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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 06/30/2025 has been entered.
Election/Restrictions
Claims 1, 3-4, 7-11, 13-14, 17-32, 34-41, 56-57 are pending.
Amended claims 1, 3-4, 7-11, 13-14, 17-25, 56 and 57 of the elected group I are under consideration.
Claims 26-32, 34-41 stand withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/06/2023.
In the prior action, it was indicated that the subject matter of claim 57 was allowable. Upon further search and consideration, claim 57 is rejected.
Priority
The domestic benefit to U.S. Provisional application 62/658,303, filed on 04/16/2018, is recognized. All the examined claims enjoy the filing date of ‘303 filing.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 06/30/2025 was filed before the mailing date of this Office Action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Claim Interpretation
Claims 1 and 11 recite “a translation termination signal”. This limitation is interpreted to mean any codon that is coded as a stop signal by the ribosome machinery in either the cytosol or mitochondria.
Claim Objections
Claims 24 and 25 are objected to for misspelling “mammalian.” Appropriate correction is required.
Claim 11 is objected to because it recites “5S mtRSS”, for consistency with claim 1, it is recommended that claim 11 recite “5S rRNA mtRSS.” Similar claim 1 recites “5s rRNA mitochondrial” while claim 11 recites “5S mitochondrial,” it is recommended that claim 11 should recite “5s rRNA mitochondrial”.
Claim Rejections - 35 USC § 112
35 U.S.C. 112(a):
The rejection of claims 1, 11 and its dependent claims 3-4, 7-11, 13-14, 17-25, 56 under 112(a) is withdrawn.
Rejection of claims 1, 3-4, 7-11, 13-14, 17-25 under 112(a) is withdrawn for reciting a mitochondrial tRNA element, the claim has been amended to a mammalian mitochondrial DNA tRNA.
Rejection of 1, 3-4, 7-10, 56 under 112(a) is withdrawn, as the amended claim recites “5s rRNA mitochondrial RNA import signal sequence (5S rRNA mtRSS)”.
Rejection of claims 5 and 15 for reciting TRNE element is withdrawn, the claims are canceled.
Response to Arguments
Applicant's arguments filed on 06/30/2025 (hereinafter referred as the Remarks) have been fully considered and are persuasive.
The persuasive argument indicated the following: “mitochondrial tRNA element” (now reworded as mitochondrial DNA tRNA) is extremely common and a patent need not teach, and preferably omits, what is well known in the art (pg. 6-7). “Providing and testing each tRNA is simply not necessary as a given tRNA provides ample proof of principle and adequately demonstrates applicant’s possession of the invention” (pg. 7).
35 U.S.C. 112(b):
Rejection of claim 21 is withdrawn, since the “such as” phrase has been removed.
Claim Rejections - 35 USC § 101
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 24 and 25 are rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
Claims 1 and 11 recite an RNA or an expression cassette, respectively. While claims immediately considered on merits recite a RNA or expression cassette, the specification describes a methods of treating a subject wherein the claimed RNA or expression cassette will be administered for treating a mitochondrial disorder (see pg. 6, line 23-24). Further, the subject to be treated is a human subject (pg. 6, line 25), thus cells of the human subject will comprise the claimed product invention. Therefore, the scope of the claims would encompass cells in a human organism and the human organism itself.
Amending the claims to an isolated mammalian host cell or a mammalian host cell in vitro or ex vivo will obviate the 35 U.S.C. 101 rejection.
Claim Rejections - 35 USC § 103
The rejection of claims 1, 3, 7, 8, 9, 10,11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 57 is maintained, as noted below.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 3, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 57 are rejected under 35 U.S.C. 103 as being unpatentable over Yamada (2017, Biomaterials, 136, pg. 56-66) and Adhya (US20100168213, pub. 07/01/2010) and Entelis et al. (2001, JBC, 276, 45642-45653).
Yamada highlights that it “would be highly desirable” to identify “a convenient and established method for achieving mitochondrial transgene” for life sciences, drug discovery and gene therapy for mitochondria, since it has its own gene expression system (i.e. transcription/translation system) and a unique codon usage (pg. 56). Yamada discloses using a DNA vector using a specific liposome-based carrier for mitochondrial delivery, a MITO-Porter system (abstract); thus the theoretically the DNA vector is delivered to the mitochondria and then is transcribed and translated in the mitochondria. Yamada demonstrated that mitochondrial DNA vector with a CMV promoter was effective in transcribing the mRNA transcript in the mitochondria (pg. 57, relevant to instant cl. 11, CMV promoter is an eukaryotic RNA polymerase II promoter; relevant to instant cl. 21); Yamada also discloses that CMV promoter has been use frequently for effective nuclear transgene expression in mammalian cells (pg. 57). The DNA vector encoded genes that were codon-optimized for mitochondrial expression and would have low expression levels, if any, in the cytoplasm. The authors used a DNA vector encoding a mitochondrial gene (ND4) with a FLAG tag and a luciferase gene at the 3’ end (relevant to instant cl. 1, 11).
