DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 1-19 are pending.
Preliminary Amendments
Applicant’s preliminary amendment filed on 12/18/2023 is acknowledged. FIG.10 was replaced with replacement sheet FIG. 10.
Applicant’s preliminary amendment filed on 12/04/2024 is acknowledged. The specification was amended to include an unintentionally omitted grant at [0001], i.e., grant W81XWH-19-1-0502 from the Department of Defense.
Applicant’s preliminary amendment filed on 01/14/2026 is acknowledged. The status identifiers of the claims were updated to indicate that claims 14-19 are withdrawn.
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on 01/14/2026 is acknowledged.
Claim(s) 14-19 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group II, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 01/14/2026.
Claims 1-13 are under consideration.
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged. Applicant has not complied with one or more conditions for receiving the benefit of an earlier filing date under 35 U.S.C. 119(e) as follows:
The later-filed application must be an application for a patent for an invention which is also disclosed in the prior application (the parent or original nonprovisional application or provisional application). The disclosure of the invention in the parent application and in the later-filed application must be sufficient to comply with the requirements of 35 U.S.C. 112(a) or the first paragraph of pre-AIA 35 U.S.C. 112, except for the best mode requirement. See Transco Products, Inc. v. Performance Contracting, Inc., 38 F.3d 551, 32 USPQ2d 1077 (Fed. Cir. 1994).
The disclosure of the prior-filed application, Application No. 63/420,923 (hereinafter, ‘923 application), fails to provide adequate support or enablement in the manner provided by 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph for one or more claims of this application.
While the ‘923 application provides support for the genus of instant claim(s) 1 and 9-12, the rest of the ‘923 application fails to provide adequate written description for claims 2-8 and 13. In the ‘923 application at paragraph [0006], the Applicant provides an “Incorporation by Reference” statement to aid in the description of invention. However, “PCU/US2022/074065”, which is being interpreted as “PCT/US2022/074065” is an international application number that corresponds to a WIPO publication, WO 2023/004426 A2 (publication date, 01/26/2023). This WIPO publication’s publicly available date came after the provisional filing date of 10/31/2022. In regard to the other publication “incorporated by reference”, “Welden et al. (“RNA editing of Microtubule associated protein tau circular RNAs promotes their translation and tau tangle formation” Nucleic Acids Res. (in press))” was not publicly available until 12/09/2022, which was after the provisional filing date. Therefore, neither reference being incorporated to support the specification was publicly available before the effective filing date of the ‘923 application.
Thus, the claims have the following effective filing dates:
Claim(s) 1 and 9-12 – 10/31/2022
Claim(s) 2-8 and 13 – 10/31/2023
Information Disclosure Statement
Receipt of the information disclosure statement(s) on 02/01/2024 is acknowledged. The signed and initialed PTO-1449 form(s) has/have been mailed with this action.
Drawings
The drawing (FIG. 10) was received on 12/18/2023. These drawing replacement sheet for FIG. 10 is acceptable.
The drawings are objected to because:
The words in FIG.3C and FIG.3F above the graphs cannot be made out.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, 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 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 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 statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete.
Applicant provided the XML file in KB, not bytes.
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 incorporation by reference paragraph, 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
Abstract
Applicant is reminded of the proper language and format for an abstract of the disclosure.
The abstract should be in narrative form and generally limited to a single paragraph on a separate sheet within the range of 50 to 150 words in length. The abstract should describe the disclosure sufficiently to assist readers in deciding whether there is a need for consulting the full patent text for details.
The language should be clear and concise and should not repeat information given in the title. It should avoid using phrases which can be implied, such as, “The disclosure concerns,” “The disclosure defined by this invention,” “The disclosure describes,” etc. In addition, the form and legal phraseology often used in patent claims, such as “means” and “said,” should be avoided.
The abstract of the disclosure is objected to because (a) “nuclkeotide” is misspelled in line 3 and (b) use of the word “that” twice in lines 4-5, “Targeting the junction ensure that that ds siRNA are limited in targeting the circular RNA produced…”. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
Claim Objections
Claim 7 is objected to because of the following informalities: “…claim 1, wherein the wherein one or more…” It would be remedial to remove “wherein the” from the sentence.
