Ex Parte KinsellaDownload PDFPatent Trial and Appeal BoardJun 29, 201713825542 (P.T.A.B. Jun. 29, 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. 13/825,542 05/28/2013 Todd M Kinsella RIGL-068 5724 83092 7590 07/03/2017 Rigel Pharmaceuticals, Inc. Bozicevic, Field & Francis LLP 201 REDWOOD SHORES PARKWAY SUITE 200 REDWOOD CITY, CA 94065 EXAMINER CHEN, SHIN LIN ART UNIT PAPER NUMBER 1632 NOTIFICATION DATE DELIVERY MODE 07/03/2017 ELECTRONIC 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. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address(es): docket@bozpat.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte TODD M KINSELLA Appeal 2016-001481 Application 13/825,542 Technology Center 1600 Before, DONALD E. ADAMS, DEMETRA J. MILLS, and JOHN G. NEW, Administrative Patent Judges. MILLS, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35U.S.C. § 134. The Examiner has rejected the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We reverse the pending obviousness rejections and enter a new ground of rejection. Appeal 2016-001481 Application 13/825,542 STATEMENT OF CASE The following claim is representative. 1. A construct system for expressing a reporter protein, comprising: a) a reporter construct comprising: i. an inducible promoter that is activated by a transcription factor; and ii. a coding sequence encoding a reporter protein, wherein said coding sequence is in operable linkage with said inducible promoter; b) a first transcription factor construct comprising: i. a first tissue-restricted promoter; and ii. a coding sequence encoding a first fusion protein comprising a first portion of a transcription factor and a first subunit of a split intein, wherein said coding sequence is in operable linkage with said first promoter; and c) a second transcription factor construct comprising: i. a second tissue-restricted promoter; and ii. a coding sequence encoding a second fusion protein comprising a second portion of said transcription factor and a second subunit of said split intein, wherein the second subunit of said split intein specifically binds to the first subunit of the split intein and said coding sequence is in operable linkage with said second promoter; wherein expression of said first and second fusion proteins in a cell results in ligation, by a protein-splicing reaction mediated by said first and second subunits of said split intein, of said first and second portions of said transcription factor to produce said transcription factor and provides expression of the reporter protein only in tissues in which expression of the promoters overlap. 2 Appeal 2016-001481 Application 13/825,542 Cited References Manfredi et al. US 2002/0106699 A1 Aug. 8, 2002 Yadev et al. US 2004/0172688 Al Sept. 2, 2004 Kanno et al., Intefm-Mediated Reporter Gene Assay for Detecting Protein-Protein Interactions in Living Mammalian Cells, Analytical Chemistry, Vol. 78, No. 2 (2006). Wikipedia definition of binding, including specific binding Pending Grounds of Rejection 1. Claims 1—3, 6, 7, 10-12 and 14—17 are rejected under pre-AIA 35 U.S.C. § 103(a) as being unpatentable over Kanno in view of Yadav. 2. Claims 1, 8, 9 and 13 are rejected under pre-AIA 35 U.S.C. § 103(a) as being unpatentable over Kanno and Yadav in view of Manfredi. Disposition of Pending Rejections We reverse grounds of rejection 1 and 2 with respect to claim 1, in favor of the following new grounds of rejection. New Grounds of Rejection Claims 1—3, 6, 7—9, 10—13 and 14—17 are rejected under pre-AIA 35 U.S.C. § 103(a) as being unpatentable over Kanno, Yadav, Manfredi, and Wikipedia definition of binding site, including specific binding. 3 Appeal 2016-001481 Application 13/825,542 FINDINGS OF FACT 1. Kanno, Fig. la is reproduced below. [principle for the intein-mediated reporter gene assay. DnaEn (amino acids 1-123) and DnaEc (amino acids 1-36) are connected with mlexA (amino acids 1-229) and VP 16AD (amino acids 411-456), respectively. Interested protein X and Y are linked to the ends of DnaEs. Interaction between X and Y accelerates the folding of DnaEn and DnaEc, and protein splicing results. mlexA and VP16AD are linked together by a peptide bond to obtain a transcriptional activity. P. 558, col. 1. 