DETAILED ACTION
Status of Application, Amendments and/or Claims
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The claim listing filed on 3/11/26 is entered; no amendments are indicated. Claims 1-4, 6, 11, 13, 15, 25-27, 29-30, 32-33, 35, 39, 41, 51-52 and 55-56 are pending. (It is noted that the previous Office action inadvertently included claim 34 in the pending claims despite being canceled by Applicants in the 3/21/24 amendments to the claims).
Election/Restrictions
Applicants’ election of Group I, claims 1-4, 6, 11, 13, 15 and 27, in the reply filed on 3/11/26 is acknowledged. There is no indication of whether the election is with or without traverse, but because the response 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 § 818.03(a)).
Claims 25, 26, 29-30, 32-33, 35, 39, 41, 51-52 and 55-56 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.
The election of SEQ ID NO: 8 as the species of GPCR in the reply is also acknowledged. Applicants indicate the elected species reads on each claim in the elected group.
Claims 1-4, 6, 11, 13, 15 and 27 are under consideration.
Drawings
Corrected drawings in compliance with 37 CFR 1.121(d) are required because the drawings do not comply with 37 C.F.R. 1.84(U)(1), which states that partial views of a drawing which are intended to form one complete view, whether contained on one or several sheets, must be identified by the same number followed by a capital letter.
Figure 8 of the instant application, for example, is presented on two separate sheets, labeled "FIG. 8" and "FIG. 8 (CONT’D)". These two sheets should be renumbered "FIG. 8A" and "FIG. 8B". In addition, each of Figures 14 (two sheets), 18 (three sheets) and 19 (two sheets) should be corrected in the same manner.
Applicants are advised to employ the services of a competent patent draftsperson outside the Office, as the USPTO no longer prepares new drawings. The corrected drawings are required in reply to the Office action to avoid abandonment of the application. The requirement for corrected drawings will not be held in abeyance.
Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d).
Applicants are reminded that once the drawings are changed to meet the separate numbering requirement of 37 C.F.R. 1.84(U)(1), Applicants are required to file an amendment to change the Brief Description of the Drawings and the rest of the specification accordingly.
Specification
The disclosure is objected to because of the following informalities:
(1) The title is not descriptive because it refers to any type of fluorescent biosensor, but the claims are limited to one that comprises a cpFP and an inhibitory molecule. A new title is required that is clearly indicative of the claimed invention. The following title is suggested: “Fluorescent Biomarkers Comprising cpFP and an Inhibitory Molecule and Methods of Use for Detecting Cell Signaling Events”.
(2) The Brief Description of the Drawings should be updated to refer to Figures 8B, 14B, 18B, 18C and 19B for the reasons set forth above.
Appropriate correction is required.
Claim Objections
Claims 1-4, 6, 11, 13, 15 and 27 are objected to for the following informalities:
In claim 1, line 4, “wherein inhibitory molecule” should be “wherein the inhibitory molecule”. The remaining claims are objected to for depending from an objected claim.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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 1-4, 6, 11, 13, 15 and 27 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 pre-AIA the applicant regards as the invention.
Claim 1 recites the limitation “the basal state” in line 4. There is insufficient antecedent basis for this limitation in the claim. Specifically, there is no preceding reference to “a basal state” to provide antecedent basis for the recitation in line 4. The could be rendered definite in this regard, for example, if “the basal state” in line 4 is amended to recite “a basal state”.
Claims 11 and 13 each depend from claim 5, which has been canceled. As such, all of the limitations of claims 11 and 13 lack antecedent basis, and the scope of the claims is indefinite. For purposes of advancing prosecution, these claims will be interpreted as depending from claim 6.
The remaining claim(s) included in the rejection are dependent claims that depend from one of the claims rejected above, and encompass the same indefinite subject matter.
Claim Rejections - 35 USC § 112(a), written description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.-The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 2, 4, 6, 11, 13, 15 and 27 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Per MPEP 2163, 35 U.S.C. 112(a) requires, “separate and distinct from the enablement requirement”, that the “specification shall contain a written description of the invention…” (Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1355 (Fed. Cir. 2010)). In making a determination of whether the application complies with the written description requirement of 35 U.S.C. 112(a), it is necessary to understand what Applicants are claiming and what Applicants have possession of.
The instant claims are directed to a product; specifically, a genetically-encoded fluorescent indicator (GEFI) comprising two parts: (a) circularly-permutated fluorescent protein (cpFP), and (b) an inhibitory molecule (IM) bound the cpFP, where in a basal state the IM inhibits fluorescence from the cpFP, and wherein disinhibition occurs upon conformational change of the GEFI and/or disruption of the bond between the cpFP and the inhibitory molecule. As the entirety of the GEFI is “genetically-encoded”, the molecule is limited to the product of a gene; i.e., a fusion protein comprising a cpFP and an inhibitory protein.
