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 .
Claims 2-4, 9, 11-12, 14, 17, 19-21, 25-29, 32, and 49-51 are pending.
Election/Restrictions
Applicant's election with traverse of Invention Group I, drawn to a method of modulating expression of a transgene… comprising… administering… chemical epigenetic modifier [CEM] wherein the CEM increases expression of the transgene in the reply filed on 01 June 2026 is acknowledged. The traversal is on the ground(s) that Applicant submits Groups I and II should be examined together. The Examiner has not provided any explanation why Groups I and II are considered to be separate inventions… There is no apparent reason why the two groups were separated. This is not found persuasive because the two methods are plainly different. An artisan would not use a method of increasing gene expression in the place of a method of decreasing gene expression. A method of increasing gene expression is not interchangeable with a method of decreasing gene expression. In addition and as explained in the restriction, WO426 teaches methods of increasing and methods of decreasing gene expression; therefore there is no unity of invention for the two methods.
However, since both methods were found searchable, the requirement for restriction between Invention Groups I and II is withdrawn in the interest of compact prosecution. The requirement for restriction between Groups I/II and III is maintained.
The requirement between Groups I/II and III is still deemed proper and is therefore made FINAL.
Claims 28, 32, and 49-51 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 01 June 2026.
Applicant’s election without traverse of the following species:
DNA-binding domain: a zinc finger binding domain,
RNA-binding domain: MS2, and
CEM: CEM87.
in the reply filed on 01 June 2026 is acknowledged.
The species CEM87, CEM114, and CEM23 were found searchable so the requirement for election of those species is withdrawn. The requirement for election of all other species is maintained
Claims 21 and 29 are examined to the extent that they read on the elected species. Election was made without traverse in the reply filed on 01 June 2026.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29are examined.
Information Disclosure Statement
The Spec. cites references.
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The IDS(es) has been considered.
Drawings
The drawings are objected to because of the following informalities:
Fig 1: the chemical structures are blurry,
Fig. 13: Text in Spec. (¶228) indicates [i.e., AAV9-CEMtrol (or vehicle) will be administered] the text under AAV-CEMtrol should read (OR VEHICLE) but currently it just says (VEHICLE).
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.
Specification
The disclosure is objected to because of the following informalities:
The Spec. discusses (¶216-217) that Fig. 6, left panel shows 48 hours post CEM87 addition, cells were imaged and flow cytometry run to determine the eGFP expression after transfection of HEK293 cells with plasmids, and that Fig. 6, right panel shows 48 hours post CEM87 addition, cells were imaged and flow cytometry run to determine the eGFP expression after HEK293 cells were transduced with AAV. However, Figure 6 itself says GFP expression within transfected AAV plasmids. That is confusing because both ¶ disclose cells were imaged and flow cytometry run to determine the eGFP expression but there is one panel with representative images and one panel with quantification of fluorescence. Please confirm that the text is correct or clarify, for the purposes of examination, what the Figs. show. What panel corresponds to what text? Reminder: new matter may not be added to the Spec. or Drawings.
Appropriate correction is required.
The lengthy specification has not been checked to the extent necessary to determine the presence of all possible minor errors. Applicant’s cooperation is requested in correcting any errors of which applicant may become aware in the specification.
Claim Interpretation
Claim 2 recites a transgene. That is interpreted as encompassing any transgene.
Claim 3 recites a method of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector. The term a disorder that is treatable by expression of a transgene is interpreted as any disorder.
Claim 9 recites the transgene encodes a protein or a functional nucleic acid. The terms a protein or a functional nucleic acid is interpreted as any protein or any nucleic acid.
Claim 14 recites optionally wherein the DNA binding domain is from…Cas9, Cas3… [emphasis added]. The claim is interpreted as meaning exactly what it says: the optional limitation requires the DNA binding domain—and only the DBD—is from one of the recited nucleases. Since, if the entire enzyme were present, it would cleave the polynt which could lead to problems of enablement, the optional limitation is interpreted as meaning that if the entire enzyme is present, it is required to be a catalytically inactive nuclease (e.g., deadCas9).
Claims 14, 21, and 29 recite optionally… two times. Claim 17 also recites optionally…. Any optional limitation(s) is interpreted as fully optional and not required.
Claims 21 and 29 recite a transcriptional activator or inhibitor protein or complex. That is interpreted as encompassing any protein or complex that is known/shown to activate or inhibit transcription.
Claim Objections
Claims 14 and 27 are objected to because of the following informalities:
Claim 14 should remove the parentheses so it recites: optionally wherein the DNA binding domain is from…Cas5, Cas5e or CasD….Csy3, Cse1 or CasA, Cse2 or CasB, Cse3 or CasE, Cse4 or CasC…
Claim 14 should also replace or in the lists of optional DNA binding domains with and, and modify the second list of optional items so it recites: …optionally wherein the DNA binding domain comprises one of a zinc finger DNA binding domain… a transcription factor DNA binding domain and a restriction endonuclease DNA binding domain…; optionally wherein the DNA binding domain is from one of: GAL4… and TALES.
Note: is the intention for Claim 14 to recite: …, or a restriction endonuclease DNA binding domain; optionally wherein the restriction endonuclease DNA binding domain is from GAL4…? If so, the claim should be amended accordingly. If not, the claim should be amended so all the optional DNA binding domains are on a single list.
Claim 27 should recite: The method of claim 20, further comprising a step of blocking the increased expression of the transgene by stopping (a) contacting the transgene delivery vector with the chemical epigenetic modifier or (b) administering to the subject the chemical epigenetic modifier.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29 are 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 claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a written description rejection.
Claim 2 recites:
a method of modulating expression of a transgene from a transgene delivery vector in a subject, the method comprising:
administering to the subject a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence;
administering to the subject a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier; and
administering to the subject the chemical epigenetic modifier; thereby modulating expression of the transgene.
That broad claim encompasses the large genera of: any transgenes and transgene expression cassettes, transgene delivery vectors and polynucleotides (polynt) comprising any transgene expression cassette and any nucleic acid binding domain recognition sequence, any nucleic acid binding domain recognition sequence, any fusion proteins comprising any nucleic acid binding domain that binds to any recognition sequence fused to any domain that binds any chemical epigenetic modifier; and any chemical epigenetic modifiers.
Any kind of transgene, any expression cassette/delivery vector/polynt encoding any transgene, any fusion proteins comprising a nucleic acid binding domain that binds to any recognition sequence fused to any domain that binds any chemical epigenetic modifier, any nucleic acid binding domain and any nucleic acid binding domain recognition sequence, any domain that binds any chemical epigenetic modifier (CEM), and any chemical epigenetic modifier would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of encoding any transgene, serving as a nucleic acid-binding domain (NBD) or NBD recognition sequence, and serving as a CEM or CEM-binding domain.
There is a written description (WD) problem because Applicant hasn’t demonstrated possession of a representative number of transgene delivery vectors/expression cassettes/polynt encoding any transgene or a representative number of transgenes. The WD problem exists because Applicant hasn’t demonstrated possession of any fusion protein(s) comprising the recited components, any NBD, any NBD recognition sequence, any domain that binds any CEM, and/or any CEM, or a representative number of any of those. The WD problem exists because Applicant hasn’t disclosed or adequately described structures responsible for the functions of encoding any transgene, serving as a fusion protein(s) comprising the recited components, serving as an NBD or NBD recognition sequence, and serving as a CEM or CEM-binding domain.
Claims 11-12 have the same problem because they recite/encompass any fusion protein…. Claims 20-21, 25, 27-29 have the same problem because they recite/encompass any CEM.
Claim 3 recites a method of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector….
In addition to reciting the same genera that are recited in Claim 2 (see above), that broad claim encompasses the large genus of transgenes that can be used to treat any disorder that is treatable by expressing a transgene. Any kind of transgene that can be used to treat a disorder that is treatable by expression of a transgene would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of treating any disorder.
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the functions of treating any disorder.
Claim 9 recites the method of claim 2, wherein the transgene encodes a protein or a functional nucleic acid.
That broad claim encompasses the large genus of transgenes that encode any protein or any functional nucleic acid. Any kind of transgene encoding any nucleic acid would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of encoding a protein or a functional nucleic acid.
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the functions of being a functional nucleic acid or encoding any protein.
Claim 11 recites the method of claim 2, wherein the polynt further comprises a sequence encoding the fusion protein.
That broad claim encompasses the large genus of polynt that encode the fusion protein comprising a nucleic acid binding domain…. Any kind of polynt that encode the fusion protein comprising a nucleic acid binding domain… would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of encoding the any fusion protein comprising an NBD ….
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the functions of encoding the any fusion protein comprising a NBD….
Claims 14 and 17 recite the nucleic acid binding domain is a DNA binding domain (Claim 14) and the nucleic acid binding domain is a RNA binding domain (Claim 17).
Those broad claims encompass the large genera of NBDs that are DNA- or RNA-binding domains. Any kind of DNA- or RNA-binding domain would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of binding DNA or RNA.
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the function of binding DNA or RNA.
Claim 20 recites the method of claim 2, wherein the CEM... increases expression of the transgene and Claim 28 recites the method of claim 2, wherein the CEM... decreases expression of the transgene.
