A federal judge has stalled the Trump administration’s attempt to slash research funding, but top universities in Cambridge are tightening their belts in response to extreme uncertainty.
A Massachusetts federal judge on March 5 blocked a federal policy that would have drastically reduced National Institutes of Health funding available to universities and other research institutions. The NIH under Donald Trump planned to impose a 15 percent reimbursement cap on “indirect costs” for all research grant recipients, including the Massachusetts Institute of Technology, Harvard and the region’s top medical centers such as Boston Children’s Hospital.
“Indirect costs” refer to money the agency disburses to support overhead expenses, such as utilities, lab space rentals and maintenance staff. Previously, reimbursement rates for these costs were negotiated by individual grantees: The NIH reported the average rate was 28 percent but some organizations went as high as 60 percent. Harvard, for example, is reimbursed at 69 percent, which means it gets 69 cents to cover indirect costs on top of every dollar it gets to conduct research.
The nationwide injunction prohibits the agency from implementing the proposed funding cuts “in any form with respect to institutions nationwide,” although the government has 60 days to appeal the ruling. Despite this temporary reprieve, the mere threat of funding reductions – and the uncertainty surrounding the future of other federal programs and agencies – is affecting Cambridge research institutions.
Hiring frozen, admissions reduced
MIT president Sally Kornbluth announced on March 4 a hiring freeze on “all staff positions that are not required for safety, compliance or other critical needs,” citing “financial uncertainty and new constraints” and “an evolving set of pressures.” The university plans to impose 5 percent to 10 percent cuts next year for academic and administrative units, including the Office of the President. In addition, many departments have reduced the number of graduate students they are admitting this year. “For an institution grounded in research and education,” Kornbluth said in a video message, “having to turn away superb young talent is a striking loss.”
Less than a week later, Harvard followed with an immediate pause on staff and faculty hiring. The announcement, signed by Harvard president Alan Garber and three top university officials, cited “substantial financial uncertainties driven by rapidly shifting federal policies” but stressed that the hiring freeze was temporary. The pause is slated to remain in effect for the remainder of the spring 2025 semester. In addition, the Harvard Faculty of Arts and Sciences opted to reject all graduate students on the waitlist for admission in the fall of 2026, and the Harvard School of Public Health has reduced the number of doctoral admissions offers in its biostatistics department and population health sciences program.
Critical research in jeopardy
As the Trump administration prepared to slash federal research funding last month, MIT joined 13 other universities – including Tufts in Somerville and Medford and Brandeis in Waltham – in a lawsuit against the NIH and the Department of Health and Human Services.
“We oppose these cuts because they will erode America’s global scientific leadership and deprive the American people of the fruits of research with untold potential benefits for their health and well-being,” said MIT’s Kornbluth.
According to the legal complaint filed by the universities, MIT got approximately $156 million in NIH grant funding in fiscal year 2024, while Brandeis was awarded $37 million. For fiscal year 2025, Tufts is getting $115.2 million. For Harvard, the agency alone accounted for $488 million in federal research funding in 2024 – making it the university’s most important source of funding.
If the Trump administration finds a way to impose NIH cuts despite the court ruling, MIT stands to lose $35 million in indirect cost reimbursements. In an emailed statement, deputy director of media relations Sarah McDonnell emphasized that indirect costs of research are “foundational to a thriving, world-class research enterprise” and “make it possible to do serious research to begin with.” These include, among others, data storage, hazardous materials management, radiation safety and the costs of maintaining research facilities and equipment.
Reducing indirect cost reimbursements will have a far-reaching, cascading effect on universities’ ability to conduct critical research. Long-term capital projects, including space renewals and equipment installations, might need to be deferred. Budget cuts pursued to absorb the loss of federal dollars, will lead to reduced graduate student admissions – already seen at Harvard and MIT – and affect other staff positions.
All this puts life-saving research that’s already being carried out into jeopardy. Some examples of NIH-funded research being conducted at MIT include: detecting lung cancer at an earlier stage, predicting how cancer cells in adults with acute leukemia will respond to treatment, improving the accessibility, safety and efficacy of therapeutic interventions for Alzheimer’s disease, and detecting preovarian cancer lesions.
Far-reaching community effects
As MIT pointed out in its suit against the NIH, nearly 14,000 Massachusetts residents are employed by the university, many of them Cambridge residents. Harvard has been the largest employer in the city for more than 20 consecutive years, and MIT is in second place. Federal funding reductions are likely to have longer-term economic repercussions.
“The vibrancy of our city is built on a lot of the young people that are here and who come for graduate school, who center around the university,” city manager Yi-An Huang said. “We have a lot of concern over how significant the [hiring] freeze might become and how long that pause would be there.” But Huang acknowledged the challenges facing universities in this period of uncertainty. “It’s really hard right now for the universities to commit if they’re not sure of the stability of the research funding and lab space,” he said.
As new executive orders are handed down in Washington, D.C., at a dizzying pace, the city is coordinating with the state administration, the Attorney General’s Office and local nonprofits to understand how federal actions might affect the community and how the city could help. “I don’t think the city can fully backfill for the level of federal funding,” Huang said. “We’re certainly thinking about what would happen if really important services or … programs were cut.”
Although research universities are a critical part of Cambridge, Huang explained that the city is focused primarily on how it can support vulnerable communities targeted by the Trump administration and its policies – including immigrants and the unhoused. “We’re all in this together,” the city manager said. “The city’s here to support people.”
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MIT’s endowment is 24.6 billion dollars. They are describing a doomsday scenario about the potential loss of 35 millions dollars, or .14% of 24.6 billion, that goes to things like purchasing copy paper for the office, rent and meals and incidentals when they go to trade shows. Political theater is wrong on either side.