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 .
Information Disclosure Statement
The information disclosure statement (IDS) filed 29 September 2023 is considered, initialed, and attached hereto.
The listing of references in the specification (pages 1-3) 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, they have not been considered.
Drawings
The drawings are not acceptable because:
Figure 1 has text that is illegible. Figure text must be plain and legible. See 37 CFR 1.84(p)(1).
Figure 1 contains portions that are blurry, and therefore are not electronically reproducible. See 37 CFR 1.84(l).
Accordingly, replacement drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to this Office action. The replacement sheet(s) should be labeled “Replacement Sheet” in the page header (as per 37 CFR 1.84(c)) so as not to obstruct any portion of the drawing figures.
Nucleotide and/or Amino Acid Sequence Disclosures
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 - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”. The following sequences disclosed in this application require a “Sequence Listing”: (AAG)6 and (AAA)6 in Figure 1a, CUCAUAACCCG and CCCUCACAAG in Table 1 (specification pages 8-9).
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, 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.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Specification
The use of the term Nanoluc, Promega, Stop and Glo, TECAN, and Infinite, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
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
Claims 3, 7, and 14 are objected to because of the following informalities:
Claims 1, 2, 14, and 15 are objected to for using internal periods (e.g. “a.”). Formatting such as “(a)” is suggested.
Claim 1 uses a comma in line 36 to delimit a list that has otherwise been delimited using semicolons, consistent use of the same delimiter in a list is required.
Claim 2 recites the codon “AUG” twice in entries ‘t.’ and ‘u.’ in a Markush group of tRNA modification-sensitive codons.
Claim 2 ends “hh. GUA”, claims must end in a period.
In Claim 3, line 2, “t-RNA” should read “tRNA”.
Claim 7 needs to have a period at the end of the claim.
Claim 14 recites an extraneous “the” in line 2, deletion is suggested.
Claim 14 uses a comma in line 17 to delimit a list that has otherwise been delimited using semicolons, consistent use of the same delimiter in a list is required.
Appropriate correction is required.
Claim Interpretation
Claim 1 recites “for detecting a modulator of a tRNA-related condition” in lines 1-2 and claim 14 recites “for the detection of a modulator of a tRNA-related condition” in lines 1-2. These recitations are of an intended use of the invention of the respective claim. Neither the body of claim 1 nor the body of claim 14 requires a modulator of a tRNA-related condition or the detection of such a modulator, instead setting forth a method and a kit, respectively. MPEP §2111.02(II) states: “If the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.” As the body of both claim 1 and 14 fully sets forth all the limitations of the claimed invention and the preamble merely states an intended use, the intended use of the preamble of claims 1 and 14 is not given patentable weight.
Claim 1 recites in lines 26-28 an optional limitation, which is not given patentable weight. See MPEP §2111.04: “Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed”.
Claim Rejections - 35 USC § 112(b) - Indefiniteness
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 1-14 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 1 recites the limitation "the luminescence emission" in line 18. There is insufficient antecedent basis for this limitation in the claim, since no luminescence emission is previously recited and two possible sources of luminescence (the first and the second luminescence-based reporter genes) are recited. Claims 2-13 are rejected based on their dependency on claim 1.
Claim 1 recites the limitation "the signal" in line 23. There is insufficient antecedent basis for this limitation in the claim. Claims 2-13 are rejected based on their dependency on claim 1.
Claim 1 recites the limitation "the recombinant DNA constructs" in lines 29 and 34. There is insufficient antecedent basis for this limitation in the claim, as it is unclear what portion of the “one or more recombinant DNA constructs” recited in line 3 of claim 1 is referred to. Claims 2-13 are rejected based on their dependency on claim 1.
Claim 1 recites the limitation "the synonymous codon of the first codon" in line-38. There is insufficient antecedent basis for this limitation in the claim, since the first codon may have multiple possible synonymous codons, such as GCC having GCU, GCA, and GCG as synonymous codons. Claims 2-13 are rejected based on their dependency on claim 1.
