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 .
Priority
Applicant’s claim to priority from Foreign Application EP14165504.3 filed 04/22/2014 and from US Application Nos. 16/017,375 filed 06/25/2018 and 15/305,976 filed 10/21/2016, and from PCT/EP2015/058684 filed 04/22/2015, is hereby acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in parent Application No.15/305,976, filed on 10/21/2016.
Election/Restrictions
Applicant’s election without traverse of Invention group II (claims 25-29 and 36
46) in the reply filed on 09/09/2025 is acknowledged.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Application Status
This Application is a DIV of US Application No. 16/017,375 filed 06/25/2018.
Amendments to claims filed 09/09/2025 are hereby acknowledged.
Claims 1-24 and 30-35 are cancelled. Therefore, claims 25-29 and 36-46 are under consideration in this office action.
Information Disclosure Statement
The information disclosure statements (IDSs) submitted on 06/24/2022 and 09/08/2025 are hereby acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
However, 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, or listed on a submitted IDS, they have not been considered.
Drawings
Replacement sheets for Drawings submitted 06/24/2022 are hereby acknowledged.
The drawings are objected to for the following reasons:
37 C.F.R. 1.84 states “Character of lines, numbers, and letters. All drawings must be made by a process which will give them satisfactory reproduction characteristics. Every line, number, and letter must be durable, clean, black (except for color drawings), sufficiently dense and dark, and uniformly thick and well-defined.”
In the current case, the words in Figures 13A, 13B, 13C, 32, 33A, 33B and 33C are illegible.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Nucleotide and/or Amino Acid Sequence Disclosures
Objection: Applicant needs to submit a sequence listing incorporation by reference paragraph and/or amendments to Drawings Fig. 13B and Fig. 13C.
Reminder:
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the
definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Figures 13B and 13C. Nucleotide and/or amino acid sequences appearing in the drawings are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specification
The disclosure is objected to because of the following informalities: Periods are missing (examples in § [0029], [0038], [0170]); usually these are very minor informalities, however it can make reading difficult in the case of § [0052], line 11.
Appropriate correction is required.
The use of the terms “NCode” ([0059]), “Arraystar” ([0059], [0145], [0181]-[0184], [0200]-[0202]), “Genzyme” ([0075]), “Biacore” ([0089]), which are trade names or marks used in commerce, has been noted in this application. The terms should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claim 25 is objected to because of the following informalities: the claim recites: “the lncRNA of SEQ ID NO: 1”. The claim should read: “an lncRNA having the sequence of SEQ ID NO: 1”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Description Rejection
Claims 25-29 and 36-46 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.
For claims drawn to a genus, MPEP § 2163 states 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.
Nature of the Invention:
Claim 25 recites “A method of treating or preventing pathological cardiac
hypertrophy in a subject, comprising administering a compound inhibiting the expression and/ or the activity of the IncRNA of SEQ ID NO: 1, wherein the compound is
a nucleic acid sequence which comprises or consists of a nucleotide
sequence being complementary to at least 12 continuous nucleotides of SEQ ID NO: 1,
a nucleic acid sequence which comprises or consists of a nucleotide
sequence which is at least 69% identical to the complementary strand of the IncRNA of SEQ ID NO: 1,
( c) a nucleic acid sequence which comprises or consists of a nucleotide
Sequence according to (a) or (b), wherein U is replaced by T,
an expression vector expressing the nucleic acid sequence as defined
in any one of (a) to (c), preferably under the control of a heart-specific promoter, or
a host comprising the expression vector of (d).”
It is therefore expected in the instant application a disclosure of a method using a
specific compound/agent capable of hybridizing and inhibiting the lncRNA of SEQ ID NO: 1.
The broadness of the claim suggests that this agent/compound can be any inhibitory nucleic acid, an miRNA (natural or synthetic), an miRNA mimic, a siRNA, a shRNA, or a hybrid (i.e. gapmer). These nucleic acid molecules are different inventions in themselves, as they each comprises base sequences and structures different and specific of each genus. Within each genus, it is expected a description and enumeration in residues for sequences corresponding to species at least 69% to 100% identical to the complementary strand of the lncRNA of SEQ ID NO: 1. It is also expected a description of specific means for delivery of the molecule, targeting moieties and tissue-specific conjugated combinations of molecules as carriers, and/or vectors. The vector can be a plasmid, a viral or retroviral vector, comprising a different and unique structure, according to the host in which it is delivered.
