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 .
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on 03/18/2026 is acknowledged.
Claims 6-7, and 11-12 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 03/18/2026.
Claim Status
Claims 1-5, 8-10 are examined on the merits.
Priority
The applicant’s application is a U.S. National Stage application of
of a Indian Application Serial No. IN202211019412, filed March 29, 2022 is acknowledged.
Receipt is acknowledged of certified copies of papers required by 37
CFR 1.55.
Claim Objections
Claim 1 is objected to because of the following informalities: Claim 1 recites “vector” in the first line. It should be “vectors”.
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 1-5, 8-10 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.
Claim 1 requires the provision of a genus of post-translationally modified TRF2. The claim encompasses any post-transnationally modification of any type, such as an phosphorylation, acetylation, glycosylation, ubiquitination, sumoylation or combination thereof, relative to SEQ ID NO 1, as long as the modification has a TRF2 activity or lack of thereof. Thus, the claim encompasses the provision of a large genus of amino acid (nucleotide) sequences that must function as an TRF2.
Claim 8, requires the provision of a genus of post-translationally modified TRF2. The claim encompasses any post-transnationally modification of any type, such as an phosphorylation, acetylation, glycosylation, ubiquitination, sumoylation or combination thereof, relative to SEQ ID NO 1, as long as the modification has a TRF2 activity or lack of thereof. Thus, the claim encompasses the provision of a large genus of amino acid (nucleotide) sequences that must function as an TRF2.
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof.
The specification envisions a to provide a targeted molecular biological approach to precisely suppress ILlR1 (interleukin 1 receptor type 1) expression in cancer cells in the tumor microenvironment (e.g., paragraph 005). The specification envisions provides two plasmids to impede IL1R1 (interleukin 1 receptor type 1) expression. One of the plasmids encodes a deadCas9 conjugated PTM (post translational modification) (K293R) of TRF2 (telomeric repeat-binding factor 2). The other plasmid expresses a guide RNA designed against IL1R1 (interleukin l receptor type 1) promoter. Combination of these two will inhibit the wild type TRF2 (telomeric repeat-binding factor 2) binding to the promoter region, which can activate IL1R 1 (interleukin 1 receptor type I) in a feed forward loop manner. The plasmids can be delivered in cell culture using commercially available transfection reagents (e.g., paragraph 007). The specification envisions a CRISPR Cas based gene-editing system of a target gene comprising vector encoding: a) post-translationally modified TRF2 (telomeric repeat-binding factor 2) operably linked to a nucleotide sequence encoding a RNA-directed dead Cas9 (dCas9) having SEQ ID 1; b) a promoter operably linked to a nucleotide sequence encoding a CRISPR-Cas9 system gRNA (guide RNA) having SEQ ID 2, wherein the gRNA (guide RNA) targets and hybridizes with the target sequence and directs the RNA-directed dead Cas9 to the DNA locus; wherein, components a) and b) are located on different vectors (e.g., paragraph 0032). The specification envisions the gRNA (guide RNA) sequence (SEQ ID 3) is targeting IL1R1 (e.g., paragraph 0034). The specification envisions a method of preparing the construct as disclosed herein comprising the steps of: a. providing TRF2 (telomeric repeats binding factor 2): b. mutating TRF2 obtained in step (a) by site directed mutagenesis on the lysine 293 residue; and c. cloning the sequence obtained in step (b) into the dCas9-VP64_GFP backbone (e.g., paragraph 0037). The specification envisions the dCas9 (dead Cas9) fusion protein comprises dCas9 (dead Cas9) fused with a post-translationally modified TRF2 (telomeric repeat-binding factor 2) acting as a transcriptional repressor of the target gene IL1R1 (interleukin 1 receptor type 1 ) (e.g., paragraph 0039).
