Meditations of an oncology geek

D Fence: My PhD Finale

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28 April 2014

Dear Reader,

The primary focus of the last five years of my life has been the pursuit of a PhD, culminating with my PhD dissertation and defense. A week ago I defended my PhD and was awarded a Doctor of Philosophy in Biomedical Sciences, more colloquially known as a “PhD” or “doctor of science.” I’ve decided to coalesce some thoughts and impressions into something resembling a narrative on the process.

Images: On April Fools’ Day, three weeks before my PhD defense, I sent my good friend Eric Murphy an email: “Hey Eric, I’ve attended a few PhD defenses, but I’m still at a loss whether this would be proper attire?” and included a link to the image below. His response was short: “I’m doing it.” Being April Fools’ Day, the mischievous ambiguity of his response made me unsure whether he was actually planning something. Following the vein of mischievous ambiguity, I opted to not ask him to clarify, and he showed up to my PhD defense with, yes, a D Fence. Friends and family in attendance signed the D Fence after the talk.

The dissertation is a written document describing any and all of my even remotely meaningful work from my PhD. It included some published work, and some work that has not yet been published. I wish I could go into detail about the work I’ve spent several years of my life performing, but some of it needs to go through peer review before I can open it up to the world. C’est la vie.

To complete a PhD, one must host a defense, or public lecture followed by questions by curious specialist and non-specialist minds alike. The public lecture is the first formal occasion for a new doctor to open up their research, ideas and insights to society, to be pondered and questioned by anyone.

More practically, a PhD defense is the final meeting between the PhD candidate and their thesis committee. The main difference from previous meetings is that the public is invited to attend and interrogate the logic, reasoning, research, and knowledge of the PhD Candidate. The public lecture must make something highly esoteric understandable to curious non-specialist minds. But, the talk must remain technical enough to satisfy the Thesis Committee as well. It’s also a rare chance for a PhD Candidate to display their work to friends and family, and making a presentation that can meet all of these demographics is no easy task.

I have many friends and family in the area, many of whom I’ve had to somewhat neglect in my long hours (years?) pursuing new knowledge through research. It’s entirely possible for a PhD candidate to have very few people attend their defense, but where’s the fun in that? I had given many scientific talks to scientists, but rarely to the audience I was expecting. I saw it as a tremendous opportunity to practice my presentation skills, and perhaps have some fun in the process. I’m not referring to a hedonistic, lost-in-the-moment type of enjoyment, but the rare, fleeting satisfaction of doing something well, wrought by blood, sweat and tears.

After all, my original reasons for pursuing medical research were because I wanted to learn to wield the tools of science to have a shot at making a small contribution to medicine. Medicine is a physical manifestation of humanity’s will to live longer and more free of physical ailments and pain. The last century has seen a significant maturation of the relationship between medicine and science, the process by which we reproducibly uncover and define the way the world works. In tandem we can do incredible things like cure infections, eradicate communicable diseases, and make a dent in perhaps the most difficult of diseases to treat: cancer.

Image: Dated to 2600 BCE, the Edwin Smith Papyrus is an ancient Egyptian combination of surgical trauma manual with recommended therapies for fractures, dislocations, lacerations, infections, etc. Among the nearly 50 cases are two describing cancer, for which there was no recommended therapy. The ancient Egyptians clearly recognized cancer as a very difficult disease to treat, perhaps also recognizing the futility of trying to treat it with their medical tools at the time; that intervention was worse than leaving patients to slowly perish. Image courtesy U.S. National Institutes of Health

Along this theme, I dedicated the first chapter of my dissertation to the history of cancer metastatic theory from ancient times until the 20th Century: from fossilized clues about cancer metastasis to the 4700 year old written case studies on cancer patients, to Hippocrates, Galen, Paget, Halstead, and Fisher. At some point in the future I hope to be able to reproduce (with permission) this chapter of my dissertation here on my blog.

I opened my defense talk with a short historical context on cancer, stressing that ancient societies clearly recognized cancer as a very difficult disease to treat. Hippocrates is credited with coining the term “cancer” because he likely recognized the ability of it to crawl throughout a cancer patient, or the physical appearance of autopsied tumors reminded him of a crab. He is also credited with the term “Metastasis” which translates loosely to “dislodgment” or “to be set free.”

For visceral effect, I also included a PET scan of an advanced stage cancer patient (to the right, courtesy with metastatic tumors throughout the body. I then asked my audience to imagine being a surgeon tasked with removing the tumors with a scalpel, stressing the difficulty in treating advanced disease, and how imperative it is for us to understand the process by which this happens so we may target it in means more precise than, well, a surgeon’s scalpel.

I really wish I could go into details about my talk from this point out, but as I mentioned before some of the data has not yet been published, and even more is not yet available via open access (i.e. the publications are owned by entities that charge a fee to the public to view). A discussion on the merits and pitfalls of the antiquated publication model and its (mal?)adaption to 21st century medical research is warranted, but perhaps not here right now.

The abbreviated version of the rest of my talk: Cells have mechanisms that allow for recognition of their physical surroundings and biological zip codes in the body. The means by which they interpret these signals and decide to commit cell suicide or to migrate and grow are integral to the behavior of cancer cells, and at the center of this is my favorite protein: Caspase-8. Through rigorous experimentation employing recombinant protein biochemistry, cell culture models and experiments in vivo, I demonstrated how this protein can play a dual role in cancer malignancy. My research model suggests that this behavior might be toggled by combining two yet-to-be-tested-together classes of drugs that are currently in the clinic and in late phases of clinical development.

Image: A slide from my talk, introducing the concept of metastasis as a multi-step process with hurdles for a cancer cell at every step using very crude illustrations.

