DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Status
Claims 1-17 are pending.
Claims 1-17 are examined on the merits.
Claim Objections
Claim 7 is objected to because of the following informality: “… plant cell comprises a soybean plant or seed” has a logical error. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Scope of Enablement
Claims 3, 5, 10, 14, 16, and 17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the expressly disclosed sequences (e. g., SEQ ID NO: 21, 22, 23) and any narrow set of closely related constructs actually described and tested, does not reasonably provide enablement for the full scope of the claimed genera encompassing “fragment or variant” and/or “a sequence having at least 80% homology” without undue experimentation. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e. commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
Claim 3 regards “extensin signal peptide… according to SEQ ID NO: 21, or a fragment or variant thereof” by “a fragment or variant”; Claims 5, 14, and 17 regard “comprises a peptide according to SEQ ID NO: 22, or a fragment or variant thereof” by “a fragment or variant”. Claims 10 and 16 regard “a sequence having at least 80% homology with SEQ ID NO: 23” by “having at least 80% homology”.
Broad genus
The claims encompass broad genera of polypeptides and polynucleotides defined by sequence identity thresholds and functional outcomes. These limitations collectively cover large numbers of undisclosed sequence permutations (includes amino-acid substitutions /insertions /deletions; truncations; domain boundary changes; junction/linker changes; codon changes; and DNA sequence with ≥80% identity) that are not constrained by clear structural rules in the claims.
Contrast with disclosed embodiments
The specification primarily describes and exemplifies specific sequences (SEQ ID NO:21, 22, and 23) and selected constructs/conditions. In contrast, the claims extend far beyond the disclosed embodiments to include any “fragment” or “variant” of the stated peptide sequences and any nucleotide sequence with ≥80% homology to SEQ ID NO:23, regardless of whether the resulting construct still functions as a signal peptide that exports the fused protein, still yields a functional exportable chimeric OPN, and /or still achieves adequate expression /processing /localization in the plant cell.
Structure-function gap and essential structural features
Enablement is not shown across the full scope because the claims rely on functionally critical sequence regions whose essential structural features are not defined across the genus:
Signal peptide (SEQ ID NO:21) “fragment or variant”: signal peptides depend on specific structural characteristics (e.g., N-region features, a sufficiently hydrophobic core, and a cleavage region) that are highly sensitive to substitutions and truncations.
The specification does not provide claim-bounding guidance identifying which residues/regions of SEQ ID NO:21 can be changed (or removed) while still retaining export function, nor a rule that would allow a POSITA to generate and screen the full universe of fragments/variants without undue experimentation.
Chimeric peptide (SEQ ID NO:22) “fragment or variant”: SEQ ID NO:22 is a fusion of at least two domains (signal peptide + OPN domain) and may include junction/linker and processing elements. Export, processing, stability, glycosylation/processing, and accumulation depend on domain boundaries and junction context, which are not predictable across arbitrary “fragment or variant” sequences.
The specification does not identify the minimum OPN features that must be preserved (e.g., required motifs/regions) nor the allowable fusion/junction variants that maintain export and functional proteins.
Nucleotide sequence (SEQ ID NO:23) “≥80% homology”: at 80% identity, an enormous number of DNA sequences are encompassed, including sequences with extensive amino-acid changes, frameshifts, altered signal peptide cleavage, altered junctions, altered codon usage, altered mRNA stability motifs, etc. The claim does not restrict “≥80% homology” to synonymous codon variants or otherwise preserve the encoded amino-acid sequence.
The specification does not provide sufficient guidance to identify which changes within that 20% divergence would still encode a secretable, functional chimeric peptide and still be expressed /processed as intended.
This is a structure-function gap, the claims cover broad sequence space while the specification provides only limited examples and lacks principles that correlated structural variation with the required functions (export/secretion and production of the intended chimeric OPN).
Representative species/genus size (Eli Lilly-type analysis)
The claimed genera are broad: for a peptide of length 24 (e.g., SEQ ID NO:21), even a two-amino-acids (less than 10%) of permitted substitutions yields a combinational 99636 (361x276) of variants; “fragment” further multiplies possibilities by permitting many truncation endpoints.
A ≥80%identity nucleotide genus covering a multi-hundred -base coding region includes astronomical numbers of sequences, many of which will encode materially different proteins and /or fail expression/export.
The specification does not provide representative species spanning this breadth (e. g., multiple distinct fragments/variants with demonstrated export and function), nor does it provide common structural characteristics defining the genus boundaries such that a POSITA could practice the full scope without undue experimentation.
Accordingly, disclose does not enable a POSITA to make and use the full scope of the claimed “fragment”, “variant”, and/or “≥80% homology” embodiments for SEQ ID NO: 21, 22 and 23 without undue experimentation, because the claims encompass extensive sequence space without sufficient structural guidance, representative working examples, or predictable rules trying the permitted sequence variation to retain export expression functionality.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 2, 4, 6, and 11-13 are rejected under 35 U.S.C. §103 as being unpatentable over Rattanapisit (Kaewta Rattanapisit et. al., Scientific Reports (2017) 7: 17358, pp1-9), in view of Wang (Xiaoting Wang et. al., Process Biochemistry (2021) 100 pp39–48).
