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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-6, 8-18, and 41, alongside the species of CGG repeats and decitabine, in the reply filed on 18 June 2026 is acknowledged.
Claim 21 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 18 June 2026.
Claim Objections
Claims 2, 8-9, and 16 are objected to because of the following informalities:
Regarding claims 2, 8-9, and 16, each of the claims have a first recitation of “an inactive Cas9 protein”, or are depend on a claim that previously recited “an inactive Cas9 protein”, followed by “the dCas9” without reference to a previously recited “dCas9”. This is inconsistent claim language and Examiner suggests amending the claims to either recite “the inactive Cas9 protein” at each instance of “dCas9”, or “a dCas9” at every instance of “an inactive Cas9 protein” in order to rectify the inconsistent language.
Appropriate correction is required.
Claim Interpretation
Regarding claims 1 and 8-9, the claims are directed towards method of contracting an expansion of nucleotide repeats in a genome. It is noted that the instant specification does not provide a formal definition for what it means to “contract” the claimed repeats in the genome. However, the working examples present in the instant specification do teach that the claimed contraction of nucleotide repeats were generated by site-specific R-loops mediated by a dCas9 that was targeted to a nucleotide repeat region through the use of a gRNA, followed by excision of the trinucleotide repeat by BER enzymes (pg. 61-64; see Example 5). Therefore, for the purposes of examination, the claimed contraction of nucleotide repeats in a genome is going to be treated as synonymous with the generation of an R-loop at a nucleotide repeat region within a genome and subsequent base excision repair enzymes acting on the R-loop structure to promote the deletion of the trinucleotide repeat.
Regarding claims 2, 8-9, and 16, the claimed “dCas9” will be interpreted as referring to the previously recited “inactive Cas9 protein” for the purposes of examination.
Claim Rejections - 35 USC § 112
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 10-12 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.
Regarding claims 10-12, the claims recite the phrase “the reference number” in line 1 of the claims. There is insufficient antecedent basis for this limitation in the claims. It is unclear what number or trinucleotide repeats the claims are making reference to. It is unclear if the claims are intended to be further limiting the amount of trinucleotide repeats in the cell of claim 9 or if the claims are intended to limit a different cell that has not been contacted with the claimed dCas9.
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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 5-6, 9, 13, and 17 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992).
Regarding claims 1 and 9, Liu is directed towards a study concerned with the rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene (Abstract). Liu teaches that Fragile X syndrome (FXS), the most common genetic form of intellectual disability in males, is caused by silencing of the FMR1 gene associated with hypermethylation of the CGG expansion mutation in the 5' UTR of FMR1 in FXS patients (Abstract). Liu teaches that targeted demethylation of the CGG expansion by dCas9-Tet1/single guide RNA (i.e., an inactive Cas9 protein and a guide RNA that directs the dCas9 to the gene comprising the repeats) in iPSCs from a subject who had FXS switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state, restoring a persistent expression of FMR1 in FXS iPSCs (Abstract).
Regarding the preamble limitations claiming that the method results in “contracting nucleotide repeats in a gene” and “in an amount sufficient to reduce the number of nucleotide repeats in the cell” (see Claims 1 and 9), MPEP 2111.02 teaches that “During examination, statements in the preamble reciting the purpose or intended use of the claimed invention must be evaluated to determine whether or not the recited purpose or intended use results in a structural difference (or, in the case of process claims, manipulative difference) between the claimed invention and the prior art. If so, the recitation serves to limit the claim.” In the instant case, the limitations reciting the intended result of the method does not result in a manipulative difference when compared to the disclosure of Liu. Accordingly, because Liu’s method meets all of the required limitations of the body of the claim, the claimed intended result is an inherent characteristic of the prior art method.
Regarding claims 5 and 13, Liu teaches that the cell from the subject had 450 CGG repeats (pg. 981).
Regarding claim 6, Liu teaches that the dCas9 system was administered to multiple cells (i.e., a population of cells) (pg. 981; see Figure 1).
Regarding claim 17, Liu teaches that the dCas9 system was administered to post-mitotic neurons (i.e., somatic cells) were derived from the methylation-edited FX52 iPSCs (pg. 985-986; see Figure 5).
Claim(s) 2-4 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) as applied to claims 1, 5-6, 9, 13, and 17 above, as evidenced by Zhou ("CGG-repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells and stem cell-derived neurons." Molecular autism 7.1 (2016): 42).
Regarding claims 2-4, Liu anticipates claims 1, 5-6, 9, 13, and 17 as described above. Liu teaches that the CGG expansions are within the 5’UTR of an FMR1 gene (Abstract). Liu teaches that the dCas9 system was administered to post-mitotic neurons (i.e., somatic cells) were derived from the methylation-edited FX52 iPSCs (pg. 985-986; see Figure 5).
