DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s response and amendments received November 20, 2025 are acknowledged.
Claims 1-11 and 14 have been canceled.
Claims 13, 16, and 17 have been amended.
Claims 18-32 are newly presented.
Claims 12, 13, and 15-32 are pending in the instant application.
Claim 12 is independent.
Applicant’s election of the invention of group III, drawn to luciferase proteins, and the luciferase protein species of SEQ ID NO:8 (i.e. a mutant of SEQ ID NO:1 with the 4 mutations Y18R/L48K/W134E/W163E as compared to SEQ ID NO:1) in the reply filed on November 20, 2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)). It should be noted that the species of SEQ ID NO:8 appears to be novel relative to the prior art. As such, the species search was extended and stopped upon finding other species enunciated in the independent claim as set forth in the rejections below.
It should be noted that applicant has submitted new claims 18-32 which are not presently assigned to any inventive grouping. These new claims are assigned as follows:
Group I – claims 22 and 23
Group II – claims 24-26
Group III – claims 18-21 and 27-28
Group IV – claim 29
Group V, claims 30-32, drawn to polynucleotides, vectors and host cells.
The finding of lack of unity is maintained as set forth in the restriction requirement mailed August 28, 2025. Applicant is remined of the possibility of rejoinder as set forth in section 6 of said restriction.
Claims 15, 20-26, and 29-32 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected species or invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on November 20, 2025.
Claims 12, 13, 16, 17, 19, 27, and 28 are under examination in this office action.
Information Disclosure Statement
The IDS forms received 10/21/2022 and 4/24/2025 are acknowledged and the references cited therein have been considered.
The listing of references in the specification on pages 61-62 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.
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 12, 16, 17, 19, 27, and 28 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The disclosure of the instant specification is not sufficient to enable a skilled artisan to practice the claimed invention without conducting an undue amount of experimentation. Undue experimentation must be considered in light of factors including: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill in the art, the level of predictability of the art, the amount of direction provided by the inventor, the existence of working examples, and the quantity of experimentation needed to make or use the invention.
Applicant has claimed mutant luciferase proteins relative to the polypeptide of SEQ ID NO:1, fusion proteins wherein such luciferase mutants are joined to a peptide antigen, and kits comprising such polypeptides. The specification discloses that SEQ ID NO:1 is a prior art luciferase derived from the deep sea shrimp Oplophorus gracilirostris called NanoKAZ/nanoLuc which is a truncation comprising only the KAZ domain that further contains 16 substitution mutations which increase catalytic activity (and thus reporter gene activity) as compared to the wild type protein (see particularly page 42 of the instant specification as well as the entirety of WO 2012/061530 and Inouye et al., and note that “NanoKAZ” is a codon optimized nucleic acid sequence encoding the exact same polypeptide as “nanoLuc” and thus at the polypeptide level the terms are synonymous). Independent claim 12 recites that the claimed polypeptides are a) a luciferase (and thus necessarily has catalytic activity that releases a photon upon substrate cleavage) and b) a mutant of SEQ ID NO:1 that i) is 80% or more identical in sequence to SEQ ID NO:1 and ii) comprises one or more substitution mutations as positions defined relative to SEQ ID NO:1. SEQ ID NO:1 is 173 amino acid residues in length, such that “at least 80% sequence identity” allows for 34 mutations (139/173 x 100 = 80.34). Claim 12 recites 7 positions that are to be mutated, with two positions having alternate substitutions such that 9 total point mutations are recited, but the language “at least one” makes it clear that while combinations of the explicitly recited substitution point mutations are encompassed they are not required, with dependent claim including 19 and 13 requiring defined combinations of point mutations or exact full length sequences respectively. To support such claims the specification discloses mutating SEQ ID NO:1 at various positions singly or in combination, and constructs comprising duplicated or triplicated domains to increase catalytic activity (see particularly working Example 1 and Table 1 beginning on page 7 of the specification). Note that mutations at positions other than those outlined in Table 1 do not appear to have been made or disclosed in the instant specification.
