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 .
Applicant’s response of 02/25/2026 has been received and entered into the application file.
Claims 1, 2, 13-15, 18, and 25 were amended in the claim set filed 02/25/2026.
Claims 3, 5, and 17 were cancelled in the claim set filed 02/25/2026.
Accordingly, claims 1, 2, 4, 6-16, and 18-25 are pending and under consideration.
Status of Prior Objections/Rejections
RE: Claim Objections
►Claims 1, 15, 17, and 25 were previously objected to for various informalities.
The amendments to the instant claim set have obviated the basis of the objections of record. The objections of record are hereby withdrawn.
However, new objections are set forth below.
RE: Improper Markush Rejection
►Claim 17 was previously rejected on the basis that it contains an improper Markush grouping of alternatives.
The cancellation of claim 17 has rendered the rejection thereof moot. The Examiner notes that the subject matter of claim 17 has been incorporated into amended instant claim 13.
RE: Claim Rejections - 35 USC § 112
►Claims 1-25 were previously rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement.
The cancellation of claims 3, 5, and 17 renders the rejection thereof moot.
The amendments to instant claim 1 have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
►Claims 13 and 17 were previously rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The cancellation of claim 17 renders the rejection thereof moot.
Applicant has traversed the rejection of record, asserting that the application demonstrates a remarkable success rate when AONs are split according to the three disclosed splitting strategies, all of which achieved successful RNA editing 100% of the time. Applicant further asserts that while the genetic disorders recited in claim 13 have varied mechanisms of pathogenesis, claim 13 is not directed to any and all variants of each one of the claimed genetic disorders. Per Applicant, claim 13 relates to the treatment of genetic disorders in which the genetic disorder is caused by a mutation involving the appearance of an adenosine, and in which deamination of that adenosine to an inosine would alleviate, prevent, or ameliorate the disorder. Applicant provides Examples within the instant specification that target APP and asserts that the art provides specific tests to evaluate ADAR-mediated gene editing in other genetic disorders. Thus, Applicant asserts that undue experimentation would not have been required for a person of ordinary skill in the art to make and use the claimed Editing AON-Helper AON sets in the methods of claim 13 in light of the detailed description in the specification and state of the art.
In response, while Applicant’s arguments have been fully considered, they are not found persuasive.
Regarding Applicant’s assertion that claim 13 relates to the treatment of genetic disorders in which the genetic disorder is caused by a mutation involving the appearance of an adenosine, and in which deamination of that adenosine to an inosine would alleviate, prevent, or ameliorate the disorder, the Examiner notes that the amended instant claim language does not limit the variants of the claimed genetic disorders, as the composition of claim 1 is explicitly drawn to targeting of adenosines to deaminate the same into inosines. Therefore, the amended limitation of “wherein the method comprises the deamination of a target adenosine into an inosine” does not further limit the diseases to be treated via the claimed method, as the composition of claim 1 is explicitly drawn to targeting of adenosines to deaminate the same into inosines.
Additionally, as set forth in the previous action, the instant claim set encompasses a wide range of genetic disorders with highly variable mechanisms of pathogenesis, even within the disease itself. For example, specific types of cancer (which is broadly claimed to be treatable via the instantly claimed method at amended claim 13) such as Acute Myeloid Leukemia, generally present with heterogenous genetic and molecular signatures, meaning treatment and prognosis vary widely-even as they relate to a single type of cancer (reviewed in Prada-Arismendy et al., 2017; of record). Even diseases with consistent mechanisms of pathogenesis, such as CADASIL, remain life-threatening and disabling diseases without any therapies available to limit disease progression (reviewed in Bersano et al., 2017). Even diseases such as Hurler disease and Hunter disease (which are 2 of the 7 types of mucopolysaccharidoses) that are known to be treatable to at least some extent with therapies such as enzyme replacement therapy and/or hematopoietic cell transplantation are not necessarily easily treatable with gene-based therapies. As reviewed in van den Broek et al., 2020 the tissues most impacted by these diseases are “hard to reach” with known therapies due to tissue-specific barriers such as the blood brain barrier, the blood-retina barrier and including, in some cases, avascularity. These barriers to treatment are disclosed to not be specific to Hurler disease, Hunter disease, or even mucopolysaccharidoses-they also apply to other metabolic diseases in which systemic treatments are not sufficient to completely cure the disease. van den Broek et al., 2020 discloses that other diseases suffering from the same barriers to treatment include Niemann-Pick disease, Tay-Sachs disease, Pompe disease, and Gaucher disease, all of which are claimed (see “conclusions” of van den Broek et al., 2020).
In view of the breadth of diseases claimed to be treatable via the method of amended claim 13, lack of supporting working examples in the instant specification, and lack of support for treatment of diseases such as CADASIL in the prior art, amended claim 13 is not considered to be fully enabled. Accordingly, the rejection of record is hereby maintained, with greater detail set forth below.
RE: Claim Rejections - 35 USC § 112(b)
►Claim 25 was previously 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.
The amendments to instant claim 25 have obviated the basis of the rejection of record. The rejection of record is hereby withdrawn.
RE: Claim Rejections - 35 USC § 103
►Claims 1-24 were previously rejected under 35 U.S.C. 103 as being unpatentable over WO 2017/220751 A1 (hereinafter Turunen; as cited in the IDS filed 09/14/2023) in view of WO 2016/097212 A1 (hereinafter Klein; as cited in the IDS filed 09/14/2023), Merkle et al., 2019 (as cited in the IDS filed 09/14/2023), and Woolf et al., 1995 (as cited in the IDS filed 09/14/2023).
►Claim 25 was previously rejected under 35 U.S.C. 103 as being unpatentable over WO 2017/220751 A1 (hereinafter Turunen; as cited in the IDS filed 09/14/2023) in view of WO 2016/097212 A1 (hereinafter Klein; as cited in the IDS filed 09/14/2023), Merkle et al., 2019 (as cited in the IDS filed 09/14/2023), and Woolf et al., 1995 (as cited in the IDS filed 09/14/2023) as applied to claim 13 above, and further in view of Chang et al., 2018 and Jonsson et al., 2012.
The cancellation of claims 3, 5, and 17 renders the rejection thereof moot.
Applicant has traversed the rejections of record, asserting that both Merkle and Klein disclose AONs comprising a targeting/editing portion and an ADAR recruiting stem-loop portion. Applicant asserts that separating the single-stranded antisense oligonucleotides into Turunen into targeting and recruiting portions for individual administrations, as disclosed in Klein, would require excising a portion of Turunen’s AON corresponding to the targeting/editing portion of the AON and coupling it to a stem-loop portion such as those disclosed in Klein and Merkle, thereby generating a self-complementary AON, not one that is complementary to the target RNA as in the claimed Helper AON.
In response, while Applicant’s arguments have been fully considered, they are not found persuasive. The AONs of Turunen explicitly do not form an intramolecular hairpin or stem-loop structure, nor do they comprise a non-complementary portion, yet they are capable of recruiting endogenous ADAR enzymes (abstract; page 3, line 30-page 4, line 4). The Examiner’s rationale relies on the disclosure of Turunen to establish that ADAR enzymes may be recruited by single-stranded AONs that do not form an intramolecular hairpin or stem-loop structure and that are complementary to the targeted region. The disclosure of Klein is relied upon to establish that targeting and recruiting portions of such AON-based systems may be separated and administered consecutively while maintaining function thereof.
