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 .
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 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.
DETAILED ACTION
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 9/30/2025 has been entered. Claims 1 and 4 were amended.
Claims 1, 3-4, and 11-20 are pending in the instant application.
Priority
This application claims priority to the provisional application 63158089 filed on 3/8/2021.
Election/Restriction
Applicant’s election without traverse of 1-10 in the reply filed on 11/21/2023 remains in effect.
Claims 11-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected group, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 11/21/2023.
Claims 1 and 3-4 are examined herein.
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.
Claim 1 is 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.
claim 1(b)
Regarding claim 1(b), a composition comprising a heterologous nucleic acid comprising FMR1 and a ≥99 tandem CGG repeat is not a description of a composition with the required functions of being able to target megabase-sized domains of DNA to de-repress any gene. Applicant did provide an example of shortening a previously-existing, mutated version of the FMR1 gene comprising 346 tandem CGG repeats to 180 tandem repeats using CRISPR to target the FMR1 locus in subjects with Fragile X (instant pg 86, para 2). The instantly claimed composition lacks a means of targeting heterochromatinized DNA in individuals without a mutation at a Fragile site comprising 40-200 CGG repeats. Thus applicant has failed to meet the written description of a composition comprising a ≥99 tandem CGG repeats that has the property of de-repressing any gene in any subject.
claim 1(c)
Regarding claim 1(c), a lipid nanoparticle comprising a non-coding RNA comprising ≥50 tandem CGG repeats is not a description of a composition with the required functions of being able to target megabase-sized domains of DNA for the purpose of gene de-repression in any subject. Inhibition of a CGG tandem repeat gene is not directly correlated with gene re-activation, thus the interfering RNA molecule described lacks of means of targeting the cellular machinery involved in gene silencing in order to promote gene activation. The instant specification cites that this interfering RNA achieves this task by being operably linked to a promoter/regulatory sequence capable of modifying the target’s expression (pg 53, para 2). Because applicant has not described the core structure responsible for the function of targeting megabase-sized heterochromatinized DNA for de-repressing a gene, applicant has also failed to meet the written description requirement by supplying the core structure responsible for the function of de-repressing megabase-sized heterochromatinized DNA. Because applicant has not disclosed any interfering RNAs with ≥50 tandem CGG repeats capable of re-activating megabase-sized heterochromatinized DNA with or without this promoter/regulatory sequence in any subject, applicant has failed to meet the written description requirement by supplying a representative number of species.
Applicant can meet the written description by either (1) supplying the core structure of the composition responsible for the function of modulating megabase-sized H3k9me3-marked heterochromatin and re-activating a gene; or (2) describing a representative number of species that have the function of targeting megabase-sized H3k9me3-marked heterochromatin and re-activating a gene. Because applicant has (1) incompletely described the core structure required for the composition to function as claimed; and (2) failed to provide a representative number of species of which to describe these genera; applicant has failed to meet the written description requirement of these genera.
Claim Rejections – 35 USC § 112(a) Enablement
Claim 1(b) is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to 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.
claim 1(b)
The specification does not reasonably provide enablement for a composition comprising a nucleic acid comprising ≥99 tandem CGG repeats that is capable of de-repressing any H3K9me3-marked gene in any individual. The claims contain subject matter which was not described in the specification in such a way as to 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.
Attention is directed to In re Wands, 8 USPQ2d 1400 (CAFC 1988) at 1404 where the court set forth the eight factors to consider when assessing if a disclosure would have required undue experimentation. Citing Ex parte Forman, 230 USPQ 546 (BdApls 1986) at 547 the court recited eight factors: (1) the nature of the invention; (2) the state of the prior art; (3) the relative skill of those in the art; (4) the predictability or unpredictability of the art; (5) the breadth of the claims; (6) the amount of direction or guidance presented; (7) the presence or absence of working examples; and (8) the quantity of experimentation necessary.
All of the Wands factors have been considered with regard to the instant claims, with the most relevant factors discussed below.