Claim 5 recites the limitation "the recombinant DNA constructs" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 6 recites the limitation "the target codons" in line 3. There is insufficient antecedent basis for this limitation in the claim.
Claim 6 recites the limitation "the corresponding synonymous codon" in line 4. There is insufficient antecedent basis for this limitation in the claim.
Claim 8 contains the trademark/trade name Nanoluc. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a specific luciferase and, accordingly, the identification/description is indefinite.
Claim 8 recites “wherein the luminescence-based reporter genes are Nanoluc, Firefly; Nanoluc-PEST or Firefly-PEST” in lines 2-3. It is unclear whether these are two specific pairs of genes that may be selected, whether any two different genes may be selected, or if the same gene may be selected as both the first and second luminescence-based reporter gene. Therefore, one of ordinary skill in the art would not be reasonably appraised of the metes and bounds of the claim.
Claim 12 recites the limitation "the tRNA modification modulator" in line 2. There is insufficient antecedent basis for this limitation in the claim.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claim 13 recites the broad recitation “wherein the tRNA-related condition is cancer”, and the claim also recites "in particular metastatic cancer" which is the narrower statement of the range/limitation. The claim is considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims. For the purpose of examination, the claim is interpreted as requiring the broadest recitation.
Claim 14 recites the limitation "the recombinant DNA constructs" in lines 11 and 15. There is insufficient antecedent basis for this limitation in the claim.
Claim 14 recites the limitation "the synonymous codon" in line 18. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 112(d) - Dependent Form
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.
Claim 13 is 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 13 contains the sole limitation "wherein the tRNA-related condition is cancer, in particular metastatic cancer". As the tRNA-related condition is not part of any required limitation of the claimed method of claim 1 on which it depends, only being present in an optional limitation and in the preamble as part of an intended use that does not have patentable weight (see Claim Interpretation section above), the restriction of the tRNA-related condition to cancer or metastatic cancer does not restrict the scope of claim 1. Therefore, claim 13 does not further limit claim 1 upon which it depends. 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.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 15 is rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim does not fall within at least one of the four categories of patent eligible subject matter (a process, machine, manufacture, or composition of matter) because it claims the use of a product. See MPEP §2173.05(q). As claim 15 is not drawn to one of the four categories of patent eligible subject matter, it is not further treated on the merits.
Claim Rejections - 35 USC § 103
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 1-7, 9-10, and 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Grentzmann et al. (US Patent 6,143,502, issued 7 November 2000), herein Grentzmann, in view of Rapino et al. (NPL Cite No 2 in IDS filed 29 September 2023)(“Codon-specific translation reprogramming promotes resistance to targeted therapy” Nature 558, pages 605-609 (2018)), herein Rapino, and Letzring et al. (“Control of translation efficiency in yeast by codon–anticodon interactions” RNA 16(12), pages 2516-2528 (2010)), herein Letzring, and as evidenced by Tuorto and Lyko (“Genome recoding by tRNA modifications” Open Biol 6(12), article 160287 (2016)), herein Tuorto.
