The Research Policy Dispatch
For decades, federal research funding has largely enjoyed broad bipartisan support from congressional appropriators. But the ground is shifting. In less than a year, administrators and researchers have faced a tsunami of executive orders and agency rules that feel destructive and threatening. Managing the day-to-day remains essential in this chaos, but it’s worth stepping back to ask: what does this moment mean for the future—both short and long term?
To get a handle on that question, it helps to look at two storylines that are now colliding. The first is a series of recent court cases that have reshaped how institutions can seek relief and how agencies exercise authority. The second is a set of executive actions that introduce political gatekeeping in grantmaking. Together, they set the stage for a more uncertain—and more legally contested era of federal funding.
To understand how these forces are reshaping federal funding, it’s useful to look at the contours of a few pivotal cases and decisions that have redefined the rules of engagement for institutions. Each one, in its own way, has narrowed traditional avenues of relief, raised the stakes of participation, or attempted to shift power back toward the executive branch. Let’s unpack.
CASA v. Trump: The End of the Nationwide Injunction
The first plot point is Trump v. CASA, Inc. (SC Docket #: 25A884) — better known simply as CASA. The case arose after the Trump administration, on its first day back in power, issued an Executive Order (EO-14160) targeting birthright citizenship. CASA de Maryland, a community advocacy group, along with others, challenged the order and sought to block it through the courts.
Here’s what makes CASA important: the Supreme Court didn’t weigh in on the constitutionality of Trump’s order. Instead, on the “shadow docket” (where emergency orders are decided without full briefing), the Court addressed the scope of injunctive relief. For decades, challengers could often secure nationwide injunctions that stopped enforcement of a federal policy across the board. CASA pulled that back. The Court held that relief must be limited to the plaintiffs before the court, not extended to everyone.
Adding to the uncertainty, Justices Barrett and Kavanaugh wrote in separate footnotes that the Court was not deciding whether Administrative Procedure Act (APA) challenges remained viable. In other words, the door to APA litigation wasn’t shut, but it wasn’t left clearly open either.
What is the APA? The Administrative Procedure Act (APA) of 1946 sets the rules for how federal agencies make and enforce regulations. It requires agencies to follow transparent processes—like publishing proposed rules, taking public comments, and providing reasoned explanations for decisions. The APA also gives courts the power to review agency actions, which is why it’s the backbone of most litigation challenging federal rules and executive orders under the Trump Administration.
Why this matters: higher education institutions can no longer assume that relief secured by one university or advocacy group will automatically extend to all. Nationwide injunctions are no longer an explicit tool that can be used by lower courts. Instead, institutions that want protection from harmful federal policies will need to participate directly in litigation or demonstrate their own injury in order to secure relief. A recent Kaiser Family Foundation analysis validates this, finding blue states that sued kept most of their CDC grants, while red states experienced the brunt of the administration’s clawbacks.
APHA v. NIH: Funding Disputes Belong in Federal Claims Court
Another important ruling came in APHA v. NIH (SC Docket #: 25A103). The American Public Health Association and affiliated institutions challenged NIH over grant termination decisions, arguing the agency had overstepped its authority under the APA.
The Court, again on the shadow docket, took a narrower view. It held that disputes over funding termination and payments belong in the Court of Federal Claims — a specialized court that handles monetary suits against the federal government — not in federal district courts.
The Court essentially told universities and organizations: if you want to fight for your grant dollars, your remedy is contractual, not regulatory. You go to the Court of Federal Claims, not to federal court under the APA.
Why this matters: the path to relief is narrower, slower, and more technical.
Chevron v. NRDC (1984) and Loper Bright v. Raimondo (2024): The Death of Agency Deference
The CASA and APHA cases were procedural rulings rather than decisions on the merits, but they interact with a larger doctrinal earthquake: the fall of Chevron deference in 2024.
For forty years, Chevron v. NRDC (1984) structured administrative law around one principle: when Congress left a statute ambiguous, courts would defer to an agency’s reasonable interpretation. This doctrine gave agencies like NIH and NSF wide latitude to define terms, enforce rules, and adapt statutory language to new realities.
That era is over. In Loper Bright v. Raimondo (2024), the Supreme Court overturned Chevron. Courts now review agency interpretations de novo — without deference. Judges, not agencies, get the last word on statutory meaning. In short, agency interpretations are now more vulnerable to litigation, and contested policies are resolved in the courts rather than unilaterally by agency leaders.
