Notice of Pre-AIA or AIA Status
1. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restrictions
2. Applicant’s election without traverse of Group I, claims 1-16, in the reply filed on 23 October 2025 is acknowledged.
Claim Rejections - 35 USC § 112
3. 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.
4. 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.
5. Claims 2-5 and 8 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’s specification describes the terms “Gluc” and “Nluc” as “…refers to Gaussia luciferase polypeptide (SEQ ID NO: 1) or a variant thereof, provided the variant is substantially identical in amino acid sequence to Gluc (SEQ ID NO: 1) and also has substantially the same activity as Gluc (SEQ ID NO: 1)” and “…refers to NanoZac luciferase polypeptide (SEQ ID NO: 2) or a variant thereof, provided the variant is substantially identical in amino acid sequence to Nluc (SEQ ID NO: 2) and also has substantially the same activity as Nluc (SEQ ID NO: 2),” respectively. Applicant’s specification provides no examples, descriptions or limitations on the what a “variant” of Gluc or Nluc entails or encompasses (e.g., the number and type of variations: additions to the ends of the polypeptide, insertions, deletions, substitutions, etc.) nor do they provide any context regarding what degree of amino acid sequence similarity or activity is considered “substantially” the same as that of SEQ ID NO: 1 or SEQ ID NO: 2. A critical feature of the claimed invention lies in the ability of coeleterazine and f-coeleterazine to be used as orthogonal substrates in the claimed method of corresponding positions on an array (see claim 1 and claim 4). There is no proper description and/or guidance regarding how to modify Gluc or Nluc in a way to maintain their activity and selectivity towards their respective substrates (see claim 5). The number of potential options that satisfy the claimed genus is highly variant and insufficient description has been provided to describe the genus encompassed by the terms “Gluc” and “Nluc” and therefore the specification does not satisfy the written description requirement of 35 U.S.C. 112(a) with respect to the full scope of claims 2-5.
Similarly, regarding the use of DTT as a deactivation reagent selective for one luciferase and not another in claim 8, applicant’s specification only provides “Gluc” and “Nluc” as examples for DTT acting as a selective deactivation agent ([0026] and [0100]-[0103]). Applicant does not adequately describe in their specification what traits, properties or sequence motifs render a luciferase susceptible or not to DTT treatment, they do they describe how one of ordinary skill in the art would be able to predict how and when DTT would function as a suitable selective deactivation reagent, nor do they describe if they are in possession of the entire genus of luciferase combinations where DTT is selective for one luciferase but not another when they are combined together. For these reasons, the specification does not satisfy the written description requirement of 35 U.S.C. 112(a) with respect to the full scope of claim 8.
6. Claims 10 and 13-16 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.
A. Claim 10 recites the phrase “…terminator deoxyribonucleotide associated with if the affinity reagent for the type of…” There appears to be a typographical error in this phrase, however the typo is such that it makes the claim difficult to parse and unclear, therefore the claim is indefinite. For the purpose of prosecution, this claim is being interpreted as though the claim recites “…terminator deoxyribonucleotide associated with the position if the affinity reagent for the type…”
B. Claim 13 recites the limitations "first protein" and “second protein” in lines 3 and 6 of the claim. Claim 1, upon which claim 13 depends, does not recite either a first or second protein. There is insufficient antecedent basis for this limitation in the claim.
C. Claims 14-16 are further rejected for being dependent on a previously rejected claim.
Claim Rejections - 35 USC § 103
7. 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.
8. 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.
9. Claims 1, 6-7, and 9-10 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac et al (United States Patent Application No. US20180223358, published 09 August 2018) in view of Sarrion-Perdigones et al (Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying, Nature Communications, 10, 5710, published 13 December 2019).
Regarding claim 1, Drmanac teaches a method of corresponding positions on an array with differently labeled affinity reagents, wherein the arrays provide a plurality of positions (i.e., a first and second position; [0020] and [0054]). Drmanac teaches that primary antibodies (i.e., affinity reagents) are added to the array simultaneously (i.e., the array comprises a first affinity reagent immobilized at a first position and a second affinity reagent immobilized at a second position; [0184]), and that the primary antibodies are labeled with a luciferase (i.e., a luciferase polypeptide; [0176]). Drmanac teaches a two-color sequencing method wherein an array is contacted with a first affinity reagent comprising a first label (e.g., luciferin) and a second affinity reagent comprising a second label (e.g., a second luciferin) and determining the positions at which the first and second affinity reagents are immobilized based on the detection of these labels ([0187] and [0210]). Drmanac teaches that the first and second labels are distinguishable from each other ([0210]).
