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 .
The office action of 8/14/26 is vacated in favor of the present office action.
The IDS references previously supplied in the 8/14/26 office action are not supplied as they were present in the 8/14/26 office action. A new copy of the signed IDS of 12/4/26 is provided again.
Applicant’s amendment and argument of 7/23/26 are entered.
Claims 19 and 29 are amended.
Claims 22-24 are canceled.
Claims 1-21 and 25-30 are pending.
Notice: Examiner Reassignment
The present Application has been reassigned to Robert M. Kelly, AU1633. The Examiner’s information is available in the last paragraphs of this action. Please address future correspondence accordingly.
Election/Restrictions
The restriction/election requirements are withdrawn, given that the claims now all come down to the same polyA tail. At this point, there is no bar to double patenting rejections in the future.
Nucleotide and/or Amino Acid Sequence Disclosures
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, 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.
Paragraphs 52, 56, 58, 59, 61, 84-85, 178, 180-181, 183, and 185 each contain sequences of nucleotides that comprise more than 9 specifically defined nucleotides (e.g., 19A is a specifically defined sequence of 19 nucleotides. Also, an element c is non-A nucleotide, which is specifically defined in sequence listing requirements as “b”. The rules for the same may be found in 37 CFR 1.821 through 1.835.
See also: PTO-2301, Attached.
The specification is objected to.
In addition to the sequence requirements, above, paragraph 181 provides conflicting information. To wit, it states
In terms of the expression level in liver, when the miR-142 binding site is inserted at a position after 14A, 19A, 30A, and 60A, the expression level in liver is basically unaffected; when it is inserted at a position after 14A and 30A, the expression level is even better than that in the control group without the miR-142 binding site; and when it is inserted at a position after 0A, the expression level in liver decreases obviously.
(emphasis added).
14A cannot occupy both instances, being unaffected and being even better than that in the control group, without the miR-142 binding site.
Also, the specification recites “RAW 246.7 cells”, while the proper name is “RAW 264. 7 cells” in paragraph 190.
Appropriate correction is required.
Claim Objections
Claims 12-14 are objected to. Claims 12-14 each contain sequences of nucleotides that comprise more than 9 specifically defined nucleotides (e.g., 19A is a specifically defined sequence of 19 nucleotides. Also, an element c is non-A nucleotide, which is specifically defined in sequence listing requirements as “b”. The rules for the same may be found in 37 CFR 1.821 through 1.835.
See also: PTO-2301, Attached.
Claims 9 and 11 are objected to because of the following informalities:
Claim 9 recites “the number of element c comprised is 2 to 10”. Because c is a non-A nucleotide, it is mathematically the same to call it 2-10 non-A nucleotides, or there exist 10 of element c. However, “comprised is” is awkward and is confusing. It is recommended to recite “wherein the number c elements is 2-10”.
Claim 11 recites “wherein the number of element d comprised is 0-5.” The use of “comprised is” is awkward and confusing. It is recommended to recite “wherein the number of d elements is 0-5.”
Appropriate correction is required.
Applicant is advised that should claim 2 be found allowable, claim 3 will be objected to under 37 CFR 1.75 as being a substantial duplicate thereof. When two claims in an application are duplicates or else are so close in content that they both cover the same thing, despite a slight difference in wording, it is proper after allowing one claim to object to the other as being a substantial duplicate of the allowed claim. See MPEP § 608.01(m). Claim 3 recites that N is chosen from 0, 1 or more than 1. However, Claim 2 requires n is a natural number from 0 to 150. Thus, Claim 3, despite having a slightly different wording, is of the same substantial scope as Claim 2.
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 12, 13, and 28 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.
Claim 12 recites “element c” and “element d”, and does not define the structure within the claim. Therefore, the Artisan must look to the specification to find the definition. There is no strict definition, but there is a statement that “Element d” and “element c” are determined according to a protocol. Element d is determined from a target sequence (which is, from the specification, an miRNA binding site, e.g., paragraph 115), and is a fragment comprising a non-A base and contains 2 or more nucleotides. Also, element d has non-A nucleotides at the 3’ and 5’ ends of the element, and element d does not contain more than 3 consecutive A nucleotides. Finally, the terminal ends of element d must be adjacent to at least 2 As. (Must these As be consecutive?) After the determination of element d, all non-A bases are determined to be “element c” in those parts of the miRNA binding site that are not element d. All of this comes from paragraph 114 of the specification. However, it is not clear from this what is element d and what is element c. Must element d include the largest sequence possible, containing no more than 3 consecutive As, and no terminal As, or can smaller sequences be utilized? Could there be more than two element d? Must there be any element d? If so, are all non-As element c, and the As are nothing? If not, how do we know we can determine anything to be element c? It is very confusing and although it appears that a definition is attempted to be provided, it is not fleshed out such that the Artisan would understand the boundaries of the claim provided by element d and element c. Moreover, for the second instance, i.e., “element c-19A-element c-17A”, there is not element A, but the specification defines element c as only being found AFTER defining element d (“After element d is determined, all non-A bases are determined to be “element C” from the parts other than element D in the target sequence”, paragraph 114). Simply put, the structure of element d and element c are not provided with enough certainty to know what is being claimed, and these sequences are not known motifs/sequences from the prior Art. Therefore, the metes and bounds of the claim are not clear.
