Biotech Strategy Blog

Commentary on Science, Innovation & New Products with a focus on Oncology, Hematology & Cancer Immunotherapy

Posts from the ‘Diagnostics’ category

Today in the plenary session of the 102nd Annual Meeting of the American Association for Cancer Research (AACR), Lynda Chin from Dana-Farber Cancer Institute in Boston provided an excellent overview of the challenges and opportunities of translating insights from cancer genomics into personalized medicine that will benefit patients.

I unequivocally recommend listening to the webcast of the plenary when it is posted on the AACR website.

As Dr Chin stated at the start of her presentation, “cancer is fundamentally a disease of the genome.”  The goal of all cancer research is to make progress with prevention, detection and cure.

In the plenary presentation she highlighted some of the successes that have come from understanding the genome e.g. the knowledge of BRAF mutation in melanoma led to the identification of a target and development of a new drug in 8 years.  In addition to the development of novel therapeutics, genomics research has helped companies reposition drugs and she highlighted crizotinib as an example (move from C-Met to ALK inhibition in NSCLC).

These successes have “motivated researchers” according to Chin.  However, it is transformative new technology such as the next generation of sequencing technology that has heralded “a new era of cancer genomics.”  Massively parallel sequencing enables comprehensive genome characterization.

Not only has innovative new sequencing technology increased the throughput, but it has dramatically decreased the costs.  As Dr Chin noted, some have questioned whether cancer genomics is worth it?  She outlined some of the recent successes, such as BAP1 in ocular melanoma (see my previous post on this) as examples of its value.

Challenges remain such as the management of the vast amount of data that genome sequencing produces.  Data management, processing and storage remain issues, as does the need to develop a reference human genome against which a patient’s tumor profile could be compared.

And even when you find a mutation, the challenge is to separate the “drivers” from the “passengers.” This according to Chin requires a “robust statistical framework”.

Cancer signaling is not linear, but is a highly interconnected and redundant network, so it remains a big task to translate genomics into personalized medicine.  According to Dr Chin using mice as models to bridge the gap between sequencing and man may be the way forward in translating cancer genomics into personalized medicine.

It’s a busy day of science at the 102nd American Association for Cancer Research (AACR) annual meeting in Orlando, You can follow what’s happening on twitter, #AACR.  Pharma Strategy Blog has an excellent “Cover it Live” widget that shows everyone’s #AACR tweets. It allows you to go back in time, so you can see what happened earlier.  AACR also has some excellent webcasts and podcasts from the meeting.

However, what caught my attention this morning was the launch of a new journal, Cancer Discovery; preview copies were handed out to attendees at the plenary session this morning.

In a world where we are already overwhelmed by data, publications and sources of information, why is this journal both important and worth reading?

Firstly, this team has a distinguished group of editors, Lewis Cantley, PhD and José Baselga MD PhD are Editors-in-Chief.  However, what attracted me was the way this journal, in a highly readable way, covers a wide range of topics from news, updates on current research to mini reviews and research articles.

In the news section, the journal picked up on nanodiamonds for drug delivery (a topic previously mentioned on this blog), and discussed the Gilead acquisition of Calistoga from perspective of bringing PI3K delta inhibitors to market.

I liked the selected highlights of recent articles of exceptional significance from the cancer literature.  The mini review on the “stumbling blocks on the path to personalized medicine in Breast Cancer” summarized the challenges in the clinical development of PARP inhibitors. The research articles reminded me of those I’ve read in other journals such as Science, with high quality figures and tables.

If AACR and the editors can keep up the high standard of the April 2011 preview copy they have published, Cancer Discovery will definitely be on the reading list of those involved with cancer research, new product development and translational medicine.

You can find out more about Cancer Discovery and read online articles on the AACR website.

Yesterday, I posted the first part of my interview with Dr Todd Sherer, Chief Program Officer at the Michael J Fox Foundation.

Next week, I will be posting the second part of the interview that discusses the significant research the foundation is funding on biomarkers that can help the diagnosis of the disease and monitor its progression.

If you are interested in learning more about the latest developments around Parkinson’s disease biomarkers, then you may wish to consider the April 27, 2011 webinar from the American Association for the Advancement of Science (AAAS) on the “Early Detection of Parkinson’s Disease: The Challenges and Potential of New Biomarkers.”