Those broad claims encompass the large genera of CEMs that cause increased/decreased expression of the transgene (which encompasses any gene). Any kind of CEM(s) that causes increased/decreased expression of the transgene would be encompassed by the claims as instantly presented. The term includes any CEM that results in direct or indirect increased/decreased expression of the transgene. Those are groups of molecules described solely by their function(s) of being a CEM that increases or decrease expression of a gene.
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the function of increasing or decreasing transgene expression.
Claim 21 recites the method of claim 2, wherein the CEM... binds to a transcriptional activator protein or complex and Claim 29 recites the method of claim 2, wherein the CEM... binds to a transcriptional inhibitor protein or complex.
Those broad claims encompass the large genera of CEMs that bind to a transcriptional activator/inhibitor protein or complex. Any kind of CEM(s) that binds to a transcriptional activator/inhibitor protein or complex would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of being a CEM that binds to a transcriptional activator/inhibitor protein or complex.
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the function of binding to a transcriptional activator/inhibitor protein or complex.
Claim 25 recites the method of claim 2, further comprising… administering… an agent that inhibits binding of the fusion protein to the CEM.
That broad claim encompasses the large genus of agents that inhibit binding of the fusion protein to the CEM. Any kind of agent that inhibits binding of the fusion protein to the CEM would be encompassed by the claims as instantly presented. Those are groups of molecules described solely by their function(s) of inhibiting binding of the fusion protein to the CEM.
There is a WD problem because Applicant hasn’t disclosed or adequately described structures responsible for the function of inhibiting binding of the fusion protein to the CEM.
An original claim may lack written description support when a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. See MPEP 2163.
The Spec. discusses (¶102-105, ¶131) transgene delivery vectors, cassettes, and transgenes. Those descriptions are inadequate because those terms encompass any transgene delivery vector and transgene but the Spec. doesn’t disclose any structure responsible for the function of being a transgene delivery vector or a transgene, and it hasn’t disclosed a representative number of transgene delivery vectors and transgenes. The Spec. discloses (¶131) the nucleic acid can be any nucleic acid of interest. Although the Spec. discusses (¶221-226) some cassettes (e.g., comprising JET-GFP), those are inadequate to provide WD support for the broad genus claimed. An artisan wouldn’t know what transgene delivery vectors, cassettes, and transgenes are suitable to use in the invention. (Fig. 8 shows the vector AAV8 didn’t produce any significant changes in luminescence, indicating that at least that vector is not suitable.)
The Spec. discusses (¶87-90, ¶105-109) some NBD recognition sequences: The nucleic acid binding domain recognition sequence serves as a binding site for a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a CEM and:
the nucleic acid binding domain recognition sequence may be any nucleotide sequence that is specifically recognized and bound by a nucleic acid binding protein such that the presence of the nucleic acid binding domain recognition sequence in the transgene delivery vector recruits a fusion protein comprising the nucleic acid binding protein.
The Spec. discusses (¶109) that portions of the fusion protein may bind a CEM: the portion of the fusion protein that is a domain that binds a CEM may be any polypeptide that specifically recognizes and binds to a portion of the CEM that is a ligand for the domain. Those § discuss the function of NBD, DNA-BD, and RNA-BD, and provide examples, but they do not disclose what structure(s) are responsible for the nucleic acid-binding function or the CEM-binding function. The Spec. doesn’t disclose NBDs or what specific protein structures/amino acid (AA) sequences are responsible for producing the function of binding nucleic acids.
The Spec. discusses (¶90) a domain that binds a CEM: The portion of the fusion protein that is a domain that binds a CEM may be any polypeptide that specifically recognizes and binds to a portion of the CEM that is a ligand for the domain. That § discloses the sole examples of FK506 or mutant FK50. However, that § doesn’t describe the structure(s) that imparts the function of CEM binding.
The Spec. discusses (¶91-95) some CEMs and (¶95-100) CEMs and agents that inhibit binding between the CEM and the fusion protein that binds a CEM. The Spec. describes that the agent that inhibits binding of the fusion protein to the CEM may be any agent that interferes with fusion protein. At none of those § (or elsewhere) does the Spec. disclose what structure(s) is responsible for inhibit binding between the CEM and the fusion protein that binds a CEM.
The Spec. doesn’t disclose the structure of fusion proteins that comprise a NBD (which binds to a recognition sequence) that is fused to a domain that binds a CEM. The Spec. discloses (§Examples, starting at ¶213) examples of only the ZF-FKBP fusion protein.
The Spec. discloses (¶84/¶104/¶130/¶134) examples of functional nucleic acids (e.g., an antisense…or [RNAi]) but doesn’t define the term. Furthermore, the Spec. provides no evidence of possession of any transgenes encoding any functional nucleic acid(s).
The Spec. discusses (¶92-94, ¶97-100) the CEM can increase/decrease expression of a transgene by bind[ing] to a transcriptional activator or inhibitor protein or complex that when recruited to the transgene delivery vector increases or decreases expression of the transgene. Examples… include BRD4 or…. That § doesn’t disclose any structure(s) that is responsible for or causes increasing or decreasing expression of the transgene—by recruiting epigenetic machinery or by any other mechanism.
The Spec. discusses (¶130-212) treating disorders or diseases. Those § specify that the disclosures are nonlimiting .Once again, the Spec. does not adequately describe, by disclosing structure–function relationships, disorders that are treatable by expression of a transgene.
Regarding what structures are encompassed by the transgenes and transgene expression cassettes, transgene delivery vectors and polynt comprising any transgene expression cassette and any NBD recognition sequence; NBD domain recognition sequences, fusion proteins comprising a NBD domain that binds to any recognition sequence fused to a domain that binds a CEM; NBDs and NBDs that are DNA- or RNA-binding domain; CEMs, CEMs that cause increased/decreased expression of the transgene, CEMs that bind to a transcriptional activator/inhibitor protein or complex; transgenes that encode functional nucleic acids; agents that inhibit binding of the fusion protein to the CEM; and transgenes that can be used to treat any disorder that is treatable by expressing a transgene, the Spec. does not provide information describing their features. The Spec. does not disclose what physical structure responsible for the claimed functions.
Applicant’s examples show the transgenes GFP and luciferase, the delivery vector AAV2, the fusion protein comprising ZF-FKBP which binds the CEM FK506 (which is linked to another CEM that induces increased expression), the CEM CEM87, the specific agent FK506 alone (i.e., not linked to another CEM that blocks increased expression) which blocks the increased expression. However, those examples are not sufficient to provide written description support for the full breadth of the broad genera claimed. Although the claims claim the functional characteristics (i.e., encoding any transgenes and polynt or expression cassettes for encoding any transgene and any NBD recognition sequence; being a transgene delivery vector; recognizing a NBD domain or being a NBD that binds DNA or RNA; binding a CEM, being a fusion protein comprising a NBD domain that binds to any recognition sequence fused to a domain that binds a CEM; NBDs and NBDs that are DNA- or RNA-binding domains; being a CEM or CEM that causes increased/decreased transgene expression; binding a transcriptional activator/inhibitor; encoding a functional nucleic acid; inhibiting binding between the fusion protein and the CEM; and being a transgene capable of treating any disorder), none of the functional characteristics is coupled with any known structure.
Although the Specification teaches the examples discussed above, it does not identify a core structure necessary for performing the claimed function(s). The Spec. does not disclose any core structure, partial structure, physical or chemical property, or functional characteristic coupled with a known or disclosed structure/function relationship responsible for each claimed function in such a way to demonstrate possession of the full invention as claimed at time of filing. The genera of molecules claimed (vectors, transgenes, fusion proteins, NBDs/DNA-binding domains (BD)/RNA-binding domains, NBD/DNA-BD/RNA-BD recognition sequences, domains that bind a CEM, CEMs, CEMs that cause increased or decreased expression or bind to a transcriptional activator or inhibitor protein or complex, transgenes for treating disorders, CEMs comprising FK506, functional nucleic acids, CEMs that bind to a transcriptional activator or inhibitor protein or complex) and species within those genera do not share any core structure.
The specification teaches only the few species discussed above (i.e., the transgenes GFP and luciferase, the delivery vector AAV2, the fusion protein comprising ZF-FKBP which binds the CEM FK509, the CEM CEM87, the specific agent FK506 alone which blocks the increased expression) but those are only a paltry number compared with the breadth of what is claimed. Altogether, the number of species disclosed by complete structure is not sufficient to provide the written description support for the huge genera and subgenera that are encompassed by the claims.
While none of these elements is specifically required to demonstrate possession, in combination their absence means that one skilled in the art at the time of filing would conclude that the inventors lacked possession of the full breadth of the invention claimed. Claims 2-3, 9, 11, 14, 17, 20-21, 25, and 28-29 are rejected for failing to demonstrate possession of the claimed invention. Claims 3-4, 9, 11-12, 14, 17, 19-21, and 25-29 are rejected because they depend from Claim(s) 2-3, 9, 11, 14, 17, 20-21, 25, and/or 28-29 and do not remedy the issues.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for:
Claim 2. A method of modulating expression of a transgene from a transgene delivery vector in a cell or organoid, the method comprising:
administering to the cell or organoid a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence;
administering to the cell or organoid a fusion protein comprising a nucleic acid binding domain fused to a domain that binds a chemical epigenetic modifier, wherein the nucleic acid binding domain binds to the recognition sequence; and
administering to the cell or organoid the chemical epigenetic modifier;
thereby modulating expression of the transgene;
Claim 3. An in vitro method of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector, the method comprising:
administering a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence;
administering a fusion protein comprising a nucleic acid binding domain fused to a domain that binds a chemical epigenetic modifier, wherein the nucleic acid binding domain binds to the recognition sequence; and
administering the chemical epigenetic modifier;
thereby modulating expression of the transgene; and
Claims 2-3 and 11-12: the claims should specify that the polynt encodes the recited components up to the size limit of the delivery vector, does not reasonably provide enablement for methods of modulating expression of a transgene in any subject or methods of treating in any subject any disease by expressing any transgene. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims. This is a scope of enablement rejection.
