Charlton no longer had money to pay her staff or any of her researchers. On Monday afternoon, she called and fired the center’s executive director — who just months earlier had uprooted her family and relocated from Los Angeles.

“It breaks my heart to see years of work wiped off the map,” said Charlton, associate professor and founding director of the LGBTQ Health Center of Excellence at the Harvard T.H. Chan School of Public Health. “I’m not sure we will ever recover.”

In what has become a weekly ritual, the NIH on Friday afternoon abruptly terminated tens of millions of health research grants in New England and around the country. The latest round of cuts strikes deep at the heart of the medical research infrastructure in Greater Boston, imperiling years of research into disease prevention and health disparities among traditionally underserved populations, according to a half-dozen health researchers whose funding was cut Friday.

Among those hardest hit is the research arm of Fenway Health, which for five decades has pioneered infectious disease research in the gay and lesbian community. On Friday, the NIH terminated five of its research grants. These included multi-year studies into prevention and treatment of HIV for adolescents and the effects of social isolation among older LGBTQ people. Including Friday’s cuts, the Fenway Institute has seen a dozen of its 27 NIH grants terminated since Trump took office — amounting to $1.8 million in lost funding.

“It’s being called a bloodbath,” said Dr. Kenneth Mayer, medical research director at Fenway Health. “The government is essentially saying that, only certain people with certain characteristics matter… and the less you know the better.”

An NIH spokesperson did not respond to questions about the scale and legality of the NIH cuts, instead sharing a link to an agency website and a list of terminated grants. The list shows that more than 300 NIH research grants — with anticipated funding of nearly $200 million — were cancelled between Feb. 20 and last Thursday, March 20th. The cancellations from last Friday are not included in the latest tally.

The cuts are part of the Trump administration’s crackdown on research focused on gender and diversity issues, and appear to violate federal court orders blocking the NIH cuts.

Two legal experts who reviewed NIH termination letters shared with the Globe said they violate federal administrative process law, which prohibits “arbitrary and capricious” policy changes. The mass cancellations also violate contract law because the NIH is imposing conditions on research projects that did not exist at the time the grants were awarded, the legal experts said.

“These terminations are illegal,” said David Super, a constitutional law expert at Georgetown Law, who reviewed the termination letters at the Globe’s request. “NIH has no authority to cancel these contracts without individualized assessments, and doing so violates court orders against blanket cutoffs of legally obligated federal funding.”

The financial impact of the grant cuts has rippled through universities, hospitals and other research institutions in Massachusetts, which is the largest recipient of NIH grant funding per capita. Already, academic scientists are warning of a massive brain drain, as graduate students and post doctoral researchers rethink their futures and consider whether to abandon medical research entirely.

More than a dozen universities, including Harvard, MIT, Brown, and the University of Pennsylvania, have frozen hiring, and the University of Massachusetts’ medical school has rescinded dozens of admissions offers to Ph.D. candidates.

“This could destroy a generation of scientists,” said Dr. Bruce Fischl, a professor of radiology at Harvard Medical School. “A lot of young people see the potential dismantling of medical research and they don’t want to stick around for it.”

Julia Marcus, an infectious disease epidemiologist and associate professor of population medicine at Harvard Medical School, said she burst into tears after the NIH abruptly terminated three of her research grants late last week. Among them was a $2.5 million grant that funded a five-year study exploring the implementation of a long-acting, injectable drug that has been shown to be highly effective at preventing HIV.

Now, she is scrambling to find money to issue paychecks to her research team.

“It’s peak inefficiency,” Marcus said of the cuts. “We poured so much time and effort into this study and then to have it terminated, on the verge of a payoff is, well, I’m running out of words.”

Nearly all biomedical researchers in academia rely to some extent on support from the NIH. Laboratories are run like small businesses, with scientists constantly applying for grants to pay for salaries, supplies and computers. Preparing a grant proposal for the NIH is a monthslong process, with many grant applications running more than 100 pages long, say university researchers.

Some researchers said they were hopeful the NIH cuts that began in earnest last month would slow, or even stop, after the courts intervened. A federal judge in Maryland twice over the past six weeks blocked the administration from terminating funding, saying in his most recent decision that the cuts “punish, or threaten to punish, individuals and institutions based on the content of their speech, and in doing so they specifically target viewpoints the government seems to disfavor.”

But the NIH continues to send out large batches of termination notices, which often arrive in researchers’ email inboxes on Friday afternoons. Many share nearly identical phrasing, including, “This award no longer effectuates agency priorities.”

“Research programs based primarily on artificial and non-scientific categories, including amorphous equity objectives, are antithetical to the scientific inquiry… and ultimately do not enhance health, lengthen life, or reduce illness,” one of the form letters says.

Ariel Beccia, an instructor at the LGBTQ center at the Harvard T.H. Chan School of Public Health, has spent the past two years studying how the COVID-19 pandemic caused health disparities to widen among LGBTQ people; and had entered the most important phase of the study exploring the factors causing the diverse outcomes. A grant from the NIH funded her data analysis work as well as her salary.

Like many of her peers, Beccia has been anxious about losing her grant money since February when Trump issued a series of directives aimed at rooting out “gender ideology.”

Then last Friday afternoon, Beccia was anxiously rebooting her email when a termination letter appeared in her inbox at 4:30 p.m. In a moment, she learned that her sole source of income, including the money she needs to buy groceries and pay rent on her Cambridge apartment, had vanished. Like many of her peers, Beccia is now scrambling to raise money from private funding sources — but the grants are smaller than those awarded by the NIH and the competition is fierce.

In her case, the NIH form letter said diversity, equity and inclusion studies “are often used to support unlawful discrimination” and harm the health of Americans. “It’s disgusting and wildly incorrect,” Beccia said of the letter. “Everyone has a gender identity. So research related to gender is critically important to improving health.”

On Tuesday afternoon, Charlton held a Zoom call to deliver the grim news about the NIH cuts to a dozen members of her research team. They were already reeling from an earlier round of notifications that had terminated a five-year, $4 million study to explore how discriminatory laws, such as so-called “Don’t Say Gay” bills, impact mental health among LGBTQ adolescents and how the laws can potentially lead to suicide. Charlton’s team had interviews lined up with more than 100 adolescents across the country when the termination note arrived.

On the call, Charlton became emotional as she explained that she no longer had the money to pay them but was aggressively seeking private donations to fill the gap.

“I am feeling really hopeful that we’ll figure this out,” she said. “But I also believe it’s going to get a lot worse before it gets better.”

Chris Serres can be reached at chris.serres@globe.com. Follow him @ChrisSerres.