Given the ubiquity of recombinant molecular biology techniques, making a polypeptide any given percent identity to a reference sequence is trivial. Ensuring that such variants maintain desired functional properties is highly non-trivial typically requiring extensive trial and error research and experimentation. For example, Binkowski et al. (WO 2012/061530, of record 4/24/2025 IDS) disclose making numerous mutants of luciferase in an effort to increase catalytic activity and while some of their mutants did increase activity other effectively eliminated it (see entire document, most notably Figures 6-27 and the working examples). Loss of functional activity subsequent to mutagenesis is reasonably expected, and indeed the art has long taught that assigning functional activities for any particular protein or protein family based upon sequence homology is inaccurate, in part because of the multifunctional nature of proteins (Skolnick et al, see entire document, particularly the Abstract and the section titled Sequence-based approaches to function prediction on page 34). Even in situations where there is some confidence of a similar overall structure between two sequences, only experimental research can confirm the artisan's best guess as to the function of the structurally related sequence (see in particular the Abstract and Box 2 on page 36). It is also known that the complexity of the problem of assigning function based on homology rises as the percent similarity or identity falls (see Whisstock et al., Quarterly Reviews of Biophysics, 2003, 36:307-340, particularly the sentence that spans pages 321 and 323).
As previously stated, the instant claim language allows for randomization of up to 20% of the total polypeptide sequence, and there is no evidence that the specifically called out point mutations are sufficient to ensure enzymatic activity in the absence of additional supporting sequence (i.e. the point mutations alone do not confer enzymatic activity) based upon the evidence presently of record. Note that the specification does not appear to disclose any reasonable use for “luciferases” that are unable to cause the release of a photon upon cleavage of a substrate. As such the instant claims encompass sequence variations far in excess of that tested by applicant and shown to work through the working examples, and elucidating what additional variants encompassed by the instant claim language do or do not maintain functional activity requires additional extensive unpredictable basic science research and experimentation beyond the experimentally verified polypeptides of SEQ ID NOs:2-17 as set forth in the working examples of the instant specification.
Claims 12, 16, 17, 19, 27, and 28 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.
Applicant has claimed luciferase polypeptides which are variants of SEQ ID NO:1, wherein the claimed variants must be at least 80% identical in sequence to SEQ ID NO:1 and must comprise at least one specifically identified substitution mutation as set forth in independent claim 12. Given that SEQ ID NO:1 is 173 residues long, 80% identical language allows for up to 34 mutations relative to the polypeptide of SEQ ID NO:1. To support such breadth, the specification discloses introducing the specific substitutions recited in claim 12 into the starting polypeptide sequence of SEQ ID NO:1, with such substitutions occurring singly or in combinations as set forth in the full length polypeptide sequences od SEQ ID NOs:2-17 (see particularly Table 1 of the instant specification for a clear indication of what mutations relative to SEQ ID NO:1 are in each variant). Data that speaks to substitution mutations made at positions outside of those specifically enunciated in claim 12 do not appear to be disclosed in the instant specification, but are necessarily present in polypeptides 80% identical to SEQ ID NO:1 as simultaneously introducing mutations at the 7 positions identified in claim 12 into the starting polypeptide of SEQ ID NO:1 yields 96% identity (166/173 x 100 = 95.95). .
The guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112, § 1 "Written Description" Requirement make clear that if a claimed genus does not show actual reduction to practice for a representative number of species, then the Requirement may be alternatively met by reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the genus. See MPEP 2163. In The Regents of the University of California v. Eli Lilly (43 USPQ2d 1398-1412) 19 F. 3d 1559, the court held that disclosure of a single member of a genus (rat insulin) did not provide adequate written support for the claimed genus (all mammalian insulins). In this same case, the court also noted: “A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is. See Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen). It is only a definition of a useful result rather than a definition of what achieves that result. Many such genes may achieve that result. The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming rejection because the specification does “little more than outlin [e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate."). Accordingly, naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material.” The court has further stated that “Adequate written description requires a precise definition, such as by structure, formula, chemical name or physical properties, not a mere wish or plan for obtaining the claimed chemical invention.” Id. at 1566, 43 USPQ2d at 1404 (quoting Fiers, 984 F.2d at 1171, 25 USPQ2d at 1606). Also see Enzo-Biochem v. Gen-Probe 01-1230 (CAFC 2002). Further, courts have long ruled that “When a patent claims a genus using functional language to define a desired result, the specification must demonstrate that the applicant has made a generic invention that achieves the claimed result and do so by showing that the applicant has invented species sufficient to support a claim to the functionally-defined genus.” See Capon v. Eshhar, 418 F.3d 1349 (Fed. Cir. 2005). Also, “A sufficient description of a genus . . . requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can "visualize or recognize" the members of the genus.” See AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69.