Regarding claim 1, Grentzmann teaches an assay (“a dual luciferase reporter system” col 5 line 21) comprising the steps of: a. providing one or more recombinant DNA constructs comprising i. A DNA oligonucleotide sequence encoding a first luminescence-based reporter gene operatively linked to a first promoter; ii. A DNA oligonucleotide sequence encoding a second luminescence-based reporter gene operatively linked to a second promoter (“a single construct has been designed (FIGS. 1 and 2). The firefly luciferase gene (fluc) has been cloned behind the renilla luciferase gene (rluc) into an altered vector pRL-SV40 vector […]. Expression features for initiation and termination of transcription and translation” col 5 lines 22-28; Fig. 1 and Fig. 2, note the SV40 and T7 promoters operatively linked to the two luciferase genes that are luminescence-based reporter genes, the claimed first and second promoter is considered to be able to be same promoter); b. Introducing the one or more recombinant DNA constructs of step a) into a system so as to allow for replication and translation in order to obtain a transduced system (“For in vitro transcription, PmlI-linearized plasmids were used as templates for T7 RNA polymerase […]. For in vitro translation in reticulocyte lysate (Promega Corp.), 1 µg of each RNA preparation was used per 7.5 µl of reaction mixture, complemented at 130 µM with all amino acids except methionine, and 3.3 µM (35S)-met (1,200 mCi/mM) was added” col 8 lines 37-48); d. Inducing the luminescence emission of the transduced system of step b) to obtain an induced system (“For luciferase activity measurements, samples of 3 µl or 0.6 µl of reticulocyte lysate mixtures were diluted in 100 µl of 1 X lysis buffer and analyzed for renilla and firefly luminescence activity using the Dual-Luciferase™ reporter assay (Promega Corp.)” col 8 lines 48-52; “measured between 2 and 12 seconds after luminescence substrate injection” col 8 lines 53-55); e. Measuring the luminescence emission of the first and of the second luminescence-based reporter genes in the induced system of step d) (“analyzed for renilla and firefly luminescence activity using the Dual-Luciferase.™ reporter assay (Promega Corp.) on a Dynatech MLX Microtiter Plate Luminometer. For both reactions, light emission was measured between 2 and 12 seconds after luminescence substrate injection” col 8 lines 50-55)).
Regarding claim 1, Grentzmann also teaches that the dual luciferase reporter system is useful for analyzing recoding (“A dual luciferase reporter system for measuring recoding efficiencies in vivo or in vitro from a single construct” col 5 lines 21-22). Though Grentzmann only teaches recoding as encompassing stop codon readthrough, +1 frameshifting, and -1 frameshifting (“In mammalian cells, three kinds of recoding have been described. First, redefinition of stop codons to sense codons (i.e., readthrough) […] Second, +1 frameshifting […] Third, -1 frameshifting” col 1 lines 40-58), Tuorto provides evidence that prior to the effective filing date of the claimed invention one of ordinary skill in the art would understand recoding to also encompass the usage of synonymous codons that vary in their dependance on tRNA modifications for translation (Tuorto title; pages 5-6, section titled “7. Genome recoding by tRNA modifications”). Therefore, one of ordinary skill in the art would understand the assay of Grentzmann to be useful for analyzing the effect of tRNA modifications.
However, Grentzmann does not teach a step c) of exposing the transduced system of step b) to one or more candidate tRNA modification modulators to obtain a modulated system, doing step d) on the modulated system of step c), step f) of correlating the signal measured in step e) to the one or more candidate tRNA modification modulators, that the one or more recombinant DNA constructs comprise 3 to 10 in frame repetitions of a first codon upstream of the first luminescence-based reporter gene and of a second codon upstream of the second luminescence-based reporter gene, that the first codon is a tRNA modification-sensitive codon, and that the second codon is a synonymous codon of the first codon. These deficiencies are made up for in the teachings of Rapino and Letzring.
Regarding claim 1, Rapino teaches that translation of HIF1A mRNA that contains codons requiring U34 tRNA modification is defective in cells depleted for genes involved in U34 tRNA modification (ELP3 and CTU1) and that replacement of the U34 codons in HIF1A with synonymous codons that do not require U34 tRNA modification rescues the translation defect (page 606, right column, paragraph 2; Fig. 2; Extended Data Fig. 5). This specific teaching more broadly informs one of ordinary skill in the art that comparison of translation of mRNA containing codons that require tRNA modification with mRNA containing synonymous codons that do not require tRNA modification can detect whether a depleted gene is required for the relevant tRNA modification, since depletion with control shRNAs did not show the codon-dependent changes in translation that shRNA-based depletion of ELP3 and CTU1 did for U34 codons. Therefore, the combination of Grentzmann and Rapino teaches an assay for detecting a tRNA modulator comprising steps a) and b) (see teachings of Grentzmann above), step c) of exposing the transduced system of step b) to one or more candidate tRNA modification modulators (for example, an shRNA targeting ELP3, as taught by Rapino) to obtain a modulated system, step d) of inducing luminescence emission of the modulated system of step c) to obtain an induced system (see teachings of Grentzmann above now applied to the combination of Grentzmann and Rapino), step e) (see teachings of Grentzmann above), and correlating the signal measured in step e) to the one or more candidate tRNA modification modulators (the correlation of translation and tRNA modification taught by Rapino).
