DETAILED ACTION
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 10/31/2025 has been entered.
2. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
3. Claims 6 and 8-18 are pending. Claims 1-5, 7 and 19 are canceled. Claims 16 and 17 are withdrawn. Claims 6 and 8 are amended.
4. Claims 6, 8-15 and 18 are under examination.
Priority
5. Independent claim 6 recites “a relative amount of the steroid hormone receptor to the nucleic acid response element in the test kit is x:1, where x is the amount of steroid hormone receptor and is defined as [0.2 < x < 20].” As indicated in the previous office action mailed on 5/5;/2023, the disclosure of the prior-filed application, Application No. 62/581,260 and 62/614,680 does not mention this limitation. As such, the effective filing date for claims 6, 8-15 and 18 is 11/2/2018.
Rejections Withdrawn
6. All 103 rejections are withdrawn in view of applicant’s amendments.
Rejections Maintained
Double Patenting
7. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/ patents/apply/applying-online/eterminal-disclaimer
8. Claims 6, 8-15 and 18 remain provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 3, 5-7, 10-15 and 17-20 of copending Application No. 17/608,590, in view of Fernandez-Millan et al (RNA, September 2017, 23(12):1788-1795).
This is a provisional nonstatutory double patenting rejection.
Claims 3, 5-7 and 10-20 of copending Application No. 17/608,590 disclose a test kit for screening a sample for the presence of a ligand capable of eliciting a steroid hormone genomic response, the test kit comprising: (i) a steroid hormone receptor that is capable of forming a receptor-ligand complex with a ligand from the sample; and (ii) a nucleic acid reporter construct comprising: (a) a hormone response element that is capable of being bound by the receptor-ligand complex; and (b) a fluorescence generating moiety,
wherein the kit further comprising a steroid hormone receptor cofactor selected from heat shock protein 90 (HSP90), a complex of HSP90 and heat shock protein 70 (HSP70), a complex of HSP90, HSP70 and heat shock protein 40 (HSP40),
wherein the relative amount of HSP90 to steroid hormone receptor is x:1, where x is the amount of HSP90 and is defined as [1≤ x ≤5],
the relative amount of steroid hormone receptor to nucleic acid reporter construct is y:1, where y is the amount of steroid hormone receptor and is defined as [1≤ y ≤5],
wherein the steroid hormone receptor is selected from the group consisting of androgen receptor (AR), estrogen receptor alpha (ER-a), estrogen receptor beta (ER-p), progesterone receptor A (PRA), progesterone receptor A (PRB), mineralocorticoid receptor (MR); and glucocorticoid receptor (GR),
wherein the steroid hormone receptor is an endogenous steroid hormone receptor purified from a cell, a recombinant steroid hormone receptor or a synthetic steroid hormone receptor,
wherein a change in fluorescence of the reporter construct provides information about the doping status of the athlete,
wherein the athlete is selected from a human athlete, an equine athlete, a canine athlete and a camelid athlete.
Claims 3, 5-7, 10-15 and 17-20 of copending Application No. 17/608,590 teach every limitation of claims 6, 8, 9, 13-15 and 18.
Claims 3, 5-7, 10-15 and 17-20 of copending Application No. 17/608,590 do not teach that the reporter comprises an RNA aptamer such as iSpinach which is capable of binding to DFHBI.
Fernandez-Millan et al teaches that fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their
fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI, a GFP mimicking dye that is nontoxic, bio-orthogonal and cell permeable), is one of the most promising, the best characterized and most widely used (abstract and page 1788, column 2). Fernandez-Millan et al teaches that iSpinach is an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability (abstract). Fernandez-Millan et al teaches that similarly to fluorescent proteins, fluorescent RNAs have a wide application spectrum, e.g., live-cell gene expression imaging, biosensing of proteins, nucleic acids or even metabolites (page 1788, column 1).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the light-up RNA aptamer iSpinach for the fluorescence reporter of the copending application. One of ordinary skill in the art would have been motivated to do so because Fernandez-Millan et al teaches that Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI, a GFP mimicking dye that is nontoxic, bio-orthogonal and cell permeable), is one of the most promising, the best characterized and most widely used (abstract and page 1788, column 2) and iSpinach is an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability (abstract). One of ordinary skill in the art would have had a reasonable expectation of success because Fernandez-Millan et al teaches that similarly to fluorescent proteins, fluorescent RNAs have a wide application spectrum, e.g., live-cell gene expression imaging, biosensing of proteins, nucleic acids or even metabolites (page 1788, column 1).
