Institut Pasteur & Universite v. Focarino: Claim Amendment of Patent Expired During Post-Grant Proceeding Leads to Dismissal

By: Jesus Hernandez, Blog Editor/Contributor  
TitleInstitut Pasteur & Univ. Pierre et Marie Currie v. Focarino, No. 2012-1485, -1486, -1487 (Fed. Cir. Dec. 30, 2013).
[A] Pasteur proposed amendments both to independent claim 1 and to dependent claim 14 that limited the targeted “DNA of an organism” to chromosomal DNA only. While agreeing that the amendments changed the scope of claim 1, which is not at issue, Pasteur argues that they did not change the scope of claim 14, because the unamended claim 14 itself was implicitly limited to chromosomal DNA [and thus should not be dismissed during post-grant proceedings, during which the patent expired].
Institut Pasteur at *12-13 (text added).
[B] Pasteur challenges the Board’s determinations of obviousness as to […] claims 10 and 12 of the ’545 patent [because (1) the cited art did not actually teach the claimed subject matter; (2) the Board ignored a Nucleic Acids Research article which underscored the extreme difficulty of the proposed combination; and (3) the Board did not give proper weight to Pasteur’s objective indicia of non-obviousness (licensing and industry praise).] […].
Id. at *12 (text added).
[A] Non-chromosomal DNA, such as mitochondrial DNA or DNA in an additional plasmid, can be homologous to chromosomal DNA. Thus, the original claim covered situations where non- chromosomal DNA is the targeted DNA. The amendment substantively narrowed the claim in requiring chromosomal DNA as the target. Because amending the claim to target only “chromosomal” DNA substantively altered (narrowed) its scope, the PTO may not issue the amended claim now that the patent has expired, as stated in applicable provisions of a PTO regulation, 37 C.F.R. § 1.530(j), (k).
Institut Pasteur at *13.
[B] Here, in ascertaining the scope and content of the prior art, the Board made factual determinations that were not supported by substantial evidence. The Board also failed to give proper consideration to at least two categories of evidence–[1 and 2] teachings in the prior art that targeting a cell’s chromosomal DNA could be toxic to the cell and [3] industry praise and licensing of Pasteur’s invention– that are important to the obviousness evaluation.
Id. at *15 (text added). 

