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Posts tagged ‘personalized medicine’

Earlier this year, I announced that there were two people I was hoping to interview next as part of the ongoing Making a Difference series, where thought leaders share their ideas and vision on emerging and important topics in cancer research. Previous discussants have included the following:

Today, I am delighted to announce that one of those identified thought leaders, Gordon Mills (MD Anderson), kindly agreed to be filmed while at last week’s ECCO (European Multidisciplinary Cancer Conference). Dr Mills is Chairman of the Department of Systems Biology, Chief of the Section of Molecular Therapeutics, Professor of Medicine and Immunology, and Anne Rife Cox Chair in Gynecology. He is also one of the best strategic thinkers I’ve come across in cancer research who not only understands the big picture, but also the detailed subtleties.

Originally, we collected audio-visual to ensure an accurate recording for the usual transcript that gets posted here on the blog, but it came out well and the subject was so compelling that we deemed it well worth watching as the first thought leader video interview here on Pharma Strategy Blog.

Dr Mills gave one of the three keynotes in the first Presidential Symposium at the Stockholm meeting, along with Drs José Baselga (MGH) and Tak Mak (U. Toronto) in a fascinating session on Personalized Medicine. This session covered the whole gamut from therapeutics, biomarkers, assays and to metabolism. I took the liberty to include a couple of Dr Mill’s slides to illustrate the points we were discussing in the video below.

We’ve come a long way over the last decade in terms of progress, but hopefully, as technology and our knowledge improve further, the best is yet to come.

This is the fifth interview in the series with thought leaders in the Making a Difference series – it covers a wide range of critical topics including BRAF, mTOR, PI3K, EGFR and RAS – please do check it out:

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Ruby (@divabiotech) talking at Singularity U

My friend Ruby Gadelrab is the very dynamic and vivacious Head of Marketing and Clinical Development for International Markets at Affymetrix.

She was recently invited to give a talk at the prestigious Singularity University meeting.

I was thrilled to see that Ruby has generously posted her talk online on her blog, Diva Biotech, which I’m a big fan of, and check out regularly in my RSS feeds.   The excellent presentation well worth reading if you want to come up to speed on the basics, as well as see her personal view on where the field is going in the near future.

I learned a lot from her synopsis and thought it was a nice thing to share here with PSB readers who may be interested in the topic, as this is a subject that will be very much to the fore in the next 5-10 years.

You can read all about it and download Ruby’s slides on Biotechnology, Genomics and Personalized Medicine.

Check it out!

One of the highlights of the recent American Association for Cancer Research annual meeting was a plenary session updating the results of the ongoing BATTLE trial at MD Anderson in non-small cell lung cancer (NSCLC).

The more scientific readers will want to check out the academic paper and commentaries published in Cancer Discovery, (see below) or listen to the complimentary AACR webcast of the plenary talk including Dr Hong’s Reverse Migration Strategy, but I realised that not everyone is familiar with, or understands the background, to this ground breaking study.

It therefore seems a great opportunity to use Storify to collate resources and snippets from social media sources to create a story around the events that have happened over the last year…

 

References:

ResearchBlogging.orgKim, E., Herbst, R., Wistuba, I., Lee, J., Blumenschein, G., Tsao, A., Stewart, D., Hicks, M., Erasmus, J., Gupta, S., Alden, C., Liu, S., Tang, X., Khuri, F., Tran, H., Johnson, B., Heymach, J., Mao, L., Fossella, F., Kies, M., Papadimitrakopoulou, V., Davis, S., Lippman, S., & Hong, W. (2011). The BATTLE Trial: Personalizing Therapy for Lung Cancer Cancer Discovery DOI: 10.1158/2159-8274.CD-10-0010

Sequist, L., Muzikansky, A., & Engelman, J. (2011). A New BATTLE in the Evolving War on Cancer Cancer Discovery DOI: 10.1158/2159-8274.CD-11-0044

Rubin, E., Anderson, K., & Gause, C. (2011). The BATTLE Trial: A Bold Step toward Improving the Efficiency of Biomarker-Based Drug Development Cancer Discovery DOI: 10.1158/2159-8274.CD-11-0036

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Two articles and an accompanying editorial published in the Journal of the American Medical Association (JAMA) today look at whole genome sequencing in a small number of cancer patients with Acute Myeloid Leukemia (AML) and Acute Promyelocytic Leukemia (APL) to determine what mutations had developed and whether that knowledge would aid in clinical decision making.