2. Kanno discloses an intein-mediated reporter gene assay for detecting protein-protein interactions in living mammalian cells” (e.g. Title). Kanno discloses cDNA encoding fusion protein, protein-DnaEn-mLexA (modified LexA DNA binding domain), cDNA encoding fusion protein protein- DnaEc-VP 16AD and the cDNA encoding each fusion protein are inserted into pcDNA3.1( + ). Kanno also discloses a reporter construct comprising a major late promoter of adenovirus, eight-repeated LexA operators, and 4 Appeal 2016-001481 Application 13/825,542 DNA sequence encoding Firefly Luciferase (e.g. Figure la, lb, p. 558, right column, 2nd paragraph). Kanno teaches “the principle of the present method is shown in Figure la. When X interacts with Y, the DnaEs are brought in proximity and undergo correct folding, which induces protein splicing. Consequently, mLexA and VP 16AD directly linked to each other by a peptide bond. Until mLexA is ligated with VP 16AD, the firefly luciferase reporter gene is not transcribed into mRNA” (e.g. bridging pages 558 and 559). CHO-EGFR cells were transfected with 0.5 ug of pmLDn_Ras and pDcv_Raf-l and all cells to be assayed were transfected with 0.5 ug of pX81uc. The luminescence from firefly luciferase was measured (e.g. Figure lb and Figure 3). The pcDNA3.1(+) plasmid contains T7 promoter and CMV immediately early promoter. The DnaEn and DnaEc are subunit of intein protein. The CHO- EGFR cells are mammalian cells. When both the promoters in pmLDn_Ras and pDcv Raf-1 are stimulated, those promoters have overlapping expression pattern. The T7 or CMV promoter is constitutive promoter (claim 4). The major late promoter of adenovirus is conditionally inducible and promoters containing LexA operators are inducible by LexA containing transcription factor (claim 6). 3. Kanno does not specifically teach the promoters on both transcription factor constructs are tissue-restricted/tissue specific, and expression of the reporter protein only in tissue in which expression of the promoters overlap. 4. Yadav discloses an isolated polynucleotide comprising a nucleotide sequence that encodes a polypeptide comprising an N terminal portion of the polypeptide (ExtN), a C- terminal portion of the polypeptide (ExtC), an intein (Int) interposed between the ExtN and the ExtC (e.g. 119). The polynucleotide further comprises a regulatory sequence, such as a constitutive plant promoter or a plant tissue specific promoter. || 95, 96, 126. 5 Appeal 2016-001481 Application 13/825,542 5. Manfredi discloses: A method for detecting protein-protein interactions ..., in which two fusion proteins are prepared and allowed to interact with each other. The interaction between the two fusion proteins leads to protein trans-splicing, generating an active and detectable reporter. Abstract. 6. Manfredi discloses that: Suitable transcription activators include, but are not limited to, GAL4, GCN4, ARD1, the human estrogen receptor, E. coli LexA protein, herpes simplex virus VP 16 (Triezenberg et al., Genes Dev. 2:718-729 (1988)), the E. coli B42 protein (acid blob, see Gyuris et al., Cell, 75:791- 803 (1993)), NF- KB p65, and the like. In addition, hybrid transcriptional activators composed of a DNA binding domain from one transcriptional activator and an activation domain from another transcriptional activator are also useful. ... The corresponding transcriptional elements specifically interacting with the transcriptional activators or repressors are well known in the art. See e.g., Hanna-Rose and Hansen, Trends. Genet., 12:229-234 (1996). 199. 7. Manfredi further discloses that a transcriptional activator or repressor protein can be divided into an N-terminal portion and a C-terminal portion which are fused to the N-terminus of N-intein and C-terminus of C-intein, respectively. Upon protein trans splicing, a full-length protein emerges as a functional transcriptional activator or repressor which subsequently activates or represses the expression of the detectable gene in the reporting vector. 1100. 6 Appeal 2016-001481 Application 13/825,542 8. Manfredi discloses that: [M]any . . . reporters can be used in a similar manner in the present invention. Such other reporters include, for example, the green fluorescent protein (GFP), which can be detected by fluorescence assay and sorted by flow-activated cell sorting (FACS) (See Cubitt et al., Trends Biochem. Sci., 20:448-455 (1995)), secreted alkaline phosphatase, horseradish peroxidase, the blue fluorescent protein (BFP), and luciferase photoproteins such as aequorin, obelin, mnemiopsin, and berovin .... 195. 