While Applicant asserts that it would have been unpredictable whether a split AON would be able to recruit ADAR and/or to edit a target RNA, this is not found persuasive for the reasons set forth above. Although none of the cited art individually discloses the instantly claimed invention in its entirety, as set forth above, Turunen discloses that single-stranded AONs that are complementary to the targeted region successfully recruit ADAR for targeted editing, while Klein discloses that targeting and ADAR-recruiting portions of AONs are separable and maintain their respective functions. Therefore, it would have been predictable that splitting the longer, single-stranded AONs of Turunen (lengths up to 100 nucleotides are disclosed at page 18, lines 19-28) as taught in Klein would recruit ADAR for targeted deamination.
Accordingly, the rejections of record are hereby maintained, with the grounds of rejection updated as necessitated by amendment as set forth in greater detail below.
New/Maintained Grounds of Objection/Rejection
Claim Objections
Claim 18 is objected to because of the following informalities:
Regarding claim 18, item (iv) of instant claim 18 recites “the Helper AON is complementary to a sequence of nucleotides in the target RNA that is separate from the sequence of nucleotides that are complementary to the Editing AON” (bolded emphasis added), which is grammatically improper. As is also recited in item (iv) of instant claim 18, a sequence of nucleotides is complementary to a sequence (bolded emphasis added). It would be remedial to amend the instant claim language to recite “the sequence of nucleotides that is complementary to the Editing AON” (bolded emphasis added).
Appropriate correction is required.
Applicant is advised that should amended claim 1 be found allowable, amended claim 18 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). The amendments to instant claim 1 render it indistinguishable from amended instant claim 18.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claim 13 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Enablement is considered in view of the Wands factors (MPEP 2164.01(A)). These include: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, and the quantity of experimentation needed to make or use the invention. All of the Wands factors have been considered with regard to the instant claims, with the most relevant factors discussed below.
Nature of the invention: Claim 13 is drawn to a method of treating genetic disorders in a subject in need thereof, including Cystic fibrosis, Hurler Syndrome, alpha-1-antitrypsin (A1AT) deficiency, Parkinson’s disease, Alzheimer’s disease, albinism, Amyotrophic lateral sclerosis, Asthma, β-thalassemia, CADASIL, Charcot-Marie-Tooth disease, Chronic Obstructive Pulmonary Disease (COPD), Distal Spinal Muscular Atrophy (DSMA), Duchenne/Becker muscular dystrophy, (Dystrophic) Epidermolysis bullosa, Fabry disease, Factor V Leiden associated disorders, Familial Adenomatous Polyposis, Galactosemia, Gaucher’s Disease, Glucose-6-phosphate dehydrogenase deficiency, Haemophilia, Hereditary Hemochromatosis, Hunter Syndrome, Huntington’s Disease, Inflammatory Bowel Disease (IBD), Inherited polyagglutination syndrome, Leber Congenital Amuaurosis, Lesch-Nyhan syndrome, Lynch syndrome, Marfan syndrome, Mucopolysaccharidosis, Muscular Dystrophy, Myotonic dystrophy type I or II, neurofibromatosis, Niemann-Pick disease type A, B, or C, NY-eso1 related cancer, Peutz-Jeghers Syndrome, Phenylketonuria, Pompe’s disease, Primary Ciliary Disease, Prothrombin mutation related disorders, Pulmonary Hypertension, (autosomal dominant) Retinitis Pigmentosa, Sandhoff Disease, Severe Combined Immune Deficiency Syndrome (SCID), Sickle Cell Anemia, Spinal Muscular Atrophy, Stargardt disease, Tay-Sachs Disease, Usher syndrome, X-linked immunodeficiency, Sturge-Weber Syndrome, or cancer.
Breadth of the claims: Amended claim 13 is broadly drawn to the treatment of a wide range of genetic disorders with highly variable mechanisms of pathogenesis. For example, Alzheimer’s disease is a neurodegenerative disease (reviewed in Bennett et al., 2019; of record); whereas, asthma (also recited in claim 17) is characterized by airway inflammation that is influenced by a number of inflammatory mediators (reviewed in Isidoro-García and Dávila, 2007; of record). Additionally, cancer is known to be a multifactorial disease with both intrinsic and non-intrinsic risk factors (reviewed in Wu et al., 2018; of record). In fact, even specific types of cancer, such as Acute Myeloid Leukemia, generally present with heterogenous genetic and molecular signatures, meaning treatment and prognosis vary widely-even as they relate to a single type of cancer (reviewed in Prada-Arismendy et al., 2017; of record). The instant claim set recites more than 50 genetic diseases that are purportedly treatable with the antisense oligonucleotides of the instant invention. However, when considering just 3 of the claimed genetic diseases (Alzheimer’s disease, asthma, and cancer), it will be appreciated by one of ordinary skill in the art that these diseases have highly variable causes (some of which may be multifactorial and not simply genetic) with associated mechanisms of pathogenesis that are also highly variable. When extrapolating these considerations to the over 50 genetic diseases recited in amended instant claim 13, one of ordinary skill in the art will appreciate that the complex nature of the subject matter of this invention is greatly exacerbated by the breadth of the claims.
Guidance of the specification and existence of working examples: While the specification envisions treatment of Cystic fibrosis, Hurler Syndrome, alpha-1-antitrypsin (A1AT) deficiency, Parkinson’s disease, Alzheimer’s disease, albinism, Amyotrophic lateral sclerosis, Asthma, β-thalassemia, CADASIL, Charcot-Marie-Tooth disease, Chronic Obstructive Pulmonary Disease (COPD), Distal Spinal Muscular Atrophy (DSMA), Duchenne/Becker muscular dystrophy, (Dystrophic) Epidermolysis bullosa, Fabry disease, Factor V Leiden associated disorders, Familial Adenomatous Polyposis, Galactosemia, Gaucher’s Disease, Glucose-6-phosphate dehydrogenase deficiency, Haemophilia, Hereditary Hemochromatosis, Hunter Syndrome, Huntington’s Disease, Inflammatory Bowel Disease (IBD), Inherited polyagglutination syndrome, Leber Congenital Amuaurosis, Lesch-Nyhan syndrome, Lynch syndrome, Marfan syndrome, Mucopolysaccharidosis, Muscular Dystrophy, Myotonic dystrophy type I or II, neurofibromatosis, Niemann-Pick disease type A, B, or C, NY-eso1 related cancer, Peutz-Jeghers Syndrome, Phenylketonuria, Pompe’s disease, Primary Ciliary Disease, Prothrombin mutation related disorders, Pulmonary Hypertension, (autosomal dominant) Retinitis Pigmentosa, Sandhoff Disease, Severe Combined Immune Deficiency Syndrome (SCID), Sickle Cell Anemia, Spinal Muscular Atrophy, Stargardt disease, Tay-Sachs Disease, Usher syndrome, X-linked immunodeficiency, Sturge-Weber Syndrome, or cancer with the antisense oligonucleotides of the instant application, the only disclosed working examples target mouse APP RNA with a limited number of disclosed antisense sequences (see examples 1-5). However, not even these examples disclose any tested or otherwise envisioned treatment of any claimed disease. While the examiner notes that APP RNA is known to be of interest to those developing treatments for Alzheimer’s disease (reviewed in Jonsson et al., 2012 and Chang et al., 2018-set forth in greater detail below; of reocrd), the specification is silent as to the applicability of the disclosed mouse APP RNA-targeting antisense oligonucleotides for treating Alzheimer’s disease. Furthermore, the instant specification is silent as to any tested or envisioned treatment of any of the diseases claimed or otherwise disclosed therein, such as experimentation with an animal model to address the practical barriers to treatment known in the art and set forth below. The only working examples are drawn to in vitro biochemical models assaying the effect(s) of the claimed antisense oligonucleotides on mouse APP RNA. Thus, it is not apparent from the experimentation disclosed in the specification what manipulated expression level or amount of the antisense oligonucleotide is required to observe a therapeutic effect in a subject having the genetic disease.
