The allegations go to the heart of integrity in medical research - the rigorous process that scientists use to prove that a new therapy works.
The allegations call into question whether the novel gene therapy was what the Jefferson researchers purported it to be: Specifically, could it have worked as reported since it was missing a piece of DNA that might have been critical to its success?
Gene therapy is in its infancy and still unproven. But if it pans out, it might allow AIDS patients to get treated just once and avoid having to take complicated and expensive medicines. Jefferson's therapy never got as far as human testing.
In its report, the Jefferson committee said ``the total evidence does not sufficiently support a finding of willful fabrication of data and scientific misconduct.'' It said ``no misconduct in research appeared to have been committed,'' but it identified ``significant problems.''
The committee ordered the scientists to send extensive correction notices to the medical journals that had published the data. The first correction was published this month in the Journal of Virology.
The committee also recommended the dismissal of the scientist, Lingxun Duan, who had the day-to-day oversight of the research project at Jefferson's Center for Human Virology. He took a leave of absence during the investigation and said he later agreed not to seek renewal of his contract.
Copies of official documents provided to the federal government and obtained by The Inquirer describe numerous allegations: missing data, a nonfunctioning gene, genetic material of an enzyme unrelated to the research that mysteriously turned up in the lab, threats against a whistle-blower, and finger-pointing among scientists on the far frontier of modern molecular medicine.
All this allegedly happened in a premier research laboratory, which has won significant funding from the National Institutes of Health and whose work has passed muster in scientific journals.
Dr. Roger J. Pomerantz, a nationally recognized AIDS researcher who is chief of the division of infectious diseases at Jefferson and director of the research center, acknowledged in an interview that he had failed to fully appreciate the problem flagged by the lab worker.
``The buck stops here,'' he said. ``I have to take responsibility.''
Nevertheless, Pomerantz said the gene therapy, which was supported by more than $800,000 in federal funds, worked in lab experiments to stop the AIDS virus from reproducing. He said a scientist unconnected with the original studies had recently repeated the experiment from scratch and found that ``it works.''
Pomerantz, who was criticized by the committee for poor management of the research, praised the thoroughness of the university's probe.
``We abided by the NIH [National Institutes of Health] and got this huge report, taller than I am,'' said Pomerantz, 41, who stands 5 feet 9 inches. ``You couldn't do anymore.''
The final report was completed in September and fills more than a dozen volumes. It has been forwarded to the Office of Research Integrity, a branch of the U.S. Department of Health and Human Services.
Under ORI procedures, allegations of possible scientific misconduct in federally sponsored research are usually first investigated by the institution where they reportedly occurred. The institution's findings are then sent to ORI for review.
Negative findings by ORI can lead to a loss of federal grants.
ORI officials declined to confirm or deny that they were reviewing the case. The agency's procedures require that unless proven correct, charges of scientific misconduct remain confidential.
THE FINDING BY POMERANTZ'S lab of a new way to attack the AIDS virus was welcome news when it hit the medical journals in 1994.
Back then, traditional medicine was losing the battle against AIDS. While chemical compounds such as AZT worked for a while, their effects soon wore off.
The Pomerantz team turned to an approach called intracellular immunization. Normally, antibodies do their disease-fighting work outside cells, but this method would get antibodies inside the cells where HIV - the AIDS virus - lives.
Lingxun Duan, now 36, a rising star in the lab, headed the project.
Duan constructed a gene that, when inserted into cells, would order up the production of an antibody that would bind to a key HIV protein, called Rev. The hope was that the antibodies would disable HIV, making it impossible to reproduce.
If the technique worked, it had far-reaching - and potentially lucrative - applications. It could be used not just to combat AIDS but possibly for other infectious diseases.
Beginning in 1994, the Jefferson team reported success in lab experiments. The next step was to check its safety in a small number of people. The NIH cleared the way, and the Jefferson team submitted an application to the FDA to test the therapy in six AIDS patients.
With a handful of other scientific groups at other medical centers working on similar approaches, the Jefferson team was eager to shepherd its invention through successful human tests. The team already had a collaborator in private industry - a Seattle-area firm, now known as Intracel Co., which was supplying raw material from which Duan constructed his gene. The company also helped fund the project.
As the Jefferson scientists were moving forward, a researcher in Pomerantz's lab, Yong Wu, found something unusual: A chunk of DNA was missing from the gene that Duan had constructed.
Wu, 41, was a virologist from China who had done research at the University of Alabama at Birmingham. He joined the Pomerantz lab in December 1994 as a post-doctoral fellow.
Wu declined to discuss the case for this story. His account of events is taken from correspondence to Jefferson officials and testimony before the investigative committee and a preliminary inquiry group.
Not long after he arrived, Wu began comparing the chemical code - known as the sequence - of Duan's gene with the sequences of genes for other antibodies, he later testified.
