Ex Parte Cannon et alDownload PDFPatent Trial and Appeal BoardMar 14, 201712913174 (P.T.A.B. Mar. 14, 2017) Copy Citation United States Patent and Trademark Office UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O.Box 1450 Alexandria, Virginia 22313-1450 www.uspto.gov APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 12/913,174 10/27/2010 MARTIN J. CANNON 110.022US2 3398 66981 7590 03/15/2017 HT KW MPTAVTSH EXAMINER MCTAVISH PATENT FIRM HA, JULIE 7460 Pinehurst Road Pine Springs, MN 55115 ART UNIT PAPER NUMBER 1675 MAIL DATE DELIVERY MODE 03/15/2017 PAPER Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte MARTIN J. CANNON, KRISTINA L. BONDURANT, and TIMOTHY J. O'BRIEN1 Appeal 2015-007470 Application 12/913,174 Technology Center 1600 Before ERIC B. GRIMES, JOHN G. NEW, and JOHN E. SCHNEIDER, Administrative Patent Judges. GRIMES, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134 involving claims related to antigenic peptides, which have been rejected on several grounds: anticipation, nonenablement, ineligible subject matter, and (for one claim) broadening in a dependent claim. We have jurisdiction under 35 U.S.C. § 6(b). We affirm the rejection based on patent-ineligible subject matter. 1 Appellants identify the Real Party in Interest as The Board of Trustees of the University of Arkansas. (Br. 3.) Appeal 2015-007470 Application 12/913,174 STATEMENT OF THE CASE “Matriptase ... is overexpressed in many tumors of epithelial origin.” (Spec. 2:9—11.) “Antigens are presented as short peptides bound to HLA class I or class II proteins on the surface of target cells for recognition by T cells. . . . CD4+ T cells recognize antigenic peptides bound to HLA class II proteins.” (Id. at 2:29 to 3:1.) “CD4+ T cells are crucial to activate the CD8+ T cell response and crucial for maintaining long-term immune memory that will recognize cancer cells in the future to prevent disease recurrence.” (Id. at 2:25—27.) Claims 1—11, 34, 35, 38, and 40-43 are on appeal.2 Claim 1 is illustrative and reads as follows: 1. A purified peptide of 7-50 amino acid residues comprising an antigenic matriptase sequence of 7-50 amino acid residues; wherein when the purified peptide is contacted with dendritic cells to generate peptide-loaded dendritic cells and the peptide-loaded dendritic cells are contacted with T cells, the peptide-loaded dendritic cells amplify CD4+ T cells (helper T cells) that recognize the matriptase sequence. The claims stand rejected as follows: Claim 43 under 35U.S.C. § 112, fourth paragraph, as being in improper dependent form (Ans. 17); Claims 1—5 under 35 U.S.C. § 102(e) as anticipated by Dickson3 (Ans. 16); 2 Claims 44 and 45 are also pending but the rejections of those claims have been withdrawn. (Ans. 18.) 3 US 7,355,015 Bl, issued Apr. 8, 2008. 2 Appeal 2015-007470 Application 12/913,174 Claims 1—5, 8—11, 34, 35, 40, and 43 under 35 U.S.C. § 112, first paragraph, as nonenabled (Ans. 7); and Claims 1—7, 38, and 40-43 under 35 U.S.C. § 101 as being directed to patent-ineligible subject matter (Ans. 2). I The Examiner has rejected claim 43 on the basis that it is broader than claim 42, from which it depends, and therefore does not comply with 35 U.S.C. § 112, fourth paragraph. (Ans. 17—18.) Appellants argue that “[sjince claim 43 depends from claim 42, by definition it includes all the limitation[s] of claim 42 and thus the peptide of claim 43 must also comprise [sic, consist of] SEQ ID NO: 4, SEQ ID NO:5, SEQ ID NO:6, or SEQ ID NO:7.” (Br. 15-16.) We agree with Appellants’ interpretation of the claims. The rejection under 35 U.S.C. § 112, fourth paragraph, is reversed. II The Examiner has rejected claims 1—5 as anticipated by Dickson. The Examiner finds that Dickson teaches “peptides having DYVEINGEK (SEQ ID NO: 33) and VVGGTDADEGE (SEQ ID NO: 32) from matriptase located in aa 228-236 and aa 443-453.” (Ans. 16.) The Examiner reasons that “[s]ince the reference teaches a polypeptide of 7-50 amino acids from matriptase, the reference anticipates claims 1-5.” {Id. at 17.) Appellants argue that “[t]here is no reason to believe that either of the Dickinson [sic] peptides have this property that when they are loaded onto dendritic cells the dendritic cells amplify CD4+ T cells that recognize the 3 Appeal 2015-007470 