Claim 1 is drawn to a chimeric peptide having a first domain and a second domain, wherein said first domain encodes an osteopontin (OPN) peptide, or a fragment or variant thereof, having its localization signal disrupted or removed, and said second domain encodes a recombinant localization signal configured to export the chimeric peptide out of a plant cell.
Rattanapisit teaches heterologous expression of human osteopontin (hOPN) in a plant expression host (Nicotiana benthamiana) using a transient expression vector system and confirm expression/purification of hOPN from plant tissue (e.g., Western blot/ELISA; Ni affinity purification) (page 1, abstract). Thus, Rattanapisit teaches an OPN peptide produced in plant cells.
Rattanapisit does not teach removing (or disrupting) OPN’s signal/localization peptide, nor does Rattanapisit teach adding second domain encodes a recombinant localization signal configured to export the chimeric peptide out of a plant cell.
Osteopontin (OPN), also known as secreted phosphoprotein 1 (SPP1), is a secreted mammalian glycoprotein that is synthesized with a canonical N-terminal signal peptide and exported through the secretory pathway, where the signal peptide is cleaved during secretion (e. g., D.T. Denhardt et. al., FASEB Journal (1994), 7(15), pp1475-1482).
Wang teaches, “bacteria, yeast, and mammalian cell cultures have been successfully utilized for the production of many human growth factors and cytokines, each of these systems has limitations that are associated with safety, cost, scalability, and posttranslational modifications”, thus indicating the “need for alternative production systems, such as to develop an efficient plant cell-based bioproduction platform for high-quality” (i.e. animal-free and endotoxin-free) (page 39, introduction).
Wang further teaches fusion of “a tobacco extensin signal peptide to a heterologous protein erythropoietic growth factors–stem cell factor (SCF)” (page 40 fig 1). Wang further teaches that the extensin signal peptide directs the fused protein into the plant secretory pathway, resulting in export of the protein outside the BY2 cell into culture media (page 40, 2.1 and page 45 discussion paragraph 1).
A POSITA would have been motivated to produce hOPN in a plant expression system as taught by Rattanapisit because plant-based recombinant production is a recognized platform for generating functional therapeutic proteins at scale, leveraging inexpensive imputes, scalable cultivation, and avoidance of many mammalian-cell culture costs and constraints. In view of Wang’s teachings emphasizing improved production efficiency and reduced cost in recombinant protein manufacture, a POSITA would have had a clear economic and practical incentive to select a plant system for hOPN production to achieve higher cost-effectiveness and operational simplicity while still obtaining the desired hOPN product.
Further, a POSITA would have been motivated to engineer the hOPN construct for secretion/export from the plant cell to improve recovery and overall process efficiency.
Accordingly, a POSITA would have found it obvious to employ a secretion/export signal such as an extension signal peptide to direct the recombinant hOPN through the plant secretory pathway for export outside the plant cell. Extensin signal peptides are known plant secretion signals, and substituting one known secretion signal for another to obtain extracellular localization is a predictable design choice within ordinary skill. Accordingly, a person of ordinary skill in the art would have been motivated to replace or supplement the heterologous proteins’ native mammalian targeting information with a known plant secretion signal in order to obtain more predictable export an extracellular accumulation in plant expression system.
Accordingly, claim 1 is unpatentable over Rattanapisit and Wang.
Claim 2 is drawn to the composition of claim 1, wherein said recombinant localization signal comprises an extensin signal peptide.
For the same reasons set forth with respect to claim 1, Wang teaches an extensin signal peptide as a localization/secretion signal in plants (i. e., a signal peptide from extensin that directs secretion/export via the secretory pathway out of BY2 cell) (page 40, fig 1); therefore, it would have been obvious to employ an extension signal peptide as the recombinant localization signal recited in claim 1.
Clam 4 is drawn to the composition of claim 1, wherein said OPN peptide comprises a peptide according to SEQ ID NO. 20, wherein the localization signal has been disrupted or removed, or a fragment or variant thereof.
Rattanapisit teaches an OPN peptide sequence (GenBank: J04765.1) (page 4, table 2) that shares same sequence with SEQ ID NO:20 except for differences limited to the N-terminal region corresponding to the localization/signal peptide, as shown by sequence alignment (below). Therefore, Rattanapisit teaches SEQ ID NO:20, or at minimum a fragment or variant thereof. Therefore, it would have been obvious, for the same reasons set forth with respect to claim 1, to use a signal-disrupted hOPN sequence in the chimeric peptide when substituting a plant secretion signal to obtain predictable export in plant cells.
Accordingly, claim 2 and 4 are unpatentable over Rattanapisit in view of Wang.
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Claim 6 is drawn to a plant cell configured to express a heterologous nucleotide sequence, operably linked to a promoter, encoding a chimeric peptide having a first domain and a second domain, wherein said first domain encodes an osteopontin (OPN) peptide, or a fragment or variant thereof, having its localization signal disrupted or removed, and said second domain encodes a recombinant localization signal configured to export the chimeric peptide out of said plant cell.
