The cloud over the FDA has not yet lifted

The big picture: The FDA's high-profile rejections of a series of rare disease drugs and its reversal on Moderna's mRNA vaccine may have dominated headlines over the past few weeks. But they followed concerns about the agency's political independence and the stability of its leadership.

• And while Vinay Prasad, the agency's top regulator of vaccines and biologics, is departing next month, his exit doesn't necessarily signal a mindset shift.
• Prasad took much of the blame for the agency's controversial recent decisions. But regardless of whether that was fair, he didn't operate in a vacuum.

Where it stands: Prasad's departure is being cast as a positive for companies that develop cell and gene therapies and other rare disease treatments, despite speculation in some circles that not much will actually change.

• FDA commissioner Marty Makary vocally defended Prasad shortly before announcing his departure, and it's no secret that Health Secretary Robert F. Kennedy Jr. has long been skeptical of pharmaceutical companies.
• What's more, Tracy Beth Høeg, who played a leading role in the push to adopt Denmark's slimmed-down childhood vaccination schedule, remains the FDA's top drug regulator — the fifth person to hold that position in a little over a year.
• Prasad "was one voice within a broader agency, and the lasting ramifications of the departure will depend on who follows and whether we see a stabilization within the organization," Leerink analysts wrote in an investor note.
• HHS spokesman Richard Danker said: "FDA approvals under Commissioner Makary's leadership are at their peak thanks to the agency's commitment to first-class science rather than the single-product lobbying campaigns waged by the Swamp."

What they're saying: "The underlying leadership dysfunction and staffing issues remain under the leadership of Commissioner Makary and HHS Secretary Kennedy," Capital Alpha Partners' Rob Smith wrote in a note this week.

• "Prasad's departure will also turn a brighter spotlight on Makary, whose job could also be in danger if FDA's turbulent leadership issues don't stabilize," Smith added.
• Raymond James analyst Chris Meekins — a former senior health official in the first Trump administration — struck a more optimistic tone, writing in a note to clients that, for all of the unknowns, he thinks Makary's job is secure and expects agency actions "to more align with Commissioner Makary's rhetoric once Prasad departs."
• White House spokesman Kush Desai said: "Under Commissioner Marty Makary's leadership, the FDA has focused on restoring Gold Standard Science and streamlining the development of promising new therapies for rare diseases."

Between the lines: Market-watchers aren't the only ones who suspect that the problem hasn't been solved. Republican Sen. Ron Johnson of Wisconsin — who chairs the Senate's Permanent Subcommittee on Investigations — has said he's probing the FDA's rejection of rare disease drugs, and his concern dates as far back as 2017.

• "Commissioner Makary is saying all the right things ... but the career researchers, it just seems like their bias is 'no,'" Johnson told Axios, adding that Prasad's departure "probably" helps the problem.
• "He seemed very proud when I talked to him that he hadn't overruled any of his career researchers. I think he needs to overrule his career researchers," Johnson added.

What we're watching: In his post announcing Prasad's departure and enumerating his accomplishments, Makary said the agency will name Prasad's successor before he leaves next month.

The bottom line: "With this encouraging departure, one prominent source of perceived uncertainty has been removed, but we are mindful of potentially broader, more structural constraints that may continue to shape outcomes," the Leerink analysts concluded.