However, the combination of Grentzmann and Rapino do not specifically teach that the one or more recombinant DNA constructs comprise 3 to 10 in frame repetitions of a first codon upstream of the first luminescence-based reporter gene and of a second codon upstream of the second luminescence-based reporter gene, that the first codon is a tRNA modification-sensitive codon, and that the second codon is a synonymous codon of the first codon. These deficiencies are made up for in the teachings of Letzring.
Regarding claim 1, Letzring teaches modifying a dual luciferase construct to make a recombinant DNA construct comprising 3 to 10 in frame repetitions of a first codon upstream of a first luminescence-based reporter gene (“Codon repeats (X) were inserted upstream […] at position 4 of the coding region of Renilla luciferase (X4R)” page 2517, Figure 1 legend; Figure 1A, construct labeled X4R) wherein the first codon is a tRNA modification-sensitive codon (Figure 2A, X4R where the Codon insert is (CGA)10) and to make a recombinant DNA construct comprising 3 to 10 in frame repetitions of a second codon upstream of a second luminescence-based reporter gene (“Codon repeats (X) were inserted upstream of a firefly luciferase reporter gene either at position 4 of the coding region (X4F)” page 2517, Figure 1 legend; Figure 1A, construct labeled X4F) wherein the second codon is a synonymous codon of the first codon (“We examined the effect of repeats of 10 identical codons in both positions, for 59 codons (except [CCC]10 and [GGG]10 for technical reasons” page 2517 right column paragraph 3, note that this includes the synonymous codons CGG, CGU, and CGC, see Table 1; note also that this recitation of page 2517 and Table 1 further teach one of ordinary skill in the art all repeats of 10 codons except for CCC and GGG that could be inserted upstream of luminescence-based reporter genes). Though Letzring does not teach both recombinant DNA constructs being present together in the same system, Letzring does teach that these constructs can be used to assay the effect of the codon repeats on translation (“To assay the effects of sequences containing codon repeats, we inserted them into common flanking sequences, either near the N-terminus at amino acid 4 of the firefly luciferase gene” page 2517 right column paragraph 3; entire reference), so one of ordinary skill in the art would be able to substitute the tRNA modification-sensitive and synonymous codon in frame repeats upstream of luciferases for sequences upstream of the two luciferases in the assay taught by Grentzmann in order to differentiate the two luciferases as one luciferase requiring the tRNA modification for translation and one luciferase not requiring the tRNA modification for translation, as suggested by the teachings of Rapino. Therefore, both recombinant DNA constructs are used in the method of the combination of Grentzmann, Rapino, and Letzring.
Regarding claim 2, Letzring teaches 10 in frame repetitions of a first codon that is a tRNA modification-sensitive codon wherein the tRNA modification-sensitive codon is any of: GCC, GCA, CGC, CGA, AGA, AAC, GAC, UGC, CAA, GAA, GGC, GGA, CAC, AUC, AUG, CUC, UUA, CUA, AAA, AUG, UUC, CCC, CCA, AGC, UCC, UCA, ACC, ACA, UGG, UAC, GUG, GUC, and GUA (Table 1).
Regarding claim 3, Letzring teaches 10 in frame repetitions of a first codon that is a tRNA modification-sensitive codon wherein the tRNA modification-sensitive codon is any of AAA, GAA, and CAA (Table 1).
Regarding claim 4, Letzring teaches 10 in frame repetitions of a second codon that is any of AAG, GAG, and CAG (Table 1).
