Cool Biomarker Idea From UT - Southwestern, Scripps, and Opko Health

Most biomarkers technologies are built upon pretty stale ideas, the most common of which is performing retrospective analysis of datasets and then applying algorithms to tease out “biomarkers”.  In the most recent issue of Cell, a group from UT Southwestern, The Scripps Florida, and Opko Health came up with a decidedly different tact on finding biomarkers.  

Antigens typically have pretty funky shapes, which is one of the ways the human immune system identifies them as being “different”.

The UT Southwestern group hypothesized that oddly shaped antigens could pull down antibodies that are activated in response to disease.  The group made a library of “peptoids” (peptides with odd shapes), stuck them on a chip, and ran whole blood samples over it to see what was pulled down.  The hypothesis seemed work - the peptoids were able to bind to antibodies with great affinity.

The group then setup a series of tests to see if the peptoids could identify biomarkers for a specific disease.  They ran whole blood cell lysates from controls and Alzheimer’s patients over the chips covered with peptoids.  The output of which was a series of peptoids bound to antibodies.  The group then ran the same test with new  Alzheimer’s lysates and a negative control, Parkinson’s lysates.  Parkinson’s provides a good indicator of the peptoid test’s specificity as it is a neurocognitive disorder with disease presentations that can sometimes be misdiagnosed as Alzheimer’s.  The antibodies pulled out from the second test confirmed the results from the first test.  The researchers had found two putative biomarkers (antibodies) that circulate in Alzheimer’s patient’s blood.  

The technology is quite green and has only been tested on a rather small dataset, but it does provide a glint of hope that an Alzheimer’s diagnostic could be run with whole blood lysates.  If the researchers’ test is confirmed through clinical validation, they will have hit the holy grail of Alzheimer’s disease testing - a cheap point of care diagnostic.  

Lab on a Chip > Circulating Tumor Cells

There is no doubt that lab on a chip technologies are hot right now in the venture capital community and I would like to highlight one application that has caught my attention. The identification and isolation of rare cell populations from whole blood samples has been a persistent challenge for researchers and clinicians.  Lab on a chip technologies offer a solution to this challenge because of their miniaturization and incredible sensitivity.

Tumor cells circulate in human blood at incredibly low frequencies (1-10 CTC per ml of whole blood) relative to other cell populations, making it quite challenging for researchers to sift out a few CTCs from a heterogeneous pool of other cells.   To put this in context, only 10-20 cc (=10-20 ml) of blood is drawn during a normal physical.  Therefore, in any given blood sample there is likely to be no more than 10-200 CTCs amongst 50 million plus white blood cells and several billion red blood cells. 

In the past, quantification of CTCs was almost impossible.  Previous technologies focused on isolating and amplifying CTCs so that lab tests could be run.  Amplification of primary cancer cells through passaging could result in additional mutations, making the older CTC isolation technologies rather ineffective.  The ideal technology would be one that was so sensitive that CTC binding events could be quantified without the need for cell amplification.  But with so few cells available, isolation becomes a daunting task.  Add in a high risk for false negatives, and CTC isolation becomes all the more challenging.      

Lab on a chip startups are attempting to leverage the sensitivity and specificity of microfluidic chips to address the CTC identification challenge.  Below is a list of some university startups that have novel lab on a chip technologies to identify CTCs: 

• Biocept was spunout of Peter Kuhn’s lab at The Scripps and is commercializing the CEE™ Cell Enrichment and Extraction platform.  The CEE technology is a microfluidic device that uses a chip coated with upright polymer fibers that are of different heights and widths.  Blood travels at variable speeds – slow closer to posts and faster away from posts – which enhances the probability of a CTC binding to an antibody attached to the post. 
• On-Q-Ity was spunout of Mehmet Toner’s lab at Mass General / Harvard and is commercializing a microfluidic based technology that is similar to the Biocept technology.  On-Q-Ity uses a process similar to Biocept’s to isolate CTCs, and then uses a second proprietary process to separate CTCs from other bound cells through cell size exclusion (CTCs are typically larger than leukocytes).
• Vitatex was spunout of the State University of New York at Stony Brook. The Vitatex technology uses a substrate coated with cell adhesion matrix (CAM, a porous layer of extracellular matrix polymer coated with blood-borne adhesion molecules) that mimics the interstitial microenvironment, in which tumor cells invade.  CTCs naturally adhere to CAM allowing for their isolation and enrichment from whole blood samples.

I am still undecided if I believe CTC isolation technologies will actually work on a commercial scale.  Application-wise, the low hanging fruit is to go after solid tumors that are hard to biopsy (lung, pancreas, etc.) and therefore could benefit from a “liquid biopsy” via CTC isolation.  After the low hanging fruit is picked, I am not sure what role lab on the chip tests will play in a clinician’s arsenal. 

My guess is that clinical validation studies through retrospective analysis will look quite convincing, but most technologies won’t hold up in prospective trials.  CTCs are so rare that there is a very high probability of false negatives, which could be rather disastrous for patients that actually do have cancer.  Clinicians will most likely want to see lots of data, requiring expensive trials, before they start using lab on a chip technologies to indentify malignancies.  I look forward to tracking the progress of Biocept, On-Q-Ity, and Vitatex, with the hope that my pessimism will be converted to optimism.

Update on January 5, 2011 by Martin Lehr

Even if a diagnostic is capable of identifying CTCs, what does that really mean to the patient?  To be honest, I am not entirely sure.  Some thoughts:

• There is a strong chance that any two people with the same number of CTCs and similar cancer subtypes could have wildly different clinical outcomes (one patient gets cancer while the other does not).
• Just because CTCs are there does not mean a person will get cancer.  A strong immune systems most likely renders most of the CTCs.
• A floating CTC could end up anywhere.  
• Are these CTCs progenitors or fully determined cancer cells?  Does that matter if they are floating around?