In the instant application, applicant is claiming mutants of the prior art luciferase polypeptide of SEQ ID NO:1. The specification discloses that SEQ ID NO:1 is a 19 kilodalton protein called nanoLuc/NanoKAZ, and that nanoKAZ itself is a truncation of the wild type luciferase from the deep sea shrimp Oplophorus gracilirostris wherein NanoKAZ also comprises 16 point mutations relative to the wild type sequence (see most particularly working example 1 beginning on page 42 of the instant specification as well as the entirety of WO 2012/061530 and Inouye et al.). Thus applicant has disclosed mutated luciferases demonstrating enhanced light generation as compared to the starting sequence, wherein the staring sequence already is a mutant demonstrating improved properties relative to the naturally occurring polypeptide (or in other words “mutants of a mutant”).
The polypeptide structures encompassed by the breadth of the instant claims goes far beyond that of SEQ ID NOs:2-17 which were made and tested by applicant and shown to display improved functional activity relative to SEQ ID NO:1 (see Table 1 as well as the working examples). Making luciferase mutants is not a novel concept, and Binkowski et al. (WO 2012/061530, of record 4/24/2025 IDS) disclose making numerous mutants of luciferase in an effort to increase catalytic activity and while some of their mutants did increase activity other effectively eliminated it (see entire document, most notably Figures 6-27 and the working examples). Loss of functional activity subsequent to mutagenesis is common, and indeed the art has long taught that assigning functional activities for any particular protein or protein family based upon sequence homology is inaccurate, in part because of the multifunctional nature of proteins (Skolnick et al, see entire document, particularly the Abstract and the section titled Sequence-based approaches to function prediction on page 34). Even in situations where there is some confidence of a similar overall structure between two sequences, only experimental research can confirm the artisan's best guess as to the function of the structurally related sequence (see in particular the Abstract and Box 2 on page 36). It is also known that the complexity of the problem of assigning function based on homology rises as the percent similarity or identity falls (see Whisstock et al., Quarterly Reviews of Biophysics, 2003, 36:307-340, particularly the sentence that spans pages 321 and 323). As previously stated, “at least 80% identity” relative to SEQ ID NO:1 encompasses 34 mutations, a number far in excess of that experimentally tested by applicant, and as shown by Binkowski et al. luciferase mutants cannot be assumed to have functional activity in the absence of experimental validation, especially as blanket percent identity allows for mutations to occur anywhere within the reference sequence. As such, there does not appear to be a reasonable correlation between the recited amount of mutation relative to SEQ ID NO:1 while maintaining activity as a luciferase (i.e. enzymatic cleavage of a substrate to release a photon) apart from the specific mutants of SEQ ID NOs:2-17 made and tested by applicant.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 12 and 27 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Inouye et al. (reference 5 on the 10/21/2022 IDS) as evidenced by Bachmann et al. (DE 19508087A1).