Appropriate correction is required.
Applicant is advised that should claim 10 be found allowable, claim 12 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim(s) 1-13 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more.
Claim(s) 1, 9-10, and 12 recite, “An isolated double stranded (ds) silencing ribonucleic acid (siRNA) comprising a nucleotide sequence comprised of a 3’ terminal nucleic acid from exon 12 of the MAPT gene fused to a 5’ terminal nucleic acid from either exon 7 of the MAPT gene or exon 10 of the MAPT gene.”, (claim 1); “wherein the double strands are two separate annealed strands.”, (claim 9); “wherein the double strands are a self-annealed single strand.”, (claim 10); and claim 12 is a duplicate claim of claim 10. Claim 9 depends on claim 1, claim 10 depends on claim 1, claim 12 is a duplicate of claim 10 which depends on claim 1.
Claim(s) 1, 9-10, and 12 are not markedly different from the product’s naturally occurring counterpart in the natural state. Here, the claimed ds siRNA can exist as, or encompass, a naturally occurring fragment of the circularRNA of exon 12->7 or 12->10 produced from the backsplicing event of the MAPT gene. The “isolated ds siRNA” encompass fragments of naturally occurring nucleotide sequences because genes are double-stranded. Additionally, a manufactured ds siRNA can be considered an equivalent to a synthetic primer and has identical nucleotide sequence as a portion of naturally occurring nucleic acid(s).
Justin R. Welden (Cloning and Functional Characterizations of Circular RNAs from the Human MAPT Locus, Theses and Dissertations – Molecular and Cellular Biochemistry University of Kentucky, 50, pages 1-147, publicly available August 8th, 2022) teaches, “Here we present evidence that the human MAPT locus generates circular RNAs through backsplicing from exon 12 to either exon 10 or 7. Our data show that the regulation of MAPT gene expression and its molecular biology are still incompletely understood, despite numerous studies focusing on alternative splicing of MAPT.. CircRNA formation through backsplicing is facilitated by repetitive elements that form regions of complementarity in the pre-mRNA, allowing to position exons for backsplicing. Human MAPT contains at least 83 Alu elements, 56 on the sense strand and 27 on the antisense strand. Since Alu elements are primate-specific, they could cause a difference in circular RNA formation between mouse and humans.”, (see 20, section 3.18, paragraph 1 and 3). Moreover, Justin R. Welden teaches, “In summary, multiple factors control the occurrence of back-splicing and thus the formation of circRNAs. Most importantly, a double stranded pre-mRNA structure brings back-splicing sites together. Its formation is influenced by the availability of complementary sequences, which in turn are negatively influenced by RNA helicases, ADAR enzymes and single-stranded RNA binding proteins. Factors that influence intron splicing, such as splice site strength, the concentration of SR-proteins and hnRNPs as well as the availability of exon enhancers and silencers also impact on circRNA formation (Figure 2.2G).”, Justin R. Welden demonstrates in Figure 2-1 the Generation of circRNAs through back-splicing, as well as how tau pre-mRNA is processed in Figure 5-1 A-B.
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Thus, the product(s) of claim(s) 1, 9-10, and 12 are not markedly different from its natural counterpart in nature.
Claim(s) 2-4 recite, “wherein the nucleotide sequence comprises 21 nucleotides in length, with up to 20 nucleotides being derived from the 3’ end of exon 12 of the MAPT gene.”, (claim 2); “wherein the nucleotide sequence comprises 21 nucleotides in length, with up to 20 nucleotides being derived from the 5' end of exon 7 of the MAPT gene.”, (claim 3); and “wherein the nucleotide sequence comprises 21 nucleotides in length, with up to 20 nucleotides being derived from the 5' end of exon 10 of the MAPT gene.”, (claim 4). Claims 2-4 depend on claim 1. Claim(s) 2-4 are not markedly different from the product’s naturally occurring counterpart in the natural state because Claycomb (Ancient Endo-siRNA Pathways Reveal New Tricks, Current Biology, Volume 24, Issue 15, Pages R703-R715, Published August 4th, 2014) teaches, “Endogenously produced small interfering RNAs (endo siRNAs, 18–30 nucleotides) play a key role in gene regulatory pathways, guiding Argonaute effector proteins as a part of a functional ribonucleoprotein complex called the RISC (RNA induced silencing complex) to complementarily target nucleic acid. Enabled by the advent of high throughput sequencing, there has been an explosion in the identification of endo-siRNAs in all three kingdoms of life since the discovery of the first microRNA in 1993.”, (see abstract). More specifically, “In both flies and mice, endo-siRNAs have a discrete 21-nt signature.”, (page R704, column 2, paragraph 4; also see Table 1). Thus, the product(s) of claim(s) 2-4 are not markedly different than their natural counterpart in nature.
