The Johns Hopkins University once had a friend in the federal government like few others.

The National Institutes of Health poured billions of dollars into Baltimore’s premier university in exchange for cutting-edge studies in biomedical research designed to save and improve lives.

But Hopkins is now anticipating a sharp reversal of fortune, on the verge of losing more than $200 million a year in federal research grants if a controversial rule change under President Donald Trump’s administration is allowed to stand, according to Laurent Heller, the university’s executive vice president for finance and administration.

As the largest public funder of biomedical research in the world, the NIH shocked the scientific community earlier this month when it announced an immediate 15% cap on its grant funding for indirect costs.

The NIH said the estimated $4 billion per year in cost-cutting moves will enable more funding to go to direct scientific research rather than “overhead.” But critics of the change say strong government support for maintaining laboratories, paying administrative staff and covering utilities remains essential to help cutting-edge biomedical research flourish.

“You’re basically destroying the system,” said Richard Huganir, a neuroscientist at Hopkins who receives NIH funds to help develop drugs to treat children with learning differences, seizures and sleep problems. “The ripple effect, I think, could be devastating to Baltimore City itself.”

For Hopkins, frequently the top recipient of NIH grants, the funding formula change could threaten the lifeblood of the nonprofit university: research dollars. For many years, Hopkins had negotiated with federal officials to receive more than 60% in funding for indirect costs. The estimated loss of NIH support, as spelled out in recent court filings, could lead to a sharp decline in research and an untold number of layoffs.

In an urgent email sent out to the Hopkins community three days after the Feb. 7 NIH announcement, University President Ron Daniels and Johns Hopkins Medicine CEO Theodore DeWeese said the funding cuts “pose an extraordinary challenge to the important and lifesaving work” of faculty, staff and students.

The $200 million figure was quietly disclosed as part of an ongoing lawsuit filed by Hopkins and other universities against the Trump administration. (A federal judge in a related case has temporarily blocked the NIH cuts pending further review.)

In an interview this week, Mayor Brandon Scott called the cuts “a devastating blow to Baltimore,” adding such moves would not only be detrimental to scientific research, but also the city’s economy. Hopkins employs more than 16,000 people who live in Baltimore and creates multiple billions of dollars of impact each year for the city, according to the school.

“I think about the people and families impacted if their jobs are gone,” Scott said. “They provide for their families based on our city’s standing as a medical and research hub.”

NIH grants extend far beyond Hopkins in Maryland, which received more money from the agency last fiscal year than all but three other states.

Other leading public universities in the state expect annual losses of about $75 million, according to estimates provided by the schools. That would mean nearly $50 million less for the University of Maryland, Baltimore; $22 million for the University of Maryland, College Park; more than $1.2 million for the University of Maryland, Baltimore County; and $1 million for Morgan State University.

The ripple effects of such cuts could be substantial in a state far more dependent than most on federal health research spending.

Maryland received more than $2.7 billion in NIH awards in fiscal year 2023, supporting more than 23,000 jobs and 5.7 billion in economic activity, according to United for Medical Research, an organization that advocates for federal grant funding increases.

At Hopkins, more than half of the university’s operating budget is from research, with a significant portion coming from the U.S. Department of Health and Human Services, home to the NIH. By contrast, educating students and providing patient care — perhaps the two things Hopkins is best known for — each make up only about 10% of its revenue.

When researchers receive grants, most of the money goes to expenses related to their work, such as equipment, supplies and salaries. The government also negotiates to provide additional funding based on a percentage of the original grant. That extra funding can be used for indirect costs such as building maintenance, library resources and administrative support.

Hopkins’ negotiated indirect cost rate is 55%, down from about 64% in recent years, according to university records. Nationwide, indirect costs have crept up over the decades. They were capped at 20% in the 1960s before the federal government began negotiating rates with individual institutions.

The NIH has long seen Hopkins as one of its premier institutions. In 2005, the NIH awarded Hopkins about $607 million, according to federal grant data. That figure has grown over the last two decades, reaching $1 billion during last fiscal year, about $281 million of which were for indirect costs, according to Hopkins.

University officials credit the massive influx of federal grants for indirect costs with helping to create the world in which critical medical breakthroughs are possible, including developing a blood test that detects early stage cancer and proving that treating hearing loss reduces risk of cognitive decline.

Part of those dollars helps keep the lights on at a lab associate professor Jamie Spangler shares with other research teams. The nearly 9,000-square-foot center with sophisticated scientific instruments allows Spangler and her colleagues to study how to manipulate proteins to treat different diseases, she said. Without it, Spangler’s team could not research ways to prevent and treat conditions ranging from lung cancer to the flu to Type 1 diabetes.

“It would just be catastrophic,” she said.

At the NIH-funded CHARMED Center, director Marsha Wills-Karp worries cuts to indirect costs — as well as an executive order that banned federal funding to “environmental justice” programs — could hurt the center’s partnerships with immigrant employees of livestock farms fighting for workers’ rights and high school students teaching homeowners how to test for lead in their pipes.

