RNAi Litigation

Archive for January, 2012

This change was made on October 31, 2011 (for seemingly obvious reasons).

Lead attorney from Hagens Berman is Debra G. Josephson. Steve W. Berman is also lised in the case according to court documents. Also, Nicholas S. Boebel at Hagens Berman is on the case according to the law firm website. Links to the web pages for these attorneys have been placed in the Left SideBar along with Links for the attorneys for the Defendants.

Dr. Bass cites Hammond’s work (Hammond et al. Nature 404: 293–296, 2000) to implicate 21- to 25- dsRNA as the active siRNA:

“The nuclease activity was partially purified from cells that had been transfected with dsRNA, but dsRNA was not added to in vitro assays of the partially purified nuclease. So, how did the nuclease know which mRNA to degrade? Sure enough, the small 21- to 25-mers co-purify with the nuclease, suggesting that these pieces somehow template degradation of the mRNA. Further, if the S2 extracts are treated with micrococcal nuclease prior to adding the mRNA, RNAi is not observed.”

Dr. Bass’ speculation on how the RNAi catalytic activity persists and can be passed on to subsequent generations:

“…the enzyme bound to its small dsRNA template is regenerated with each round of annealing and cleavage, which could explain how RNAi appears to act catalytically.”

Dr. Bass’ uncertainty about the mechanism of RNAi:

“There are still many mysteries about the mechanism of PTGS (post-transcriptional gene silencing), but we know enough to consider the tantalizing possibility that dsRNA is an important signaling molecule in this process.”

Hearing. Status Conference set for 2/28/2012 at 03:00 PM in Courtroom 19 before Judge Patti B. Saris

[from Case 1:11-cv-10484-PBS Document 42 Filed 12/27/11]

The University of Utah (Utah) has dropped UMass as a defendant in their lawsuit against Max-Planck, Whitehead, MIT, and Alnylam and instead named the following UMass employees as defendants in this case:

ROBERT L. CARET, President of the University of Massachusetts in
his official capacity;
JAMES R. JULIAN, Executive Vice President and Chief Operating Officer of the University of Massachusetts, in his official capacity;
DAVID J. GRAY, Senior Vice President for Administration, Finance &
Technology and University Treasurer of the University of Massachusetts, in his official
capacity; and
JAMES P. MCNAMARA, Executive Director, Office of Technology Management of the University of Massachusetts, in his official capacity, their predecessors and successors in office.

How Dr. Bass asserts her inventorship of siRNA

31. Dr. Bass conceived the inventions of all of the issued claims of Tuschl II patents and at least some pending claims of Tuschl I, as well as of the still pending Tuschl II applications, well before any date asserted by the currently named inventors. Dr. Bass’ idea for the patents at issue was so well defined in her mind that it could have been reduced to practice by someone with ordinary skill in the art without further research. Moreover, she had a specific, particular solution to the problem at hand, not just general research goals.

32. Dr. Bass reduced her inventions to practice well before any date asserted by the currently named inventors of Tuschl I and II. Dr. Bass, with the assistance of her postdoctoral fellow, Dr. Scott Knight, reduced to practice her conception that the RNase III enzyme Dicer was the key agent of RNAi, and hence, that the resultant molecule would have, inter alia, a 3’ overhang, by treating multicellular animals with dsRNA corresponding to C. elegans Dicer (K12H4.8) well prior to any date asserted by the currently named inventors of Tuschl I and Tuschl II.

33. Dr. Bass conceived treating mammals, including humans, using dsRNA of 21-23 nucleotides with a 3’ overhang well before any date asserted by the currently named inventors of Tuschl I and Tuschl II.

Chronology

34. As an Assistant Professor at the University, Dr. Bass researched and analyzed dsRNA binding proteins. She identified a sequence in these proteins, known as a dsRNA binding motif, and searched various gene databases to identify genes that would produce proteins with this dsRNA binding motif.

35. In the course of her search, Dr. Bass identified the C. elegans gene, K12H4.8, that is now known to produce the RNase III enzyme colloquially known as “Dicer.” As far back as 1993, Dr. Bass understood that Dicer cleaves longer strands of dsRNA into short dsRNA and makes staggered cuts that leave 3’ overhangs (pronounced “3 prime overhangs”) of about two nucleotides in length.