Application 12/913,174 matriptase sequence (that is, the peptide sequence loaded onto dendritic cells).” (Br. 14.) Appellants point out that neither of Dickson’s peptides overlaps any of the peptides identified in the Specification, and “[t]he Examiner has provided no rationale why the Dickinson [sic] peptides must inherently have the property recited in the claims.” (Id.) We agree with Appellants that the Examiner has not pointed to evidence that suffices to support a finding of anticipation. The claims on appeal require that the claimed peptides, when contacted with dendritic cells, result in dendritic cells that amplify T helper cells that recognize the matriptase sequence. Dickson discloses the deduced amino acid sequence for a matriptase cDNA clone, and indicates that the two peptide sequences that the Examiner cites “agreed with the internal sequences obtained from matriptase.” (Dickson 6:49—50.) As Appellants pointed out, though, neither of Dickson’s peptides shares any sequence with the four sequences identified in the Specification. The Specification states that “[t]he inventors have utilized an algorithm to predict peptides that will bind to three common HLA class II variant proteins (1).” (Spec. 3:5—6.) Reference (1) is Southwood et al., Several Common HLA-DR Types Share Largely Overlapping Peptide Binding Repertoires, 160 J. Immunol. 3363—3373 (1998). (Spec. 24.) The Specification states that “[t]he algorithms calculate a binding affinity value of a hypothetical 9-mer peptide by multiplying the ARB [adjusted relative binding] values of each residue of the peptides.” (Id. at 11:22—23.) Thus, the evidence shows that the peptides disclosed in the Specification were identified based on their particular amino acid sequences. 4 Appeal 2015-007470 Application 12/913,174 The Examiner has not pointed to evidence that shows it would be reasonable to expect the two peptide sequences disclosed by Dickson to share the property that is required by the claims on appeal. See Ex parte Skinner, 2 USPQ2d 1788, 1789 (BPAI 1986) (“[T]he examiner must provide some evidence or scientific reasoning to establish the reasonableness of the examiner’s belief that the functional limitation is an inherent characteristic of the prior art” before the burden is shifted to the applicant to disprove the inherency.). Ill The Examiner has rejected claims 1—5, 8—11, 34, 35, 40, and 43, on the basis that the Specification “does not reasonably provide enablement for all peptides of 7-50 amino acids of matriptase sequence or fragments thereof, or fragments of peptide comprising SEQ ID NOs: 4-7.” (Ans. 7.) The Examiner finds that the significance of specific amino acids for biological activity of a protein is unpredictable, as is prediction of a protein’s structure based on its amino acid sequence, and that even small mutations can have large effects on a protein’s activity. (Id. at 8—13.) The Examiner also calculates that the claims encompass a large number of possible peptides. (Id. at 14—15.) The Examiner concludes that [gjiven that one could not determine the structure of a protein computationally, and that the effect of amino acid substitution is unpredictable, it flows logically that one would be unduly burdened with experimentation to determine the effect of amino acid substitution(s) in a peptide or protein, with regards to structure, function, or physical/chemical properties. (Id. at 15.) 5 Appeal 2015-007470 Application 12/913,174 Appellants argue that the Specification identifies the algorithm that was used to calculate the binding affinity of various matriptase peptides, and also describes the testing method to determine whether any given peptide has the activity recited in the claims. (Br. 11—12.) Appellants also argue that the claims require the actual matriptase sequence and do not allow for substitutions, and that predicting a protein’s structure is irrelevant to the claims. {Id. at 12.) We agree with Appellants that the Examiner has not shown that undue experimentation would be required to practice the full scope of the claims. The Specification states that the inventors used a known algorithm to identify peptides in matriptase that are likely to bind to three common HLA class II variants. (Spec. 3:5—6.) The Specification identifies the source of