Predictability and state of the art: While it is acknowledged that some of the recited genetic diseases have been treated by inhibiting expression of a gene in the subject using an antisense oligonucleotide (such as spinal muscular atrophy-reviewed in Bennett et al., 2019; of record). However, many more of the recited genetic diseases have not been treated using an antisense oligonucleotide. For example, CADASIL remains a life-threatening and disabling disease without any therapies available to limit disease progression (reviewed in Bersano et al., 2017; of record). Even diseases such as Hurler disease and Hunter disease (which are 2 of the 7 types of mucopolysaccharidoses) that are known to be treatable to at least some extent with therapies such as enzyme replacement therapy and/or hematopoietic cell transplantation are not necessarily easily treatable with gene-based therapies. As reviewed in van den Broek et al., 2020 (of record) the tissues most impacted by these diseases are “hard to reach” with known therapies due to tissue-specific barriers such as the blood brain barrier and the blood retina barrier and including, in some cases, avascularity. These barriers to treatment are disclosed to not be specific to Hurler disease, Hunter disease, or even mucopolysaccharidoses-they also apply to other metabolic diseases in which systemic treatments are not sufficient to completely cure the disease. van den Broek et al., 2020 (of record) discloses that other diseases suffering from the same barriers to treatment include Niemann-Pick disease, Tay-Sachs disease, Pompe disease, and Gaucher disease, all of which are claimed (see “conclusions” of van den Broek et al., 2020; of record).
Amount of experimentation necessary: The skilled artisan could not reasonably extrapolate from the teaching in the as-filed specification to the genus of diseases claimed or otherwise envisioned because each disease requires a different targeted gene, region of a gene, or even group(s) of genes. A great deal of future work in the inhibition of any gene(s) connected to any of the claimed disease(s) would have to be developed to demonstrate efficacy of the claimed antisense oligonucleotides in a model of the disease. Without evidence that the claimed diseases may be treated using the instantly claimed antisense oligonucleotides that deaminate a target adenosine in a target RNA sequence, it is unpredictable that this would be an effective treatment.
Furthermore, other than contemplating administering the oligonucleotide to treat a genus of genetic diseases in a subject in need thereof, the specification does not disclose how to design or use the claimed antisense oligonucleotides to treat a subject in need thereof. As clearly stated in Genentech Inc. v. Novo Nordisk A/S (CAFC) 42 USPQ2d 1001: “Patent protection is granted in return for an enabling disclosure of an invention, not for vague intimations of general ideas that may or may not be workable. See Brenner v. Manson, 383 U.S. 519, 536, 148 USPQ 689, 696 (1966) (stating, in the context of the utility requirement, that “a patent is not a hunting license. It is not a reward for the search, but compensation for its successful conclusion.”) Tossing out the mere germ of an idea does not constitute enabling disclosure. While every aspect of a generic claim certainly need not have been carried out by an inventor, or exemplified in the specification, reasonable detail must be provided in order to enable members of the public to understand and carry out the invention.” Applicant cannot rely on the knowledge of one skilled in the art to supply information on the novel aspects of the claimed invention, to which the instantly filed disclosure is largely silent as set forth above.
In view of the breadth of the claims and the lack of guidance provided by the specification as well as the unpredictability of the art, the skilled artisan would have required an undue amount of experimentation to make and/or use the claimed invention. Therefore, claim 13 is not considered to be enabled by the instant disclosure.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 19 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 19 depends from amended instant claim 13, which has been amended to recite a method of treating or ameliorating a genetic disorder in a subject in need thereof, said method comprising administering the composition of claim 1 to the subject, wherein the method comprises the deamination of a target adenosine into an inosine. In comparison, instant claim 19 recites that the composition (administered to the subject in need thereof per amended instant claim 13) “mediates the deamination of the target adenosine in the target RNA in a cell.” This recitation does not further limit the subject matter of instant claim 13, which already recites deamination of a target adenosine into an inosine in a subject in need thereof. Therefore, claim 19 is rejected under 35 U.S.C. 112(d).
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
Claims 1, 2, 4, 6-16, and 18-24 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2017/220751 A1 (hereinafter Turunen; as cited in the IDS filed 09/14/2023; of record) in view of WO 2016/097212 A1 (hereinafter Klein; as cited in the IDS filed 09/14/2023; of record), Merkle et al., 2019 (as cited in the IDS filed 09/14/2023; of record), and Woolf et al., 1995 (as cited in the IDS filed 09/14/2023; of record).
With regard to amended claim 1, which recites “a composition comprising a set of two single stranded antisense oligonucleotides (AONs), wherein
(i) one AON is the “Editing AON” and the other AON is the “Helper AON”,
(ii) the Editing AON is complementary to a sequence of nucleotides in a target RNA that includes a target adenosine,
(iii) the Editing AON comprises a nucleotide that is directly opposite the target adenosine and is a cytidine that is not modified with 2’-OMe or 2’-MOE (“orphan nucleotide”),
(iv) the Helper AON is complementary to a sequence of nucleotides in the target RNA that is separate from the sequence of nucleotides that is complementary to the Editing AON,
(v) the Helper AON has a length of 16 to 22 nucleotides,
(vi) the Editing AON has a length of 16 to 22 nucleotides, and
(vii) the composition can mediate the deamination of the target adenosine in the target RNA, wherein
the Helper AON and Editing AON can form a double stranded complex with the target RNA in a consecutive manner;
the Helper AON is 100% complementary to a sequence of nucleotides in the target RNA that is located at the 3’ side of the sequence of nucleotides in the target RNA that are complementary to the Editing AON;
there is no nucleotide gap, or there is a 1 nucleotide gap, a 2 nucleotide gap, or a 3 nucleotide gap in between the sequence of the Helper AON and the sequence of the Editing AON; and
the set, after forming a double stranded complex with the target RNA, is configured to recruit an endogenous ADAR enzyme to bring about the deamination of the target adenosine into an inosine,”
compositions comprising antisense oligonucleotides capable of mediating the deamination of a target adenosine in a target RNA are known in the art. In brief, Turunen discloses single-stranded RNA-editing antisense oligonucleotides (AONs) capable of mediating the deamination of a specified target adenosine in a target RNA by recruiting an ADAR enzyme endogenously present in the cell (page 3, lines 30-34; page 4, lines 3-4). Per Turunen, the antisense oligonucleotides taught therein are shorter than prior AONs, which makes them easier to produce, use, and manufacture (page 8, lines 12-13). However, while the AONs of Turunen are shorter than those previously disclosed in the art, they are nonetheless longer than those of the instant claim set, as they are recited to comprise a length of up to 100 nucleotides, preferably comprising 18 to 70 nucleotides (page 18, lines 19-28). Thus, Turunen discloses that single-stranded AONs that are complementary to a target RNA comprising the target adenosine (the only non-complementary residue) are capable of binding to the specified target, recruiting an endogenous ADAR enzyme, and editing the specified target (abstract; page 3, lines 34-35; page 8, lines 15-19).
