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 .
Application Status
Claims 1-9, filed 8/18/2022 are under examination in this Office action. It is noted that amended claims were filed on 8/18/2022, absent the multiple dependency found in the original claims, filed on the same date. In the amended claims of 8/18/2022, claims 7 and 9 were amended to drop multiple dependency. The multiple dependency exists in the claims filed on 8/29/2023. It is presumed that the submission on this date is the English translation of the Japanese application.
Priority
This application claims priority to foreign parent to JP2020028547, field 2/21/2020. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statements (IDS’s) submitted on 11/07/2022, 09/20/2024 and 03/03/2025 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
The drawings, filed 8/18/2022, are accepted.
Claim Rejections - 35 USC § 112(a)
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 1,2, 3, 4, 6, 9 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, for failing to comply with the enablement requirement. This is a scope of enablement rejection, because the specification is considered to be partially enabling for the use of siRNA with disclosed SEQIDNo’s in mouse organ and cell cultures and human cell cultures, does not reasonably provide enablement for topical administration in any physical location, for any RNA molecule targeting USAG-1, or a wide-array of variants of the SEQ ID NO provided, or for tooth regeneration therapy as a treatment in any taxonomic species. The claims contain subject matter which was not described in the specification in such a way as to fully enable one skilled in the art to which it pertains or with which it is most nearly connected, to make and/or use the invention.
The MPEP §2164.01(a) recites, “There are many factors to be considered when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any necessary experimentation is “undue.” 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).
(A) Breadth of claims: The claims are very broadly drawn to use of any topical administration in any physical location in any species/cell line/organ culture, for any RNA molecule targeting USAG-1 (claim 1), or one of five types (claim 2), or two types (claim 3) for a wide-array of variants of the SEQ ID NO provided (claims 4 and 6), or for tooth regeneration therapy as a treatment in any taxonomic species (claims 1 and 9).
(B) Nature of invention: The invention relates to tooth regeneration as a function of affecting USAG-1 expression with RNA. Particular RNA are disclosed, that may be modified, for use as the RNA.
(C) The state of the prior art: Presents challenges and unknowns: i. Zheng et al (hereafter Zheng, 2012, Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation, PNAS 109: 11975-11980) disclosed topical application of siRNA conjugates and pointed out that for example, the there is an epidermal barrier that typically precludes entry of gene suppressing therapy, and in-fact has been a major technological challenge (Pg 11975, right col, para 1), one example of how the broad claim of topical administration (claim 1) may typically prove ineffective (Pg 11975, Para 1 (Abstract)) ii. While varied small RNAs may be used to alter gene expression, the classes of small RNAs have explicitly different requirements, as outlined in detail in the written description rejection below. These requirements being met are essential to proper functioning of the different microRNAs, which have different stringency requirements, as discussed below. iii. The art does not disclose that a wide array of SEQID replacement/deletion/insertion mutations will meet the stringency requirements, especially of siRNA and shRNA binding, to successfully employ their use in impacting mRNA. As indicated below, the art does demonstrate differences in stringency requirements for the classes of small RNAs proposed for the invention. iv The art does not disclose tooth regeneration in a wide taxonomic array of organisms or treatment for tooth conditions. Togo et al (hereafter Togo, Antagonistic Functions of USAG-1 and RUNX2 during Tooth Development PLoS ONE 11(8), 2016) discloses regeneration of precursors to teeth in organs in cell lines and in mandible explant to organs in mice. Liang et al (hereafter Liang, 2015, Down-regulation of SOSTDC1 promotes thyroid, Oncotarget 6:31,31780-31791) demonstrate that SOSTDC1 is relevant to cancer development down-regulation of SOSTDC1 (another term for USAG-1), is associated with, for example, renal carcinoma and gastric tumors (Pg. 31780, left col, final para to right col, top para).
(D) The level of one of ordinary skill: High. Generally, skilled artisans in biotechnology are highly-skilled with a PhD. Enzo Biochem, Inc. v. Calgene, Inc., 188 F.3d 1362, 1373 (Fed. Cir. 1999) (citing Enzo Biochem, Inc. v. Calgene, Inc., 14 F. Supp. 2d 536, 567 (D. Del 1998)) (district court did not abuse discretion in finding that “a person of ordinary skill in the art would be ‘a junior faculty member with one or two years of relevant experience or a postdoctoral student with several years of experience’”).