Moderated by Dr Todd Sherer, the webinar will discuss the only FDA approved biomarker, DaTscan that provides for imaging of dopamine transporters at dopaminergic nerve terminals in the nigrostriatal pathway.  It will also discuss the Parkinson’s Progression Markers Initiative (PPMI) that the foundation is funding.

Today is the deadline to take advantage of the early bird discounts on offer for this webinar.

Innovation in drug delivery presents opportunities for biotechnology companies, and is an area I expect we will see major leaps forward through nanotechnology.

Nanotechnology is the application of science and engineering to materials that are between 1 and 100 nanometers (nm) in size.  The Environment Protection Agency (EPA) defines nanotechnology as “the creation and use of structures, devices, and systems that have novel properties and functions because of their small size.”

1nm is one-billionth of a meter.  To put this in context, 1nm is one seven-thousandth of the width of a red blood cell or one eighty-thousandth of the width of a human hair. These are unimaginably small materials that are engineered to operate at the molecular and atomic level.

What’s more, there are now more than 1000+ consumer products on the market that utilize nanotechnology from the titanium particles in sunscreens to the silver contained in advanced first aid strips/plasters.  Nanotechnology will impact more than $2.5 trillion of manufactured goods by 2015.

Lux Research predicts that by 2014, 16% of manufactured goods in healthcare and life sciences will include nanomaterials.

To date, the United States leads the way in the fast evolving field of nanotechnology.  Between 2001 and 2010, the U.S. Government invested $12.4 billion in nanoscale science, engineering and technology through the U.S. National Nanotechnology Initiative (NNI).

The National Cancer Institute’s “NCI Alliance for Nanotechnology in Cancer” has an excellent website that outlines the potential impact of nanotechnology.

Some of the promising new cancer diagnostics and therapies based on nanotechnology include:

  • Positron Emission Tomography (PET) imaging agents that can be used to assess the responsiveness of tumors to chemotherapy
  • Chemically engineered adenovirus nanoparticle that stimulates the immune system. This is in phase 1 trials for chronic lymphocytic leukemia (CLL).
  • Cyclodextrin-based nanoparticle that encapsulates a small-interfering RNA (siRNA) agent that shuts down a key enzyme in cancer cells
  • CRLX101, a cyclodextrin-based polymer conjugated to camptothecin is in clinical trials with solid tumor patients
  • A nanoparticle based magnetic resonance imaging (MRI) contrast agent that binds to αvβ3-intregrin, a protein found on newly developed blood vessels associated with tumor development. This is in early clinical trials
  • Technology for the detection of cancer biomarkers such as prostate specific antigen (PSA)
  • Use of carbon nanotubes to improve colorectal cancer imaging.

Emerging companies such as Bind Biosciences are focusing on targeting cancer, inflammatory, cardiovascular diseases and infectious diseases with therapeutic nanoparticles.  Their lead product BIND-014 is currently in phase 1 development.

Innovations in nanotechnology will continue to present new product opportunities for biotechnology, pharmaceutical, medical imaging and diagnostics companies, and should be on everyone’s radar.

 

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One of the challenges with cancer is being able to detect the disease early enough for effective treatment. The staging or progression of the cancer at time of diagnosis is correlated with 5 year overall survival (OS) rates. Biomarkers that may be expressed by a cancer are, therefore, potentially useful for diagnosis and monitoring of treatment.

There is an ongoing debate about the effectiveness of prostate specific antigen (PSA) as a biomarker for early detection of Prostate Cancer (PC). As Sally Church on Pharma Strategy Blog discusses, PSA measurements can offer false positives and up to 75% of men have a negative biopsy. There is clearly a need for alternatives to PSA measurements.

In the March 1, 2011 online edition of Clinical Cancer Research (a journal of the American Association for Cancer Research, AACR), Richard Morgan and colleagues from the Postgraduate Medical School at the University of Surrey in Guildford, assessed the potential of the Engrailed-2 (EN2) protein as a prognostic biomarker for PC.

Their research found that EN2 is secreted into the urine of men with PC (92%, n=104), but does not appear in the urine of those without PC (0%, n=11). Presence of EN2 in the urine showed a 66% sensitivity for the detection of PC without a digital rectal exam (DRE) when compared to biopsy findings of those with confirmed PC (54 of 82 men). The specificity of the test is almost 90%, i.e. it can pick out men with prostate cancer versus those without cancer.

