RNAi Litigation

Archive for May, 2011

[from Case 1:11-cv-10484-RGS Document 1 Filed 03/22/11]

28. Dr. Bass conceived the inventions of all of the issued claims of Tuschl II and at least some pending claims of Tuschl I well before any date asserted by the currently named inventors.

29. 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 post-doctoral 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

Chronology

31. 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.

32. 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 base pairs—or two nucleotides—in length.

33. 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. …

34. 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.

35. 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 beginning in 1999.

36. 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.

37. 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 called “RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals” (the “Zamore Article”). The Zamore Article 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. … Read the rest of this entry »

[This comes from his declaration filed with the court on July 21, 2009 and in the Univ. Utah Complaint (Case 1:11-cv-10484-PBS) Exhibit 8 Filed 03/22/11]

Dr. Tuschl states:

‘Synthetic Production of siRNA

19. The Tuschl II co-inventors and I were the first in the field to devise a protocol for isolating and identifying small RNAs through a process called cloning. [They cloned (copied) for the first time the siRNAs that were active in RNAi in large numbers (my wording).] Before this time, it was impossible, without undertaking extraordinary efforts, to isolate and characterize the sequences of small RNAs from an uncharacterized mixture of RNA fragments such as the one produced by the Drosophila lysate system.

20. The cloning protocol allowed us to characterize the small RNAs responsible for RNAi and, once characterized, allowed us to directly synthesize the molecules active in RNAi without the need for enzymes present in the Drosophila lysate system….. In the Tuschl II method, the production of small dsRNAs does not require the enzyme or the longer dsRNAs; rather small dsRNAs can be produced synthetically (i.e., from scratch [chemically synthesized]).

21. siRNAs produced synthetically have several advantages over RNA fragments from the prior Tuschl I Drosphila lysate system.

22. Whereas the Drosophila lysate system does not produce a pure population of RNA fragments that are uniform in size and sequence and free from other cellular RNA, the synthetic molecules are efficient and precise, because the siRNAs are uniform in size and sequence…

23. Prior to the development of the cloning protocol, it was impossible, without undertaking extraordinary efforts, to identify the molecules in the Drosophila lysate system that were responsible for silencing genes by RNAi. It was only after we developed the method for cloning small RNAs that we could create, study, and characterize the isolated components produced by the Drosophila lysate system and identify the molecules responsible for RNAi. [The details regarding the nature of the siRNA molecules derived from cloning, and characterization of the resulting target mRNA degradation process, are major features of the Tuschl II priority application EP ‘325 filed on December 1, 2000 and the first Tuschl II paper published in Genes & Development on January 15, 2001 (left sidebar)]

Tuschl II Invention of 3’ Overhangs

24. In the Fall of 2000, approximately several months after we made the first synthetic isolated siRNAs, we used them to discover that the most effective siRNAs are those that have 3’ overhangs…. [This was accomplished by testing many alternative structures and opened up the possibility of using modified nucleotides to make the siRNA molecules more stable in living systems.]

Mammalian Cell Data

27. Shortly after the Tuschl II ‘325 application was filed, the other Tuschl II co-inventors and I discovered that our synthetically produced, 21-nucleotide siRNAs with 3’ overhangs could cause RNAi in mammalian cells. [Including human cells; May 26 2001 Nature paper (left sidebar) submitted on February 20, 2001; the assay demonstrating knock down of the endogenous gene encoding human nuclear lamin is shown at the bottom of the left sidebar]. This was a phenomenal discovery because, prior to the Tuschl II inventions, researchers believed that small dsRNAs, including siRNAs would not silence genes in mammalian cells….

38. As explained above, the Tuschl II inventors were the first to invent a synthetic dsRNA molecule with features that allow it to perform RNAi in mammalian cells. This invention is groundbreaking, in large part, because it opens the door for using RNAi technology as a human therapeutic agent….’

The following quote comes from the end of the first Tuschl II paper (left sidebar): “The finding that synthetic 21- and 22-nt siRNA duplexes can be used for efficient mRNA degradation demonstrates that the targeting step can be uncoupled from the dsRNA-processing step. This raises the prospects of using siRNA duplexes as new tools for sequence-specific regulation of gene expression in functional genomics as well as biomedical studies. The siRNAs may be effective in mammalian systems, where long dsRNAs can not be used because they activate the dsRNA-dependent protein kinase (PKR) response…” (i.e. the toxic, non-tissue-specific interferon response mechanism).

