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Cellumen: Chasing Cellular Systems Biology

By John Russell

February 19, 2009 | Founded in 2004 and based in Pittsburgh, Cellumen is one of a small but growing number of biotechs working to use high content screening in cell-based assays to identify promising drug candidates and to red-flag troublesome tox-causing compounds. Better reagents, less expensive and improved scanners, advancing informatics and human cell handling techniques are all propelling the community forward.

It will be interesting to watch the march forward of imaging based methods. No less than Eugene Myers, inventor of BLAST and now concentrating informatics for imaging, has said he thinks the amount of imaging-based data will eventually overwhelm even the genomics data flood (See, “Imaging Informatics,” Bio-IT World, Jan/Feb 2009). What sets Cellumen apart, says Don Taylor, director of marketing and son of Cellumen founder Donald Lansing Taylor, is its ‘cellular systems biology’ approach.

The company labels its approach as Cellular Systems Biology (CSB). Like several of its counterparts, Cellumen treats cells with compounds, uses a fluorescent reporter system to monitor molecular activities, and develops “fingerprints” which may be associated with disease, toxicology, or health. Two major differentiators, according to Taylor, are its proprietary “gene-activation” systems which enables effective targeting of entities to be tracked and Cellumen’s ability to measure and readout many parameters in a single assay.

“We’re a Delaware corporation and we really spun out of the experience of Cellomics. The two co-founders of Cellumen actually were the co-founders of Cellomics, which was acquired some years ago by then Fisher Scientific,” said Taylor. Cellumen is also an alumnus of the Pittsburgh Life Sciences Greenhouse, which provided some funding as did Novitas Capital. “Our first venture funding came from Safeguard Scientifics, a publicly held venture capital company. They led a Series B $8.7 million round back in July of 2007.”
“The driver [for starting the company] was to be able to address the more advanced cell-based high content screening assays that would be required to meet the new demands in drug discovery and drug development,” he says. Cellumen’s brand of cellular systems biology currently involves using single cell types in multiplexed cell-based assays which can measure six or more parameters per cellular screen, according to Taylor.

The company offers both products and services. Early on, the focus was somewhat more on drug discovery. Today, the emphasis has shifted more to tox screening. The idea, of course, is to identify problems (or promising candidates) much earlier in the drug discovery process. It has been working primarily with an immortalized HepG2 human cell line and primary rat hepatocytes. Assays are compared with “CellCiphr” profiles, fingerprints Cellumen has already developed by screening a library of compounds, and characterizing them. The revealed biology can be fairly detailed.

“In the case of cell models of disease for protein-protein interactions these are actually recombinant proteins that we co-express using adenoviral vector delivery,” explains Taylor. “On each one of those expressed proteins we attach a fluorescent label. One is a GFP and the other is an RFP. And for one of the proteins, they will actually attach an anchor to the nucleus. Then the conjugate protein is tagged with a shuttling signal so that basically shuttles back and forth freely between the nucleus and the cytoplasm. When co-expressed, those two proteins are actually connected and they bind together in the nucleus so that you get a signal that is orange basically.”

“Then when you start screening for compounds, as soon as there’s a disruption there’s a rapid response so if there’s a disruption in the protein binding the shuttling, the anchor to the nucleus holds but the shuttling component disrupts. It goes into the cytoplasm and then you can very quickly detect the green versus red signal and that’s also a reversible process so that you can wash out the reagent and perform the process over again. So that’s a way to actually in a high throughput capacity using high content screening screen for compounds that have this protein disruption capacity.”

Cellumen’s HepG2 panel has ten parameters ranging from oxidative stress to mitochondrial potential, to nuclear morphology and so on. “What’s important is the ability to identify the right biological activity that one is looking to measure and it’s not just a single endpoint,” says Taylor. The entire process is highly automated.  Cellumen receives compound from customers in powder or as a solution and produces fingerprints associated with the compounds.