Nature of the invention:
A composition comprising a nucleic acid comprising a ≥99 tandem CGG repeats that is effective for de-repressing the subset of H3K9m3-marked genes of:
FMR1, FMR1NB, FMR1-AS1, C5orf38, CTD-2194D22.4, LOC100506858, IRX2, LOC105374620, LINC01377, LINC01019, LINC01017, IRX1, LINC02114, DPP6, LINC01287, LOC101929998, CSMD1, FAM135B, LOC101927815, COL22A1, KCNK9, TRAPPC9, MYOM2, LOC101927845, LINC01591, LOC101927915, SPANXN4, SPANXN3, SLITRK.4, SPANXN2, UBE2NL, SPANXN1, SLITRK.2, TMEM257, MIR892C, MIR890, MIR888, MIR892A, MIR892B, MIR891B, MIR891A, CXorf51B, CXorf51A, MIR513C, MIR513B, MIR513A1, MIR513A2, MIR506, MIR507, MIR508, MIR514B, MIR509-2, MIR509-3, MIR509-1, MIR510, MIR514A1, MIR514A2, MIR514A3, TCERG1L, MIR378C, TCERG1L-AS1,
LINC01164, TMEM132C, TMEM132D, LOC100996671, LOC101927592, LINC00508, LOC100996679, GLT1D1, RIMBP2, LINC00939, LOC101927464, LOC100128554, LINC00944, LINC00943, LOC440117, LOC101927616, LOC101927637, LOC105370068, FLJ37505, LINC00507, CRAT8, LOC101927694, MIR4419B, MIR3612, SLC15A4, LOC283352, LOC101927735, LOC100190940, FZD10-AS1, FZD10, PIWIL1, RBFOX1, MIR8065, TMEM114, DNAH9, SHISA6, PTPRT, LOC101927159, LINC01441, LINC01440, CBLN4, and MC3R.
Note: All of these genes are deactivated in the presence of a fragile site at FMR1 in those with Fragile X.
Breadth of claims:
The method is drawn to de-repressing any H3K9me3-marked gene in any subject. This includes those who do not have Fragile X and are expressing a normal amount of FMR1, thus lack a motivation for de-repressing the genes listed above. This also comprises the administration of this nucleic acid as an ectopic species and insertion of this nucleic acid into any location in the host’s genome.
State of the prior art/Predictability or unpredictability of the art:
Vengoechea teaches an individual with an FMR1 duplication still suffers cognitive deficits such as motor and speech delay, focal seizures, absence seizures and hyperactivity, which are clinical traits frequently observed in individuals with an altered function of the FMR1 gene (doi: 10.1038/ejhg.2012.78; Vengoechea, pg 1199, col 2, para 2). Surprisingly, Vengoechea teaches that this individual displayed normal levels of FMR1 expression (abstract), thus this gene duplication event did not result in overexpression of FMR1 as one would expect. Furthermore, as Fragile X disease is caused by having an excessive number of CGG repeats in FMR1, resulting in the suppression of a variety of genes (doi: 10.1016/j.cell.2023.11.019; Thomas, pg 5840, col 1-2). One would expect the introduction of a Fragile site (i.e. an excessive number of CGG tandem repeats) in a healthy individual would cause gene repression, as opposed to gene de-repression as claimed.
Amount of guidance/Existence of working examples:
Applicant has not provided any examples of inserting a ≥99 tandem CGG repeat in healthy subjects. Applicant has not provided any example of administering a nucleic acid comprising a ≥99 tandem CGG repeat to a subject that experience repression of a gene that isn’t FMR1 (e.g. BRCA1). Thus the gene-suppressing effect of adding a fragile site to an individual with repressed BRCA1 is unknown.
Quantity of experimentation:
Given that Vengoechea teaches that FMR1 duplication doesn’t necessarily result in overexpression of FMR1 and that the insertion of a Fragile site (i.e. a nucleic acid comprising 20-400 CGG repeats) has been shown to repress, as opposed to de-repress several genes including FMR1; a person of skill in the art would have no expectation that the instantly claimed composition would be capable of de-repressing any gene in any individual. Given the teachings of Vengoechea, a person of skill in the art would not have a reasonable expectation that the duplication of FMR1 would even result in the de-repression of FMR1 in those with Fragile X. A person of skill in the art, in undertaking the experimentation necessary to determine if this therapy is effective, one would have no reasonable expectation that this claimed therapy would be effective in the de-repression of any gene in any individual.
Lack of a working example is a critical factor to be considered, especially in a case involving an unpredictable and undeveloped art. See MPEP § 2164.
