The FDA told Dendreon Corp. to stop enrolling patients in a second Phase III trial of its therapeutic vaccine, Provenge, in hormone-resistant prostate cancer.

The FDA instructed Seattle-based Dendreon to suspend new patient enrollment, but said those already enrolled could continue in the trial, called D9902. The FDA’s action does not affect the first Provenge Phase III trial, called D9901.

“[The FDA’s questions] relate to specific composition of cellular components [of Provenge], which is prepared by isolating dendritic cells from patients’ blood and combining them with recombinant protein,” Dendreon CEO Christopher Henney said in a conference call after the markets closed on Tuesday, explaining that the FDA’s request does not involve safety or trial design issues.

The company is “preparing a detailed response” to the FDA, Henney said. He also said he believes one reason for the scrutiny is that Provenge is the first of a new class of drugs and is a late-stage product. Henney said that the agency simply “wants to be comfortable that they have a good grasp of clinical questions” and a grasp on the product being used in clinical trials.

“We think the questions are not unusual,” he said.

Henney said the company is encouraged by the progress of D9901.

“We’ve always said we will have efficacy results from the 9901 trial in the June-July time frame,” he said. “With respect to 9902, it is a pivotal trial and sister trial to 9901.”

D9902 is the supporting trial to D9901 and needed for filing a biologics license application.

Leading up to the filing, however, he said Dendreon would need to have the drug fully characterized, noting that there are components in the vaccine “other than the antigen-presenting cells.” One of the functions of Provenge is to stimulate T cells, he said.

The primary endpoint for both trials is a twofold delay in time-to-disease progression, with a secondary endpoint of time to development of disease-related pain. The vaccine candidates have been developed as a result of the identification and engineering of tumor antigens that can be recognized by the immune system. Dendreon then uses a proprietary technique to isolate and manipulate dendritic cells to produce the T-cell response.

Dendreon Chief Financial Officer Martin Simonetti said the company did not change formulations of Provenge from the D9901 trial to the D9902 trial. He added that not only has knowledge of dendritic cells increased in the field, but also within the agency another factor that might have prompted the inquiry.

In light of the news, Pacific Growth Equities Inc., of San Francisco, lowered its rating for Dendreon’s stock.

“The reason for the FDA’s request at this late period is unclear,” wrote analyst Thomas Dietz in a research note issued Wednesday. “Management indicated that throughout the ongoing trials, the company has been in continuing dialogue as to the level of characterization required for the product.

“We believe that during this period of uncertainty, it is most appropriate to step back from the Dendreon story, and we are lowering our rating to neutral,” the note said.

Dendreon has the vaccine Mylovenge in Phase II trials for multiple myeloma and APC8024 in Phase I trials for breast, ovarian and colon cancers.

Dendreon’s stock (NASDAQ:DNDN) fell 22 cents Wednesday to close at $4.11.