Regarding the claimed limitation wherein “the FMR1 gene is inactive due to the presence of expansion of CGG nucleotide repeats in the 5’ UTR of the FMR1 gene” (see Claim 2) and “a disorder caused by the expansion of nucleotide repeats” (see Claim 3-4), Liu does not explicitly teach that the CGG expansions seen in the 5’UTR of the FMR1 gene are alone sufficient to cause fragile X syndrome (i.e., FXS). However, Zhou teaches that the presence of the CGG expansions in Liu inherently cause FXS.
Zhou is drawn towards a study concerned with CGG repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells (Abstract). Zhou teaches that FXS is caused from the expansion of a CGG-repeat tract in the 5′ untranslated region of the FMR1 gene to >200 repeats (Abstract).
Therefore, the FXS described in Liu is inherently caused by the expanded CGG repeats present in the 5’ UTR of the FMR1 gene because the 5’UTR of the FMR1 gene of Liu had 450 CGG repeats (i.e., greater than 200 repeats).
Regarding claim 4, Liu teaches that the dCas9 system was administered to post-mitotic neurons (i.e., somatic cells) were derived from the methylation-edited FX52 iPSCs (pg. 985-986; see Figure 5).
Claim(s) 10-12 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) as applied to claims 1, 5-6, 9, 13, and 17 above, as evidenced by Seltzer ("Prevalence of CGG expansions of the FMR1 gene in a US population‐based sample." American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 159.5 (2012): 589-597).
Regarding claims 10-12, Liu anticipates claims 1, 5-6, 9, 13, and 17 as described above.
For the purposes of claim interpretation, based on the wording of claim 11, the claims are interpreted as claiming a reference number of repeats, wherein the reference number is the amount of repeats in a healthy cell that does not have FXS (see Claim 11).
Liu does not specifically teach that the reference number is 30-100 repeats (Claim 10) or 0-50 repeats (Claim 12). Liu does not specifically teach that the reference number is a number of nucleotide repeats in a control cell that does not have the condition associated with nucleotide repeat expansion (Claim 11).
Seltzer is drawn towards a review study concerned with the prevalence of CGG expansions of the FMR1 gene in a US population-based sample (Abstract). Seltzer teaches that FXS is caused by an expansion of CGG trinucleotide repeats in the FMR1 gene of a subject (pg. 589). Seltzer teaches that in individuals with FXS, there are over 200 CGG repeats in the FMR1 gene, compared to the 5–40 repeats in the normal gene (pg. 589).
Therefore, the reference value of repeats in a healthy cell not having a condition associated with nucleotide repeat expansions (i.e., FXS), wherein the reference value is 0-50 or 30-100, inherently falls within the claimed range of reference values as evidenced by Seltzer.
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 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, 5-6, 9, 13, and 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) in view of Szczelkun ("Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes." Proceedings of the National Academy of Sciences 111.27 (2014): 9798-9803), and Laverde ("R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities." Journal of Biological Chemistry 295.40 (2020): 13902-13913).
Regarding claims 1 and 9, Liu is directed towards a study concerned with the rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene (Abstract). Liu teaches that Fragile X syndrome (FXS), the most common genetic form of intellectual disability in males, is caused by silencing of the FMR1 gene associated with hypermethylation of the CGG expansion mutation in the 5' UTR of FMR1 in FXS patients (Abstract). Liu teaches that targeted demethylation of the CGG expansion by dCas9-Tet1/single guide RNA (i.e., an inactive Cas9 protein and a guide RNA that directs the dCas9 to the gene comprising the repeats) in iPSCs from a subject who had FXS switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state, restoring a persistent expression of FMR1 in FXS iPSCs (i.e., the demethylation of the expanded nucleotide repeat region resulted in FMR1 expression in the cell) (Abstract).
Liu does not teach or suggest that the method results in “contracting nucleotide repeats in a gene” and “in an amount sufficient to reduce the number of nucleotide repeats in the cell” (see Claims 1 and 9)
Szczelkun is drawn towards a study concerned with R-loop formation by Cas9 (Abstract). Szczelkun teaches that Cas9 proteins utilize a bound RNA that hybridizes to complementary sequence stretches (i.e., a guide RNA) (Abstract). Szczelkun teaches that on DNA targets, the resulting structure formed by the bound RNA interacting with the complementary sequence is an R-loop (Abstract).