See the decision in Rasmusson v. SmithKline 413 F.3d 1318, 1325 (Fed. Cir. 2005) which stated: “Thus, at the end of the day, the specification, even read in the light of the knowledge of those skilled in the art, does no more than state a hypothesis and propose testing to determine the accuracy of that hypothesis. That is not sufficient. [Citation omitted.] ‘If mere plausibility were the test for enablement under §112, applicants could obtain patent rights to “inventions” consisting of little more than respectable guesses as to the likelihood of their success. When one of the guesses later proved true, the “inventor” would be rewarded the spoils instead of the party who demonstrated that the method actually worked.’”
Therefore, in view of the Wands factors as discussed above, e.g., the amount of guidance provided, the predictability of the art and the lack of working examples, to practice the full scope of the claimed invention herein, a person of ordinary skill in the art would have to engage in undue experimentation, with no assurance of success.
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.
Claims 1, 3, and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Jaenisch et al. (US20190359959) in view of Park et al. (doi: 10.1016/j.celrep.2015.08.084), and Stephan et al. (doi: 10.3390/cancers12040876), Chavez (doi: 10.1038/nmeth.3312), and Savage (WO2018089664). This rejection has been modified to solely address the amendments.
Claim 1(a)
The claims are drawn to the composition selected from the group consisting of:
Regarding claim 1, JAENISCH discloses [Abstract]: “methods of modifying DNA methylation by contacting a catalytically inactive site specific nuclease fused to an effector domain having methylation or demethylation activity and one or more guide sequences.”
As to claim 1(a), specific to the composition of an epigenomic editor, comprising catalytically dead (dCas9) operably linked to a composition for removing a methylation mark, JAENISCH discloses: [0007] methods of modulating the methylation of one or more genomic sequences in a cell, the methods comprising introducing into the cell a catalytically inactive site specific nuclease fused to an effector domain having methylation or demethylation activity; and a guide sequence or a nucleic acid that encodes a guide sequence, thereby modulating the methylation of one or more genomic sequences in a cell… [0021] In some embodiments, the effector domain comprises Tet1 or Dnmt3a. In some aspects, the catalytically inactive site specific nuclease is a catalytically inactive Cas protein (e.g., a dCas9 protein).” JAENISCH teaches a catalytically inactive dCas9 fused to an effector domain, which meets the claim limitation of claim 1a because the effector domain having demethylation activity (such as a Ten-Eleven Translocation [TET] protein), is a composition which functionally acts in the process of removal of a methyl group from cytosines (see claim 2). JAENISCH teaches a composition comprising an epigenomic editor (dCas9-Tet1 fusion protein) comprising dCas9 fused to effector domain for removing a methylation mark, to reactivate FMR1. Thus meeting the limitation of a composition comprising a catalytically dead Cas9, linked to an effector domain. JAENISCH also teaches the Cas9-effector domain can further bind to an effector molecule (pg 12, para 0088), wherein the effector molecule is a DNA demethylase (pg 12, para 0089). JAENISCH teaches their invention as part of a method of treating Fragile X syndrome, to specifically demethylate the hypermethylated CCG region of the gene FMR1 (pg 18, para 0131).
JAENISCH and PARK are silent on the gene FMR1 being a H3K9me3-heterochromatin mark containing gene. JAENISCH and PARK are silent on the H3K9me3-heterochromatin mark containing gene qualifying as a “megabase-sized domain”. Jaenisch does not teach fusing the dCas9 to VP64 or NF-κB p65, or a histone lysine demethylase (KDM).
PARK discloses: (pg. 235) “We show that removal of the CGG repeats can induce reactivation of silenced FMR1 gene expression… we demonstrate complete DNA demethylation of the FMR1 promoter… histone 3 K9 methylation (H3 K9meth), which indicates a repressed chromatin state and is associated with FMR1 silencing… were markedly upregulated following the CGG repeat editing, and the repressive chromatin marker H3K9meth was significantly downregulated… These results indicate that the ablation of the CGG repeats had an epigenetic effect on the methylation status and chromatin state of the FMR1 promoter.” PARK teaches a composition comprising RGENS for overexpression of one or more H3K9 methylation heterochromatin mark containing gene, such as FMR1, where the gene is silenced in a heterochromatic genomic region.