Claim 13 is rejected for the same reasoning given against claim 12, above. Thus, the metes and bounds of the claim are not clear. Moreover, exacerbating the same, the sequence provided has a separate miRNA binding site location “miRNA binding location”, and elements d and c. How can these sequences be present when the binding site, which is the target sequence, be outside the binding site? The specification teaches specifically that Element d is determined from the target sequence, and all non-A bases left over after defining the element d, are determined to be element c’s. Again, the metes and bounds of the claim are not clear.
Claim 28 recites “The engineered DNA molecule according to Claim 21”. However, there is no engineered DNA in Claim 21. Thus, there is a lack of antecedent basis.
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 1-21 and 25-33 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.
The claims are generic for the breadth of miRNA binding sites (e.g., Claim 1), which specifically includes a large number of specifically claimed miR binding sites (e.g., Claims 15-16) and miR-142, miR-122, miR-126, and miR-148a binding sites (e.g., Claim 27). Additionally, the claims are generic for the organ, tissues and cells, including prokaryotic and eukaryotic cells (e.g., Claims 21 and 30). All of this is in the context of miRNA binding sites being placed within a polyA tail (e.g., Claim 1).
The specification teaches that the purpose of miRNA binding sites within the polyA tail, is to attach them to mRNA coding sequences and to express the mRNA in various cell types, with regulation provided by way of miRNA binding to the binding sites, and having particular activities in silencing or expressing the encoded gene, thereby achieving selective regulation (e.g., paragraphs 4-15). Further, antecedent basis is provided for the list of miRNAs and binding sites (e.g., paragraphs 62-87). Antecedent basis is provided prokaryotic and eukaryotic cells (paragraph 92). Antecedent basis provided for E. coli (e.g., paragraph 93). As far as cells, organs and tissues: liver, spleen and hepatic parenchymal cells are taught (e.g., paragraph 95), RAW 264.7 cells, which are immortalized mouse macrophage like cells from a tumor induced by a murine leukemia virus in BALB/c mice (paragraph 107), along with LSEC (liver sinusoidal endothelial cells), hematopoietic stem cells, and acute myeloid leukemia cells (paragraph 108) and a long list of prokaryotic cells (e.g., paragraph 163).
The prior Art is silent on the issue of miRNA binding sites being placed within the polyA tail of coding sequences. To wit, miRNA binding sites are typically found in the 3’ UTR of mRNAs (e.g., Zhang, et al. (2017) “The Pattern of microRNA Binding Site Distribution”, Genes, 8:296, 11 pages long, see ABSTRACT). In fact, the Examiner’s search has provided no information of miRNA binding sites in the polyA tail. Thus, the sole description for the same must be within the specification and claims. All of this is in the context of about 2300 miRNAs in just humans (e.g., Alles, et al. (2019) “An estimate of the total number of true human miRNAs”, Nucleic Acids Research, 47(7): 3353-64, last paragraph). Additionally, there exist over 200 cell types in just humans (e.g., Khan YS, Farhana A. Histology, Cell. [Updated 2025 Mar 27]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2026 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK554382/, 18 pages as printed, see paragraph 2).
The specification teaches the purpose of these polyA tails is their use in organs/cells/tissues, where expression is lower in those cells/tissues/organs, due to the high level of miRNA expression (e.g., paragraph 94), specific expression of a target gene in an organ/tissue/cell, which may be preferentially lver or spleen or hepatic parenchymal cells (paragraph 95). That is, by integrating a miRNA binding site into a polyA tail, the mRNA expression in an organ/tissue/cell where it is undesired is specifically turned off, to reduce the off-target side effects of such expression (e.g., paragraph 110).
In example 1 luciferase genes are placed before alpha-globin 3’UTR, followed by a polyA tail, the tail having particular characteristics. In the set of miR sites, they are alternatively placed in the 3’UTR, at the beginning of the polyA, or after 14, 19, 30, or 60 As, into the sequences. Two sets are made this way, one with miRNA site for miRNA-142, and the other set for miRNA-122.
Example 2 is the preparation of mRNA-LNPs for delivery.