While Drmanac teaches that the antibody labels are luciferin proteins, and that the labels are distinguishable from each other, Drmanac does not specifically teach a fist luciferin polypeptide and a second luciferin polypeptide, nor do they specifically teach contacting the array with a first substrate and a second substrate wherein the first luciferase polypeptide does not cross react with the second substrate and the second luciferase polypeptide does not cross react with the first substrate.
However, Sarrion-Perdigones teaches a range of luciferin molecules with strong preference for a particular substrate (i.e., the first and second luciferin do not cross react with the second a first substrates respectively; Table 1, pg. 2 column 2 ¶ 4 and pg. 3 column 1 ¶ 1-2).
It would have been obvious to one having ordinary skill in the art to have substituted the generic luciferase taught by Drmanac with an appropriate first and second luciferase taught by Sarrion-Perdiones to arrive at the instantly claimed invention with a reasonable expectation for success. The ordinary artisan would have been motivated to make this substitution because Drmanac specifically teaches that antibodies are labeled with luciferase and that the first and second labels are distinguishable ([0176] and [0210]). In addition, the ordinary artisan would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in luciferase-based reagents with high substrate specificity.
Regarding claim 6, Drmanac teaches that the array comprises third and fourth positions, wherein a third affinity reagent is immobilized at the third positions and a fourth affinity reagent is immobilized at the fourth positions ([0210]). Drmanac teaches that the third affinity reagent is associated with both the first and second labels (e.g., the first and second luciferin proteins) and the fourth affinity reagent is associated with no label ([0210]). Drmanac teaches that the first label is detected at the fist position, the second label is detected at the second position, the first and second labels are detected at the third position, and no label is detected at the fourth position ([0210]).
Regarding claim 7, Sarrion-Perdigones teaches that a first luminescence signal is detected before a second luminescence, that a deactivation reagent is added after detection of the first luminescence signal, and that the deactivation reagent selectively deactivates the first luciferase (e.g., FLuc and Renilla luciferases, FIG 1b and caption, and pg. 5 column 1 ¶ 2).
Regarding claim 9, Drmanac teaches that the first affinity reagent specifically binds to a first non-labeled reversible terminator (NLRT; i.e., a 3'-O-reversible terminator deoxyribonucleotide; [0122]).
Regarding claim 10, Drmanac teaches that the method comprises identifying a particular NLRT (i.e., a 3'-O-reversible terminator) associated with a particular position based on the binding of an affinity reagent to that particular position ([0187] and [0210]).
10. Claim 2-4 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac et al (United States Patent Application No. US20180223358, published 09 August 2018) in view of Sarrion-Perdigones et al (Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying, Nature Communications, 10, 5710, published 13 December 2019) as applied to claim 1 above, and further in view of Inouye et al (United States Patent Application No US20150299675, published 22 October 2015).
Regarding claims 2-4, the method of claim 1 is discussed fully above and incorporated here.
Neither Drmanac nor Sarrion-Perdigones teach that the first substrate is f-CTZ and the first luciferase polypeptide is Nluc.
However, Inouye teaches that NanoKaz (i.e., reference SEQ ID NO: 2) does not use coeleterazine (CTZ) as an efficient substrate and does use f-coeleterazine (f-CTZ) as a substrate ([0004], [0051] and Table 2). It is noted that applicant’s specification defines Nluc as “…NanoZac luciferase polypeptide (instant SEQ ID NO: 2) or a variant thereof, provided the variant is substantially identical in amino acid sequence to Nluc (instant SEQ ID NO: 2) and also has substantially the same activity as Nluc (instant SEQ ID NO: 2).” The NanoKaz luciferase polypeptide taught by Inouye (reference SEQ ID NO: 2) utilizes f-CTZ as a substrate (i.e., has substantially the same activity as Nluc) and is merely two amino acids different than instant SEQ ID NO: 2, therefore NanoKaz satisfies the limitations of claims 2 and 3 wherein “the first luciferase polypeptide is Nluc” and “the second luciferase polypeptide is Nluc,” respectively.
