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 .
Claim Status
This action is in response to the papers filed on October 21, 2025. Claims 23-44 were previously pending in the instant application.
Applicant’s election without traverse of the species of exon 22 of the ATP2A1 gene in the reply filed on 13 March 2025 was previously acknowledged. The species election of exon 22 of the ATP2A1 gene is being applied to all pending claims.
Claims 23-27, 29-31, 37, and 43-44 are amended. Claims 35 and 42 are cancelled. No claims are newly added.
Therefore, claims 23-34, 36-41, and 43-44 are pending and under examination in the present Official Action.
Priority
The present application is a 35 U.S.C. 371 national stage filing of International Application No. PCT/EP2020/075574, filed 11 September, 2020, which claims priority to European patent application No. EP19306099.3, filed 12 September, 2019. Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copies of papers required by 37 CFR 1.55 have been filed in this application on 11 March, 2022.
Therefore, the earliest possible priority for the instant application is 12 September, 2019.
Drawings
The drawings submitted on 11 March, 2022 are accepted by the Examiner.
Maintained Objections/Rejections in view of Applicant’s Amendments/Arguments
Claim Objections
Claims 36, and 37 remain objected to because of the following informalities: abbreviations/acronyms must be spelled out upon their first encounter in the claims (for example: ATP2A1, RYR1, CAPZB, INSR, CAM2B, ITGB, BIN1, TAU, DMD). Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 23-34, 36-41, and 43-44 remain 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. This rejection has been modified as necessitated by amendment of the claims in the response filed on October 21, 2025
Claim 23 recites “primary transcript” in the second line of the claim and “a mature transcript” eighth and tenth lines of the claim. However, the claim is directed to a chimeric nucleic acid molecule and not a transcript. Thus, it is unclear what applicant is referring to in the claim and why a primary transcript is distinguished from a mature transcript. Further, the Specification provides no definition of “primary transcript” nor “mature transcript” nor why they are distinguished nor whether primary transcript is the major species of transcript selected from several possible primary, secondary, tertiary, etc. transcripts or merely a transcript that hasn’t been spliced yet. Therefore, claim 23 is unclear and a person having ordinary skill in the art would not be apprised of the scope of the patent protection sought. Claims 24-34, 36-41, and 43-44 are further rejected for their dependency on a rejected base claim.
Claim 23 is indefinite because of its recitation of “said exon is designed to inhibit expression of a functional form of said product of interest” in line 9. It is unclear as to “the design” or designs that are intended as being encompassed by the noted phrase. Exon encoding portions of DNA or RNA are known in the prior art to have numerous designs, both specific and general. For example, exons are joined together to form coding sequences that produce proteins. It is suggested that applicant clarify the intended meaning of the noted phrase.
Amended claim 23 now reads “flanked by two intronic regions”. This language is unclear because it is unclear whether Applicant intends the exon to be flanked on each side by two introns or by one intron on either side. Further, “intronic regions” is unclear insofar as it is unclear how to determine an intronic region. It but a single base sufficient to meet the scope of intronic region or is an entire intronic sequence required? The answer is unclear. Thus, the metes and bounds of claim 23 cannot be determined and a person having ordinary skill in the art would not be apprised of the scope of the patent protection sought. Claims 24-34, 36-41, and 43-44 are further rejected for their dependency on a rejected base claim.
Claim 27 is indefinite in its recitation of “modified MBNL protein having an YGCY-binding property to binding partners” because it is unclear whether the amino acid sequence “YGCY” is in the modified MBNL protein or in the binding partner. As such the metes and bounds of the claim are indefinite. This rejection has been modified to address Applicant’s amendment to claim 27. Claim 27 remains unclear for the same reasons previously identified.
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.
Applicant has amended claim 23 to specify MBNL protein and to require flanking intronic regions. Applicant has not amended claim 43 or 44 to further specify any of the identified issues of lack of enabled scope. Further, claim 23 continues to read on any MBNL protein and any intronic regions rather than the specific regions and modified MBNL protein previously identified as enabled. Consequently, this rejection is maintained.
