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USPTO Allows Claims in Two Rosetta miRNA Patent Apps, Raising Patent Primacy Questions

Rosetta Genomics this week said that the US Patent and Trademark Office has allowed claims in two of the company’s microRNA patent applications, one covering a human miRNA gene and one covering an HIV miRNA gene.
“This is an important milestone for Rosetta Genomics," Amir Avniel, the firm’s president and CEO, said in a statement. "Our extensive intellectual property portfolio is an integral part of our business strategy, and these patent allowances are a significant milestone for Rosetta Genomics and the microRNA field."
Rosetta’s announcement comes a little more than a week after Alnylam Pharmaceuticals and partner Isis Pharmaceuticals reported that the patent office had allowed claims in an miRNA patent application the companies exclusively licensed from the Max Planck Institute for therapeutic applications.
At the time, Alnylam and Isis said their in-licensed patent — No. 10/490,955, which Max Planck also co-exclusively licensed to Rosetta, Asuragen, Stratagene, and Exiqon for diagnostic uses — would be the first US patent specifically related to the nascent miRNA field.
Max Planck’s patent application was filed with the USPTO on Sept. 15, 2004, and carries a PCT filing date of Sept. 27, 2002. Rosetta’s patent application covering the human miRNA gene was filed with the US patent office on Dec. 6, 2002, while its HIV miRNA patent was filed on Aug. 28, 2003.
Both Rosetta and Alnylam have said they expect the USPTO to issue patents on the claims in their applications within six months.
Regardless of which patents are issued first, challenges to the validity of the IP seem a distinct possibility. Both Alnylam and Rosetta have commonly made their patent estates the centerpiece of any discussion about the companies’ potential. Additionally, Alnylam has not been shy about asserting itself when it comes to IP.
Claiming Dibs
Rosetta’s first application, No. 10/310,914, is entitled “Bioinformatically Detectable Group of Novel Regulatory Genes and Uses Thereof” and covers “a novel group of regulatory, non-protein coding genes, which are functional in specifically inhibiting translation of other genes, some of which are known to be involved in various diseases.”
The application, which lists Rosetta founder and Chief Architect Isaac Bentwich as the sole inventor, also covers methods for detecting and inhibiting translation of these novel genes, which belong “to the miRNA genes group.” It was filed on Dec. 6, 2002.
Rosetta said that the USPTO has allowed claims in this patent application related to miR-492, a human miRNA about which little data is publicly available. A PubMed search on the miRNA results in a single paper, published last year in The Journal of Heredity by researchers from Integrated DNA Technologies, indicating that miR-492 lies together with another miRNA within a processed pseudogene.
The second patent application, No. 10/604,944, is entitled “Bioinformatically Detectable Group of Novel HIV Regulatory Genes and Uses Thereof.” It claims “a novel group of bioinformatically detectable, viral regulatory RNA genes, which repress expression of host target … genes by means of complementary hybridization to binding sites in untranslated regions of these host target … genes.
“It is believed that this novel group of viral genes represent a pervasive viral mechanism of attacking hosts, and that therefore knowledge of this novel group of viral genes may be useful in preventing and treating viral diseases,” the application adds.
Rosetta said that US patent office has allowed claims in the application, which also lists Bentwich as the sole inventor, related to an undisclosed HIV miRNA gene.
In reporting the two notices of allowance, Rosetta also noted that the patent office had cleared claims in the Max Planck patent application. Like Alnylam and Isis in their announcement earlier this month, Rosetta did not mention the other licensees to that piece of IP.
Unlike Alnylam and Isis, however, Rosetta did not tout the yet-to-be-issued claims in its ‘914 patent application as “the first US patent covering human microRNAs,” nor did it cite its ‘944 application as the first US patent covering a viral miRNA.

"Our extensive intellectual property portfolio is an integral part of our business strategy, and these patent allowances are a significant milestone for Rosetta Genomics and the microRNA field."

Although the USPTO typically issues a patent within six months of sending out a notice of allowance, it is under no obligation to do so, making it uncertain that the IP Alnylam and Isis have licensed would, in fact, be the first US patent covering an miRNA.
Re-Exams on the Horizon?
Given recent developments in the RNAi IP landscape, as well as the competitive nature of the miRNA field, there is a possibility that the validity of these miRNA patents could be called into question.
Recently, the USPTO rejected claims in a patent awarded to Sirna Therapeutics (now a part of Merck) covering the use of nucleic acids such as siRNAs to modulate the expression of IKK-gamma genes (see RNAi News, 2/8/2007). 
When the patent was issued last year, Sirna called the IP an indicator that it was on track to win patents for roughly 250 similarly broad target-specific applications it had filed with the US patent office. In contrast, Alnylam officials have publicly stated that the company does not expect RNAi patents covering an entire gene target will stand.
Although Alnylam itself did not itself ask the patent office for the re-examination that led to the preliminary rejection, the law firm that did ask for the review is known to have provided corporate finance services to Alnylam institutional investor Polaris Venture Partners. One of Alnylam’s co-founders Christoph Westphal, was also previously a general partner at Polaris.
But whether there will be similar re-exam requests for any of the three miRNA patents coming down the pike — either from Alnylam, Rosetta, or another company playing in the miRNA field — is not certain. Officials from Alnylam did not return requests for comment, and Rosetta continues to be under a US Securities and Exchange Commission-mandated quiet period in relation to its recent initial public offering (see RNAi News, 3/1/2007).

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