DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s Response to Election/Restriction Filed, filed 02 March 2026, has been entered. Claims 1-9, 11-12, 14-16, 18, 20-21, 25, 27, and 30 are currently pending. Claims 1, 4, 9, 11, 12, 16, 18, and 20 are independent claims. Applicant’s election without traverse of the invention of Group I, drawn to a recombinant nucleic acid, a vector comprising the recombinant nucleic acid, a cell comprising the vector, an AAV particle comprising the vector, and a pharmaceutical composition comprising the AAV particle, is acknowledged.
Claims 12, 18, 20-21, 25, 27, and 30 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-9, 11, and 14-16 are currently pending in the application and under examination to which the following grounds of rejection are applicable. An action on the merits follows.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/US2022/021249, filed 22 March 2022, which claims priority to U.S. Provisional Application No. 63/164,069, filed 22 March 2021.
Thus, the earliest possible priority for the instant application is 22 March 2021.
Information Disclosure Statement
The information disclosure statements filed 21 September 2023 and 25 January 2024 have been considered by the Examiner.
Drawings
The drawings are objected to because: 37 CFR 1.84 (u)(1) states “Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter.” In the instant case, the view numbers for the partial views for Figure 1 that appear on several sheets are followed by "(CONT.)" instead of a capital letter such as FIG. 1A, FIG. 1B, etc.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-9, 11, and 14-16 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. Claims 4-9, 11, and 14-16 are included in this rejection due to their dependence on claims 1 and/or 11.
Independent claim 1 recites, “the nucleotide sequence” in line 2. There is insufficient antecedent basis for this limitation in the claim. Claim 1 recites “A recombinant nucleic acid comprising a sequence encoding human arylsulfatase B” in lines 1-2, but does not have any recitation of “a nucleotide sequence”. As such, the metes and bounds of the claim cannot be determined.
Claim 2, which depends on claim 1, is indefinite in its recitation of “a nucleotide sequence at least 90% identical to”. It is unclear if the sequence recited in claim 2 is the same sequence of claim 1 or a different nucleotide sequence. As such the metes and bounds of the claim are indefinite.
Claim 3 depends on claim 1 and recites “the nucleotide sequence”. It is unclear if the sequence recited in claim 2 is the same sequence of claim 1 or a different nucleotide sequence. As such the metes and bounds of the claim are indefinite.
Claim 11 recites, “the AAV vector genome of claim 6”, which is indefinite because claim 6 is directed to a vector and not a vector genome. As such, the metes and bounds of the claim cannot be determined.
Claim Rejections - 35 USC § 112(a)- Written Description
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.
Claims 1-9, 11, and 14-16 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Independent claim 1 recites, “A recombinant nucleic acid comprising a sequence encoding human arylsulfatase B (ARSB), wherein the nucleotide sequence has been codon-optimized for expression in human cells”. Dependent claim 2 recites “The recombinant nucleic acid of claim 1, comprising a nucleotide sequence at least 90% identical to SEQ ID NO: 1 or SEQ ID NO: 2”.
The claims are broadly but reasonably interpreted as a genus of recombinant nucleic acid molecules comprising any human codon-optimized sequence encoding any human ARSB protein, including ARSB protein variants. The scope of the claims as written encompasses any variation in the nucleic acid sequences, which include variations which change the amino acid sequence at any position to any other amino acid. As such, the claim as written, encompasses variations which may change the structure sufficiently to adversely affect the function and/or alter the function of the ARSB polypeptide.
The disclosure does not provide structure/function correlations for the genus of human codon-optimized sequence encoding any human ARSB protein variant.
The specification teaches a wild-type nucleic acid sequence (SEQ ID NO: 4) and two codon-optimized nucleic acid sequences encoding human ARSB, SEQ ID NO: 1 and SEQ ID NO: 2, which were generated by two different commercially-available codon optimization tools [0014-0016, 0097-0098, Figure 1, 2, 3]. Sequence identities among the three sequences are as follows: 4 and 1: 62.8% identity; 4 and 2: 65.0% identity; and 1 and 2: 76.5% identity.