In the case of one of the patients, the information learned from the sequencing led to a change in treatment, but sadly the AML patient died soon after.

There is a big caveat here – whole genome sequencing is not yet ready for prime time – the technique currently costs in the range of $20-40K per person, but in the future as costs come down, the $1K genome should be a viable goal to aid oncologists make clinical decisions through a more personalised medicine approach.  By that, I mean selecting a patient’s therapy based on the underlying molecular biology of their cancer – an individual thumbprint, if you like.

In the case of Welch et al’s, (2011) study, they wanted to see if sequencing could be taken out of the lab and into the clinical arena.  They had a particularly challenging case – a woman with a family history of cancer who was diagnosed with early onset breast and ovarian cancers in her thirties and unfortunately developed treatment-related AML (t-AML) and sadly died soon after.

The question here is what factor(s) might contribute to the cancer susceptibility?

BRCA1 and 2 analysis was not particularly useful in this case.  However, whole genome sequencing from the skin and leukemic cells identified a new TP53 mutation – essentially the technique picked up unknown structural variants that are missed by conventional assays.  As Pasche and Absher summarised it in their editorial:

“The patient was heterozygous for a novel deletion of 3 exons of the TP53 gene and that the intact copy of TP53 had been lost in the leukemic cells due to uniparental disomy.

This mutation in TP53 would not have been discovered without whole-genome sequencing.”

This finding also has important implications for the offspring of carriers of this mutation.

Link et al’s (2011) study was a little different.  They also had a challenging case – a patient diagnosed and being treated for AML who was awaiting an allogeneic stem cell transplant.  The pre-treatment bone marrow cells were used for the whole genome sequencing.

The sequencing results produced a surprise from the analysis – they revealed the presenece of a novel and cytogenetically invisible fusion oncogene normally associated with APL, thus enabling the clinical team to reconsider a new treatment plan for the patient based on the differential diagnosis.

The editorial concluded that:

“Hence, recent advances in genomics are likely to change the molecular characterization of cancer rapidly and provide a path for the personalized treatment of patients with cancer.”

To which I would add the caveat that whole genome sequencing, while intuitively very useful, is unlikely to have a wider impact until sequencing costs come down to more sensible and practical levels.

However, this time is fast approaching since genome sequencing costs are beating Moore’s Law in the rate they are decreasing.  The research papers published in JAMA this week are an important milestone on the road to personalised medicine.

References:

ResearchBlogging.orgWelch, J., Westervelt, P., Ding, L., Larson, D., Klco, J., Kulkarni, S., Wallis, J., Chen, K., Payton, J., Fulton, R., Veizer, J., Schmidt, H., Vickery, T., Heath, S., Watson, M., Tomasson, M., Link, D., Graubert, T., DiPersio, J., Mardis, E., Ley, T., & Wilson, R. (2011). Use of Whole-Genome Sequencing to Diagnose a Cryptic Fusion Oncogene JAMA: The Journal of the American Medical Association, 305 (15), 1577-1584 DOI: 10.1001/jama.2011.497

Link, D., Schuettpelz, L., Shen, D., Wang, J., Walter, M., Kulkarni, S., Payton, J., Ivanovich, J., Goodfellow, P., Le Beau, M., Koboldt, D., Dooling, D., Fulton, R., Bender, R., Fulton, L., Delehaunty, K., Fronick, C., Appelbaum, E., Schmidt, H., Abbott, R., O’Laughlin, M., Chen, K., McLellan, M., Varghese, N., Nagarajan, R., Heath, S., Graubert, T., Ding, L., Ley, T., Zambetti, G., Wilson, R., & Mardis, E. (2011). Identification of a Novel TP53 Cancer Susceptibility Mutation Through Whole-Genome Sequencing of a Patient With Therapy-Related AML JAMA: The Journal of the American Medical Association, 305 (15), 1568-1576 DOI: 10.1001/jama.2011.473

Pasche, B., & Absher, D. (2011). Whole-Genome Sequencing: A Step Closer to Personalized Medicine JAMA: The Journal of the American Medical Association, 305 (15), 1596-1597 DOI: 10.1001/jama.2011.484

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This week I'm adjusting to the high altitude of Denver while at the American Association of Cancer Research (AACR) meeting on molecular diagnostics and cancer therapeutics. It's a great little meeting, networking opportunities are excellent and I'm learning a lot about what new cutting edge ideas are being explored.