Regarding claim 5, Letzring teaches recombinant DNA constructs comprising 4 to 8 repetitions of the first or second codon (“We also examined the effect of repeats of four identical codons in the N-terminal position” page 2518 left column paragraph 1; Table 1 rightmost columns labeled X4F-4mer, note that it includes tRNA modification-sensitive codons such as AAA as well as synonymous codons such as AAG).
Regarding claim 6, Letzring teaches recombinant DNA constructs comprising 4 or 10 in frame repetitions of codons. Though Letzring does not teach specifically 6 in frame repetitions of codons as claimed, in view of Letzring’s teachings of 4 or 10 in frame repetitions the specific 6 in frame repetitions claimed would have been prima facie obvious to one of ordinary skill in the art because the disclosed number of repetitions in the art are near to the claimed “range” of 6 repetitions. MPEP §2144.05(I): “a prima facie case of obviousness exists where the claimed ranges or amounts do not overlap with the prior art but are merely close.”
Regarding claim 7, Letzring further teaches that recombinant DNA constructs comprising 3 to 10 in frame repetitions of codons upstream of a reporter gene wherein the reporter gene is a fluorescence-based reporter gene (“Codon repeats (X) were inserted […] at position 4 of the coding region of […] superfolder GFP (X4G)”, page 2517, Figure 1 legend; Figure 1A, construct labeled X4G).
Regarding claims 9 and 10, Grentzmann teaches a dual recombinase assay wherein the system allowing for replication and translation are living human cells (“For in vivo translations, human kidney 293 cells (ATCC) were cultivated in minimum essential medium supplemented with 10% fetal bovine serum. Transient transfections were performed by lipofection using reagents from GIBCO/BRL (Gaithersburg, Md.). In vivo expression of the reporter genes was dependent on cell density and transfection efficiency, but was consistent in a given series of transfection experiments. Luciferase activity was determined 24 hours after transfection. One-hundred microliters of lysate was assayed by the Dual-Luciferase™ reporter assay as described above” col 9 line 60 - col 10 line 3).
Regarding claim 12, Rapino teaches assaying the effect of a tRNA modification modulator wherein the candidate tRNA modification modulator is an inhibitor (page 606 right column paragraph 2; Fig. 2; note that the shRNAs targeting ELP3 or CTU1 or the control shRNA are the modulators the system is being exposed to, so they are inhibitors since they inhibit translation, see Fig. 2f columns 3-6 where exposure to shELP3 or shCTU1 reduces translation of the FLAG tag attached to WT HIF1α).
Regarding claim 13, the combination of Grentzmann, Rapino, and Letzring teaches the assay of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above) and the limitation “wherein the tRNA-related condition is cancer, in particular metastatic cancer” does not carry patentable weight (see 35 U.S.C. 112(d) rejection of claim 13 above), so claim 13 is taught by the combination of Grentzmann, Rapino, and Letzring.
The combination of Grentzmann and Rapino would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention. Grentzmann teaches an assay for analyzing the effect on translation of recoding and Tuorto provides evidence that one of ordinary skill in the art would recognize tRNA modifications as recoding, so one of ordinary skill in the art would be motivated to apply the assay of Grentzmann to questions pertaining to analyzing tRNA modifications. Since Rapino teaches a relationship between the translation of an mRNA containing or lacking codons that are dependent on tRNA modifications and the presence or absence of tRNA modification modulators (e.g. the shRNAs taught by Rapino), one of ordinary skill in the art would be motivated, able to apply, and have a reasonable expectation of success in the combining the assay of Grentzmann with the relationship taught by Rapino in order to analyze the effect of tRNA modification modulators on recoding by codon choice and tRNA modification. Therefore, the combination of Grentzmann and Rapino would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date.