Cancer is actually a group of many heterogeneous diseases with overlapping etiology and behavior. My research alone is a far cry from a “cure.” Medical research is the combined efforts of thousands (millions?) of scientists past and present, and my work builds heavily upon work performed by those that came before me. It’s a tremendous honor and privilege to take part in this tradition. By communicating my results and ideas, I am closing a small piece of that loop and contributing (a very small part) to this process.

On a personal side, perhaps the most important and practical thing I have learned in the process is that, after five years of blood sweat and tears (and a healthy helping of head banging) I want some more. I have tested the depths of my motivations and I have found that I am indeed very deeply passionate about using science to improve the physical well-being of cancer patients. There are many times where I could have thrown in the towel, but at every hurdle and hill in my way I found motivation to continue. I remain easily excited by new prospects and developments in science as they pertain to oncology, and when I grab my morning coffee I often get distracted by reading scientific papers and oncology clinical trials results.

In terms of my career, I am allowing myself to be guided by the onus of finding the most impactful, efficient way to improve cancer diagnosis, risk assessment, and therapy. I am currently exploring several options in academia and the biotech industry toward these ends.

If you’ve made it this far I thank you, dear reader.


Written by Ryon

April 28th, 2014 at 10:44 am

Posted in Science Blog

Precision Oncology Needs Neoadjuvant Clinical Trials like I-SPY2

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4 March 2014

The emerging view of cancer is an increasingly diverse set of rare diseases with overlapping etiology and molecular drivers (1). The evolving definition of personalized oncology centers on the development and vetting of many specific, targeted, low-toxicity molecular scalpels that can be used individually or in combinations to tailor a patient’s cancer treatment. The bottleneck of drug development is the testing phase, and there are numerous barriers to novel chemotherapeutic introduction to the clinic.

The I-SPY2 trial has received a lot of press lately, and rightfully so: it’s a bayesian study designed to adaptively match patient genotypes of appropriate therapies in a rotating 5-arm clinical trial that can quickly take on a new agent once one of the test arms graduates, ready for Phase III trials that (theoretically) have a might higher chance for success, with fewer patients (2, 3). The trial has been engineered to make cancer drug trials quicker and less expensive, and more information can be found here.

The I-SPY2 trial is co-directed by Laura Esserman, who gave an illuminating talk at the UCSD Moores Cancer Center last week. Most targeted therapies are tested in clinical trials in heavily pre-treated patients in the metastatic setting, and often without molecular biomarkers. Agents tested in the metastatic setting often see a 2-4 year knowledge turn, while those in the adjuvant setting often come with a 6-9 year knowledge turn. This is simply too slow (and uses too many patients and is too expensive) to realize the vision of personalized oncology.

In the neoadjuvant setting (pre-surgery, chemo-naive patients) the turnaround can be much faster. Instead of disease recurrence, the trial readout is volumetric change in tumors. Tumor samples are subject to panomic (genomic, proteomic, methylomic, etc) analysis before and after neoadjuvant therapy, enabling post-therapy clues to efficacy or failure of tested agents. While this sounds straightforward, this is not the norm for current oncology clinical trials, especially ones for targeted therapies. The reasons for this are beyond the scope of this post. There has been an extreme paucity of information for why certain drugs do not work, and very limited information on what –omics background produce responders.

While pre-operative administration could permit greater organ conservation in the patient, I am also interested in this approach for two additional reasons:

1) Chemotherapy-naive patients might be less susceptible to drug resistance out of the gate. Many drug resistance mechanisms are shared, and patients will not have been weakened from systemic chemotherapy in the neoadjuvant setting (4, 5).

2) Surgery is a highly invasive procedure that damages tissue, releasing cytokines and growth factors that can promote inflammation and tumor growth (6).

The neoadjuvant is a better stage to test for agent efficacy, and opens the door to glimpses of tumor biology that might enable more curative approaches. The neoadjuvant drug administration combined with panomics approaches could be a boon for the emerging “Rapid Learning Precision Oncology” paradigm proposed as part of “Personalized Oncology 3.0” by Shrager and Tenenbaum (7). Eventually, it may be possible to consider each patient encounter as an experiment, with each additional “experiment” better informed than the last.

I-SPY2 has already graduated two agents to Phase III trials: the small molecule dual HER2 and EGFR inhibitor Neratinib, and the PARP inhibitor Veliparib. The speed at which they passed through Phase II trials is encouraging. Because the trial actively adapts with genotype efficacy, it’s anticipated that Phase III trials will have a greater chance of success. I will be watching this with great anticipation, and at this point in time I am skeptically optimistic about I-SPY2. We need more bullets, big or small, and every new target and every new agent adds another small step toward realizing the vision of personalized oncology.



1. Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, et al. Mutational landscape and significance across 12 major cancer types. Nature. 2013 Oct 17;502(7471):333-9. PubMed PMID: 24132290. Epub 2013/10/18. eng.
2. Berry DA. Adaptive clinical trials in oncology. Nature reviews Clinical oncology. 2012 Apr;9(4):199-207. PubMed PMID: 22064459. Epub 2011/11/09. eng.
3. DeMichele A, Berry DA, Zujewski J, Hunsberger S, Rubinstein L, Tomaszewski JE, et al. Developing safety criteria for introducing new agents into neoadjuvant trials. Clinical cancer research : an official journal of the American Association for Cancer Research. 2013 Jun 1;19(11):2817-23. PubMed PMID: 23470967. Epub 2013/03/09. eng.
4. Junttila MR, de Sauvage FJ. Influence of tumour micro-environment heterogeneity on therapeutic response. Nature. 2013 09/19/print;501(7467):346-54.
5. Lord CJ, Ashworth A. Mechanisms of resistance to therapies targeting BRCA-mutant cancers. Nature medicine. 2013 Nov;19(11):1381-8. PubMed PMID: 24202391. Epub 2013/11/10. eng.
6. Costanzo ES, Sood AK, Lutgendorf SK. Biobehavioral influences on cancer progression. Immunol Allergy Clin North Am. 2011 Feb;31(1):109-32. PubMed PMID: 21094927. Pubmed Central PMCID: PMC3011980. Epub 2010/11/26. eng.
7. Shrager J, Tenenbaum JM. Rapid learning for precision oncology. Nature reviews Clinical oncology. 2014 Feb;11(2):109-18. PubMed PMID: 24445514. Epub 2014/01/22. eng.

Written by Ryon

March 4th, 2014 at 3:26 pm

Posted in Science Blog

New Publication, Dissertation Approved, and Histology

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18 February 2014

It’s been a busy month! Well, most months are busy, but this one has been especially so, and I have some good news to show for it:

1) I am pleased to announce that my review article “Caspase-8 as a Regulartor of Tumor Cell Motility” has been published in Current Molecular Medicine and is available on PubMed.

2) About a week ago I had my pre-thesis defense meeting with my Thesis Committee. After a grueling two hour meeting my Committee Chair gave their verdict: “We are pleased with your progress, we accept your proposed graduation timeline and would like a draft of your dissertation in six weeks’ time.” Looks like I’ll be defending my thesis in the spring! I have not yet set a date, but it’s most likely going to be mid-May.

3) On top of all of that excitement I have been in the midst of my Med Into Grad program. It’s hard to appreciate the nuances and challenges of clinical oncology from the lab bench, and there are so many things that I see on a daily basis that could be aided with new technology. Often, the applications are not groundbreaking or miraculous or ideas that come down from the sky on sunbeams with chariots of angels singing a chorus; they are often subtle, but the sum of all of small innovations will aid modern oncology.

For instance, today I heard a surgeon describe being mid-surgery deep in the peritoneal cavity, his patient open on the operating table. He came across a lesion that looked very much like fibrosis, but was later revealed to be tumor after analysis of biopsy that he sampled just to be sure. A team of physicians then discussed how to move forward on the patient, who was still recovering from surgery with residual tumor cells remaining.

In another instance, a minor stir almost ensued when a patient was staged (via histology) as having a low-grade primary ovarian tumor, when it was more low-ish. The distinction matters tremendously, as the high grade (and more common) tumors will receive systemic, and sometimes preoperative, chemotherapy along with surgery, while the low grade tumors will be treated with surgery alone. The decision to give systemic chemotherapy is not taken lightly by clinical oncologists, and they absolutely need the most un-ambiguous information possible to do be the most effective with the least amount of harm.

I want to find out how subjective and reproducible the measures are that are currently used for diagnosis and guidance of treatment. I want to find means for emerging technology to help remove ambiguity in diagnosis and aid treatment. Could the emerging sequencing technologies and avenues like liquid biopsy provide a better means to asses tumor burden, extent of vascular invasion and prognostic response to existing and emerging therapies? Could this provide a more precise means of who needs what therapy?

In less than a week I’ll be starting my clinical rotations with histology. I’ll be observing how pathologists grade tumors and what sort of clinically relevant information is gleaned from microscopic observation of tumor samples, and how precise and / or subjective such measures are. It should be fun!


Written by Ryon

February 18th, 2014 at 6:26 pm

Posted in Science Blog

Heterogeneity in clinical molecular profiling: a case study

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9 January 2014

Happy New Year! This week continues my Med Into Grad clinical exposure, and last night I was privileged to attend Molecular Tumor Board at the UCSD Moores Cancer Center.

Tumor boards are weekly meetings where clinical oncologists discuss their patients and solicit opinions of their peers and others in attendance.  Meetings usually cluster cases together by organ type, i.e. breast cancer.  To address the challenges of the recent flood of new molecularly targeted chemotherapeutics to the clinic, about a year ago the Molecular Tumor Board began, drawing attendance of about 15-20 clinical physicians as well as pathologists, radiologists, genetic counselors, and a few research scientists. It’s an honor for me to attend; many attending scientists have at least some gray hair. I could wax poetic about witnessing the dawn of genetically tailored medicine in front of my eyes, but I’ll spare you, dear reader.

The cases are presented with information like age, date of diagnosis, treatment history, and for molecular tumor board, molecular profile as well. Yesterday the case was presented for a woman with malignant colon cancer. Unlike every other case I’ve seen presented, the patient had molecular profiling performed by no less than five different diagnostic centers: Foundation Medicine, Caris, Clarient, Consultive Proteomics, and Oncopath.

The tests range from immunohistochemical to whole exome sequencing, so variability between the tests would be expected. Also, sample biopsies are from colon, secum, peritoneum and lymph node over a two year period, representing differing geographical and temporal snapshots of what is already (assumed to be) a heterogeneous, evolving disease. Perhaps it is not surprising that among the 15 actionable targets indicated by these tests combined, only three of these targets were reported by more than one test.

After a few minutes of discussion, another shared “target” was revealed with similar mRNA elevation consistent between two tests, but was included in only one of the two official reports because of different thresholds of significance used by different companies.

So, what are the actual actionable targets for this patient?!? It would be easy to dismiss this as gibberish, but what this does represent, however, are five example clinical information scenarios of the same patient. Depending on the time of diagnosis, previous therapy, location of biopsy, and preference of diagnostic center, any of these five test results could have reasonably found their way to this patient’s oncologist’s iPad.