At first, he said, he had trouble because the published sequence of Duan's gene had an error: Two segments of DNA were transposed.
Once he straightened out that confusion, Wu said, he found that the gene was missing a small but critical piece of DNA. It was a chunk that helped direct the antibody to bind to Rev, the HIV protein.
Since antibodies work by binding to an infectious agent, Wu said the missing sequence made Duan's gene a ``pseudogene,'' meaning it could not function. He took his discovery to Duan, his superior. Duan, a graduate of the Shanghai Second Military University, had come to Philadelphia in 1989 to work on cancer research, first at Fox Chase Cancer Center and then at Jefferson.
``When I told Dr. Duan that this was a pseudogene, Dr. Duan admitted it, but said not to say anything,'' Wu testified.
Duan, in an interview, said he did not tell Wu to keep quiet. Duan said the research team was aware the gene had an unusual structure. But no one thought much about it because the gene therapy worked to stop HIV in lab experiments, he said.
Wu testified that he did not go directly to Pomerantz because ``for me it doesn't make sense because he cannot trust me, but he trusts Duan. So it scary for me to talk truth with him.''
Over the next year, Wu went about his work in the lab. In July 1996 Pomerantz told Wu that he would be terminated as of Sept. 1. Pomerantz said Wu ``has a talent in research,'' but noted that because of personal problems, ``he has not done well on his own as an independent researcher,'' according to a Pomerantz memo in the committee report.
Soon after, Wu went to a senior researcher in the lab, Dr. Omar Bagasra, who oversaw the molecular testing involved in the gene therapy work.
``So he called me one weekend, he came over, and explained to me, `Look at this sequence, something is wrong with this sequence. There's no way it can bind,' '' Bagasra later testified.
He said that he told Pomerantz of Wu's claims. Pomerantz decided it wasn't necessary to redo the experiments, but he agreed to have Duan's gene sequenced again to see if the coding was correct, according to testimony.
That check confirmed Wu's discovery that the published sequence of the gene was incorrect. Pomerantz submitted the correct information to Human Gene Therapy, a medical journal.
Left unaddressed, though, was Wu's major concern - that the missing chunk of DNA made it unlikely that the gene produced antibodies that would bind to Rev. So how could it work?
In December 1996, after leaving Jefferson, Wu took his concerns to the top.
In a letter to George F. Kalf, Jefferson's assistant dean for scientific affairs, Wu filed a complaint of scientific misconduct against Duan and pointed out what he considered to be irregularities in the gene therapy work.
He said there were ``several gross mistakes'' in papers published by the Jefferson team.
Wu also alleged that Duan was using the Jefferson lab ``for his own personal cloning factory'' and was possibly preparing to sell genetically engineered products to China.
He wrote that Duan hired scientists from the same military school that Duan had attended so ``they can follow his orders and keep his secrets.''
Wu said that after filing the complaint, he got a threatening phone call from Duan.
``Dr. Duan told me that since, in the letter, I had said things that attacked the Chinese government, or the People's Liberation Army, he would send the letter to the Chinese government to punish me when I returned to China,'' Wu testified.
He was so fearful, he said, ``it has been necessary for me to move from my residence and to make myself very scarce.''
Duan said in an interview that while he did call Wu in anger, he never threatened him. Duan said his ties to the Chinese military were remote and ended when he graduated from the military medical school in Shanghai. He said Wu's allegations of suspect business dealings were groundless.
Three days after Wu made his charges to Kalf, Pomerantz sent a letter to Kalf. ``Nothing that I have seen has given me any reason to question Dr. Duan's integrity or his scientific excellence,'' he wrote.
WU'S LETTER SET IN MOTION Jefferson's system for dealing with allegations of scientific misconduct. The first step was to set up an inquiry committee to determine whether a full investigation was warranted.
Meanwhile, Bagasra was checking out Wu's contentions by conducting his own experiments. His name was among the researchers listed on many of the papers published by the Jefferson team.
A Pakistani who had come to the United States in 1972, Bagasra joined Pomerantz's lab in 1991. He had developed a way to measure even the smallest amount of the genetic material of HIV inside cells.
Bagasra's account of events is taken from his testimony and documents in Jefferson's reports.
Drawing from a test tube labeled as containing Duan's gene, Bagasra, 49, inserted the gene into cells growing in the laboratory. The cells turned yellow and looked sickly, as if they were dying, he later testified.
To see what might be making the cells sick, Bagasra and a graduate student sequenced the gene they had inserted into the cells. They found it wasn't Duan's gene at all, but a portion of the gene for asparaginase, an enzyme used to kill cancer cells in some leukemia patients. Asparaginase had never been part of the experiments at Jefferson, or described in the team's published papers or applications for testing in people.
Then came another surprise. When a lab worker checked the published sequence of Duan's gene using an international gene database, she found it was remarkably similar to the published sequence of a gene for an antibody to asparaginase. Both were missing the same chunk of DNA, according to a report given to the inquiry committee.