the algorithm, as well as the testing that was done to determine whether the identified peptides had the activity recited in the claims. While most of the rejected claims are not limited to human matriptase peptides, the Examiner has not provided sufficient basis for concluding that applying the same techniques to other matriptase sequences, or identifying peptides of different lengths between seven and fifty amino acids, would require undue experimentation. As Appellants have pointed out, the Examiner’s concerns about amino acid substitutions and prediction of protein structure are not relevant to the claimed invention. We therefore reverse the rejection under 35 U.S.C. § 112, first paragraph. IV The Examiner has rejected claims 1—7, 38, and 40-43 as being directed to patent-ineligible subject matter. The Examiner finds that the 6 Appeal 2015-007470 Application 12/913,174 claimed peptides are fragments of a human protein and the claims do not recite features that demonstrate a marked difference from the naturally occurring protein. (Ans. 2—3.) The Examiner concludes that the claimed peptides are not significantly different from a natural product, and are therefore directed to a judicial exception to patentability. {Id. at 7.) We agree with the Examiner that claim 1 is not patent-eligible subject matter. Claim 1 is directed to a peptide that is made up of a fragment of the naturally occurring matriptase protein. Thus, the Supreme Court opinion in Association for Molecular Pathology v. Myriad Genetics, Inc., 133 S.Ct. 2107 (2013), is controlling. In Myriad, the Court considered claims directed to isolated DNA encoding the BRCA1 polypeptide and fragments of at least 15 nucleotides of that DNA. Id. at 2113. The Court held that “Myriad did not create anything. To be sure, it found an important and useful gene, but separating that gene from its surrounding genetic material is not an act of invention.” Id. at 2117. “Myriad found the location of the BRCA1 and BRCA2 genes, but that discovery, by itself, does not render the BRCA genes ‘new . . . composition^] of matter,’ § 101, that are patent eligible.” Id. “Nor are Myriad’s claims saved by the fact that isolating DNA from the human genome severs chemical bonds and thereby creates a nonnaturally occurring molecule.” Id. at 2118. The same analysis applies here. Claim 1 is directed to fragments of a naturally occurring protein, separated from the rest of the protein. Appellants have identified certain peptides, with naturally occurring amino acid sequences, that have the property of causing peptide-loaded dendritic 7 Appeal 2015-007470 Application 12/913,174 cells to amplify helper T cells but that does not render the peptides new compositions of matter that are patent eligible. Rather, claim 1 is directed to products of nature. Appellants argue that “[mjatriptase is more than 50 amino acids. So a purified peptide of 50 amino acids or less comprising matriptase sequence is not matriptase and is not a natural product. . . . Claim 1 uses information about the natural product matriptase, but it is not matriptase and is not a natural product. Accordingly, it is patent eligible.” (Br. 7.) This argument is not persuasive because the Myriad Court expressly held that the isolated BRCA genes were not patent eligible even though isolating the DNA required severing chemical bonds. Myriad, 133 S.Ct. at 2118. See also In re BRCA1- and BRCA2-based Hereditary Cancer Test Patent Litigation, 774 F.3d 755, 760 (Fed. Cir. 2014) (“The Supreme Court held ineligible claims directed to segments as short as 15 nucleotides, the same length as the primer claims at issue here, suggesting that even short strands identical to those found in nature are not patent eligible.”). The logic of the Myriad Court also applies when the naturally occurring product is a fragment of a protein rather than a gene. We therefore affirm the rejection of claim 1 under 35 U.S.C. § 101. Claims 2—7, 38, and 40-43 fall with claim 1. 37 C.F.R. § 41.37(c)(l)(iv). SUMMARY We affirm the rejection under 35 U.S.C. § 101 but reverse the other rejections on appeal. 8 Appeal 2015-007470 Application 12/913,174 TIME PERIOD FOR RESPONSE No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED-IN-PART 9 Copy with citationCopy as parenthetical citation