Instead, these are all presented for one patient, underscoring the tremendous challenge posed to the clinical translation of this knowledge for personalized medicine, likely representing not only highly heterogeneous disease, but highly heterogeneous therapy courses, and heterogeneous outcomes as well.

So, why not get this five dimensional testing done for all cancer patients? There are a few barriers. The first is cost: each test is upwards of $5000. The second is ethical: tissue biopsies are invasive, and multiple biopsies are only feasible for patients with highly accessible disease.

How will we standardize this knowledge? Should we? To what degree? How should it be presented? What sort of continuing education could be necessary / appropriate for clinical oncologists at centers without access to a molecular tumor board?

I will be pursuing these questions as Med Into Grad continues!


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Written by Ryon

January 9th, 2014 at 5:03 pm

Posted in Science Blog

FDA regulating hype? What about supplements and e-medicine?

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6 December 2013


As a follow-up to last week’s post, I can’t help but wonder about the future of the FDA, more than the future of medical genomic testing.

The FDA appears to have its beef not with sequencing, per se, but the hype of the interpretations of that sequencing. As far as genomic sequencing goes, it would be unreasonable for the FDA to prevent people from sequencing their own genes, and this is not what it’s doing for the time being. The real beef that the FDA has with 23andMe was the interpretation of that sequencing, taking what has been called a “paternalistic” role to vet / regulate the quality of information that could directly affect the actions taken by patients.

Along those lines, why not intervene and regulate online health info amalgamations like and Is this not medical diagnostic hype? (see image)

This point was touched upon by Rahul Rekhi in The Guardian:

And what of services like WebMD – the hypochondriac’s haven – which offer patients checklists by which to self-diagnose their perceived symptoms? Do these not pose similar public health concerns? Yet, they persist largely uninhibited.

While half a million customers for 23andMe is nothing to laugh at, it still pales in comparison to the massive tide of people making significant personal health decisions based off ill-vetted pseudoscientific information on the internet. If the FDA wants to expand its reach and do the maximum public good, perhaps they should step in here, or perhaps the poorly regulated, multi-billion dollar supplements industry? An anti-cancer drug needs 15+ years and multiple stages of clinical trials and upwards of a billion dollars to show efficacy by our standards, but nothing is preventing snake oil salesmen from marketing homeopathic water to promote “vitality” to cancer patients.

Also, companies like 23andMe could easily make themselves over in countries without an overly paternalistic FDA. Its rather easy to sidestep regulatory oversight of transporting biological specimens (like cheek swabs) across international boundaries: one could have their genome sequenced in California and instantly uploaded the Cloud with something like Illumina’s BaseSpace and immediately have it analyzed by medical genomics teams in India, Singapore, etc.

The FDA has put its finger firmly in the hole in the dam, but it looks like the rising tide of genomic sequencing will soon spill it all over anyway. The plot thickens…

Written by Ryon

December 6th, 2013 at 4:31 pm

Posted in Science Blog

23andMe, the FDA, and evolving science ethics

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27 November 2013

I’ve got a thesis to write, manuscript to edit, and a pesky microscope problem to work around, but I just cannot help but follow the current discussions surrounding the battle between 23andMe and the FDA. There’s a LOT of hype and charged discussions going on in social media at the moment, and I’ve had the pleasure of watching it all unfold. All in all, I have seen some very healthy ethical discussion on many fronts. I thought I’d share a few enlightened points I’ve come across.

First, came the announcement:

The actual letter from the FDA is a fantastic read:

Your company submitted 510(k)s for PGS on July 2, 2012 and September 4, 2012, for several of these indications for use. However, to date, your company has failed to address the issues described during previous interactions with the Agency or provide the additional information identified in our September 13, 2012 letter for (b)(4) and in our November 20, 2012 letter for (b)(4), as required under 21 CFR 807.87(1). Consequently, the 510(k)s are considered withdrawn, see 21 C.F.R. 807.87(1), as we explained in our letters to you on March 12, 2013 and May 21, 2013.  To date, 23andMe has failed to provide adequate information to support a determination that the PGS is substantially equivalent to a legally marketed predicate for any of the uses for which you are marketing it; no other submission for the PGS device that you are marketing has been provided under section 510(k) of the Act, 21 U.S.C. § 360(k).  {emphasis added}

Matthew Herper in Forbes gives a great introduction to what is a highly nuanced ethical debate quickly becoming a macrocosm of a battle between 23andMe and the FDA:

I’d like to be able to start here by railing against our medical system, which prevents patients from getting data about our own bodies because of a paternalistic idea that people can’t look at blood test results, no less genetic information, without a doctor being involved or the government approving the exact language of the test. I’d like to be able to argue that the Food and Drug Administration is wantonly standing in the way of entrepreneurism and innovation by cracking down on 23andMe, a company that is just trying to give patients the ability to know about their own DNA, to understand their own health risks, and to participate in science.

I wish that was the story I’m about to write, but it’s not, and it all really comes down to one fact in the FDA’s brutally scathing warning letter to 23andMe, the Google GOOG +0.36%-backed personal genetics startup. It’s this quote from the letter by Ileana Elder, in the agency’s diagnostics division: ‘FDA has not received any communication from 23andMe since May.’

more here:

The blog Genotopia makes some very important distinctions about what the FDA is trying to regulate:

We must be clear that the FDA letter does not prohibit 23andMe from selling their test. It demands they stop marketing it. The difference may not amount to much in practice—how much can you sell if you don’t market your product?—but the distinction does help clarify what is actually at stake here. FDA is not attempting to instigate a referendum on the public’s access to their own DNA information. They are challenging the promises 23andMe seems to make. This is, in short, not a dispute about access, but about hype.