Stephan teaches fragile sites of chromosomes are at greater risk of deregulation than non-fragile sites and that the FRAXA site in FRM1 is a conserved hotspot for miRNAs that silence genes and inhibit double strand break repair (abstract). Stephan teaches that FRAXA is a portion of the FMR1 gene which harbors trinucleotide repeat expansions in Fragile X syndrome correlated with disease severity (pg 3, para 4). Stephan teaches this gene region comprises over 1 megabase pairs of nucleotides (pg 4, Fig 1). Taken together, Stephan teaches the FMR1 gene comprises over 1 megabase pairs, thus meeting the limitation of the domain of heterochromatin comprising megabase-sized domains of chromatin.
Chavez teaches fusing dCas9 to VP64, p65, and combinations thereof, resulting in increased transcriptional activity (pg 326, col 2, para 3). Chavez teaches the dCas9 fusions were able to activate expression of the repressed genes, NGN2 and NEUROD1 (pg 328, col 1, para 2).
Savage teaches a CRIPSR method comprising a catalytically inactive dCas9 (para 0006) fused to a fusion partner such as lysine demethylase (KDM) (abstract; para 00127). Savage teaches this system can target long non-coding RNAs (lncRNA) (para 0254) comprising CGG repeats in order to guide their excision (para 0083-0084).
It would have been obvious to combine the teachings of Jaenisch, Park, Stephan, Chavez, and Savage, arriving at a composition comprising a catalytically dead Cas9 linked to an effector molecule p65 or VP64 (1) Jaenisch teaches a composition comprising these two components (dead Cas9 and decitabine) as being effective for demethylating FMR1; (2) Park discloses FMR1 being a H3K9 heterochromatin marking gene; (3) Stephan corroborates that FMR1 contains megabase-sized domains; (4) Chavez teaches the effector molecules VP64 and p65 can be fused to dCas9 in order to activate the expression of a repressed gene; and (5) Savage teaches using CRISPR to generate long non-coding RNAs using dCas9 fused to a lysine demethylase. One of skill in the art would have had a reasonable expectation of success because Jaenisch and Chavez teach all the elements of the composition claimed and they disclose that those components are effective for activating transcription and demethylating the FMR1 gene, which is qualifies as both a megabase-sized and H3k9me3-heterochromatin mark containing gene. Thus by extension, one of skill in the art would have found it obvious to apply the composition of Jaenisch/Chavez to other H3k9me3-heterochromatin mark containing genes containing megabase-sized domains, because Jaenisch has already disclosed that their composition is capable of reactivating genes in those marked domains. Savage further adds that dCas9 can be fused to KDM in order to target CGG repeats for excision, said repeats which are H3K9 marked, as taught by Park.
Claim 3
As to claim 3, specific to the composition further comprising a guide RNA specific for at least one silenced gene, JAENISCH discloses: [claim 26] “A method of modulating the methylation of one or more genomic sequences in a cell comprising introducing into the cell a. a catalytically inactive site specific nuclease fused to an effector domain having… demethylation activity; and b. a guide sequence or a nucleic acid that encodes a guide sequence, thereby modulating the methylation of one or more genomic sequences in a cell”… [claim 37] “The method of claim 26, wherein the guide sequences are ribonucleic acid guide sequences”… [0051] “FIG. 19E demonstrates targeted in vivo DNA methylation editing by dCas9-Tet1 to activate a silenced GFP reporter”... [0052] “FIG. 20 depicts the reversal of hypermethylation of FMR-1 in Fragile X Syndrome. A cell exhibiting Fragile X Syndrome is contacted with dCas9-Tet1 fusion protein to specifically demethylate… to reactivate FMR-1…” JAENISCH teaches an epigenomic editor having RNA guide sequences modulating one or more silenced genes, including reactivating gene FMR1 for example, because FMR1 epigenetic silencing is governed by DNA methylation.
Claim 4
As to claim 4, specific to the composition further comprising a guide RNA specific to the selected silenced gene FMR1, JAENISCH discloses: [0052] “FIG. 20 depicts the reversal of hypermethylation of FMR-1 in Fragile X Syndrome. A cell exhibiting Fragile X Syndrome is contacted with dCas9-Tet1 fusion protein to specifically demethylate… to reactivate FMR-1…” JAENISCH teaches an epigenomic editor having RNA guide sequence specific for silenced gene FMR1.