Interestingly, there was no correlation between serum PSA levels and the presence or absence of EN2. EN2 is measured in small quantities of unprocessed urine (100μl) by means of a simple enzymatic assay.

The investigators state in their paper that a multicenter clinical trial is planned to investigate whether EN2 measurements can be used as a tool for monitoring disease progression after hormonal treatment, radiotherapy or surgery.

However, despite the promising preliminary results in this paper, it is still too early to say whether EN2 will evolve into a clinically useful predictive biomarker for PC.  The fact that EN2 was secreted in patients with non-PSA secreting PC, raises the possibility that it might have a diagnostic role to play in combination with other biomarkers.

EN2 has also been shown to be an oncogene in breast cancer, so it will be interesting to see if there is any further information presented at the forthcoming AACR annual meeting from April 2 to 6 in Orlando.

I recommend reading Pharma Strategy Blog for further insight on cancer biomarkers.

That is the interesting question that struck me after reading Sam Kean’s informative article in the February 4 edition of Science.  Ten years on from the sequencing of the Human Genome, the patenting of human genetic information presents unique challenges at the interface of science, law and innovation.

Researchers have obtained patents for isolating different sections of DNA that occur naturally in our bodies.  Whether this should be permitted is still open to debate. Currently, diagnostic companies who want to launch a new cancer test face the challenge that patents now cover many genes.

The Science article cites start-up Foundation Medicine in Cambridge, MA who estimated the cost of investigating possible patent infringement for a new diagnostic test at $35M, a cost that exceeded the company’s $25M of VC funding.

Add in the costs of any royalties or licensing fees and the issue of prior patents is now a nightmare for any diagnostics company.  It is simply not practical to license every gene that may be implicated in a multifactorial disease such as diabetes.  Pre-existing patents have become a barrier to market entry.

As the Science article reports, gene patents cover not only very small snips of DNA, as short as 15 nucleotides, but can prohibit the sequencing of associated DNA. Companies such as 23andMe that sequence an individual’s genome to test for the presence of certain genes may be violating patent rights of others.

What’s more so called “method” patents cover the linking of a gene sequence with a specific medical condition.

As advances in personalized medicine continue, there is a need to balance the competing interests of protecting scientific discovery and rewarding innovation, while at the same time allowing access to human genetic information that many think should be “free to all men and reserved exclusively to none.” Quotation from Bilski v. Kappos, 130 S.Ct. 3218, 3225 (2010)

A law suit currently on appeal to the US Court of Appeals for the Federal Circuit may lead to a change in the current practices of the US Patent & Trademark Office.  The American Association of Pathologists and others have challenged several patents relating to the breast cancer genes BRCA1 and BRAC2 held by Myriad Genetics and the University of Utah Research Foundation.

BRCA1 and BRCA2 genes are associated with an increased risk of breast and ovarian cancer.  The US district court for the Southern District of New York in a surprise decision by Judge Robert Sweet, invalidated Myriad’s patents.  The New York Times article about the case has a link to the Judge’s 156 page opinion.  The decision that isolated but otherwise unaltered DNA should not be patentable is now being appealed by Myriad.

In their legal brief, arguing for the decision to be upheld, the United States Government states:

“The fact that a particular segment of the human genome codes for the BRCA1 protein in a human cell, for example, rather than for adrenaline or insulin or nothing at all, is not within the power of science to alter. Such basic natural relationships may not be the subject of a patent.”

If the District Court’s decision is upheld on appeal, it would represent a fundamental policy shift on what patents can be obtained for human genetic information. Such a decision would prevent Myriad from charging royalties and exclusivity for the genetic testing of BRCA1 and potentially invalidate similar types of patents. Depending on your point of view this will either harm the biotechnology industry or increase the market opportunities.

Given the stakes involved, it is likely the Myriad case will end up being considered by the United States Supreme Court, and what they may decide is anyone’s guess.

To read more in-depth analysis about the Myriad case and the legal issues involved with the patenting of genomic information, I strongly recommend the “Genomics Law Report”, a blog written by Dan Vorhaus and others.

Ten years after the human genome was sequenced we are still working out the intellectual property rights. The question as to whether companies should be allowed to patent unaltered human genes is one that will be answered in the not too distant future.

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