Cytomedix‘s (OTC:CMXI) Aldagen acquisition signaled the company’s intention to establish a strong presence in regenerative medicine therapies and the deal fills needs for both companies.

Aldagen, who had tried twice to go public only to withdraw both times amid poor market conditions, gets a partner interested in developing its stem cell treatments. Cytomedix gains prospective regenerative medicine therapies for its pipeline.

But for Aldagen and its investors such as Intersouth Partners and Aurora Funds, the acquisition announced Wednesday is not quite an exit. It’s more like another door that allows the company to continue moving forward with its stem cell therapy research.

For both companies to see this deal pay off, they need a successful phase 2 clinical trial for Aldagen’s experimental ischemic stroke therapy. And even then, the ultimate goal is for Aldagen’s therapy to draw interest from a Big Pharma partner.

Aldagen’s “bright cell” technology isolates stem cells that express high levels of the ALDH enzyme, which have the potential to promote cell and tissue regeneration. The Durham, North Carolina company was formed in 2000 as StemCo Biomedical based on technology licensed from Duke University and Johns Hopkins University.

With Aldagen now in the fold of Gaithersburg, Maryland-based Cytomedix, the focus now turns to Aldagen’s clinical trials on ALD-401, its experimental treatment for ischemic stroke. Dr. James Hinson, Cytomedix’s chief medical officer, said that the stroke opportunity comes down to time. Stroke patients have a small time window for treatment, which gives patients few treatment options. But Hinson said that Aldagen’s bright stem cells widen that window to days rather than hours.

Although the deal is valued at up to $40 million, Aldagen gets just $16 million up front in the form of preferred Cytomedix shares. The rest of the payoff is heavily linked to milestones.

That leaves Aldagen shouldering a lot of the development risk. Cytomedix chief financial officer Andrew Maslin explained that the company structured the deal in a way that reduces risks to its own shareholders. Depending on the progress of clinical trials, Aldagen could gain up to an additional 20.3 million Cytomedix shares in three milestone payments. But more than just spreading the risk and deferring the payoff, Aldagen is also sharing the costs.

The more than $10 million cost for clinical trials will be partially covered by $5 million kicked in by Aldagen’s investors in the form of a private placement investment in Cytomedix. In other words, Aldagen investors — who according to securities filings have pumped more than $50 million into Aldagen already — are paying Cytomedix to study its experimental stroke treatment in clinical trials.

Aldagen’s $16 million up-front payment in stock represents a 17.3 percent stake in Cytomedix. In a conference call with analysts, Cytomedix CEO Martin Rosendale noted that it wasn’t long ago that Cytomedix’s entire valuation was $16 million. He did little to disguise his satisfaction at acquiring Aldagen for discount compared to the valuations of other stem cell therapy companies.

Cytomedix expects to see its valuation climb and Aldagen must see that, too. Rosendale said Cytomedix is close to a licensing deal with a “top 20 global pharmaceutical company” on its Autologel wound care system. The company is also seeking to add indications for its Angel Whole Blood Separation System. A 510(k) clearance could give the company a piece of the $800 million-a-year biologics market associated with spinal fusion procedures.

Cytomedix sees Aldagen as another key piece to building the company’s regenerative medicine heft. Both companies believe in the technology’s promise in stroke and other indications. That means the investors who bet on stem cell regenerative therapies must continue to be patient. The financial and therapeutic payoff is still further down the road.

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