Claims 23-34, 36-41, and 43-44 remain 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:
A chimeric nucleic acid molecule comprising:
a first nucleic acid sequence whose primary transcript comprises exon 22 of the ATP2A1 gene flanked by intron 21 of the ATP2A1 gene at the 5’ end of the primary transcript and flanked by intron 22 of the ATP2A1 gene at the 3’ end of the primary transcript, said primary transcript being subject to splicing by a modified Muscleblind Like Splicing Regulator (MBNL) protein; and
a second nucleic acid sequence comprising a transgene of interest encoding a product of interest;
wherein the modified MBNL protein enhances inclusion of said exon 22 of the ATP2A1 gene in a mature transcript of the chimeric nucleic acid molecule, and
wherein said exon 22 of the ATP2A1 gene is designed to inhibit expression of a functional form of said product of interest when included into the mature transcript of the chimeric nucleic acid molecule,
A method of treating a disease or disorder linked to sequestration of MBNL, myotonic dystrophy, myotonic dystrophy type 2, or myotonic dystrophy type 2 comprising administering intramuscularly an AAV9 vector comprising a chimeric nucleic acid molecule comprising:
a first nucleic acid sequence, the primary transcript of which comprises exon 22 of the ATP2A1 gene flanked by intron 21 of the ATP2A1 gene at the 5’ end of the primary transcript and flanked by intron 22 of the ATP2A1 gene at the 3’ end of the primary transcript, said primary transcript being subject to splicing by a modified Muscleblind Like Splicing Regulator (MBNL) protein; and
a second nucleic acid sequence comprising a transgene of interest encoding a product of interest;
wherein the modified MBNL protein enhances inclusion of said exon 22 of the ATP2A1 gene in the mature transcript of the chimeric nucleic acid molecule, and
wherein said exon 22 of the ATP2A1 gene is designed to inhibit expression of a functional product of interest, when included into the mature transcript., and
An in vitro method for controlling the expression of a transgene of interest, depending on the endogenous level of MBNL protein, comprising the expression of a chimeric nucleic acid molecule comprising:
a first nucleic acid sequence, the primary transcript of which comprises exon 22 of the ATP2A1 gene flanked by intron 21 of the ATP2A1 gene at the 5’ end of the primary transcript and flanked by intron 22 of the ATP2A1 gene at the 3’ end of the primary transcript, said primary transcript being subject to splicing by a modified Muscleblind Like Splicing Regulator (MBNL) protein; and
a second nucleic acid sequence comprising a transgene of interest encoding a product of interest;
wherein the modified MBNL protein enhances inclusion of said exon 22 of the ATP2A1 gene in the mature transcript of the chimeric nucleic acid molecule, and
wherein said exon 22 of the ATP2A1 gene is designed to inhibit expression of a functional product of interest, when included into the mature transcript.