Procedural HistoryOn appeal, the Board of Patent Appeals and Interferences (now the Patent Trial and Appeal Board) affirmed the rejections, concluding that the claimed inventions were obvious extensions of two prior-art references disclosing similar methods of targeting non-chromosomal DNA in prokaryotic cells. Pasteur appeals the Board’s conclusions to this court.
Institut Pasteur at *4.
Legal Reasoning (Newman, Clevenger, Taranto)
[A] Dismissal of the '605 Patent based on Narrowing Amendment
Claim 1 (with amendment)1. A method for inducing at least one site directed double-stranded break in the chromosomal DNA of an organism comprising: (a) providing an isolated, viable cell of said organism containing at least one Group I intron encoded endonuclease recognition site at a location in the chromosomal DNA of the cell […].
Institut Pasteur at *7.
Amendment Cause of DismissalFor the ’605 patent, we dismiss Pasteur’s appeal as moot, because Pasteur presented only substantively amended claims to the Board and to this court, and amended claims cannot be entered now that the patent has expired.
Id. at *4.
Ex Ante and Ex Post Analysis Of Altering Amendment At End of Patent Life
Ex ante Looking backward, if the claim were to issue on reexamination, Pasteur could not enforce it for the period before issuance of the reexamination certificate. That is because, for inter partes reexaminations under the pre-2013 version of 35 U.S.C. § 316(b) applicable here, as for reissues under 35 U.S.C. § 252, when a claim is substantively amended, the analysis of intervening rights after issuance, considering pertinent references and prosecution history, treats the amendment as raising an irrebuttable presumption that the original claim was materially flawed, so there can be no liability for acts of infringement before the amended claim issues.
Id. at *13-14 (internal citations omitted).
Ex postLooking forward, the PTO may not grant Pasteur a patent right extending beyond the statutorily authorized term, which has already ended.
Id. at *14 (internal citations omitted).
[B] Obviousness Grounds to invalidate '545 Patent are Deficient
Claim 7 (with amendment)7. A method for in vivo site directed genetic re- combination in an organism comprising:
(a) providing a transgenic eukaryotic cell having at least one Group I intron encoded endonuclease recognition site inserted at a unique location in a chromosome; (b) providing an expression vector that expresses said endonuclease in said transgenic cell; (c) providing a plasmid comprising a gene of interest and a DNA sequence homologous to the sequence of the chromosome, allowing homologous recombination;
Institut Pasteur at *8-9.
(1) The cited art did not actually teach the claimed subject matter.
[W]e conclude that the Board erred in finding that two references in the prior art, Frey and Dujon, “showed that a GIIE endonuclease cleaved yeast chromosomal DNA when expressed in yeast cells.” ’545 Board Decision, at * 7. In fact, neither reference discloses a GIIE endonuclease cleaving yeast chromosomes while those chromosomes are in yeast cells.
Id. at *16.
Frey discloses cleaving yeast chromosomes that had already been extracted from yeast cells and purified, not chromosomes still “in yeast cells.” […] [C]ontrary to the Board’s finding that the reference “describe[s] results using GIIE endonucleases in yeast,” ’545 Board Decision, at *7, the reference discloses only that a GIIE endonuclease could cleave yeast chromosomes extracted from yeast cells. Nor does Dujon disclose cleaving yeast chromosomes in yeast cells; the reference is silent about what type of DNA is cleaved. […] It teaches that a GIIE endonuclease “can be expressed in the yeast nucleus from artificial constructs and the protein is able to cleave efficiently both its natural site within mitochondria and an artificially placed site within the nucleus.” […] Nowhere else does the reference clarify what is meant by cleaving “an artificially placed site within the nucleus.”
Id. at *16-17.
(2) The Board ignored a Nucleic Acids Research article which underscored the extreme difficulty of the proposed combination.The Board compounded its erroneous findings by ignoring teachings that targeting a GIIE endonuclease to chromosomal DNA in a living cell could be highly toxic to the cell. The sole prior-art reference identified by the Board that discloses such a method warns of such dangers: a 1990 article in Nucleic Acids Research specifically teaches that introducing a GIIE endonuclease could be “highly toxic” to the cell, which might not be able to repair double-stranded breaks in the chromosome using homolo- gous recombination. J.A. 10314. Such a teaching counts significantly against finding a motivation to take the claimed steps with a reasonable expectation of success.
Id. at *17.
(3) The Board did not give proper weight to Pasteur’s objective indicia of non-obviousness
LicensingThe Board too finely parsed Pasteur’s licensing activities. It rejected the evidence because “Dr. Choulika did not establish that the third parties specifically licensed the patent family to gain access to the subject matter claimed in the ’545 patent, rather than other technology described in the patent but not claimed or claimed in related patents.” ’545 Board Decision, at 10. But that theoretical possibility does not undermine the strong probative value of the licensing of the ’545 patent. The central success described in the patent is the one prior art hoped for and is captured in the claims at issue: a method that uses GIIE endonucleases and homologous recombination to achieve the targeted modification of chromosomal DNA in living cells, specifically in yeast and, indeed, in
mammals. […]
Id. at *20-21 (internal citations omitted).
Industry PraiseThe Board also erred in dismissing Pasteur’s second category of objective indicia—industry praise—[...]. The Board acknowledged that Pasteur established a connection between “the praise by the industry and the homologous recombination step which is claimed,” but it found that step “was possessed by the prior art” and, thus, “not a proper basis to rebut the prima facie case of obviousness.” […] That finding, however, simply repeats the Board’s misreading of Dujon. […] Under a correct reading of the reference, a method that uses GIIE endonucleases and homologous recombination to achieve the targeted modification of chromosomal DNA was not “possessed by the prior art.”
Id. at *21 (internal citations omitted).
For the foregoing reasons, we dismiss Pasteur’s appeal with respect to the ’605 patent, reverse the Board’s rejection of claims 10 and 12 of the ’545 patent, […]
Institut Pasteur at *25. 

Editor Note
The Court reiterated the resoning with regard to the '545 Patent to the '252 patent. For further reading, click here.
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