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
Claims 1, and 62-120 are pending.
Applicant’s election with traverse of Group III (claims 97-120) in Remarks file 1/14/26 is acknowledged. Applicant’s traversal argument is on the grounds that Aznarez does not disclose identifying retained introns 5, 8, 9, 12, 13, and/or 14 and that the teachings of retained introns in Aznarez do not extend to introns 5, 8, 9, 12, 13, and/or 14. Applicant’s further argue that the secondary reference, Michaud, fails to teach or suggest the claimed antisense oligonucleotides. Applicant’s arguments have been thoroughly reviewed and found unpersuasive. In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See the §103 below for the explanation of the combination of references sufficient for one skilled in the art to be motivated to modify the cited references to make the claimed invention. See also In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Furthermore, “Obviousness can be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so. In re Kahn, 441 F.3d 977, 986, 78 USPQ2d 1329, 1335 (Fed. Cir. 2006) (discussing rationale underlying the motivation-suggestion-teaching test as a guard against using hindsight in an obviousness analysis). A "motivation to combine may be found explicitly or implicitly in market forces; design incentives; the ‘interrelated teachings of multiple patents’; ‘any need or problem known in the field of endeavor at the time of invention and addressed by the patent’; and the background knowledge, creativity, and common sense of the person of ordinary skill." Zup v. Nash Mfg., 896 F.3d 1365, 1371, 127 USPQ2d 1423, 1427 (Fed. Cir. 2018) (quoting Plantronics, Inc. v. Aliph, Inc., 724 F.3d 1343, 1354 [107 USPQ2d 1706] (Fed. Cir. 2013) (citing Perfect Web Techs., Inc. v. InfoUSA, Inc., 587 F.3d 1324, 1328 [92 USPQ2d 1849] (Fed. Cir. 2009) (quoting KSR, 550 U.S. at 418-21)).”
Applicant elects, without traverse, the species of:Species I: intron 8.
Species II: specific SynGAP1 associated disorder of “intellectual disability”.
Species III: antisense oligonucleotide binding specific target of an intron splicing silencer (ISS).
Species IV: the specific ISS position +17-28.
Species V: the target region span of the retained intron position +4-35.
Species VI: SEQ ID NO: 93, wherein the antisense oligonucleotide is at least 70% complementary to the target region, comprises at least 8 contiguous nucleobases that are 100% complementary to the target region, and consists of from 8 to 50 nucleobases.
Species VII: about every 3 months.
Claims 1, 62-96, 102, and 106-111 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.
Examination on the merits commences on claims 97-102, 104, 105, and 112-120.
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.
Claim(s) 97 and 120 are rejected under 35 U.S.C. 103 as being unpatentable over Aznarez (Aznarez, I., WO 2017/106377 A1) in view of Michaud (Michaud, J., WO-2010051632-A1).
Regarding claims 97 and 120, Aznarez teaches methods of treating a MRD5 in a subject by increasing the expression of a target protein or functional RNA by cells of the subject [0005]. Aznarez teaches wherein the cells have a retained-intron- containing pre-mRNA (RIC pre-mRNA), the RIC pre-mRNA comprising a retained intron, an exon flanking the 5' splice site, an exon flanking the 3' splice site, and wherein the RIC pre-mRNA encodes the target protein or functional RNA [0005]. Aznarez teaches wherein the method comprises contacting the cells of the subject with an antisense oligomer (ASO) complementary to a targeted portion of the RIC pre-mRNA encoding the target protein or functional RNA, whereby the retained intron is constitutively spliced from the RIC pre-mRNA encoding the target protein or functional RNA, thereby increasing the level of mRNA encoding the target protein or functional RNA and increasing the expression of the target protein in the cells of the subject [0005]. Aznarez teaches this design and use of antisense oligonucleotides (ASO) targeting pre-mRNA retaining introns 15, 18 and 19 of SynGAP1 the gene (Claim 1, Examples 1-3 and Figure 4 and 6). Aznarez teaches the ASO designed using the ASO walk method (moved every 5 nucleotide intervals), including 18-mers, 2 'O-Me, and PS modifications (Example 2, Figures 4 and 6). Aznarez teaches ASOs increase gene expression in cell lines when transfected, demonstrating ASOs used to improve splicing efficiency of retained introns in SynGAP1 (Example 4). Aznarez teaches the use of these oligonucleotides for treatment of disorders associated with mutations in SynGAP1. Aznarez further demonstrates that ASOs significantly improved splicing efficiency, e.g. targeting +36 to +41 region of intron 18 (Figure 7E).
Aznarez does not disclose specifically targeting intron 8 for increasing SynGAP1 expression.
However, Michaud teaches antisense oligonucleotide to SynGAP1 with 100% identity to the claimed introns. For example, Michaud teaches SEQ ID NO: 31 is a 20-mer, complementary to SEQ ID NO: 121 of the present application and spanning the position +58-77 of intron 8 (See Table 2: Primer pairs used for PCR amplification of SYNGAP1 exons and their intronic junctions) [00119].
A person skilled in the art, when solving the problem of increasing SynGAP1 expression, would have been motivated to apply the method of Aznarez to other known retained introns in SynGAP1 and combine an ASO such as disclosed by Michaud in order to target SYNGAP1 intron 8 for improved splicing efficiency. Aznarez performed RNA sequencing of SynGAP1, yielding RNA-seq data and nuclear components (see Figure 3, cytoplasmic for upper track and nuclear for lower track). Therefore, one of skill in the art, upon reviewing RNA-seq data, would appreciate that other introns are also retained. Relative to exon sequences, there were observable RNA-seq reads aligned to introns 5, 8, 9, 12, 13, and 14 (within boxes noted in FIG. 3). For example, the read density for introns 8, 9 and 12 was comparable to intron 19 and higher than introns 15 and 18 studied for Aznarez. Thus, these introns would appear as distinct targets, likely suitable for regulation of SynGAP1 expression. In addition, the sequencing data for Aznarez was aligned to NM_006772.2 (NCBI Reference Sequence for SynGAP1, as used in this instant application) and was identical to the data for NM_006772. 2. Thus, it would be apparent to those skilled in the art that there were a number of other retained introns in SynGAP1 and therefore those skilled in the art would be motivated to apply the method of Aznarez to the claimed intron 8 with reasonable expectations of success to arrive at the claimed invention.
