This Just In: Help NCI Develop Pharmacodynamic Assays

PD_ Assay RFI – S09-205 – Issued 8-11-09

Follow the link above if you’re interested in helping NCI-Frederick develop novel, PD tests for point of care cancer diagnostics. The link is a download (Word Doc) of the entire RFI.

Here’s the gist:

The purpose of this Request for Information (RFI) is to provide potential subcontractors an overview of one strategic goal of the Division of Cancer Treatment and Diagnosis (DCTD) at NCI which is to promote the introduction of promising cancer therapeutics through the integration of appropriate pharmacodynamic (PD) tests into Phase 0 clinical trials with the focus on gathering evidence of targeted drug action that enables early Go/NoGo decisions. Information is requested from non-profit organizations, academics, clinical centers, and industry on the following topics:

1. Provide comment on the technologies and key cancer related pharmacodynamic targets for the next generation of PD assays that are to be developed using readily clinically adoptable state-of-the-art tools.

a. Utilization of multiplexed assay platforms that enable multiple PD readouts from small amounts of specimens coupled with robust annotation and data management to include: multi-channel microscopy, ELISAs, Laser Capture, PCR, etc. The goal is to maximize the amount of PD information that can be obtained from a single specimen. Combinatory markers have the greatest potential for providing valid and clinically relevant drug action and patient response information in genetically diverse populations.

b. The next generation of PD Assays must query multiple validated cancer specific analytes simultaneously to include the following categories:

1) Interrogate multiple targets within a molecular pathway, such as PTEN/Akt/PI3K/mTORC1 & 2.

2) Measure informative analytes that span across multiple core signaling pathways, of which the specific pathways driving the disease are often unique for different cancers.

3) Quantify multiple molecular events on the same target molecule, for example, activating and suppressing modifications of individual Akt isozymes or multiple phosphorylation sites on the MET receptor.

4) Identification of tumor stem cells using multiple known or novel stemness markers.

5) Filter target detection and quantitation to allow measurement in specific cellular compartments (e.g. plasma membrane and nucleus).

6) Develop assays for multiple new or known markers that are indicators of apoptotic commitment of tumor cells upon therapeutic treatment.

c. Establish an infrastructure to provide access to key reagents (antibodies, primers & probes, calibrators, references, etc), specimens (repositories, storage, processing, etc)), and accessory technologies (software, robotics, etc) that are essential for development of robust, sensitive, reproducible tests. This topic includes quality controlled production of critical reagents, regulatory (FDA/CLIA/CAP) knowledge and compliance, antibody diagnostic imaging, pattern recognition software, data analysis software that gives easily interpretable results, nanotechology for biopsies, and much more.

2. To provide institutions the opportunity to indicate their level of interest in responding to, and participating in, any future subcontracting opportunities in support of the pharmacodynamic assay initiative.

3. Provide institutions the opportunity to elaborate on their specific expertise in the core areas listed above.

Let me know if I can help or introduce you to the right people, if interested.

UPDATE 8/13  I should also point out that all of these “Business Opportunities” are available on SAIC-Frederick’s web site.

Here’s what’s there today:

A list of current business opportunities is provided below.

Name	Description	SBSA*	Organization	Contact
X09-003	Blanket Purchase Agreement covering Chemicals, Water Treatments, Parts, Supplies, and Services	No	SAIC-Frederick, Inc	C. Jean Eyler
SW09-003	Blanket Purchase Agreement for Recycled Paper	Yes	SAIC-Frederick, Inc.	Nancy Mayo
E08-075	Solicitation/Contract/Order for Commercial Items	No	SAIC-Frederick, Inc.	Kay Ecker
S09-170	Solicitation/Contract/Basic Ordering Agreement	No	SAIC-Frederick	Gary Krauss
X10-001	Solicitation/Contract/Order For Commercial Items	Yes	SAIC-Frederick	Nancy Mayo
S09-198	RFI: Insect Cell Based Biopharmaceutical Development	No	SAIC-Frederick
S09-202	HIV Vaccine Strategies	No	SAIC-Frederick
S09-205	RFI – Pharmacodynamic (PD) tests into Phase 0 clinical trials	No	SAIC-Frederick	Howard Souder, Jr.

FredCoBio and the Immaculate Confection

This may be a bit of a stretch to link Mary Spiro’s piece, “Gummi guts: artist Jason Freeny bestows rubbery confection with internal organs“ in the Baltimore Examiner with FredCoBio, but here’s the catch:  The artist is from Middletown and it’s biotech, geeky stuff.  Also, really cool stuff.

"Immaculate Confection" by Jason Freeney via Baltimore Examiner

There are a number of cool images on Jason’s web site MoistProuctions, and a neat slide show on Mary’s Baltimore Examiner piece as well as an interview.  Although he’s in Manhattan now, you can find more of the former FredCo resident on his blog and his Facebook Page:  Gummi Fetus.