Inouye et al. disclose making and testing substitution mutants of the 19 kilodalton catalytic protein KAZ which is a truncation derived from native Oplophorus luciferase to enhance luminescence (see entire document, particularly the abstract). They disclose that in the prior art, the KAZ protein was mutated at 16 positions to make “nanoLuc” which displayed increased luminescence intensity as compared to wild type sequence KAZ, and that a codon optimized version of nanoLuc was made and called “nanoKAZ” (see most particularly the paragraph spanning pages 157 and 158). Inouye et al. made variants of KAZ comprising only one of the 16 present in nanoLuc/nanoKAZ, a limited number of double mutants, and a triple mutant they termed eKAZ (see particularly the first full paragraph of the left column of page 158 as well as Tables 1-5). The locations of such substitution mutations are explicitly identified (see Figure 1, most particularly 1B and note that the black boxes are the site of mutation while the sequence presented in 1B is that of the wild type KAZ protein). Instant claim 12 claims polypeptides that are at least 80% identical to SEQ ID NO:1, and since SEQ ID NO:1 is 173 residues in length this allows for 34 changes relative toe SEQ ID NO:1. Notably, the specification discloses that SEQ ID NO:1 is nanoKAZ (see page 42). Thus all of the KAZ mutants disclosed by Inouye et al. other than those comprising A54I meet the limitations of claim 12. This is because 80% identity allows for up to 34 mutations and nanoKAZ has only 16 relative to the wild type sequence, and because the instant recited “I56A” mutation relative to SEQ ID NO:1 is actually a mutation back to the wild type sequence which comprises an alanine at this position. It is noted that the sequence depicted in Figure 1B is only 169 residues while SEQ ID NO:1 is 173, and that comparison of these sequences reveals a two amino acid extension on both the amino and carboxyl termini of SEQ ID NO:1 as compared to that of the figure. Thus “A54I” as reported by Inouye et al. is the same location as “I56A” relative to SEQ ID NO:1 in the luciferase construct, and again the 80% identity language more than allows for such minor sequence changes at the amino and carboxy termini. Further, as presently recited, claim 12 only requires one of the specifically enunciated substitution mutations to actually be present, and since alanine is the residue found in the wild type sequence of the KAZ luciferase at position 56 relative to SEQ ID NO:1, any KAZ luciferase wherein this residue hasn’t been mutated necessarily meets the instant claim limitations. Additionally, Inouye et al. disclose that their mutant luciferases were expressed as a fusion construct comprising an N-terminal histidine tag (see most particularly Figure 1C as well as the paragraph spanning pages 158 and 159), and given that His tags are peptides that can be bound by an antibody as evidenced by Bachmann et al. (see entire document, and note that “antigen” is simply anything that can be bound by an antibody) the luciferase mutants of Inouye et al. were expressed as a fusion protein comprising an N-terminal peptidic antigen.
Claim Rejections - 35 USC § 103
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.
Claim 16, 17, and 28 are rejected under 35 U.S.C. 103 as being unpatentable over Inouye et al. (reference 5 on the 10/21/2022 IDS) as applied to claims 12 and 27 above and further in view of Janin et al. (WO 2018/197727).
The teachings of Inouye et al. have been discussed above and differ from the instant claimed invention in that even though they disclose testing their luciferases with various substrates and detection of the resultant visible light signal, they never disclose putting such components together in a “kit” form.
Janin et al. disclose numerous novel luciferase substrates and the combination of such substrates with luciferase in kits for the purpose of detection in various biological assays (see entire document, particularly the abstract, claims, and page 12). Notably the specific substrate recited in instant claim 17 is explicitly disclosed and claimed by Janin et al. (“Q-108” see particularly page 27, Table 1, and claim 11).
Therefore it would have been obvious to artisans at the time of the invention to place the luciferases of Inouye et al. into kits as disclosed by Janin in order to gain the advantage of being able to be used for diagnostic purposes as was also disclosed by Janin et al.
Claim Objections
Claim 13 is objected to as being dependent upon a rejected independent claim, but would be allowable if rewritten in independent form including all of the limitations of the independent claim and any intervening claims.
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Michael Szperka whose telephone number is (571)272-2934. The examiner can normally be reached Monday-Friday 8:30-5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Misook Yu can be reached at 571-272-0839. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Michael Szperka
Primary Examiner
Art Unit 1641
/MICHAEL SZPERKA/Primary Examiner, Art Unit 1641