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 .
Priority
Applicant’s claim to priority from Foreign Application No. GB2020549.9 filed 12/23/2020 and International Application PCT/GB2021/053413 filed 12/22/2021 is hereby acknowledged. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Election/Restrictions
Applicant’s election without traverse of Invention group I (claims 1, 3, 6-9, 11-18 and 21-24, drawn to a method of treating a disorder of the saccharopine pathway of lysine degradation in a subject) and Species Group A (1) (a disorder to treat that is a deficiency in ALDH7A1 and the disorder is pyridoxine-dependent epilepsy), Group B(1)( RNA, DNA or combination RNA and DNA) and Group C (3) (a nucleic acid molecule with a generic sequence of SEQ ID NO: 35 and a specific sequence of SEQ ID NO: 41) in the reply filed on 07/07/2026 is acknowledged.
Claims 10 and 25 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 07/07/2026.
Application Status
This Application is a National Stage entry under 35 U.S.C. §371 of PCT/GB2021/053413 filed 12/22/2021.
This Office Action is in response to Amendments and Remarks filed 07/07/2026.
Amendments to claims filed 07/07/2026 are hereby acknowledged.
Claim 23 is currently amended. Claims 2, 4-5, 10, 19-20 and 25 are cancelled. Therefore, claims 1, 3, 6-9, 11-18 and 21-24 are pending and under
consideration in this office action.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 06/22/2023 and 01/03/2024 are hereby acknowledged. The submissions 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 06/22/2023 are hereby acknowledged and are acceptable.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). See page 39, TABLE 1.
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The use of the terms “Lipofectamine” (page 35, lines 21, 23; page 39, line 27; page 40, lines 8, 19; page 41, line 24; page 43, lines 7, 9, 11, 14), “ Millipore” (page 35, line 32), “Eppendorf” (page 35, line 33; page 36, line 2), “Waters”, “Xevo” and “Acquity” (page 36, line 18; page 44, lines 19-20), “Discovery” (page 36, line 19), “Amberlyst 15” (page 36, line 33), “RNeasy Plus Mini kit” (page 37, line 5), “NanoDrop” (page 37, line 7), “SuperScript” (page 37, line 10), “GraphPad Prism” (page 37, line 25; page 5, lines 4 and 26), which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore, the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 22 is objected to because of the following informalities: The claim seems to recite an alternative number (v), without introducing the other limitations from (i) to (iv).
Claim 23 is objected to because of the following informalities: semi-colon “;” and/or term “or” are missing at the end of alternative (c).
Appropriate correction is required.
Claim Interpretation
Regarding claim 1, it recites “A method of treating a disorder of the
saccharopine pathway of lysine degradation in a subject, comprising administering to the subject a composition comprising a nucleic acid silencing molecule that reduces the expression of alpha-aminoadipic semialdehyde synthase (AASS).”
Examiner interprets that the disorder can be any disorder involving the saccharopine pathway. Examiner also interprets the “subject” can be an animal model of disease, since the Specification teaches that the subject “can be a mammal” (see page 31, line 1). Examiner also interprets that the “nucleic acid silencing” is a knockdown nucleic acid and not a knockout nucleic acid, since it is claimed to “reduces the expression of alpha-aminoadipic semialdehyde synthase”. Examiner interprets that the reduction of expression via a silencing nucleic acid is performed at the mRNA level and is not a complete abolishing of the expression by gene deletion at the genomic level.
Regarding claims 3, 9, 12, 18, 22 and 23, they recite the term “optionally”. According to MPEP 2173.05(h), section II, the term is used to indicate “alternative” recitations. Examiner interprets that in the case of claims 3, 9, 18, 22 and 23, the claims recite alternative options to limitations that are not absolutely required by the claims.