With regard to the cpFP, the specification teaches that “[a]ny suitable cpFP may be used, including commercially available circularly-permuted fluorescent proteins or fluorescent proteins that are circularly-permuted in a custom fashion. Exemplary cpFPs, include, for example, circularly-permuted variants of green fluorescent protein (cpGFP), red fluorescent protein (cpRFP) blue fluorescent protein (cpBFP), cyan fluorescent protein (cpCFP), yellow fluorescent protein (cpYFP), violet-excitable green fluorescent protein (cpSapphire), or enhanced green fluorescent protein (cpEGFP)” (¶ 61, published application). The specification further provides the amino acid sequences of cpGFP (SEQ ID NO: 1; 241 amino acids) and cpRFP (SEQ ID NO: 26; 412 amino acids). The specification further provides examples of GEFIs including five that are recited in dependent claim 15, including SEQ ID NO: 17 (termed K-SPOTIT1.0, 778 amino acids); SEQ ID NO: 21 (K-SPOTIT1.1, 752 amino acids); SEQ ID NO: 18 (M-SPOTIT1.1, 761 amino acids), SEQ ID NO: 27 (red-SPOTIT for KOR; 950 amino acids) and SEQ ID NO: 28 (red-SPOTIT for MOR; 933 amino acids). The first three of these comprise the cpGFP of SEQ ID NO: 1 and the latter two comprise the cpRFP of SEQ ID NO: 26.
With respect to the “inhibitory molecule”, while it must be a protein as it is genetically-encoded, it is otherwise limited only by its functionality as an inhibitor of the cpFP. Thus, the claims are genus claims, encompassing a fusion protein comprising a cpFP and a genus of proteins that inhibits fluorescence from the cpFP in a basal state. Said genus of inhibitory proteins encompasses antibodies, as evidenced by dependent claim 2, which is limited to a nanobody, and claim 3, which is further limited to nanobody Nb39. The term “nanobody” is defined in the specification as “an antibody fragment having a single monomeric variable antibody domain” (¶ 55). The specification describes Nb39 as a “Gαi protein mimic”, and provides its amino acid sequence as SEQ ID NO: 2 (¶ 63, published application). The specification describes the mechanism of action of the inhibitor vis-à-vis the cpFP: “When Nb39 is distanced from or cleaved from the cpFP, such as by an agonist binding to the GPCR (e.g. Gαi-coupled GPCR) and thereby inducing binding of Nb39 to a site on the GPCR, the fluorophore is allowed to mature, thereby permitting a fluorescent signal” (¶ 63). The specification also provides another example of an inhibitor that is Nb80, “a Gαs-mimic nanobody” (¶ 139), which has the sequence of SEQ ID NO: 3.
The prior art recognizes that antibodies (and thus nanobodies comprising antibody fragments) bind to epitopes of 5-7 amino acids (Benjamini et al, 1991. Immunology: A Short Course, 2nd edition, page 40 only). While the general structure of an antibody was well-known in the prior art, it is the structure of the complementarity-determining regions (CDRs) that determines the specificity of a particular antibody, and said CDR structure is not predictable based on the epitope to which it binds. Thus, even knowing the structure (CDRs) of one antibody does not allow the skilled artisan to predict the structure of other antibodies that bind to the same epitope or to the other epitopes in the same protein. The relevant art, Ferrara et al (2015. mAbs. 7(1): 32-41) teaches that there is substantial variation in the structure of antibodies that bind to a single protein, on the order of hundreds of different sequences; specifically, see page 36: "The number of different HCDR3s selected against the test antigens ranges from 74 to 460 (Table 3), with the actual number of different antibodies likely to be significantly higher when different VL chains and additional VH mutations are taken into account” (pg 36). Thus, there are at least hundreds of different antibody structures that will bind to a GPCR and act as a mimic of a G protein, but the specification has only provided examples of two such sequences.
Furthermore, dependent claim 15 encompasses GEFI molecules comprising variants of SEQ ID NO: 17, 21, 18, 27 or 28 that are at least 90% identical to the respective reference sequence, which encompasses variants with mutations in up to 10% of the protein sequence. For example, the amino acid sequence of SEQ IN NO: 17 is 778 amino acids in length, and thus the variants encompassed by the claim include those with up to 77 amino acids changed throughout the amino acid sequence. If all of these mutations are found within the 124 amino acids of the Nb39 portion (SEQ ID NO: 2), this would be over 60% of the Nb39 protein. The prior art appreciates that "Mutations … are generally destabilizing, and can reduce protein … fitness" and "In general, more comprehensive understanding of how mutations affect protein fitness within living cells is needed, including their combined effects on function, thermodynamic and kinetic stability, and clearance through aggregation and degradation" (pg 602 of Tokuriki et al, 2009, Current Opinion in Structural Biology. 19: 596-604). Thus, knowledge of the amino acid sequence of Nb39 alone is not sufficient for the skilled artisan at the time of the effective filing date to predict which mutations (substitutions, additions and deletions) will result in a nanobody that retains functionality. Furthermore, the specification does not provide a description of mutations that can be in the Nb39 protein and that will retain functionality; i.e., inhibition of a cpFP.
