cells intermingled with the tumor cells.  In one study, WNT16B growth factor secretion was induced in stromal fibroblasts, which in turn protected the cancer cells from programmed cell death.  In another pair of studies (here and here), stimulated secretion of hepatocyte growth factor from stromal cells attenuated the sensitivity of melanoma cells to BRAF inhibitors, one of our newest targeted therapeutic classes.  It seems that the effects of treatment are more complicated than we had thought.  Our cell-autonomous approach to drug development is probably too simplistic.  In retrospect, it seems obvious that we should account for the effects of other cells that, with the tumor cells, create the environment in which the cancer develops.

Rethinking cancer therapy has been proposed by Robert Gatenby and colleagues for some time now (see, for example, their article in Cancer Research in 2009).  Over the summer, Gillies, Gatenby, and colleagues published another paper describing how these concepts impact targeted therapy as progress in cancer therapy.  These folks have brought concepts from evolutionary biology and the control of invasive species to bear on cancer therapy.

Gatenby and colleagues describe a model for how evolutionary dynamics operate in the tumor microenvironment: phenotypic diversity, courtesy of genetic instability, provides the substrate for selective forces, provided by cytotoxic drugs, resulting in selection of tumor cells that can survive almost any insult.  Under this scenario, toxic drugs will select for some variant that will then proliferate to fill the niche vacated by the cells killed by the therapy.  Adaptive therapy is described as a potential solution to this problem.  In essence, adaptive therapy uses interventions that strategically impose a substantial evolutionary cost on cancer, thereby reducing its fitness to survive and ability to adapt to its new environment.

A high evolutionary cost means that interventions are difficult to evolve around.  To illustrate what these might be like, they draw examples from control of invasive species.  Might cancer be better handled as if it were an invasive species?  Two points that they make are 1) that eradication is often not possible and control of population size is the goal; and 2) the high-evolutionary cost interventions are often biological.

Although the cancer genome is an important component of the disease, it is becoming clear that there are additional facets of the disease, such as the interaction of the cancer genome with genomes in its environment.  Consideration of the role of tumor microenvironment modulation of therapy is a welcome expansion of how we think about cancer and our response.  Likewise, radically new strategies for cancer therapy, possibly like adaptive therapy, are welcome, as well.  Incorporating these new concepts into our view of cancer helps put us on the path to effective new treatments.

Lessons learned from tumor heterogeneity

Tuesday, April 10th, 2012

My recent blog post, Tumor heterogeneity, revealed…, discussed the New England Journal of Medicine article by Gerlinger and colleagues describing the genetic heterogeneity found both within a patient’s individual tumor nodules and between spatially separate nodules.  There has been a substantial amount of discussion of this work and angst about how it might signal the end of personalized medicine even before it really got started.  I don’t believe that will be the case at all.  To the contrary, this paper made interesting contributions in three conceptual areas that may help pull the field forward.  These areas are the 1) relevance of prognostic gene expression profiles, 2) the nature of “driver” genetic mutations, and 3) the pathogenesis of cancer itself.  All of these areas are, in my opinion, very important to make headway in before personalized cancer medicine can become a truly effective tool in medicine.

Heterogeneity in gene expression profiles across the tumor specimen

The result that most seized on to proclaim the demise of personalized medicine was the finding that gene expression signature from spatially separated parts of a tumor nodule yielded different assessments of prognosis.  The implication is that a single biopsy specimen is inadequate to generate an accurate prediction of clinical course or response to treatment.  Most likely that is at least partially true.  However, the issue is with sampling, rather than the molecular biology.  We have known for decades that tumors have variable histology within their mass, with some regions reflecting poorer prognosis than others via their histologic grade.  Rather than reflecting a conceptual disconnect that dooms a new paradigm, it looks more like a technical problem to solve, which should be no surprise along this new path.

Convergent evolution

Both the Gerlinger paper, as well as others (e.g. Walter et al, NEJM), using NGS have now demonstrated that within a single patient the same gene can be found to be mutated multiple independent times, suggesting that this mutation creates a change in gene function that participates in the development of the cancer.  This had not been shown in humans before.  This finding will be useful for clinical diagnostics  and it may be game changing in basic research.  In clinical diagnostics identification of a multiply-mutated gene would give additional confidence that the damage it represents is causal and may help select targeted therapy.  In basic research, identification of such genes would represent novel evidence of the causality of specific genetic changes in the disease process.  This type of evidence is a smoking gun, a sign post saying “Needs to be mutated to reach this disease state”.  This type of evidence, which only deep sequencing can yield, is a new and useful application of NGS that was not previously available.