The factors to be considered in determining whether a disclosure would require undue experimentation include: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the specification; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 8 USPQ2d, 1400 (CAFC 1988) and MPEP 2164.01.
The breadth of the claims and the nature of the invention: With respect to claim breadth, the standard under 35 U.S.C. §112(a) entails determining what the claims recite and what the claims mean as a whole. Claim 2 recites a method of modulating expression of a transgene from a transgene delivery vector in a subject. The broadest reasonable interpretation (BRI) of the method of Claim 2 is that the methods encompass modulating expression of any transgene in a subject. The nature of the invention is a method of modulating transgene expression in a subject. Methods of Claims 2 and claims depending therefrom have been interpreted as methods of treatment because they recite modulating transgene expression in a subject. This interpretation is consistent with the contemplated use of these methods as treatment claims in specification (¶3, ¶9-10, ¶130, and others). The Spec. explicitly discloses (¶3) the invention relates to methods and compositions for gene therapy.
Claim 3 recites a method of treating any condition that is treatable by expression of a transgene from a transgene delivery vector in a subject in need thereof. The BRI of the method of Claim 3 is that the methods encompass treating in a subject any disorder that is treatable by expressing in a subject any transgene from a transgene deliver vector, wherein the method comprises…. The nature of the invention is methods for modulating expression of any transgene in a subject and for treating any disorder that is treatable by expression of a transgene in a subject.
The BRI of Claims 2-3 (and claims depending therefrom) encompasses that the polynt encodes any size of transgene.
Claims 11-12 recite the same polynt encodes the fusion protein and the transgene. The BRI of Claims 11-12 is just that: the same polynt encodes the fusion protein and any size of transgene. The nature of the invention of Claims 11-12 is a method of modulating expression of any transgene in a subject by administering to the subject a transgene delivery vector comprising a polynt comprising a transgene expression cassette and a NBD recognition sequence and further encoding a fusion protein comprising a NBD, wherein the NBD is fused to a domain that binds a chemical epigenetic modifier and wherein the NBD binds the NBD recognition sequence.
A skilled artisan would not be able to use the methods as claimed with a reasonable expectation of success based solely on what is disclosed in the specification.
The state of the art and prior art, the level of one of ordinary skill, and the level of predictability in the art: The art of Patnaik (et al. 2023. Epigenetic Modulators as Therapeutic Agents in Cancer. Int. J. Mol. Sci. 24:14964, “Patnaik”) discusses modulating epigenetics in therapeutic contexts. Patnaik is generally drawn to using drugs to modulate endogenous epigenetics, but the teachings are still relevant to the claimed invention. Patnaik teaches (Table 1, §6. Current Challenges and Discoveries, ¶1) some epigenetic modifier drugs suffer from toxicity and inefficient delivery to tumor sites (which affects their efficacy), and have issues of durability and long-term stability. Patanik teaches (same § and ¶) some epigenetic drugs are cytotoxic and that in general, cytotoxicity is one of the main reasons epigenetic drugs need to undergo thorough testing. To that point, Patanik shows (Table 1) many epigenetic modifiers have been discontinued. Patanik discusses (§6. Current Challenges and Discoveries, ¶2) while CRISPR technologies have the potential for targeted manipulation of epigenetic shifts, epigenome editing is still in its early stages… Precision is one of the main issues. For example, a stud[y] shows the potential error in the system, raising concerns about potential off-target effects. An artisan would understand that means epigenetic modifying drugs require thorough testing before they can be administered to a subject, especially a subject suffering from a disorder.
Patanik’s teachings indicate (same § final ¶) it’s difficult to even determine whether epigenetic treatment is working because the epigenome is both tissue-specific and condition-specific… [which] leads to issues because the risk markers must be present in bodily fluids, such as blood or saliva for detection. An artisan would understand that means it’s difficult to determine whether the claimed method is actually working because making such a determination would require testing a variety of bodily fluids for markers and knowing which fluids to test, which varies depending on gene, tissue, and condition. Those are variables that Applicant’s Spec. simply hasn’t addressed.
In addition, Lu (2022. Dissertation: Development and Optimization of Chemical Epigenetic Modifiers. Dissertation submitted at UNC Chapel Hill, “Lu”) teaches (PDF p. 29, full ¶1) the art of gene-specific control of chromatin is not currently possible in the clinical setting. That statement was made in 2022, which is after the filing date of the claimed invention.
Furthermore, the prior art of Rittiner (et al. 2020. Gene-Editing Technologies Paired With Viral Vectors for Translational Research Into Neurodegenerative Diseases. Front. Mol. Neurosci. 13:148, “Rittiner”) teaches (Table 3, §In vivo Applications and Size Constraints) there is an upper limit to the size of a gene that can be placed on a vector. That teaching indicates that, without evidence to the contrary, it would not be possible to modulate expression of any transgene of any size, especially when (Claims 11-12) the transgene is placed on the same polynt as the fusion protein.
The prior art shows there are disorders whose cause is unknown. For example, the art of Raising Children Network (2025. Syndromes without a name [SWAN]. Available online at raisingchildren.net.au. Accessed on 25 June 2026, “RCN”) teaches (§About syndromes without a name [SWAN] ¶2) ‘Syndromes without a name’ is a term that doctors might use when a child has symptoms of a genetic condition, but these symptoms can’t yet be diagnosed [as any particular disease]. RCN teaches (§Why are conditions not diagnosed?) some conditions can’t be diagnosed because symptoms of genetic conditions often overlap, which makes it hard to diagnose or recognize them and because many rare conditions don’t have diagnostic tests available because the genes causing the condition have not yet been identified.
For those reasons, it would not be possible to determine whether or not any disorder is treatable by expression of a transgene. Furthermore, although Applicant teaches (¶170) some illustrative disease states that can be treated, the prior art of Espe (2018. Malacards. J. Med. Libr. Assoc. 106[1]:140-141, “Espe”) teaches (¶2) one database records there are more than 26,000 diseases that affect the human body. Applicant hasn’t provided guidance that discloses how to determine whether or not any of those disorders—or a representative number of them—is treatable by delivering a transgene.
Additionally, even if it were possible to know that certain disorders are theoretically treatable by expression of a transgene, Applicant hasn’t shown it would be able to treat all or any of them using their method. The art of Abou-el-Enein (et al. 2021. Evidence generation and reproducibility in cell and gene therapy research: A call to action. Molec. Ther. 22:11-14, “Abou”) teaches that (p. 1 ¶1-2) although cell and gene therapies (CGT) are expected to transform into treatment options for a wide spectrum of conditions, inadequate evidence on actual therapeutic efficacy has led several CGTs to be withdrawn from market due to heterogeneity in treatment response and toxicities, targeting rare diseases with low patient accrual and lack of suitable comparators in clinical trials, and the need for long-term safety and efficacy follow up studies, among others. Abou also discusses CGT are risky: the mode of action for gene therapies, in many cases, relies on introducing permanent changes to human cells and tissues, which, in turn, increases the risk of unforeseen and delayed adverse events. Abou continues (p. 1 ¶3) preclinical testing of CGTs has, in some instances, limited capability for generating informative evidence. Abou teaches (same ¶) cell and mouse models often fail to adequately reproduce features of the target patient population and do not accurately reflect later findings in treated patients. Abou teaches (same ¶) pre-clinical studies, such as toxicokinetics and mode of action, are technically difficult to perform for CGTs.
Abou’s teachings indicate that CGT that appear to be efficacious—even if they pass regulatory testing and move to market—may not actually treat a condition (i.e., several CGTs have been withdrawn from market due to lack of actual efficacy). Abou’s teachings indicate obtaining data about efficacy can be difficult due to low patient accrual and lack of suitable comparators in clinical trials. That means it’s difficult to determine that a CGT treats a condition, even as a CGT moves through clinical trials. Abou’s teachings indicate there are pitfalls to preclinical studies even if they have been performed using model mice and model cells. Abou’s teachings relate to the claimed invention because Claim 3 encompasses a method of treating any disorder. However, Abou teaches that even when there are ample preclinical (i.e., relevant cell and mouse studies investigating efficacy of a specific CGT for a specific disorder) and clinical disease-specific data (i.e., from humans afflicted with a disease), it is still difficult to determine that any CGT is capable of treating a disorder. In the case of the instant invention, Applicant hasn’t provided any data showing any sort of treatment whatsoever. Therefore an artisan would reasonably conclude that it is certainly not possible to make any declaration about treating a disorder without at least preclinical, disease-specific data.