The State of the Art:
lncRNAs and lncRNA of SEQ ID NO: 1:
Mattick (Mattick, J.S. et al. “Long non-coding RNAs: definitions, functions,
challenges and recommendations”. Nature Reviews Molecular Cell Biology, Vol. 24 (2023), pp: 430-447) reviews and discloses a consensus statement about long non-coding RNAs (lncRNAs). Mattick teaches that many lncRNAs are spliced and polyadenylated, which led to their description as “mRNA-like” (see page 431, right column, “Definition and nomenclature of lncRNAs” section, second paragraph). They are also derived from pseudogenes and occur frequently in human genome (more than 15,000 identified) and derived from sequences acting as 3’ untranslated regions of mRNAs or regulatory regions (same paragraph).
Mattick teaches that these lncRNAs have important functions with visible impact in mutated mice (see Figure 1 and below):
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Mattick teaches that lncRNAs range from 1kb to 100kb or longer in size, often
multi-exonic and highly alternatively spliced (see page 437, right column, “lncRNA structure-function relationships” section first paragraph).
It is therefore interpreted that given the important functions and sizes of lncRNAs, designing a specific inhibitory molecule 15 to 30 base pair-long would be a difficult and critical aspect of lncRNA silencing.
Boon (Boon, R.A. et al. “Long Noncoding RNAs. From clinical genetics to
therapeutics targets”. Journal of the American College of Cardiology, Vol 67, No. 10 (2016), pp:1214-1226) teaches the importance of lncRNAs in cardiovascular system health and diseases (see abstract and figure, page 1217).
Boon teaches that depending on the subcellular localization, lncRNAs can act via various mechanisms, mimicking transcription factor sites and binding to transcription factors, functioning as decoy and interfering with gene expression (see summary in figure, page 1217). LncRNAs can also be chromatin modifiers and contribute to epigenetic silencing or activation of expression. They can bind to miRNAs and act as sponges, or affect splicing of mRNA or their stability (see figure, page 1217).
Boon also teaches that knocking down lncRNAs such as TERMINATOR, ALIEN and PUNISHER results in cardiovascular defects in developing zebrafish embryos (see page 1218, right column, last paragraph and page 1219, left column, first paragraph), while dysregulation of others such as Novlnc6 results in dilated cardiomyopathy (see page 1219, left column, “Regulation of lncRNAs during pathology” section).
Therefore, Boon teaches that lncRNAs can have multiple functions in cells, and that multiple lncRNAs are known to be important in cardiovascular health and diseases.
Viereck (Viereck, J. et al. “ Long noncoding RNA Chast promotes cardiac
Remodeling”. Science Translational Medicine, Vol. 8, No. 326 (2016), p:326ra22) teaches the isolation of lncRNA of SEQ ID NO: 1, identified in instant Specification as lncRNA Gm11641 or ENSMUST00000130556, renamed “Chast” for “cardiac hypertrophy-associated transcript” ( see instant Specification § [0020], [0143]-[0144], Table 1; and Viereck page 1, right column, 2nd paragraph and Figure 1A). Viereck teaches that lncRNA Gm11641 overlaps untranslated regions of two other genes, Arhgap 27 and Plekhm1. See Figure 1F and below:
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Inhibitory nucleic acid molecules: MiRNA, miRNA mimic, siRNA, shRNA and gapmers:
Lam (Lam et al. “ siRNA versus miRNA as therapeutics for gene silencing”.
Molecular Therapy--Nucleic Acids, Vol. 4 (2015), p:e252) teaches the differences between miRNA and siRNA for gene silencing (see title and abstract). Lam teaches miRNAs are produced in a cell following post-transcriptional processing (Table 1). First the primary miRNA transcript (pri-miRNA) produces a 70-100 nucleotide precursor (pre-miRNA). The pre-miRNA precursors are then processed by Dicer into a 18-25-mer miRNA duplex which associates with RISC and binds to the target RNA through partial complementary base pairing with the consequence that the target gene silencing occurs via translational repression, degradation, and/or cleavage.
Lam further teaches:
“Since this phenomenon can occur with both siRNA and miRNA,48,49,50 the RNA duplex needs to be carefully designed to warrant correct guide strand selection by the RISC. Two major sequence parameters are known to determine the guide strand selection: (i) the asymmetry rule and (ii) 5′ nucleotide preference; both of which can be applied to … miRNA design” (page 5, section “Design of therapeutic siRNA”-Strand selection paragraph).