does not reasonably provide enablement for (1) a genus of chimeric nucleic acid molecules comprising just exon 22 of the ATP2A1 gene along with any flanking intronic sequences wherein any protein regulating alternative splicing enhances inclusion of exon 22 of the ATP2A1 gene in the mature transcript, (2) a method of treating any disease linked to any dysfunction of any protein regulating alternative splicing comprising administering in any form a chimeric nucleic acid molecule comprising just exon 22 of the ATP2A1 gene along with any flanking intronic sequences wherein any protein regulating alternative splicing enhances inclusion of exon 22 of the ATP2A1 gene in the mature transcript, or (3) an in vivo method for controlling the expression of a transgene of interest depending on the endogenous level of any protein regulating alternative splicing, comprising the expression of a nucleic acid molecule comprising just exon 22 of the ATP2A1 gene along with any flanking intronic sequences wherein any protein regulating alternative splicing enhances inclusion of exon 22 of the ATP2A1 gene in the mature transcript. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
Claim 23 broadly reads on a chimeric nucleic acid molecule comprising just exon 22 of the ATP2A1 gene along with any flanking intronic sequences (literally any sequence identified as intronic) wherein the chimeric nucleic acid molecule possesses the functional property of any MBNL protein (MBNL1, MBNL2, MBNL3) enhances inclusion of exon 22 of the ATP2A1 gene in the mature transcript. Claim 26 specifies that the protein regulating alternative splicing is MBNL1, MBNL2, or MBNL3 or a variant and claim 27 specifies that the protein regulating alternative splicing is a modified MBNL protein having YGCY binding property and reduced splicing activity. Claim 28 specifies that the MBNL protein binds CUG repeats, claim 29 specifies that the MBNL protein lacks C-terminal domain, and claim 30 specifies that the MBNL protein lacks amino acids corresponding to exons 5-10 of MBNL1. It is noted that the broadest embodiment encompasses any MBNL protein (having any modifications or no modifications at all) and that dependent claim 26 still reads on an MBNL protein that does not bind to CUG repeats or have the YGCY binding property. Claim 37 specifies that exon 22 of the ATP2A1 gene is flanked by introns 21 and 22 of the ATP2A1 gene. However, all pending claims excluding claim 37 continue to read on a nucleic acid having only exon 22 of the ATP2A1 gene as elected along with any possible intronic sequences. Claims 43-44 are directed to methods wherein the nucleic acid of claim 23 is used. The breadth of claim 23 is captured above but the breadth is expanded on further in the context of the methods claims because of the functional outcomes claimed. Claim 43 broadly encompasses a method of treating a disease linked to sequestration of MBNL, myotonic dystrophy, myotonic dystrophy type 1, and myotonic dystrophy type 2 comprising administering the nucleic acid of claim 23 in any form (plasmid, any viral vector, double-stranded RNA) and by any route of administration. It is noted that the nucleic acid of claim 23 only requires exon 22 of the ATP2A1 gene as elected along with any flanking intronic sequences and does not require it be flanked by introns 21 and 22 of the ATP2A1 gene, MBNL protein function, or a modified MDNL protein transgene. Claim 44 broadly encompasses a method for controlling expression of a transgene of interest in vitro/ex vivo or in vivo depending on the endogenous level of MBNL protein, comprising the expression of the nucleic acid of claim 23 (again, this reads on a nucleic acid of claim 23 only requiring exon 22 of the ATP2A1 gene as elected and not requiring it be flanked by introns 21 and 22 of the ATP2A1 gene).
The specification does not provide sufficient guidance for determining (1) whether any MBNL protein can be used to enhance inclusion of exon 22 of the ATP2A1 gene in the mature transcript of a chimeric nucleic acid molecule comprising just exon 22 of the ATP2A1 gene as elected along with any flanking intronic sequences, (2) whether a chimeric nucleic acid molecule according to claim 23 comprising just exon 22 of the ATP2A1 gene as elected along with any flanking intronic sequences can be administered to treat any disease disease linked to sequestration of MBNL, myotonic dystrophy, myotonic dystrophy type 1, or myotonic dystrophy type 2 by any route, or (3) whether a chimeric nucleic acid molecule according to claim 23 comprising just exon 22 of the ATP2A1 gene as elected along with any flanking intronic sequences can be expressed to control the expression of a transgene of interest in vivo or in vitro depending on the endogenous level of any MBNL protein.