Example 3 utilizes the miR-142 set, and injects via tail vein into C57BL/6 mice. It is found that the miR-142 binding sites at 14A and 30A express higher than without miR-142, in the liver, and decreased expression is found for all in the spleen. Thus, 14A and 30A are chosen for this advantage over miR-142 at other positions in the polyA tail, and it is deemed suitable for applications for expression in the liver, with less expression in the spleen.
Example 4 utilizes the miR-122, inserted at the same sites, as above, and tests expression in mouse liver and spleen. 0A, 14A, and 19A are found as optimal for expression in the spleen, while not expressing much in liver.
Example 5 clones plasmids in E. coli, and finds the 14A and 30A variants exhibit lower base deletion than at 0A, 60A and the in the 3’UTR.
Example 6 tests miR-142 insertions at 0A, 1A, 2A, 3A, 4A, 5A, 10A, and 14A in mouse RAW 164.7 cells. In this case, the RAW 264.7 cells degrade all of the mRNAs tested.
Example 7 makes 0A inserts that are miR-142 linked to miR-122, and miR-122 linked to miR-142 (upstream – linked – downstream on mRNA). These are then tested in RAW 264.7 cells. The cells degrade both forms, without preference for order of miRs.
Example 8 provides for 0A inserts comprising three miR sites, 142, 148a, and 126, in each possible order, then expressed in LSECs (expressing miR-126), Stellate cells expressing miR-148a, and hepatic parenchymal cells. Expression is lowered in each cell type, but the 126-148a-142 and 148a-142-126 silences it better than the other combinations.
Comparing examples 3 and 4 indicates that expression control differs for the miRs by position in the polyA tail. I.e., while miR-142 is best expressed in liver cells at positions 14A and 30A, miR-122 works at positions 0A, 14A, and 19A. Thus, the cell specificity of each miR site depends on position on the polyA. Also, 0A-14A seem to work for miR-142 in RAW 264.7 cells. Finally, the multiple miR sites depend on order and cell type (e.g., examples 7-8), but this does not determine the position beyond at the end of the 3’UTR.
Given the breadth of cell types, tissues, and organs, which amount to 200+ tissues/cells in humans, and also in other animals, along with the extremely large number of miRNAs (about 2000 in just humans), along with the extremely large number of positions in the polyA tail(the tails tested are limited to the same overall size and structure), and the polyA tail structure itself, in view of the limited demonstrations in the specification and absence of miRs in polyA tails in the Art, the Artisan cannot envision where to put any particular miR site(s) in the polyA tails to get preferential expression or silencing in the breadth of which tissues/cells/organs expression or silencing is desired. Therefore, the Artisan would not have understood Applicant to have been in possession of the breadth of the claimed invention, beyond those embodiments specifically shown in the specification.
Prior Art
The closest prior art to Applicant’s claims is Graveley (2011) “Getting in the Loop: New Insights into the Mechanism of Poly(A) Site Recognition”, Structure, 19: 279-81. Figure 2A-2C teaches a hypothetical mRNA containing three UGUA CFIm binding sites and AAUAAA canonical polyA sites, with an intervening miRNA binding site. It is postulated that the processing occurs when the CFIm interacts with the upstream polyA site, yielding an mRNA lacking the miRNA, and if the CFIm instead interacts with the first and third UGUA site, the downstream polyA will be processed, yielding an miRNA binding site in the 3’ UTR. It is proposed that this might be a form of control in cell types. However, while the nucleic acid itself meets the structure of the broad claims, it is hypothetical, and would need to be tested to see if such took place. In addition, while it implies the possibility of naturally occurring structures that infringe the broad claims, the Examiner has found no evidence of it in the prior Art. Thus, no rejection is made for any form of judicial exception under 101. Additionally, because the nucleic acid is hypothetical, and the resulting answer cannot be determined, the Artisan would not be reasonably confident of obtaining the stated results postulated by Graveley. Furthermore, the Examiner has looked to the prior art for testing this hypothesis, or utilizing it, and has found none. It appears the prior art looking to this aspect is closest found in Ghosh, et al. (2022) “CFIm-mediated alternative polyadenylation remodels cellular signaling and miRNA biogenesis”, Nucleic Acids Research, 50(6): 3096-3114. In these studies, a screening is performed for genes differentially polyadenylated in the presence and knock down of CFIm25 and CFIm68 (subunits of CFIm). In such, differential regulation is found for several genes, and it is suggested that miRNAs regulate certain forms, but no direct teaching is provided for the structure as presently claimed Thus, the Examiner finds the claims free of the Art of record.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ROBERT M KELLY whose telephone number is (571)272-0729. The examiner can normally be reached M-F: 8a-5p.
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ROBERT M. KELLY
Examiner
Art Unit 1638
/ROBERT M KELLY/ Primary Examiner, Art Unit 1638
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