(E) The Level Of Predictability In The Art: Very low. Generally, the level of predictability in the biotechnology arts is low. C.f. In re: Kubin, 561 F.3d 1351 (Fed. Cir. 2009); Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348 (Fed. Cir. 2007). This finding is further evidenced by the state of the prior art as explained below, particularly as it relates to the type of small RNA employed and the many mutations allowed in the sequences of those RNAs, as disclosed in the claims.
(F) The Amount Of Direction Provided By The Inventor: Adequate description is found for a particular scope of these claims, as articulated below, however the amount of direction provided by the inventor regarding replacing one small RNA species with another, or mutating the relevant sequences, or using different taxa or cells lines is insufficient to be enabled.
(G) The existence of working examples; Few. In the Specification, the pharmaceutical composition is disclosed as technically preferably administered within the maxilla or mandible; it may cause side effects on sites other than tooth missing site, and local admin to a tooth missing site or tooth formation site allow regeneration without serious side effects (Pg 34). The potential for such side effects is good rationale for limited scope of topical administration to the area necessary for tooth regrowth. There is no data presented beyond this scope and no working example outside application to mandible explant to organ (kidney) in mice.
In the working examples (Pg 36), ‘two’ siRNA (each sense + anti-sense; SEQ ID NO 5-6 and 7-8) are indicated as knocking down mouse Usag-1, in mouse enamel epithelial cell cultures and mandibular organ culture of embryonic mouse (Pg 37-38). Next, knockdown of Usag-1 on tooth germ in mandibular culture was demonstrated (Pg 38-39), followed by work on the tooth development stage, which depicted no development stage change with siRNA #903 (SEQID NOs:7- 8) and #304 (SEQIDNO 5-6), but #304 increased number of tooth germs (Pg 39) and when combined with knockdown of Runx2, promoted tooth development (Pg 40). Example 2 relates to the hydrogel carrier, used in mandible explant that was transplanted to mouse, to the kidney (Pg 41). Example 3: Mouse mandibular explant was transplanted, with gel containing Usag-1 siRNA, to kidney of mouse; tooth germ from explant was counted; and tooth number, otherwise decreased by Runx2, was recovered by siRNA targeting Usag1. Example 4: mandibular explant in mouse, plus siRNA targeting Usage1 in kidney of live mouse, demonstrated tooth germ / tooth like tissue formation (FIG4A,B 5A). Example 5: Human USAG-1 knockdown by siRNA #1706 (SEQ ID NO: 1, 2) and 1347 (SEQ ID NO: 3,4) was demonstrated in human embryonic kidney cells (Pg45).
(H) The Quantity Of Experimentation Needed To Make Or Use The Invention Based On The Content Of The Disclosure: Very high. The factors disclosed in these 112(A) rejections make clear that a skilled artisan would be required to engage in extensive optimization that amounts to undue experimentation. Although “an extended period of experimentation may not be undue if the skilled artisan is given sufficient direction or guidance,” here, the specification and prior art provides little to no guidance, on myriad issues, including for example use of a ribozyme in place of an siRNA, or use of another species, or organism, or successful use of the mutated SEQIDs presented. See In re Colianni, 561 F.2d 220, 224 (CCPA 1977). In fact, the specification seems to be missing information as to which other sample types actually work, much less work together. Therefore, this factor weighs heavily against full enablement.
In conclusion, there is insufficient support for complete enablement, but support is provided for scope of enablement, where the claims are not enabled beyond these SEQ IDs presented, or beyond mice with explants, and cell lines, as described (e.g. explant kidney in live mouse, or cultures) or human cell line, as described. However, the claims are enabled for this limited scope, inclusive of siRNA, the SEQIDs presented, and the culture lines/taxonomic species presented.
Claims 1,2, 3, 4 and 6 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.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states 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, reduction to drawings, 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 Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Nature of the Invention:
Claim 1 recites pharmaceutical composition for topical administration for tooth regeneration therapy, comprising an RNA molecule targeting USAG-1 or a nucleic acid molecule that produces the RNA molecule, and a pharmaceutically acceptable carrier.
Claim 2 recites the pharmaceutical composition according to claim 1, wherein the RNA molecule is selected from the group consisting of a siRNA, a shRNA, an antisense RNA, a miRNA, and a ribozyme.
Claim 3 recites The pharmaceutical composition according to claim 2, wherein the RNA molecule is a siRNA or a shRNA.