However, in the case of claim 12, Examiner interprets the term “optionally” to be used to mean “preferentially” and indicate preferred embodiments.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 12 and 17 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 claim 12, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
In the present instance, claim 12 recites the broad recitation “the nucleic acid silencing molecule comprises or consists of an antisense oligonucleotide (AON), a small interfering RNA (siRNA), a short hairpin RNA (shRNA), a microRNA (miRNA), or a CRISPR guide RNA”, and the claim also recites “optionally…an antisense oligonucleotide (AON) or a small interfering RNA (siRNA)” which is the narrower statement of the range/limitation. The claim is considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
The term “optionally” usually indicates a feature/limitation that is not absolutely required by the claim and is used in the claim in an inconsistent manner compared to its use in other claims comprising the term “optionally”.
Regarding claim 17, it recites “The method of claim 16, wherein (i) the
composition comprises two or more nucleic acid silencing molecules as defined in claim 16; (ii) each of the two or more nucleic acid silencing molecules are of one stereoisomer; and (iii) no further nucleic acid silencing molecules are comprised in the composition”.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 17 recites the broad recitation “two or more nucleic acid silencing molecules”, and the claim also recites “no further nucleic acid molecule” which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
It is unclear what number of nucleic acid molecules is an acceptable number within the composition, to then adding no further nucleic acid silencing molecule to the composition.
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.
Claims 1, 3, 6, 11-12, 18 and 22 are rejected under 35 U.S.C. § 103 as being unpatentable over Leandro (Leandro, J. et al. “Deletion of a-aminoadipic semialdehyde synthase limits metabolite accumulation in cell and mouse models for glutaric aciduria type 1”. Journal of Inherited Metabolic Diseases, Vol, 43 (2020), pp:1154-1164; First published online June 21, 2020; printed November 2020; cited on IDS filed 01/03/2024), in view of Pena (Pena, I.A. et al. “Mouse lysine catabolism to aminoadipate occurs primarily through the saccharopine pathway; implications for pyridoxine dependent epilepsy (PDE)”. Biochemica et Biophysica Acta, Vol. 1863 (2017), pp: 121-128; cited on IDS filed 01/03/2024), Perez (Perez, B. et al. “Clinical, biochemical, and molecular studies in pyridoxine-dependent epilepsy: Antisense therapy as possible new therapeutic option”. Epilepsia, Vol. 54, No. 2 (2013), pp: 239-248) and Cleveland (Cleveland, B.M. et al. “[Symbol font/0x61]-Aminoadipate ẟ-semialdehyde synthase mRNA knockdown reduces the lysine requirement of a mouse hepatic cell line”. The Journal of Nutrition, Vol. 138 (2008), pp: 2143-2147, and cited in the IDS filed 01/03/2024).
Regarding claim 1, it recites “A method of treating a disorder of the
saccharopine pathway of lysine degradation in a subject, comprising administering to the subject a composition comprising a nucleic acid silencing molecule that reduces the expression of alpha-aminoadipic semialdehyde synthase (AASS).”
Leandro teaches an animal model glutaryl-CoA dehydrogenase (GCDH) Knock-out (KO) mice that is a model for Glutaric aciduria type 1 (GA1) (see page 1155, right column, section 2.3).
Leandro teaches that crossing this animal to obtain a double KO animal GCDH/AASS (page 1157, section 3.3) leads to the rescue of the GCDH KO phenotype, i.e., normalization in glutarylcarnitine and carnitine levels in GCDH-deficient mice (page 1158, section 3.4).
Leandro does not teach a silencing nucleic acid capable of reducing AASS gene expression.
However, Pena teaches that the saccharopine and the pipecolate pathways are linked, are central to lysine catabolism in the body, both converging to the synthesis of α-aminoadipic-δ-semialdehyde (AASA), substrate for ALDH7A1, and piperidine-6-carboxylate (P6C), and also linked to disorders such as pyridoxine dependent epilepsy (PDE), caused by mutations in ALDH7A1, and glutaric aciduria type 1, caused by mutations in GCDH (see Introduction, page 121, and page 122, left column, and Figure 1).