This shift has immediate implications for politically driven executive actions, such as the Federal Grantmaking Oversight executive order signed on August 7, 2025 (EO-14332). Without Chevron deference, agencies can no longer rely on judicial deference to implement policies quickly or stretch statutory language unchecked. Coupled with the Government Accountability Office’s (GAO) finding (B-337397) that HHS’s March 3, 2025 “Policy on Adhering to the Text of the Administrative Procedure Act” did in fact remove a judicially enforceable expectation of notice-and-comment, agency actions now face heightened scrutiny both in courts and with concurrence of GAO, by Congress under the Congressional Review Act (CRA). Judicial oversight tempers agency discretion, constraining the unilateral implementation of politically driven grantmaking decisions.
Why this matters for institutions:
Agency rules and guidance are more vulnerable to legal challenges.
Policies may be unsettled for lengthy periods of time while litigation plays out.
Courts, not scientific agencies, will increasingly decide what statutory text means — often with less technical expertise.
Institutions should expect less predictable public notice before rule changes, and increased litigation risk. If and when congress decides to take back its recently lacking oversight responsibilities, we may expect greater oversight via the CRA.
In short: the administration will likely continue to push the boundaries of rulemaking that will invite legal challenge, but external checks on agency discretion — from both courts and Congress — are stronger. Perhaps a momentary silver lining of the overturning of Chevron.
From Legal Shifts to Institutional Strategy
What does this mean for universities, research hospitals, and other grant-dependent institutions? The rules of engagement have shifted. Litigation around federal grants is likely to become more common, but the avenues for relief are narrower (vis-à-vis CASA, APHA). At the same time, courts are giving agencies less deference after Loper Bright, making agency interpretations and rulemaking more vulnerable to challenge. And while political appointees now play a larger role in initial funding decisions, projects that survive that review may face fewer risks of termination later. In this environment, institutions cannot rely on agency discretion or outside lawsuits to protect their funding. Resilience depends on proactive pre-award planning, airtight grantsmanship, and deliberate alignment with statutory and executive priorities. These investments protect the momentum of research, allowing discovery to advance without costly interruptions.
Tactical Playbook: Pre-Award Investment
In today’s environment, institutions best positioned to secure and defend federal funding are those that treat pre-award infrastructure and grantsmanship as strategic priorities. These approaches and investments are probably no longer optional—they determine whether proposals are competitive, defensible, and durable to political or legal scrutiny. Possible focus areas for consideration include:
Strategic intake & triage – Create processes to assess every proposed submission for program fit, quality, and risk. Early vetting ensures capped proposal slots are used effectively and that submissions align with statutory and administrative expectations. With NIH’s new proposal cap (NOT-OD-25-132), internal prioritization or competitive review becomes critical to allocate opportunities strategically.
Grantsmanship specialists – Invest in staff expertise or training to translate methods and aims into narratives that demonstrate alignment with congressional and administration priorities. This isn’t spin; it’s clear, documented evidence of fit. Agencies now expect proposals to show societal impact as well as scientific merit.
Documentation & provenance – Maintain a defensible trail of authorship, tools (including AI) used, and approvals obtained. This is increasingly vital if NIH questions originality or if proposals face later scrutiny in litigation or review. While NIH has not yet detailed enforcement of NOT-OD-25-132, robust audit trails are a prudent best practice.
Internal “political clearance” – Short, structured reviews of EO-sensitive or high-visibility topics can identify risks before submission, reducing vulnerability to shifting political priorities.
AI governance policies – Adopt explicit rules for acceptable AI use, paired with internal attestations of human authorship for critical sections, to safeguard integrity and auditability.
Scenario planning & legal briefing – Use “what if” simulations—EO reversals, APA/CRA implications, judicial challenges—to prepare for uncertainty and guide risk management.
Proposals that clear these internal checkpoints and convincingly demonstrate societal impact will be more resilient under the new political appointee model outlined in the Federal Grantmaking Oversight Executive Order. In practice, awards obtained through these processes should be less likely to face termination for misalignment with administration priorities.
If you need to track federal policy changes in real time, understand which executive or congressional actions affect funding risk, and see how those shifts impact specific programs and agencies, the Research Policy Atlas provides a centralized, actionable view to guide institutional strategy and pre-award decision-making.
Until next time,
Sarah Trimmer, MPH
The Research Policy Dispatch
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