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the recombinant DNA constructs comprising 3 to 10 in frame repetitions of tRNA modification-sensitive codons or synonymous codons upstream of luminescence-based reporter genes taught by Letzring for the sequences upstream of each of the luciferases in the dual luciferase assay taught by Grentzmann in the combination of Grentzmann and Rapino. One of ordinary skill in the art could have performed the substitution because Letzring teaches creating their constructs using dual luciferase assay plasmids (see Methods section of Letzring) and techniques to construct plasmids with desired sequences in frame and upstream of a second sequence are standard in the art. One of ordinary skill in the art would also expect the results of the substitution to be predictable because both Letzring and Grentzmann are concerned with constructs that express luciferase under various regulatory situations, so applying the method of regulating expression (via repeated codons) in Letzring to the assay of Grentzmann should be predictable. Therefore, the combination of Grentzmann, Rapino, and Letrzing and the invention as a whole of claims 1-7, 9-10, and 12-13 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Grentzmann et al. (US Patent 6,143,502, issued 7 November 2000), herein Grentzmann, in view of Rapino et al. (NPL Cite No 2 in IDS filed 29 September 2023)(“Codon-specific translation reprogramming promotes resistance to targeted therapy” Nature 558, pages 605-609 (2018)), herein Rapino, and Letzring et al. (“Control of translation efficiency in yeast by codon–anticodon interactions” RNA 16(12), pages 2516-2528 (2010)), herein Letzring, and as evidenced by Tuorto and Lyko (“Genome recoding by tRNA modifications” Open Biol 6(12), article 160287 (2016)), herein Tuorto, as applied to claims 1-7, 9-10, and 12-13 above, and further in view of Promega (https://www.promega.com/products/luciferase-assays/reporter-assays/nano-glo-dual-luciferase-reporter-assay-system/ accessed from Wayback Machine snapshot dated 17 November 2019).
Regarding claim 8, the combination of Grentzmann, Rapino, and Letzring teach the assay of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, they do not teach the assay wherein the luminescence-based reporter genes are Nanoluc, Firefly; Nanoluc-PEST or Firefly-PEST (interpreted as requiring the first and second luminescence-based reporter genes to be two separate genes from this list). This deficiency is made up for in the teachings of Promega.
Regarding claim 8, Promega teaches a dual luciferase assay using firefly and Nanoluc luciferases as the reporters (page 3).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the Nanoluc and firefly reporter combination taught by Promega for the Renilla and firefly reporter combination taught by Grentzmann. One of ordinary skill in the art could have performed the substitution and the results of the substitution would be predictable because both reporter combinations are used for dual luciferase assays. Additionally, Promega teaches Nanoluc is a stable and brighter reporter than Renilla luciferase (page 5), which would motivate one of ordinary skill in the art to perform the substitution in order to improve the assay with a bright and stable reporter. Therefore, the invention as a whole of claim 8 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Grentzmann et al. (US Patent 6,143,502, issued 7 November 2000), herein Grentzmann, in view of Rapino et al. (NPL Cite No 2 in IDS filed 29 September 2023)(“Codon-specific translation reprogramming promotes resistance to targeted therapy” Nature 558, pages 605-609 (2018)), herein Rapino, and Letzring et al. (“Control of translation efficiency in yeast by codon–anticodon interactions” RNA 16(12), pages 2516-2528 (2010)), herein Letzring, and as evidenced by Tuorto and Lyko (“Genome recoding by tRNA modifications” Open Biol 6(12), article 160287 (2016)), herein Tuorto, as applied to claims 1-7, 9-10, and 12-13 above, and further in view of Kisly et al. ("Ribosomal protein eL24, involved in two intersubunit bridges, stimulates translation initiation and elongation" Nucleic Acid Res 47(1), pages 406-420 (2019)), herein Kisly.
Regarding claim 11, the combination of Grentzmann, Rapino, and Letzring teach the assay of claim 1 (see 35 U.S.C. 103 rejection of claim 1 above). However, they do not teach that the system allowing for replication and translation is a prokaryotic or eukaryotic cell-free extract containing endogenous ribosomes, endogenous transfer RNA, and endogenous amino acids.