Furthermore, as noted above, the elected invention under consideration also encompass inhibitors that are proteins other than antibodies. The specification does not provide a description of other proteins that will function to inhibit cpFP as required by the claims.
Thus, the claims are genus claims because they encompass use of a genus of protein, including antibodies, having the required functionality, i.e., inhibition of a cpFP and activation upon conformation change or bond disruption. However, a product defined by function is not in and of itself sufficient to describe the product because it is only an indication of what the product does, rather than what it is; i.e., the specific structure of the product. It is only a definition of a useful result rather than a definition of what achieves that result. Per MPEP 2124, "describing a composition by its function alone typically will not suffice to sufficiently describe the composition". Furthermore, in the instant case the specification does not establish a correlation between structure and function; i.e., the structure of one inhibitory antibody does not provide predictability regarding other antibody structures having the same functionality. Furthermore, the decision of the Federal Circuit in Amgen v. Sanofi, 872 F.3d 1367 (Fed. Circ. 2017) held that a claim directed to an antibody requires written description of the antibody itself rather than being satisfied solely by a written description of the antigen to which it binds (the so-called "newly characterized antigen" test). Thus, a description of the target protein (e.g. a GPCR) is not in and of itself sufficient to provide a description of the genus of antibodies binding to said target.
Written description for a genus may also be satisfied through sufficient description of a relevant number of species. This is dependent on whether one of skill in the art would recognize necessary common attributes or features possessed by the members of the genus. Generally, in an unpredictable art, adequate description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. Also, “[w]hen 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" (Capon v. Eshhar, 418 F.3d 1349 (Fed. Cir. 2005)). “[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” (AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69).
A description of two inhibitors (Nb39 and Nb80) is not representative of the claimed genus. Per MPEP 2163, "A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that "only describe[d] one type of structurally similar antibodies" that "are not representative of the full variety or scope of the genus.")
Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111 (Fed. Cir. 1991), clearly states “applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed” (pg 1117). The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed” (pg 1116).
Therefore, only genetically-encoded fluorescent indicator (GEFI) comprising (a) a circularly-permuted fluorescent protein (cpFP), and (b) an inhibitory molecule (IM) bound to the cpFP, wherein the IM inhibits fluorescence from the cpFP in the basal state, and wherein cpFP fluorescence is disinhibited upon conformational change of the GEFI, and wherein the inhibitory molecule bound to the cpFP is a nanobody that is Nb39 (SEQ ID NO: 2) or Nb80 (SEQ ID NO: 3), but not the full breadth of the claim meets the written description provision of 35 U.S.C. §112(a). Applicants are reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. §112 is severable from its enablement provision (pg 1115).
Note on Prior Art Rejection(s)
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 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.
Claim Rejections - 35 USC § 102
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.
Claims 1, 6 and 27 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Tian et al, WO 2018/098262, published 5/31/2018. The earliest date to which the instant application claims priority is 2/26/21.
Claim 1 encompasses a genetically-encoded fluorescent indicator (GEFI) comprising (a) a circularly-permuted fluorescent protein (cpFP), and (b) an inhibitory molecule (IM) bound to the cpFP, wherein the IM inhibits fluorescence from the cpFP in the basal state, and wherein cpFP fluorescence is disinhibited upon conformational change of the GEFI.
Tian teaches an inactive GPCR with a cpGFP inserted into the intracellular Loop3 (Figure 2, ¶ 22). The cpGFP is integrated into coding sequence of the protein (e.g., ¶ “a polynucleotide encoding the GPCR having a cpFP sensor integrated into its third intracellular loop, as described above and herein”. Furthermore, as shown in Figure 2, structure of the GFP in the basal state keeps the cpGFP inactive, and thus meets the definition of an inhibitor, and cpFP fluorescence is activated upon a conformational change of the GFP in the presence of an active GPCR (Figure 2). As such, the teachings of Tian anticipate claim 1.
Claim 6 encompasses a GEFI of claim 1 wherein the cpFP is bound to a G-protein coupled receptor. In the teachings of Tian described above, the cpFP is inserted into, and therefore covalently bound to, a GPCR. As such, the teachings of Tian also anticipate claim 6.
Claim 27 encompasses a kit comprising the GEFI of claim 1. Tian further teaches “a kit comprising the GPCR having a cpFP sensor integrated into its third intracellular loop, as described above and herein” (¶ 12). As such, the teachings of Tian also anticipate claim 27.
Conclusion
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ZACHARY C HOWARD whose telephone number is (571)272-2877. The examiner can normally be reached on Monday to Friday from 9 AM to 5 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Vanessa Ford, can be reached at telephone number (571) 272-0857. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ZACHARY C HOWARD/Primary Examiner, Art Unit 1674
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