9. Claims 6, 8-15 and 18 remain provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-13 and 17-22 of copending Application No. 17/608,602. Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection.
Claims 1-15 of copending Application No. 17/608,602 disclose a cell-free test kit for screening a test sample for the presence of a ligand capable of eliciting a steroid hormone genomic response, the test kit comprising: (i) a steroid hormone receptor that is capable of forming a ligand- receptor complex with a ligand from the test sample; and (ii) a nucleic acid molecule comprising: (a) a polymerase promoter sequence; (b) a response element that is capable of being bound by the ligand- receptor complex; and (c) a reporter construct where the response element (b) is located between the promoter sequence (a) and the reporter construct (c), and (a), (b) and (c) are operably linked; and (iii) a single polypeptide polymerase; and wherein, the presence of a ligand in the test sample is detected by measuring a reduction or inhibition in transcription of the reporter construct caused by binding of the ligand-receptor complex to the response element when the sample is combined with the test kit,
wherein the test kit further comprising a steroid hormone receptor cofactor selected from heat shock protein 90 (HSP90), a complex of HSP90 and heat shock protein 70 (HSP70), a complex of HSP90, HSP70 and heat shock protein 40 (HSP40), a complex of HSP90, HSP70, HSP40 and p23,
wherein the relative amount of HSP90 to steroid hormone receptor is x:1, where x is the amount of HSP90 and is defined as [1≤ x ≤5],
the relative amount of steroid hormone receptor to nucleic acid reporter construct is y:1, where y is the amount of steroid hormone receptor and is defined as [7≤ y ≤10],
wherein the reporter construct comprises a sequence encoding an RNA aptamer capable of binding to a fluorophore., wherein the RNA aptamer is Mango II, and optionally comprises the F30 scaffold,
wherein the steroid hormone receptor is selected from the group consisting of androgen receptor (AR); estrogen receptor alpha (ER-a) and estrogen receptor beta (ER-p); progesterone receptor A (PRA) and progesterone receptor B (PRB); mineralocorticoid receptor (MR); and glucocorticoid receptor (GR).
The kit is for determining the doping status of an athlete, wherein the athlete is selected from a human athlete, an equine athlete, a canine athlete and a camelid athlete.
The claims of copending Application No. 17/608,602 teach every limitation of the instant claims and anticipate instant invention.
10. Claims 6, 8-15 and 18 remain provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of copending Application No. 18/036,594.
This is a provisional nonstatutory double patenting rejection.
Claims 1-15 of copending Application No. 18/036,594 disclose a test kit for screening a test sample for the presence of a ligand capable of eliciting a steroid hormone genomic response, the test kit comprising:(i) a cell lysate comprising a steroid hormone receptor that is capable of forming a ligand-receptor complex with a ligand from the test sample; and (ii) a nucleic acid molecule comprising: (a) a polymerase promoter sequence comprising or consisting in SEQ ID NO: 85; (b) a response element that is capable of being bound by the ligand-receptor complex; and (c) a reporter construct where the response element (b) is located between the promoter sequence (a) and the reporter construct (c), and (a), (b) and (c) are operably linked; and (iii) optionally, a T7 RNA polymerase,
wherein the kit further comprising at least one steroid hormone receptor coactivator selected from erythroblast transformation-specific transcription factor ERG; one or more p160 coactivators inclusive of steroid receptor coactivators, SRC-1, SRC-2, SRC-3; Vav3 a Rho GTPase guanine nucleotide exchange factor; E2F1; ATAD2; CBP/p300; Leupaxin; FHL2; the ARA family of proteins; GRIP1; BRAC1; and Zac1,
The kit further comprising a steroid hormone receptor corepressor comprising at least one of:(i) heat shock protein 90 (HSP90);(ii) a complex of HSP90 and heat shock protein 70 (HSP70);(iii) a complex of HSP90, HSP70 and heat shock protein 40 (HSP40);(iv) a complex of HSP90, HSP70, HSP40 and p23; (v) a complex of HSP90, HSP70, HSP40, p23 and heat shock protein organizing protein (Hop); (vi) a complex of HSP90, HSP70, HSP40, p23, Hop and 48kD Hip protein (Hip); (vii) a complex of HSP90, HSP70, HSP40, p23, Hop, Hip and p60 (viii) a complex of HSP90, HSP70, HSP40, p23, Hop, Hip, p60 and FKBP52;and (ix) any combination of (i) to (viii).