Claims 1 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Chandler et al. (doi: 10.1186/1471-2199-4-3). This rejection has been modified to solely address the amendments.
claim 1(b), 4
Regarding claim 1(b) and 4, Chandler teaches a plasmid containing 27, 70, and 105 CGG repeats (Fig 1) that are operably linked to a promoter sequence (pg 4, col 2, para 2; Fig 1). Chandler teaches abnormal expansion of CGG repeats is associated with a length dependent hypermethylation and loss of flanking gene expression (pg 2, col 1, para 1). Chandler teaches chromatin architecture across the fragile X expansion is consistent with a transcriptionally silenced state, with the region becoming late replicating and extensively hypermethylated (pg 2, col 1, para 2). Chandler teaches fragile X CGG associated repeats can direct transcriptionally repressive chromatin to adjacent promoters (pg 2, col 2, para 1). MPEP § 2112.01(II) states:
“Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable. Therefore, if the prior art teaches the identical chemical structure, the properties applicant discloses and/or claims are necessarily present.”
Because the composition of Chandler is a narrower embodiment to what is claimed, it necessarily possesses the properties of “modulating megabase-sized domains of heterochromatin” and “de-repressing at least one H3K9me3-heterochromatin mark containing gene,” such as FMR1. Furthermore, this inherent feature need not be recognized at the relevant time. “There is no requirement that a person of ordinary skill in the art would have recognized the inherent disclosure at the relevant time, but only that the subject matter is in fact inherent in the prior art reference. Schering Corp. v. Geneva Pharm. Inc., 339 F.3d 1373, 1377, 67 USPQ2d 1664, 1668 (Fed. Cir. 2003)” See MPEP § 2112(I). Chandler teaches that the native human promoter for FMR1 didn’t provide sufficient transcriptional activity in the Xenopus model organism, thus they used the constitutively active human herpes virus promoter of HSVtk (pg 4, col 2, para 2). Given this teaching, one of skill in the art would have found it obvious to modify the promoter so that it is compatible with the species that is intended to be treated.
Claims 1 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Green et al. (US20180256749), in view of Chandler (doi: 10.1186/1471-2199-4-3), Stephan et al. (doi: 10.3390/cancers12040876), Kariko et al. (US20150038558), and Weissman et al. (doi: 10.1586/14760584.2015.973859). This rejection has been modified to solely address the amendments.
claim 1(c)
As to the composition of 1(c), comprising a noncoding RNA molecule comprising a premutation length CGG repeat, Green teaches that transcriptionally inactive FMR1 is marked by histone H3 lysine 4 trimethylation (H3K4me3) (pg 9, para 0083). Green teaches silenced FMR1 has increased DNA methylation by DNA methyltransferase (DNMT1); thus, in some embodiments, an epigenetic modulator of FMR1 is an agent that inhibits DNMT1 activity or expression, wherein said epigenetic modulator is a nucleic acid (pg 5, para 0063). Green teaches in some embodiments, an epigenetic modulator of FMR1 is a histone methyltransferase inhibitor, wherein example histone methyltransferases include, but are not limited to, EZH2, SETDB1, SUV39H1, EHMT1/2 (pg 6, para 0066). Green teaches in some embodiments, the epigenetic modulator of FMR1 is an interfering RNA (pg 7, para 0075). Green teaches the interfering RNA de-represses FMR1 via repressing one of the repressive markers of FMR1 (pg 9, para 0083, 0089; Fig 1).