The RNA editing approach disclosed in Turunen is similar to the approach disclosed in Woolf et al., 1995, in which relatively long single-stranded antisense RNA oligonucleotides ranging from 25 to 52 nucleotides in length recognize an RNA sequence targeted for editing and direct the modification of said sequence by recruiting or otherwise providing editing machinery such as deaminating enzymes (abstract; page 8298, column 1, paragraph 1-column 2, paragraph 1; figure 1). Woolf et al., 1995 discloses that the antisense oligonucleotide constructs with lengths of 34 and 52 nucleotides mediated effective and efficient correction of a premature stop codon in the dystrophin gene (figure 3). Thus, both Turunen and Woolf et al., 1995 disclose the utility of administering single-stranded RNA-editing antisense oligonucleotides for purposes of mediating the deamination of a specified target adenosine in a target RNA. The AONs of both Turunen and Woolf et al., 1995 are longer than the instantly claimed Editing AON and the instantly claimed Helper AON.
Klein discloses a targeted approach to RNA editing using oligonucleotide constructs comprising a targeting portion (more than 16 or 17 nucleotides in length but shorter than 25 nucleotides in length (page 10, lines 16-18)) specific for the target nucleic acid sequence to be edited and a stem-loop recruiting portion capable of binding and recruiting a nucleic acid editing entity naturally present in the cell, such as an ADAR enzyme (page 3, lines 2-6; page 6, lines 1-5; page 12, lines 5-10). It is of note that Klein discloses that the targeting and recruiting oligonucleotides may be administered separately (page 7, lines 21-24). This separate administration is considered to read on the instantly claimed consecutive binding of an Editing AON and Helper AON as recited at amended instant claim 1. The RNA editing approach disclosed in Klein is similar to the approach disclosed in Merkle et al., 2019 (see figure 1), in which the antisense oligonucleotides of the system comprise a specificity domain (comparable to the targeting portion of Klein) and a stem-loop ADAR-recruiting domain (comparable to the recruiting portion of Klein). Thus, both Klein and Merkle et al., 2019 disclose the utility of administering RNA-editing antisense oligonucleotides comprising a targeting portion and a recruiting portion for purposes of mediating the deamination of a specified target adenosine in a target RNA, while Klein explicitly discloses that the targeting and recruiting oligonucleotide portions may be administered separately.
While none of the cited art individually discloses a composition comprising a set of two single stranded antisense oligonucleotides for mediating the deamination of a target adenosine in a target RNA, the collective disclosures of the cited art render the instantly claimed composition obvious. As set forth above, Woolf et al., 1995 established that single-stranded antisense oligonucleotides with lengths of 34 and 52 nucleotides mediated effective and efficient correction of a premature stop codon in the dystrophin gene by recruiting the cellular enzyme dsRAD (figure 3; page 8301, column 1, paragraphs 2-3). Additionally, Woolf et al., 1995 explicitly discloses that a therapeutic RNA editing reagent must have two activities: a component that specifically recognizes the sequence to be edited and a sequence modifying activity (page 8298, column 1, paragraph 2). While Klein discloses RNA-editing antisense oligonucleotides in which a targeting portion and a recruiting portion are administered separately for purposes of deaminating a specified target adenosine in a target RNA, and Merkle et al., 2019 similarly discloses RNA editing antisense oligonucleotides comprising a specificity domain and a recruiting domain, both Klein and Merkle et al., 2019 disclose recruiting portions or domains that have a double-stranded stem-loop structure. However, as set forth above and similar to Woolf et al., 1995, Turunen discloses the utility of single-stranded RNA-editing antisense oligonucleotides capable of mediating the deamination of a specified target adenosine in a target RNA by an ADAR enzyme endogenously present in the cell even in the absence of an intramolecular stem-loop structure. Thus, both Woolf et al., 1995 and Turunen establish that single-stranded RNA-editing antisense oligonucleotides are capable of mediating deamination of a specified target adenosine in a target RNA in which the single-stranded RNA-editing antisense oligonucleotides must have two activities: a component that specifically recognizes the sequence to be edited and a sequence modifying activity. While Klein and Merkle et al., 2019 also disclose deamination of a specified target adenosine in a target RNA by antisense oligonucleotides albeit with a targeting portion and a double-stranded stem-loop structure recruiting portion, Klein’s disclosure that the targeting and recruiting oligonucleotides may be administered separately (page 7, lines 21-24) establishes that the targeting and recruiting oligonucleotides are capable of functioning even when they are unlinked and administered at different times (i.e. are two separate oligonucleotides).
Klein discloses that the single-stranded targeting portion taught therein (which reads on the instantly claimed “Editing AON”) is complementary to the target RNA sequence over the entire length of the targeting portion except for a mismatch in which a cytidine is found opposite the adenosine to be edited (page 15, lines 6-8 and lines 17-19). Additionally, Turunen discloses that the single-stranded antisense oligonucleotides taught therein comprise a cytidine or a deoxycytidine with a 2’-OH or a 2’-H group opposite the targeted adenosine (page 10, lines 26-28 and 31-32). Neither Klein nor Turunen discloses or otherwise suggests that this cytidine is modified. These disclosures satisfy the limitations of (ii) and (iii) of instant claim 1.
Regarding the sequence complementarity of the Helper AON, Turunen discloses single-stranded antisense oligonucleotides comprising a targeting portion and a recruitment portion, respectively reading on the instantly claimed Editing and Helper AONs, as set forth above. Turunen discloses that this entire antisense oligonucleotide is capable of forming a double stranded complex with a target RNA in a cell due to being complementary to a target RNA region comprising the target adenosine (page 10, lines 3-6) with the exception of a cytidine or deoxycytidine mismatch opposite the targeted adenosine (page 10, lines 31-32). Thus, the disclosure of Turunen satisfies the limitations of (iv) of instant claim 1.