Claim 6 recites a plant cell configured to express a chimeric peptide as recited in claim 1, and Rattanapisit teaches plant expression of hOPN while Wang teaches secretion/export using an extension signal peptide; therefore, it would have been obvious to configure a plant cell to express the chimeric peptide for the same reasons as claim 1.
Claim 11 is drawn to the plant cell of claim 6, wherein said recombinant localization signal comprises an extensin signal peptide.
Claim 11 further specifies that the recombinant localization signal comprises an extension signal peptide, as taught by Wang.
Claim 12 is drawn to the plant cell of claim 11, wherein said extensin signal peptide comprises a peptide according to SEQ ID NO. 21, or a fragment or variant thereof.
Claim 12 further specifies that the recombinant localization signal comprises an extension signal peptide, as taught by Wang.
Claim 13 is drawn to plant cell of claim 6, wherein said OPN peptide comprises a peptide according to SEQ ID NO. 20, wherein the localization signal has been disrupted or removed, or a fragment or variant thereof.
Claim 13 further specifies that the OPN peptide comprises SEQ ID NO:20 with the localization signal disrupted/removed (or a fragment/variant thereof), which corresponds to the hOPN sequence with N-terminal localization/signal disruption/removal (per sequence alignment) and is obvious modification consistent with rationale for claim 1.
The claimed invention in claims 6, and 11- 13 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Claim 7 rejected under 35 U.S.C. §103 as being unpatentable over Rattanapisit (2017), in view of Wang (2021) as applied claim 6, and Philip (Reena Philip et. al., Plant Science (2001) 161 pp323–335).
Claims 6 as the teaching of Rattanapisit and Wang is discussed above.
Claim 7 is interpreted as depend of claim 6.
Claim 7 is drawn to the plant cell of claim 6, wherein said plant cell comprises a soybean plant or seed.
Philip teaches expression of a heterologous mammalian protein (bovine β-casein) in transgenic soybean seeds under control of a soybean seed expression cassette (page 323, abstract), thereby teaching a soybean plant/seed cell as a host for heterologous protein production and processing (page 324, paragraph 1-2).
A person of ordinary skill in the art would have been motivated to express the recombinant hOPN construct of Rattanapisit, removed/modified mammalian N-terminal peptide, included the extension signal peptide secretion strategy taught by Wang, in a soybean plant or seed cell as taught by Philip, with a reasonable expectation of success because Philip teaches successful heterologous mammalian protein expression and processing in soybean seeds therefore, claim 7 would have been obvious.
Claim 15 rejected under 35 U.S.C. §103 as being unpatentable over Rattanapisit (2017), in view of Wang (2021) as applied claim 6, and Philip (2001), and further in view of Sun (Xianjun Sun et. al., Scientific Reports (2015) 5:10342, pp1-10).
Claims 6 as the teaching of Rattanapisit and Wang is discussed above.
Claim 15 is interpreted as depend of claim 6.
Claim 15 is drawn to the plant cell of claim 6, wherein said nucleotide sequence is codon optimized for expression in Glycine Max.
Sun teaches use of a soybean codon-optimized coding sequence (codon-optimized Cas9) for expression in soybean (page 8, Vector construction).
A person of ordinary skill in the art would have been motivated to employ, in soybean (Glycine max), the recombinant protein expression and signal-peptide-directed export approach taught by Rattanapisit as modified by Wang, and to codon-optimize the heterologous nucleotide sequence for soybean expression as taught by Sun, with a reasonable expectation of success because Philip demonstrated heterologous protein expression/
processing in soybean seeds and Sun demonstrates soybean codon optimization to improve expression in soybean.
Therefore, the limitation of claim 15 would have been obvious.
Claim 8 rejected under 35 U.S.C. §103 as being unpatentable over Rattanapisit (2017), in view of Wang (2021) as applied claim 6, and Roberts (Gethin R. Roberts, et.al., Plant Physiology (2005), Vol. 138, pp. 1259–1267).
Claims 6 as the teaching of Rattanapisit and Wang is discussed above.
Claim 8 is interpreted as depend of claim 6.
Claim 8 is drawn to the plant cell of claim 6, wherein said promoter comprises an inducible promoter.
Roberts teaches an inducible promoter system for plants (alc-based gene switch) thereby teaching an inducible promoter for regulated expression in plant tissue culture (page 1260, abstract).
Claim 9 is drawn to the plant cell of claim 8, wherein said inducible promoter comprises an ALCR/alcA ethanol switch.
Roberts teaches “The ALCR/alcA (alc) two-component, ethanol-inducible gene expression system provides stringent control of transgene expression in genetically modified plants” (page 1259 abstract).
A person of ordinary skill in the art would have been motivated to express the recombinant hOPN construct of Rattanapisit, modified to include the extension signal peptide secretion strategy taught by Wang using an inducible promoter as taught by Roberts to control expression, with a reasonable expectation of success because Roberts teaches inducible control of transgene expression in plants. Therefore, claims 8 and 9 would have been obvious.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
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/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/ Primary Examiner, Art Unit 1663