Note on the “interferon response mechanism”: This is a first line of defense in mammals against infection by viruses that leads to intracellular production of larger dsRNAs. This response, which has been known and characterized since the 1960s, causes fever (among other things) which helps to slow the viral infection.

[This comes from his declaration filed with the court on July 21, 2009 and in the Univ. Utah Complaint (Case 1:11-cv-10484-PBS) Exhibit 8 Filed 03/22/11]

Dr. Tuschl states:

‘General Overview of the Tuschl II Invention

16. Dr. Zamore and I left Dr. Bartel’s Whitehead (lab) to become independent investigators in our respective (labs) in November, 1999, and July, 1999, respectively. I started my (lab) at (Max-Planck) in September, 1999, and hired Sayda Elbashir and Winfried Lendeckel. The Tuschl II patent applications name Dr. Elbashir, Dr. Lendeckel, and myself as inventors, and all of us worked in my (lab) at (Max-Planck).

17. From September, 1999, to mid-March, I dedicated part of my work toward completion of the Zamore et al., 2000, Cell paper which I published with my Tuschl I co-inventors (on March 31, 2000). At the same time I worked solely with Drs. Elbashir and Lendeckel, the Tuschl II group, to perform independent work that led to the Tuschl II inventions, which are described below. After about March 16-18, 2000, I worked solely with the other Tuschl II co-inventors on research that resulted in the Tuschl II inventions. However, I continued to communicate with Dr. Sharp and Dr. Bartel, two of my co-inventors. [ There is an email from Tuschl to Zamore on April 5, 2000 complimenting Brenda Bass after reading a pre-print of her soon to be published review saying that it is ‘obvious that RNase III would cut dsRNA because there aren’t many dsRNA nucleases’ ].

18. The Tuschl II inventions relate to compositions and methods for RNAi. In contrast to the work of the Tuschl I inventors, the Tuschl II inventors, including myself were the first to characterize the structural features of of siRNA, which enabled us to synthesize them and subsequently discover that they could act to silence genes in mammals. This finding, of course is essential to using RNAi for therapeutic purposes in humans. The key characteristics of the siRNA molecules described by our work, and which are discussed in more detail below, are as follows:

• Substantially free from non-target RNA molecules, meaning that it does not contain celluar contaminants that may be present in the (Drosophila) lysate;
• Synthetically, or non-enzymatically, prepared, meaning that it can be prepared from scratch;
• Double stranded;
• 19-23 nucleotides in length’
• At least one strand has a 3’ overhang, meaning at least one of the two strands of the dsRNA has a single-stranded region of 1-3 nucleotides on its 3’ end; and
• Capable of targeting and modifying/silencing specific mammalian genes in mammalian cells (I would have added “live” or “living” in front of “mammalian”).

Figure 1 (below) illustrates on example of a Tuschl II siRNA, in which each box represents an RNA nucleotide and the top and bottom rows of boxes each represent a strand of the double stranded RNA molecule.’

[This comes from his declaration filed with the court on July 21, 2009 and in the Univ. Utah Complaint (Case 1:11-cv-10484-PBS) Exhibit 8 Filed 03/22/11]

Dr. Tuschl states:

The Drosophila Lysate System

‘10. In mid-1999, Dr. Sharp, Dr. Bartel, Dr. Zamore and I decided to pursue an in vitro system for studying the recently-discovered phenomenon of RNAi. … At the time, Dr. Zamore and I were working as post-doctoral fellows in Dr. Bartel’s lab at …Whitehead. The system we developed is…the Drosophila lysate system. … The lysate contains the contents originally found in cells, including the cells’ naturally occurring DNA, RNA, enzymes, and debris. In this system, we introduced long strands of dsRNA, which were previously made separately, in test tubes containing Drosophila lysate.We observed that the long dsRNAs initiated RNAi. The other Tuschl I co-inventors and I published the result in Tuschl et al., …Genes & Development … December 15, 1999 …

11. Using the Drosophila lysate system (“the lysate”), we were able to show that the introduction of long dsRNA into test tubes containing the lysate could cause silencing of genes. … Though we were able to observe that the introduction of long dsRNAs was causing silencing of genes, we did not know how it was happening. At the time of publication, we acknowledged that “the molecular mechanisms by which dsRNA generates the RNAi effect are unknown>” That is, we did not know what components in the lysate or what characteristics of the long dsRNA molecules were responsible for triggering the RNAi response.