Laverde is drawn towards a study concerned with how R-loops promote trinucleotide repeat deletion (i.e., interpreted as encompassing the claimed “contraction”) through DNA base excision repair enzymes (Abstract). Laverde teaches that R-loops are generated when a nascent RNA strand hybridizes back to its DNA template to create an RNA:DNA hybrid (i.e., an RNA:DNA hybrid analogous to the guide RNA:DNA hybrid described in Szczelkun) (pg. 13902). Laverde teaches that R-loops on expanded GAA, CAG, CTG, or CGG trinucleotide repeats result in a guanine-rich single-stranded region on a nontemplate strand of the DNA, which can be damaged by endogenous and exogenous DNA base-damaging agents (pg. 13902). Laverde teaches that endogenous APE1 can efficiently incise an abasic site located between genomic (GAA)20 and (CAG)20 trinucleotide repeats present in the nontemplate strand (pg. 13902-13903; see Figure 1). Laverde teaches that base excision repair enzymes acting on the R-loop structure promotes the deletion of the trinucleotide repeats (pg. 13907-12909; see Figure 8).
Therefore, the claimed result of trinucleotide contractions are not a surprising result compared to the closest prior art because, before the effective filing date of the claimed invention, one of ordinary skill in the art would have recognized and expected the R-loop generated by the trinucleotide repeat-targeting guide RNA of the dCas9 system of Liu to result in the contraction of the genomic nucleotide repeats. Because Szczelkun teaches that Cas9 proteins can form R-loops with target DNA of interest through its guide RNA’s interaction with the target DNA, one would have expected the dCas9 system of Liu to have similarly formed an R-loop at the trinucleotide repeat region of the FMR1 gene that was targeted by the gRNA. Additionally, because Laverde teaches that R-loop formation at trinucleotide repeat regions resulted in the deletion (i.e., contraction) of the trinucleotide repeats by base excision repair enzymes, one would have expected the R-loop formed by the dCas9 system of Liu to have similarly resulted in the deletion of the trinucleotide repeat regions.
Regarding claims 5 and 13, Liu teaches that the cell from the subject had 450 CGG repeats (pg. 981).
Regarding claim 6, Liu teaches that the dCas9 system was administered to multiple cells (i.e., a population of cells) (pg. 981; see Figure 1).
Regarding claim 17, Liu teaches that the dCas9 system was administered to post-mitotic neurons (i.e., somatic cells) were derived from the methylation-edited FX52 iPSCs (pg. 985-986; see Figure 5).
Claim(s) 2-4 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) in view of Szczelkun ("Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes." Proceedings of the National Academy of Sciences 111.27 (2014): 9798-9803), and Laverde ("R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities." Journal of Biological Chemistry 295.40 (2020): 13902-13913) as applied to claims 1, 5-6, 9, 13, and 17 above, further in view of Zhou ("CGG-repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells and stem cell-derived neurons." Molecular autism 7.1 (2016): 42).
Regarding claims 2-4, Liu in view of Szczelkun and Laverde renders obvious claims 1, 5-6, 9, 13, and 17 as described above. Liu teaches that the CGG expansions are within the 5’UTR of an FMR1 gene (Abstract). Liu teaches that the dCas9 system was administered to post-mitotic neurons (i.e., somatic cells) were derived from the methylation-edited FX52 iPSCs (pg. 985-986; see Figure 5).
Liu in view of Szczelkun and Laverde does not teach or suggest that the FMR1 gene is inactive due to the presence of expansion of CGG nucleotide repeats in the 5’ UTR of the FMR1 gene (see Claim 2), or wherein the cell, or somatic cell, is from a subject who has a disorder caused by the expansion of nucleotide repeats (Claims 3-4).
Zhou is drawn towards a study concerned with CGG repeat dynamics and FMR1 gene silencing in fragile X syndrome stem cells (Abstract). Zhou teaches that FXS is caused from the expansion of a CGG-repeat tract in the 5′ untranslated region of the FMR1 gene to >200 repeats (Abstract).
Therefore, one of ordinary skill in the art would have recognized that the reference value of present within an FMR1 gene that was from a subject that did not have FXS comprises 5-40 repeats. Because Liu teaches that the 5’UTR of the FMR1 gene derived from a subject who had FXS had 450 CGG repeats, and Zhou teaches that FXS is caused when the 5’ UTR of an FMR1 gene has >200 CGG repeat expansions, one of ordinary skill in the art would have recognized and expected that the FXS seen within the subject of Liu to have been caused by the >200 CGG repeat expansions as described by Zhou.
Regarding claim 4, Liu teaches that the dCas9 system was administered to post-mitotic neurons (i.e., somatic cells) were derived from the methylation-edited FX52 iPSCs (pg. 985-986; see Figure 5).