“What I mean by fingerprint is that Cellumen, not only do we measure six or more, 10, even 11 parameters per assay but we also offer a 10-point dose response curve. So for each compound we use 10 concentrations from nanomolar to micromolar. We also measure the compounds across three time points. We have acute, early, and late stage time points that range between one hour, 24 hours, and 48 hours or 72 hours, depending on the cell background.” Taylors adds that turnaround time can be two to four weeks depending on the nature of the screens and the granularity of data and interpretive results requested.

One practice, which may be unique to Cellumen, is an effort to quantify the savings its tox testing can produce. This work is based on a project with consultant Cambridge Healthtech Associates.

Taylor says, “So the sensitivity of our test is something that we take very seriously and when we actually quantify this in a financial value proposition. We’ve been able to use the empirical data that we’ve received from our Cambridge Healthtech Associates Study, a consortia of over 10 pharmaceutical companies that send Cellumen compounds. We were able to demonstrate using those results that Cellumen projects a cost savings to any one typical big pharma of more than $91 million per year by applying CellCiphr as a filter at the start of the hit-to-lead phase assuming that one has approximately 400 compounds at the start of the hit-to-lead phase.”

Recently the company added a panel to predict cardiac hypertrophy earlier in the drug discovery and development process. “In the past 10 years, nearly 30 percent of all drugs in the United States have been withdrawn due to cardiotoxicity,” says Kate Johnson, CSO. “There are many tests available to detect electrophysiological abnormalities of the heart, but Cellumen’s Cardiac Hypertrophy Panel is the first systems-based panel to detect other development-limiting toxicities in cardiac cells.”

The cardiac tox panel is designed to measure eight distinct toxicity indicators in drug compounds including mitochondrial function, oxidative stress, apoptosis, and cellular hypertrophy and  Cellumen says its panel quantifies both the mechanism and time course of toxicity.

Cellumen has worked with several partners—Eli Lilly and Mitsubishi’s Tanabe Pharma are two—and last June it announced a research collaboration with the National Center for Toxicology Research (NCTR). Under the agreement, Cellumen uses its CellCiphr toxicity risk assessment technology to profile blinded samples of known liver toxicity compounds including both failed and marketed drugs for the NCTR. The NCTR will incorporate the knowledge generated by Cellumen to develop a liver toxicity knowledge base. Cellumen will use the profiling data and compound safety data from the collaboration to further develop the diversity in the CellCiphr database and the types of cell panels, as well as to advance the classifier informatics tools.

The company is also collaborating with the Alzheimer’s Drug Discovery Foundation. “We’re actually developing biosensors and gene switch cell lines to emulate Alzheimer’s disease to allow for the exploration of compounds that may help treat that disease so it incorporates the ability for us to over-express certain proteins coupled with protein-protein interaction biosensors in a complete cellular model.”

Despite the progress, Taylor says the competitive landscape is broad: “Probably the most formidable competitor is the status quo. What pharma typically does and what they have been doing forever is a small animal study as primary filter for any significant toxicity studies. It’s been difficult [to win acceptance] even though there is all this talk about identifying toxic liabilities early on with ‘predictive’ approaches.”

“From my perspective, industry is adopting it slower than they ought to. I don’t fault them because there have been many technologies over the past five-ten years that have been touted to be predictive but ultimately did not prove their point of view. So in today’s very difficult financial times pharma naturally needs to be very selective in what they choose to license.”

Too true. Even so, Cellumen is hardly standing still. “We’re moving from what we call kind of these mono-layer cultures, plating HepG2, plating rat primary hepatocytes to human tissue model microarrays, a 3D array if you will. And these are going to be created from stem cells, primary cells and so on. So these will be tissue-specific panels of functional biomarkers that will then go into an augmented CellCiphr classifier that then becomes a predictive tool for human toxicity and so this is to support the FDA’s reduce, refine, and replace, the 3Rs Initiative and to help be on the cutting edge of within ten years being able to replace animals as the filter for toxicity.”
This article first appeared in Bio-IT World’s Predictive Biomedicine newsletter. 
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