21-23 Nucleotide Length

12. In or about January, 2000, the other Tuschl I co-inventors and I determined that in the lysate system, there was some process occurring in the lysate that was causing cleavage of the long input dsRNA into fragments of about 21-23 nucleotides. It was further determined that if we removed the RNA fragments that we believed to be about 21-23 nucleotides in length from the lysate system in which they were created, and added them to a brand new lysate to which a long dsRNA precursor had never been added, the roughly 21-23 nucleotide fragments alone could result in silencing of genes.

13. Based on these findings, the first Tuschl I provisional patent application, the ‘594 application, was filed in the USPTO on March 30, 2000, naming the (four Tuschl I inventors)…. The following day, March 31, 2000, the Tuschl I inventors published the data … (in the journal Cell).

14. All of the information and figures included in the ‘594 application can be traced back to (the December 1999 paper and this more recent Cell paper except) Figure 12 of the ‘594 application was described as unpublished data in the … (Cell paper)…

15. In a contemporaneous paper by Bass (et al in Cell published on April 28, 2000), the research described in the (March 30, 2000 Cell paper) was recognized as an in vitro Drosophila lysate system that produces 21-23 nucleotide RNA fragments that cause RNAi. However, the author (Bass) recognized that the in vitro (i.e. test tube) observations of the (March 31) Cell paper have not yet been directly connected to RNAi in vivo (i.e. in a living organism).” … In other words, our research generated no evidence that our Tuschl I invention could silence genes in living … Drosophila cells that were the source of the lysate for the artificial system, much less in humans – or for that matter in any mammalian species. …’

In paragraph 53 of the University of Utah complaint against the five owners of Tuschl I and II (Max-Planck, Alnylam, UMass, Whitehead, and MIT), the plaintiff (Univ. of Utah) states as follows:

“These successful experiments reduced to practice Dr. Bass’ conception that Dicer was responsible for RNAi, and that therefore, short interfering dsRNA of about 21–23 nucleotides in length with 3’ overhang were the mediators of RNAi in life and could be used to accomplish RNAi as a treatment for disease.” The problem with this statement is everything that comes after “therefore”.

This is a simple, neat experiment in which Bass et al silenced the gene in the worm (C. elegans) that encoded RNase III (Dicer) and subsequently showed that RNA interference was lost if the Dicer gene was silenced. But this is not a reduction to practice of the efficacy of siRNA or siRNA treatment of disease. Am I missing something here?

I’m baffled by this lawsuit because if Dr. Bass succeeds in proving inventorship in court against the wishes of the owners of Tuschl I and II, my limited understanding of patent law tells me that this will cause invalidation of these patent families. Of course, we now know that cases like these may likely be settled between the plaintiff and defendant parties before the case goes to trial and before too much damage has been done. For UMass in the previous case, settlement seems all about creating a satisfactory option for Merck - thus preserving both Tuschl patent families. When I read the assertions of the Utah complaint, these read more like a form of extortion designed to get a share of the Tuschl royalties for the University of Utah.

There can be no argument against the tremendous insight into the mechanism of RNAi displayed by Dr. Bass in her laudable mini-review in Cell (April 28th, 2000; a follow-up to the Tuschl I paper in Cell published on March 31, 2000).

However, the following two statements were taken from the concluding remarks of Dr. Bass’ review:

“The in vitro observations of Zamore et al. (2000) have not yet been directly connected to RNAi in vivo.”