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Claim(s) 5 and 6 recite, “wherein the nucleotide sequence comprises 21 contiguous nucleotides in length from SEQ ID NO: 28.”, (claim 5) and “wherein the nucleotide sequence comprises a sequence selected from SEQ ID NOs: 8-19 and 29-36.” Claim 5 depends on claim 1 and claim 6 depends on claim 5. Claims 5 and 6 are not markedly different from the product’s naturally occurring counterpart in the natural state because SEQ ID NO: 28 and its varied fragments (SEQ ID NOs: 8-19 and 29-36) can be found in Figure 1E of Welden et al, see marked-up image below. Thus, the product of claim(s) 5 and 6 are not markedly different than their naturally occurring counterparts in nature.
Claim(s) 7 and 8 recite, “wherein the wherein one or more nucleic acids are modified.”, (claim 7), and “wherein the modification includes incorporation of 2'-O-methylation, 2'-0-ethylation, 2'-fluorination, 2'-desoxylation, and/or 5'- phosphorylation, mono-phosphothionate, or di-phosphothionate.”, (claim 8). Claim 7 depends from claim 1 and claim 8 depends from claim 7. Claim(s) 7 and 8 are not markedly different from the product’s naturally occurring counterpart in the natural state because Claycomb teaches, “Interestingly, Drosophila endo-siRNAs are distinguished by a 2’-O-methylmodification at their 3’ end. This modification is catalyzed by the methylase Hen1, and is also found on piRNAs in animals and small RNAs in plants.”, (see, page R704, column 2, paragraph 4; and Table 1). Also, Zlatev et al (5′-C-Malonyl RNA: Small Interfering RNAs Modified with 5′ Monophosphate Bioisostere Demonstrate Gene Silencing Activity, ACS Chem Biol, Vol 11, Pages 953-960, Published December 17th, 2015) teaches, “5′-Phosphorylation is a critical step in the cascade of events that leads to loading of small interfering RNAs (siRNAs) into the RNA-induced silencing complex (RISC) to elicit gene silencing.”, (abstract). Thus, the product of claim(s) 7 and 8 are not markedly different than their naturally occurring counterparts in nature.
Claim 11 recites, “further comprising a spacer of 3 to about 20 unmatching nucleotides in length between a sense portion and an antisense portion.”, (claim 11). Claim 11 depends on claim 10 and claim 10 depends on claim 1. Claim 11 is not markedly different from the product’s naturally occurring counterpart in the natural state because, as mentioned above by Welden et al , “In addition to the well known linear RNAs, pre-mRNAs generate circular RNAs through a backsplicing mechanism, where a downstream 5’ splice site is joined with an upstream 3’ splice site. In most cases, circRNAs are generated when the pre-mRNA forms a loop containing the exons undergoing backsplicing. This loop can be formed by either a large lariat or more commonly through intramolecular RNA base pairing, leading to double stranded RNA regions as short as 30–40 nt in length... Due to their self complementarity Alu elements form extensive double stranded RNA structures in pre-mRNA, which can influence alternative splicing and promote the formation of circRNAs.”, (see page 2753, column 2, paragraph 3 to page 2755, column 1, paragraph 1).
