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Carlsbad-based Isis Pharmaceuticals Inc. announced Monday it will collaborate with a unit of Johnson & Johnson to develop new drugs to to treat autoimmune disorders of the gastrointestinal tract.

The agreement with Johnson & Johnson’s Janssen Biotech unit includes a $35 million upfront payment plus up to $800 million in in development, regulatory and sales milestone payments and license fees.

The deal combines Isis’ RNA-targeted technology platform with Janssen’s expertise in autoimmune disorders and therapeutic formulation.

“We are excited to be working with Janssen to apply our drug discovery and development efforts in this therapeutic area.  This collaboration broadens the utility of our drug discovery technology to new targets in the GI tract and expands the administration of antisense drugs to local delivery, including oral delivery, to the gut,” said B. Lynne Parshall, chief operating officer at Isis Pharmaceuticals.

“We are the leader in RNA-targeted therapeutics and our innovation and the successes of our pipeline drugs enable us to form collaborations, like this one, with leaders in specific therapeutic areas.  This partnering strategy ensures that we have access to resources that support and enhance our drug discovery efforts and also provides us with collaborators, like Janssen, who are uniquely capable of conducting development, marketing and commercial efforts for these drugs.”

Chris Jennewein is founder and senior editor of Times of San Diego.