Lam also teaches the asymmetry rule means the guide strand should have a more thermodynamically unstable 5’ end vs. the passenger strand and the 5’ nucleotide preference rule instructs that the guide strand should have a U or A at the 5’ end whereas the passenger strand should always contain C and G at the 5′ end to minimize the risk of being incorrectly selected as a guide strand (same paragraph).
An incorrect loading orientation into RISC results in the intended guide strand being discarded and off-target effects produced since the remaining (intended passenger strand) strand base-pairs to non-intended mRNA (Lam, section “Design of therapeutic siRNA”-“Strand selection” paragraph).
With respect to the use of claimed miRNA for in vivo use in a subject, Lam teaches RNA therapies face barriers of stability, delivery challenges, and off-target effects (page 1, right column, first paragraph). Lam teaches synthetic miRNA precursors with longer sequences (from a few extra nucleotides to a full-length pri-miRNA) have been proposed as therapeutic agents and these pri-miRNAs require processing in the nucleus, whereas pre-miRNAs and miRNAs do not, so different strategies are required for delivery of different types of miRNA to their cellular targets (see page 6, section “Design of therapeutic miRNA”, paragraph 2). Lam teaches miRNA has an intracellular site of action but is poorly permeable across biological membranes ( see page 9, left column, section “Delivery of siRNA and miRNA Therapeutics”). Lam teaches viral vectors can be effective for delivery but are associated with serious safety concerns (same section, paragraph “Viral vectors”). Regarding stability, Lam teaches RNA exhibits poor stability and chemical modifications can address that (see page 7, left column, section “Chemical modification”). Different modifications are available as tools to mitigate nuclease degradation and facilitate delivery (same section).
Gorski (Gorski, S. et al. “RNA-based recognition and targeting: sowing the
seeds of specificity”. Nature Reviews-Molecular Cell Biology, Vol. 18 (2017), pp: 215–228 ) teaches that essential to a regulatory RNA’s function is the presentation of short 'seed sequences' in a target (abstract). While regulatory RNAs may vary in length, 1) secondary and tertiary structures are important in target recognition and 2) target binding usually involves partial complementarity with only a short stretch of nucleotides (Fig. 1). For example, duplexes containing 8 nucleotides are unstable, whereas a 20-nucleotide RNA–RNA duplex is nearly irreversible under physiological condition (see page 215, right column, first paragraph). While mismatches are allowed within the seed region, the location of these mismatches can have different effects on guide–target binding: mismatches at nucleotides 2–5 of the guide reduce the association rate more than mismatches at positions 6–8. In the absence of a matched seed sequence, the RNP finds targets more slowly and binds to them less stably (see page 219, right-side column,1st paragraph). For 21-nucleotide miRNA and siRNAs, nucleotides 2–8 make the largest contribution to the energy of target binding, with mismatches at the center of the seed decreasing binding the most (see page 224, left-side column, 1st paragraph).
- Van den Berg (Van den Berg, F.T. et al.“ Design of effective primary microRNA mimics with different basal stem conformations”. Molecular Therapy—Nucleic Acids, Vol. 5 (2016), p: e278) teaches that primary microRNA mimics (pri-miRNA) are important mediators of effective gene silencing and are well suited for sustained therapeutic applications (see Abstract). Van den Berg teaches the design of effective primary microRNA mimics with different basal stem conformations (see page 2, “Results” section and Figure 1). While the entire reference is relied on, applicant is directed to the “Design and functionality of pri-miRNA mimic” starting at page 4. On page 5, Van den Berg recites, “The processing and silencing efficacy of guides derived from pri-miRNA mimics was again assessed by northern blot analyses and luciferase reporter assays (Figure 4b–e).” Further recitation, “In contrast to the original pri-miRNAs, functional miRNAs were not effectively derived from all pri-miRNA mimics”. Van den Berg concludes this section of the reference with the following significant recitation, “Together, these results indicated that exogenous miRNAs can indeed be effectively derived from expressed pri-miRNAs with a variety of basal stem lengths and motifs, where the canonical hairpin was present in almost all, most, or none of the predicted structures including the extended flanking sequence, but the level of target silencing differed for mimics with the same scaffold or core guide sequence” (page 5).