Pena also suggests that inhibition of the enzyme AASS could constitute a new strategy to treat PDE patients and other inherited diseases of lysine catabolism (see Abstract, last three lines).
Perez teaches antisense therapy as a new possible therapeutic option of PDE (see title). Perez teaches the use of antisense morpholino oligonucleotides (AMO) targeted to splice site to correct aberrant splicing caused by mutations in ALGH7A1 exon 1 (see page 242, left column, second paragraph) in patient lymphoblasts (see Figure 3).
Cleveland teaches a nucleic acid molecule that reduces the expression of [Symbol font/0x61]-Aminoadipate ẟ-semialdehyde synthase (AASS) (see title and abstract). Cleveland teaches the use of two plasmids pSilencer4.1-CMVneo and pSilencer4.1-CMVpuro selected for stable expression of short hairpin RNA (shRNA), the sequences used as antisense for interfering with mouse AASS expression (see page 2144, left column, “Materials and Methods” section, “Plasmid construction” paragraph).
Therefore, Cleveland teaches the feasibility of silencing AASS using RNA interference.
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have tried and rescue the phenotype of an animal model for Glutaric aciduria type 1 as taught by Leandro, with an antisense oligonucleotide directed against AASS mRNA as suggested by Pena and taught by Perez and Cleveland. One with ordinary skills in the art motivated in developing a treatment modality that can be applied to human and personalized medicine such as an antisense therapy, could have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding claims 3 and 6, Leandro teaches a glutaric aciduria type 1 model, knocking down glutaryl-CoA dehydrogenase (GCDH) (see title), which is a model of deficiency in GCDH.
Pena teaches that inhibiting AASS enzyme could constitute a strategy not only to treat PDE but also other inherited diseases of lysine catabolism (see abstract).
Perez teaches that antisense therapy against ALDH7A1 gene expression can treat PDE (see title and abstract).
Cleveland teaches decreasing AASS mRNA via RNA interference (see title and abstract).
The description of the combination of references Leandro, Pena, Perez and Cleveland is described above. The combination renders elements of claim 1 obvious, therefore, the elements of claim 3 are also rendered obvious by the combination of references.
Regarding claims 11, 12 and 22, Perez teaches antisense morpholino oligonucleotides that are 25-mer targeting the pre-mRNA; Perez teaches DNA sequences (see page 242, left column, second paragraph).
Cleveland teaches shRNA expressed in two plasmids (see page 2144, left column, “Materials and Methods” section, “Plasmid construction” paragraph).
The description of the combination of references Leandro, Pena, Perez and Cleveland is described above. The combination renders elements of claim 1 obvious, therefore, the elements of claims 11, 12 and 22 are also rendered obvious by the combination of references.
Regarding claim 18, Cleveland teaches a sequence that is a nucleotide sequence that has at least 75% sequence identity to a nucleotide sequence comprised in a mRNA transcribed from AASS; Cleveland teaches 4 sense sequences chosen to design shRNA1, shRNA2, shRNA3 and shRNA4 (see page 2144, left column, “Materials and Methods” section, “Plasmid construction” paragraph).
An alignment of sequences (according to the Specification, AASS mRNA is described in instant SEQ ID NO: 10; see page 6, line 16) with the sense sequences taught by Cleveland shows that the sense sequence of shRNA3 (5’- UCACUGCAAGCTACAUUAC- 3’) is 91.6% identical to SEQ ID NO: 10; see below (Qy = Query: Cleveland’s sense shRNA3; Db = database: instant SEQ ID NO: 10):
Query Match 91.6%; Score 17.4; DB 1; Length 5825;
Best Local Similarity 78.9%;
Matches 15; Conservative 3; Mismatches 1; Indels 0; Gaps 0;
Qy 1 UCACUGCAAGCTACAUUAC 19
:|||:||||||||||: ||
Db 1825 TCACTGCAAGCTACATCAC 1843
The description of the combination of references Leandro, Pena, Perez and Cleveland is described above. The combination renders elements of claim 1 obvious, therefore, the elements of claim 18 are also rendered obvious by the combination of references.