The specification also teaches generally, as claimed, that the nucleic acid sequence has at least 90% sequence identity to SEQ ID NO: 1 or SEQ ID NO: 2 [0096]. The specification also teaches a limiting definition for a percentage nucleic acid sequence identity as the percentage of nucleotide residues in the candidate sequence that are identical with the nucleotides in the polynucleotide specifically disclosed within the instant disclosure [0058]. The specification does not teach any specific sequences out to 90% identity with either of the recited codon-optimized sequences encoding ARSB (i.e., SEQ ID NO: 1 or SEQ ID NO: 2) other than SEQ ID NO: 1 and SEQ ID NO: 2 themselves. Example 1 discloses that two different codon-optimized version of the ARSB open reading frame (ORF) were prepared (GW and GS), wherein the GS ORF exhibits increased expression relative to the wild-type or GW ORF, such that GS was selected for further studies [0162, Figure 1, 2].
The specification does not disclose which variants of the sequence of SEQ ID NOs: 1 or 2 would encode an amino acid sequence which would retain the essential functional properties of the ARSB nor which variants would disrupt such functions. The specification additionally does not disclose any % identity which would retain the necessary identity and functionality in the encoded ARSB polypeptide. As such, the specification fails to provide any specific guidance as to which up to 10% of the sequence of SEQ ID NOs: 1 or 2 could be changed to allow for a functional ARSB polypeptide of the instant invention. Therefore, the description is not sufficient to adequately describe and demonstrate possession of any variants of SEQ ID NOs: 1 or 2, and particularly variants of SEQ ID NOs: 1 or 2 which comprise up to 10% sequence differences.
The following guidance provided in MPEP 2163 is informative. To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. An invention described solely in terms of a method of making and/or its function may lack written descriptive support where there is no described or art-recognized correlation between the disclosed function and the structure(s) responsible for the function. In other words, describing a composition by its function alone typically will not suffice to sufficiently describe the composition. See for example Eli Lilly, 119 F.3 at 1568, 43 USPQ2d at 1406 (Holding that description of a gene’s function will not enable claims to the gene "because it is only an indication of what the gene does, rather than what it is."); see also Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen Inc. v. Chugai Pharm. Co., 927 F.2d 1200, 18 USPQ2d 1016 (Fed. Cir. 1991)). An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed. See, e.g., Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 927, 69 USPQ2d 1886, 1894-95 (Fed. Cir. 2004) (The patent at issue claimed a method of selectively inhibiting PGHS-2 activity by administering a non-steroidal compound that selectively inhibits activity of the PGHS-2 gene product, however the patent did not disclose any compounds that can be used in the claimed methods. While there was a description of assays for screening compounds to identify those that inhibit the expression or activity of the PGHS-2 gene product, there was no disclosure of which peptides, polynucleotides, and small organic molecules selectively inhibit PGHS-2. The court held that "[w]ithout such disclosure, the claimed methods cannot be said to have been described."). Furthermore, written description issues may also arise if the knowledge and level of skill in the art would not have permitted the ordinary artisan to immediately envisage the claimed product arising from the disclosed process. See, e.g., Fujikawa v. Wattanasin, 93 F.3d 1559, 1571, 39 USPQ2d 1895, 1905 (Fed. Cir. 1996). While it has been held that what is conventional or well known to one of ordinary skill in the art need not be disclosed in detail, for inventions in emerging and unpredictable technologies, or for inventions characterized by factors not reasonably predictable which are known to one of ordinary skill in the art, more evidence is required to show possession.
The specification, as discussed in detail above, provides guidance for only two disclosed species of codon-optimized sequence encoding ARSB (i.e., SEQ ID NOs: 1 and 2), which each encode the same polypeptide sequence with some alternative codon usage, without providing sufficient detailed descriptions of the various variants which would encode a polypeptide with sufficient structural and functional properties of ARSB. As such, the specification fails to provide a description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of any of the claimed genus of variants of SEQ ID NOs: 1 or 2 comprising up to 10% differences in nucleic acid sequence.
At the time of filing, codon optimization was well known in the art; however, the claim as written does not require that any variants within the at least 90% identity limitation encode the same amino acid sequence as encoded by SEQ ID NOs: 1 or 2. There is not a disclosure of regions or domains of the protein that are essential to ARSB activity. There is no disclosure of what amino acids are in the active site, the binding pocket, or the hydrophobic core of the protein. There is no structure/function relationship taught at all for SEQ ID NOs: 1 or 2. The specification mentions only the full length of three disclosed species of ARSB coding sequences (non-codon optimized and codon optimized versions) corresponding to nucleotides of SEQ ID NOs: 1, 2, and 4.