9. Manfredi discloses that: [T]he fusion constructs are designed such that intein mediated trans-splicing produces an active reporter that is a transcriptional activator or repressor capable of activating or repressing the expression of a detectable gene. Thus, the trans-splicing event will be detected based on the expression or suppression of the detectable gene. In this embodiment, a “reporting vector” containing the detectable gene operably linked to a transcriptional regulatory sequence is also introduced into the host cells. 198. 10. Figure 2A of Manfredi is reproduced below. 7 Appeal 2016-001481 Application 13/825,542 Figure 2A, top two scheme lines of Manfredi show an example of an N-intein and C-intein pairing or specific binding. When the inteins pair and interact with each other, an active reporter will be detectable in the host cell. 148. 11. Manfredi teaches introducing into an yeast cell a first chimeric gene and a second chimeric gene, said first chimeric gene encoding a first fusion protein having a first test polypeptide, an N-intein, and a first inactive reporter polypeptide fused to the N-terminus of the N-intein, said second chimeric gene encoding a second fusion protein having a second test polypeptide, a C- intein, and a second inactive reporter polypeptide fused to the C-terminus of the C-intein, wherein ligation between the C- terminus of said first inactive reporter polypeptide and the N- terminus of said second inactive reporter polypeptide forms an active reporter protein (e.g. claim 12). The reporter protein can be luciferase, green fluorescence protein or blue fluorescence protein (e.g. claim 18). The fusion constructs can be designed such that intein mediated trans-splicing produces an active reporter that is a transcriptional activator or repressor capable of activating or repressing the expression of a detectable gene (e.g. [0098]). The suitable transcription activator includes GAL4, GCN4 and herpes simplex virus VP 16 etc. (e.g. [0099]). 12. “In biochemistry, a binding site is a region on a protein or piece of DNA or RNA to which ligands (specific molecules and/or ions) may form a chemical bond.” “A more specific type of binding site is the transcription factor binding site present on DNA. Short, recurring patterns in DNA often indicate sequence-specific binding sites for proteins such as nucleases and transcription factors; ribosome binding, mRNA processing, and transcription termination are also signaled by these sequence motifs.” See, https://en.wikipedia.org/wiki/Binding site 8 Appeal 2016-001481 Application 13/825,542 PRINCIPLES OF LAW In making our determination, we apply the preponderance of the evidence standard. See, e.g., Ethicon, Inc. v. Quigg, 849 F.2d 1422, 1427 (Fed. Cir. 1988) (explaining the general evidentiary standard for proceedings before the Office). “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSRInt’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). Claim interpretation Claim 1 uses the transitional phrase “comprising” and, therefore, does not exclude other claim elements, for example, Protein X and Protein Y of Kanno, Fig. 1. The Specification does not define the term “specifically binds,” as used in claim 1. During ex parte prosecution, claims are to be given their broadest reasonable interpretation consistent with the description of the invention in the specification. See In re Zletz, 893 F.2d 319, 321 (Fed. Cir. 1989). See also, Cuozzo Speed Technolgies, LLC v. Lee, 136 S. Ct. 2131, 2144 (2016). “Without evidence in the patent specification of an express intent to impart a novel meaning to a claim term, the term takes on its ordinary meaning.” Optical Disc Corp. v. Del Mar Avionics, 208 F.3d 1324, 1334 (Fed. Cir. 2000). We find that the ordinary meaning of the term “specifically binds” means, “In biochemistry, a binding site is a region on a protein or piece of DNA or RNA to which ligands (specific molecules and/or ions) may form a chemical bond.” FF 10. “A more specific type of 9 Appeal 2016-001481 Application 13/825,542 binding site is the transcription factor binding site present on DNA. Short, recurring patterns in DNA often indicate sequence-specific binding sites for proteins such as nucleases and transcription factors; ribosome binding, mRNA processing, and transcription termination are also signaled by these sequence motifs.” FF10. Thus, we read the term “specific binding” in the claims to mean a specific association, attraction between molecules. Prima Facie Case Kanno discloses a construct system for expressing a reporter protein, (Fig