The specification teaches that myotonic dystrophy type 1 (DM1) is caused by unstable CTG repeat expansion in the DMPK gene resulting in aggregates of DMPK transcripts with CUG repeats in nuclear foci, that these aggregates occur in muscle cells in DM1, that MBNL proteins bind tightly to CUG repeats resulting in sequestration and loss of function of MBNL, and that this loss of function results in mis-regulation of pre-mRNAs targeted by MBNL (Specification, page 1, lines 12-27). The specification also teaches that supplying MBNL1 as a gene therapy corrects splicing of MBNL targets and cites Kanadia et al. for this teaching, and that supplying a non-functional variant of MBNL having no splicing activity could be used according to WO2015/158365 to compete with sequestered MBNL1 proteins for CUG binding to release sequestered MBNL1 proteins and recover MBNL1 activity (Specification, page 1, lines 29-34; page 2, lines 1-5). The specification then teaches that overexpression of a therapeutic transgene generally may have unwanted effects and that controlling expression of the therapeutic transgenes would be desirable to avoid unwanted effects (Specification, page 2, lines 7-12). The specification generally teaches the chimeric nucleic acid molecule of claim 23 and teaches exon 22 of the ATP2A1 gene as the exon of the first nucleic acid sequence in claim 23 alongside teachings of 8 other exons that could be used in the invention (Specification, page 3, lines 1-6). The specification provides particular embodiments in which the transgene of interest is a MBNL protein, in particular MBNL1, MBNL2, or MBNL3, preferably MBNL1 or a variant thereof in particular a modified MBNL1 having YGCY binding property and reduced splicing activity, more particularly a modified MBNL protein lacking C-terminal domains, more particularly lacking amino acids corresponding to exons 5-10 of the MBNL mRNA, in particular the modified MBNL has the sequence of SEQ ID NO: 5 (Specification, page 3, lines 8-21). The specification also teaches that, in a gene therapy context, gene therapy vectors containing the chimeric nucleic acid molecule are used to restore the functional activity of MBNL as a treatment for myotonic dystrophy (Specification, page 8, lines 7-12). It is noted that the specification does not provide any teachings for any other diseases which may be treated with a chimeric nucleic acid molecule comprising exon 22 of the ATP2A1 gene. The specification describes a list of other proteins regulating alternative splicing that could be used (TDP-43, FUS, NOVA, and RBM20) (Specification, page 9, lines 28-31) but again specifies that MBNL1 is preferred (Specification, page 10, lines 1-2). The specification also defines “splice-sensor” as the first nucleic acid sequence of the chimeric nucleic acid molecule and requiring “intron-exon-intron” sequence wherein the exon able to inhibit expression of the transgene is flanked by two intronic regions (Specification, page 10, lines 6-10). The specification also teaches that the “intron-exon-intron” sequence of the splice sensor must be flanked by two exonic sequences providing a splice donor and splice acceptor for the protein regulating alternative splicing to be able to splice the splice-sensor sequence (Specification, page 12, lines 1-6). It is noted that, as elected, instant claim 23 does not require the native intronic sequences flanking exon 22 of the ATP2A1 gene nor do they require the further flanking splice donor and splice acceptor exonic sequences taught by the specification as required for the protein regulating alternative splicing to be able to splice the splice-sensor of the first nucleic acid sequence. The specification also teaches that the splice-sensor can be 5’ of the sequence encoding the transgene, in the 3’ UTR of the sequence encoding the transgene, or within the sequence encoding the transgene, and, in particular, the splice-sensor is introduced between exon 1 and exon 2, between exon 2 and exon 3, or between exon 3 and exon 4 of MBNL1 (Specification, page 12 whole page; page 13, lines 1-3). The specification also teaches that exon 22 of the ATP2A1 gene contains two stop codons (Specification, Figure 1). Thus, it is noted that in the preferred embodiments where exon 22 of the ATP2A1 gene is inserted within the transgene, at least three different truncated proteins will be produced in cells expressing the transgene in the absence of MBNL1. The specification also teaches particular embodiments wherein exon 22 of the ATP2A1 gene is flanked by introns and other exons of the ATP2A1 gene, “3’ end of exon 21 – intron 21 – exon 22 – intron 22 – 5’ end of exon 23” (Specification, page 15, lines 1-17). The specification also teaches four specific modified MBNL proteins having C-terminal deletions and being of all three MBNL subtypes (Specification, page 19, lines 17-33; page 20, lines1-33).