I will be doing some highlights from each day series later in the week once I've had time to process all the information, as there is a lot to digest here.

What is interesting though, is to look at big picture trends, both in academia and basic research and also what industry are doing in their research teams, since these ideas may well get incorporated into early phase I clinical trials for validation and pilot purposes. More about this later in the week.

Although a lot of the attendees are from the diagnostics end of the business (either academic or industry), there are quite a few serious researchers and thinkers here too. Gordon Mills from MD Anderson gave one of the best talks I've seen at an opening session in a long while. David Parkinson from Nodality also laid out a strategic and thoughtful overview of how things are currently, and how they will continue to change in cancer research with new approaches. 

One thing really struck me here in Denver. While outsiders and FDA become more paranoid about conflicts of interest, it is clear to me that what we actually need is closer and more collaborative relationships between basic and clinical research in order to translate the knowledge and ideas into practice or the clinic more quickly.  To do this requires fresh ideas, a fresh approach and better communication and collaboration. 

By collaboration, I don't just mean between academia and industry, but between labs and between companies, rather than competition. Increasingly, I'm seeing smart researchers presenting data that was generated on behalf of several groups, often in different cities or even countries, each providing different skills and expertise to the research. This used to happen sporadically between friends and former colleagues, but now it's starting to become more commonplace. It's a good sign and a great way to synergies resources and bring more expertise to projects.

Industry are typically very slow to change and tend to see other companies as rivals rather than for collaborative purposes, which is a great shame given that we're all working towards the same goal: fight cancer. 

That said, there are some exciting new, albeit subtle changes afoot. When I think of cancer research, the first two industry research powerhouses I think of are Genentech, who have traditional sought strong relationships with academia and Novartis, who have the Novartis Institute for Biomedical Research (NIBR) and the Genomics Institute of the Novartis Research Foundation (GNF).  

More recent examples include Novartis and GSK, who appear to have been collaborating on research projects and the other major one that surprised many was the Merck-Astra-Zeneca hookup on specific, but related compounds with relevant cancer pathways.

Which brings me to Gordon Mills stirring talk on Monday evening. He made the case that this is the time for systems biology to make it's mark. Rather than looking at adding in a targeted therapy eg an EGFR, a MEK or whatever inhibitor (TKI or monoclonal antibody) to shut off one particular piece of a complex pathway, we need to start looking at a broader concept, which he called 'pathwayness'. That is, we have learned that cancer biology is highly complex and shutting off one aberrant or overexpressed protein, won't shut down the whole engine because either the cancer adapts or other parts continue to function and drive the tumour's survival.

For me, what was spooky about this well thought and well argued talk was that it was eerily similar as a concept to what Frank McCormack was describing earlier this year using PI3K as an example. Both McCormack and Mills are probably ahead of their time.

What we need to see is industry listening to what they have to say and start to think more strategically about what to do with all the inhibitors we already have out there for the 12 critical cancer drivers that Bert Vogelstein discussed at AACR earlier this year.  

Mills argued cogently that we actually have many of the potential tools we need to take a deeper systems biology approach to personalized medicine and by looking at each patients cancer biology we could potential develop a treatment approach relevant to them. He called this 'listening to what the patient tells us'.

This reminded me that recently, there was an article in Forbes about why personalized medicine is bunk, written by a MD at a VC firm. The article annoyed me, mainly for it's lack of critical thinking, fair balance or even a basic understanding of what is happening in medicine and clinical research. Rather than vent in the comments, I turned up at this AACR meeting and was greatly reassured that cancer research is in good hands and we have many excellent people and resources focused on the whole concept of matching treatment to a patients tumour. It will happen. In many ways the revolution has already begun; we just need to get better at it. Every failure tells us something new and important about what to do next.