Wang (Wang, X. et al. “Silencing of Long Noncoding RNA MALAT1 by miR-
101 and miR-217 inhibits proliferation, migration, and invasion of esophageal squamous cell carcinoma cells”. The Journal of Biological Chemistry, Vol. 290, No.7 (2015), pp: 3925-3935) teaches that naturally occurring miRNAs (miR-101 and miR-217) are capable of silencing lncRNA MALAT1 (see title and abstract). Wang teaches that the silencing of MALAT1 leads to inhibition of growth, invasion, and metastasis of esophageal squamous cell carcinoma cells (see title, abstract and page 3926, left column, first paragraph, and Figures 3 and 4). Wang teaches that expressing miRNA mimics (L-miR-101 and L-miR-217) are capable of reducing the level of MALAT1 expression (see Figure 2C).
Therefore, Wang’s teachings suggest that overexpressing these miRNAs or their mimics could be used as anti-lncRNA therapeutics for cancer treatment.
Chen (Chen, M. et al. “Tetracycline-inducible shRNA targeting antisense long
non-coding RNA HIF1A-AS2 represses the malignant phenotypes of bladder cancer”. Cancer Letters, Vol. 376 (2016), pp: 155-164) teaches inhibition of long non-coding RNA HIF1A-AS2 with a shRNA represses the proliferation of bladder cancer cells (see title, abstract and page 157, right column, “Knockdown of HIF1A-AS2 inhibited cell proliferation of bladder cancer” section, and Figure 2). Chen teaches the sequence of the shRNA used on page 156, left column, “Materials and methods” section, “Short hairpin RNA (shRNA)” paragraph.
Maruyama (Maruyama, R. et al. “ Knocking Down Long Noncoding RNAs
using antisense oligonucleotides Gapmers”. Methods and Protocols, Methods in Molecular Biology, Vol. 2176 (2020), pp: 49-56) teaches the use of gapmers as promising tools for therapeutics (see page 52, section 4). However, Maruyama discloses that the design of good gapmers is a critical step (see page 51, section 3). Maruyama teaches that chemical modifications, especially LNA lead to higher RNA binding affinity. Maruyama also discloses that GC content is one of the most important parameters in the design of gapmers, and off-target effects are to be avoided using software tools (see section 3). Maruyama concludes acknowledging that using gapmers for lncRNA inhibition as a therapeutic tool is still in its infancy, tissue-specific delivery being a challenge, as well as delivery route, toxicity, treatment duration, dosage adjustment and off-target effects (see page 54, section 5).
Viereck (see above) teaches that lncRNA of SEQ ID NO: 1, called Chast,
is capable of inducing pressure overload in mice and cardiac hypertrophy in cardiomyocytes in vitro (see Figures 1 and 2). Viereck also teaches the use of LNA gapmer to silence Chast in HL-1 cardiomyocytes cells in vitro results in significant upregulation of Plekhm1 gene expression; Viereck also teaches that using siRNA against Plekhm1 gene results in increase in Chast expression level (see page 5, left column, 2nd paragraph). Viereck teaches that using Gapmer against Chast in mice prevents cardiac remodeling and reduces the size of heart compared to control (see Figures 6 and 7). Viereck teaches a gapmer sequence for Chast , i.e. “ 5’-TGGATTGGAGGTTGG-3’ (see page 10, right column, “Cell culture, transfection, and treatment” section). Although other details on the gapmer, i.e. chemical modifications and formulation, were not provided, Viereck teaches that other siRNA molecules targeting a gene related to Chast, e.g. Plekhm1, can have an effect on Chast’ s expression (same paragraph).
A review of the art and prior art shows that there are challenges associated with the use of an antisense RNA molecule to function as an inhibitor of lncRNA in a cell in vitro or in vivo in a subject, requiring proper processing, adequate length and specific sequence requirements. It is also notable that modifying a lncRNA’s expression using an inhibitory nucleic acid affects other genes located in proximity.
These challenges make it obvious that there is a need for adequate written description of the agent/compound to be used in the claimed method of treating or preventing pathological cardiac hypertrophy. It is also obvious that a lncRNA of SEQ ID NO: 1 is fairly recent as a discovery, and only one specific agent, i.e. a gapmer, with little information on structure and formulation, has been described in the literature so far.
Guidance from the Specification:
Regarding lncRNA of SEQ ID NO: 1 specifically, Applicant discloses in the
Specification, the validation of expression of lncRNA Gm11641, i.e Chast in heart tissue (see Figure 1, § [0145]), the validation that lncRNA Gm11641 is a non-coding RNA (see § [0147]), and its upregulation in a model of cardiac hypertrophy (see Figure 2A).
