Emma-Victoria Banos

Donnelley Biological Sciences Learning Center houses much of the University’s NIH funded research.

Continuing coverage of UChicago’s lawsuit and the NIH’s “indirect” funding cuts can be found here and here.

Three separate lawsuits were filed against the Department of Health and Human Services (HHS) and the National Institutes of Health (NIH) in the Massachusetts District Court on Monday, following a Friday NIH directive that slashed funding for “indirect” costs of university research. 

The University of Chicago, alongside three academic associations and 12 other universities, is a plaintiff in one of the lawsuits. 

All plaintiffs in that suit are represented by law firm Jenner & Block LLP, which could not be reached for comment. 

Two other lawsuits were also brought against the NIH on Monday. One was filed by a group of 22 states including Illinois, all of which have Democratic attorneys general; the other, by five medical organizations, including Boston and New York hospitals.

Judge Angel Kelley, who is presiding over all three lawsuits, issued a temporary restraining order (TRO) in the states’ lawsuit, applying only within the 22 states, and later issued a nationwide TRO in the medical organizations’ lawsuit.

At the time of publication, no judicial action had been taken in the suit brought by UChicago.

The “indirect” costs that the NIH directive cuts support administrative functions and maintenance expenses for buildings, utilities, and equipment for researchers and their labs. Generally, researchers cannot use grant money intended for direct research costs to pay indirect expenses.

When the NIH awards research grants to a scientist at an institution of higher education (IHE), the agency includes additional funding for indirect costs at a rate negotiated between the HHS and the institution. 

The NIH currently covers indirect costs of on-campus organized research at UChicago at a rate of 64 additional cents for every dollar of direct grant funding, a number in line with rates at other major research universities. 

The University negotiated an indirect costs funding rate with HHS for a five-year period ending in June 2026, but, under the new directive, all indirect costs would be set at a flat rate of 15 cents per dollar. This change to the flat rate would apply to all new grants and to “existing grants to IHEs retroactive” to February 9, per the NIH announcement. 

For fiscal year 2024, the University received approximately $338 million in NIH funding, of which $241 million went to direct costs and $97 million supported indirect costs.

Katie Miller, spokesperson for Elon Musk’s Department of Government Efficiency (DOGE), called NIH funding for indirect costs a “Liberal DEI Deans’ slush fund” in a post on X.

Neither the NIH nor the HHS responded to requests for comment. 

DOGE could not be reached for comment.

The University did not respond to a request for comment.

All three lawsuits against the NIH allege violations of the Administrative Procedure Act (APA). The APA regulates the process by which federal agencies engage in rulemaking and requires agencies to provide advance notice of rules and an opportunity for public comment.

Georgetown University administrative and constitutional law professor David Super and UChicago Law constitutional lawyer Alison LaCroix told the Maroon those APA violations were likely part of an intentional plan to challenge the confines placed on the executive branch through “overtly illegal actions.”

According to Super, NIH’s directive “doesn’t even attempt to comply with the APA.”

“Even if there are potentially problems with the indirect cost rates, the whole system is built up around those rates, and universities have made their budgets based on the current policy. The suddenness of this change alone could be deemed arbitrary and capricious,” Super told the Maroon. 

The TRO, issued by Judge Kelley, temporarily blocks the Trump administration from reducing the NIH’s indirect cost rate. 

Judges can issue a TRO if they believe that a plaintiff will suffer immediate, irreparable injury without the order. TROs cannot be appealed and typically expire after 14 days. They last only until the court holds a hearing on whether to grant a preliminary injunction—a more enduring form of court order.

Over the weekend, Vice President JD Vance posted on X, “Judges aren’t allowed to control the executive’s legitimate power,” prompting many lawyers to raise concerns about a “constitutional crisis” in which the Trump administration refuses to abide by judicial rulings limiting the scope of Trump’s executive actions.

House Speaker Mike Johnson agreed with Vance, saying that although “the branches have to respect our constitutional order… there’s a lot of game yet to be played.” 

When asked about Vance and Johnson’s statements, Super said: “Those claims are absurd and the people saying them know that. The courts’ powers here have been clear since the early days of the Republic.”

Neither Vance’s nor Johnson’s office could be reached for comment. 