She goes on to further discuss her model in saying that it “predicts that introducing 21- to 25-mer dsRNAs into a cell should trigger gene silencing, but so far all RNAi systems require dsRNAs greater than (about) 100 base pairs for efficient inhibition of gene expression.” In fact, Figure 12 of the earliest published Tuschl I patent application (WO 01/75164) demonstrated that 21-23 nucleotide dsRNA was far less efficient in performing RNA interference compared to a 505 nucleotide dsRNA. Read the rest of this entry »

“Our proprietary LNP delivery technology is also enabling the product development efforts of our partners. We expect to see multiple data points throughout 2011 from four different therapeutic products currently in clinical trials that utilize our LNP technology, including Tekmira’s PLK-1 and Alnylam’s ALN-VSP, ALN-TTR and ALN-PCS products. …”

“…On March 16, 2011, Tekmira filed a complaint against Alnylam for misappropriation and misuse of trade secrets, know-how and other confidential information. On April 6, 2011, Alnylam filed an answer and counterclaim to Tekmira’s complaint. Tekmira has taken appropriate steps to ensure that it can pursue this lawsuit without interruption to its core business activities and intends to fulfill all of its manufacturing obligations to Alnylam.

Tekmira’s LNP technology is enabling the systemic RNAi product pipeline of Alnylam Pharmaceuticals, Inc. Tekmira continues to be the exclusive manufacturer of any LNP based drug products required by Alnylam through to the end of Phase 2 clinical trials, including the products ALN-VSP, ALN-TTR and ALN-PCS. As reported in Alnylam’s First Quarter 2011 Financial Results: Read the rest of this entry »

This is part of the Settlement Agreement between the plaintiffs and defendants Exhibit 10.2 struck on March 14, 2011 relating to the offer to UMass of the right to license Tuschl II to Merck.

3.4 UMass Payments to Alnylam. In consideration of the rights granted under the Merck Option Agreement, UMass shall pay Alnylam (i) [**] percent ([**]%) of any additional payments or other consideration (exclusive of any milestone payments due under the UMass-Sirna Agreement) that UMass receives from Merck solely for rights to the US Tuschl II Family, and (2) [**] percent ([**]%) of royalty income (exclusive of any milestone payments due under the UMass-Sirna Agreement) that UMass receives from Merck solely for rights to the US Tuschl II Family. For the avoidance of any doubt, the Parties acknowledge and agree: (i) UMass shall have no obligation to make any payment to Alnylam in the event that UMass and Merck agree that the milestone payment provided for in the UMass-Sirna Agreement upon issuance of a patent in the US Tuschl I Patent Family shall be due if a patent issues in either the US Tuschl I Patent Family or the US Tuschl II Patent Family; (ii) if UMass increases the consideration it receives from Merck above the consideration described in the UMass-Sirna Agreement in exchange for rights to the US Tuschl II Patent Family, then Alnylam shall be entitled to [**] percent ([**]%) of such increased amount; and (iii) if UMass receives income under the UMass-Sirna Agreement solely as a result of the license of the US Tuschl II Patent Family (i.e., such payments would not have been made on account of the license to the US Tuschl I Patent Family), then Alnylam shall be entitled to [**] percent ([**]%) of such amount. UMass shall make such payments to Alnylam not later than [**] days after receipt of the corollary payment from Merck.

3.5 No Termination of Merck Option Agreement. No challenge to the validity, enforceability, or inventorship of any application or patent in the Non-US Tuschl II Patent Family made by Merck outside of the United States shall have the effect of terminating Merck’s rights under Merck Option Agreement. [This section appears to acknowledge the expected appeal (by Merck et al.) of a recent decision by the EPO to uphold Tuschl II. This appeal was filed on April 4th.]

3.6 No Use of Merck License. Max Planck and Alnylam agree that neither the existence nor the terms of any license entered into by Merck pursuant to a Merck Option Agreement for rights to the US Tuschl II Patent Family shall be admissible for any purpose in any infringement action, opposition proceeding, nullity proceeding, or other judicial or administrative proceeding in which the validity of any member of the Tuschl II Patent Family may be challenged.

…

10.1.3 Merck. The terms of this Confidential Settlement Agreement may be disclosed to Merck, but only so long as Merck is informed of this confidentiality provision and agrees in writing to take reasonable measures to keep the terms of this Confidential Settlement Agreement strictly confidential and prevent their disclosure to any third party except as permitted by Section 10.1.5 and 10.1.6. Read the rest of this entry »

This is part of the Settlement Agreement between the plaintiffs and defendants Exhibit 10.3 struck on March 14, 2011 relating to the offer to UMass of the right to license Tuschl II to Merck.