Claim 4 recites, “The pharmaceutical composition according to claim 3, wherein the siRNA or shRNA comprises: (1) a sense strand comprising a nucleotide sequence shown in SEQ ID NO: 1, or a nucleotide sequence that differs from the nucleotide sequence shown in SEQ ID NO: 1 by deletion, substitution, insertion and/or addition of one to several nucleotides, and an antisense strand comprising a nucleotide
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sequence shown in SEQ ID NO: 2, or a nucleotide sequence that differs from the nucleotide sequence shown in SEQ ID NO: 2 by deletion, substitution, insertion and/or addition of one to several nucleotides, or (2) a sense strand comprising a nucleotide sequence shown in SEQ ID NO: 3, or a nucleotide sequence that differs from the nucleotide sequence shown in SEQ ID NO: 3 by deletion, substitution, insertion and/or addition of one to several nucleotides, and an antisense strand comprising a nucleotide sequence shown in SEQ ID NO: 4, or a nucleotide sequence that differs from the nucleotide sequence shown in SEQ ID NO: 4 by deletion, substitution, insertion and/or addition of one to several nucleotides”.
Claim 6 recites: The pharmaceutical composition according to claim 5, wherein the antisense RNA comprises: (1) a nucleotide sequence shown in SEQ ID NO: 2, or a nucleotide sequence that differs from the nucleotide sequence shown in SEQ ID NO: 2 by deletion, substitution, insertion and/or addition of one to several nucleotides, or (2) a nucleotide sequence shown in SEQ ID NO: 4, or a nucleotide sequence that differs from the nucleotide sequence shown in SEQ ID NO: 4 by deletion, substitution, insertion and/or addition of one to several nucleotides.
Claim 1 is broadly directed to a composition with any RNA molecule or NA molecule that produces the RNA, that targets a gene. Claim 2 limits claim 1 to five species, and claim 3, to two species. Claim 4 addresses sequence and variants that will comprise strands of the molecule.
Focusing on the phrases in bold, it is therefore expected that the instant application will provide disclosure of a composition using these types of RNA molecules, these sequences with the variants described, namely deletions substitutions, insertions, additions of one to several nucleotides, to satisfy the written description and demonstrate possession of the invention. In this type of work, reduction to practice, with examples of compositions meeting these varied limitations (e.g. multiple deletions or insertions, in a given SEQ ID recited that are able to be used successfully in the invention as a pharmaceutical composition RNA molecule that targets USAG-1 would be expected and necessary to demonstrate functionality of the modified sequence for its purpose.
State of the art:
RNAs: Claim 1 addresses “RNA molecules” that target a gene, or “nucleic acids” that produce them, which comprise a very large Genus. For Claims 2 and 3, Notably, RNA sequences of varied types (species) are recognized as having substantive differences relevant to their specificity and function. Further they may be natural or synthetic. A brief review is presented which points to the issue that the assumption of mere replacement of one species of RNA with another, is not sufficient to meet the expectation of equal functionality between them in their knock down or silencing effects, given for example they are structurally different, and this can affect their functioning. Further greater sequence specificity is required for some of these than others, for complementary binding to target to be successful.
O’Brien et al. (hereafter O’Brien, 2018, Overview of MicroRNA Biogenesis Mechanisms of Actions and Circulation, Front Endorcinol 9:402, 1-12) taught that miRNAs interact with 3’ UTR of target mRNAs to degrade the mRNA or repress translation (Pg 1, para 1). However, binding to 5’UTR and coding regions may induce gene expression silencing (Pg 3, left col last ling to right col lines 1-2). They bind with either full or partial complementarity to target miRNA response elements (MRE) (Pg 4 left col, para 2) where in partial complementary, there may be mismatches between target and central sequence of the miRNA guide strand (Pg 4, left col, first full para) and functional interaction often occurs via the 5’ seed region (e.g. nucleotides 2-8), with additional pairing at 3’ end to aid stability and specificity of miRNA-target interaction (Pg 4 left col, para 2). A total number of binding sites exists (MRE load) for each miRNA and retention is longer for higher, relative to lower, affinity MREs target sites, and so higher affinity MREs result in greater sensitivity to (post transcriptional) repression for those target mRNAs (Pg. 7, left col, first full para, lines 3-7, 11-13).
siRNAs are small interfering RNAs, potent gene silencers, usually l21 bp long, and mediate sequence specificity Lück et al. (hereafter Lück, 2019, siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Front Plant Sci 10: 1023, Pg 1 para 3). They are generated from cleaved dsRNA cut into 19-25 nt ds oligonucleotides, with 3’ overhangs of 2 nucleotides (Lück, Pg 1, para 3). Sequence asymmetry is highly relevant to selecting a strand incorporated into an RNA-induced silencing complex, and mRNA targets are then identified by specific nucleotide pairing between the antisense strand of the silencing complex siRNA and the target mRNA, which after pairing is hydrolyzed to knock down gene expression (Lück Pg 1 final para final few lines, to Pg 2 left col lines 3-5, 8-11). Design of artificial constructs aims for a 21 nt RNA linear sequence, per Mickiewicz, et al (hereafter Mickiewicz, 2016, Acta Biochimica Polonica, V63 (1)71-77), Pg 72, left col, para 3, lines 13-14). Xu (2018 Antisense RNA: the new favorite in genetic research, Biomed & Biotech, 19:739-749) lays out a Table of similarities between miRNA and siRNA (Table 1) and of most value here, a Table of differences (Table 2), for comparative purposes (Zheng, Pg 743).