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GREEN discloses: [0058] “a subject is referred to as ‘premutation’ and the number of CGG repeats ranges from about 55 repeats to about 200 repeats”; [0075] “an epigenetic modulator of FMR1 is an interfering RNA. Examples of interfering RNA include, but are not limited to double stranded RNA (dsRNA), siRNA, shRNA, miRNA, and antisense oligonucleotide (ASO). Inhibitory oligonucleotides may interfere with gene expression, transcription and/or translation. Generally, inhibitory oligonucleotides bind to a target polynucleotide via a region of complementarity. For example, binding of inhibitory oligonucleotide to a target polynucleotide can trigger RNAi pathway-mediated degradation of the target polynucleotide (in the case of dsRNA, siRNA, shRNA, etc.), or can block the translational machinery (e.g., antisense oligonucleotides). Inhibitory oligonucleotides can be single-stranded or double-stranded. In some embodiments, inhibitory oligonucleotides are DNA or RNA. In some embodiments, the inhibitory oligonucleotide is selected from the group consisting of: antisense oligonucleotide, siRNA, shRNA and miRNA. In some embodiments, inhibitory oligonucleotides are modified nucleic acids”; and [0120] “an inhibitory oligonucleotide (e.g., interfering RNA) can be delivered to the cells via an expression vector engineered to express the inhibitor oligonucleotide.” Green discloses the method [claim 28] “wherein the epigenetic modulator of FMR1 is a nucleic acid”… [claim 29] “The method of claim 28, wherein the nucleic acid is an interfering nucleic acid selected from the group consisting of: double stranded RNA (dsRNA), siRNA, shRNA, miRNA, and antisense oligonucleotide (ASO)”… [claim 30] “The method of any one of claims 1 to 29, wherein the epigenetic modulator of FMR1 is an interfering nucleic acid comprising a sequence (e.g., a guide sequence)… [claim 39] “presence of expansion of a polymorphic CGG repeat within the 5′UTR of the FMR1 gene”… [claim 40] “the expansion comprises between about 55 CGG repeats and about 200 CGG repeats.” GREEN teaches a noncoding RNA molecule, siRNA, a composition comprising sequences specific to premutation length CGG repeat, which meets the claim limitation composition comprising a noncoding RNA molecule of at least 50 CGG repeats because Green teaches the siRNA sequence is specific to the premutation CGG length of 55-200 repeats. GREEN teaches a noncoding RNA molecule, siRNA, a composition comprising sequences specific to premutation length CGG repeat, which meets the claim limitation composition of 1(c), comprising a noncoding RNA molecule because an siRNA is classified as a noncoding RNA molecule. Green teaches various techniques may be employed to introduce nucleic acid molecules into cells, such as commercially available nanoparticle transfection systems that are lipid-based (e.g. Sigma Aldrich’s N-TER and Invitrogen’s Lipofectamine) (pg 13, para 0125). Thus satisfying the limitation of the composition being delivered in a lipid nanoparticle.
Green is silent on the H3K9me3-heterochromatin mark containing gene qualifying as a “megabase-sized domain”. Green does not teach long non-coding RNAs.
Chandler teaches a plasmid containing 27, 70, and 105 CGG repeats (Fig 1) that are operably linked to a promoter sequence (pg 4, col 2, para 2; Fig 1). Chandler teaches abnormal expansion of CGG repeats is associated with a length dependent hypermethylation and loss of flanking gene expression (pg 2, col 1, para 1). Chandler teaches chromatin architecture across the fragile X expansion is consistent with a transcriptionally silenced state, with the region becoming late replicating and extensively hypermethylated (pg 2, col 1, para 2). Chandler teaches fragile X CGG associated repeats can direct transcriptionally repressive chromatin to adjacent promoters (pg 2, col 2, para 1).
Stephan teaches fragile sites of chromosomes are at greater risk of deregulation than non-fragile sites and that the FRAXA site in FRM1 is a conserved hotspot for miRNAs that silence genes and inhibit double strand break repair (abstract). Stephan teaches that FRAXA is a portion of the FMR1 gene which harbors trinucleotide repeat expansions in Fragile X syndrome correlated with disease severity (pg 3, para 4). Stephan teaches this gene region comprises over 1 megabase pairs of nucleotides (pg 4, Fig 1). Taken together, Stephan teaches the FMR1 gene comprises over 1 megabase pairs, thus meeting the limitation of the domain of heterochromatin comprising megabase-sized domains of chromatin.
It would have been obvious to combine the teachings of Green and Stephan because (1) Green supplies the interfering RNA comprising 55-200 CGG tandem repeats in order to inhibit DNA methylation machinery involved in silencing FMR1; and (2) Stephan supplies the information that FRM1 in those with fragile X comprises a megabase-sized domains of heterochromatin. Green further corroborates that this heterochromatinized DNA is silenced via methylation of histone proteins, such as H3K9me3. One of skill in the art would have had a reasonable expectation of success because Green teaches that this strategy of inhibiting an inhibitor of FMR1 expression using an interfering RNA is effective strategy in de-repressing that gene and Stephan teaches that the long CGG repeats within mutated FRM1 are megabase-sized.
