Harvard University appeared to be bracing for federal funding cuts before it publicly pronounced on Monday that it will not submit to the Trump administration’s demands that it cede unprecedented control to the government.

Last week, the school borrowed $750 million from Wall Street to shore up its coffers. Then on Monday, just as it announced it was not capitulating to President Donald Trump, it posted a sweeping summary of the kinds of research innovations that are at risk if federal officials cut grants that fund research on illnesses from cancer to diabetes.

The Trump administration’s $2.2 billion freeze on funds to Harvard began Monday night as a trickle of stop-work orders on major contracts that support projects ranging from research on a deadly infection to the effects of spaceflight on the human body. The damage assessment on which research had been stopped was occurring throughout the day Tuesday, with more cancellations expected.

Sarah Fortune, a professor and chair of the department of immunology and infectious diseases at Harvard T.H. Chan School of Public Health, woke up Tuesday to a stop-work order for a large contract focused on unraveling how the immune system fights tuberculosis, with the goal of creating better detection and vaccines.

The contract, worth $60 million over seven years, supports work at Harvard and at multiple other institutions across the country. Because the contract supports research on nonhuman primates, Fortune said there is now a question of whether a vaccine trial in rhesus macaque monkeys that is set to end in December can go to completion. There is a painful, real-time discussion of whether the monkeys may have to be euthanized, now that funding has been abruptly pulled.

“We’re halfway through,” Fortune said. “To have to euthanize these animals is so morally repugnant to me.” Fortune has other grants from the National Institutes of Health that support her 20-person laboratory focused on tuberculosis, an infectious disease that kills more than 1 million people each year. She does not yet know if those will be terminated. Asked how she felt, she simply said: “Scared.”

Harvard is a leader in cutting-edge medical, scientific and technology research that heavily relies on federal funding. Without those dollars, the university said the work will grind to a halt as researchers lack the resources to complete ongoing projects or finance new ones.

Federal funding is the largest source of support for research at Harvard, according to the university. In fiscal 2024, federal funding of $686 million made up approximately 68 percent of total sponsored revenue at Harvard.

The university has been preparing for the fallout since the Trump administration last month said it was reviewing nearly $9 billion in federal funding to Harvard and its affiliates amid allegations of antisemitism and illegal diversity, equity and inclusion programs on the campus.

The Trump administration sent the school a five-page letter last week that called for changes to leadership, student discipline and extensive government oversight as well as cooperation with federal immigration officials. The multiagency Joint Task Force to Combat Anti-Semitism on Monday night paused $2.2 billion in multiyear grants and $60 million in multiyear contract value to Harvard after the school rebuffed the government’s demands for changes.

The administration declined to specify which contracts or grants are affected, while Harvard is getting a handle on the extent of the pause.

Harvard is the wealthiest college in the nation with a $53 billion endowment, a collection of tax-exempt donations and investments that pays for salaries, research, financial aid and other expenses in perpetuity. A lot of that money, however, is restricted by donors and cannot be easily accessed.

The university would not say whether it plans to increase its endowment distribution to offset the potential loss of federal funding, but a university spokesperson said that “as part of ongoing contingency planning for a range of financial circumstances, Harvard is evaluating resources needed to advance its academic and research priorities.”

Harvard issued $750 million of taxable bonds last week to shore up liquidity, with the proceeds earmarked for general corporate purposes, according to the university.

Harvard took a calculated risk when it became the first university to formally push back against the government’s efforts to force change in higher education. Rebuking the administration could ratchet up funding cuts or inspire other punitive measures. Trump is now threatening to revoke Harvard’s tax-exempt status.

“Perhaps Harvard should lose its Tax Exempt Status and be Taxed as a Political Entity if it keeps pushing political, ideological, and terrorist inspired/supporting ‘Sickness?’” Trump said in a Truth Social post on Tuesday. “Remember, Tax Exempt Status is totally contingent on acting in the PUBLIC INTEREST!”

The president does not have unilateral authority to revoke the school’s tax exemption, but the IRS can eliminate it if Harvard is found to be participating in political campaigning or lobbying.

After the task force said it was reviewing $9 billion in funds to the university, Harvard President Alan M. Garber said the university would engage with the group while protecting its community and academic freedom. Things changed Friday after the task force issued its wide-ranging demands. By Monday, Garber told Harvard’s community that the university “will not surrender its independence or relinquish its constitutional rights.”

Faculty cheered on the decision, even those whose funding is on the line.

“It’s pure punitive lunacy. They’re just trying to bring the golden goose of American science, technology and education pipeline to a halt,” said Donald E. Ingber, founding director of the Wyss Institute for Biologically Inspired Engineering at Harvard. Late Monday night, he received a stop-work order on two parts of a larger contract that support about 20 employees and are collectively worth nearly $20 million.

One project, supported by the Biomedical Advanced Research and Development Authority, was devoted to using models to understand the effects of radiation exposure on human biology to develop new medical countermeasures. The other project seeks to help elucidate the impact of spaceflight on human biology.

“It goes against everything this administration talks about with international competitiveness,” Ingber said. “We are turning away the future workforce. The brain drain has started already.”