Moore et al (hereafter Moore, 2010, Short hairpin RNA (shRNA) Design, delivery and assessment of gene knockdown Methods Mol Biol 629 141-158) discussed shRNAs, a valuable form of siRNA using a similar silencing complex. shRNAs are hairpin in shape, comprised of two single strands, with complementary, 19-22 bp RNA sequences (stem), linked by a 4-11 nt loop, and they also have an overhang like siRNA but unlike siRNA (where concentration dilutes with cell division and where off-target effects may be high), shRNA, can be used to generate stable knock down cell lines (Moore, Abstract, and Pg 2 para 1 and 2). Unlike siRNA where incomplete knockdowns may result from incomplete transfection, viral-based, shRNAs can skirt this issue for untransfectable cells (Moore, Pg 2, para 2). Of particular note for this evaluation, Moore points out that there is no guarantee of effective gene silencing for a given siRNA until experimentally proven (Moore, Pg 2, para 3, line 5-6).
Xu disclosed that antisense RNA are unique DNA transcripts, comprising 19-23 nucleotides complementary to mRNA target, required for their function (Xu, Pg 739, Para 1 (Abstract)). They may impact DNA, RNA, chromosome structure, transcription, translation, RNA and protein stability (Xu Pg 740, right col para 2). Xu considers synthetic antisense RNA in regulation of gene expression of microorganism (Pg 746, right col, para 1, lines 3-5).
Scott (2013, The hammerhead ribozyme: structure catalysis and gene regulation Prog Mol Biol Transl Sci 120 1-23) addressed hammerhead ribozyme as a single-folded RNA strand that self-cleaves separating the RNA into an enzyme and substrate strand (Page 2, para 1). The ribozyme has a core of 15 mostly invariant nucleotides flanked by three helical stems with required tertiary interaction between stems (Pg. 2 last two lines to Pg 3 first para). Metal ions or positive charge are needed for these to function properly (Pg 3, para 3 and 4). In mammalian lectin genes, for example, ribozymes between the stop codon and poly A signal sequence cleave the 3’ UTR and reduce gene expression (Pg 9, para 4). Tertiary interactions stabilize active sites and structure, and are necessary for cleavage as the RNA folds to bring reactive groups together (Pg 9, para 4).
Nucleotide sequence of strands: A review of the literature does not obviously reveal any suite of particular RNA nucleotide sequences inclusive of deletions, insertions, substitutions, known to impact USAG-1. However, one of ordinary skill recognizes that many mutations impact sequence functionality, particularly as it relates to binding complementary strands of nucleic acid.
This is of significance in a number of ways for microRNAs in general, as disclosed by Mickiewicz et al (2016, AmiRNA new method of artificial miRNA design, Acta Biochimia Polonica, 63 71-77), since miRNAs have particular features related to their functionality, including size (e.g. for srRNAs, 20-30 nt; Mickiewicz , Pg 71, left col, para 1) and shape and complementarity requirements that differ for different categories of small RNAs Mickiewicz , Pg 71, right col, first part lines 2-3), as disclosed above.
In sum, these species of RNA structures are not identical and have sequence lengths that are restrained to varied degrees, related to structure and number of nucleotides in different parts, including complementary binding sites with target, and these structures have specific shapes that differ from one another, and particular structural arrangements. Complementary regions with target that are required to match to different degrees, with miRNAs for example tolerant to partial complementarity but with siRNAs and shRNAs requiring precise matches to function. These are clearly not instantly interchangeable, particularly incorporating the SEQ ID Nos or their wide array of potential variants recited. It is not reasonable to expect random mutations, including insertions and deletions, to a specific sequence (SEQ ID NO), that modify sequence length which may impact RNA species shape and which will alter complementary binding, not to effect functionality.