Klein discloses that the single-stranded targeting portion taught therein is more than 16 or 17 nucleotides in length but shorter than 25 nucleotides in length (page 10, lines 10-20), which reads on the instantly claimed Editing AON having a length of 16 to 22 nucleotides, satisfying the limitations of (vi) of instant claim 1. Furthermore, while the nucleotide length of the Helper AON is not explicitly addressed, as set forth above, Woolf et al., 1995 discloses that 34 and 52-mer single stranded antisense oligonucleotides effectively and efficiently mediated correction of a premature stop codon (figure 3). Therefore, one of ordinary skill in the art prior to the effective filing date of the claimed invention would have known that antisense oligonucleotides of at least 34 to 52 nucleotides in total length are capable of mediating targeted deamination. Thus, if the Editing AON is more than 16 or 17 nucleotides in length but shorter than 25 nucleotides in length (as disclosed in Klein), then the Helper AON must be long enough to increase the total length to at least 34 to 52 nucleotides (as disclosed in Woolf et al., 1995). For example, if the Editing AON is 16 nucleotides in length, the Helper AON must be at least 18 nucleotides in length, satisfying the limitations of (v) and (vi) of instant claim 1.
Finally, regarding the limitations of (vii) of instant claim 1, as repeatedly set forth above, the disclosures of Woolf et al., 1995, Merkle et al., 2019, Klein, and Turunen all establish that antisense oligonucleotides are capable of mediating the deamination of a target adenosine in the target RNA via the action of endogenous enzymes such as ADAR (page 3, lines 30-34; page 4, lines 3-4).
Regarding the amended limitations (b)-(d), if one of ordinary skill in the art were to separate the single-stranded, ADAR-recruiting AON of Turunen as per Klein, the Helper AON would necessarily be 100% complementary to a sequence of nucleotides in the target RNA that is located at the 3’ side of the nucleotides in the target RNA that are complementary to the Editing AON, as instantly claimed, given that the shorter Editing and Helper AONs were derived from the same AON with greater length, with the shorter length making them easier to produce, use, and manufacture (Turunen: page 8, lines 12-13). As depicted in Figure 1 of Klein, the Helper (or recruiting) portion of the AON may be located 3’ to the nucleotides in the target RNA that are complementary to the Editing AON, as instantly claimed.
Furthermore, such separation of the single-stranded, ADAR-recruiting AON of Turunen (as per Klein) would necessarily produce a targeted region wherein there is no nucleotide gap between the sequence of the Helper AON and the Editing AON, as instantly claimed.
Finally, regarding the limitations of (d) of amended instant claim 1, as repeatedly set forth above, the disclosures of Woolf et al., 1995, Merkle et al., 2019, Klein, and Turunen all establish that antisense oligonucleotides are capable of mediating the deamination of a target adenosine in the target RNA via the action of endogenous enzymes such as ADAR (page 3, lines 30-34; page 4, lines 3-4).
Therefore, given that both Woolf et al., 1995 and Turunen disclose that the single-stranded antisense oligonucleotides taught therein are capable of recruiting endogenous deaminating enzymes such as ADAR to specifically edit targeted sequences and are easier to manufacture and use (as disclosed in Turunen), and that Klein and Merkle et al., 2019 disclose antisense oligonucleotides capable of deaminating a target adenosine in the target RNA and comprising targeting and recruiting portions (which are separable per Klein), it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the claimed invention to separate the single-stranded antisense oligonucleotides taught in Turunen and Woolf et al., 1995 into “targeting” and “recruiting” portions (as disclosed in Merkle et al., 2019) for individual administration (as disclosed in Klein) to predictably generate a composition comprising a set of two single-stranded antisense oligonucleotides capable of mediating the deamination of a specified adenosine base for therapeutic purposes. One would have been motivated to make such a modification in order to receive the expected benefit of more easily generating a therapeutic RNA editing reagent with a component that specifically recognizes the sequence to be edited and a sequence modifying activity (as disclosed in Woolf) that is more easily capable of deaminating a specified adenosine base for therapeutic purposes, as set forth in greater detail below.
With regard to amended claim 2, which recites “the composition according to claim 1, wherein there is no nucleotide gap between the sequence of the Helper AON and the sequence of the Editing AON,” as set forth above regarding amended instant claim 1, separation of the single-stranded, ADAR-recruiting AON of Turunen (as per Klein) would necessarily produce a targeted region wherein there is no nucleotide gap between the sequence of the Helper AON and the Editing AON, as instantly claimed.
With regard to claim 4, which recites “the Editing AON [of the composition of claim 1], besides the mismatch between the cytidine opposite the target adenosine, is 100% complementary to the target RNA,” as set forth above Turunen discloses that the entire length of the antisense oligonucleotides taught therein is capable of forming a double stranded complex with a target RNA in a cell due to being complementary to a target RNA region comprising the target adenosine (page 10, lines 3-6). The notable exception to this is that the “targeting portion” (or Editing AON) comprises a cytidine or deoxycytidine mismatch opposite the targeted adenosine (page 10, lines 31-32). Put another way, Turunen discloses that with the exception of the editing site mismatch, the remaining portions of the antisense oligonucleotides taught therein (i.e. the recruiting portion or Helper AON as well as the remaining sequence of the targeting portion or Editing AON) are perfectly complementary to the target RNA (page 20, lines 23-25), as instantly claimed.
With regard to claim 6, which recites “the Editing AON [of the composition of claim 1] comprises one or more phosphorothioate (PS) linkages,” both Turunen and Klein disclose that the editing portions of the antisense oligonucleotides taught therein may comprise phosphorothioate linkages (Turunen page 20, lines 12-14; Klein page 17, lines 9-21), as instantly claimed.
With regard to claim 7, which recites “the Editing AON [of the composition of claim 1] comprises at least one nucleotide with a sugar moiety that comprises a 2’-OMe modification, and/or at least one nucleotide with a sugar moiety that comprises a 2’-MOE modification,” both Turunen and Klein disclose that the editing portions of the antisense oligonucleotides taught therein may comprise modified sugar moieties, such as those comprising a 2’-OMe or a 2’-MOE (Turunen page 20, lines 8-14; Klein page 17, lines 9-21), as instantly claimed.
With regard to claim 8, which recites “the orphan nucleotide [of the composition of claim 1] comprises a 2’-H in the sugar moiety (DNA),” Turunen discloses that the antisense oligonucleotides taught therein (comprising the targeting and recruiting portions of Klein, as set forth above) are capable of forming a double stranded complex with a target RNA in a cell due to being complementary to a target RNA region comprising the target adenosine (page 10, lines 3-6). The notable exception to this is that the “targeting portion” (or Editing AON) comprises a cytidine or deoxycytidine mismatch opposite the targeted adenosine (page 10, lines 31-32). Turunen further discloses that this mismatch opposite the targeted adenosine preferentially comprises a deoxyribose sugar moiety with a 2’-H group (i.e. deoxycytidine) (page 4, lines 5-7), as instantly claimed.
With regard to claim 9, which recites “the nucleotide at the 5’ side and/or the nucleotide at the 3’ side of the orphan nucleotide [of the composition of claim 8] is DNA,” Turunen discloses that the antisense oligonucleotides taught therein (comprising the targeting and recruiting portions of Klein, as set forth above) are capable of forming a double stranded complex with a target RNA in a cell due to being complementary to a target RNA region comprising the target adenosine with the notable exception of a mismatched cytidine or deoxycytidine opposite the targeted adenosine (page 10, lines 3-6 and lines 31-32). Turunen further discloses that the nucleotide 5’ and/or 3’ of the mismatched cytidine opposite the target adenosine also comprises a deoxyribose with a 2’-H group (page 9, line 35-page 10, line 2), as instantly claimed.