The company seems to promise self-knowledge. The ad copy for 23andMe promises to tell you what your genome ‘says about you.’ ‘The more you know about your DNA,’ they trumpet, ‘the more you know about yourself.’ On one level, that’s perfectly, trivially true: your genome does have a lot to do with your metabolism, body structure, how you respond to disease agents, and so forth. The problem is, we as yet know very little about how it all works. The 23andMe marketing exploits a crucial slippage in the concept of ‘knowledge,’ which FDA correctly finds misleading. In short, the marketing implies a colloquial notion of knowledge as a fixed and true fact, while the science behind the test is anything but.

Genotopia continues:

…The 23andMe product, like every genome test, provides probabilities of risk, not mechanisms. Probabilities are messy and hard to understand. They carry an almost irresistible tendency to be converted into hard facts. If you flip a coin 9 times and it comes up heads every time, you expect the next flip to come up tails. And if you get heads 49 times in a row, the next one has got to be tails, right? Even if you know intellectually that the odds are still 50:50, just like on every previous flip. You can know you have a particular gene variant, but in most cases, neither you nor anyone else knows exactly what that means. Despite the language of probability that dots the 23andMe literature, their overall message—and the one clearly picked up by many of their clientele—is one of knowledge in the colloquial sense. And that is oversell.

…the 23andMe test is being sold directly to individuals who may not have any knowledge of genetics. The tendency to convert risks into certainty is higher than ever. The knowledge they sell is a set of probabilities, and further, those probabilities are not stable. The consumer may not—indeed probably doesn’t—appreciate how much we know, how much we don’t know, and how much we don’t even know we don’t know. The company claims to be selling knowledge but in fact they are selling uncertainty.

More here:

David Dobbs’s NEURON CULTURE has created a fantastic list of diverse, intelligent commentary on the ethics, regulations, and science surrounding the current story:

He also offers some of his own commentary, perhaps advocating that a little messiness in the system must be weighed against the potential for positive impacts:

But do those apparently rare errors inflict more harm than the sorts of errors our medical system makes every day? Do they inflict more harm than a lack of information about important risk genes inflict? Does any harm done outweigh the great good that people gain from having inexpensive access to lots of information about medical risk?

A person learning the status of hundreds of genes of medical interest (along with information about their ancestry) with a simple spit-test may learn much actionable information — not to mention an education about genetics — that would otherwise depend on … what? Expensive access to doubtless heavily marked-up genetic tests prescribed by physicians and executed by companies happy to charges hundreds of dollars per gene? We need more such information; not less. I pray this will soon be reversed.

Lastly, there is the discussion about whether the FDA is hindering what could be a fantastic new dawn of public interest in science, not just for of un-health aversion, but just for the sake of inquiry, curiosity and education in itself. I have to admit, that this arena plucks a special chord in my heart. At the very least, I’m so glad to see these types of discussions continue, and move forward general public interest in science and genetics.


Written by Ryon

November 27th, 2013 at 1:44 pm

Posted in Science Blog

N of 1 Study Insightful to Prostate Cancer Evolution, Therapy?

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18 November 2013

(back to science blog)

It’s tantalizing (and extremely important) to factor the fourth dimension in cancer: time. Cancer is a microcosm of evolution, the most lethal versions of which are bestowed with an immense reservoir of genetic heterogeneity, providing the raw resources to adapt to changing environments. The physical manifestations of this are the same that thwart treatment: chemotherapy resistance and metastasis (1).

Tumor heterogeneity over time is difficult to study, owing to a rarity in genomics-grade longitudinal samples in cancer patients. Last week I had the pleasure of presenting a curious N=1 study to our weekly journal club here at the Moores Cancer Center. Haffner and colleagues performed genomic and histological analyses on unusually well-preserved specimens collected over a man’s 17 year disease course with prostate cancer (2). (article available for free here)

The ensuing analyses revealed a few interesting pieces of information:

The region of the prostate surveyed that likely gave rise to a wave of lethal metastases 17 years after diagnosis (and radical prostatectomy) was of low histological grade compared to the rest of the prostate tumor region.

The lymph node metastasis removed the same time as the radical prostatectomy differed in molecular signature to the lethal metastases 17 years later, indicating a diverging evolution and suggesting, at least in this patient, that the palpable lymph node tumor did not act as a way station for the lethal, visceral metastases 17 years later in the lung, liver, and thoracic lymph nodes. This gives weight to the “embolization” theory of metastasis in prostate cancer, which posits that lymphatic and hematogenous dissemination are two separate paths, the lethal one being hematogenous. In breast cancer, this distinction was the subject of much debate until clinical trials very clearly demonstrated that aggressive removal of regional lymphatics does not reduce the risk of distant organ dissemination in breast cancer (3, 4). Perhaps the same could be true for prostate cancer? While not “essential” organs, aggressive surgical removal of regional lymphatics is far from innocuous. Even small hints at tumor evolution can glean valuable information for the most effective, least invasive means to treat prostate cancer.

Lastly, the metastatic clones that aggressively arose 17 years after diagnosis were all highly similar in both driver and passenger mutations, indicating a temporally recent progenitor. The questions that I would like to ask are:

Where were these metastatic clones hiding out for 17 years? The patient had multiple gaps without detectable disease. Also, what caused re-immergence from metastatic latency? Why then and not 10 years prior or 10 years in the future? Was there an undetected watershed moment mutation after decades of genomic Russian roulette and genomic instability that enabled the emergence of a lethal clone? Or, were there coordinated changes in many tissues at once that could have given rise to a more favorable environment for metastasis (i.e. perhaps some threshold related to aging)?

