Billionaire philanthropist Paul Allen died two months ago, but before he passed away, he passed along a $125 million commitment to a new research frontier: the Allen Institute for Immunology.

The Allen Institute’s newest division, unveiled today at the institute’s Seattle headquarters, will focus on the human immune system and how it can be tweaked to fight cancer and autoimmune diseases such as rheumatoid arthritis.

“None of this would have been possible without the extraordinary vision and generosity of our late founder, Paul Allen,” Allan Jones, president and CEO of the Allen Institute, said at the unveiling. “Paul challenged us to go after the really hard problems, to unravel the complexities of biology, and make a lasting impact on science that advances health.”

In its initial phase, the immunology institute will focus its energy on five diseases: two types of cancer known as multiple myeloma and melanoma, plus rheumatoid arthritis and two types of inflammatory bowel disease — specifically, ulcerative colitis and Crohn’s disease.

Multiple myeloma is the second most common blood cancer, after leukemia, and is said to cause 12,500 deaths annually. Melanoma is a skin cancer that’s expected to cause more than 9,300 deaths in the U.S. this year. More than 1.3 million Americans have rheumatoid arthritis, which affects the joints, and as many as 1.6 million Americans have to cope with chronic inflammatory bowel disease.

Although the immune system is known to play a role in all those conditions, for good or for ill, the mechanisms involved are poorly understood. Those are the knowledge gaps that the Allen Institute for Immunology aims to fill.

The new institute’s executive director is Thomas Bumol, who worked for more than 35 years at Lilly Research Laboratories. His work at Lilly focused on drug discovery and early clinical development of treatments for maladies including arthritis and inflammatory bowel disease.

Bumol said his new gig, which drew him out of retirement, will present an “unprecedented opportunity” to advance a field that’s crucial to disease prevention and treatment.

“The immune system is enormously complex. It’s what’s keeping all of us in the room healthy without even being aware of it,” he said. “It takes care of that bee sting you got on that hike last summer, or helps heal your hand from that cut you got making Thanksgiving dinner, or stops that cold you picked up last week from your family. In other words, a silent ‘Guardians of the Galaxy’ of you.”

Boosting the immune system can cause a patient’s own body to target cancer cells more accurately, but when the immune system goes wrong, that can lead to conditions including arthritis and inflammatory bowel disease as well as diabetes, lupus and a wide assortment of allergies. Progress is being made with cutting-edge procedures such as immunotherapy, but to accelerate that progress, scientists need a deeper understanding of the immune system’s basic mechanisms.

“We are just scratching the surface of a huge unmet need,” Bumol said.

To gain that deeper understanding, the immunology institute will build upon the open-science, big-science model set by the Allen Institute’s two existing research divisions. The Allen Institute for Brain Science focuses on brain structure and the crucial role played by gene expression, while the Allen Institute for Cell Science delves into the mechanisms that govern cellular processes.

Jones said that Allen was intimately involved in laying out the plans for the immunology effort, going back to an internal survey of biomedical frontiers several years ago. “Something that thematically came up over and over again was that Immunology was really ripe for a big investment in some way,” he recalled.

Bumol said he met with Allen and other members of the billionaire’s team over the summer, building to a climax in August. “Those meetings were amazing,” Bumol said. “You knew you were in the presence of an incredible intellect. The challenge to dig deeper, to go way beyond the data … was there.”

Two months later, Allen announced that his case of non-Hodgkin’s lymphoma had returned. Two weeks after that, Allen was dead. But the Allen Institute had the commitments it needed to move ahead with its five-year, $125 million plan.

“The new focus on immunology draws on the Allen Institute’s 15-year history of groundbreaking basic and translational scientific discovery,” Marshall Horwitz, associate dean of UW Medicine and chair of the new institute’s scientific advisory board, said in a news release.

Bumol’s division will coordinate detailed studies of the foundational components of the immune system — its cell types and networks — and how those components change over the course of one to three years in healthy volunteers as well as patients with immune-related diseases. Eventually, the immunology institute will employ 60 to 70 people, Bumol said.

The institute is partnering with five other research organizations: the Benaroya Research Institute at Virginia Mason and the Fred Hutchinson Cancer Research Institute in Seattle, as well as the University of California at San Diego, the University of Colorado Anschutz Medical Campus and the University of Pennsylvania.

“This is truly a group of six institutions, basically working together for these goals,” Bumol said.

It’s likely to take several months to flesh out the institute’s staff and put the procedures in place for the institute’s collaborations. Gary Firestein, director of UCSD’s Clinical and Translational Research, told GeekWire that such collaborations will open the way to research strategies that are “beyond the reach of any of us individually.”

“The technologies will be a huge aspect of this, and the data integration will also be huge,” said Michael Holers, chief of the division of rheumatology at CU Anschutz.

In keeping with the precedent set by Paul Allen for the institute’s other research divisions, the immunology institute will make all of its data and tools openly accessible online for anyone in the scientific community to use.

Update for 2:20 p.m. PT Dec. 12: This report has been updated with comments from today’s briefing at the Allen Institute.