Regarding ds RNA spacers/loops, Groebe and Uhlenbeck (Characterization of RNA hairpin loop stability, Nucleic Acids Research, Vol 16, Iss 24, Pages 11725-11735, published December 23rd, 1988) teach that “Hairpins are the basic units of RNA secondary structure. Although the secondary structure of the 16S RNA can be divided into several large domains, about 70 percent of the molecule consists of 31 small hairpins that vary in sequence and size. A review of 21 16S-like RNA secondary structures from a number of organisms reveals that 268 of the 590 phylogenetically proven RNA hairpins have four nucleotides in the loop. 66 hairpins with eight nucleotides in the loop are the second most common class. Previous thermodynamic studies have determined that the most stable RNA hairpin occurred when six nucleotides were present in the loop.”, (see page 11725-11735, paragraph 2). Thus, the product of claim 11 is not markedly different than their naturally occurring counterparts in nature.
Claim 13 recites, “A lipid nanoparticle comprising the isolated ds siRNA of claim 1 and a lipid membrane.” Claim 13 is dependent on claim 1. Claim 13 is not markedly different from the product’s naturally occurring counterpart in the natural state. He et al (Targeting circular RNAs as a therapeutic approach: current strategies and challenges, Signal Transduction and Targeted Therapy, Vol 6, Issue 185, pages 1-14, published May 21, 2021) discloses, “Exosomes are extracellular vesicles that typically range from 30 to 100nm in diameter. They are secreted from and received by many types of cells to facilitate intercellular communication. Exosomes naturally carry a wide variety of molecules, including circRNAs, miRNAs, long noncoding RNAs, proteins, lipids, and DNA fragments.”, (see page 9, column 1, paragraph 4). Thus, the product of claim 13 is not markedly different from its naturally occurring counterpart in nature.
Therefore, this judicial exception is not integrated into a practical application because claim(s) 1-13 do not include any element in addition to the judicial exception.
Claim(s) 1-13 are rejected under 35 U.S.C. 101 because no inventive concept is provided or more than what is well-known, routine, and conventional in the art. The claimed invention does not have any elements in addition to the judicial exception, therefore, the claims are not directed to a product of nature without significantly more.
Claim Rejections - 35 USC § 102
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) 1-6, 10 and 12 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Welden et al (The human MAPT locus generates circular RNAs, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1864, Issue 9, Part B, Pages 2753-2760, September 2018) as evidenced by Justin R. Welden (Cloning and Functional Characterizations of Circular RNAs from the Human MAPT Locus, Theses and Dissertations – Molecular and Cellular Biochemistry University of Kentucky, 50, pages 1-147, publicly available August 8th, 2022).
Of note: Claim 12 is a duplicate of claim 10, thus art applied to claim 10 is applicable to claim 12.
Welden et al discloses, “The pre-mRNA of MAPT is well studied and its aberrant pre-mRNA splicing is associated with frontotemporal dementia. Using a PCR screen of RNA from human brain tissues, we found that the MAPT locus generates circular RNAs through a backsplicing mechanism from exon 12 to either exon 10 or 7. MAPT circular RNAs are localized in the cytosol and contain open reading frames encoding Tau protein fragments… In summary, we report the identification of new bona fide human brain RNAs produced from the MAPT locus. These may be a component of normal human brain Tau regulation and, since the circular RNAs could generate high molecular weight proteins with multiple microtubule binding sites, they could contribute to taupathies.”, (Abstract). “In addition to the well known linear RNAs, pre-mRNAs generate circular RNAs through a backsplicing mechanism, where a downstream 5’ splice site is joined with an upstream 3’ splice site. In most cases, circRNAs are generated when the pre-mRNA forms a loop containing the exons undergoing backsplicing. This loop can be formed by either a large lariat or more commonly through intramolecular RNA base pairing, leading to double stranded RNA regions as short as 30–40 nt in length…. Due to their self complementarity Alu elements form extensive double stranded RNA structures in pre-mRNA, which can influence alternative splicing and promote the formation of circRNAs.”, (see page 2753, column 2, paragraph 3 to page 2755, column 1, paragraph 1).