Senator Chuck Grassley (R-Iowa), said during a meeting with reporters Tuesday that, while he believes the Trump administration will appeal court decisions blocking his priorities, Trump “has taken an oath to follow the law. And I assume he’s going to do that [if he loses on appeal].”

Just two weeks into the new administration, many parts of Trump’s agenda have been blocked in federal courts by TROs, including a Federal Bureau of Prisons policy denying gender-transition medical care and a sweeping attempt to freeze federal grants and loans.

On Monday, after states provided Federal District Judge John McConnell with evidence that Trump’s grant freeze had continued despite the TRO blocking it, McConnell directed the White House to comply with court orders.

“The broad categorical and sweeping freeze of federal funds is, as the Court found, likely unconstitutional and has caused and continues to cause irreparable harm to a vast portion of this country. These pauses in funding violate the plain text of the TRO,” McConnell wrote.

​​McConnell also ordered, “The Defendants must resume the funding of institutes and other agencies of the Defendants (for example the National Institute for Health) that are included in the scope of the Court’s TRO.”

Both Super and Northwestern Pritzker School of Law administrative law professor James Speta told the Maroon that McConnell’s rulings will likely benefit the plaintiffs, including UChicago, in their lawsuits against NIH.

According to Alison LaCroix, “While [TROs] are not verdicts, they have the full force of the law. It is extremely well-settled constitutional law that these judgments of the federal court are binding.”

What that “bind” means in practice is up to some interpretation, especially in the face of an administration signaling a willingness to defy judicial orders. 

Quoting Maness v. Meyers (1975) in his latest order, McConnell wrote: “Persons who make private determinations of the law and refuse to obey an order generally risk criminal contempt even if the order is ultimately ruled incorrect.”

“The issue with contempt of court is who enforces it,” LaCroix told the Maroon. “When it comes to [contempt of court] there are normal answers and there are ‘it’s a huge crisis’ type of answers, and these days we seem to always be in ‘it’s a huge crisis’ mode.”

According to Super, the judiciary has “extensive” means with which to guarantee compliance with a court order. 

“People who’ve thwarted court orders universally come to regret that day,” Super said. “If it gets far enough, the courts can attempt to ascertain which officials are engaged in noncompliance and hold them in contempt of court—criminal or civil.” 

In the case of civil contempt, which typically carries a financial penalty, courts can tell banks to deduct from offenders’ funds without any executive enforcement necessary, Super explained.

If the President refuses to abide by a court order, “that’s where we would fall back on the notion that it is emphatically the province and duty of the judiciary to say what the law is,” LaCroix said. “But past impeachment and removal, or not re-electing, there’s no other real check on the executive.”

“One thing that can get lost in all these [executive orders and directives] is that the principles [the Administration are opposing] are in the Constitution. That’s the highest law we have,” LaCroix continued. “That’s the ceiling, and it can’t be changed except by the incredibly onerous amendment process. So no matter what Trump says, there’s no way an executive order can, pardon the pun, trump the Constitution.”

“They are intentionally and overtly violating a number of statutes—choosing to act unlawfully to make changes that they could make legally,” Super said. “When the VP tweets, that certainly suggests the administration is seriously considering defying the courts in addition to Congress.”

Super told the Maroon the Trump administration’s regulatory strategy was “absolutely a constitutional crisis. This is the biggest effort to reshape the U.S. Constitution since the Civil War.”

“There have been debates over the long course of American history about the relationship between the executive and the courts, but [these questions of authority] have been settled since at least Marbury v. Madison in 1807 and probably since the U.S. Constitution in 1788,” LaCroix explained.

James Sparrow, an associate professor of American history at UChicago, told the Maroon that the Trump administration’s attempts to reshape the executive branch were unprecedented since at least the late 1800s. 

In a post on his Substack blog, Harvard constitutional law professor and conservative legal scholar Adrian Vermeule offered a different perspective. 

“Even where courts have jurisdiction to decide, it is always legally valid to argue that their decisions ought themselves to respect the separation of powers, and are thus subject to limitations internal to the law, as it were,” Vermeule wrote.

Vermeule could not be reached for comment.

The White House did not respond to repeated requests for comment. 

This is a developing story.

Anushree Vashist contributed reporting.