Applicant shows tissue-specific expression of lncRNA Gm11641, with higher expression in lung, spleen, kidney and brain (see figure 3).
Applicant shows expression of lncRNA Gm11641 in cardiomyocytes, cardiac fibroblasts and endothelial cells in culture (see Figure 4).
Applicant shows overexpression of lncRNA Gm11641 using a lentiviral vector in cardiomyocytes in culture and the result, i.e. modification in cell sizes and gene expression (see § [0155]-[0156]).
More importantly, Applicant discloses repression of lncRNA Gm11641 using a Gapmer antisense oligonucleotide in cardiomyocytes in culture (see Figure 9 and § [0157]). Applicant discloses only one dosage, i.e. 50nM of Gapmer used, with significant but small reduction in relative expression of lncRNA Gm11641.
Applicant’s description of the gapmer’s structure is as follow: “LNATM GapmeRs (Exigon) contain a central stretch of DNA monomers flanked by blocks of modified nucleotides (LNA, locked nucleic acids).”
What the Specification does not teach:
The Specification does not provide examples with subjects other than mice and
cells in culture. The Specification does not teach any siRNA directed against lncRNA Gm11641, nor shRNA, nor miRNA nor mimics. The Specification discloses only one gapmer, without any specific information on its structure, the enumeration of the residues, the localization of the sequence used, nor the chemical modification and pattern of modification of the oligonucleotide.
The Specification does not disclose species of inhibitory nucleic acid comprising a nucleotide sequence at least 69% identical to the complementary strand of the lncRNA of SEQ ID NO: 1. There is no enumeration of residues in specific species having 69% to 100% identity to the complementary strand of the lncRNA of SEQ ID NO: 1.
One of ordinary skills in the art, relying upon the prior art and the guidance of the Specification would not be able to reproduce the claimed invention and treat cardiac hypertrophy in a subject such as a non-human primate or a human, using an siRNA, a shRNA or a miRNA mimic, or even using the gapmer “disclosed”.
Conclusion:
Taking into consideration the factors outlined above, including the nature of the
invention, the state of the art, the guidance provided by the applicant and the specific example, it is the conclusion that Applicant does not possess the invention as broadly claimed. There is no specific written example within the Specification that would lead one with ordinary skills in the art to a different conclusion.
Since claims 26-29 and 36-46 are depending on claim 25, and do not remedy its deficiencies, they are rejected as well.
Scope of enablement Rejection
Claims 25-29, 36-46 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because, while being enabling for a method of treating a pathological cardiac hypertrophy in mice using a specific gapmer, the Specification does not reasonably provide enablement for preventing the disease in any subject, nor does it provide guidance for other species of compounds encompassed in claim 25, i.e. any type of inhibitory nucleic acid.
The test of enablement is whether one skilled in the art could make and use the claimed invention from the disclosures in the specification coupled with information known in the art without undue experimentation (United States v. Telectronics., 8 USPQ2d 1217 (Fed. Cir. 1988)). Whether undue experimentation is needed is not based upon a single factor but rather is a conclusion reached by weighing many factors. These factors were outlined in Ex parte Forman, 230 USPQ 546 (Bd. Pat. App. & Inter. 1986) and again in In re Wands, 8 USPQ2d 1400 (Fed. Cir. 1988), and the most relevant factors are indicated below:
Nature of the invention:
Claim 25 recites : “A method of treating or preventing pathological cardiac
hypertrophy in a subject, comprising administering a compound inhibiting the expression and/ or the activity of the IncRNA of SEQ ID NO: 1, wherein the compound is
a nucleic acid sequence which comprises or consists of a nucleotide
sequence being complementary to at least 12 continuous nucleotides of SEQ ID NO: 1,
a nucleic acid sequence which comprises or consists of a nucleotide
sequence which is at least 69% identical to the complementary strand of the IncRNA of SEQ ID NO: 1,
( c) a nucleic acid sequence which comprises or consists of a nucleotide
Sequence according to (a) or (b), wherein U is replaced by T,
an expression vector expressing the nucleic acid sequence as defined
in any one of (a) to (c), preferably under the control of a heart-specific promoter, or
a host comprising the expression vector of (d).”