With regard to claim 10, which recites “the Editing AON [of the composition of clam 1] comprises at least one phosphonoacetate internucleoside linkage, at least one methylphosphonate internucleoside linkage, and/or at least one nucleotide comprising an unlocked acid (UNA) ribose modification,” both Turunen and Klein disclose that the editing portions of the antisense oligonucleotides taught therein may comprise methylphosphonate internucleoside linkage(s) (Turunen page 16, lines 28-31; Klein page 30, lines 1-4), as instantly claimed.
With regard to claim 11, which recites “the Editing AON [of the composition of claim 1] is 19, 20, or 21 nucleotides in length, wherein the orphan nucleotide is the 6th, 7th, or 8th nucleotide from the 5’ end, and wherein the Helper AON is 17, 18, or 19 nucleotides in length,” as set forth above, Klein discloses that the single-stranded targeting portion taught therein is more than 16 or 17 nucleotides in length but shorter than 25 nucleotides in length (page 10, lines 10-20), which reads on the instantly claimed Editing AON having a length of 19 to 21 nucleotides, satisfying the limitations of (vi) of instant claim 1. Furthermore, while the nucleotide length of the Helper AON is not explicitly addressed, as set forth above, Woolf et al., 1995 discloses that 34 and 52-mer single stranded antisense oligonucleotides effectively and efficiently mediated correction of a premature stop codon (figure 3). Therefore, one of ordinary skill in the art prior to the effective filing date of the claimed invention would have known that antisense oligonucleotides of at least 34 to 52 nucleotides in total length resulting from both the targeting (or editing) and recruiting (or helper) portions are capable of mediating targeted deamination and would have tailored the exact length of the recruiting (or helper) portion to ensure sufficient length and sufficient activity through routine experimentation guided by these disclosures (see MPEP § 2143). Furthermore, Figure 1b of Merkle et al., 2019 depicts the location of the claimed orphan nucleotide. As shown in Figure 1b of Merkle et al., 2019, the orphan cytidine nucleotide is located at the residue positioned 8th from the 5’ end of the targeting portion of the antisense oligonucleotide of Merkle et al., 2019, as instantly claimed.
With regard to claim 12, which recites “the composition according to claim 1, further compris[es] a pharmaceutically acceptable carrier,” Turunen discloses that the antisense oligonucleotides taught therein (comprising the targeting and recruiting portions of Klein, as set forth above) are particularly suitable for therapeutic use and may be provided to a patient in the form of a pharmaceutical composition comprising a pharmaceutically acceptable carrier (page 27, lines 4-9), as instantly claimed.
With regard to amended claim 13, which recites “a method of treating or ameliorating a genetic disorder in a subject in need thereof comprising administering the composition according to claim 1 to the subject, wherein the genetic disorder is selected from the group consisting of Cystic fibrosis, Hurler Syndrome…or cancer, wherein the method comprises the deamination of a target adenosine into an inosine” as set forth above, Turunen discloses that the antisense oligonucleotides taught therein (comprising the targeting and recruiting portions of Klein, as set forth above) are particularly suitable for therapeutic use in treating genetic diseases such as those recited (i.e. cystic fibrosis, Hurler syndrome, cancer, and others) (page 28, lines 23-40), as instantly claimed. Furthermore, as repeatedly set forth above, the disclosures of Woolf et al., 1995, Merkle et al., 2019, Klein, and Turunen all establish that antisense oligonucleotides are capable of mediating the deamination of a target adenosine in the target RNA via the action of endogenous enzymes such as ADAR (page 3, lines 30-34; page 4, lines 3-4), as instantly claimed.
With regard to amended claim 14, which recites “a method for the deamination of at least one target adenosine in a target RNA in a cell, the method comprising:
providing the cell with a composition of claim 1;
allowing annealing of the AONs to the target RNA to form a double stranded nucleic acid molecule; and
allowing the ADAR enzyme endogenously present in said cell to complex with the double stranded nucleic acid molecule and to deaminate the target adenosine in the target RNA to an inosine,”
as set forth above regarding the composition of claim 1, the disclosures of Turunen, Klein, Woolf et al., 1995, and Merkle et al., 2019 render the composition of claim 1 obvious. Turunen further discloses a method for the deamination of at least one specific target adenosine present in a target RNA in a cell, said method comprising the steps of providing said cell with an antisense oligonucleotide taught therein (comprising the targeting and recruiting portions of Klein, as set forth above), allowing uptake by the cell of said antisense oligonucleotide, allowing annealing of said antisense oligonucleotide to the target RNA sequence, and finally allowing a mammalian ADAR enzyme comprising a natural double-stranded RNA binding domain as found in the wild type enzyme to deaminate said target in said target RNA sequence to an inosine (page 27, lines 15-21), as instantly claimed.
With regard to amended claim 15, which recites “the method [of claim 14] further comprises: a) sequencing a region of the target RNA, wherein the region comprises the position of the target adenosine; b) assessing the presence of a functional, elongated, full length and/or wild type protein when the target adenosine is in a UGA or UAG stop codon, which is edited to a UGG codon through the deamination; c) assessing, when the target RNA is pre-messenger RNA (pre-mRNA), whether splicing of the pre-mRNA was altered by the deamination; or d) using a functional read-out, wherein the target RNA after the deamination encodes a functional, full length, elongated and/or wild type protein,” Turunen discloses that the method set forth above regarding deaminating at least one target adenosine (page 27, lines 15-21) further comprises sequencing the target RNA to determine whether the target adenosine was successfully converted to an inosine, assessing the presence of a functional, elongated, full-length and/or wild type protein when said target adenosine is located in a UGA or UAG stop codon, which is edited to a UGG codon through said deamination, assessing whether splicing of the pre-mRNA was altered by said deamination, or using a functional read-out, wherein the target RNA after said deamination encodes a functional, full length, elongated, and/or wild type protein (page 27, lines 23-36), as instantly claimed.
With regard to claim 16, which recites “a method for the deamination of at least one target adenosine present in a target RNA in a human cell comprising contacting the cell with the composition of claim 1,” as set forth above, Turunen discloses a method for the deamination of at least one specific target adenosine present in a target RNA in a cell (page 27, lines 15-21). Turunen further discloses that this cell may be a human cell (page 4, line 29), as instantly claimed.
With regard to claim 19, which recites “the composition [of the method of claim 13] mediates the deamination of the target adenosine in the target RNA in a cell,” as set forth above, Turunen discloses a method for the deamination of at least one specific target adenosine present in a target RNA in a cell, such as a human cell (page 4, line 29; page 27, lines 15-21) for therapeutic use in treating diseases such as genetic disorders (page 28, lines 23-40), as instantly claimed.