Regarding claim(s) 1, 10 and 12, Welden et al discloses, “We concentrated on exon 10, since this exon is alternatively spliced and deregulated in both Alzheimer's disease and FTLD-MAPT. To amplify circular RNAs, we used a reverse primer upstream of the forward primer, i.e. a reverse primer in exon 10 and a forward primer in exon 11, which amplifies circular, but not linear RNAs (Fig. 1A, C)… The bands from RNAse R treated RNA generated by the circular RNA primers were subcloned and sequenced. Two of the bands corresponded to circular RNAs made from exon 12 back splicing, either to exon 10 or 7 (Fig. 1C). The exon sequences present in the linear MAPT mRNA were completely present in the circular RNAs, indicating usage of the linear splice sites. Both circRNAs were divisible by 3 (288, and 681 nt, respectively) and circ12→7 contained an in frame AUG start codon. No AUG start codon was present in circ12→10 (Fig. 1D, E). The other bands contained noncanonical splice sites and thus their mechanism of generation is unclear and they could be PCR artifacts.”, (see page 2755, column 2, paragraph 5-6 to page 2756, column 1, paragraph 1).
Welden et al is silent regarding double-stranded RNA, however, double-stranded RNA is an inherent feature of the MAPT exon 12 [Wingdings font/0xE0] 10 or 12 [Wingdings font/0xE0]7 backsplicing event to form the circularRNA as evidenced by Justin R. Welden (evidentiary document). Justin R. Welden discloses, “Here we present evidence that the human MAPT locus generates circular RNAs through backsplicing from exon 12 to either exon 10 or 7. Our data show that the regulation of MAPT gene expression and its molecular biology are still incompletely understood, despite numerous studies focusing on alternative splicing of MAPT... CircRNA formation through backsplicing is facilitated by repetitive elements that form regions of complementarity in the pre-mRNA, allowing to position exons for backsplicing. Human MAPT contains at least 83 Alu elements, 56 on the sense strand and 27 on the antisense strand. Since Alu elements are primate-specific, they could cause a difference in circular RNA formation between mouse and humans.”, (see 20, section 3.18, paragraph 1 and 3). Moreover, Justin R. Welden teaches, “In summary, multiple factors control the occurrence of back-splicing and thus the formation of circRNAs. Most importantly, a double stranded pre-mRNA structure brings back-splicing sites together. Its formation is influenced by the availability of complementary sequences, which in turn are negatively influenced by RNA helicases, ADAR enzymes and single-stranded RNA binding proteins. Factors that influence intron splicing, such as splice site strength, the concentration of SR-proteins and hnRNPs as well as the availability of exon enhancers and silencers also impact on circRNA formation (Figure 2.2G).”, Justin R. Welden demonstrates in Figure 5-1A-B the double-stranded nature of single-stranded pre-mRNA for the generation of MAPT circRNAs
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through back-splicing and the complementarity of alu elements.
Since the disclosed exons and sequences are the same, the compositions must necessarily exhibit the same properties, including dsRNA. See MPEP 2112.02(II). Accordingly, the feature of a self-annealed single strand forming a dsRNA is considered inherent.
Regarding claim(s) 2-6, Welden et al further discloses a nucleotide sequence comprised of a 3' terminal nucleic acid from exon 12 of the MAPT gene fused to a 5' terminal nucleic acid from either exon 7 of the MAPT gene or exon 10 of the MAPT gene (claim 1); a nucleotide sequence comprises 21 nucleotides in length, with up to 20 nucleotides being derived from the 3' end of exon 12 of the MAPT gene (claim 2); a nucleotide sequence comprises 21 nucleotides in length, with up to 20 nucleotides being derived from the 5' end of exon 7 of the MAPT gene (claim 3); a nucleotide sequence comprises 21 nucleotides in length, with up to 20 nucleotides being derived from the 5' end of exon 10 of the MAPT gene (claim 4); a sequence comprises 21 contiguous nucleotides in length from SEQ ID NO: 28 (claim 5); and nucleotide sequence(s) comprising a sequence selected from SEQ ID NOs: 8-19 and 29-36 (claim 6) (see Welden et al. Fig. 1C-E, Fig. 2B). Fig.1D and Fig. 1E below to highlight sequences.
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Therefore, claim(s) 1-6, 10 and 12 are anticipated by Welden et al as evidenced by Justin R. Welden.
Claim(s) 2-4, 6, and 13 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Justin R. Welden (Cloning and Functional Characterizations of Circular RNAs from the Human MAPT Locus, Theses and Dissertations – Molecular and Cellular Biochemistry University of Kentucky, 50, pages 1-147, publicly available August 8th, 2022).