For Bagasra, the finding couldn't be explained by chance, he later testified.
Putting it all together, Bagasra came up with a theory that he shared with the inquiry committee: It wasn't Duan's gene that was stemming the growth of HIV in lab experiments. Instead, asparaginase, combined with an antibody for asparaginase, was making it work.
He speculated to the committee that this wasn't an accident, but a well-thought-out plan to make the research appear successful. He alleged that the doctored gene therapy, had it ever reached AIDS patients, could have been ``toxic.''
On April 18, 1997, following a three-month probe, the Jefferson inquiry committee concluded that ``one or more acts of scientific misconduct may have been committed,'' and that it was possible asparaginase, not Duan's gene, was responsible for inhibiting HIV in the team's experiments. But the committee said there was no evidence to substantiate Wu's allegation of possible business dealings with China.
The scientific concerns were enough to trigger a full-blown investigation.
TWENTY-ONE TIMES between May and September 1997, a three-member investigation committee, along with assorted advisers and staff, met in a Jefferson conference room. The sessions started around dinnertime and sometimes went late into the night.
They heard from 14 witnesses, looked over documents and scientists' notebooks and ordered lab tests to sort out the tangled web of accusations.
In a report delivered on Sept. 29, the committee concluded that the research was fraught with ``careless'' and ``sloppy'' science and that Duan's gene had ``an extraordinary number of problems.''
It confirmed Wu's allegation that Duan's gene contained ``a large deletion'' in an area that governed the ability of the antibody to bind to the HIV protein, Rev. The deletion probably occurred by accident in the engineering of the gene, the committee said.
But given the missing DNA, it was ``very questionable'' whether the gene could work as reported, the report said.
The committee concluded that the binding data presented by the Pomerantz lab in medical journals was ``grossly inadequate.'' In some experiments, no original data were kept, making the committee question whether the work was ever done.
While the committee acknowledged that Jefferson's experiments found that the therapy had anti-HIV activity in cell culture, all of those experiments were, to some extent, dependent on Duan, the committee noted.
The committee confirmed the presence of genetic material for asparaginase in one vial.
However, it knocked down Bagasra's theory that asparaginase was responsible for the reported success of the experiments. It said the asparaginase gene found in the lab was incomplete and therefore unlikely to do anything, much less kill cells.
The committee criticized Bagasra for making unsubstantiated claims, including ``very speculative'' assertions that the asparaginase would have been harmful had it gotten into AIDS patients.
Still, the committee found no answer to a big mystery: How did a gene for asparaginase get into a test tube labeled as containing Duan's gene - a gene that, with its missing segment, was a close relative to the gene for an asparaginase antibody?
The committee called this a ``striking coincidence'' and said the probability that it happened by chance was ``exceedingly low.''
Overall, the committee found Wu ``more credible'' than Duan. It concluded that ``Dr. Duan probably did threaten [Wu] with retaliation when Wu returned to China.'
While the committee recommended that Duan be fired for careless science and misleading testimony, it cleared him of misconduct in research because it found no ``direct evidence'' that he had willfully ``altered [gene] constructs to include toxins'' or otherwise intentionally falsified data.
Pomerantz, the committee said, did not appropriately supervise Duan and did not pay enough attention to the possibility there was a problem in his lab. It told him to draw up a corrective-action plan to prevent future problems.
``In our opinion, most scientists would have quickly done carefully controlled experiments to determine the validity of the [gene] construct and the validity of previously published experiments,'' the committee said. At the same time, the committee said Pomerantz's actions were ``on the whole appropriate.''
The committee said Bagasra not only had lost his scientific objectivity during the investigation, but also broke the committee's confidentiality rules.
Bagasra since then has told federal officials that the committee failed to fully explore the evidence, according to Bagasra's lawyer, Alan Epstein.
Last month Bagasra was placed on administrative leave by Jefferson, pending a hearing on his dismissal, Epstein said. He said Bagasra was ``being punished for making allegations regarding various instances of scientific misconduct.''
Jefferson officials declined to comment, saying they could not discuss personnel matters unless they got approval from Bagasra.
``The university actively attempted to get permission from Dr. Bagasra to speak with . . . The Inquirer with as much detail as possible, but Dr. Bagasra refused through his lawyer,'' said Phyllis Fisher, a university spokeswoman.
AS THE FEDERAL OFFICE of Research Integrity reviews what went on at Jefferson, Pomerantz said the controversy has not set back his research. While the experiment under scrutiny has been set aside, he is now using the same genetic technique to target a different HIV protein.
``We are moving forward,'' he said.
Duan is also looking ahead. He said he was fed up with academia and was exploring his research options in private industry. He said he was convinced that the federal review would vindicate him because the data are on his side.
``Science is science,'' he said.