wherein the reporter construct comprises a sequence encoding an RNA aptamer capable of binding to a fluorophore, wherein the RNA aptamer is Mango II or iSpinach, wherein the steroid hormone receptor is selected from the group consisting of androgen receptor (AR); estrogen receptor alpha (ER-a) and estrogen receptor beta (ER-p); progesterone receptor A (PRA) and progesterone receptor B (PRB); mineralocorticoid receptor (MR); and glucocorticoid receptor (GR).
Applicant’s Arguments
The response states that the instant application has an earlier patent term filing date (November 2, 2018) than the cited reference applications, and these are provisional rejections. According to M.P.E.P 804, if a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earlier patent term filing date, the Office should withdraw the rejection in the application having the earlier patent term filing date and permit that application to issue as a patent. As explained further herein, all outstanding rejections have been rendered moot or overcome. The instant application enjoys the earlier patent term filing date with respect to the reference patent applications. As such, the provisional non-statutory double patenting rejections should be withdrawn
Response to Arguments
Applicant’s arguments have been carefully considered but are not persuasive because these provisional non-statutory double patenting rejections are not the only rejections remaining at this time.
New Grounds of Objection and Rejection
Claim Objections
11. Claims 8, 9 and 14 are objected to because of the following informalities:
Claim 8 is objected to for reciting “wherein the steroid hormone receptor cofactor is a synthetic or recombinant steroid hormone receptor” (emphasis added). Claim 8 should be amended to recite “wherein the synthetic or recombinant steroid hormone receptor cofactor is selected from….”.
Claim 9 is objected to for reciting “any one of claim 6”.
Claim 14 is objected to for reciting redundant terms, see “is either one or both” and “and/or”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
12. 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.
13. Claims 6, 8-15 and 18 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. This is a written description rejection.
The claims are rejected because the specification does not adequately describe “synthetic or recombinant transcription machinery” and “synthetic or recombinant steroid metabolism machinery” (emphasis added).
“[T]he purpose of the written description requirement is to ‘ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor’s contribution to the field of art as described in the patent specification.’” Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1353-54 (Fed. Cir. 2010) (en banc) (quoting Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920 (Fed. Cir. 2004)). To satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991). See also MPEP 2163.04.
For a claim to a genus, a generic statement that defines a genus of substances by only their functional activity does not provide an adequate written description of the genus. Reagents of the University of California v. Eli Lilly, 43 USPQ2d 1398 (CAFC 1997). The recitation of a functional property alone, which must be shared by the members of the genus, is merely descriptive of what the members of the genus must be capable of doing, not of the substance and structure of the members.
“[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.” Ariad, 598 F.3d at 1350 (quoting Eli Lilly, 119 F.3d at 1568-69). A “representative number of species” means that those species that are adequately described are representative of the entire genus. AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (“The ’128 and ’485 patents, however, only describe species of structurally similar antibodies that were derived from Joe-9. Although the number of the described species appears high quantitatively, the described species are all of the similar type and do not qualitatively represent other types of antibodies encompassed by the 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 to provide a "representative number” of species.
The “structural features common to the members of the genus” needed for one of skill in the art to ‘visualize or recognize’ the members of the genus takes into account the state of the art at the time of the invention.
Lastly, even if a selection procedure is disclosed that was, at the time of the invention, sufficient to enable the skilled artisan to identify antibodies with the recited functional properties, the written description provision of 35 U.S.C § 112 is severable from its enablement provision.
