A biotechnology company in Cambridge, Mass., with rights to a groundbreaking patent developed by three academic institutions won a key patent victory in one legal venue on Monday, but also suffered a recent defeat involving the same patent in a different legal venue.

The victory came in a federal district court in Boston, where Judge Rya W. Zobel found that a patent on an invention licensed by Ariad Pharmaceuticals in 1991 was valid and enforceable, and that a jury’s finding, in 2006, that Eli Lilly and Company had infringed the patent would stand. The jury had awarded Ariad $65.2-million plus continuing royalties.

Under its licensing deal, the company is to share royalties with Harvard University, the Massachusetts Institute of Technology, and the Whitehead Institute for Biomedical Research, whose inventors developed a technique for identifying the role played by a “messenger” protein in regulating how cells function. The patent on the invention, which was awarded in 2002, also shows how the messenger protein could have medical and therapeutic uses.

The defeat came from the U.S. Patent and Trademark Office, which, after re-examining the patent, rejected some of its claims, including those asserted by Ariad in its lawsuit against Lilly. The claims are also part of a separate lawsuit that pits Ariad against Amgen Inc. and Wyeth.

In a news release, Ariad said it would challenge the patent office’s findings. —Goldie Blumenstyk