Fig. 1 from Yamada:
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Further, Yamada notes the vector further encoding a mitochondrial gene (ND4), a FLAG-tag, and a luciferase gene optimized for mitochondrial expression, all following the CMV promoter. Fig. 1 also displays the stop codon as taa codon for the mtLuc transcript (relevant to instant cl. 1, 3, 7, 8, 9, 10, 11, 13, 17-21; displaying a 1st ORF (ND4), then 2nd (FLAG) and 3rd ORFs (mtLuc), followed by a translation terminal signal). Also note a tRNAAsp at the 3’ end. Following cellular internalization, the pDNA is transcribed into mRNA (see Supplemental figure S3, pg. 3).
Yamada does not disclose the 5s rRNA mitochondrial import signal (5S rRNA mtRSS), nor a mammalian DNA tRNA of cl. 1, 11.
Adhya (US20100168213, pub. 07/01/2010) discloses a protein-coding RNA (pcRNA, par. 12) that is operably linked to a signal tag (cl. 1). The signal tag is derived from the D domain of a yeast tRNATyr (par. 17, 110), and Adhya notes that the signal tag is transported across the mitochondrial membrane by binding to carriers (par. 11) and then the pcRNA, once delivered to the mitochondria, will provide translation templates for synthesis of normal mitochondrial proteins to replace missing or defective mitochondrial genes. Further Adhya discloses that the signal tag “may consist of part or whole of the natural substrate (i.e. tRNA) for the carrier” (par. 49). Although it discloses that the signal tag can be attached at the 5’ or 3’ end of the pcRNA (par. 109), the exemplary molecules have the signal tag at the 5’ end of the pcRNA (Fig. 3, par. 111, relevant to instant cl. 1). Adhya discloses a bacteriophage T7 promoter upstream of signal tag oligos for in vitro transcription of signal-tagged pcRNAs (par. 114, step (9)).
Adhya discloses the pcRNA comprising various ORFs, which are mitochondria genes, such as ND1, ND2, cytochrome oxidases, atp, etc. . . . see Fig. 3A-3C, relevant to instant cl. 1, 7). Since a pcRNA comprises ORFs of mitochondrial transcripts, it has a natural mitochondrial stop codons (AGA, UAG, UAA, i.e. a translation terminal signal, indicated by boxed sequence in Fig. 3A, relevant to instant cl. 1, 10, 11, 20). Using cybrid cell line from Kearns-Sayre syndrome patient for which the mitochondria genome is missing genes for COII, COIII, ATP6 and ATP8 and thus is respiratory deficient, Adhya demonstrate that respiration was restored to 75% of normal cell lines by importing pcRNA-1 (par. 161-162, relevant to instant cl. 24, 25).
Adhya does not disclose 5S rRNA nor mammalian mitochondrial DNA tRNA.
Entelis demonstrated 5S rRNA and tRNA, both yeast tRNALYS and human mitochondrial tRNALYS, imported into human mitochondria with the aid of either yeast or human soluble proteins (abstract). Entelis demonstrate quantification of in vivo and in vitro import of 5S rRNA and tRNAs (see Fig. 8; trKHm, is tRNALys of human mitochondria (relevant to instant cl. 1, 11). Entelis purified the respective tRNAs or 5S rRNA and used isolated yeast and human mitochondria, the latter of which is a mammalian mitochondria.
One of the KSR rationale that may be used to support a conclusion of obviousness is that there is some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. Therefore, it would have been prima facie obvious for one of ordinary skill in the art before the filing date of the claimed invention to have modified the expression vector of Yamada in view of Adhya and Entelis and arrive at the claimed invention with a reasonable expectation of success. Based on Yamada’s success of using a CMV promoter to transcribe a mitochondrial expression vector with Flag tag in the mitochondria and based on Adhya’s success of importing pcRNA, which encodes mitochondrial transcripts, into the mitochondria by incorporating a sequence of tRNA in between the T7 promoter and mitochondrial protein-coding mRNA, a skilled artisan would reasonably expect success of incorporating Adhya’s tRNA sequence in between CMV and mitochondrial protein-coding mRNA. Further based on the success of importing a mammalian mitochondria tRNA and/or 5S rRNA into human mitochondria of Entelis, a skilled artisan would reasonably expect success of substituting the tRNA sequence of Adhya with 5S sRNA and/or mitochondrial tRNA of Entelis in between the promoter sequence and mitochondrial specific genes to transcribe an RNA sequence that is transported into and expressed in the mitochondria. Thus, cl. 1, 3, 7, 8, 9, 10, 11, 13, 17, 18, 19, 20, 21, 25 are obvious.
Regarding instant cl. 22 and 23, Yamada discloses the use of modified AAV vector to express genes in the mitochondria. Thus it would be obvious to incorporate the expression cassette in an AAV vector and a skilled artisan would reasonably expect success in transcribing the fusion-transcript in the cytoplasm from the CMV promoter, followed by importation of fusion-transcript to the mitochondria by the 5S rRNA and tRNA sequence and expressed in the mitochondria due to the mRNA transcript being optimized for mitochondrial expression.