What the specification does and does not teach
The specification broadly defines what the RNA species are, and that they may be modified (Pg 19, line3, 11-20, Pg 21, lines 16-end, Pg 24, line 25 to Pg 26, line 11, Pg 26 line 11-22, Pg 27, line 8 to Pg 28, line 15, and more). The specification discusses preferred examples, which includes discussion of modifying the sense strand SEQID NO:1 or 3, or antisense strand SEQID NO:2 or 4, of an siRNA by, for example deletion/insertion/addition of up to three nucleotides (Pg. 23), which may interfere with, or eliminate proper functioning and this preferred embodiment is not a working example. Pg 26-27 is similar in scope, here for anti-sense RNA, and variant sequences to SEQID NO: 2 or 4. There are no working examples, of ribozymes or miRNAs or shRNAs, or examples that disclose any of the many types of mutation recited for the SEQ ID No’s, that would demonstrate functionality.
In the working examples (Pg. 36), ‘two’ siRNA (sense + anti-sense sequence), and four SEQ ID NO (1) SEQ ID NO 5 and 6 and 2) SEQ ID NO: 7 and 8), are indicated as knocking down mouse Usag-1, in a) mouse enamel epithelial cell cultures and b) mandibular organ culture of embryonic mouse (Pg 37-38). An interaction with RunX2 was also provided, where siRNA SEQID NO: 5 and 6 increased number of tooth germs (Pg 39 (Pg 39). Mouse mandibular explant into kidney of live mouse, and finally human kidney cells were used as systems. No additional mutated sequences are used or are presented even in these examples. No additional species of RNA are used or discussed in the context of these examples. No additional cell lines or additional taxonomic classes are used or presented.
Conclusion regarding possession
Taking into consideration the factors outlined above, including the nature of the invention, the state of the art, the guidance provided by the applicant and the specific example, it is the conclusion that Applicant does not possess the invention as recited in the claims.
There is not sufficient specific written example in the Specification that would lead one with ordinary skill in the art to a different conclusion. Alternate RNA species are not used beyond the above articulated siRNA, despite the unpredictable nature of altering the species of RNA used and/or altering the sequences employed in the knock down, and despite clear differences in requirements for RNAs serving the purpose of functioning in altering gene expression. The lack of RNA species testing (e.g. replacing one species for another in the working examples) and lack of SEQID variant testing, results in high expectation of unpredictability. The varied levels of mismatch tolerance in the species of RNA are not addressed, and particularly for siRNA and shRNA that have low tolerance to complementarity mismatch, the null expectation is for unpredictability in functionality, when modifying these species.
Written description (possession) does not extend beyond the SEQ IDs disclosed for siRNA use, for the taxa and type of use, beyond the mouse model (e.g. explant kidney in live mouse, or cell cultures) or human cell lines described, to include any additional taxa.
Claim interpretation
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The claims are broadly drawn to a composition comprising an RNA, or nucleic acid that produces RNA, that targets USAG-1, and a carrier.
For clarity of the record, a definition of “pharmaceutical acceptable carrier”, is found in Law Insider (www.lawinsider.com/dictionary/pharmaceutically-acceptable-carrier) and states:
Pharmaceutically acceptable carrier means a carrier that is useful in preparing a pharmaceutical composition that is generally safe, non-toxic and neither biologically nor otherwise undesirable, and includes a carrier that is acceptable for veterinary use as well as human pharmaceutical use.
Since this definition appears to arise from a single source, to ensure broadest reasonable interpretation, Lichtenstein et al (WO 2018/085753 A1, published 11 May 2018) also addressed pharmaceutical carriers and disclosed (Pg 10, line 6) “Pharmaceutically acceptable carriers are well known in the art and include, for example, aqueous solutions such as water or physiologically buffered saline or other solvents or vehicles such as glycols, glycerol, oils such as olive oil, or injectable organic esters.”
Claim Rejections - 35 USC § 103
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 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 non-obviousness.
Claims 1, 2, and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Togo et al (hereafter Togo, PLoS ONE 11(8), 2016) in view of Zheng et al (hereafter Zheng, 2012, Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation, PNAS 109: 11975-11980), further in view of Mickiewicz et al (hereafter Mickiewicz, 2016, Acta Biochimica Polonica, V63 (1)71-77), further in view of Lück et al. (hereafter Lück, 2019, siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Front Plant Sci 10: 1023), further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov).
Re: Claim 1 A pharmaceutical composition for topical administration for tooth regeneration therapy], comprising an RNA molecule targeting USAG-1 or a nucleic acid molecule that produces the RNA molecule, and a pharmaceutically acceptable carrier.