“What’s upsetting to me and my colleagues is not being able to follow through on our promise to the communities to work with them,” said Wills-Karp, a professor of environmental health and engineering.

Hopkins recently took the fight to Washington last week as protesters and their elected leaders rallied in sub-freezing temperatures to make their case for restoring funds.

Funding cuts “will only lead to the further detriment of America’s ability to make discoveries, develop treatments and advance technology,” Jaime Eugenin von Bernhardi, a Hopkins Medicine postdoctoral fellow, told a crowd of about 100 rallying outside the federal Department of Health and Human Services.

Eugenin von Bernhardi said many like him work long hours, sacrifice weekends and postpone starting families in order to advance their research, which is now more difficult than ever under the threat of layoffs.

“I cannot tell you how difficult it is to do this life-altering work with the constant anxiety and the mental health toll that looms over us,” he said.

Hopkins remains a wealthy university, but officials insist the school won’t be able to weather the NIH cuts unscathed.

Budget documents show the university ended last fiscal year with an excess of nearly $423 million in revenue. The school also has a $13 billion endowment, according to data released last year from the National Association of College and University Business Officers and the Commonfund, an asset management firm.

Even so, the university has “little margin to absorb unexpected funding gaps” because much of the money comes with legally binding restrictions from funders on how and when it can be spent, Heller, the school’s executive vice president for finance and administration, wrote in court papers.

Hopkins insists the school’s unspent revenue is not meant to be used as “a rainy day fund.”

“A small portion can help weather short-term disruptions — such as a brief government shutdown — but not for long and not nearly enough to make up for sweeping cuts in federal funding for lifesaving medical research and care,” university spokesman J.B. Bird wrote in a statement to The Banner.

A reduction in grant funds would “necessarily and immediately result in staffing reductions,” Heller wrote in court papers. Among the jobs at risk: compliance officers who check for adherence to laws and regulations, and the staff of boards that review research plans involving human subjects.

Already, department leaders at Hopkins are considering limiting the number of new Ph.D. students, whose tuitions and stipends depend largely on NIH funding, according to Huganir. Within the neuroscience program, Huganir predicts they will probably cut the number of offers by 25%.

Current students are feeling the pinch too. “They’re all worried about whether they will survive,” he said.

Michael Rosenbaum — a Hopkins trustee and founder of Catalyte, a company that trains Baltimore residents from diverse backgrounds to be software developers — said it’s difficult to overstate how important research is to the region’s ability to create jobs.

“This kind of stuff puts Maryland on the map, on the cutting edge of research,” Rosenbaum said. “For our region, it generates growth.”

The amount of research money coming into Maryland has become crucial for revenue and economic growth, said Kelly Schulz, CEO of the Maryland Tech Council and former Maryland secretary of commerce. “Maryland is at the very top of the list for potential harm.”

But some have cast doubt on the assertion that indirect cost cuts would affect the university’s research output and economic impact.

“The bluff threat is unless you pay us more, we’re going to have to stop some of this critically important work. I don’t believe it for a second,” said Jay Greene, senior research fellow at The Heritage Foundation, a conservative think tank. Heritage was behind Project 2025, a Republican policy blueprint that called for cutting indirect cost rates because, the organization claims, they may be funding diversity, equity and inclusion initiatives.

Greene argued that universities have been overcharging taxpayers for indirect costs and can turn to other sources of funding, adding that it’s in their interest to continue conducting research because it helps them make money and elevate their status.

NIH’s new indirect cost rate of 15% is similar to that of private foundations and could allow more funding to “go directly to critical scientific research, instead of funding bloated university bureaucracies,” said Maryland Rep. Andy Harris, a Republican representing parts of Baltimore County, Harford County and the Eastern Shore, and former Johns Hopkins Hospital anesthesiologist.

But Sen. Chris Van Hollen, a Democrat, disagreed, saying that “this has nothing to do with government efficiency. It will waste important federal dollars if clinical trials are cut short, if labs are closed and there aren’t jobs created.”

Last week, all nine Democratic U.S. lawmakers from Maryland signed a letter addressed to the new U.S. Health and Human Services Secretary Robert F. Kennedy Jr., condemning cuts to NIH funding that they said will “leave a significant wake of destruction across the state.”

“To arbitrarily and illegally cut it threatens Maryland’s health, safety, and economy,” the letter said. “Slashing research funding will ultimately harm patients and even cost lives – many of them Marylanders.”

Caught in the crossfire of the funding debate may be patients like Kyle Lewis.

In 2020, doctors told Lewis he would only have weeks to live after they discovered 40 tumors on his major organs, Lewis said. He joined an NIH-funded trial at Hopkins to treat Stage 4 metastatic melanoma with “very aggressive” immunotherapy, he said. Now, five years later, the 46-year-old Navy veteran is helping to raise his three kids in Columbia.

“It gave me this time, it saved my life,” Lewis said, adding, “It’s hard to think about the next guy that this happens to not getting the treatment that I got, not being able to extend his life.”

An earlier version of this story misspelled the name of Michael Rosenbaum, the Hopkins trustee.