Claims 1 is rejected under 35 U.S.C. 103 as being unpatentable over Rovozzo et al. (doi: 10.1371/journal.pone.0168204) in view of Green (US 20180256749).
claim 1(c)
Regarding claim 1(c), Rovozzo teaches CGG repeats upstream of the FMR1 gene media RNA localization and translation (abstract). Rovozzo teaches exogenous CGG repeat RNA inhibits the translation of other RNA’s (e.g. ARC RNA), thus representing a potential pathogenic mechanism for Fragile X (abstract). Rovozzo teaches injecting RNAs comprising 99 CGG repeats into hippocampal neurons (pg 8, para 2). Thus meeting the limitation of generating a non-coding RNA comprising at least 50 CGG repeats. Because the instantly claimed vaccine of claim 9 comprises no other components other than the RNA described in claim 1 and Rovozzo teaches their composition (1) contains RNA and (2) is injectable, this meets the limitation of the composition comprising an RNA vaccine. The immunostimulating properties of the CGG containing RNA are inherent to the compound. As an evidentiary reference, Derbis et al. (doi: 10.1038/s41467-021-21021-w) teaches enhancement of immune system-related markers being elevated in mice models of fragile X that express RNA comprising 90 CGG repeats (Fig 5; pg 10, Fig 5 caption; pg 8, col 2, para 3).
MPEP § 2112.01(II) states:
“Products of identical chemical composition can not have mutually exclusive properties.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). A chemical composition and its properties are inseparable. Therefore, if the prior art teaches the identical chemical structure, the properties applicant discloses and/or claims are necessarily present.”
Because the composition of Rovozzo is a narrower embodiment to what is claimed, it necessarily possesses the properties of “modulating megabase-sized domains of heterochromatin” and “de-repressing at least one H3K9me3-heterochromatin mark containing gene,” such as FMR1.
Rovozzo teaches that the CGG repeats are microinjected (pg 4, para 4), and is silent on them being delivered via a lipid nanoparticle.
Green teaches a method of derepressing FMR1 in those with fragile X (pg 1, para 0007-0008) comprising administering an RNA molecule that re-activates FMR1 gene expression (pg 2, para 0023). Green teaches various techniques may be employed to introduce nucleic acid molecules into cells, such as commercially available nanoparticle transfection systems that are lipid-based (e.g. Sigm-Aldrich’s N-TER and invitrogen’s Lipofectamine) (pg 13, para 0125). Thus satisfying the limitation of the composition being delivered in a lipid nanoparticle.
It would have been obvious to combine the teachings of Rovozzo and Green because both references are aimed at derepressing a gene affected by Fragile X using an RNA molecule and Green teaches lipid nanoparticle systems that are commercially available are effective in introducing said RNA molecules in these individuals. One of skill in the art would have had a reasonable expectation of success because Green teaches lipid nanoparticle systems are effective at delivering RNA into cells, even those affected by Fragile X.
Response to Arguments
Applicant's arguments filed 9/30/2025 have been fully considered but they are not persuasive.
112(a) WD; pg 9, para 3 - pg 10, para 1
Applicant argues the newly added amendment specifying the genomic locus (e.g. FMR1, CSMD1, etc) is sufficient to meet the written description requirement.
These amendments add specificity requirements to the targeting and the structure for targeting these specific genes is lacking more so than the more generic genus of “H3K9me3 marked” genes. The invention described in the specification achieves this specific targeting by the individual having Fragile X, which results in the repression of FMR1 and the adjacent genes of CSMD1, etc.
112(a) WD, pg 10, para 2
Applicant argues that the expression plasmid does not require any sequence of the FMR1 gene, what it requires is a 99 CGG tandem repeat linked to a promoter to generate a long noncoding RNA molecule that is capable of titrating methylases away from genomic DNA. Applicant asserts this titration of methylases is all that is required to de-repress any gene.
Examiner has never argued that the expression plasmid requires the sequence of the FMR1 gene. Examiner is arguing that the subject needs to have Fragile X disorder in order for the invention to function. The written description rejection of claim 1(b) and 1(c) is based on the claim failing to meet the pre-requisite condition of the subject having Fragile X. The written description rejection of claim 1(c) is based on the fact that removing methylases does not result in spontaneous demethylation of already methylated heterochromatin. Examiner recognizes that flooding methylases with CGG repeats is a means of targeting methylases, and not a means of targeting H3K9me3-heterochromatin mark containing genes. Thus applicant has not satisfied the written description requirement of targeting (i) H3K9me3- heterochromatin mark containing genes; nor (ii) derepressing a gene that is not FMR1. Claims 1(b) and 1(c) are drawn to a method of de-repressing any gene, but neither supply a means of doing so except in the sole case of the subject having Fragile X.