Regarding targeting USAG-1, Togo disclosed development of extra, or supernumerary teeth in Usag-1 deficient mice Pg 2, Para 1, lines 12-13), which are used as a supernumerary tooth model (Pg 3, para 1, lines 1-2). Usag-1 deficiency causes signaling changes that result in tooth formation (Pg 2, Para 1, lines 12-13). Usag-1 mRNA is expressed in rudiment and normal incisors, as well as in the forming molar region (Pg 2, para 2, line 25-26). In a mouse line that does not form bone and has poorly developed teeth (Runx2 null mice), damping Usag-1 expression allows for tooth development (Pg 3, para 4; (Table 1, last col)). Togo literally states “Our investigations and related studies clearly validate the hypothesis that the de novo repression of target genes such as Usag-1 could be used to stimulate arrested tooth germs in order to induce new tooth formation in mammals. (Pg 11, para 1, lines 7-9). Togo continues, “Molecular targeted therapy could be used to generate teeth in patients with congenital tooth agenesis by stimulating arrested tooth germs.” (Pg 11, para 1, penultimate and final lines).
Togo taught decreased expression of USAG1, but did not teach a composition of an RNA molecule to perform this function, or a carrier.
Zheng taught a composition. Zheng topically delivered an RNA as a therapeutic to suppress gene activity, using carrier nanoparticles (Pg 11975 left col, para 1 (Abstract), Pg 11977, left col, final para).
Mickiewicz taught the significance of RNA molecules, namely the ubiquitous nature of miRNA and the wide-ranging role of RNA interference in gene expression, driven specifically by small regulatory RNAs (Pg 2015, left col, Para 1 (Abstract), left col Para 2, lines 1-4). Given the widespread role of miRNAs, Mickiewicz taught a method, available for public use, to design miRNA constructs, though primarily for plants. Mickiewicz then did not teach an ideal software for design of RNA outside of for use in plants.
Lück similarly addressed RNA molecule design and disclosed multiple available software programs, including BLOCK-iT used in a wide array of taxa, for successful design of an RNA molecule, particularly an miRNA sequence (Pg 2, left col, para 2, all; meeting instant claim 2).
Togo, nor Mickiewicz, nor Lück disclosed the mRNA sequence that would be used in the design of the RNA in the composition.
Ensembl (USEAST.ENSEMBL.ORG) contains Usag-1 sequence that would be the target of the composition. DNA sequence and transcript for USAG1 are known, e.g. for Mus musculus, in ensembl.org, as Transcript: ENSMUST00000041407.7 Sostdc1-201, with mRNA alignment to M. musculus presented from a blast search (blast.ncbi.nlm.nih.gov):
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Re: claim 9, the composition of claim 1, wherein the tooth regeneration is a treatment of tooth agenesis or regeneration of a missing tooth. The claim is directed at the intended use of the composition and does not change the composition itself and therefore is not further limiting to the composition and as such is met by the rejection of claim 1.
Prior to the effective filing date of the invention, it would have been prima facie obvious to one of ordinary skill in the art to have improved upon the work of Togo by having designed a topical composition in the manner of Zheng, with a nanoparticle carrier, with an RNA that would silence or knock down the expression of Usag-1, based upon the known properties of regeneration and development of teeth that occurred when Usag-1 functionality was abrogated, as disclosed by Togo (described above). It would have been obvious to try to make the composition given the success of Zheng’s work with ramping down expression of a gene in this form of a composition, akin to what Togo needed to do, and particularly given the knowledge and foresight of Togo regarding the value of knockdown of Usag-1, and Togo’s own anticipated predicted results, a reasonable expectation of success was in hand. Motivation for this composition was provided by Togo who explicitly stated that Usag-1 could be used to stimulate arrested tooth germs to induce new tooth formation in mammals.
It would have been prima facie obvious to one of ordinary skill to design an RNA impacting the expression of USAG1, to be used in the composition of Togo as developed by Zheng, to knock down USAG1 expression, given the motivation provided by Mickiewicz, namely the ubiquitous and functional nature of miRNAs. It would have been further obvious to have designed that RNA for Togo in view of Zheng in view of Mickiewicz, using an appropriate available online too, as disclosed by Lück, to provide a reasonable expectation of success, with the motivation to generate a well-designed RNA for use in the composition of Togo provided by Mickiewicz.