Finally, FDA (2025. FDA News Release: FDA Requests Sarepta Therapeutics Suspend Distribution of Elevidys and Places Clinical Trials on Hold for Multiple Gene Therapy Products Following 3 Deaths. Available online at fda.gov. Accessed on 25 June 2026, “FDA”) indicates there are risks associated with gene therapies which means that practically speaking, they are not necessarily suitable for treating, in any subject, any disorder that is theoretically treatable by expression of a transgene. The Sarepta drug, designed to deliver into the body a gene that leads to production of Elevidys micro-dystrophin, killed three children because the AAV serotype used led to liver failure. A person of ordinary skill would conclude that FDA indicates it is simply not practically possible to treat any disorder that is theoretically treatable by expressing a transgene.
Altogether, a person of ordinary skill would conclude that Patnaik, Rittiner, Lu, RCN, Espe, Abou, and FDA indicate the full scope of the method of Claims 2-3 and 11-12 (and claims depending therefrom) is not enabled.
The amount of direction provided by the specification and the existence of working examples: What is enabled by the working examples does not enable the breadth of the claims. Regarding Lu and the basis for the claimed invention, the Spec. discusses (¶213) CEMs recruit endogenous chromatin modifying enzymes to modulate transcription. That indicates that the claimed invention works because the CEMs result in chromatin modification. But Lu teaches (as of 2022, cited above) the art of gene-specific control of chromatin is not currently possible in the clinical setting.
The Examples (which start at ¶213) show administering to HEK293 cells the transgene delivery vector AAV2 comprising a polynt comprising a transgene expression cassette (wherein the transgene is luciferase or GFP) and a NBD recognition sequence (i.e., zinc finger binding domain) and administering to the cells a fusion protein comprising a NBD fused to a domain that binds a CEM (i.e. zinc finger–FK506-binding protein [ZF–FKBP]), wherein the NBD binds the recognition sequence, and administering to the subject the CEM (i.e., FK506 linked to CEM87) (which constitutes the method of Claim 2 whose scope is described here as enabled), and finding increased GFP fluorescence and luciferase luminescence. The Examples (e.g., Figs. 7-10 and 15-18) show administering the CEM, CEM87, increases transgene expression to protein. Those experiments show the method of Claim 2 successfully results in transgene delivery and expression.
Those experiments do not show a method of successfully modulating transgene expression in a subject or treating any disorder that is treatable by expression of a transgene. Those experiments do not show a method of successfully treating any disorder at all.
Nothing in the Spec. shows any administration to a subject or any preclinical model of any disorder or disease. The only examples show transgenes encoding GFP or luciferase.
The Spec. provides no evidence of using the claimed method to administer anything to a subject or to treat any disorder whatsoever. As discussed above, Abou describes demonstrating efficacious CGT requires carrying out certain preclinical experiments. Nothing in the Spec. indicates any experiments were carried out in any subject or model of any disorder/disease—neither in vitro nor in vivo models. Nothing in the Spec. demonstrates any expression control in any subject or any improvement in any particular disorder, let alone the full breadth of disorders claimed.
Although the level of an artisan is high, the art of merely identifying disorders treatable by expression of a transgene is unpredictable (as taught by RCN). The art of treating disorders is even more unpredictable (as discussed in Abou and demonstrated by FDA). The art of modulating epigenetics is also unpredictable (as discussed by Patnaik). The art of gene-specific control of chromatin is not currently possible in the clinical setting (as of 2022 which is after the filing date of the claimed invention), as taught by Lu. Rittiner described other practical considerations that indicate using the full breadth of the claimed invention is unpredictable.
To overcome a prima facie case of lack of enablement, applicant must present argument and/or evidence that the disclosure would have enabled one of ordinary skill in the art to make and use the claimed invention at the time of filing. [emphasis added.]
MPEP §2164.05
Specification Must Be Enabling as of the Filing Date [R-07.2022]
Whether the specification would have been enabling as of the filing date involves consideration of the nature of the invention, the state of the prior art, and the level of skill in the art. The initial inquiry is into the nature of the invention, i.e., the subject matter to which the claimed invention pertains. The nature of the invention becomes the backdrop to determine the state of the art and the level of skill possessed by one skilled in the art.
The state of the prior art is what one skilled in the art would have known, at the time the application was filed, about the subject matter to which the claimed invention pertains. The relative skill of those in the art refers to the skill of those in the art in relation to the subject matter to which the claimed invention pertains at the time the application was filed. See MPEP § 2164.05(b). See Pac. Biosciences of Cal., Inc. v. Oxford Nanopore Techs., Inc., 996 F.3d 1342, 1352, 2021 USPQ2d 519 (Fed. Cir. 2021). [emphasis added.]
MPEP §2164.05(a)
An artisan would necessarily conclude that the method could not be used as claimed in a subject or to treat any disorder(s) encompassed by the claims.
The quantity of experimentation needed to make or use the invention: The standard of an enabling disclosure is not the ability to make and test if the invention works but one of the ability to make and use with a reasonable expectation of success. A patent is granted for a completed invention, not the general suggestion of an idea (MPEP 2164.03 and Chiron Corp. v. Genentech Inc., 363 F.3d 1247, 1254, 70 USPQ2d 1321, 1325-26 (Fed. Cir. 2004). The instant specification is not enabling because one cannot follow the guidance presented therein or within the art at the time of filing, and practice the claimed method without first making a substantial inventive contribution. Given teachings of Patnaik, Lu, Rittiner, RCN, Espe, Abou, and FDA, an artisan of ordinary skill would not be able to use the invention as claimed with a reasonable expectation of success. The amount of experimentation required for enabling guidance commensurate in scope with what is claimed goes beyond what is considered “routine” within the art and constitutes undue further experimentation in order to successfully use the method of modulating expression of a transgene in a subject (Claim 2) or method of treating any disorder that is treatable by expression of a transgene in a subject (as recited in Claim 3) with any reasonable expectation of success. Claims 2-3 and 11-12 are rejected for those reasons. Claims 4, 9, 11-12, 14, 17, 19-21, and 25-29 are rejected because they depend from Claims 2 and/or 11 and don’t remedy the issues.
In conclusion, the specification provides enablement for:
Claim 2. A method of modulating expression of a transgene from a transgene delivery vector in a cell or organoid, the method comprising:
administering to the cell or organoid a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence;
administering to the cell or organoid a fusion protein comprising a nucleic acid binding domain fused to a domain that binds a chemical epigenetic modifier, wherein the nucleic acid binding domain binds to the recognition sequence; and
administering to the cell or organoid the chemical epigenetic modifier;
thereby modulating expression of the transgene; and
Claim 3. An in vitro method of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector, the method comprising:
administering a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence;
administering a fusion protein comprising a nucleic acid binding domain fused to a domain that binds a chemical epigenetic modifier, wherein the nucleic acid binding domain binds to the recognition sequence; and
administering the chemical epigenetic modifier;
thereby modulating expression of the transgene.
Claims 2-3 and 11-12 should specify that the polynt encodes the recited components up to the size limit of the delivery vector.
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
A claim may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173. In the present instance, Claims 2 and 3 recite …administering to the subject a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier…. The claim(s) are considered indefinite because there is a question or doubt as to what are the metes and bounds of the claim. It is not clear what structure is fused to a domain that binds a chemical epigenetic modifier.
Claims 2 and 3 are rejected for those reasons. Claims 3-4, 9, 11-12, 14, 17, 19-21, and 25-29 are rejected because they depend from Claim 2 and do not remedy the issues.
In the interest of compact prosecution, the claims are interpreted as reciting: …administering to the subject a fusion protein comprising a nucleic acid binding domain fused to a domain that binds a chemical epigenetic modifier, wherein the nucleic acid binding domain binds to the nucleic acid binding domain recognition sequence…
In the present instance, Claim 3 recites a method of treating a disorder that is treatable by expression of a transgene…. The claim(s) are considered indefinite because there is a question or doubt as to what are the metes and bounds of the claim. It is not clear what constitutes a disorder that is treatable by expression of a transgene. It is not clear what disorder(s) is or is not treatable by expression of a transgene. Although the Spec. discloses (¶170) some diseases/disorders that the transgene delivery vectors of the present invention can be employed… to treat, those are merely illustrative disease states but are not limiting. An artisan wouldn’t know what disorders are or are not included in the genus of disorders that are treatable by expression of a transgene. Furthermore, despite the fact that the Spec. defines (¶64) “treating”, what is deemed to reduce or to at least partially improve or ameliorate the severity of the subject's condition and/or to alleviate, mitigate or decrease in at least one clinical symptom and/or to delay the progression of the condition can vary depending on the eye of the beholder.
Claim 3 is rejected for those reasons. In the interest of compact prosecution, the claims are interpreted as reciting a method of attempting to address any symptom or characteristic of any disorder.
In the present instance, Claim 9 recites a functional nucleic acid. The claim(s) are considered indefinite because there is a question or doubt as to what are the metes and bounds of the claim because the term isn’t defined in the Spec. and because what constitutes a functional nucleic acid can vary depending on the eye of the beholder.
Claim 9 is rejected for those reasons. In the interest of compact prosecution, the claims are interpreted as reciting the transgene encodes any nucleic acid that produces, by itself without being translated to protein, any function: any aptamer, any antisense oligonucleotide, any RNAi, any miRNA.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c).
In the present instance, Claim 14 recites the broad recitation wherein the nucleic acid binding domain is a DNA binding domain, and the claim also recites optionally wherein the DNA binding domain comprises one of a zinc finger… or TALES which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower “optional” language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. It is not clear whether the DNA binding domain is intended to be any DNA binding domain or is limited to the “optional” species recited in the claim. In the interest of compact prosecution, the DNA binding domain is interpreted as encompassing any DNA binding domain and those recited in the claim are interpreted as exemplary and fully optional.