The working examples teach a splice-sensor derived from the human ATP2A1 gene and containing partial exon 21 (34 nucleotides from the 3’ end of the intron), intron 21, exon 22, intron 22, and partial exon 23 (22 nucleotides from the 5’ end of the intron) inserted in front of an EGFP protein or a V5-MBNLdelta sequence in a pcDNA3.1(+) vector (Specification, page 28, lines 20-26). The working examples also teach the same splice-sensor inserted upstream of a sequence encoding a dCas9-eGFP (Specification, page 28, lines 28-30; page 33, lines 7-13). Thus, the specification provides 3 examples of “exon-intron-exon-intron-exon” splice-sensors inserted upstream of a transgene. The working examples also teach a splice-sensor comprising intron 21-exon 22-intron 22 of the human ATP2A1 gene inserted between exons 2 and 3, or between exons 3 and 4 of the V5-MBNLdelta sequence with an extra (T) inserted into exon 22 to keep the 2 stop codons within exon 22 in frame (Specification, page 28, lines 32-34). The working examples also teach the insertion of the “exon-intron-exon-intron-exon” splice sensor directly after the stop codon of the V5-MBNLdelta transgene before the polyA signal (Specification, page 29, lines 1-6). The working examples also teach a murine ATP2A1-derived splice sensor containing partial exon 21 (50 nucleotides from the 3’-end of the intron), intron 21, exon 22, intron 22, and full exon 23 inserted just after the stop codon of V5-MBNLdelta transgene before the polyA signal (Specification, page 29, lines 8-11). Thus, when the working examples provide exon 22 at either end of a transgene, it is provided only along with flanking MBNL exonic sequence to provide splice donor and splice acceptor sequence and when inserted within a transgene, the working examples only provide exon 22 flanked by introns 21 and 22. The working examples do not ever teach exon 22 of the ATP2A1 gene as a splice-sensor without its native intronic sequences nor do they teach exon 22 of the ATP2A1 gene as a splice sensor without flanking intronic and exonic sequence when used at the 5’ end or within the 3’ UTR of a transgene.
In the context of methods of using the splice-sensors of the specification, the working examples teach their use in HEK293T cells containing tetracycline-inducible MBNL1 (Specification, page 29, lines 15-24; page 31, lines 6-32), and their intramuscular injection into DM1 model mice (HSALR) via AAV9 vector (Specification, page 29, lines 27-32; page 32, lines 1-22). The working examples also teach that the “splice-sensor” makes it possible to control the expression of MBNLdelta (SEQ ID NO: 5) depending on the functional level of endogenous MBNL1 protein (Specification, page 32, lines 24-28) and that, when MBNL1 level is high in induced HEK293T cells, V5-MBNLdelta protein with splice-sensor embedded between exons 2 and 3 is reduced by 60% and V5-MBNLdelta protein with splice-sensor embedded between exons 3 and 4 is reduced by 70% (Specification, page 34, lines 2-6). The working examples also teach that when injected into mice, WT mice do not express the V5-MBNLdelta indicating inclusion of exon 22 in the mature transcript and DM1 mice do express the V5-MBNLdelta protein indicating skipping of exon 22 of the ATP2A1 gene (Specification, page 32, lines 1-22). No working example is given which provides support for the use of any nucleic acid other than one containing a splice-sensor derived from the human ATP2A1 gene and containing partial exon 21 (34 nucleotides from the 3’ end of the intron), intron 21, exon 22, intron 22, and partial exon 23 (22 nucleotides from the 5’ end of the intron) and a V5-MBNLdelta transgene which housed within an AAV9 vector, and is subject to splicing by MBNL1 to treat anything other than DM1 in a mouse model of DM1 in vivo. Further, even when injected into mice, the specification lacks a description of a therapeutic effect at all and merely provides support for the functioning of the splice-sensor in vivo.