With regard to claim 20, which recites “the cell [of the method of claim 19] is a skin cell, a lung cell, a heart cell, a kidney cell, a liver cell, a pancreas cell, a gut cell, a muscle cell, a gland cell, an eye cell, a brain cell, or a blood cell,” Turunen discloses that the method taught therein can be used with cells from any organ e.g. skin, lung, heart, kidney, liver, pancreas, gut, muscle, gland, eye, brain, and blood (page 20, line 37-page 21, line 1), as instantly claimed.
With regard to claim 21, which recites “the administration of the composition [of the method of claim 13] is in vivo or ex vivo,” Turunen discloses that the method taught therein can be practiced in vitro, in vivo, or ex vivo (page 21, lines 9-11), as instantly claimed.
With regard to claim 22, which recites “the composition [of the method of claim 13] is formulated for intravenous administration,” Turunen discloses that the method taught therein can be practiced by administering the antisense oligonucleotides taught therein (comprising the targeting and recruiting portions of Klein, as set forth above) intravenously (page 28, lines 18-21), as instantly claimed.
With regard to claim 23, which recites “the target RNA [of the method of claim 13] is a messenger RNA (mRNA) or a pre-mRNA,” Turunen discloses that the target RNA may be any cellular RNA sequence but is usually a pre-mRNA or an mRNA with a protein coding function (page 22, lines 34-35), as instantly claimed.
With regard to claim 24, which recites “the composition [of the method of claim 13] targets a 5’ non-coding sequence, a 3’ non-coding sequence, an intron, or an exon in the target RNA,” Turunen discloses that the invention taught therein (comprising antisense oligonucleotides that themselves comprise the targeting and recruiting portions of Klein, as set forth above) can be practiced on any RNA target comprising an adenosine, whether in a coding region, an intron, or a non-coding exon (such as a 5’ or 3’ untranslated region) (page 22, line 40-page 23, line 1), as instantly claimed.
Given that both Woolf et al., 1995 and Turunen disclose that the single-stranded antisense oligonucleotides taught therein are capable of recruiting endogenous deaminating enzymes such as ADAR to specifically edit targeted sequences and are easier to manufacture and use (as disclosed in Turunen), and that Klein and Merkle et al., 2019 disclose antisense oligonucleotides capable of deaminating a target adenosine in the target RNA and comprising targeting and recruiting portions (which are separable per Klein), it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to separate the single-stranded antisense oligonucleotides taught in Turunen and Woolf et al., 1995 into “targeting” and “recruiting” portions (as disclosed in Merkle et al., 2019) for individual administration (as disclosed in Klein) to predictably generate a composition comprising a set of two single-stranded antisense oligonucleotides capable of mediating the deamination of a specified adenosine base for therapeutic purposes, as disclosed in both Klein Turunen. One would have been motivated to make such a modification in order to receive the expected benefit of more easily generating a therapeutic RNA editing reagent with a component that specifically recognizes the sequence to be edited and a sequence modifying activity (as disclosed in Woolf) that is more easily capable of deaminating a specified adenosine base for therapeutic purposes (as disclosed in both Klein and Turunen).
With regard to amended claim 18, which recites “a composition comprising a set of two single stranded antisense oligonucleotides (AONs), wherein
one AON is the “Editing AON” and the other AON is the “Helper AON”,
the Editing AON is complementary to a stretch of nucleotides in a target RNA that includes a target adenosine,
the Editing AON comprises a nucleotide that is directly opposite the target adenosine and is a cytidine that is not modified with 2’-OMe or 2’-MOE (“orphan nucleotide”),
the Helper AON is complementary to a sequence of nucleotides in the target RNA that is separate from the sequence of nucleotides that are complementary to the Editing AON,
the Helper AON has a length of 16 to 22 nucleotides,
the Helper AON and Editing AON form a double stranded complex with the target RNA in a consecutive manner,
the Helper AON is complementary to a sequence of nucleotides in the target RNA that is complementary to the Editing AON, and
there is no nucleotide gap between sequences complementary to the sequence of the Helper AON and the sequence of the Editing AON;
and wherein the set, after forming a double stranded complex with the target RNA is configured to recruit an endogenous ADAR enzyme to bring about the deamination of the target adenosine into an inosine,”
as set forth above regarding the composition of instant claim 1, given that both Woolf et al., 1995 and Turunen disclose that the single-stranded antisense oligonucleotides taught therein are capable of recruiting endogenous deaminating enzymes such as ADAR to specifically edit targeted sequences and are easier to manufacture and use (as disclosed in Turunen), and that Klein and Merkle et al., 2019 disclose antisense oligonucleotides capable of deaminating a target adenosine in the target RNA and comprising targeting and recruiting portions (which are separable per Klein), it would have been obvious to someone of ordinary skill in the art prior to the effective filing date of the claimed invention to separate the single-stranded antisense oligonucleotides taught in Turunen and Woolf et al., 1995 into “targeting” and “recruiting” portions (as disclosed in Merkle et al., 2019) for individual administration (as disclosed in Klein) to predictably generate a composition comprising a set of two single-stranded antisense oligonucleotides capable of mediating the deamination of a specified adenosine base for therapeutic purposes. One would have been motivated to make such a modification in order to receive the expected benefit of more easily generating a therapeutic RNA editing reagent with a component that specifically recognizes the sequence to be edited and a sequence modifying activity (as disclosed in Woolf) that is more easily capable of deaminating a specified adenosine base for therapeutic purposes. Furthermore, as set forth above, Turunen discloses that the double-stranded structures formed by binding of the AONs taught therein to their respective targeted sequences are capable of harnessing ADAR enzymes to edit the target adenosine, even in the absence of a stem-loop recruitment structure (page 8, lines 10-19).
When separating the single-stranded antisense oligonucleotides taught in Turunen into “targeting” and “recruiting” portions for individual administration, as disclosed in Klein, to predictably generate a composition comprising a set of two single-stranded antisense oligonucleotides capable of mediating the deamination of a specified adenosine base for therapeutic purposes (as set forth above), the “targeting” portion is considered to read on the instantly claimed “Editing AON,” while the “recruiting” portion is considered to read on the instantly claimed “Helper AON,” satisfying the limitations of (i) of instant claim 18.
Klein discloses that the single-stranded targeting portion taught therein (which reads on the instantly claimed “Editing AON”) is complementary to the target RNA sequence over the entire length of the targeting portion except for a mismatch in which a cytidine is found opposite the adenosine to be edited (page 15, lines 6-8 and lines 17-19). Additionally, Turunen discloses that the single-stranded antisense oligonucleotides taught therein comprise a cytidine or a deoxycytidine with a 2’-OH or a 2’-H group opposite the targeted adenosine (page 10, lines 26-28 and 31-32). Neither Klein nor Turunen discloses or otherwise suggests that this cytidine is modified. These disclosures satisfy the limitations of (ii) and (iii) of instant claim 18.
Regarding the sequence complementarity of the Helper AON, Turunen discloses single-stranded antisense oligonucleotides comprising a targeting portion and a recruitment portion, respectively reading on the instantly claimed Editing and Helper AONs, as set forth above. Turunen discloses that this entire antisense oligonucleotide is capable of forming a double stranded complex with a target RNA in a cell due to being complementary to a target RNA region comprising the target adenosine (page 10, lines 3-6) with the exception of a cytidine or deoxycytidine mismatch opposite the targeted adenosine (page 10, lines 31-32). Thus, the disclosure of Turunen satisfies the limitations of (iv) of instant claim 18.