The working examples discloses the construction of two plasmids to impede IL1R1 expression. One of the plasmid encodes a dCas9 (dead Cas9) conjugated PTM (post translational modification) K293R of TRF2 (telomere repeats-binding factor 2). The other one expresses a gRNA (guide RNA) designed against IL1R1 (interleukin 1 receptor type l) promoter. Combination of these two inhibits the wild type TRF2 (telomere repeats-binding factor 2) binding to the promoter region which activates IL1R1 (interleukin 1 receptor type 1) in a feed forward loop manner (e.g., paragraph bridge [0046-0087]). The working example discloses that MDAMB231 and HT1080 cell lines expressing of dCas9 K293R TRF2 and IL1R1 guide RNA have reduced expression of IL1R1 as compared to cells transfected with dCas9 WT TRF2 (e.g., paragraph 0091; Figs. 1, 4). In addition, Further, dCas9 K293R TRF2 and dCas9 WT TRF2 expression in
MDAJVrB231 resulted in altered NFkB signaling. WT TRF2 mediated higher IL1R1 led to phosphorylated NFkB (activation of NFkB signaling pathway) compared to the K293R TRF2 counterpart (e.g., paragraph 0092; Fig. 3).
The examples described in the specification does not meet the limitation of the rejected claims containing a post-translationally modified TRF2. The specification only provides data for post translational modification K293R of TRF2. This is not representative of the very large variations allowed by the claims, there is insufficient guidance provided indicating any of the elements that are critical to the functioning of the modified TRF2 variants, thus it cannot be determined which amino acid can be changed without disrupting the function of the TRF2; thus, further experimentation would be required to determine which variants of e.g., TRF2 (SEQ ID NO: 1) are functional and which are not. There is insufficient guidance provided indicating any of the elements that are critical to the functioning of TRF2.
The state of the art with respect to using post-translationally modified TRF2 is under developed and unpredictable. Amiard et al. (Nature Structural & Molecular Biology, 2007) teaches that Telomere repeat factor-1 (TRF1) and TRF2 and protection of telomeres-1 (POT1) are telomeric DNA-binding proteins that organize large nucleoprotein complexes involved in essential telomeric functions (e.g., left column, paragraph 2nd, page 147). Amiard teaches that TRF2 appears to require DNA binding to stimulate strand invasion, as the truncated mutant form TRF2ΔBΔM, which does not
bind DNA, does not stimulate invasion (e.g., right column, paragraph 2nd, page 149; Table 1). Amiard teaches that the truncated forms TRF2ΔB, TRF2ΔM and TRF2ΔLΔM stimulate strand invasion, whereas TRF2ΔBΔM and BTRF2 do not. This shows that the TRF-homology (TRFH) domain is necessary but not sufficient for strand invasion. The linker domain seems dispensable for strand invasion, and it might even cause a decrease in the efficiency of the invasion reaction (e.g., left column, paragraph 2nd, page 150; Table 1). Benarroch-Popivker et al. (Molecular Cell, 2016) teaches that the wrapping activity of TRF2 requires the presence of seven lysine and two arginine residues on the surface of the TRFH domain. Mutation of these residues to alanine (resulting in the ‘Topless’ mutant of TRF2) abrogates the DNA wrapping activity. Mutants with different numbers of mutated lysines were constructed: K241, K242, and K245 in mutant 3K; K158, K173, K176, and K179 in mutant 4K; and all seven of them in mutant 7K (e.g., right column, paragraph 2nd, page 277; Figs. S3C, 3A). Mutated of two arginines to alanines in combination with the seven lysines, giving
the 7K2R mutant (Figure S3A). This mutant showed reduced topological
activity (Figure 3A) and wrapping efficiency (e.g., right column, paragraph 1st, page 278; Figs. S3A, 3A-B). Similarly, Timashev et al. (Nucleus, 2020) teaches that topless version of TRF2 is deficient in all aspects of telomere protection, suggesting that this is a loss-of-function mutant and therefore not readily interpretable (e.g., left column, paragraph 3rd, page 2; Fig. 1). Konishi et al. (Genes & Development, 2008) teaches that several mutations
appeared to interfere with TRF2 function in a temperature-independent manner, whereas others had no discernable effect on the behavior of TRF2. Three mutations in helix 1 of TRF2 (positions 450, 460, and 462
in human TRF2) resulted in TRF2 variants with slight differences in their ability to protect telomeres at different temperatures. One mutation in helix 2 (I468A) resulted in a mouse TRF2 allele that was fully capable of
protecting telomeres at 32°C but not at 37° or 40°C (e.g., left column, paragraph 1st, page 2; Fig. 1B, Suppl. Table 1).