At the time of filing, it was known that MBNL1 binds YGCY domains within RNA through zinc finger domains located on exons 1-2 and 4 (Konieczny et al., Nucleic acids research 42.17 (2014): 10873-10887., hereinafter “Konieczny”, Figure 1.). Konieczny teaches that MBNL1, MBNL2, and MBNL3 differ from each other with respect to where their zinc finger domains are located and which exons can be alternatively spliced, that human MBNL proteins differ from mouse MBNL proteins with respect to the same, and that one of the zinc finger domains in each MBNL protein spans two exons (exons 1 and 2 for MBNL1 and 2, and exons 1 and 4 for MBNL3) (Konieczny, Figure 1.). Konieczny also teaches that MBNL1 is the most highly expressed of the three subtypes and that it is most highly expressed in skeletal muscles and heart tissue (Konieczny, Figure 2.). Konieczny also teaches that the ATP2A1 RNA binding site for MBNL1 is located 116 nucleotides downstream of exon 22 within intron 22 and that binding sites downstream of exons facilitates inclusion whereas binding upstream facilitates exclusion of alternative exons generally (Konieczny, Figure 5., Figure 6.). Thus, it was known at the time of filing that native flanking intronic sequences are required for MBNL splicing of ATP2A1 transcripts, that, in particular, the YGCY binding region of MBNL proteins binds downstream of exon 22 to facilitate its inclusion in mature transcripts, that human and mouse MBNL proteins as well as MBNL1, MBNL2, and MBNL3 are distinct from each other with respect to where their zinc fingers are located, and that in humans one of the zinc finger domains spans exons 1 and 2 of MBNL1 and exons 1 and 4 of MBNL3. At the time of filing, it was also known that misfolded proteins are normally eliminated through proteolytic mechanisms but that in response to genetic events, misfolded proteins can form aggregates that lead to toxicity in vivo (Holmes et al., Critical reviews in biochemistry and molecular biology 49.4 (2014): 294-303., hereinafter “Holmes”, Abstract). Holmes teaches that truncated proteins can misfold and lead to toxicity as well (Holmes, page 4, last paragraph). A skilled artisan knew from the teachings of Holmes at the time of filing that producing truncated proteins in unknown amounts throughout an organism would carry a risk of toxicity. Further, at the time of filing it was known that different AAV serotypes possess different tissue tropism (Lisowski et al., Current opinion in pharmacology 24 (2015): 59-67., hereinafter “Lisowski”, Abstract). Lisowski teaches that specific AAV capsids show unpredictable species and cell-type specificity (Lisowski, Abstract). Lisowski also teaches that, while most AAV serotypes display skeletal muscle tropism, this tropism is dependent on the species infected and AAV4 shows no skeletal muscle tropism to-date (Lisowski, Table 1). Thus, a skilled artisan knew from the teachings of Holmes and Lisowski that different AAV vectors would express genetic payloads in different tissues and that, depending on the AAV serotype used, truncated proteins could be produced throughout an organism. Further, at the time of filing modified MBNL proteins possessing increased YGCY activity were known (Hale et al., Nucleic acids research 46.6 (2018): 3152-3168., hereinafter “Hale”, Abstract). Hale teaches an MBNL protein modified to possess duplicate zinc finger domains which increases ATP2A1 exon 22 inclusion in HeLa cells (Hale, Abstract, Figure 2.). The prior art of record only teaches MBNL proteins regulating ATP2A1 exon 22 inclusion and no reference has been located to-date which provides support for any protein regulating alternative splicing which possess the functional property of enhancing exon 22 of the ATP2A1 gene inclusion in mature transcripts other than MBNL proteins.
Therefore, in view of the breadth of the claims, the lack of sufficient guidance in the specification for any protein regulating alternative splicing other than MBNL protein or for any splice-sensor other than exon 22 of the ATP2A1 gene flanked by its native introns (and further exons when inserted at the terminal end of a transgene), the limitation of the working examples to a single in vivo example using AAV9 to deliver a modified MBNL protein intramuscularly to mice and only to exon 22 of the ATP2A1 gene splice-sensors possessing flanking intronic sequences (and further exons when inserted at the terminal end of a transgene), the unpredictability evidenced by the prior art at the time of filing with respect to the use of various AAV serotypes, the expression of truncated proteins, and the ability of MBNL proteins to enhance inclusion of exon 22 of the ATP2A1 gene when no intronic sequence or splice donor/acceptor pair is present, and the lack of teachings in the prior art at the time of filing for any protein other than MBNL proteins which regulate exon 22 inclusion into ATP2A1 transcripts, it would require undue experimentation to make/use the invention commensurate in scope with the claims.