Pathogenesis

The picture that the Gerlinger paper, Walters paper, and others paints is one of clonal evolution of cancer.  This type of work paints this picture with clarity that has not been achievable before.  What is striking to me is that these results make it harder to ignore the concept that these molecular alterations, as important as they clearly are in the progression of cancer, may not be the cause of cancer.  They beg the question, “what initiated this evolutionary process?”.  Certainly, oncogenes, tumor suppressors, and the like are a part of cancer pathogenesis, carrying the developing disease along.  But it seems to me that there is still a “first cause” of some sort that we have not put our collective fingers on.  Genomic instability is certainly key, but then what is the genesis of the genomic instability?  What are the inputs that kick this process off?  Efforts to answer these questions will move us closer to effective treatments for cancer and other diseases that may share these pathogenic processes.

Tumor Heterogeneity, Revealed…

Thursday, March 8th, 2012

A very interesting and timely article on tumor heterogeneity was published in the New England Journal of Medicine today.  Gerlinger and colleagues from the UK used next-generation sequencing to look for heterogeneity across various regions of renal tumors and metastases in four patients.  They report that indeed there is a great deal of heterogeneity within individual tumor nodules–in fact, most of the many alterations to the tumor genome were not shared across all nodules.  Further, analysis of the pattern of mutations revealed branching evolution of the primary tumor and its metastases, rather than a linear pattern of progression of the cancers.

A couple of important conclusions suggested by this work:

  • Single biopsies of the primary tumor may give you a very misleading understanding of the cancer.
  • Cancer stem cells may not be what we thought they were, if they exist.
  • Confirms the adaptability of cancers by demonstrating convergent evolution of functional gene alterations.

None of what was reported is inconsistent with evidence from previous decades of cancer research.  It was work that really needed to be done and I’m happy it appears to have been completed in a careful, thoughtful way.

Failure of the Genome?

Thursday, May 19th, 2011

I recently read an article written by Jonathan Latham in the Guardian (UK) online with the title, “Failure of the Genome” (credit to Genome Web for pointing the post out to their readers).  Following the eye-grabbing headline, the article goes on to posit that the Human Genome Project has not turned up much of use.  Indeed, the author asserts that there is scant evidence supporting the genetic underpinnings of disease paradigm.  To a geneticist or one of the many others who have backed the various genome projects, this is provocative indeed.

So, why did this provocative headline catch my eye?  I have to admit, I am one of those who have become weary of seeing the “Gene For…” headlines ad nauseum over the last couple of decades, only to see those claims vanish into the twilight of yesterday’s news time and again.

The magically vanishing claims of genetic causation that show up daily certainly have jaded even a dedicated molecular biologist like me* to an extent.  As such, I can understand how this pattern of hype of research results followed by disillusion when the claims quietly die would dishearten others who see these stories.

So, maybe what grabbed me was the sense that we, as a society, have swallowed the genetic-cause-of-disease hype hook, line, and sinker—and this article is evidence of rising discontent the emptiness of those hyped promises that come in company and university press releases.  The real story about genes and disease is more complicated than will fit in the easy to digest news bits that are our common food in these information-intense times.

I hope that we scientists will recognize this backsplash as a signal to examine how we communicate our science.  What I most value in the scientific enterprise are the truthfulness and credibility that are a part of this culture.  I hope we will work to preserve these qualities.

 

*I come to this as a molecular biologist with a couple of decades of experience doing research in oncology, in particular, the role of oncogenes in the development and progression of cancer.  Based on my own hands-on experience in trying to understand the role of genes in a disease, I’d be hard pressed to simply dismiss genetic variation as a factor is disease causation, as Mr. Latham does.  It is pretty clear to me that variation in genetic makeup leads to variation in phenotype, some of those phenotypes being what we call “disease”.

 

Recent Developments in DTC Genomic Testing

Wednesday, January 5th, 2011

It’s been relatively quiet on the DTC Genomic Testing front since the turmoil over the FDA’s decision to consider regulating DTC genetic/genomic testing last summer died down.  Nevertheless, there have been a few news items that yielded glimpses of what is going on in the industry.

In November 2010, 23andMe received additional investments from Google, New Enterprise Associates, and Johnson and Johnson Development Corporation.  In the last few days, the company announced that it would “experiment” with new pricing models.

In mid-December 2010, the Institute of Medicine (US) announced that it would be researching, then issuing a report on possible ways forward for and possible legitimate uses of predictive ‘omics-based tests.

Also in mid-December, DeCode Genetics published findings in Science Translational Medicine of a study of SNPs related to PSA expression in prostate cancer.  The DeCode group interprets their results as refining the utility of the PSA protein marker for prostate cancer.  In essence, the SNP markers described can be used to individualize PSA test results by predicting whether the individual’s range of PSA expression can be expected to be higher or lower than average.