These questions cannot be answered with the current study, and I agree with Brannon and Sawyers (5) that N=1 studies could be immensely more powerful if we are able to better transpose genomics to the spatial and temporal disease course of many patients. At this point we have the technology; the real challenges in implementation are clinical and logistical, which can be overcome.


1. Klein CA. Selection and adaptation during metastatic cancer progression. Nature. 2013 09/19/print;501(7467):365-72.
2. Haffner MC, Mosbruger T, Esopi DM, Fedor H, Heaphy CM, Walker DA, et al. Tracking the clonal origin of lethal prostate cancer. The Journal of clinical investigation. 2013 Nov 1;123(11):4918-22. PubMed PMID: 24135135. Pubmed Central PMCID: PMC3809798. Epub 2013/10/19. eng.
3. Donker M, Straver ME, van Tienhoven G, van de Velde CJ, Mansel RE, Litiere S, et al. Comparison of the sentinel node procedure between patients with multifocal and unifocal breast cancer in the EORTC 10981-22023 AMAROS Trial: Identification rate and nodal outcome. Eur J Cancer. 2013 Mar 19. PubMed PMID: 23522754. Epub 2013/03/26. Eng.
4. Fisher B, Redmond C, Fisher ER, Bauer M, Wolmark N, Wickerham DL, et al. Ten-year results of a randomized clinical trial comparing radical mastectomy and total mastectomy with or without radiation. The New England journal of medicine. 1985 Mar 14;312(11):674-81. PubMed PMID: 3883168. Epub 1985/03/14. eng.
5. Brannon AR, Sawyers CL. “N of 1” case reports in the era of whole-genome sequencing. The Journal of clinical investigation. 2013 Nov 1;123(11):4568-70. PubMed PMID: 24135144. Pubmed Central PMCID: PMC3809802. Epub 2013/10/19. eng.

Written by Ryon

November 18th, 2013 at 10:11 am

Posted in Science Blog

An Amazing Weekend with Pedal the Cause

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30 October 2013

Pedal the Cause is many things. It’s a cancer research fundraiser. It’s a bike ride. It’s a celebration of trial, tribulation, and growth. It’s a metaphorical and physical act honoring the stamina of cancer patients. It’s a community.

For one weekend a group of cancer patients, friends of cancer patients, researchers, caretakers, doctors, and kindred spirits made their way from the UCSD Moores Cancer Center to the mountain town of Julian and back. Via bicycles. The entire experience was simply amazing. There are too many things I could say about it, so instead I will guide my story with photographs.

Image: I’m up there, I promise!

My Saturday started pretty early. I refused to drive to the start and had a nice warmup hauling my 30lb backpack up Gilman Drive. I dropped it off, said hello to many familiar faces, and quickly found my way to the starting chute.

The course profile to Julian is pretty much up, up, and up. A long bike ride in San Diego County can take one through many microclimates. Saturday did not disappoint. Gray skies at the start transitioned to mist and fog as we ascended up to Poway, then as we hit Scripps Poway Parkway we ascended above that as well, finding clear skies.

Image: My buddy Andrew Ulvestad shot this (while moving, yes he’s talented!) as we ascended above the clouds and up to the desert air of Ramona.

Within a matter of miles mist and fog gave way to Ramona and desert air. I managed to find company with those that just love to ride hard and fast, so I tagged along. Before I knew it we were at the Santa Ysabel aid station snacking on orange slices, which at that moment in time was quite possibly the most pleasant thing in the world.

Our extraordinarily ambitious friends headed north from there to circle around Julian and ascend from the east side. My friend Andrew Ulvestad and I felt that lunch sounded like a better idea, and ascended the final 7 miles straight up to Julian.

Image: I had the honor of being the first cyclist into the riders’ village

Throughout the afternoon and evening I met so many amazing people at the riders’ village. It was inspiring to hear the stories of those that not only survived, but were made stronger by their experiences with cancer. Everyone there had no facade. Any metaphorical mask was magically discarded somewhere on the road to Julian.

Image: It’s hard to find better company. Here I am with Bill Koman, Diane Hyat, Robert Kaplan, and Mike McHale

Hundreds of people present were completely open and exchanging their incredible, extremely personal life experiences and stories. I was somewhat apprehensive that perhaps a depressed or sad mood might underly an event associated with something (cancer) that causes grief to so many people. What I found instead was an honesty, openness, and kinship with almost complete “strangers” that became the theme of my Pedal the Cause. It’s taken a few days, but it’s still registering how uplifting, enlightening, and rich that was. The spice of life was served up all night.

Image: The evening’s ceremonies flawlessly transitioned the vibe, with cancer survivor Bill Koman laying down some extremely ambitious goals for the coming years, including 1000 riders for next year’s event.

As expected, the night was pretty cold up on the mountain. And also as expected, this coast-loving weakling didn’t pack warmly enough. Lesson learned! The next morning saw clear skies, and a FAST descent down the mountain to Santa Ysabel. We also descended the stunning Highway 78 down to Escondido. Again, those microclimates… we went from clear and cold, to clear and warm-ish, to borderline hot in Ramona, all the way down to the fog bank that met us at the base of the 78.

Up Torrey Pines and on to UCSD, we were greeted by a finishing chute lined with cheering people and cowbells! I wanted to thank everyone there at the same time, but realizing the absurdity of that wish rolling by at 15mph I simply sat up and pointed and smiled at everyone that came to cheer.