Regarding instant cl. 56 and 57, Adhya indicates that signal tag can be other tRNA sequences as natural or artificial substrates for the protein carrier complex and thus indicate that “in principle any large number of sequences from different organisms may serve as signal tag” (par. 110) and may consist of part or whole of the natural substrate (i.e. tRNA) (par. 49). Adhya used a non-mammalian yeast tRNA along with specific protein complex to transport the pcRNA into a human cybrid cell line. The full mitochondrial tRNA sequences are known; in fact, Adhya’s pcRNA-2 in Fig. 3B sequence comprises the reverse complement of SEQ ID NO: 1, a precursor tRNAGlu sequence (see underlined portion, excerpt of Fig. 3B below; because it is transcribed from the opposite strand of the mitochondria’s double stranded genome. Further, Entelis demonstrates that mitochondrial tRNA-Lys with specific carriers was imported into the mitochondria (Fig. 8, Table 1, pg. 45650).
Excerpt of Fig. 3B below, underlined portion is reverse complement of instant SEQ ID NO: 1
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The KSR’s “obvious to try” rationale for supporting conclusion of obviousness requires the following three findings:
(1) a finding that at the relevant time, there had been a recognized problem or need in the art, which may include a design need or market pressure to solve a problem; (2) a finding that there had been a finite number of identified, predictable potential solutions to the recognized need or problem; (3) a finding that one of ordinary skill in the art could have pursued the known potential solutions with a reasonable expectation of success.
As Yamada highlighted the need to identify a “convenient and established method for mitochondrial transgene expression” and with observation of Adhya and Entelis’s demonstration of importing mitochondrial tRNA into the mitochondria, and with a finite number of mitochondrial tRNAs (see Fig. 2 of Adhya, ~20 tRNAs), a skilled artisan could have pursued the known potential solution with a reasonable expectation of success.
One of the KSR rationale that may be used to support a conclusion of obviousness is obvious to try. Therefore, it would have been prima facie obvious for one of ordinary skill in the art before the filing date of the claimed invention to have modified 5S rRNA and tRNA modified vector of Yamada, Adhya, Entelis and view of Entelis and arrive at the claimed invention with a reasonable expectation of success. Based on Adhya’s observation that any large number of tRNA sequences from different organisms may serve as signal tag and Entelis demonstrating that a mitochondrial tRNA is capable of being imported into the mitochondria, it would be obvious to try to test, as an initial point, the various full mitochondrial pre-tRNA sequence, including pre-tRNA-glutamate of SEQ ID NO: 1. Thus, cl. 56 and 57 are obvious.
Claims 4 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Yamada et al. (2017, Biomaterials, 136, pg. 56-66) and Adhya (US20100168213, pub. 07/01/2010) and Entelis et al. (2001, JBC, 276, 45642-45653) as applied to claims 1, 3, 7, 8, 9, 10,11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 57, 4 and 14 above, and further in view of Wang et al. (2012, Biochemistry, 109, 4840-4845).
Disclosure pertaining to rejection of claims 1, 3, 7, 8, 9, 10,11, 13, 17, 18, 19, 20, 21, 22, 23, 24, 25, 56, 57, 4 and 14 is noted above.
Yamada, Adhya, Entelis do not disclose a 3’-UTR.
Wang discloses correcting human mitochondrial mutations with targeted RNA import (title) by fusing a 20-ribonucleotide stem-loop sequence from the H1 RNA to tRNAs and mRNAs to import the hybrid RNA into the mitochondria (abstract). Wang further discloses including a 3’-UTR of some genes localizes the mRNA to the mitochondrial outer membrane, and that 3’UTR is not required for mRNA import but for corrective mitochondrial-encoded tRNAs, appending the 3’-UTR localization sequence was essential for efficient fusion-transcript translocation in mitochondria (abstract).
One of the KSR rationale that may be used to support a conclusion of obviousness is that there is some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention. Therefore, it would have been prima facie obvious for one of ordinary skill in the art before the filing date of the claimed invention to have modified the teaching of Yamada in view of Wang and arrive at the claimed invention with a reasonable expectation of success. Based on the Wang’s demonstration that a specific 3’UTR aids in localization of mRNA to the mitochondrial outer membrane and mitochondrial-encoded tRNAs required 3’-UTR for efficient translation, a skilled artisan would reasonably expect success in combining mRNA of Yamada with a 3’ UTR of Wang for improved delivery to or translocate into the mitochondria.
Response to Arguments
Applicant’s arguments with respect to examined claims have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
The claims were amended. However, the art of record, cited in this action, indicate using “carriers” or proteins to assist tRNA appended mRNAs to cross the mitochondrial membrane. The Remarks note the following (pg. 9):
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The argument is not persuasive, since the Remarks nor the specification provide evidence that protein “carriers” are not required. The ideal test would be to solely use the tRNA either alone or ideally appended with mRNA along with purified mitochondria to demonstrate that no other cellular factors/proteins are required. Here, the specification nor the Remarks provide such evidence.
Thus, the rejection is maintained.
Allowable Subject Matter
No claim allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEYUR A. VYAS whose telephone number is (571)272-0924. The examiner can normally be reached M-F 9am - 4 pm (EST).
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/KEYUR A VYAS/Examiner, Art Unit 1637
/Soren Harward/Primary Examiner, TC 1600