In the present instance, Claim 17 recites the broad recitation wherein the nucleic acid binding domain is a RNA binding domain, and the claim also recites optionally wherein the RNA binding domain binds a MS2… or Qβ hairpin motif which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower “optional” language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. It is not clear whether the RNA binding domain is intended to be any RNA binding domain or is limited to the “optional” species recited in the claim.
In the interest of compact prosecution, the RNA binding domain is interpreted as encompassing any RNA binding domain and those recited in the claim are interpreted as exemplary and fully optional.
In the present instance, Claim 21 recites the broad recitation …wherein the CEM binds to a transcriptional activator protein or complex, and the claim also recites optionally BRD4 or CBP/p300, optionally wherein the CEM comprises compound 1 (CEM87)… which is the narrower statement of the range/limitation. Claim 29 recites the broad recitation …wherein the CEM binds to a transcriptional inhibitor protein or complex, and the claim also recites … optionally wherein the CEM binds to a histone deacetylase, optionally wherein the CEM comprises… which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower “optional” language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. It is not clear whether the transcriptional activator or inhibitor protein or complex is intended to be any transcriptional activator or inhibitor protein or complex or is limited to the “optional” species recited in the claim. It is not clear whether the CEM is intended to be any CEM or is limited to the species recited in the claim.
In the interest of compact prosecution, the CEM of Claim 21 is interpreted as encompassing any CEM that binds to a transcriptional activator protein or complex and the CEM of Claim 29 is interpreted as encompassing any CEM that binds to a transcriptional inhibitor protein or complex. The optional limitations recited in the claims are interpreted as exemplary and fully optional.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 2-4, 9, 14, 17, 19-21, and 25-29 are rejected under 35 U.S.C. 103 as being unpatentable over International Publication Number WO 2019/028426 (published 07 February 2019, “WO426”, of record) and Alhaji (et al. 2018. Silencing of transgene expression in mammalian cells by DNA methylation and histone modifications in gene therapy perspective. Biotechnol. Genetic Engineer. Rev. 35[1]:1-25, “Alhaji”).
NOTE: references to p. # of WO document refer to PDF p. #. References to ¶ # count ¶1 as the first full ¶ on a p. ¶0 is the first partial ¶ on a p.
WO426 teaches (§Abstract) methods of using bifunctional chemical epigenetic modifiers (CEM). Regarding some limitations of Claims 2-3: WO426 teaches (pp. 4-5 ¶4-1):
methods of increasing expression of a target gene in a cell, the method comprising:
a) expressing a fusion protein in the cell, wherein the fusion protein comprises a catalytically inactive Cas9 (dCas9) and a FK506 binding protein (FKBP), wherein the catalytically inactive Cas9 (dCas9) is bound to a [sic] one or more guide RNAs, wherein the one or more guide RNAs bind upstream or downstream of a target gene;
b) contacting the cell with a bifunctional chemical epigenetic modifier (CEM) comprising a FK506 or a derivative thereof, a linker and a bifunctional ligand, wherein the FK506 binds to the FKBP of the fusion protein; and
c) mobilizing effector proteins to the target gene, wherein the effector genes are activated by the bifunctional ligand; wherein the expression of the target gene is increased.
WO426 (Figs. 1, 9-10, and 19) show that FK506 may be connected to a CEM.
WO426 simply uses different terminology to describe the same concept as the instant claims: WO426 describes expressing in a cell (i.e., administering to a cell) a fusion protein comprising a dCas9 and an FKBP wherein the dCas9 is bound to a guideRNA that binds upstream of a target gene. That describes a fusion protein that comprises a NBD fused to a domain that binds a CEM, wherein the NBD binds to a recognition sequence. The instantly claimed fusion protein is WO426’s dCas9–FKBP. The dCas9 bound to a guide RNA is what comprises a NBD that binds upstream (or downstream) of a target gene. Then WO426’s step (b)—contacting the cell with a bifunctional chemical epigenetic modifier (CEM) comprising aFK506 or a derivative thereof, a linker and a bifunctional ligand, wherein the FK506 binds to the FKBP of the fusion protein—discloses what is instantly claimed as administering to the subject [or the enabled scope to a cell] a CEM, thereby modulating expression of the transgene. WO426’s step (c)—mobilizing effector proteins to the target gene, wherein the effector genes are activated by the bifunctional ligand—is an inevitable outcome of administering the FK506-linker-CEM because WO426 teaches (Example 11, starts on p. 68 ¶2) the bifunctional molecule system redirects chromatin machinery to a specific gene locus.
Regarding Claims 14 and 28: WO426 teaches (p. 29) ¶2) their methods use dCas9 which interacts with guide RNAs to place the desired editing proteins to specific sites, and the methods can be used to repress or activate expression of one or more target genes. WO426 teaches (p. 30 ¶1-3) their methods can use other agents including GCN4, zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALENs). WO426 teaches (p. 39 ¶2) a GAL4 DNA-binding array. A variety of DNA binding domains and DNA binding domain recognition sites are shown in the WO426 Figs.: Figs. 1-2, 5, 7, 9-10 show a Gal4 NBD recognition site binding to Gal4-FKBP. Figs. 9B and 19 show guide RNA–dCas9–FKBP binding to a NBD recognition site (i.e., the target site of the guide RNA or the dCas9-binding site).
Regarding Claim 17: WO426 teaches (p. 30 ¶2) the methods can incorporate ms2-compatible gRNAs which have a modified stem loop capable of recruiting dCas9 or MS2 coat protein (MCP)-fusion and that such incorporation can increase the number of FKBPs which physically increases the proximity of recruited CEM to chromatin.
Regarding Claim 19: WO426’s Fig. 19A shows that the domain that binds a CEM is FKBP and the CEM comprises FK506:
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In this case FKBP is the domain that binds a CEM and it binds the CEM comprising FK506–linker–recruitment warhead.
Regarding Claim 20: WO426 teaches (Figs. 21 and 30 and their captions, p. 20 ¶3, and as described above: p. 5 ¶1) contacting the cell with the CEM comprising FK506 and a bifunctional ligand mobilizes effector proteins to the target gene and activates them which increases expression of the target gene.
Regarding Claim 21: WO426 teaches (Fig. 19 and its caption) a dCas9 CEMa system that recruits endogenous chromatin modifying machinery to regulate transcriptional activity and teaches the CEMs CEM87, CEM88, and CEM114 respectively recruit the specific activating chromatin-modifying machinery BRD2,3,4, BRF1, and CBP/p300.
Regarding Claims 25-26: WO426 teaches (p. 24 ¶0) their bifunctional CEMs can repress or activate gene transcription. WO426 teaches (same §, Fig. 28) excess FK506 outcompetes CEM23 for the FKBP binding site. This is useful to tightly regulate changes to gene transcription allowing for rapid reversal of biological action. That indicates WO426 teaches blocking the effect of their bifunctional ligands—whether the effect of the bifunctional ligands is increased or decreased gene expression—by administering FK506 because FK506 outcompetes the bifunctional ligand. Administering excess FK506 would outcompete the binding between the bifunctional ligand and the fusion protein and would thereby block the increased expression that was previously induced by binding between the bifunctional ligand and the fusion protein. Therefore WO426 teaches limitations of Claims 25-26.
Regarding Claims 28-29: WO426 teaches (p. 24 ¶0) their bifunctional CEMs can repress gene transcription by binding to HDAC inhibitors which recruit HDAC activity and cause target gene repression. WO426 teaches (p. 41, §Example 2, Figs. 1B and 2) the inhibitor CEM23 which represses transcription of the gene encoding GFP. A person of ordinary skill knows that HDACs are transcriptional inhibitors. Therefore WO426 teaches limitations of Claims 28-29.
Regarding methods of treatment, WO426 teaches (p. 25 §Methods of Treatment ¶1 and entire §) methods of treating various conditions in a subject and (p. 26 ¶1-2) methods of reducing or increasing target gene expression in a cell.
Altogether, WO426 teaches the general idea of the claimed invention.
WO426 does not teach using their methods or system to modulate transgene expression.
However, Alhaji teaches (§Abstract) transgene silencing by epigenetic modifications is a major challenge to achieving effective gene therapy for many genetic conditions. Alhaji teaches (§Introduction ¶2) epigenetic silencing of a transgene affects genes carried on both integrating and non-integrating systems, including (§Epigenetics transgene silencing effect on non-integrating vectors ¶4) the non-integrating viral vectors most commonly used in gene therapy, adenovirus (AdV) and adeno-associated virus (AAV).
Regarding Claim 4: Alhaji’s teachings (§Introduction ¶2) indicate that it is common to deliver a transgene on a viral vector or a nonviral vector.
Regarding Claim 9: Alhaji teaches (§Introduction ¶1) transgenes can encode fluorescent proteins or can be used for therapeutic intervention, in which a therapeutic gene is delivered to mammalian cells to augment, supplement, or replace a defective disease-causing gene in order to correct a genetic defect. Alhaji provides the example of using AAV to express the protein human clotting factor IX.
Altogether, Alhaji teaches that modulating epigenetic silencing of a transgene was of interest in the field of gene therapy.