It is therefore expected a disclosure of a method of preventing cardiac hypertrophy in any subject, healthy, genetically predisposed and/or at risk. The subject can be a non-human primate or a human, as encompassed by the claim. It is also expected a disclosure of different types of inhibitory nucleic acid molecules, their enumeration in residues accompanied with specific SEQ ID NOs. It is also expected a disclosure of species showing variations in residues to encompass nucleic acid sequences which are at least 69% identical to the complementary strand of the lncRNA of SEQ ID NO: 1. It is expected a disclosure of different vectors and their structures, delivery methods for specifically targeting the heart, as well as chemical modifications of the oligonucleotides, conjugated ligands and/or targeting moieties, carriers and excipients for the compounds. It is also expected a step by step guidance for both methods of preventing and treating cardiac hypertrophy.
State of the Art:
Challenges identified in the Art for an inhibitory nucleic acid molecule
A review of the art and prior art discussed in “Written Description Rejection” above, shows that the following are challenges associated with the use of a silencing RNA molecule to function in a cell in vitro or in vivo in a subject:
Proper processing of nucleic acid sequences (e.g. to produce pri-miRNAs in the nucleus).
Length considerations for designing a functional siRNA and miRNA.
Sequence requirements on the region of complementarity with the target RNA, such regions of complementarity referred to as a “seed region”.
Testing of candidate silencing RNAs is essential because of the unpredictability whether a candidate siRNA or miRNA will work in a cell.
While it is recognized that introduction of exogenous nucleic acids that are
targeted to a specific gene may result in attenuation of expression of the targeted gene, nucleic acid based therapies are highly unpredictable:
Denzler (Denzler R et al.” Impact of MicroRNA levels, target-site
complementarity, and cooperativity on competing endogenous RNA-regulated gene expression.” Molecular Cell, Vol. 64, No.3 (2016), pp:565-579) teaches that several factors unduly influence miRNA-induced target-gene repression (1st line of introduction). Some of these as described in the entire reference are: competing endogenous RNA-mediated derepression counteracts intended miRNA activity, miRNA decay, almost complementary sites can contribute to target-site competition without imparting repression (see page 566, “Results” section, first paragraph), and closely spaced sites of the same or different miRNAs cooperatively sequester miRNAs (see page 573, left column, 2nd paragraph). Denzler concludes their study by suggesting testing of putative miRNAs in two different cell types and testing several different miRNA families.
Therefore, Lam, Gorski, Van Den Berg (see in “Written Description Rejection” above) and Denzler, all teach that miRNA should be complementary to its target RNA. All references teach there is unpredictability in miRNA function. Gorski teaches a seed sequence is necessary, Lam teaches, specifically, unpredictability with respect to miRNA design, miRNA delivery, lack of stabilizing chemical modifications to miRNA, and miRNA function. Van Den Berg also teaches that secondary structures of designed sequences matter and may differ in effects. Denzler teaches about competing endogenous sequences creating unpredictability, hence the need for multiple specific tests for each species of inhibitors.
Other Challenges in using an anti-lncRNA inhibitor as therapeutics:
Boon (see in “Written Description Rejection” above) also emphasizes in a
section named “Promise and challenges in using lncRNAs as therapeutic targets or biomarkers” that many lncRNAs are not conserved at the sequence level and are expressed only in primates, based on disclosures in prior art (see page 1223, left column). Boon states that “Humanized models or organoid cultures will be necessary to screen for biological properties of primate-specific lncRNAs before embarking on costly and ethically disputed nonhuman primate studies”. Boon also reminds that antisense oligonucleotide delivery is lower in the heart compared with the liver, although antimiRs and antagomirs can be used to improve cardiovascular diseases in small animals (see page 1223, right column). Boon also teaches that inhibiting a lncRNA may have unforeseen consequences, because some lncRNAs have been found to code for proteins or short peptides, as it was reported for a cardiac lncRNA (LINC00948) encoding myoregulin ( see Boon, reference#114).
The court has indicated that the more unpredictable an area is, the more specific enablement is necessary in order to satisfy the statute. (See In re Fisher, 427 F.2d 833, 166 USPQ 18 (CCPA 1970)). This is because it is not obvious from the disclosure of one species, what other species will work.