Claims 7-9 are rejected under 35 U.S.C. § 103 as being unpatentable over Leandro (Leandro, J. et al. “Deletion of a-aminoadipic semialdehyde synthase limits metabolite accumulation in cell and mouse models for glutaric aciduria type 1”. Journal of Inherited Metabolic Diseases, Vol, 43 (2020), pp:1154-1164; First published online June 22, 2020, printed November 2020; cited on IDS filed 01/03/2024), in view of Pena (Pena, I.A. et al. “Mouse lysine catabolism to aminoadipate occurs primarily through the saccharopine pathway; implications for pyridoxine dependent epilepsy (PDE)”. Biochemica et Biophysica Acta, Vol. 1863 (2017), pp: 121-128; cited on IDS filed 01/03/2024), Perez (Perez, B. et al. “Clinical, biochemical, and molecular studies in pyridoxine-dependent epilepsy: Antisense therapy as possible new therapeutic option”. Epilepsia, Vol. 54, No. 2 (2013), pp: 239-248) and Cleveland (Cleveland, B.M. et al. “[Symbol font/0x61]-Aminoadipate ẟ-semialdehyde synthase mRNA knockdown reduces the lysine requirement of a mouse hepatic cell line”. The Journal of Nutrition, Vol. 138 (2008), pp: 2143-2147, and cited on IDS filed 01/03/2024), as applied to claim 1 above, and further in view of Sauer (Sauer, S.W. Et al. “Therapeutic modulation of cerebral L-lysine metabolism in a mouse model for glutaric aciduria type I”. Brain, Vol. 134 (2011), pp: 157-170).
Regarding claim 1, the rejection of claim 1 is described above. The elements of claim 1 are rendered obvious by the combination of references Leandro, Pena, Perez and Cleveland.
Regarding claims 7 and 9, Leandro teaches that GA1 is treated by restricting
lysine intake and carnitine supplementation, and emergency treatment (see page 1154, Introduction section, left column).
Cleveland teaches that hyperlysinemia can be caused by a defective AASS enzyme and that hyperlysinemic children consuming a diet deficient in lysine exhibit a decline in plasma lysine concentrations to near-normal levels and under these conditions both growth and development improve (see page 2143, right column). Cleveland teaches that using RNAi to reduce expression of the AASS gene at the mRNA, protein, and protein activity levels, however the reduction is to about 20% of original level for mRNA and only to about 70% for protein levels (see Figure 2). Cleaveland teaches that using RNAi against AASS decreases the nutritional Lysine requirement (see page 2146, right column, third paragraph; and Table 1).
This teaching also suggests that RNAi against AASS mRNA may not be sufficient to obtain complete control over Lysine catabolism.
The combination of references Leandro, Pena, Perez and Cleveland does not render obvious an additional therapeutic regimen in a subject as described in claim 1.
However, Sauer teaches therapeutic modulation of L-lysine metabolism in a mouse model for glutaric aciduria type I (GA1) (see title).
Sauer teaches an animal model of GA1 having hyperlysinemia, a GCDH -/- knock-out mice, and diet intervention to reduce the level of lysine in the brain and liver (see page 159, left column, lines 12-19). Sauer teaches four types of intervention: low L-lysine diet, L-Arginine supplementation, L-carnitine supplementation and clofibrate treatment (see page 159, “Materials and methods”; and “Results” pages 161-165).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have used RNAi against AASS mRNA to reduce its levels in subjects experiencing hyperlysinemia and glutaric aciduria type 1 (GA1) as taught by Leandro modified by Pena, Perez and Cleveland, in a combination therapy further comprising a diet therapy consisting in a lysine-restricted diet as taught by Sauer.