It would have been obvious to have obtained the known Usag-1 DNA sequence from public access databases (e.g. Ensembl.org) and with this, obtained the mRNA sequence from Genbank, to have designed an RNA mechanism to knock down USAG-1 expression given sequence knowledge for Usag-1 for Togo in view of Zheng in view of Mickiewicz in view of Lück. The motivation to conduct these design steps would have come from the basic need for this genetic information to successfully design the RNA of the composition and from Togo’s idea on tooth formation from stimulated Usag-1, and given the point that Mickiewicz made regarding the widespread nature of RNAi and small, regulatory RNAs role in gene expression control (Pg 71, left col lines 1-5), and the fact that online tools were available as disclosed by Lück, to then make the RNA molecule that served the purpose desired.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Togo et al (hereafter Togo, PLoS ONE 11(8), 2016) in view of Zheng et al (hereafter Zheng, 2012, Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation, PNAS 109: 11975-11980) in view of Mickiewicz et al (hereafter Mickiewicz, 2016, Acta Biochimica Polonica, V63 (1)71-77), further in view of Lück et al. (hereafter Lück, 2019, siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Front Plant Sci 10: 1023), further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov), further in view of Agarwal (2007, Online siRNA Designing Tool: BLOCK-iT™ RNAi Designer From Invitrogen, www.biocompare.com/ Product-Reviews/40578-Online-siRNA-Designing-Tool-BLOCK-iT-RNAi-Designer-From-Invitrogen/).
The contributions of Togo, Zheng, Mickiewicz, Lück, Ensembl, and Blast have been discussed.
Re: claim 3, the RNA is an siRNA or a shRNA: Agarwal explicitly discusses the fact that shRNA can be efficiently designed with BLOCK-iT, the software previously discussed.
Prior to the effective filing date of the invention, it would have been prima facie obvious to one of ordinary skill in the art to have designed a shRNA using the BLOCK-iT designer for the invention of Togo in view of Zheng, Mickiewicz, Lück, Ensembl, and Blast because the software was in existence for this purpose, and the likelihood of success was very high to develop a functional shRNA. The motivation to design an shRNA, and a reasonable expectation of success, came directly from Agarwal, who stated that shRNA was a typical mechanism to induce silencing of gene expression, and that shRNA specifically, were valuable for stable integration (Para 2, 8-11). Further, Agarwal pointed out that BLOCK-iT allowed for custom RNA design for any organism (Para 2 line 2), and that the algorithm used was highly effective for efficient design (Para 2, line 4), including of shRNA (Para 2, line 5). Agarwal pointed to the fact that the program takes all of the relevant sequence information (e.g. size range from target gene, spacer/loop, reverse complement of target sequence) into account if you merely provide input sequence of the gene of interest (Para 4, lines 3-10), which as addressed above, was easily available.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Togo et al (hereafter Togo, PLoS ONE 11(8), 2016) in view of Zheng et al (hereafter Zheng, 2012, Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation, PNAS 109: 11975-11980) in view of Mickiewicz et al (hereafter Mickiewicz, 2016, Acta Biochimica Polonica, V63 (1)71-77), further in view of Lück et al. ((hereafter Lück, 2019, siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Front Plant Sci 10: 1023), further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov), , further in view of Agarwal (2007, Online siRNA Designing Tool: BLOCK-iT™ RNAi Designer From Invitrogen, www.biocompare.com/ Product-Reviews/40578-Online-siRNA-Designing-Tool-BLOCK-iT-RNAi-Designer-From-Invitrogen/), further in view of Xu et al (Hereafter Xu, 2018 Antisense RNA: the new favorite in genetic research, 19:739-749).
The contributions of Togo, Zheng, Mickiewicz, Lück, Ensembl, and Blast have been discussed.
Re: claim 5, the composition of claim 1, consisting of an antisense RNA, Xu disclosed antisense RNAs for regulating expression of target genes. (Pg 740 left col, lines 2-4). The reference includes miRNAs and siRNAs (Pg 740 right col, lines 10-12) and Fig 1 notes for antisense RNA small RNA is used as repressor (Pg 740, FIG 1 and its legend). In addressing siRNAs for RNA interference use, Xu points to siRNA antisense strand as identifying and degrading target mRNA (Table 2 right col, 4th cluster of text for siRNA addressing mechanism of action). Xu then addresses strictly antisense RNA as powerful tools in regulating expression of genes of myriad types, including examples of inhibiting translation of RNAs in cells (Pg 744 right col, Pg 745 left col, line 4-6) and as suppressing or inhibiting expression of genes (Pg 745, para 2 lines 4-6).
Prior to the effective filing date of the invention, it would have been prima facie obvious to one of ordinary skill in the art to have improved upon the work of Togo in view of Zheng, in view of Mickiewicz, in view of Lück, in view of Ensembl, and in view of Blast, and to have accepted the teaching of Xu that antisense RNA is a powerful mechanism for inhibition of gene expression, and used antisense RNA in composition made. There was reasonable expectation of success given and motivation provided by the fact that damped expression of USAG-1 was the known function of importance in the work presented by Togo, and given that all of the materials needed to construct an antisense RNA were available from the aforementioned references in the ways described.