As such, the prior art teaches about the unpredictability of the use of post-translationally modified TRF2.
The claims encompasses significantly more than what is disclosed in the specification and does not satisfy the written description requirement under 35 U.S.C 112(a).
Therefore, the skilled artisan would have reasonably concluded applicants were not in possession of the claimed invention for claims 1--5, 8-10.
The claims listed in the statement of rejection but not otherwise discussed are rejected because they are similarly not limited to particular amino acids that are considered to be adequately described by the specification.
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 1, 9-10 is 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.
Claim 1: The claim is directed to a CRISPR Cas system comprising structural components, including a vector encoding dCas and TRF2 and a vector encoding a guide RNA. However, the claim further recites that “the gRNA (guide RNA) targets and hybridizes with the target sequence and directs the RNA-directed dead Cas9 to the DNA locus”. It is unclear whether the quoted language is intended to define a structural characteristic of the claimed system or instead recites actions or operations performed by the system. Because the claim is drawn to a product, but includes language reciting actions performed by the product (“targets”, “hybridize” and “directs”), it is unclear when infringement occurs and what structural limitations are required by the claim. Therefore, the claim is indefinite because it improperly mixes product limitations with method-like operational steps, rendering the scope of the claim unclear. It would be remedial to replace the phrase “the gRNA (guide RNA) targets and hybridizes with the target sequence and directs the RNA-directed dead Cas9 to the DNA locus” with the phrase “the gRNA (guide RNA) is capable of targeting and hybridizing with the target sequence and directing the RNA-directed dead Cas9 to the DNA locus”.
Claim 9: The claim refers to “the construct”, and “the delivery agent”, which lacks of antecedent basis, because its specific identity has not been previously introduced in claim 1. It is unclear whether “the construct” refers to a specific construct previously introduced in the claim, a construct recited in claim 1 (the CRISPR-Cas system comprise vectors “a” and “b”), or a particular component. As a result, the scope of the claim cannot be determined with reasonable certainty. It would be remedial to replace the phrase “the construct” with the phrase “the vectors”.
Additionally, the phrase “the delivery agent” lacks antecedent basis because no delivery agent has been introduced in claim 1. Therefore, it is unclear what substance, composition or class of materials constitutes “the delivery agent”. It would be remedial to replace the phrase “the delivery agent” with the phrase “a delivery agent”.
Claim 10: The claim recites “wherein the CRISPR-dCas based gene- editing system is used for targeting other genes including, but not limiting to, ILiR1”. The phrase “including, but not limited to” renders the claim indefinite because it introduces an open-ended and undefined set of genes without establishing the boundaries of the claimed subject matter. Specifically, it is unclear which genes in addition to IL1R1 are encompassed by the claim. As drafted, the claim expressly indicates that genes other than IL1R1 are included within the scope of the claim but fails to indicate those genes.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2-5, 8, 10 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 2 recites “wherein the RNA-directed nuclease is a dCas9 protein”. Claim 2 depends from claim 1, which recites “nucleotide sequence encoding a RNA-directed dead Cas9 (dCas9) having SEQ ID NO 1”. Thus, Claim 1 already claims a dCas9 protein comprised in SEQ ID NO 1. Claim 2 is merely recasting the same dCas9 without further limiting the dCas9 in any manner. Thus, despite the difference in language, these claims have substantially the same scope, claim 2 provides no additional structural narrowing.