One with ordinary skills in the art motivated in an optimal control of lysine catabolism in subjects in need thereof could have performed this modification to the treatment as suggested by the teachings of Cleveland and as taught by Sauer, with a reasonable expectation of success and would have arrived at the claimed invention.
Regarding claim 8, Leandro teaches that lysine degradation proceeds mainly via the mitochondrial saccharopine pathway and defects in two enzymes cause severe inborn errors of metabolism, PDE, caused by mutations in ALDH7A1 gene, and GA1 caused by mutations in GCDH gene (see “Introduction” section, page 1154). Leandro teaches that PDE is a condition treated by pyridoxine supplementation and lysine-restricted diet, and GA1 is treated by restricting lysine intake and carnitine supplementation (see page 1154, Introduction section).
Pena teaches that mutations in ALDH7A1 result in accumulation of aminoadipic semialdehyde (AASA) and piperidine-6-carboxylate (P6C) (see Introduction section, page 121). Pena also teaches high doses of pyridoxine are used for treatment of PDE ( page 121, Introduction section); pyridoxine is a form of vitamin B6 (according to instant Specification, page 1, line 19).
Perez teaches PDE is controlled pharmacologically with pyridoxine (see page 239, “Summary”, “Purpose” section). Perez also teaches different pyridoxine doses for patients listed in Table 1. Perez teaches that the symptoms of patients were not limited to seizures, with other associated neurological dysfunctions that persist even with early and adequate treatment with pyridoxine (see page 246, left column, last paragraph). Perez concludes that treatment with vitamin B6 is effective for suppressing the seizures and normalizing EEG, but that it is not so effective to ensure normal neurodevelopment (see page 246, right column, last sentence). Perez proposes that antisense therapy may hold promise as a means to rescuing splicing changes in ALDH7A1 thereby avoiding the production of toxic metabolites (see page 247, left column, last paragraph).
Sauer teaches L-Arginine supplementation amplified the biochemical effect of low-lysine diet and inhibits mitochondrial L-lysine uptake (see page 162, left column, second and third paragraphs).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have used RNAi against AASS mRNA to reduce its levels in subjects having a deficiency in ALDH7A1. One with ordinary skills in the art could have substituted the subjects having GA1 for subjects having PDE, since they both experience hyperlysinemia treatable using RNAi against AASS mRNA as taught by the combination of references Leandro, Pena, Perez and Cleveland. Cleveland also teaches that the decrease in mRNA levels of AASS may not be 100%, therefore, unwanted metabolites can still accumulate under RNAi treatment. One with ordinary skills motivated in treating PDE by decreasing AASS expression using RNAi and decreasing the toxic metabolites further, would have considered a multiple modalities treatment, and would have combined a lysine-restricted diet with supplement of vitamin B6/pyridoxine in addition to the RNAi treatment. One with ordinary skills in the art would have performed this modification with a reasonable expectation of success and would have arrived at the claimed invention.
Claims 13-17 and 24 are rejected under 35 U.S.C. § 103 as being unpatentable over Leandro (Leandro, J. et al. “Deletion of a-aminoadipic semialdehyde synthase limits metabolite accumulation in cell and mouse models for glutaric aciduria type 1”. Journal of Inherited Metabolic Diseases, Vol, 43 (2020), pp:1154-1164; First published online June 22, 2020, printed November 2020; cited on IDS filed 01/03/2024), in view of Pena (Pena, I.A. et al. “Mouse lysine catabolism to aminoadipate occurs primarily through the saccharopine pathway; implications for pyridoxine dependent epilepsy (PDE)”. Biochemica et Biophysica Acta, Vol. 1863 (2017), pp: 121-128; cited on IDS filed 01/03/2024), Perez (Perez, B. et al. “Clinical, biochemical, and molecular studies in pyridoxine-dependent epilepsy: Antisense therapy as possible new therapeutic option”. Epilepsia, Vol. 54, No. 2 (2013), pp: 239-248) and Cleveland (Cleveland, B.M. et al. “[Symbol font/0x61]-Aminoadipate ẟ-semialdehyde synthase mRNA knockdown reduces the lysine requirement of a mouse hepatic cell line”. The Journal of Nutrition, Vol. 138 (2008), pp: 2143-2147; cited on IDS filed 01/03/2024), as applied to claim 1 above, and further in view of Setten (Setten, R. L. et al. “The current state and future directions of RNAi-based therapeutics”. Nature Reviews, Vol. 18 (2019), pp: 421-446) and Liu (Liu, L. et al. US 2008/0293142 A1; published November 27, 2008).