Justin R. Welden discloses, “Lastly, I show that the circular tau RNAs can be reduced by siRNAs targeting against the backsplice junction preventing translation. The translated protein could be neurotoxic and with the siRNAs specifically targeting the circular and not the linear RNA the siRNAs could be used as a therapeutic drug for Alzheimer’s disease and other tauopathies.”, (Page 2, paragraph 2).
Regarding claim 2 Justin R. Welden discloses, in table 5-1 on page 83, double stranded siRNA of sequence(s) 21 nucleotides in length, and 8 nucleotides from exon 12 in the sense strand for the 12to10 junction and 13 nucleotides from exon 12 in the sense strand for the 12to7 junction (reading on “with up to 20 nucleotides being derived from the 3’ end of exon 12 of the MAPT gene”). (See table 5-1 below).
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Regarding claim(s) 3-4 Justin R. Welden discloses, in table 5-1 on page 83, double stranded siRNA of sequence(s) 21 nucleotides in length, and 11 nucleotides from exon 10 in the sense strand for the 12to10 junction and 6 nucleotides from exon 7 in the sense strand for the 12to7 junction (reading on “with up to 20 nucleotides being derived from the 3’ end of exon 10 (claim 4) or 7 (claim 3) of the MAPT gene”). (See table 5-1 below).
Regarding claim 6, Justin R. Welden discloses, in table 5-1 on page 83, a sequence comprising a sequence selected from SEQ ID NO: 15 (i.e., siRNA 12to7 junction version 3). See table 5-1 below.
Regarding claim 13, Justin R. Welden discloses on page 75, encapsulating the siRNA in a lipid nanoparticle with Lipofectamine 2000 ®. More specifically, “Transient transfection was performed in HEK 293T cells. Cells were plated in a 6-well plate (VWR, 10062-892) at a density of 300,000 cells per well. All of the samples had 200 ng of eGFP for transfection efficiency and loading control. One microgram of the tau expression construct, zkscan 7-12 WT, was mixed with 150 μl of sterile Opti-MEM medium (ThermoFisher Scientific, 31985062). The 12to7 junction siRNA was added to the mix at different concentrations, 0.40 μM, 2 μM, and 4 μM, and then vortexed and incubated at room temperature for 5 minutes. In another tube, 150 μl of sterile Opti-MEM medium and 10 μl of Lipofectamine 2000 (Fisher Scientific, 11668030) were mixed. The two mixtures were combined, vortexed and incubated for 10 minutes at room temperature. After 10 minutes, the media was removed, and the DNA mixture was added to the cells. The cells were incubated for 20 minutes at 37˚C 5% CO2. After 20 minutes, 2 ml of DMEM 10% FBS media were added to the cells and incubated for 24 hrs. After 24hrs, the media was replaced with fresh media for 48 hrs. After 48 hrs, the cells are lysed and analyzed for protein. The same was done for the zkscan 10-12 VM expression construct and 12to10 junction siRNAs. The siRNAs sequences are shown in Table 5.1.”.
Therefore, claim(s) 2-4, 6, and 13 are anticipated by Justin R. Welden.
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.
Claim(s) 7 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Justin R. Welden (Cloning and Functional Characterizations of Circular RNAs from the Human MAPT Locus, Theses and Dissertations – Molecular and Cellular Biochemistry University of Kentucky, 50, pages 1-147, publicly available August 8th, 2022)as applied to claim(s) 2-4, 6, and 13above, in view of Lam et al (siRNA versus miRNA as Therapeutics for Gene Silencing, Molecular Therapy-Nucleic Acids, Vol 4, Pages 1-20, Published September 15th, 2015.
The teachings of Justin R. Welden are describe above and applied as before.
Justin R. Welden does not teach one or more nucleic acid modifications, wherein the modification includes incorporation of 2'-O-methylation, 2'-0-ethylation, 2'-fluorination, 2'-desoxylation, and/or 5'- phosphorylation, mono-phosphothionate, or di-phosphothionate. =
Lam et al teaches gene silencing mechanisms of siRNA and miRNA, stabilizing modifications, and ds siRNA for therapeutic use.