The scope of the claims as written encompasses any variation in the nucleic acid sequences, which include variations which change the amino acid sequence at any position to any other amino acid. As such, the claim as written, encompasses variations which may change the structure sufficiently to adversely affect the function and/or alter the function of the ARSB polypeptide.
Tomanin teaches that MPS VI is an autosomal recessive lysosomal storage disorder caused by pathogenic ARSB gene variants [Tomanin et al. 2018, Human Mutation, 39, 1788-1802, abstract]. Tomanin further teaches 198 non-polymorphic ARSB variants associated with MPS VI which include missense, small deletion, nonsense, splicing, small duplication, large deletion, synonymous, insertion/deletion, and stop-loss mutations [Figure 1]. Tomanin also teaches that pathological variants in ARSB do not appear to be concentrated in any particular region or domain of the ARSB protein, such that variants were located alternatively in or near the active site pocket as well as remotely from the active site [column 10 ¶ 2, Figure 2, 4]. Tomanin additionally teaches that genotype-phenotype correlations in MPS VI have remained elusive due at least in part to the large proportion of rare or private mutations, limited phenotypic reporting, and overall heterogeneity of the disease, particularly for missense mutations whose effect on ASRB enzyme function may not be immediately apparent [column 10 ¶ 2]. Accordingly, given the dramatic effects single missense mutations or small indel mutations within the coding sequence for ARSB can have on the function of the ARSB protein, sufficient to induce MPS VI, the scope of the claim encompasses variants of the ARSB coding sequence which would result in non- or dys-functional ARSB polypeptides.
As such, variations of the ARSB coding sequences of up to 10% non-identities relative to the sequences of SEQ ID NOs: 1 or 2, such that a functional ARSB protein is still encoded, were neither conventional nor predictable at the time of filing, and the knowledge and level of skill in the art at the time of filing would not have permitted the ordinarily skilled artisan to immediately envisage all the variations of the sequence of SEQ ID NOs: 1 or 2, up to 10% variation, which would still produce a functional ARSB protein from the generic description provided by the specification. In view of these considerations, an ordinarily skilled artisan would not have viewed the teachings of the specification to as sufficient to show that the Applicant was in possession of the claimed invention.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1 and 4-9 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Makino & Pearson [US20240123040A1, published 18 April 2024, with priority to US Provisional Application No. 63/146,340, filed 05 February 2021].
Regarding claim 1, Makino discloses a recombinant nucleic acid comprising a sequence encoding human arylsulfatase B (ARSB), wherein the nucleotide sequence has been codon-optimized for expression in human cells [0050].
Regarding claim 4, Makino discloses a vector comprising the codon-optimized nucleic acid sequence encoding human ARSB [0050].
Regarding claims 5-6, Makino discloses wherein the vector is an adeno-associated viral vector [0053].
Regarding claims 7-8, Makino discloses wherein the nucleic acid encoding human ARSB is operably linked to a constitutive EF1α promoter [0061, 0110-0111, Table 2A Figure 8A, 9A, 10A].
Regarding claim 9, Makino discloses a cell in vitro comprising the vector comprising the nucleic acid sequence encoding human ARSB [0004, 0050, Figure 12].
Accordingly, by teaching all of the limitations of claims 1 and 4-9, Makino anticipates the instant invention as claimed.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 4-9, 11, and 14-16 are rejected under 35 U.S.C. 103 as being unpatentable over Makino & Pearson [US20240123040A1, published 18 April 2024, with priority to US Provisional Application No. 63/146,340, filed 05 February 2021]; in view of Vance et al. [2016, Scientific Reports, 6:22131, 1-10].
Regarding claim 1, Makino discloses a recombinant nucleic acid comprising a sequence encoding human arylsulfatase B (ARSB), wherein the nucleotide sequence has been codon-optimized for expression in human cells to treat mucopolysaccharidosis type VI, which is caused by deficient activity of ARSB [0002, 0050].
Regarding claim 4, Makino discloses a vector comprising the codon-optimized nucleic acid sequence encoding human ARSB [0050].
Regarding claims 5-6, Makino discloses wherein the vector is an adeno-associated viral vector [0053].
Regarding claims 7-8, Makino discloses wherein the nucleic acid encoding human ARSB is operably linked to a constitutive EF1α promoter [0061, 0110-0111, Table 2A Figure 8A, 9A, 10A].