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods for modulating gene expression of WO426 with the teachings regarding silencing of transgenes in gene therapy of Alhaji for the benefit of using the WO426 methods to regulate transgene expression in gene therapy. One would have been motivated to do so with a reasonable expectation of success because WO426 teaches methods of regulating gene expression—either increasing or decreasing it—by recruiting epigenetic machinery and because Alhaji teaches transgene silencing by epigenetics impedes gene therapy and that regulating transgene expression was of interest in the gene therapy field. One would have been motivated to do so with a reasonable expectation of success because WO426’s method uses guide RNA to target their system to any target gene and there is no reason why the system couldn’t be used to target the system to a transgene of interest (which Alhaji teaches can be silenced by endogenous epigenetic silencing mechanisms).
Specifically regarding Claims 2-3, it would have been obvious to modify WO426’s method of modulating gene expression by targeting their fusion protein or fusion protein–guide RNA to Alhaji’s transgene delivery vector wherein the transgene had been epigenetically silenced. It would have been obvious to design a transgene delivery vector to comprise a NBD recognition sequence that would bind WO426’s fusion protein or fusion protein comprising a target-specific guide RNA because an artisan would have known they would use the system of WO426 to target any nucleic acid and that doing so would require placing appropriate NBD recognition sequence(s) in the polynt. One would have been motivated to do so because Alhaji teaches (§DNA methylation and gene expression ¶2; §Histone modification and gene expression ¶4; §Silencing of transgene expression in gene therapy ¶1-2; §Epigenetics transgene silencing effect on non-integrating vectors ¶4) methylation of transgene promoters leads to the decline of transgene expression.
Specifically regarding Claim 27, it would have been obvious to block the increased expression of the transgene by stopping administering the CEM because WO426 teaches (p. 24 ¶0, p. 68 §Example 11) their bifunctional CEM recruits transcriptional activation machinery, so an artisan would have known that withdrawing the CEM or interrupting the contact between the transgene delivery vector and the CEM would have blocked the increased expression.
Modifying the method of WO426 to target a transgene that was epigenetically silenced would have produced all the limitations of Claims 2-4, 9, 14, 17, 19-21, and 25-29.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29 are rejected under 35 U.S.C. 103 as being unpatentable over WO426 and Alhaji as applied to Claims 2-4, 9, 14, 17, 19-21, and 25-29 above, and further in view of Santos-Moreno (et al. 2020. Multistable and dynamic CRISPRi-based synthetic circuits. Nat. Comm. 11:2746, “Santos”) and Bashor (and Collins. 2018. Understanding Biological Regulation Through Synthetic Biology. Annu. Rev. Biophys. 47:399-423, “Bashor”).
The teachings of WO426 and Alhaji as applicable to Claims 2-4, 9, 14, 17, 19-21, and 25-29 have been described above.
WO426 and Alhaji teach methods of modulating expression of a transgene from a transgene delivery vector and methods of treating a disorder in vitro, the method comprising administering to the subject a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence; administering to the subject a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier; and administering to the subject the chemical epigenetic modifier; thereby modulating expression of the transgene.
WO426 and Alhaji do not teach that the polynt encoding the transgene further comprises a sequence encoding the fusion protein (Claim 11) or that the transgene expression cassette and the sequence encoding the fusion protein are operably linked to the same promoter or separate promoters (Claim 12).
However, Santos, drawn to CRISPR-based synthetic circuits, teaches genetic circuits that comprise a transgene expression cassette (i.e., encoding GFP), and a nucleic acid binding domain recognition sequence (i.e., a PAM + gRNA binding site), and a single guide RNA (sgRNA) all on the same plasmid or genetic circuit. Santos teaches (Fig. 1) the following circuit, shown here as a simplified excerpt of Fig. 1:
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That shows the transgene, NBD, and sgRNA are encoded on the same plasmid.
Regarding Claim 12, Santos shows the sgRNA and GFP are each operably linked to their own promoter (i.e., “separate promoters”). Therefore Santos teaches limitations of Claim 12.
Santos teaches (§Results and discussion-Design features and CRISPRi testing ¶1-2) their sgRNA was induced by Ara and that dCas9 was expressed from a separate plasmid to keep the levels constant.
However, a person of ordinary skill in the art would have understood that there is no reason why dCas9—or the fusion protein of WO426—could not have been expressed from the same single plasmid as the sgRNA (i.e., NBD) and transgene + NBD recognition sequence. Santos teaches (§Results and discussion-Design features and CRISPRi testing ¶1) the main circuit components were all expressed from a single vector (so-called variable vector) to avoid fluctuations in their stoichiometry.
To that end, Bashor, drawn to a review about genetic circuits, teaches biological components are modular and can be combined as desired to produce a synthetic, user-controlled genetic circuit. Bashor teaches (§2. SYNTHETIC GENE CIRCUITS AS PHYSICAL MODELS FOR STUDYING REGULATORY FUNCTION ¶1) biological systems are organized according to a scalable, modular hierarchy and their network motifs often appear in analogous physiological contexts, implying a modularity of function. Bashor teaches (same §, ¶2) a bioengineer is fully capable of constructing a circuit comprising various modular components, including establishing user control over circuit input, and iteratively adjusting the design until the desired behavior is achieved.
It would have been obvious to encode all the elements necessary for the method of WO426 and Alhaji, namely the transgene and the NBD recognition sequence upstream of it, as well as the fusion protein–guide RNA, on the same plasmid to avoid fluctuations in their stoichiometry and make sure that the entire system necessary for the method was delivered to each cell. An artisan would have known it is possible to encode the system of WO426 on a single plasmid because WO426 teaches it is possible to encode the fusion protein comprising a NBD fused to a domain that binds a CEM (wherein the NBD binds to a NBD recognition sequence) on a polynt and Santos and Bashor would have shown an artisan that polynt can be combined in a modular way.
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods of modulating transgene expression or methods of treating a disorder in vitro of WO426 and Alhaji with the synthetic circuit of Santos and teachings of Bashor. One would have done so for the benefit of producing a single polynt encoding the transgene and the NBD recognition sequence upstream of it (wherein the transgene is operably linked to a promoter as shown in Santos Fig. 1) and the fusion protein comprising a NBD fused to a domain that binds a CEM (wherein the NBD binds to the NBD recognition sequence) which would have made it easier to ensure that each cell of interest received the entire system of WO426 and Alhaji and would have allowed the artisan to avoid fluctuations in stoichiometry of the various components. One would have been motivated to do so with a reasonable expectation of success because Santos teaches expressing circuit components from a single vector avoids fluctuations in component stoichiometry and because the teachings of Santos and Bashor indicate that producing a genetic circuit comprising known component (which are inherently modular) s is routine and conventional in the art of synthetic biology.
Modifying the methods of WO426 and Alhaji with the teachings of Santos and Bashor would have produced the limitations of Claims 11-12 (and Claims 2-4, 9, 14, 17, 19-21, and 25-29).
Claims 2-4, 9, 14, 17, 19-21, and 25-29 are rejected under 35 U.S.C. 103 as being unpatentable over WO426 and Alhaji as applied to Claims 2-4, 9, 14, 17, 19-21, and 25-29 above, and further in view of Peng (et al. 2006. A transgenic approach for RNA interference-based genetic screening in mice. PNAS 103[7]:2252-2256, “Peng”).
The teachings of WO426 and Alhaji as applicable to Claims 2-4, 9, 14, 17, 19-21, and 25-29 have been described above.
WO426 and Alhaji teach method of modulating expression of a transgene from a transgene delivery vector and methods of treating a disorder in vitro, the method comprising administering to the subject a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence; administering to the subject a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier; and administering to the subject the chemical epigenetic modifier; thereby modulating expression of the transgene.
WO426 and Alhaji do not teach that the transgene encodes a functional nucleic acid that is an RNAi (i.e., an alternative limitation of Claim 9).
However Peng, drawn to a transgenic approach for RNA interference-based genetic screening in mice, teaches (§Abstract) they successfully induced RNAi-induced gene knockdown by introducing into a mouse small hairpin RNA-expressing constructs as transgenes. That indicates that it was routine and conventional in the art to introduce into a cell or animal transgenes encoding RNAi.
Therefore, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods of modulating transgene expression or methods of treating a disorder in vitro of WO426 and Alhaji with the transgene encoding RNAi of Peng for the benefit of using the system of WO426 and Alhaji to control expression of RNAi. One would have been motivated to do so with a reasonable expectation of success because WO426 teaches their system can be applied to any gene, because Alhaji indicates it is possible to encode any gene on a plasmid that can be administered, and because Peng teaches they successfully induced RNAi in a mouse by introducing the RNAi on a transgene.
Modifying the methods of WO426 and Alhaji with the teachings of Peng would have produced the alternative limitation of Claim 9 (and Claims 2-4, 9, 14, 17, 19-21, and 25-29).
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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Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 11905537 (“US537”) in view of International Publication Number WO 2019/028426 (published 07 February 2019, “WO426”, of record), Alhaji (et al. 2018. Silencing of transgene expression in mammalian cells by DNA methylation and histone modifications in gene therapy perspective. Biotechnol. Genetic Engineer. Rev. 35[1]:1-25, “Alhaji”), Santos-Moreno (et al. 2020. Multistable and dynamic CRISPRi-based synthetic circuits. Nat. Comm. 11:2746, “Santos”), and Bashor (and Collins. 2018. Understanding Biological Regulation Through Synthetic Biology. Annu. Rev. Biophys. 47:399-423, “Bashor”).