112(a) WD, pg 10, para 3-4
Applicant argues “The Examiner opines that there is a lack of data demonstrating a shortening of an FMR1 CGG repeat. Applicant submits that the lack of data demonstrating shortening of a CGG repeat is immaterial as that is not the mechanism by which the construct of the invention functions.”
Conversely to applicant’s assertions, Examiner stated the opposite. This is the one area where applicant did provide sufficient evidence. The verbatim statement is reiterated here: ‘Applicant did provide an example of shortening a previously-existing, mutated version of the FMR1 gene comprising 346 tandem CGG repeats to 180 tandem repeats using CRISPR to target the FMR1 locus in subjects with Fragile X (instant pg 86, para 2).’ For clarity, this statement is drawn to the method of claim 1(a) which satisfied the written description requirement. In effect, Applicant is using the technology of claim 1(b) and 1(c) as a counterargument to invalidate the method of claim 1(a).
112(a) E, pg 12, para 2-pg 13, para 1
Applicant repeats the argument regarding the CGG repeats being capable of titrating the methylases from performing further methylation. Applicant points to pg 95 regarding the generation of the expression vector and Figures 35-36 regarding the effects of the plasmid.
Applicant must recognize that the evidence provided is limited to subjects with Fragile X, as is suggested by the instant abstract. This requirement is evident in the example applicant provided, which is performed in a Fragile X subject. Examiner fully admits the data provided regarding de-repressing genes in subjects with Fragile X is well substantiated in the instant application, as elaborated in the ‘Allowable Subject Matter’ section. Unfortunately, Applicant has not provided any examples of inserting a ≥99 tandem CGG repeat in non-Fragile X subjects. Applicant has not provided any example of administering a nucleic acid comprising a ≥99 tandem CGG repeat to a subject that is experiencing repression of a gene that isn’t FMR1 (e.g. BRCA1). Thus the gene-suppressing effect of adding a fragile site to an individual with repressed BRCA1 is unknown. A person of skill in the art would have no expectation that the instantly claimed composition would be capable of de-repressing any gene in any individual. In essence, the breadth of the claims are not commensurate in scope with Applicant’s findings.
102; pg 14, para 1
Applicant argues that the invention of Chandler is a research tool and not a pharmaceutical agent.
Chandler satisfies the limitation of the preparation being a pharmaceutical because it is delivered to a biological subject (oocytes) and elicits a therapeutic effect (de-represses genes adjacent to the fragile site) (pg 8, col 1-2). Nonetheless, the teachings of Chandler have been converted to a 103 to address the newly added limitation of requiring the promoter to be human.
103; pg 15, para 5-pg 16, para 2
Applicant argues that Jaenisch does not teach a dCas9 being operably linked to KDM. Applicant argues the references of Park, Stephan, and Chavez fail to address this deficiency.
The newly added reference of Savage addresses this newly limited Markush option.
103; pg 16, para 5-pg 18, para 1
Applicant argues that siRNA as taught by Green are too short to meet the newly added claim requirements of at least 70 CGG repeats. Applicant argues siRNAs are a completely different technology than long non-coding RNAs. Applicant provided definitions of “small non-coding RNAs” described as being 20-30 nucleotides in length, as being a restraint on all siRNAs.
Using the definitions supplied by Green, Green teaches the siRNAs of their invention are 55-200 repeats in length. Absent a limitation that excludes siRNAs from the claims, the teachings of Green still render obvious the limitation of being at least 70 repeats in length. If this is not found sufficient, the reference of Chandler has been added to the rejection which more clearly refers to CGG repeats greater than 70 repeats in length.
103; pg 19, para 1-pg 20, para 1
Applicant argues that the invention of Rovozzo is a research tool and not a pharmaceutical agent. Applicant argues that Rovozzo does not teach de-repressing one of the genes listed in the newly added amendments.
Rovozzo satisfies the limitation of the preparation being a pharmaceutical because it is delivered to a biological subject (human Fragile X fibroblasts) and elicits a therapeutic effect (de-represses FMR1 and ARC) (pg 18), thus satisfying both of these limitations.
Conclusion
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/L.A.E./
Examiner, Art Unit 1675
/Adam Weidner/Primary Examiner, Art Unit 1675