We have the tools, but there are also a lot of hurdles and challenges to be addressed along the way, not least the regulatory side of things and a different way of thinking about testing and validating the ideas in clinical trials. The good news is that there is much needed activity going on behind the scenes at the policy level, as witnessed by the Cancer Caucus in DC today, where Harold Varmus is kicking off a new era at the NCI. I'm hopeful that the think tank will have open minds and the passion to change the way we think about cancer research.

 

As part of a four part series on personalized therapy for lung cancer, here is the second summary in the series based on some fascinating lectures at the AACR meeting on the molecular origins in lung cancer this week.

The second presentation I really enjoyed on biomarkers and personalized therapy looked at the ‘blind alley’ that
many are still using to distinguish patients.  Histology, as Dr David Gandara aptly
described it, is a rather ‘crude form of molecular selection’ that is likely to
be a transient one.  He provided a
telling example of two patients with a different case history:

  1. 65 yo
    male who smokes, has a squamous histology, KRAS mutation, low ERCC1 and low
    RRM1
  2. 39 yo
    female who is a non-smoker with a adenocarcinoma, EGFR mutation and high ERCC1
    and high RRM1

He then posed the question to the audience of whether it is still
appropriate to treat these two patients the same way?

What was abundantly clear at this meeting to me is that the
answer would be an emphatic ‘no’ based, not on their physical characteristics
and histology, but on the underlying biology.  Whether that is a view held by the majority of community
oncologists, I’m not so sure though. 

Excision repair cross-complementing gene (ERCC1) is an interesting biomarker that was first mooted nearly ten years ago and has received little attention, but is now coming back to the fore as clinical trials and modeling techniques catch up with basic biology. It encodes a nucleotide excision repair protein that repairs a range of lesions, including UV-induced thymine dimers and other photoproducts, and also lesions caused by a variety of chemical agents including the platinums.

Dr Gandara noted that low
levels are prognostic in early stage I/II NSCLC and predictive of a
poor response in metastatic disease, thus suggesting that platinum chemotherapy
would be optimal, e.g using a gemcitabine-cisplatin combination, whereas early
stage patients with high levels of ERCC1 would have a good prognosis and likely
do better without chemotherapy.  ERCC1 has also been shown to play a role in DNA repair after cisplatin damage.  Interestingly, high tumour tissue levels of ERCC1 mRNA in ovarian and gastric cancer patients have been associated with cisplatin resistance.

Similarly, RRM1 is useful for predicting response to
gemcitabine and TS for pemetrexed. Although pemetrexed is approved for use in treating non-squamous
patients, what about TS expression in lung cancer?  Gandara noted the general trend towards high TS in SCLC and
squamous cell carcinoma and low TS in patients with adenocarcinoma. Knowing this kind of information about
the tumour biology (ERCC1, RRM1
and TS) can therefore be potentially useful in deciding which chemotherapy
regimen to use.

What this AACR meeting really brought to the fore to me is
the gradual move from rather crude methods to more sophisticated ways of
defining patient subsets as our knowledge and understanding of biology
improves.  

Sometimes though, the
gap between published research and clinical trials also lags, mainly because of
either the cost of tumour biopsy and biomarker studies in large scale trials or
the development of new inhibitors designed to target the molecular abnormality
identified.  The impression I came
away with is that the next five years may well produce some really big advances in
both basic science and clinical practices that will contribute to a more logical and scientific approach to the treatment of a hard to treat cancer.

Times are a-changin’ and that’s great news for patients with
lung cancer. 

 

ResearchBlogging.org
Dabholkar, M., Vionnet, J., Bostick-Bruton, F., Yu, J., & Reed, E. (1994). Messenger RNA levels of XPAC and ERCC1 in ovarian cancer tissue correlate with response to platinum-based chemotherapy. Journal of Clinical Investigation, 94 (2), 703-708 DOI: 10.1172/JCI117388 

Cobo, M., Isla, D., Massuti, B., Montes, A., Sanchez, J., Provencio, M., Vinolas, N., Paz-Ares, L., Lopez-Vivanco, G., Munoz, M., Felip, E., Alberola, V., Camps, C., Domine, M., Sanchez, J., Sanchez-Ronco, M., Danenberg, K., Taron, M., Gandara, D., & Rosell, R. (2007). Customizing Cisplatin Based on Quantitative Excision Repair Cross-Complementing 1 mRNA Expression: A Phase III Trial in Non-Small-Cell Lung Cancer Journal of Clinical Oncology, 25 (19), 2747-2754 DOI: 10.1200/JCO.2006.09.7915

There were a number of fascinating talks over the last four
days covering the latest information on biomarkers and personalized
therapy.  The summary that follows
is highly incomplete, but hopefully reflects some key points I’ve learned at
this excellent AACR meeting.  Unpublished
data reported by the presenters, will not, however be discussed and thus
commentary will be limited to general observations based on published data or
hypotheses evolving from them.