All this talk almost makes me want to comment on the recent banter spewed forth by the RTLifer’s about one of our largest Biotech companies, but instead I’ll ask you to enjoy this YouTube video of a Gummi Bear (fetus)being destroyed for the sake of science (via joannelovesscience.com)

By the way, you trolls, if you’re so committed to your mission, why not take a pledge to never use a single product that was developed using Stem Cells?  Same thing to those trolls destroying Pharma Execs (and at one point in time threatening me and my family) claiming to be Aminal Rights Activists:  Don’t use any drugs or products that used Aminaml Testing?  Why not?  It would be the right things to do.

On another note, I saw an interesting article in the FNP yesterday that Emergent Biosolutions is pulling out of Frederick.  This caught me by surprise because I didn’t even know they were in Frederick.  According to their Press Room, they’ve owned these buildings since 2004, but never renovated or improved them.  Building in Gaithersburg instead.  OK, you win some and you lose some.  I thought I heard somewhere that they won a contract fo9r H1N1 vaccine, but I may be mistaken.

I somehow missed Balog’s Biotech “Battle over biosimilars” last Sunday in the FNP.  Personally, I think giving the “biosimilars” more protection, mimimizing the competition will have the opposite effect of putting new products on the shelf faster.  It will stop competition dead in it’s tracks at the expense of the people needing these new therapies and ultimately, more people will die.  The US Patent System is broken and archane and needs to be overhauled thrown out the window.

I would also be remiss if I didn’t mention a write up in FNP last week about MedImmune.  The new facility is on schedule to open in 2011.  I also learned, informally, that Synagis will be the first product produced there, but the plans are to move to more “flexible” manufacturing to permit other uses in the future.

Phot by Sam Yu via Frederick News Post

I will be making a guest appearance at the Frederick County Workforce Service’s Center at noon on Wednesday 8/12 for a “Lunch-n-Learn”.  If you’re looking for work, then I might suggest you attend.  You may not “learn” anything, but it’s all about the networking.  I know I have been through the Center more than once in the past 9 years.  I think it’s the least I can do to return the favor.

And speaking of networking, I am working on the next BioBeers with a target date of Thursday 8/27.   Pencil it in.  We can discuss fetal Gummi bear stem cell research…

When Genotyping gets Personal

Many moons ago, from about 1992-95 (Yikes, 16 years ago?), I spent most of my time in a “cold box” toiling over pouring, packing and eluting columns or slopping goo from one centrifuge bucket to the next or wheeling 40 liter tubs of one buffer or the other from the buffer kitchen to the cold box.  Making enzymes, fancy proteins that catalyzed some modification of nucleic acids or other proteins.

One we made quite frequently was DNA Polymerase-I or it’s companion, the “Large Fragment of DNA Polymerase-I” known as the Klenow fragment or simply “Klenow”.    Or maybe it was T7 DNA Polymerase or Taq Polymerase.  The thing about the DNA polymerases we dreaded were not so much the cold box as most cross column (to determine where inthe column development the enzyme was eluted in deference to contaminating activities) as the QC tests.  Most QC tests in those days involved the use of radioactive nucleotides.  Radionuclides are relatively easy to produce, inexpensive and easy to detect.  But the mother of all QC tests was the dreaded Dideoxy sequencing.

Things have changed a lot over the past 15 years in the world of sequencing.  Back then, you might see 200-300 bands if you could pour a large enough gel.  This is useful for small plasmids and viruses and such.  Not really very useful for whole genome sequencing.    But towards the end of the ’90′s a TIGER and Celera jumped into the sequencing game, called the Human Genome Project, pitting these private groups against the NIH.

To make a long story short (you can read more in the linked wikis), Craig Venter’s groups proved victorious and this generated a new Biotech bubble involved in Human Genomics.

Jump ahead to SciFoo ’08.  Some of the Rock Stars in attendance were of the Human Genomic craze, like 23andMe founders Linda Avey and Anne Wojcicki, and Harvard’s George Church, amongst others (including me).    This was truely my first real indoctrination into the Personal Genotyping hysteria, as the announcement of 23andMe (funded, in part, by Google) was made just prior to SciFoo ’08.

So when I read about the Personal Genome Project looking for volunteers, I justed straight on-line and registered a few months back.  The project’s goal is to collect 100,000 human phenotypes. The first phase was the so-called “PGP-10” , most of whom are closely related to the project.  I am hoping to get into the PGP-1000, which is the third phase, but I may just make it into the PGP-100, which is the next step in the process.

Check out this cool YouTube, which is part of a documentary being filmed by Marilyn Ness, a two-time Emmy Award-winning documentary producer:

So what should appear in my in box this morning at 10:07 AM?

Invitation

Thanks for your interest in joining with the PGP to advance personal genomic research! Your eligibility application has been reviewed. Based on the information you provided, you are eligible to continue to the next stage of enrollment!

Part of enrollment involves a Pledge. I will be asked to make a financial pledge and will recruit a community of supporters would be able to contribute over the next 6 months if I am enrolled in the project. Participants will be enrolled without regard to whether a financial pledge is made or the amount of the pledge, but contributions are encouraged and will be used to subsidize the costs of research and related activities.

I have been working on my enrollment forms this morning and through lunch.  I have so many other cool FredCoBio stories I want to cover this week, so stay tuned.

And please, if  you or your organization would like to Sponsor me through the process, do get in touch.  I may take the Google approach and look for micropayments, say like $0.01 per base sequenced.