RNAi Litigation

Professor Brenda Bass claims to have invented siRNA according to complaints and memoranda filed in this lawsuit by the University of Utah.

[from Case 1:11-cv-10484-PBS Document 61 Filed 03/21/12]

Dr. Bass has been researching RNA biochemistry since graduate school in 1980-1985, where she worked with Dr. Thomas Cech, who received the Nobel Prize in 1989 for discovering RNA molecules that catalyze reactions. Her Ph.D. studies focused on such molecules that cleave (cut) and ligate (join) RNA. In her postdoctoral work from 1985-1989, she discovered enzymes that act on dsRNA, which began her study of dsRNA and laid the foundation for the inventions at issue here. In 1989, Dr. Bass was appointed Assistant Professor at the University of Utah, where she researched and analyzed dsRNA binding proteins, searching gene databases to identify genes that would produce proteins with dsRNA binding motifs.

Dr. Bass was appointed Associate Professor in 1995, a full Professor in 1999, and a Distinguished Professor in 2007. She has been awarded numerous honors, including: a Pew Scholars Award; a David and Lucile Packard Fellowship; a named Investigator at the Howard Hughes Medical Institute; and election to the American Academy of Arts & Sciences. She is an editorial board member of the journal RNA, and was an editorial board member of the journal Science from 2004-2007. She was a founding member of the RNA Society in 1993, has been committee chair and a board member, and was elected its president in 2007.

In searching gene databases, Dr. Bass identified a gene “K12H4.8” in a species of worm “C. elegans” that is now known to produce an enzyme of a type known as “RNase III,” colloquially known as “Dicer.” Unlike the Tuschl II named inventors, Dr. Bass knew that Dicer cleaves dsRNA into 21-23 nucleotide pieces. As early as 1993, Dr. Bass understood that Dicer cleaves longer strands of dsRNA into short dsRNA and makes staggered cuts that leave 3’ overhangs of about two nucleotides in length. She was the first to discover that the K12H4.8 gene plays a role in dsRNA metabolism, well before the RNAi phenomenon was demonstrated.

When RNAi was first reported in 1998, the discoverers were unable to describe the mechanism by which it functioned in a cell. When she learned of the RNAi discovery, however, Dr. Bass recognized that Dicer was likely to be involved in RNAi because of its unique structure. In approximately 1998, she began developing experiments to test this conception that were ultimately carried out in her laboratory beginning in 1999. These successful experiments, completed in May 2000, reduced to practice Dr. Bass’s conception that Dicer was responsible for catalyzing RNAi, and that therefore, short interfering dsRNA of about 21-23 nucleotides in length with 3’ overhangs were the mediators of RNAi in living organisms and could be used to accomplish RNAi as a treatment for disease. [This, therefore statement was not actually made in Dr. Bass' insightful April 28, 2000 minireview (left sidebar) which was the published prior art at the time. The Tuschl I patent presents an experiment that suggested that the short fragments were less active than larger dsRNA (left sidebar "Figure 12 in the Tuschl I patent application) leaving open the discovery of the best mode for siRNA activity. JL]

In early 2000, the journal Cell asked Dr. Bass to write a review (a “mini-review”) of an article submitted by Dr. Tuschl and others titled “RNAi: double-stranded RNA directs the ATPdependent cleavage of mRNA at 21 to 23 nucleotide intervals.” The article described their discovery that a fruit fly “Drosophilia” cell lysate (a mixture made from the contents of cells) unexpectedly cleaved long dsRNA into short dsRNA of about 21-23 nucleotides. The article suggested that one could effect RNAi by using the short dsRNAs. The article makes no mention of 3’ overhangs or the length of the overhangs. Dr. Tuschl and the other authors admitted that they did not know how the short 21-23 nucleotide dsRNAs were produced in the lysate, and that they did not know the structure of the short dsRNA fragments.

Upon reading a pre-publication version of the article in early March 2000, Dr. Bass recognized that the K12H4.8 gene she had identified had all the properties necessary for RNAi, and that the resulting short dsRNA fragments would have the 3’ overhang. On March 21, 2000, she began drafting her review, titled “Double-Stranded RNA as a Template for Gene Silencing.” Her draft included information about the Dicer enzyme that cleaves dsRNA into short 21-23 nucleotide dsRNAs with 3’ overhangs.

On April 5, 2000, Dr. Tuschl sent an email to Dr. Zamore (click to enlarge), one of the other named Tuschl I inventors, reflecting that he had read a pre-publication draft of Dr. Bass’s review. Dr. Tuschl’s email admits that he and Dr. Zamore had not known that Dicer (RNase III) cuts dsRNA into pieces of 21-23 nucleotides in length until reading Dr. Bass’s review. Dr. Bass’s review was published in the journal Cell on April 28, 2000. It set forth her conception that Dicer’s RNase III domains were responsible for cleaving dsRNA into approximately 23 nucleotide segments with 3’ overhangs. She identified the genes that encode Dicer in various organisms, including the C. elegans worm, the Drosophila fruit fly, and humans. Her review set forth her conception that introducing dsRNA of about 21-23 nucleotides with 3’overhangs should trigger gene silencing, i.e., that genetic disease could be treated in various organisms, including humans, by administering such molecules.

On April 11, 2000, Dr. Bass presented her conception of 3’ overhangs to a group of RNA scientists at the Banbury Center, Cold Spring Harbor Laboratory. The conference was attended by 40 scientists central to the study of RNAi, including Drs. Bass and Zamore – the named Tuschl I inventor with whom Dr. Tuschl communicated by email about what he had learned from Dr. Bass’s review of their article. Dr. Bass described her conception regarding Dicer’s role in RNAi, including her conception that the short dsRNA fragments would have 3’ overhangs of about 2 nucleotides, with illustrations of the structure of the resulting short dsRNA molecule. Dr. Zamore attended her presentation.

In August 2000, Dr. Bass presented again at a program referred to as the Uppsala Conference. Tuschl II named inventors Drs. Tuschl and Elbashir attended, as did Dr. Bass, and presented on aspects of RNAi. Id. Dr. Bass talked to Dr. Tuschl at the meeting, and over dinner told him of the experiments in her laboratory in which she had reduced to practice her conception that Dicer would cleave dsRNA into fragments of 21-23 nucleotides in length with 3’ overhangs. In October 2000, two months after the Uppsala Conference, the Tuschl II inventors submitted a paper to the journal Genes and Development, in which they stated that the most effective short interfering RNAs in RNAi were those that have 3’ overhangs. The paper cited Dr. Bass’s review of the Tuschl article in Cell, and her work on RNase III (Dicer).

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