NOTE: references to p. # of WO document refer to PDF p. #. References to ¶ # count ¶1 as the first full ¶ on a p. ¶0 is the first partial ¶ on a p.
Although the claims at issue are not identical they are directed to overlapping subject matter.
The instant claims are directed to methods of modulating expression of a transgene from a transgene delivery vector and of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector, the method steps comprising: administering a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence; administering a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier; and administering the chemical epigenetic modifier; thereby modulating expression of the transgene or treating the disorder; wherein the delivery vector can be viral or nonviral, wherein the transgene can encode a protein or functional nucleic acid; wherein the polynt further comprises a sequence encoding the fusion protein and the transgene expression cassette and the sequence encoding the fusion protein are operably linked to the same promoter or to different promoters; wherein the NBD is a DNA-binding domain (that can be any of those recited in Claim 14) or an RNA-binding domain (that can be any of those recited in Claim 17); wherein the domain that binds a CEM is FKBP and the CEM is FK506; wherein contacting the delivery vector with the CEM increases transgene expression; wherein the CEM binds to a transcriptional activator protein or complex that can be BRD4 or CBP/p300 and the CEM can be CEM87 or CEM114; the method further comprising a step of blocking the increased transgene expression by contacting the vector with an agent that inhibits binding of the fusion protein to the CEM or by administering an agent that inhibits binding of the fusion protein to the CEM and wherein the fusion protein can be FKBP and the CEM can be FK506; and wherein the method comprises a step of blocking increased expression by stopping the contact between the delivery vector and the CEM or by stopping administering the CEM.
The patented claims are directed to a bifunctional CEM comprising FK506 or a derivative thereof, a linker, and a HDAC inhibitor or derivative thereof; wherein the linker can have various components; to a pharmaceutical composition comprising the composition; and to methods of using the bifunctional CEMs.
Both claim sets are directed to using bifunctional CEMs. Any element of the claimed invention that isn’t recited in the US537 claims would have been obvious in view of the prior art:
WO426 (§Abstract; pp. 4-5 ¶4-1; Figs. 1, 9-10, and 19; Example 11, starts on p. 68 ¶2; p. 29 ¶2; p. 30 ¶1-3; p. 39 ¶2; Figs. 1-2, 5, 7, 9-10; Figs. 9B and 19 and its caption; Figs. 21 and 30 and their captions, p. 20 ¶3, and as described above: p. 5 ¶1; (p. 24 ¶0; same §, Fig. 28; p. 24 ¶0; p. 41, §Example 2, Figs. 1B and 2; p. 25 §Methods of Treatment ¶1 and entire §; p. 26 ¶1-2; p. 24 ¶0, p. 68 §Example 11), Alhaji (§Abstract, §Introduction ¶2, §Epigenetics transgene silencing effect on non-integrating vectors ¶4, §DNA methylation and gene expression ¶2; §Histone modification and gene expression ¶4; §Silencing of transgene expression in gene therapy ¶1-2; §Epigenetics transgene silencing effect on non-integrating vectors ¶4), Santos (Fig. 1; §Results and discussion-Design features and CRISPRi testing ¶1-2), and Bashor (§2. SYNTHETIC GENE CIRCUITS AS PHYSICAL MODELS FOR STUDYING REGULATORY FUNCTION ¶1-2) teach all the limitations that the US537 claims don’t teach.
Therefore, it would have been obvious to a person of ordinary skill in the art to apply those teachings to the US537 claims for the benefits of using the CEM of the US537 claims to modulate transgene expression in gene therapy. One would have been motivated to do so with a reasonable expectation of success because WO426 teaches methods of regulating gene expression—either increasing or decreasing it—by recruiting epigenetic machinery and because Alhaji teaches transgene silencing by epigenetics impedes gene therapy and that regulating transgene expression was of interest in the gene therapy field. An artisan would have readily recognized that the compositions and methods of the US573 claims could be used with the teachings of WO426.
One would have been motivated to do so with a reasonable expectation of success because WO426’s method uses guide RNA to target their system to any target gene and there is no reason why the system couldn’t be used to target the system to a transgene of interest (which Alhaji teaches can be silenced by endogenous epigenetic silencing mechanisms). It would have been obvious to block the increased expression of the transgene by stopping administering the CEM because WO426 teaches (p. 24 ¶0, p. 68 §Example 11) their bifunctional CEM recruits transcriptional activation machinery, so an artisan would have known that withdrawing the CEM or interrupting the contact between the transgene delivery vector and the CEM would have blocked the increased expression. It would have been obvious to apply the teachings about synthetic circuits of Santos and Bashor for the benefit of producing a single polynt encoding the transgene and the NBD recognition sequence upstream of it (wherein the transgene is operably linked to a promoter) and the fusion protein comprising a NBD fused to a domain that binds a CEM (wherein the NBD binds to the NBD recognition sequence).
Doing so would have made it easier to ensure that each cell of interest received the entire system of WO426 and Alhaji and would have allowed the artisan to avoid fluctuations in stoichiometry of the various components. One would have been motivated to do so with a reasonable expectation of success because Santos teaches expressing circuit components from a single vector avoids fluctuations in component stoichiometry and because the teachings of Santos and Bashor indicate that producing a genetic circuit comprising known components is routine and convention in the art of synthetic biology.
Using the compositions and methods of the US537 claims with the teachings of WO426, Alhaji, Santos, and Bashor to target a transgene that was epigenetically silenced would have produced all the limitations of Claims 2-4, 9, 11-12, 14, 17, 19-21, 25-27, and 29.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 68-86 of copending Application No. 18438385 (“App385”) in view of WO426, Alhaji, Santos, and Bashor.
Although the claims at issue are not identical they are directed to overlapping subject matter.
The instant claims are directed to methods of modulating expression of a transgene from a transgene delivery vector and of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector, the method steps comprising: administering a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence; administering a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier; and administering the chemical epigenetic modifier; thereby modulating expression of the transgene or treating the disorder; wherein the delivery vector can be viral or nonviral, wherein the transgene can encode a protein or functional nucleic acid; wherein the polynt further comprises a sequence encoding the fusion protein and the transgene expression cassette and the sequence encoding the fusion protein are operably linked to the same promoter or to different promoters; wherein the NBD is a DNA-binding domain (that can be any of those recited in Claim 14) or an RNA-binding domain (that can be any of those recited in Claim 17); wherein the domain that binds a CEM is FKBP and the CEM is FK506; wherein contacting the delivery vector with the CEM increases transgene expression; wherein the CEM binds to a transcriptional activator protein or complex that can be BRD4 or CBP/p300 and the CEM can be CEM87 or CEM114; the method further comprising a step of blocking the increased transgene expression by contacting the vector with an agent that inhibits binding of the fusion protein to the CEM or by administering an agent that inhibits binding of the fusion protein to the CEM and wherein the fusion protein can be FKBP and the CEM can be FK506; and wherein the method comprises a step of blocking increased expression by stopping the contact between the delivery vector and the CEM or by stopping administering the CEM.
The copending App385 claims are directed to a bifunctional CEM comprising FK506 or a derivative thereof, a linker, and a bromodomain inhibitor or a CBP/p300 inhibitor; wherein the linker can have various components or can be cleavable; to a pharmaceutical composition comprising the composition; and to methods of using the bifunctional CEMs.
Both claim sets are directed to using bifunctional CEMs. Any element of the claimed invention that isn’t recited in the App385 claims would have been obvious in view of the prior art:
WO426 (§Abstract; pp. 4-5 ¶4-1; Figs. 1, 9-10, and 19; Example 11, starts on p. 68 ¶2; p. 29 ¶2; p. 30 ¶1-3; p. 39 ¶2; Figs. 1-2, 5, 7, 9-10; Figs. 9B and 19 and its caption; Figs. 21 and 30 and their captions, p. 20 ¶3, and as described above: p. 5 ¶1; (p. 24 ¶0; same §, Fig. 28; p. 24 ¶0; p. 41, §Example 2, Figs. 1B and 2; p. 25 §Methods of Treatment ¶1 and entire §; p. 26 ¶1-2; p. 24 ¶0, p. 68 §Example 11), Alhaji (§Abstract, §Introduction ¶2, §Epigenetics transgene silencing effect on non-integrating vectors ¶4, §DNA methylation and gene expression ¶2; §Histone modification and gene expression ¶4; §Silencing of transgene expression in gene therapy ¶1-2; §Epigenetics transgene silencing effect on non-integrating vectors ¶4), Santos (Fig. 1; §Results and discussion-Design features and CRISPRi testing ¶1-2), and Bashor (§2. SYNTHETIC GENE CIRCUITS AS PHYSICAL MODELS FOR STUDYING REGULATORY FUNCTION ¶1-2) teach all the limitations that the App385 claims don’t teach.
Therefore, it would have been obvious to a person of ordinary skill in the art to apply those teachings to the App385 claims for the benefits of using the CEM of the App385 claims to modulate transgene expression in gene therapy. One would have been motivated to do so with a reasonable expectation of success because WO426 teaches methods of regulating gene expression—either increasing or decreasing it—by recruiting epigenetic machinery and because Alhaji teaches transgene silencing by epigenetics impedes gene therapy and that regulating transgene expression was of interest in the gene therapy field. An artisan would have readily recognized that the compositions and methods of the App385 claims could be used with the teachings of WO426.