It would have been obvious to one of ordinary skill in the art to have simply substituted the generic first or second substrate and first or second luciferase polypeptide with f-CTZ and Nluc, and to have the alternate substrate be CTZ as Inouye specifically teaches that CTZ is not a substrate for Nluc, in order to arrive at the instantly claimed invention with a reasonable expectation of success. One having ordinary skill in the art would have been motivated to make this substitution because Inouye teaches that Nluc polypeptides provide the advantage of being secreted extracellularly from animal cells even in the absence of the eukaryotic secretory signal peptide sequence ([0015]). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the development of luciferase variants.
11. Claims 11-16 are rejected under 35 U.S.C. 103 as being unpatentable over Drmanac et al (United States Patent Application No. US20180223358, published 09 August 2018) in view of Sarrion-Perdigones et al (Examining multiple cellular pathways at once using multiplex hextuple luciferase assaying, Nature Communications, 10, 5710, published 13 December 2019) as applied to claim 1 above, and further in view of Hermanson (Chapter 20 – Antibody modification and conjugation, Bioconjugate Techniques (Third Edition), 867-920, published 2013).
Regarding claim 11, the method of claim 1 is discussed fully above and incorporated here. Drmanac teaches that antibodies are labeled with enzymes (e.g., luciferase), and that the enzymes are coupled to or part of a fusion protein with luciferase ([0176]). It is not here that any method of coupling an antibody to a protein inherently comprises “a linker” without further limitation to the claim.
Drmanac does not specifically teach how the luciferase is coupled to the antibody.
However, Hermanson teaches that antibodies are coupled to enzymes via heterobifunctional crosslinking reagents (i.e., linkers; pg. 871 column 1 ¶ 3).
It would have been obvious to one having ordinary skill in the art to have substituted the generic “linking” method taught by Drmanac with the heterobifunctional linker taught by Hermanson to arrive at the instantly claimed invention with a reasonable expectation of success. The ordinary artisan would have been motivated to make this substitution because Hermanson specifically teaches that heterobifunctional crosslinkers provide specific advantages such as limiting unwanted polymerization of protein conjugates and providing control over the extent and sites of crosslinking (pg. 871 column 1 ¶ 3). In addition, one having ordinary skill in the art would have recognized that the known techniques in the cited references could have been combined with predictable results because the known techniques in the cited references predictably result in the formation of antibody-enzyme conjugates.
Regarding claim 12, Hermanson teaches that the heterobifunctional crosslinker is an SMCC linker (pg. 871 column 1 ¶ 3 and FIG 20.3).
Regarding claim 13-16, Hermanson teaches that amine groups (i.e., -NH2) on the antibody are activated by the NHS ester end of SMCC (pg. 871 column 1 ¶ 3 and column 2 ¶ 4) to generate a maleimide-activated intermediate that reacts with sulfhydryl groups (i.e., -SH). Hermanson teaches that Traut’s reagent (i.e., 2-iminothiolane, a cyclic thioimidate) reacts with amine groups in proteins to generate terminal sulfhydryl residues, and that these sulfhydryl residues react with maleimide-activated proteins.
While Hermanson doesn’t specifically teach the conjugation of a maleimide-activated antibody with a sulfhydryl containing protein (e.g., luciferase), they teach that either the enzyme or the antibody is activated with SMCC, and that 2-iminothiolane is used to add terminal sulfhydryl groups to any generic protein, so it would have been obvious to one having ordinary skill in the art to have used the techniques taught by Hermanson to activate the antibody with SMCC, activate the luciferase with 2-iminothiolane, and couple with terminal sulfhydryl groups of the activated luciferase to the activated maleimide of the antibody-SMCC conjugate to arrive at the instantly claimed invention with a reasonable expectation of success. Additionally, the MPEP teaches that any order of performing process steps is prima facie obvious in the absence of now or unexpected results.
Conclusion
12. No claims are allowed.
13. Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN ELLIS YOUNG whose telephone number is (703)756-5397. The examiner can normally be reached M-F 0730 - 1700.
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/BRIAN ELLIS YOUNG/Examiner, Art Unit 1684
/JULIET C SWITZER/Primary Examiner, Art Unit 1682