36. She identified this gene well before the RNA interference phenomenon (“RNAi”) was demonstrated, and discovered that it has a dsRNA binding motif, two RNase III domains, and a helicase domain. She was the first to discover that this gene plays a role in dsRNA metabolism.

37. In 1994, Dr. Bass published a paper in the journal Current Biology characterizing proteins containing dsRNA binding motifs. In this paper, she noted that K12H4.8 is a gene that produces a protein with a double-stranded RNA binding motif, as well as RNase III and helicase domains.

38. When RNAi was first reported by Drs. Fire and Mello in 1998, they were unable to describe the mechanism by which RNAi functioned in a cell. Dr. Bass soon recognized that the K12H4.8 gene she had discovered was likely to be involved in RNAi because of its unique structure, and began to consider its features. The fact that K12H4.8 had dsRNA binding motifs, RNase III domains, and a helicase domain led her to the conception that this enzyme catalyzed RNAi. In approximately 1998, she began developing experiments to test this conception. These experiments were carried out at the University of Utah beginning in 1999.

39. Dr. Bass had members of her lab contact a C. elegans gene consortium to isolate C. elegans strains that contained a deletion mutation in the K12H4.8 gene. While waiting for this particular strain, she directed a member of her lab, Dr. Knight, to perform experiments to silence the expression of the Dicer gene using RNAi. This was a novel concept because it was not clear whether one could use RNAi to interfere with the RNAi function itself.

40. In early 2000, because of her extensive knowledge about dsRNA, the journal Cell asked Dr. Bass to write a review and comment on an article submitted by Tuschl, Zamore, and others titled “RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals.” The Zamore Article (left sidebar, paper published Marach 31, 2000) described the authors’ discovery that a Drosophila lysate (in which they were studying RNAi) unexpectedly cleaved the long 500 base pair dsRNA they were using to effect RNAi into short dsRNA of about 21-23 nucleotides.

41. The Zamore Article further indicated that one could effect RNAi by using the short dsRNAs isolated from the Drosophila lysate, although details of these experiments were not included.

42. Upon reading a pre-publication version of the Zamore Article in early March 2000, in preparation of her review and comment, Dr. Bass immediately recognized that the protein produced by the K12H4.8 gene had all of the properties necessary for RNAi, and that the resultant short dsRNA fragments would have a 3’ overhang. On March 21, 2000, she began to draft her review, titled, “Double-Stranded RNA as a Template for Gene Silencing.” As of March 21, 2000, her draft included information about RNase III enzymes and specifically an RNase III domain as part of the Dicer enzyme that cleaves dsRNA into short 21-23 nucleotide dsRNAs with 3’ overhangs.

43. Dr. Bass’ review, published April 28, 2000, set forth her conception that Dicer’s RNase III domains were responsible for cleaving dsRNA into approximately 23 nucleotide segments, and that it made staggered cuts that resulted in 3’ overhangs. In her article she specifically identified the genes that encode Dicer in various organisms, such as C. elegans, Drosophila, and humans. Her review also set forth her conception that introducing dsRNA of about 21-23 nucleotides into a cell should trigger gene silencing, i.e., that genetic disease could be treated in various organisms, including humans, by administering such molecules.

44. The Zamore Article eventually was published on March 31, 2000, and served as the basis for the Tuschl I provisional application No 60/193,594 (the “First Tuschl I Provisional”), filed with the USPTO on March 30, 2000, – one week after Dr. Bass wrote her draft review. The named inventors in the First Tuschl I Provisional are Tuschl, Sharp, Bartel, and Zamore.

45. Neither the Zamore Article nor the First Tuschl I Provisional describes cleaving long dsRNA strands into short dsRNA of about 21-23 nucleotides connected to K12H4.8, an RNase III enzyme, or Dicer. Neither the Zamore Article nor the First Tuschl I Provisional describes that these short dsRNAs have a 3’ overhang or the length of the overhang. Read the rest of this entry »