The rejection of claim 1 is described above. The elements of claim 1 are rendered obvious by the combination of references Leandro, Pena, Perez and Cleveland.
Regarding claim 17, Cleveland teaches using one shRNA in their composition at a time (see page 2144, right column, first paragraph).
Therefore, regarding claims 13-17 and 24, the combination of references does not render elements of claims 13-17 and 24 obvious, i.e., a modified oligonucleotides comprising 2’-O-methoxyethylribose modified nucleotides (claim 13), 2’-O-methyl modified nucleotides (claim 14), LNA modifications, (claim 15), phosphorothioates modified nucleotides (claim 16), two or more nucleic acid silencing molecules of one stereoisomer (claim 17), and conjugated to one or more non-nucleic acid moieties (claim 24).
However, Setten reviews all of these modifications to oligonucleotides used in RNAi and trends in their designs (see title and abstract; page 422, left column).
Setten teaches examples of modifications LNA, 2’-O-methyl, 2’-O-methoxyethyl, phosphorothioate modifications, for nuclease resistance and stability, as well as conjugation to non-nucleic acid moieties GalNAc for efficient delivery in Figure 3 (page 425).
Setten teaches that selecting stereoisomers using stereoselective phosphorothioate (PS) modifications is possible. Setten teaches that Sp-oriented PS linkages provide better resistance to nuclease cleavage, they also tend to reduce the base-pairing Tm of the flanking base compared with Rp-oriented linkages (see page 436, right column, “Stereoselective phosphorothioate synthesis” section).
Liu teaches design and construction of expression cassettes capable of delivering and expressing multiple shRNAs in one administration (see title and abstract). Liu teaches that it is recommended to screen the most effective siRNA from several potential sites of a given mRNA (see [0021], page 3, first paragraph). Liu also teaches that a single DNA vector expressing multiple shRNAs against different regions of a gene is a new strategy to improve the silencing efficiency (see [0022]).
Therefore, Liu teaches two or more silencing nucleic acid molecules in one composition comprising one expression cassette (see [0022]-[0023]).
Therefore, it would have been obvious to one with ordinary skills in the art before the effective filing date of the claimed invention to have tried and rescued the phenotype of an animal model for Glutaric aciduria type 1 as taught by Leandro, with antisense oligonucleotides directed against AASS mRNA as suggested by Pena and taught by Perez and Cleveland, and modified the oligonucleotide as taught by Setten, adding 2’-O-MOE and 2’-O-Me, LNA and Sp-oriented phosphorothioate linkages modifications. One of ordinary skills in the art motivated in increasing the efficiency of gene silencing by providing multiple silencing molecules targeting different sites of the mRNA could have combined multiple silencing molecules within the same construct as taught by Liu. One with ordinary skills in the art motivated in developing a treatment modality that can be applied to human using serum-stabilized, delivery and efficiency-optimized construct for silencing, could have performed these modifications with a reasonable expectation of success and would have arrived at the claimed invention.
Allowable Subject Matter
Claims 21 and 23 are objected to as being dependent upon a rejected base claim but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDRA G DACE DENITO whose telephone number is (703)756-4752. The examiner can normally be reached Monday-Friday, 8:30-5:00EST.
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/A.D./Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636
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