Regarding claim 9, Makino discloses a cell in vitro comprising the vector comprising the nucleic acid sequence encoding human ARSB [0004, 0050, Figure 12].
Regarding claims 11 and 14-15, Makino teaches that mutations in ARSB cause mucopolysaccharidosis type VI (MPS VI), which includes a number of problems including bone dysplasia, joint restriction, organomegaly, heart disease, and corneal clouding [0002]. Also, as described above, Makino teaches an adeno-associated viral vector comprising the human ARSB coding sequence [0053], but does not explicitly teach an AAV particle comprising the AAV vector genome.
However, Vance teaches a gene therapy vector for treating mucopolysaccharidosis type 1 (MPS1)- associated corneal clouding [page 2 ¶ 2-4]. Vance also teaches a AAV8, AAV9, and chimeric AAV8/AAV9 (8G9) particles comprising codon-optimized sequences encoding a human IDUA protein for transduction of corneal cells to treat the MPS1-associated corneal clouding in MPS1 patients [abstract, page 6 ¶ 1, Figure 2-4]. Vance further teaches that all three AAV serotypes were able to transduce human corneas, and that the AAV8/AAV9 chimeric capsid (8G9) was most efficient for transduction of human cornea explants, transducing both the stroma cells and the corneal endothelium [abstract, page 6 ¶ 1, Figure 2-4].
Therefore, given the teachings of Makino that deficiencies of ARSB cause corneal clouding; the teachings of Vance that AAV particles with AAV8, AAV9, or a chimeric AAV8/AAV9 capsid serotype are able to transduce human corneas; and the teaching of Vance that the chimeric AAV8/AAV9 capsid serotype is most efficient for transduction of human cornea explants; an ordinarily skilled artisan at the time of filing the instant application would have been motivated to package a vector genome comprising a codon-optimized sequence encoding human ARSB into an AAV particle having an AAV8, AAV9, or chimeric AAV8/AAV9 serotype for transduction of human corneas, including corneal stroma cells and corneal epithelium, to treat MPS VI-associated corneal clouding.
Regarding claim 16, Makino and Vance teach the limitations of claim 11.
Additionally, Makino teaches pharmaceutical compositions for the treatment of MPS VI comprising an engineered cell comprising the vector comprising a nucleic acid sequence encoding human ARSB [0004, 0027].
Vance teaches the intended use of the disclosed AAV particles for corneal-targeted gene therapy in patients affected with MPS1, wherein the AAV particles are able to transduce corneal cells without inducing apoptosis even at high viral doses, suggesting the safety of AAV8G9-delivered gene therapy in MPS patient corneas [page 2 ¶ 2-4, page 4 ¶ 2, page 5 ¶ 2, Figures 2-4].
Although Makino and Vance do not explicitly teach to include the AAV particles in a pharmaceutical composition, given the teachings of Makino and Vance to deliver the therapeutic gene to patient corneas for treatment of corneal clouding in MPS, an ordinarily skilled artisan at the time of filing the instant application would have been motivated to comprise the AAV particle comprising a viral genome encoding ARSB in a pharmaceutical composition for treatment of MPS VI-associated clouding in patients with MPS VI.
Therefore, given the motivation taught by Vance to package a vector genome encoding human ARSB into an AAV particle having an AAV8, AAV9, or chimeric AAV8/AAV9 serotype for transduction of human corneas to treat MPS VI-associated corneal clouding; it would have been prima facie obvious to an ordinarily skilled artisan at the time of filing the instant application to package the nucleic acid of Makino in an AAV8, AAV9, or chimeric AAV8/AAV9 particle and to include the AAV particle in a pharmaceutical composition for use in treating of MPS VI-associated corneal clouding to arrive at an AAV particle and pharmaceutical composition according to the instantly claimed invention with a reasonable expectation of success.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Dr. KATIE L PENNINGTON whose telephone number is (703)756-4622. The examiner can normally be reached M-Th 8:30 am - 5:30 pm, Friday 8:30 am - 12:30 pm CT.
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DR. KATIE L. PENNINGTON
Examiner
Art Unit 1634
/KATIE L PENNINGTON/Examiner, Art Unit 1634
/MARIA G LEAVITT/Supervisory Patent Examiner, Art Unit 1634
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