A Definition
1.7. “Gatekeeper” shall mean an independent attorney, not employed by Alnylam, registered to practice before the United States Patent and Trademark Office who shall be mutually agreed upon by UMass and Alnylam, and who shall be bound by the Confidentiality Agreement and perform the services identified in Section 2.3 of this Agreement.

2. Grant of Rights.

2.1. Exclusive License. Except as expressly set forth in Section 2.2, UMass grants to Alnylam for the Term an exclusive, unrestricted, royalty-free license, with the right to grant sublicenses, under the US Tuschl II Patent Family including without limitation the right to make, have made, sell, have sold, offer for sale, import and use any Licensed Product.

2.2. Merck License Agreement. Notwithstanding the license set forth in Section 2.1, UMass reserves the right to convey an option (and corresponding licenses) to Merck (and to no other person or entity) to acquire from UMass one or more non-exclusive licenses to make, have made, sell, have sold, offer for sale, import and use any Licensed Product, except with respect to Excluded Targets, under the US Tuschl II Patent Family, provided that the agreement conveying the option and any agreement granting any such license shall include provisions to the effect that (i) Merck shall have no right to grant any sublicenses, except to (a) an Affiliate (which sublicense shall automatically terminate at the time that the entity to which the sublicense was granted ceases to be an Affiliate of Merck); and (b) a Collaboration Partner, Distributor, or a contractor working under the direction of Merck or a Merck Affiliate to the extent such contractor assists in performing the activities licensed hereunder, and in such cases only with respect to the specific Licensed Product that is the subject of the particular collaboration, distribution or services agreement; (ii) the option agreement and all licenses shall automatically terminate if Merck files a legal proceeding in the USPTO, a United States court, or an arbitral forum, challenging the validity, enforceability or inventorship of any application or patent in the US Tuschl II Patent Family, except if Merck is sued for infringement of a US Tuschl II Patent; and (iii) the license cannot be assigned except to an Affiliate or in connection with a merger, acquisition, or sale of all or substantially all of the assets of Merck or an Affiliate relating to the subject matter of the US Tuschl II Patent Family, which sale includes the assignment of the License Agreement dated September 8, 2003, between UMass and Sirna Therapeutics, Inc. Nothing contained in this Section 2.2 shall be construed to prevent Merck from asserting non-infringement as a defense in any legal proceeding involving a patent or application in the US Tuschl II Patent Family, or to assert any defense in a legal proceeding outside the United States involving a patent or application that is not a member of the US Tuschl II Patent Family. UMass acknowledges and agrees that (a) it shall have no right to grant to Merck any rights under the US Tuschl II Patent Family with respect to any Excluded Targets, and (b) any non-exclusive license granted to Merck pursuant to this Section 2.2 shall expressly provide that Merck is prohibited from granting any sublicense, covenant not to sue, or freedom to operate under any application or patent in the US Tuschl II Patent Family except as set forth in clause (i) above. Alnylam represents and warrants that, as of the Effective Date, there are [**] Excluded Targets. Alnylam shall allow UMass to designate a single outside attorney (the “UMass Attorney”) who agrees to be bound by the Confidentiality Agreement to inspect at Alnylam’s offices, at a reasonable time and with reasonable advance notice, documents sufficient to confirm that, as of the Effective Date, there are [**] Excluded Targets. Alnylam agrees that, if at any time after the Effective Date, a Target ceases to be subject to exclusive rights granted to another entity under the US Tuschl II Patent Family, then such Target shall no longer be an Excluded Target.

2.3. Provisions Concerning Excluded Targets. Alnylam shall provide the Gatekeeper with a certified list of Excluded Targets within [**] of the Effective Date. The Gatekeeper shall maintain such list in a secure location during the Term of this Agreement. Alnylam shall update the list of Excluded Targets during the Term of the Agreement by promptly informing the Gatekeeper when a Target has been removed from the list. Merck may, from time to time, provide to the Gatekeeper in confidence a list of proposed Targets. Read the rest of this entry »