Klein discloses that the single-stranded targeting portion (which reads on the instantly claimed Editing AON) taught therein is more than 16 or 17 nucleotides in length but shorter than 25 nucleotides in length (page 10, lines 10-20). Furthermore, while the nucleotide length of the Helper AON is not explicitly addressed, as set forth above, Woolf et al., 1995 discloses that 34 and 52-mer single stranded antisense oligonucleotides effectively and efficiently mediated correction of a premature stop codon (figure 3). Therefore, one of ordinary skill in the art prior to the effective filing date of the claimed invention would have known that antisense oligonucleotides of at least 34 to 52 nucleotides in total length are capable of mediating targeted deamination. Thus, if the Editing AON is more than 16 or 17 nucleotides in length but shorter than 25 nucleotides in length (as disclosed in Klein), then the Helper AON must be long enough to increase the total length to at least 34 to 52 nucleotides (as disclosed in Woolf et al., 1995). For example, if the Editing AON is 16 nucleotides in length, the Helper AON must be at least 18 nucleotides in length, satisfying the limitations of (v) of instant claim 18.
As set forth above, the targeting AON portion disclosed in Klein broadly reads on the instantly claimed Editing AON, while the recruiting AON portion disclosed in Klein broadly reads on the instantly claimed Helper AON. The single antisense oligonucleotide disclosed in Turunen is considered to comprise both of these portions, as set forth above. Additionally, Turunen discloses that this entire antisense oligonucleotide is capable of forming a double stranded complex with a target RNA in a cell due to being complementary to a target RNA region comprising the target adenosine (page 10, lines 3-6) with the exception of a cytidine or deoxycytidine mismatch opposite the targeted adenosine in the editing portion (page 10, lines 31-32). As shown in Figure 1 of Turunen, these antisense oligonucleotides are continuous single strands of nucleotides in which sequence 3’ of the sequence targeted by the Editing AON is complementary to the sequence of the rest of the antisense oligonucleotide (i.e. the recruiting or helper portion) without any nucleotide gaps, satisfying the limitations of (vii) and (viii) of instant claim 18. Additionally, while the order of annealing regarding the Helper AON and the Editing AON is not explicitly addressed in either Klein or Turunen, Klein does disclose that the targeting and recruiting portions may be administered separately (page 7, lines 21-24). Therefore, as set forth in MPEP § 2143(I)(E), given there is a finite number of options to try regarding the order of administration, it would have been obvious to try administering either the Editing AON first in order for it to anneal first or the Helper AON first in order for it to anneal first, meaning the Helper and Editing AONs would anneal consecutively, satisfying the limitations of (vi) of instant claim 18.
Given that both Woolf et al., 1995 and Turunen disclose that the single-stranded antisense oligonucleotides taught therein are capable of recruiting endogenous deaminating enzymes such as ADAR to specifically edit targeted sequences and are easier to manufacture and use (as disclosed in Turunen), and that Klein and Merkle et al., 2019 disclose antisense oligonucleotides capable of deaminating a target adenosine in the target RNA and comprising targeting and recruiting portions (which are separable per Klein), it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to separate the single-stranded antisense oligonucleotides taught in Turunen and Woolf et al., 1995 into “targeting” and “recruiting” portions (as disclosed in Merkle et al., 2019) for individual administration (as disclosed in Klein) to predictably generate a composition comprising a set of two single-stranded antisense oligonucleotides capable of mediating the deamination of a specified adenosine base for therapeutic purposes, as disclosed in both Klein Turunen. One would have been motivated to make such a modification in order to receive the expected benefit of more easily generating a therapeutic RNA editing reagent with a component that specifically recognizes the sequence to be edited and a sequence modifying activity (as disclosed in Woolf) that is more easily capable of deaminating a specified adenosine base for therapeutic purposes (as disclosed in both Klein and Turunen).
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over WO 2017/220751 A1 (hereinafter Turunen; as cited in the IDS filed 09/14/2023; of record) in view of WO 2016/097212 A1 (hereinafter Klein; as cited in the IDS filed 09/14/2023; of record), Merkle et al., 2019 (as cited in the IDS filed 09/14/2023; of record), and Woolf et al., 1995 (as cited in the IDS filed 09/14/2023; of record) as applied to claim 13 above, and further in view of Chang et al., 2018 (of record) and Jonsson et al., 2012 (of record).
The combined disclosures of Turunen, Klein, Merkle et al., 2019, and Woolf et al., 1995 are described above and applied as before. However, these disclosures do not teach the target RNA of instant claim 25.
With regard to amended claim 25, which recites “the target RNA [of the method of claim 13] is an Amyloid Precursor Protein (APP) RNA,” while Turunen, Klein, Merkle et al., 2019, and Woolf et al., 1995 collectively disclose the method of treatment of instant claim 13, none of these disclosures teach, suggest, or motivate targeting APP RNA, as instantly claimed. However, APP is a known therapeutic target of antisense oligonucleotides, as is disclosed in Chang et al., 2018 (abstract; Figure 1A). The antisense oligonucleotides taught in Chang et al., 2018 are splice switching oligonucleotides specifically designed to skip exon 17 of APP mRNA, thereby eliminating the γ-secretase cleavage sites encoded by the exon that would facilitate Aβ release from the membrane (abstract; Figure 1). Additionally, Jonsson et al., 2012 discloses that certain point mutations in the APP sequence can dramatically impact the progression of Alzheimer’s disease. Specifically, Jonsson et al., 2012 discloses that the point mutation A673T confers strong protection against Alzheimer’s disease (page 98, column 2, paragraph 1).
Given that Turunen, Klein, Merkle et al., 2019, and Woolf et al., 1995 collectively disclose a method of treating genetic diseases, said method comprising targeted deamination by specifically-designed antisense oligonucleotides, that Chang et al., 2018 discloses therapeutic splice switching antisense oligonucleotides targeting APP mRNA, and that Jonsson et al., 2012 discloses that certain point mutations (i.e. A673T) are known to confer protective effects, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to apply the method of treating a genetic disease collectively disclosed by Turunen, Klein, Merkle et al., 2019, and Woolf et al., 1995 to the manipulation of APP mRNA (as disclosed in Chang et al., 2018), such as at target sites defined by known point mutations (as disclosed in Jonsson et al., 2012), to predictably generate APP mRNA and its resulting protein product that protects the treated patient from the progression of Alzheimer’s disease. One would have been motivated to make such a modification in order to receive the expected benefit of protecting the treated patient from the progression of Alzheimer’s disease.
Conclusion
No claims are allowed.
Claim 18 is objected to.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Sarah E Allen whose telephone number is (571)272-0408. The examiner can normally be reached M-Th 8-5, F 8-12.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Jennifer Dunston can be reached at 571-272-2916. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/SARAH E ALLEN/Examiner, Art Unit 1637
/J. E. ANGELL/Primary Examiner, Art Unit 1637
Prosecution Insights