The small intimate event of 300 people with a common focus
and a well organized format contributes significantly to the learning and
offline discussions.  That is a
tribute to not only the organizing committee, but also the co-chairs, Drs Roy
Herbst from MD Anderson and David Carbone from Vanderbilt.  Both of these gentlemen, along with Dr
Paul Bunn from the Colorado Cancer Center, were particularly giving of their
time in helping me understand some of the more complex issues and I’m extremely
grateful to their patience with my many questions.  Any inaccuracies that may result in this report are entirely
mine.

First a little bit a history. 

Not so long ago, patients with non-small cell lung cancer
(NSCLC) would be treated with series of chemotherapy doublets or singlets, with
little regard for the underlying biology. 
As such, there is very little (or small) difference reported in the
literature between the various combinations such carboplatin plus paclitaxel,
gemcitaibine or docetaxel with cisplatin, or vinorelbine or pemetrexed  combinations, for example.  It was very much an empirical way of
looking at the options based on physicians choice depending upon patient
characteristics (stage, age, performance status etc) and physician preference
or experience with managing toxicities.

More recently, it was noticed that patients taking erlotinib
(Tarceva), an EGFR inhibitor, tended to do better if they had an EGFR mutation,
were young, female, non-smoker and with an adenocarcinoma histology.  Meanwhile, pemetrexed (Alimta), was
found to have a greater efficacy benefit in non-squamous compared to squamous
patients.

This represents a small advancement in identifying which
patients are most likely to respond to therapy, thereby sparing the exposure to
a drug that is most unlikely to have any benefit.  Four presentations were particularly intriguing to me and deserve some mention in separate blog posts.

In the first one, Dr Herbst presented the BATTLE (biomarker
based targeted therapy for lung cancer elimination) concept being developed and
evolved at MD Anderson across a large multi-functional team involving
researchers, physicians, and nurses. 
Aside from oncologists, intervention radiologists, diagnostic and
molecular pathologists were also heavily involved, as were the research groups
involved with molecular biology and biomarkers. 

The basic concept was that not all patients are the same and
tumour biopsies could be critical in determining the optimal clinical approach
to therapy in a highly heterogeneous disease.  Having biomarker driven clinical trials and understanding
molecular mechanisms of response will help improve knowledge of the underlying
disease for future studies.

BATTLE1 began in November 2006 and enrolled 341 patients
with NSCLC who had received at least one prior chemotherapy, had a good
performance status and biopsy amenable disease.  Eligible patients were randomized to receive one of four
regimens, depending upon their initial biopsy result, i.e. using adaptive
randomization.  Eleven core
biomarkers were used to help stratify patients and also determine the effect of
therapy before and after treatment, with the primary end point being 8 week
disease control rate: 

  • EGFR mutation – Erlotinib
  • Ras/Raf – Sorafenib
  • VEGF – vandetanib
  • Cyclin D1/RXR – Erlotinib plus bexarotene

The trial was closed in October 2009 and 227 patients had
evaluable tumour biopsies.

The concept appears to have proven successful and BATTLE2 is
now underway, with the goal of enrolling over 300 patients being evaluated with
different therapies in four new regimens, ie: 

  • Erlotinib
  • Erlotinib + IGF-1Ri
  • Erlotinib + AKTi
  • MEKi + AKTi

However,
Herbst noted that the IGF-1R combination may need to be reconsidered following the
recent announcement of the figitumumab futility data.

What I like about this approach is that treatment is based upon a logical design with a strong rationale from the underlying biology, rather than just relying on patient characteristics and physicians (sometimes biased) opinion.  

I do think we will see more of the work from translational medicine and research start to impact patient selection in the future.  Right now, we're just scratching the surface of what's possible.

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