Regarding claim(s) 7 and 8, Lam et al further teaches in the ‘Chemical Modification’ section, “RNAs are extremely vulnerable to serum nucleases. Although double-stranded RNA is more resistant to nuclease degradation than single-stranded RNA, naked RNAs in their unmodified forms are degraded rapidly following administration by the abundant nuclease present in the bloodstream, which contributes to a short half-life in vivo. Poor stability is one of the major obstacles toward the successful application of siRNAs and miRNAs as therapeutic agents. Chemical modifications of RNA were developed initially to address this issue. In addition, chemical modification of the RNA duplexes can minimize immunogenicity and reduce off-target effects…Modification of the ribose 2′-OH group is the most diverse and also the most popular type of modification in RNA duplex design, as the gene silencing activity of siRNAs or miRNAs does not depend on this group. This strategy involves the substitution of the ribose 2′-OH group with other chemical groups, including 2′-O-methyl (2′-O-Me), 2′-fluoro (2′-F) and 2′-methoxyethyl (2′-O-MOE) (Figure 3), and can effectively enhance the stability of the RNA duplex in serum. In particular, substitutions with 2′-O-Me and 2′-F are the two most extensively studied modifications in siRNA. Although these modifications are generally well-tolerated at most siRNA positions, extensive or full modification may lead to significant loss of silencing efficiency. By alternating 2′-O-Me and 2′-F substitutions in a fully substituted siRNA, nuclease-resistant and highly potent modified siRNA can be produced. Bulky substitution such as 2′-O-MOE may enhance nuclease resistance, but is poorly tolerated in terms of activity.”, (page 7, column 1, paragraph(s) 1 and 4; and Figure 3).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the siRNA for targeting the backsplice junction of exons 12[Wingdings font/0xE0] 10 or 12[Wingdings font/0xE0]7, as disclosed by Justin R. Welden, by incorporating a 2′-O-methyl (2′-O-Me) or 2′-fluoro modification to yield the predictable results of enhancing the stability of the RNA duplex in serum, increasing nuclease resistance, and increasing potency, as taught by Lam et al.
Thus, claim(s) 7 and 8 are unpatentable over Justin R. Welden in view of Lam et al.
Claim(s) 11 is rejected under 35 U.S.C. 103 as being unpatentable over Welden et al (The human MAPT locus generates circular RNAs, Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease, Volume 1864, Issue 9, Part B, Pages 2753-2760, September 2018) as applied to claim(s) 1-6, 10 and 12 above, in view of Wilusz (Repetitive elements regulate circular RNA biogenesis, Mob Genet Elements, Vol 5, Issue 3, Pages 39-45, Published May 21st, 2015).
The teachings of Welden et al are describe above and applied as before.
Welden et al does not teach wherein the dsRNA, a self-annealed single strand, further comprises a spacer of 3 to about 20 unmatching nucleotides in length between the sense portion and antisense portion.
Wilusz teaches, “In most cases, circular RNA biogenesis appears to be initiated when complementary sequences from 2 different introns base pair to one another. This brings the splice sites from the intervening exon(s) into close proximity and facilitates the backsplicing event that generates the circular RNA. As many pre-mRNAs contain multiple intronic repeats, distinct circular transcripts can be produced depending on which repeats base pair to one another.”, (abstract).
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Regarding claim 11, Wilusz teaches the minimal intronic elements/mismatches sufficient to for human ZKSCAN1 to form circular RNA. Moreover, Wilusz teaches a 3 basepair spacer, in Figure 2, between the sense and antisense strands of dsRNA that is a self-annealed single strand. Moreover, Wilusz teaches, “Complicating the regulation of circular RNA biogenesis is the fact that introns commonly contain multiple repetitive elements. Depending on how the complementary sequences base pair to one another, very different splicing patterns can result (Fig. 3A). When base pairing occurs across different introns (as discussed above), backsplicing is induced and the intervening exon(s) form a circular RNA (Fig. 3B). If base pairing instead occurs between repeats within a single intron, canonical splicing occurs and a linear mRNA is produced (Fig. 3C). The expression of a given circular RNA can thus be largely controlled by competition for base pairing between the various complementary sequences. The number of repeats, their degree of homology, and the distance between them are likely all key determining factors. Furthermore, this competition allows multiple circular RNAs to be generated from a single protein-coding gene (Fig. 3D).”, (see page 41, column 3, paragraph 2).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the single stranded pre-mRNA that forms dsRNA, as taught by Welden et al, to contain a three basepair spacer between the sense and antisense region of the intronic alu elements, as taught by Wilusz, to yield the predictable results of containing the minimal intronic elements/mismatches sufficient to form MAPT circular RNA. One would be motivated to do so as a way to allow for multiple circular RNAs to be generated from a single protein-coding gene, as taught by Wilusz.