Regarding claim 11, Kisly teaches a dual luciferase assay being used for assaying translation wherein the system allowing for replication and translation is a prokaryotic or eukaryotic cell-free extract containing endogenous ribosomes, endogenous transfer RNA, and endogenous amino acids (“To determine processivity of ribosomes, synthesis of a fusion Renilla-Firefly luciferase over 80 minutes in cell-free translation extracts was examined” page 415 left column paragraph 2; Methods subsections “Preparation of yeast cell-free extracts” through “In vitro translation reaction” page 409 right column paragraph 1 - page 410 left column paragraph 3).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the performance of a dual luciferase assay in cell-free extract taught by Kinsly for the performance of a dual luciferase assay in in vivo or in vitro systems (“the invention relates to a reporter system and method of use thereof for quantification of translational recoding, reinitiation, and internal initiation in eukaryotes in vivo and in vitro” Grentzmann col 1 lines 13-16) taught by Grentzmann. One of ordinary skill in the art could have performed the substitution and the results of the substitution would be predictable because both references teach performing the same type of assay, dual luciferase assays. Therefore, the invention as a whole of claim 11 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 14 is rejected under 35 U.S.C. 103 as being unpatentable over Grentzmann et al. (US Patent 6,143,502, issued 7 November 2000), herein Grentzmann, in view of Rapino et al. (NPL Cite No 2 in IDS filed 29 September 2023)(“Codon-specific translation reprogramming promotes resistance to targeted therapy” Nature 558, pages 605-609 (2018)), herein Rapino, and Letzring et al. (“Control of translation efficiency in yeast by codon–anticodon interactions” RNA 16(12), pages 2516-2528 (2010)), herein Letzring, and as evidenced by Tuorto and Lyko (“Genome recoding by tRNA modifications” Open Biol 6(12), article 160287 (2016)), herein Tuorto, as applied to claims 1-7, 9-10, and 12-13 above, and further in view of Weiner et al. ("Kits and Their Unique Role in Molecular Biology: a Brief Retrospective" Biotechniques 44(5), pages 701-704 (2008)), herein Weiner.
Regarding claim 14, the combination of Grentzmann, Rapino, and Letzring teach cells comprising one or more recombinant DNA constructs comprising i. A DNA oligonucleotide sequence encoding a first luminescence-based reporter gene operatively linked to a first promoter; ii. A DNA oligonucleotide sequence encoding a second luminescence-based reporter gene operatively linked to a second promoter; Wherein the recombinant DNA constructs comprise 3 to 10 in frame repetitions of a first codon upstream of the first luminescence-based reporter gene; Wherein the first codon is a modification-sensitive codon; Wherein the recombinant DNA constructs further comprise 3 to 10 in frame repetitions of a second codon upstream of the second luminescence-based reporter gene; and Wherein the second codon is a synonymous codon of the first codon (see 35 U.S.C. 103 rejection of claim 1 above). Grentzmann further teaches the components of the dual luciferase assay in one or more vials (“Renilla and firefly luciferase activities were assayed in the same tube” Grentzmann col 9 lines 5-6). However, the combination of Grentzmann, Rapino, and Letzring do not teach these components as part of a kit.
Regarding claim 14, Weiner teaches that it is useful to put together components in a kit in order to obtain advantages such as improved quality control (“prepacked reagent kits generally—have eliminated the need for users to control quality” page 701 right column paragraph 2) and are also desirable for their consistent reagents and tested protocols (“Modern researchers’ devotion to today’s kits suggests that they consider consistent reagents and tested protocols a good buy” page 702 left column paragraph 4). Therefore, the combination of Weiner with Grentzmann, Rapino, and Letzring teaches combining the components taught by Grentzmann, Rapino, and Letzring into a kit.
The combination of Weiner with Grentzmann, Rapino, and Letzring would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention. The advantages of kits taught by Weiner would motivate one of ordinary skill in the art to combine it with the assay taught by the combination of Grentzmann, Rapino, and Letzring in order to improve it with the advantages of kits, such as improved quality control and consistency of reagents. One of ordinary skill in the art would have a reasonable expectation of success in this combination because a kit is fundamentally just packaging together the components and does not impact their function in the assay. Therefore, the invention as a whole of claim 14 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Conclusion
Claims 1-15 are rejected.
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/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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