Matching Wits with Cancer

Wednesday, April 21st, 2010

An article and a report spurred my thinking about the complexness of the cancer cell phenotype today.  Art Levinson, the long-time CEO and now Chairman of Genentech, wrote an editorial in the 9 April 2010 issue of Science supporting changes in drug approval regulations to make it easier to gain approval for drug combinations.  It has become apparent that one of the ways that cancer cells evade death from some of our most promising new genomics-based drugs is by relying on redundant signaling pathways to compensate for pathways blocked by the single drug agent.  Now, clearly redundancy is a positive feature of cells in general, but here it makes combating cancer difficult.  However, there is hope that redundancy is not infinite in cancer cells and that we may be able to block enough of critical signaling pathways with combinations of drugs to elicit cell death.  However, the world of drug regulations was designed around single agents; thus, to take advantage of the use of multiple drugs to combat cancer required each of the drugs in the combination to show statistically significant efficacy on its own in the clinic.  A very tall hurdle to clear.  The recent shift at the FDA (Wall Street Journal Health Blog, March 18, 2010) to develop guidelines to enable the development of combination drugs based on the totality of data will accelerate development of better cancer therapeutics.

At the annual AACR meeting in progress in Washington, DC, Burt Vogelstein reported that he and his colleagues had identified 3,142 driver mutations over 100,000 tumors, of which 286 were tumor suppressor genes and 33 were oncogenes.  The actual numbers are not so important as is the fact that so many genes can contribute to cancer.  The large potential number of gene products and pathways involved underscores the need for combination therapies in cancer.  It is hard to imagine, with the level of system redundancy (e.g. signaling pathways) found in cancer cells, that a single agent will have a significant impact on tumor progression.  At the same time, these results suggest that redundancy is not infinite, as suggested above, given the finite number of genes involved in cancer.  While the cancer phenotype may be complex, it may well be that this complexity will become manageable with better understanding of the disease and better therapies based on this understanding.

Cancer Genes in the News Again

Tuesday, March 30th, 2010

There seems to have been quite a bit of activity in the world of gene-based cancer diagnostics lately.  Just in the last 24 hours some of Myriad Genetics’ BRCA patents were ruled invalid in the United States (http://www.genomicslawreport.com/wp-content/uploads/2010/03/Myriad-SJ-Opinion.pdf) and a recent article in the New England Journal of Medicine (Wacholder et al., NEJM 362: 11, 2010) suggested that breast cancer-associated SNPs add little to traditional models for assessing prognosis of being diagnosed with breast cancer.  These two developments illustrate two aspects of the ongoing debate about the genetic information in health care: how should genetic information be used and who owns it?

On the “who owns it?” front, the Myriad case is all about the patenting of genes.  This debate goes back to the early days of large scale gene sequencing when companies like Myriad Genetics, Human Genome Sciences, Incyte Pharmaceuticals, etc. were filing patent applications on gene sequences nearly as fast as they could sequence them.  The question then, as now, was “what is the invention here?”  Are naturally occurring gene sequences patentable?  This recent ruling against Myriad is of the opinion that naturally occurring gene sequences, even “in isolation”, are not inventions and hence not patentable.  Seems reasonable to me.  In my experience patents and the resulting restrictions on use of something as fundamental as a gene sequence do inhibit research, primarily by driving up the cost.  My feeling is that there are plenty of opportunities for inventiveness, and therefore intellectual property, a step further away from the gene sequence in the form of compounds, devices, and methods for diagnostic and therapeutic products.

The BRCA gene alleles in question appear to have quite a bit of information regarding the phenotype of the person in question.  This implies value in so far as that information can be used to assess the future risk of developing breast cancer.  Alleles like the BRCA 1 and BRCA 2 are fairly rare, though.  Clearly it would be good to have more broadly applicable genetic tests for breast cancer and other diseases.  A number of academic laboratories have published studies suggesting that “gene signatures” are useful in classifying breast cancers (see for example Sorlie et al., PNAS 100: 8418, 2003).

Quite a few companies and other organizations are developing gene signature-based tests in this area, based on the concept that combinations of more commonly occurring alleles will provide sufficient information to facilitate improved assessments of risk.  The first of these tests to reach market is the Oncotype Dx test from Genomic Health, Inc.  Several studies have been published on the Oncotype Dx test demonstrating the utility of the Recurrence Score in facilitating risk assessment.  The product is beginning to gain traction in the market.

The publication from Wacholder et al (above) suggests that combinations of several single nucleotide polymorphisms know to be associated with breast cancer adds little to traditional models for assessing risk of developing breast cancer.  While superficially it appears that the Wacholder study and other studies, such as Oncotype Dx studies, conflict I’m not sure that is true.  It may be that the question being asked in these two situations is different.  The Oncotype Dx test is looking at risk of metastatic disease, while the Wacholder study is looking at risk of primary breast cancer occurrence.  Further, the modeling methods used are different.

The upshot to me is that we are not done yet understanding how to use genetic information in making decisions about health care.  In a few cases it is fairly straight forward.  However, to reach the expectations set for genomic information a decade ago we will have to be able to use genetic information to assess health issues much more broadly than a handful of rare alleles.  This is proving harder to do than I think many expected.