Breadth of the Claims:
Claim 25 recites in (a) “a nucleic acid sequence which comprises or consists
of a nucleotide sequence being complementary to at least 12 continuous nucleotides of SEQ ID NO: 1” or in (b) a nucleic acid sequence “at least 69% identical to the complementary strand of the lncRNA of SEQ ID NO: 1” or in (c) “a nucleic acid sequence which comprises or consists of a nucleotide sequence according to (a) or (b), wherein U is replaced by T”, or “(d) an expression vector expressing the nucleic acid sequence” or (e ) a host comprising the expression vector of (d)” .
The claim does not recite “gapmer” as only species, nor “mouse” only as a subject, nor “cardiomyocyte or cardiac fibroblast or vascular endothelial cell in culture” specifically.
Claim 25 encompasses prevention of cardiac hypertrophy in any subject,
which can be a human predisposed to the disease, but healthy. It also encompasses the use of miRNAs, shRNA and gapmers against lncRNA of SEQ ID NO: 1 for treating and preventing the disorder, in any subject as well.
Guidance from the Specification:
Applicant only discloses repression of lncRNA Gm11641 using a Gapmer antisense oligonucleotide in cardiomyocytes in culture (see Figure 9 and § [0157]). Applicant discloses only one dosage, i.e. 50nM of Gapmer used, with significant but small reduction in relative expression of lncRNA Gm11641.
Applicant’s description of the gapmer’s structure is as follow: “LNATM GapmeRs (Exigon) contain a central stretch of DNA monomers flanked by blocks of modified nucleotides (LNA, locked nucleic acids).”
Therefore, claim 25 is too broad. A legitimate question arises about the specificity and the structure of the one compound used, and about optimization efforts needed based upon individual base residues to be switched and/or modified, and tissue-specific delivery methods.
Experimentation Required:
In order to practice the claimed invention, an important amount of
experimentation would be required.
Applicant does not disclose any specific composition for a method of prevention in non-human primates or humans. Applicant does not disclose a tissue-specific method of delivery, knowing that tissue targeting can be an issue since lncRNA Gm11641 is expressed abundantly in lung, kidney and brain (see Figure 3).
In “Brief Descriptions of Drawings” sections ( § [0008]-[0046]), the
specification does not provide the base sequence of any inhibitory nucleic acid (no enumeration of residues, no SEQ ID No. entered at the time of filing), nor the chemical structure of ligands, targeting-moieties, nor structural or any other sort of limitations on potential inhibitors.
Since the applicant does not disclose any structure to permit a person of ordinary skills in the art to make the claimed inhibitor, said person of ordinary skills would have to test every compound known in the literature as capable of downregulating the specific long noncoding RNA Chast, or use any miRNA, shRNA, gapmer known to interfere with Arhgap27 and Plekhm1 mRNA. One with ordinary skills in the art would also have to design and test a plurality of synthetic miRNAs, shRNAs or gapmers, as well as conjugating ligands, linkers, targeting moieties and carriers (e.g. liposomes with structural lipids, phospholipids, PEG-lipids…), and evaluate their effectiveness in decreasing Chast lncRNA level in cells and in whole organisms.
This would require an unreasonable amount of experimentation. This constitutes “undue experimentation” and lack of enablement according to MPEP, § 2164.01, 2164.01(a) and 2164.05(a).
Conclusion:
Taking into consideration the factors outlined above, including the nature of the
invention, the breadth of the claims, the state of the art, the guidance provided by the applicant and the specific examples, it is the conclusion that an undue experimentation would be required to make and use the invention as claimed.
Since claims 26-29 and 36-46 are depending from claim 25, and do not remedy its deficiencies, they are rejected as well.
Claim Rejections - 35 USC § 112(b)
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 25-29 and 36-46 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.
Regarding claim 25, MPEP § 2173.05 (d) states “If stated in the claims, examples and preferences may lead to confusion over the intended scope of a claim”. Regarding claim 25, it recites in (d) “ preferably under the control of a heart-specific promoter”; the term "preferably" renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention.
Claims 26-29 and 36-46 depend on claim 25; these claims do not remedy the deficiencies of claim 25, therefore they are rejected as well.
Regarding claim 26, it recites the limitation " the pharmaceutical composition" in
line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 26 depends upon claim 25, in which there is no mention of a particular pharmaceutical composition, only “a compound” is mentioned. A “Pharmaceutical composition” can comprise the claimed compound and multiple other components such as carriers or excipients. A specific pharmaceutical composition is not claimed in claim 25.
Conclusion
No claim is allowed.
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/A.D./Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636