Image: well, no image yet. I’m hoping the photographer at the end got this. He might still be editing and getting them online. I’ve got my fingers crossed!

I want to thank all of my friends and family that supported me in this cycling and fundraising journey, even if it was in the smallest way. Thanks for reading, and I am already looking forward to next year’s event!


KFMB Channel 8 coverage of Pedal the Cause

Written by Ryon

October 30th, 2013 at 3:06 pm

Posted in Science Blog

Could the liquid biopsy circumvent tumor heterogeneous hurdles?

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24 October 2013

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Nature magazine recently had a special Insight on tumor heterogeneity, complete with no less than six fantastic review articles on the topic.

Barbara Marte gave an introduction on the matter:

Cancer is not one but many diseases. It is different in each patient and continuously evolves into a progressively complex interplay of diverse tumour cells with their changing environment.
In an insightful and prescient 1976 paper, Peter Nowell proposed the now prevailing view of cancer as a process of clonal evolution, in which successive rounds of clonal selection give rise to tumours with diverse genetic and other molecular alterations that may necessitate ‘personalized’ therapies.

There is great variability between cancers, but it is the variability within tumors that I see as the biggest hurdle for diagnosis, treatment, and resistance even with the multi-faceted revolution in sequencing and targeted therapies.

If every cancer, and perhaps every cancer cell, is unique, and some cancer cell populations are more ‘unique’ than others, this needs to be taken into consideration for the improvement of cancer diagnoses and prognoses, for the treatment and monitoring of each patient and for the design of clinical trials to evaluate new therapies.

I could not agree more. A caveat to every molecular analysis on tumor tissue is that it offers only a spatial and temporal snapshot of the disease. This caveat is seldom acknowledged in oncology literature, almost never directly addressed in discussions, and sometimes completely ignored in experimental methodology that would be greatly affected by the heterogeneous snapshot caveat. What was present at that moment in time might be no more in weeks’ or months’ time. While there is a potential for a malignant tumor to continue to evolve, tremendous spatial heterogeneity already exists in many tumors. (1-4)

Any targeted therapy might not hit every tumor cell even with perfect pharmacodynamics, because a particular target might not be present in every tumor, and it’s difficult to know what other targets exist in other regions of a tumor without a comprehensive survey of tumor heterogeneity. Genetic testing requires biopsies for genomic surveys, and even the most advanced sequencing technologies cannot get past a particular caveat: it is impossible to survey an entire tumor’s genetic heterogeneity. Repeat biopsies are highly invasive to cancer patients and pose logistical and ethical problems. Besides, and if a particular tumor was easily accessible, it would likely be removed surgically anyway.

So, what part of a tumor could or should be biopsied? How much weight should be put on the driver mutations detected in a particular biopsy? What essential molecular targets might evade our notice?

While there is a growing appreciation (apprehension?) at the immense heterogeneity within tumors and the associated hurdles to more effective therapy, there is also a growing interest in cell free DNA (cfDNA). It was recently reported that advanced cancer patients have an order of magnitude higher amount of DNA floating around in their blood plasma than healthy volunteers (5). Furthermore, the amount of cfDNA was shown to correlate with disease progression (6), and to carry tumor-specific mutations that can be used to track genomic evolution of metastatic cancer in response to targeted therapy (7).

The origin of this cfDNA is likely the same cells that will cause the most harm to cancer patients: the ones that escape tumor(s) and seed the bloodstream. Studies from circulating tumor cells (CTC) indicate that the vast majority of CTC’s do not form tumors (8, 9), and the detection of shards of tumor cells along with long strands of genomic DNA is consistent with many of these cells being torn apart by sheer forces in the vasculature. The genomic interrogation of this cfDNA might not be too far away with the current trends in sequencing technology, giving rise to the non-invasive “liquid biopsy” of solid tumor heterogeneity surveyed with a blood draw (7, 10).

Such analyses are amendable to serial biopsies and might give light to the kinetics of tumor heterogeneity over time, portraying patterns of tumor evolution that could be exploited therapeutically, and perhaps even prophylactically.


1. Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. The New England journal of medicine. 2012 Mar 8;366(10):883-92. PubMed PMID: 22397650. Epub 2012/03/09. eng.
2. Yachida S, Jones S, Bozic I, Antal T, Leary R, Fu B, et al. Distant metastasis occurs late during the genetic evolution of pancreatic cancer. Nature. 2010 Oct 28;467(7319):1114-7. PubMed PMID: 20981102. Pubmed Central PMCID: PMC3148940. Epub 2010/10/29. eng.
3. De Mattos-Arruda L, Cortes J, Santarpia L, Vivancos A, Tabernero J, Reis-Filho JS, et al. Circulating tumour cells and cell-free DNA as tools for managing breast cancer. Nature reviews Clinical oncology. 2013 Jul;10(7):377-89. PubMed PMID: 23712187. Epub 2013/05/29. eng.
4. Park SY, Gonen M, Kim HJ, Michor F, Polyak K. Cellular and genetic diversity in the progression of in situ human breast carcinomas to an invasive phenotype. The Journal of clinical investigation. 2010 Feb;120(2):636-44. PubMed PMID: 20101094. Pubmed Central PMCID: PMC2810089. Epub 2010/01/27. eng.
5. Perkins G, Yap TA, Pope L, Cassidy AM, Dukes JP, Riisnaes R, et al. Multi-purpose utility of circulating plasma DNA testing in patients with advanced cancers. PloS one. 2012;7(11):e47020. PubMed PMID: 23144797. Pubmed Central PMCID: PMC3492590. Epub 2012/11/13. eng.
6. Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, et al. Analysis of circulating tumor DNA to monitor metastatic breast cancer. The New England journal of medicine. 2013 Mar 28;368(13):1199-209. PubMed PMID: 23484797. Epub 2013/03/15. eng.
7. Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, et al. Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature. 2013 May 2;497(7447):108-12. PubMed PMID: 23563269. Epub 2013/04/09. eng.
8. Allard WJ, Matera J, Miller MC, Repollet M, Connelly MC, Rao C, et al. Tumor cells circulate in the peripheral blood of all major carcinomas but not in healthy subjects or patients with nonmalignant diseases. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004 Oct 15;10(20):6897-904. PubMed PMID: 15501967. Epub 2004/10/27. eng.
9. Meng S, Tripathy D, Frenkel EP, Shete S, Naftalis EZ, Huth JF, et al. Circulating tumor cells in patients with breast cancer dormancy. Clinical cancer research : an official journal of the American Association for Cancer Research. 2004 Dec 15;10(24):8152-62. PubMed PMID: 15623589. Epub 2004/12/30. eng.
10. Lianidou ES, Mavroudis D, Georgoulias V. Clinical challenges in the molecular characterization of circulating tumour cells in breast cancer. British journal of cancer. 2013 Jun 25;108(12):2426-32. PubMed PMID: 23756869. Pubmed Central PMCID: PMC3694246. Epub 2013/06/13. eng.