Response to Arguments
Applicant argues that, following the amendments to claim 23 to require MBNL protein and “flanked by two intronic regions”, the claims are enabled. This argument has been fully considered but has not been found persuasive for the following reasons.
Applicant argues “The specification provides ample guidance for MBNL protein and its use to enhance inclusion in the mature transcript of a chimeric nucleic molecule of exon 22 of the ATP2A 1 gene and other exons that are subject to splicing by MBNL. (Specification as filed, page 9, line 21 to page 10, line 2; page 10, lines 22-23; page 14, lines 1-4 and 23-26; and Figures 1C, 2B,5B,6B, 7B, and 8B). The specification also provides guidance for a method of treating a disease or disorder linked to a sequestration of an MBNL protein by administering the chimeric nucleic acid molecule of claim 23 through various routes. (Specification as filed, page 16, lines 13-14; page 25, line 34 to page 26, line 31; and page 27, lines 7-10 and 18-34)” (Remarks at 9 and 10), “The Supreme Court in Amgen Inc. v. Sanofi confirmed that a specification must not always "describe with particularity how to make and use every single embodiment within a claimed class." Amgen Inc. v. Sanofi, 598 U.S. 594, 610-11 (2023). The Court stated "it may suffice to give an example (or a few examples) if the specification also discloses 'some general quality ... running through' the class that gives it 'a peculiar fitness for the particular purpose."' Id. at 611. "In some cases, disclosing that general quality may reliably enable a person skilled in the art to make and use all of what is claimed, not merely a subset." Id. The specification teaches examples of exons (see, e.g., specification page 11, lines 4-11; page 14, lines 1-4 and 23-26; and Examples 1-6), and discloses a general quality "'running through' the class [of exons] that gives them 'a peculiar fitness for the particular purpose"' in the context of a chimeric nucleic acid molecule as claimed. The general quality of the exons taught by the specification is their susceptibility to splicing by MBNL, which combined with their presence in a first nucleic acid sequence of the claimed chimeric nucleic acid molecule enables the exons to inhibit the expression of a functional form of the product of interest encoded by the second nucleic acid sequence of the chimeric nucleic acid molecule. Therefore, the specification enables one skilled in the art to make and use all exons as claimed and not merely a subset” (Remarks at 10 and 11) and “The specification teaches examples of the method of treatment (see, e.g., specification pages 31-32, Example 2 and Figure 4), and discloses a general quality running through the class of disease treatment methods-treatment of diseases characterized by reduced functional levels of endogenous MBLN, because in these diseases inclusion of the exon into the mature transcript of an administered chimeric nucleic acid molecule will be reduced and the product of interest will be expressed. Therefore, the specification enables one skilled in the art to treat all diseases that have reduced functional levels of endogenous MBLN and not merely a subset. The specification further provides examples of controlling the expression of various transgenes, e.g., GFP, dCas9-GFP, and MBNLA (Examples 1-6 and Figures 1-8) and provides a general quality running through the class of methods of controlling transgenes-controlling transgenes depending on endogenous levels of MBNL, because such transgenes will be expressed in cells with low levels of endogenous MBNL after being contacted with a chimeric nucleic acid molecule but will not be expressed in cells with high endogenous MBNL levels due to inclusion of the exon of the first nucleic sequence of the chimeric nucleic acid molecule in the mature transcript. Therefore, the specification enables one skilled in the art to control all transgenes depending on endogenous levels of MBLN and not merely a subset” (Remarks at 11 and 12). These arguments have been fully considered but have not been found persuasive for the following reasons.