Claim 7 is rejected under 35 U.S.C. 103 as being unpatentable over Togo et al (hereafter Togo, PLoS ONE 11(8), 2016) in view of Zheng et al (hereafter Zheng, 2012, Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation, PNAS 109: 11975-11980) in view of Mickiewicz et al (hereafter Mickiewicz, 2016, Acta Biochimica Polonica, V63 (1)71-77), further in view of Lück et al. (hereafter Lück, 2019, siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Front Plant Sci 10: 1023), further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov), in view of Yan et al (hereafter Yan, 2019, International Journal of Nanomedicine 14 3645-3667).
The teachings of Togo, in view of Zheng, further in view of Mickiewicz, further in view of Lück, further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov) have been discussed.
Re: claim 7, the composition of claim 1 where the carrier is a liposome, Yan successfully used liposomes as a carrier for miRNA that was designed to silence the Slug gene (Pg 3645, Para 1 (Abstract), line 5-6) and potential target for gene therapy (Pg 3646, lef col, 3rd full para, last line). Inhibition by the miRNA liposomes was effective (Pg 3658, left col, para 2, lines 3-6). Further, physical traits of the mice used in the study, such as weight were not affected by the miRNA liposomes, and the drug caused no evidence of obvious pathology to major organs (Pg 3658, left col, para 3).
Prior to the effective filing date of the invention, it would have been prima facie obvious to one of ordinary skill in the art to have improved upon the work of Togo in view of Zheng, in view of Mickiewicz, in view of Lück, in view of Ensembl, and in view of Blast, and to have used the liposome delivery mechanism in the pharmaceutical composition of claim 1 as the carrier of the RNA of Zheng in lieu of the nanoparticle. The expectation of success with this application was high, given this replacement given the similarity of methodologies being employed, which was for Togo, carrying an miRNA to knock down Usag-1. While the carrier of Zheng has merits, the motivation to have used the carrier of Yan in place of that, would have come from providing for a safety-tested method of carry that demonstrated no evidence of harm when used for the purpose of knocking down mRNA expression of a gene in live mammals.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Togo et al (hereafter Togo, PLoS ONE 11(8), 2016) in view of Zheng et al (hereafter Zheng, 2012, Topical delivery of siRNA-based spherical nucleic acid nanoparticle conjugates for gene regulation, PNAS 109: 11975-11980) in view of Mickiewicz et al (hereafter Mickiewicz, 2016, Acta Biochimica Polonica, V63 (1)71-77), further in view of Lück et al. (hereafter Lück, 2019, siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction Front Plant Sci 10: 1023), further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov), in view of Yan et al (hereafter Yan, 2019, International Journal of Nanomedicine 14 3645-3667).
The teachings of Togo, in view of Zheng, further in view of Mickiewicz, further in view of Lück, further in view of Ensembl (USEAST.ENSEMBL.ORG), further in view of Blast (blast.ncbi.nlm.nih.gov) and Yan, have been discussed.
Re: claim 8, the composition of claim 7, the carrier is cationized gelatin, cationized gelatin hydrogel or cationized gelatin microsphere,
Murata et al (hereafter Murata, 2018, Preparation of cationized gelatin nanospheres incorporating molecular beacon to visualize cell apoptosis, Sci Reports 8:14839, Pg 1-11) disclosed the use of cationized gelatin hydrogels for controlled release of siRNA (Pg1 para 3, lines 3-5).
Prior to effective filing date it would have been prima facie obvious to one or ordinary skill in the art to have incorporated the use of cationized gelatin hydrogels into the work of Togo in view of Zheng, Mickiewicz, Lück, Ensembl Blast and Yan, given their compatibility with the work of Togo, and the release of miRNA per Zheng, that they could serve as a simple substitution for the liposomes of Yan, and given the motivation that they have a suite of valued traits, including that the gelatin is biosafe and biocompatible for medical and pharmaceutical applications, and that this material could be used for controlled release purposes (Pg 1, para 3, lines 1-5). These factors would have been meritorious for medical purposes such as tooth development.
Conclusion
Claims 1-9 are rejected. Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lisa Horth whose telephone number is (703)756-4557. The examiner can normally be reached Monday-Friday 8-4 EST.
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/LISA HORTH/ Examiner, Art Unit 1681
/NEIL P HAMMELL/ Supervisory Patent Examiner, Art Unit 1636