Claim 3 recites “wherein the gRNA (guide RNA) sequence (SEQ ID 3) is targeting IL1R1”. Claim 3 depends from claim 1, which recites “b) a promoter operably linked to a nucleotide sequence encoding a CRISPR-Cas9 system gRNA (guide RNA) having SEQ ID 2”. SEQ ID NO 3 is comprised in SEQ ID NO 2 [see alignment below]. Thus, Claim 1 already claims a gRNA targeting IL1R1 SEQ ID NO 3. Claim 3 is merely recasting the same gRNA targeting IL1R1, without further limiting the gRNA of SEQ ID NO 3 in any manner. Thus, despite the difference in language, these claims have substantially the same scope, claim 3 provides no additional structural narrowing.
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Claim 4 recites “A nucleic acid construct as claimed in claim 1 comprises nucleic acid sequence encoding a dCas9 (dead Cas9) fusion protein having SEQ ID NO 1”. Claim 4 depends from claim 1, which recites “nucleotide sequence encoding a RNA-directed dead Cas9 (dCas9) having SEQ ID NO 1”. Thus, Claim 1 already claims a dCas9 comprised in SEQ ID NO 1. Claim 4 is merely recasting the same dCas9 without further limiting the dCas9 in any manner. Thus, despite the difference in language, these claims have substantially the same scope, claim 4 provides no additional structural narrowing.
Claim 5 recites “A nucleic acid construct as claimed in claim 1 comprising a guide RNA having SEQ ID NO 2”. Claim 5 depends from claim 1, which recites “b) a promoter operably linked to a nucleotide sequence encoding a CRISPR-Cas9 system gRNA (guide RNA) having SEQ ID 2”. Thus, Claim 1 already claims a guide RNA comprised in SEQ ID NO 2 [see alignment above]. Claim 5 is merely recasting the same guide RNA sequence without further limiting the guide RNA in any manner. Thus, despite the difference in language, these claims have substantially the same scope, claim 5 provides no additional structural narrowing.
Claim 8 recites “a post-translationally modified TRF2 (telomeric repeat-binding factor 2) acting as a transcriptional repressor”. Claim 8 depends from claim 4 which depends of claim 1, which recites “a) post-translationally modified TRF2 (telomeric repeat-binding factor”. Thus, Claim 1 already claims a post-translationally modified TRF2. Claim 8 is merely recasting the same post-translationally modified TRF2 without further limiting the post-translationally modified TRF2 in any manner. Acting as a “transcriptional repressor of the target gene IL1R1” merely states an intended result or inherent function of the previously recited dCas9-modified TRF2 and it does not impose an additional structural limitation, then the dependent claim fails to further limit the parent claim.
Claim 10 recites “wherein the CRISPR-dCas based gene- editing system is used for targeting other genes including, but not limiting to, IL1R1”. Claim 10 depends from claim 9 which depend on claim 1, which recites “a CRISPR-Cas9 system gRNA (guide RNA) having SEQ ID 2 which comprises the gRNA targeting IL1R1” [see alignment above]. The system specifically targets IL1R1 based on the SEQ ID NO 2 comprising the guide RNA that targets IL1R1. Thus, Claim 1 already claims a CRISPR-Cas9 system gRNA (guide RNA) having SEQ ID 2 which comprises the gRNA targeting IL1R1. Claim 10 is merely recasting the same guide RNA targeting IL1R1 without further limiting the IL1R1 in any manner. Thus, despite the difference in language, these claims have substantially the same scope, claim 10 provides no additional structural narrowing.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JULIO GOMEZ RODRIGUEZ whose telephone number is (571)270-0991. The examiner can normally be reached Monday - Friday 8:00 am - 5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Jennifer Dunston can be reached at 5712722916. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JULIO WASHINGTON GOMEZ RODRIGUEZ/Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637
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