First, Applicant has not addressed all previously identified issues of lack of enablement. Applicant has not addressed the contextual difference taught in the specification for the use of the splice sensor within a gene (requiring intron-exon-intron) versus at either end of a gene (requiring exon-intron-exon-intron-exon). Applicant also has not addressed outstanding issues with regard to the method of treating which, as written, encompasses any route of administration, any subject (including humans) and any exonic splice sensor while no working example is given which provides support for the use of any nucleic acid other than one containing a splice-sensor derived from the human ATP2A1 gene and containing partial exon 21 (34 nucleotides from the 3’ end of the intron), intron 21, exon 22, intron 22, and partial exon 23 (22 nucleotides from the 5’ end of the intron) and a V5-MBNLdelta transgene which housed within an AAV9 vector, and is subject to splicing by MBNL1 to treat anything other than DM1 in a mouse model of DM1 in vivo. Further, the method of claim 44 still reads on an in vivo application which implicates all of the issues with the method of treatment above. Instead of addressing all of these issues, Applicant has instead amended the claims to read on MBNL protein and to require “flanked by two intronic regions” and insists that this is enough to overcome the rejection. It is noted that the amended language reads on any intronic region from any source including but a single nucleotide or introns which natively flank completely unrelated exons. The specification provides only a limited application of this principle and it is only with respect to exon 22 of the ATP2A1 gene flanked by its respective introns 21 and 22 and when it is used at the terminal end of a target gene it is required to have further flanking exonic sequence (see above rejection). While it is true that a specification must not always "describe with particularity how to make and use every single embodiment within a claimed class." Amgen Inc. v. Sanofi, 598 U.S. 594, 610-11 (2023), it is also true that merely describing a single working example within a vastly claimed genus may impose undue experimentation on the skilled artisan when there is unpredictability evidenced by the art at the time of filing. This unpredictability has been evidenced in the above rejection and has not been addressed by Applicant in their response. Although Applicant discloses a general quality "'running through' the class [of exons] that gives them 'a peculiar fitness for the particular purpose"' in the context of a chimeric nucleic acid molecule as claimed. This general quality is not one devoid of nuance and is one where the specific molecular activities of both the exons and the proteins binding the exons are required to obtain the general property. Those activities are impacted greatly by the presence or absence of specific intronic sequences flanking the specific exons used (not just any intronic regions), specific splice donor/acceptor pairs, and specific binding properties within their binding proteins (for example the claimed YGCY binding property of MBNL protein). Applicant has only disclosed one such specific example which functions as claimed and has only disclosed very specific contexts with particular nuances where the claimed chimeric molecule functions in the methods claimed. Accordingly, these arguments are not found persuasive.
Additional Comments
Arandel et al. discloses a decoy-based gene therapy targeting CUGexp-DMPK transcripts in DM1 wherein a truncated MBNL that lacks C-terminal residues to abolish splicing activity but maintain RNA binding properties in vitro (Arandel et al., International Myotonic Dystrophy Consortium Meeting IDMC-11. 2017., only paragraph).
Somarelli et al. teaches splicing reporters comprised of exon 9 of the FGFR2 gene flanked by intronic sequences and inserted within an eGFP gene to produce a fluorescent reporter for the study of epithelial-mesenchymal transition (Somarelli et al., Rna 19.1 (2013): 116-127., Abstract, Figure 1.). Somarelli et al. teaches that the system can be further improved by selecting genes with multiple splice variants other than just 2 (Somarelli et al., page 124, third paragraph).
Neither Arandel nor Somarelli teaches the use of exon 22 of the ATP2A1 gene in a splice-sensor, nor the application of a splice-sensor to inhibit expression of a functional product of interest. Thus, the claims as elected are indicated as free of the prior art of record because none of the prior art of record teaches the application of exon 22 of the ATP2A1 gene to inhibit the expression of a functional product of interest.
Matloka describes the instant invention and is, thus, relevant but is not available as prior art because the reference was published after the effective filing date of the claimed invention (Matloka, Magdalena., Diss. Sorbonne Université, 2019., Page 125). It should also be noted that this reference is authored by one of the instant inventors.
No claim is allowed.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/BRENDAN THOMAS TINSLEY/ Examiner, Art Unit 1634
/MARIA G LEAVITT/Supervisory Patent Examiner, Art Unit 1634