Accordingly, claim 11 is unpatentable over Welden et al in view Wilusz.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claim(s) 1-10, and 12 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim(s) 3 and 6-8 of copending Application No. 18/291,367 (reference application- hereinafter ‘367). Although the claims at issue are not identical, they are not patentably distinct from each other because:
Claim 3 of the ‘367 application is drawn to “The isolated ds siRNA, “to silence the expression of a backsplice circular RNA (circRNA) from exon 12 of the MAPT gene comprising a fragment of exon 12 and a fragment of the backspliced exon”, “comprising between 17 and 22 contiguous nucleic acids from SEQ ID NO: 1 and/or SEQ ID NO:39”, wherein the contiguous nucleic acids comprise at least one nucleic acid from exon 12 and one nucleic acid from either exon 10 or exon 7.”, (Claim 3 is dependent on claim 2, which is dependent on claim 1).
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SEQ ID NO:39 has 100% sequence similarity to instant SEQ ID NO: 28 (of instant claim 5). Instant SEQ ID NOs: 8-19 and 29-36 are made up of 21 nucleotide fragments of SEQ ID NO: 28.
Thus, claim 3 of ‘367 anticipates instant claim(s) 1-6.
Claim 6 of the ‘367 application is drawn to “The isolated ds siRNA, “to silence the expression of a backsplice circular RNA (circRNA) from exon 12 of the MAPT gene comprising a fragment of exon 12 and a fragment of the backspliced exon”, “comprising between 17 and 22 contiguous nucleic acids from SEQ ID NO: 1 and/or SEQ ID NO:39”, wherein one or more nucleic acids are modified.
Claim 6 anticipates instant claim(s) 7-8.
Claim 7 of the ‘367 application is drawn to “The isolated ds siRNA, “to silence the expression of a backsplice circular RNA (circRNA) from exon 12 of the MAPT gene comprising a fragment of exon 12 and a fragment of the backspliced exon”, wherein the double strands are two separate annealed strands.”
Claim 7 anticipates instant claim 9.
Claim 8 is drawn to “The isolated ds siRNA, “to silence the expression of a backsplice circular RNA (circRNA) from exon 12 of the MAPT gene comprising a fragment of exon 12 and a fragment of the backspliced exon”, wherein the double strands are a self-annealed single strand.”
Claim 8 of ‘367 anticipates instant claim(s) 10 and 12.
Claim 11 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 8 of copending Application No. 18/291,367 (reference application- hereinafter ‘367) in view of ThermoFisher Scientific (siRNA Design Guidelines | Technical Bulletin #506; Crawled by WayBackMachine on December 11th, 2015).
Claim 8 of ‘367 is drawn to “The isolated ds siRNA, “to silence the expression of a backsplice circular RNA (circRNA) from exon 12 of the MAPT gene comprising a fragment of exon 12 and a fragment of the backspliced exon”, wherein the double strands are a self-annealed single strand.”
Claim 8 of ‘367 does not require a spacer of 3 to about 20 unmatching nucleotides in length between the sense portion and antisense portion.
ThermoFisher Scientific teaches, “Various research groups have reported successful gene silencing results using hairpin siRNAs with loop size ranging between 3 to 23 nucleotides.”, (Under section – Length and Sequence of the Loop Linking Sense and Antisense Strands of Hairpin siRNA).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the ds siRNA of claim 8 from ‘367 to contain a loop size (reading on spacer) between 3 and 23 nucleotides to yield the predictable results of successful gene silencing, as taught by ThermoFisher Scientific.
Thus, instant claim 11 is unpatentable over claim 8 of ‘367 in view of ThermoFisher Scientific.
These are provisional nonstatutory double patenting rejection(s) because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims allowable.
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/L.M.T./Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637