la and b). Fig lb of Kanno shows construct pX81uc which is an inducible promoter that is activated by a transcription factor. | 66 of Kanno discloses, “In the case of a polypeptide reporter or polypeptide test agent fused to the C-terminus of the C-intein, it may also be preferred that the first amino acid of the polypeptide immediately following the C-terminus of the C-intein is cystenine, serine, or threonine.” Thus, Kanno discloses a coding sequence encoding a reporter protein, wherein said coding sequence is in operable linkage with said inducible promoter. Kanno also discloses a reporter construct comprising a major late promoter of adenovirus, eight- repeated LexA operators, and DNA sequence encoding Firefly Luciferase reporter (e.g. Figure la, 1 b, p. 558, right column, 2nd paragraph). Fig. la of Kanno, second line of scheme, further discloses a first transcription factor construct comprising a promoter, and a second promoter; and a coding sequence encoding a second fusion protein comprising a second portion of said transcription factor and a second subunit of said split intein. Kanno Fig. la and b discloses a coding sequence encoding a first fusion protein comprising a first portion of a transcription factor and a first 10 Appeal 2016-001481 Application 13/825,542 subunit of a split intein, wherein said coding sequence is in operable linkage with said first promoter. The principle of the method of Kanno, and as claimed, is shown in Figure la. When X interacts with Y, the DnaEs are brought in proximity and undergo correct folding (specific binding), which induces protein splicing. P. 558, col. 2. To yield an efficient splicing reaction, two particular amino acid sequences (KFAEY fused to DnaEn and CFNLSH fused to DnaEc) were inserted at the splicing junctions of each cDNA These two cDNAs were separately inserted into multiple cloning sites of pcDNA3.1(+) expression vectors, and we named these plasmids as pmLDn (encoding a mLexA-DnaEn fusion protein) and pDcV (encoding a VP16AD-DnaEc fusion protein) (Figure lb). P. 558, col. 2. Claim 1 and its transitional claim language “comprising,” does not exclude the additional X-Y protein interaction or drawing together of the intein molecules for their specific binding/folding interaction. Kanno does not disclose that the promoter of the intein construct is a tissue specific promoter. Yadav makes up for this deficiency in Kanno. Yadav discloses it is well known in the art to include a tissue specific promoter in an intein mediated protein splicing construct. 1195, 96, 126. Kanno discloses that the second subunit of said split intein specifically binds to the first subunit of the split intein and the coding sequence is in operable linkage with the second promoter. Expression of the first and second fusion proteins in a cell results in ligation, by a protein-splicing reaction mediated by the first and second subunits of said split intein, of the first and second portions of the transcription factor to produce the transcription factor and provides expression of the reporter protein only in 11 Appeal 2016-001481 Application 13/825,542 tissues in which expression of the promoters overlap. One of ordinary skill in the art would have recognized that the folding reactions between split inteins in Kanno, and Manfredi Fig. 2A, are specific binding reactions well known in the art and within the definition of “specific binding” of record, and which are generally useful configurations in split intein mediated protein and reporter constructs within their technical grasp. Appellant’s Previous Position Appellant previously contended that: [T]he Examiner has erred in interpreting the cited art and, in fact, the cited references do not teach or suggest all the limitations of the claims. Furthermore, the Examiner's proposed modification of the system of Kanno to arrive at the instantly claimed system would not have been obvious to the ordinary skilled artisan at least in part because such modification would render the system of Kanno unable to be used for its intended purpose. App. Br. 5—6. In particular, Appellant argues that: [T]he method of Kanno requires that, to detect a protein-protein interaction, the test proteins and not the intein subunits specifically bind to one another. If the intein subunits of Kanno were to specifically bind with one another the reporter would be activated in the absence of binding of the test proteins, making the system incapable of indicating whether or not a protein- protein interaction of the test proteins has occurred. Thus, Kanno clearly fails to teach or suggest intein subunits that specifically interact with one another. App. Br. 6. 