Written by Ryon

October 24th, 2013 at 9:50 am

Posted in Science Blog

Does the end of gene patents mean rising demand for diagnostic sequencing?

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1 October 2013

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Last week I attended a fantastic panel debate on gene patents hosted by the San Diego chapter of Oxbridge Biotech Roundtable at The Scripps Research Institute. Rachel Tsui moderated a panel of four:

Pro gene Patents:
Lisa Haile
Anthony Kuhlman

Against Gene Patents:
Lisa Madlensky (Genetic Counselor at UCSD Moores Cancer Center)
Lana Feng (Founder, Personalized Diagnostics)

The debate itself was more of a discussion, with minimal rhetorical tactics used by either side. However, the debate could have been improved with a better overview of patent law in general; the nature of audience questions indicated inadequate fundamental knowledge about what was being debated.

That said, the questions and discussions were very good. A few ideas / questions that stuck out to me:

1) Along the lines of patenting a technique for detecting something “natural”: Is the Reference Genome actually “natural” or a best-fit amalgamation of the genetic heterogeneity of mankind? If so, perhaps this is not actually natural and could be patented in itself?

2) Companies holding gene patents usually do not sue academic institutions, though they can. It is in their best interests most of the time to let academic labs do research and publish, purportedly adding value to their patents. (Lisa Haile)

3) Currently, diagnostic sequencing of patented genes (in her experience as a genetic counselor) are not dramatically more expensive than non-patented genes. (Lisa Madlensky)

After the panel discussions and audience questions concluded, I had a chance to catch up with Dr. Madlensky on the topic of diagnostic testing. As a genetic counselor with decades of experience, she has literally witnessed the birth of the genomic age through the eyes of medicine. I always see a sense of irony about the incredible multitude of what we “know” about genetics and how little is used in the clinic. The reasons for this are multifaceted, but are quickly rising from esoteric to painfully relevant with the growing tide of the genomic age.

In particular, I was interested in the impact of platforms like Understand Your Genome from Illumina that aim to put personal genomic data directly into the hands of the consumer. The Understand Your Genome conference will take place next month here in San Diego, and for a $5000 ticket and a DNA sample, Illumina will provide participants with an iPad with their genome browser application containing participant’s entire genome! I could wax poetic about the dawn of personalized genomics and science fiction becoming science fact, but for I am most immediately concerned with the way this will affect the physician-patient relationship. I wrote recently about the harms of overdiagnosis in otherwise healthy patients and many of these concerns could be carried over for considerations relating to personal genomics and genetic curation.

I relayed some of these concerns to Dr. Madlensky, and she had a few perspectives to add to the mix. Although the FDA guidelines are evolving, there is regulation in place for diagnostic-grade sequencing information, and before making any recommendations in genetic counseling it is necessary to have gene(s) in question re-sequenced, usually via the Sanger method. Critically, diagnosis today is mostly phenotype driven, not genotype driven: physicians and genetic counselors do not usually go looking for things that could be “wrong” when no obvious malady is present. Even then, they do not usually do genetic interrogation without having other reasons for doing so, like presence of disease symptoms in the patient or a family history of such.

That said, there is a changing trend, and the rising genomic tide might entice more patients and physicians to use the emerging genetic tools for screening purposes. However, there is still one major gatekeeper for any medical intervention: the physician (as it should be, in my opinion. More on that some other time). The physicians’ recommendations and prescriptions, in turn, are regulated by follow-up medical grade sequencing diagnostics of individual genes. Given this scenario, it would not be too much of a stretch to imagine a hugely increased demand for diagnostic-grade sequencing tests and centers (private or public) and for qualified genetic counselors, as most primary care physicians are are not adequately trained in the nuances of molecular diagnostics to make use of the rising tide of personal genomics.

In summary:

The recent Supreme Court rulings will not directly, dramatically change the current medical genomic landscape for patients. However, it makes a smoother landscape for sequencing enterprises.

In the near future (less than a few years) we may all have our genomes on iPads.

Given this scenario, the rate limiting steps for medical action will still remain with physicians (I hope), and their actions are in turn limited by the availability of diagnostic-grade medical sequencing tests.

There might be vastly increased demand for FDA-approved medical diagnostic sequencing tests and centers.


Written by Ryon

October 1st, 2013 at 4:06 pm

Posted in Science Blog