Claim(s) 8 and 14-18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) in view of Szczelkun ("Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes." Proceedings of the National Academy of Sciences 111.27 (2014): 9798-9803), and Laverde ("R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities." Journal of Biological Chemistry 295.40 (2020): 13902-13913) as applied to claims 1, 5-6, 9, 13, and 17 above, and further in view of “Liu2” ("Editing DNA methylation in the mammalian genome." Cell 167.1 (2016): 233-247) and Saba ("Decitabine in the treatment of myelodysplastic syndromes." Therapeutics and clinical risk management 3.5 (2007): 807-817).
Regarding claims 8 and 14-18, the applicable teachings of Liu in view of Szczelkun and Laverde are discussed above as applied to claims 1, 5-6, 9, 13, and 17.
Liu additionally teaches that previous studies, including the subsequently mentioned “Liu2” reference, had successfully introduced a catalytically inactivate Cas9 fused to Tet (dCas9-Tet) in order to allow for targeted modification of DNA methylation in the mammalian genome in vivo (pg. 981). Liu teaches that the dCas9-Tet1 was able to edit somatic neurons derived from subjects who had FXS, and that the demethylation was maintained following the engraftment of the neurons into the mouse brain (Abstract). Liu teaches that demethylation of the FMR1 gene is one potential therapeutic strategy for FXS (Abstract).
Liu in view of Szczelkun and Laverde do not teach or suggest that the inactive Cas9 protein and guide RNA are administered to a subject (Claim 8), alongside a therapeutically effective amount of a DNMT inhibitor (Claim 8). Liu in view of Szczelkun and Laverde do not teach or suggest that the cell is in a living subject (Claim 9). Liu in view of Szczelkun and Laverde do not teach or suggest that the cell is within the brain of the subject (Claim 15). Liu in view of Szczelkun and Laverde do not teach or suggest that the dCas9 and gRNA are administered systematically to the subject (Claim 16). Liu in view of Szczelkun and Laverde do not teach or suggest that the cell is a somatic cell within a subject (Claim 17).
Regarding claim 16, it is noted that the instant specification does not provide a definition for what it means for the dCas9 and gRNA to be administered “systematically” to the subject. Accordingly, the claim limitation is interpreted as encompassing an administration method selected from injection.
Liu2 is drawn towards a study concerned with targeted DNA methylation editing in vivo (Abstract). Liu2 teaches that lentiviral vectors expressing dCas9-Tet1 and gRNAs were able to be injected into a mouse’s brain (i.e., a brain that comprises somatic neurons) in order to successfully modify DNA methylation status of a GFP reporter in vivo (pg. 242, 244; see Figure 7).
Saba is drawn towards a review study concerned with the use of decitabine in myelodysplastic syndromes (Abstract). Saba teaches that decitabine is a DNMT inhibitor and low doses of decitabine are associated with demethylation (i.e., decitabine is a demethylating agent) (pg. 809, 813). Saba teaches that decitabine treatment has been shown to reverse hypermethylation of endogenous cell-cycle inhibitor genes (i.e., decitabine can be utilized to demethylate hypermethylated nucleic acids) (pg. 809).
Therefore, regarding the modification wherein the dCas9-Tet and gRNA are injected into somatic neurons present within a living subject’s brain, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have systematically injected the dCas9-Tet and gRNA of Liu in view of Szczelkun and Laverde to somatic neurons within a living subject’s brain, because it would have merely amounted to combination of prior art elements according to known methods to yield predictable results. Because Liu already teaches that the dCas9-Tet and gRNA were able to be injected into somatic neurons, and that following engraftment into a living mouse’s brain the target DNA’s methylation status was maintained, while Liu2 teaches that systematically injecting the same fusion protein into a mouse’s brain resulted in the dCas9-Tet and gRNA successfully functioning in the in vivo model, one would have expected injecting the dCas9-Tet and gRNA of Liu into somatic neurons present within a living subject’s brain to have resulted in the construct performing the same function as it did within the somatic neurons of Liu. Additionally, because both references teach the use of the same construct for the same reason, namely targeted demethylation of DNA, one would have expected the injection of the dCas9-Tet and gRNA into somatic neurons present within a living subject to have predictably resulted in a functioning dCas9-Tet and gRNA system that could edit a target DNA’s methylation status in vivo.