12 Appeal 2016-001481 Application 13/825,542 ANALYSIS We entertain, but are not persuaded by, Appellant’s previous arguments of record. As indicated herein, the additional protein-protein interaction of the test proteins X-Y in Kanno is not excluded from the scope of the pending claims. In addition, Manfredi teaches that the use of split inteins and their specific binding are well known in the art of reporter expression. See, Fig. 2A. Manfredi also teaches that: Hybrid transcriptional activators composed of a DNA binding domain from one transcriptional activator and an activation domain from another transcriptional activator are also useful. ... The corresponding transcriptional elements specifically interacting with the transcriptional activators or repressors are well known in the art. See. e.g., Hanna-Rose and Hansen, Trends. Genet., 12:229-234 (1996). Manfredi 99 and 100, Fig. 5. It would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to use tissue-restricted promoter in the vector taught by Kanno because Yadav teaches intein-mediated protein splicing, particularly trans-splicing, in plants, microbial, yeast and animal systems, the use of regulatory sequence and the regulatory sequence (promoter) can be tissue-specific, developmental stage-specific or inducible promoter. Yadav teaches that tissue-specific promoters were well known in the use of intein reporter systems. One of ordinary skill in the art would have substituted the promoter taught by Kanno with tissue-specific promoter taught by Yadav in order to provide tissue-specific expression of the fusion proteins. Since the intein-mediated protein splicing system taught by Yadav requires expression of IntN (N-terminal portion of intein) and IntC (C- 13 Appeal 2016-001481 Application 13/825,542 terminal portion of intein) and the IntN and the IntC together forms a naturally split intein to bring together ExtN and ExtC to form a functional protein, one of ordinary skill in the art at the time of the invention would have used a tissue-restricted promoter (for example, same type of tissue- restricted promoter) that promotes expression of both IntN and IntC in the same cell. Thus, it would have been obvious to one of ordinary skill that expression of the reporter protein (ExtN+ExtC) would be in tissue in which expression of both tissue-restricted promoters overlap. One having ordinary skill in the art at the time the invention was made would have been motivated to do so in order to form fused transcription factor containing mLexA and VP 16AD so as to activate expression of reporter gene as taught by Kanno with reasonable expectation of success. One of ordinary skill in the art would have recognized that the folding reactions between split inteins in Kanno, and Manfredi are specific binding reactions within the definition of record. We find that the cited prior art, in combination, teaches each element claimed. Thus we find that the preponderance of the evidence supports that the combination of the cited references teaches the invention, as claimed. CONCLUSION OF LAW The Examiner’s obviousness rejections are reversed in favor of the above new ground of rejection. All pending, rejected claims fall. This decision contains a new ground of rejection pursuant to 37 C.F.R. § 41.50(b). 37 C.F.R. § 41.50(b) provides “[a] new ground of rejection pursuant to this paragraph shall not be considered final for judicial review.” 37 C.F.R. § 41.50(b) also provides that Appellant, WITHIN TWO 14 Appeal 2016-001481 Application 13/825,542 MONTHS FROM THE DATE OF THE DECISION, must exercise one of the following two options with respect to the new grounds of rejection to avoid termination of the appeal as to the rejected claims: (1) Reopen prosecution. Submit an appropriate amendment of the claims so rejected or new evidence relating to the claims so rejected, or both, and have the matter reconsidered by the examiner, in which event the proceeding will be remanded to the examiner.... (2) Request rehearing. Request that the proceeding be reheard under § 41.52 by the Board upon the same record.... No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). See 37 C.F.R. § 1.136(a)(l)(iv). REVERSED: and 37 C.F.R, $ 41.50(b) 15 Copy with citationCopy as parenthetical citation