Claim(s) 98-102, 104, 105, and 112-119 is/are rejected under 35 U.S.C. 103 as being unpatentable over Aznarez (Aznarez, I., WO 2017/106377 A1) in view of Michaud (Michaud, J., WO-2010051632-A1) applied to claim 97, and in further view of Hua (Hua, Yimin, et al. "Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice." The American Journal of Human Genetics 82.4 (2008): 834-848.) and Piva (Piva, Francesco, et al. "SpliceAid 2: a database of human splicing factors expression data and RNA target motifs." Human mutation 33.1 (2012): 81-85.) and Khvorova (Khvorova, A., US-7820809-B2, 2010).
The teachings of Aznarez and Michaud as applied above for claim 97 are incorporated here.
Regarding claim 98-102, 104 and 105, Aznarez and Michaud do not teach rationally designed intron-targeting ASOs wherein the ASO binds to an intron splicing silencer (ISS) at positions +17-28 relative to the 5' splice site of intron 8 and the target region spans positions +4-35 and which is recognized by a heterogeneous nuclear ribonucleoproteins (hnRNP) and wherein the hnRNP is hnRNPA1.
However, Hua and Piva teach rational design systems for arriving at predicted ISS targeting ASOs such as in the claimed invention.
Hua teaches an antisense oligonucleotide (ASO)-tiling method of systematically screening the proximal intronic regions flanking exon 7 and identified two intronic splicing silencers (ISSs): one in intron 6 and a recently described one in intron 7 (abstract). Hua analyzed the intron 7 ISS by mutagenesis, coupled with splicing assays, RNA-affinity chromatography, and protein overexpression, and found two tandem hnRNPA1/A2 motifs within the ISS that are responsible for its inhibitory character (abstract). Therefore, Hua teaches the importance of the role of the ISS and the splice repressors hnRNPA1 and hnRNP I on the splicing mechanism.
Piva teaches SpliceAid 2, a database of human splicing factors expression data and RNA target motifs, to foresee the splicing pattern alteration, to guide the identification of the molecular effect due to the mutations, and to understand the tissue-specific alternative splicing (abstract). Examiner notes the instant application Specification employs these design systems for their ASO generation protocols (Specification pg 38, Example 3, Sections A-D).
Regarding claims 104 and 105, Aznarez and Michaud do not teach wherein the antisense oligonucleotide sequence comprising at least 8 contiguous nucleotides from SEQ ID NO: 93.
Khvorova teaches oligonucleotide sequences for gene modulation, SEQ ID NO: 1015942 with 74.4% identity, 93% local similarity, and 14 contiguous matches to the instant elected SEQ ID NO: 93 targeting SynGAP1.
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It would have been obvious before the effective filing date of the claimed invention for a skilled artisan to have been motivated to employ the methods of targeting an intronic splicing silencer (ISS) with hnRNPA1/A2 motifs taught by Hua and combined the guidance from the SpliceAid 2 database design tool taught by Piva of rational design of ASO in order to modify the ASO teachings of the intron 8 targeting ASO of Aznarez and Michaud to target SYNGAP1 intron 8 for improved splicing efficiency as described in the 103 rejection above applied to claim 97, to arrive at the claimed ASO with predictable success for effective ASO that binds to an intron splicing silencer (ISS) at positions +17-28 where the intron 8 target region spans from +4-35 and is recognized by a heterogeneous nuclear ribonucleoproteins (hnRNP), wherein the hnRNP is hnRNPA1, and wherein the ASO has at least 8 contiguous nucleotides of instant SEQ ID NO: 93. Hua and Piva teach effective ASO rational design systems and Khvorova teaches the existing known sequence for targeting the claimed region of SYNGAP1.
Regarding claims 112-114, Khvorova teaches the 15 base oligonucleotide sequence for gene modulation, SEQ ID NO: 1015942 with 74.4% identity, 93% local similarity, and 14 contiguous matches to the instant elected SEQ ID NO: 93 targeting SynGAP1.
Regarding claim 115, Khvorova teaches the oligonucleotides of the invention as containing modifications (12 lines 8-20).
Regarding claim 116, Khvorova (12 lines 8-20) and Michaud [00142] teach the oligonucleotides of the invention as containing modifications of the backbone or a modification of a ribose sugar.
Regarding claim 117, Khvorova (12 lines 8-20) and Michaud [00142] teach the oligonucleotides of the invention as containing 2'-MOE modifications.
Regarding claim 118, Khvorova (12 lines 8-20) and Michaud [00142] teach the oligonucleotides of the invention as containing a backbone that comprises phosphorothioates.
Regarding claim 119, Michaud [00142] teaches the an ASO or one or more component of any ASO may be modified to enhance binding affinity to a target sequence on a pre-mRNA transcript; reduce binding to any non-target sequence; reduce degradation by cellular nucleases such as RNase H.
Conclusion
All claims are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JOHN CHARLES MCKILLOP whose telephone number is (703)756-1089. The examiner can normally be reached Mon-Fri 8:30-5:30.
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/JOHN CHARLES MCKILLOP/Examiner, Art Unit 1637
/EKATERINA POLIAKOVA-GEORGANTAS/Primary Examiner, Art Unit 1637
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