One would have been motivated to do so with a reasonable expectation of success because WO426’s method uses guide RNA to target their system to any target gene and there is no reason why the system couldn’t be used to target the system to a transgene of interest (which Alhaji teaches can be silenced by endogenous epigenetic silencing mechanisms). It would have been obvious to block the increased expression of the transgene by stopping administering the CEM because WO426 teaches (p. 24 ¶0, p. 68 §Example 11) their bifunctional CEM recruits transcriptional activation machinery, so an artisan would have known that withdrawing the CEM or interrupting the contact between the transgene delivery vector and the CEM would have blocked the increased expression. It would have been obvious to apply the teachings about synthetic circuits of Santos and Bashor for the benefit of producing a single polynt encoding the transgene and the NBD recognition sequence upstream of it (wherein the transgene is operably linked to a promoter) and the fusion protein comprising a NBD fused to a domain that binds a CEM (wherein the NBD binds to the NBD recognition sequence).
Doing so would have made it easier to ensure that each cell of interest received the entire system of WO426 and Alhaji and would have allowed the artisan to avoid fluctuations in stoichiometry of the various components. One would have been motivated to do so with a reasonable expectation of success because Santos teaches expressing circuit components from a single vector avoids fluctuations in component stoichiometry and because the teachings of Santos and Bashor indicate that producing a genetic circuit comprising known components is routine and convention in the art of synthetic biology.
Using the compositions and methods of the App385 claims with the teachings of WO426, Alhaji, Santos, and Bashor to target a transgene that was epigenetically silenced would have produced all the limitations of Claims 2-4, 9, 11-12, 14, 17, 19-21, 25-27, and 29.
This is a provisional nonstatutory double patenting rejection.
Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 and 28 of copending Application No. 18843505 (“App505”) in view of WO426, Santos, and Bashor.
Although the claims at issue are not identical they are directed to overlapping subject matter.
The instant claims are directed to methods of modulating expression of a transgene from a transgene delivery vector and of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector, the method steps comprising: administering a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence; administering a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a chemical epigenetic modifier; and administering the chemical epigenetic modifier; thereby modulating expression of the transgene or treating the disorder; wherein the delivery vector can be viral or nonviral, wherein the transgene can encode a protein or functional nucleic acid; wherein the polynt further comprises a sequence encoding the fusion protein and the transgene expression cassette and the sequence encoding the fusion protein are operably linked to the same promoter or to different promoters; wherein the NBD is a DNA-binding domain (that can be any of those recited in Claim 14) or an RNA-binding domain (that can be any of those recited in Claim 17); wherein the domain that binds a CEM is FKBP and the CEM is FK506; wherein contacting the delivery vector with the CEM increases transgene expression; wherein the CEM binds to a transcriptional activator protein or complex that can be BRD4 or CBP/p300 and the CEM can be CEM87 or CEM114; the method further comprising a step of blocking the increased transgene expression by contacting the vector with an agent that inhibits binding of the fusion protein to the CEM or by administering an agent that inhibits binding of the fusion protein to the CEM and wherein the fusion protein can be FKBP and the CEM can be FK506; and wherein the method comprises a step of blocking increased expression by stopping the contact between the delivery vector and the CEM or by stopping administering the CEM.
The copending App505 claims are directed to methods of modulating expression of a transgene from a transgene delivery vector and of treating a disorder that is treatable by expression of a transgene from a transgene delivery vector, the method steps comprising: administering to the subject a transgene delivery vector comprising a polynucleotide comprising a transgene expression cassette and a nucleic acid binding domain recognition sequence; administering to the subject a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds a CEM of claim 1; and administering to the subject the CEM of claim 1; thereby modulating expression of the transgene or treating the disorder. An artisan would readily perceive that those claims are very similar to the instant claims.
The App505 claims are further directed to various CEMs that can be bifunctional CEMs comprising FK506 and another CEM as recited in the claims; to pharmaceutical compositions comprising the CEM or to compositions comprising the CEM and FKBP with a mutation and wherein the composition further comprises a gRNA binding polypeptide that can be an MS2 polypeptide; to the composition comprising a gRNA comprises a gene-targeting polynt sequence and a polynt sequence that is recognized by the gRNA-binding polypeptide and to variations of that composition, including comprising a CRISPR-Cas protein that can be Cas9, Cas12a, Cas13, or a dCas9; wherein the composition further comprises a sequence-specific DNA binding domain that can be a zinc finger or others; to a composition comprising a transgene delivery vector comprising a polynucleotide comprising a nucleic acid binding domain recognition sequence and a transgene expression cassette, and a fusion protein comprising a nucleic acid binding domain that binds to the recognition sequence fused to a domain that binds to a CEM; to methods of modulating expression of a target gene in a subject or methods of modulating expression of a transgene in a subject.
Both claim sets are directed to methods of using bifunctional CEMs to modulate transgene expression. App505 Claims 28-29 clearly encompass instant Claims 2-3.
Since the App505 claims show the CEM, CEM87, they encompass the outcome of instant Claims 20-21 wherein transgene expression is increased and the CEM binds a transcriptional activator protein or complex. That is because WO426 teaches CEM87 possesses, due to its chemical structure, the property of recruiting a transcriptional activator protein or complex.
App505 Claim 6 encompasses instant Claim 19.
App505 Claims 8 and 10 encompass instant Claim 17.
App505 Claims 12-14 encompass limitations of instant Claim 14.
An artisan wouldn’t know what kind of things the transgene of the App505 claims could encode so they’d look in the App505 Spec. and find at ¶101 the transgene can encode a protein or a functional nucleic acid. Therefore the App505 claims encompass instant Claim 9.
The App505 claims don’t recite the limitations of Claims 11-12 or 25-27 but those would have been obvious to a person of ordinary skill in view of the prior art:
Regarding Claims 25-26: WO426 teaches (p. 24 ¶0) their bifunctional CEMs can repress or activate gene transcription. WO426 teaches (same §, Fig. 28) excess FK506 outcompetes CEM23 for the FKBP binding site. This is useful to tightly regulate changes to gene transcription allowing for rapid reversal of biological action. That indicates WO426 teaches blocking the effect of their bifunctional ligands—whether the effect of the bifunctional ligands is increased or decreased gene expression—by administering FK506 because FK506 outcompetes the bifunctional ligand. Administering excess FK506 would outcompete the binding between the bifunctional ligand and the fusion protein and would thereby block the increased expression that was previously induced by binding between the bifunctional ligand and the fusion protein. Therefore WO426 teaches limitations of Claims 25-26.
Specifically regarding Claim 27, it would have been obvious to block the increased expression of the transgene by stopping administering the CEM because WO426 teaches (p. 24 ¶0, p. 68 §Example 11) their bifunctional CEM recruits transcriptional activation machinery, so an artisan would have known that withdrawing the CEM or interrupting the contact between the transgene delivery vector and the CEM would have blocked the increased expression.
WO426 teaches (§Abstract; pp. 4-5 ¶4-1; Figs. 1, 9-10, and 19; Example 11, starts on p. 68 ¶2; p. 29 ¶2; p. 30 ¶1-3; p. 39 ¶2; Figs. 1-2, 5, 7, 9-10; Figs. 9B and 19 and its caption; Figs. 21 and 30 and their captions, p. 20 ¶3, and as described above: p. 5 ¶1; (p. 24 ¶0; same §, Fig. 28; p. 24 ¶0; p. 41, §Example 2, Figs. 1B and 2; p. 25 §Methods of Treatment ¶1 and entire §; p. 26 ¶1-2; p. 24 ¶0, p. 68 §Example 11) other limitations of the instant claims.
Santos (Fig. 1; §Results and discussion-Design features and CRISPRi testing ¶1-2) and Bashor (§2. SYNTHETIC GENE CIRCUITS AS PHYSICAL MODELS FOR STUDYING REGULATORY FUNCTION ¶1-2) teach all the other limitations that the Ap505 claims don’t teach.
Therefore, it would have been obvious to a person of ordinary skill in the art to apply those teachings to the App505 claims for the benefits of producing a single polynt encoding the transgene and the NBD recognition sequence upstream of it (wherein the transgene is operably linked to a promoter) and the fusion protein comprising a NBD fused to a domain that binds a CEM (wherein the NBD binds to the NBD recognition sequence). Doing so would have made it easier to ensure that each cell of interest received the entire system of the App505 claims and WO426 and would have allowed the artisan to avoid fluctuations in stoichiometry of the various components. One would have been motivated to do so with a reasonable expectation of success because Santos teaches expressing circuit components from a single vector avoids fluctuations in component stoichiometry and because the teachings of Santos and Bashor indicate that producing a genetic circuit comprising known components is routine and convention in the art of synthetic biology.
Using the compositions and methods of the App505 claims with the teachings of WO426, Santos, and Bashor to target a transgene that was epigenetically silenced would have produced all the limitations of Claims 2-4, 9, 11-12, 14, 17, 19-21, and 25-29.
This is a provisional nonstatutory double patenting rejection.
Conclusion
No claim is allowed.
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RUTHIE S ARIETI
Examiner
Art Unit 1635
/RUTH SOPHIA ARIETI/Examiner, Art Unit 1635
/NANCY J LEITH/Primary Examiner, Art Unit 1636
Prosecution Insights