Additionally, regarding the administration of an effective amount of a DNMT inhibitor, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have contacted the cell of Liu with decitabine because it would have merely amounted to a combination of prior art elements according to known methods to yield predictable results. Because both Liu and Saba both teach the use of demethylating agents that can demethylate hypermethylated nucleic acids within target cells, one would have expected utilizing decitabine within the cell of Liu to have similarly demethylated the FMR1 gene. Additionally, because Liu teaches that demethylating the FMR1 gene through the use of the dCas9-Tet1 construct has therapeutic benefit and can aid in the restoration of FMR1 expression, one would have expected the decitabine of Saba to have predictably provided a similar therapeutic benefit through its ability to aid in the demethylation of the FMR1 gene.
Claim(s) 10-12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) in view of Szczelkun ("Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes." Proceedings of the National Academy of Sciences 111.27 (2014): 9798-9803), and Laverde ("R-loops promote trinucleotide repeat deletion through DNA base excision repair enzymatic activities." Journal of Biological Chemistry 295.40 (2020): 13902-13913) as applied to claims 1, 5-6, 9, 13, and 17 above, and further in view of Seltzer ("Prevalence of CGG expansions of the FMR1 gene in a US population‐based sample." American Journal of Medical Genetics Part B: Neuropsychiatric Genetics 159.5 (2012): 589-597).
Regarding claims 10-12, based on the wording of claim 11, the claims are interpreted as claiming a reference number of repeats, wherein the reference number is the amount of repeats in a healthy cell that does not have FXS.
Liu in view of Szczelkun and Laverde does not teach or suggest that the reference number is 30-100 repeats (Claim 10) or 0-50 repeats (Claim 12). Liu in view of Szczelkun and Laverde does not teach or suggest that that the reference number is a number of nucleotide repeats in a control cell that does not have the condition associated with nucleotide repeat expansion (Claim 11).
Seltzer is drawn towards a review study concerned with the prevalence of CGG expansions of the FMR1 gene in a US population-based sample (Abstract). Seltzer teaches that FXS is caused by an expansion of CGG trinucleotide repeats in the FMR1 gene of a subject (pg. 589). Seltzer teaches that in individuals with FXS, there are over 200 CGG repeats in the FMR1 gene, compared to the 5–40 repeats in the normal gene (pg. 589).
Therefore, one of ordinary skill in the art would have recognized and expected that the reference value of present within an FMR1 gene that was from a subject that did not have FXS comprised 5-40 repeats. Because Liu teaches that the 5’UTR of the FMR1 gene derived from a subject who had FXS had 450 CGG repeats, and Seltzer teaches that the amount of CGG repeats in a healthy cell that does not have FXS is 5-40, while cells derived from subjects who did have FXS was >200, one of ordinary skill in the art would have recognized and expected that the claimed reference values of nucleotide repeats to have fallen within the claimed range of 0-50 or 30-100 CGG repeats.
Claim(s) 41 is/are rejected under 35 U.S.C. 103 as being unpatentable over Liu ("Rescue of fragile X syndrome neurons by DNA methylation editing of the FMR1 gene." Cell 172.5 (2018): 979-992) as applied to claims 1, 5-6, 9, 13, and 17 above, and further in view of Saba ("Decitabine in the treatment of myelodysplastic syndromes." Therapeutics and clinical risk management 3.5 (2007): 807-817).
Regarding claim 41, Liu anticipates claims 1, 5-6, 9, 13, and 17 as described above.
Liu further teaches that the demethylation of the FMR1 gene switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state and restored persistent expression of FMR1 in FXS iPSCs (Abstract). Liu teaches that demethylation of the FMR1 gene is a potential therapeutic strategy for FXS (Abstract).
Liu does not teach or suggest that the cell was contacted with an DNMT inhibitor selected from decitabine (Claim 41).
Saba is drawn towards a review study concerned with the use of decitabine in myelodysplastic syndromes (Abstract). Saba teaches that decitabine is a DNMT inhibitor and low doses of decitabine are associated with demethylation (i.e., decitabine is a demethylating agent) (pg. 809, 813). Saba teaches that decitabine treatment has been shown to reverse hypermethylation of endogenous cell-cycle inhibitor genes (i.e., decitabine can be utilized to demethylate hypermethylated nucleic acids) (pg. 809).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have contacted the cell of Liu with decitabine because it would have merely amounted to a combination of prior art elements according to known methods to yield predictable results. Because both Liu and Saba both teach the use of demethylating agents that can demethylate hypermethylated nucleic acids within target cells, one would have expected utilizing decitabine within the cell of Liu to have similarly demethylated the FMR1 gene. Additionally, because Liu teaches that demethylating the FMR1 gene through the use of the dCas9-Tet1 construct has therapeutic benefit and can aid in the restoration of FMR1 expression, one would have expected the decitabine of Saba to have predictably provided a similar therapeutic benefit through its ability to aid in the demethylation of the FMR1 gene.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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