The specification defines the term "steroid metabolism machinery" as any enzyme or non- enzyme cofactor, and includes combinations of enzyme and non-enzyme cofactors, sufficient to convert a ligand from a physiologically inactive form to a physiologically active form or from a physiologically active form to a more physiologically active form, or from a physiologically active form to a less physiologically active form, or from a physiologically active form to a physiologically inactive form (page 25, lines 10-15). Steroid metabolism machinery isn’t a single enzyme. It is a multi-enzyme pathway including cytochrome P450s, reductases, dehydrogenases, cofactors membrane context. Although individual steroid-metabolizing enzymes have been made recombinantly in the art, making reconstituted multi-enzyme systems for using in the claimed method are technically demanding because it requires careful balancing of multiple enzymes and cofactors, etc. Each steroid requires different enzymes and cofactors. Zhang et al. (Chinese J of Catalysis 2022, 43: 1749-1760) discloses that although the construction of a cell‐free multienzyme system is highly flexible and adaptable, it is challenging to make all enzymatic reactions act in concert (abstract). Zhang et al. teaches that with the increasing number of enzymes involved, the complexity of a cell‐free system would increase exponentially, and unexpected interactions among the reaction entities may occur, leading to difficulties in the construction of a synthetic route with reaction compatibility and optimized catalytic performance (page 1749, column 1).
The specification does not define the term “synthetic or recombinant transcription machinery”. To get transcription one would need RNA polymerase II, general transcription factors, mediators, and chromatin context, which are provided in the art by nuclear extract. Neither the art nor the instant specification discloses a fully defined cell-free transcription system based, response-element-driven, cell-free hormone receptor assay as claimed. Swank et al. (PNAS, 2019, 116(13): 5892-5901) disclose “Gene-regulatory networks (GRNs) are of central importance in both native and engineered systems. They integrate, compute, and transduce input signals, leading to specific changes in gene expression. Many components contribute to the function of GRNs, and transcription factors and their interaction with promoters are core players. Due to the complexity of even a single transcription factor promoter interaction, it has proven difficult to quantitatively study these systems in vitro or in vivo. Although the development of new technologies is steadily enabling progress in this area, our understanding of GRNs remains limited, as exemplified by our inability to predict in vivo gene-expression levels in essentially any organism and the difficulty associated with de novo engineering of GRNs.” (page 5899, column 1). Swank et al. discloses “As engineered systems become more complex, it will become increasingly important that a large number of standardized characterized components become available. It will be equally important to develop a comprehensive mechanistic understanding of these components and systems to allow parts to be standardized and rationally assembled without requiring extensive trial-and-error cycles or large screens, which may not be feasible for large systems. As work progresses on cellular subsystems such as gene regulation, DNA replication, ribosome biogenesis, metabolic networks, and membrane and protein superstructures, it will be intriguing to contemplate whether it may be possible to integrate these individual systems to create a synthetic cell or cell-like mimic.” (page 5900, column 2).
The specification discloses that machinery is provided by a cell-free extract and/or in a recombinant or synthetic form (page 29, last paragraph). The specification further discloses that a cell-free extract provides transcription and/or translation machinery as well as the steroid metabolism machinery (page 37-38); the transcription and/or translation machinery is provided by a nuclear or cell-free extract (page 36, lines 29-30, Example 1, pages 57, line 4 and 64).
Therefore, the specification only discloses cell-free extract or nuclear extract for “transcription machinery” and “steroid metabolism machinery”. The specification does not disclose any synthetic or recombinant transcription machinery” and any “synthetic or recombinant steroid metabolism machinery”. The identity and amount of each components (e.g. enzymes, transcription factors, cofactors) of “synthetic or recombinant transcription machinery” and “synthetic or recombinant steroid metabolism machinery are not disclosed in the specification. There is insufficient written description regarding “synthetic or recombinant transcription machinery” and any “synthetic or recombinant steroid metabolism machinery because the relevant identifying characteristics of machinery such as components and their relative amounts are not set forth in the specification as-filed. The disclosed cell-free extract and nuclear extract are not synthetic or recombinant.
In the absence of structural characteristics that are shared by members of the genus of machinery, and absence of a representative number of species to describe the genus, one of ordinary skill in the art would not consider that applicant was in possession of synthetic or recombinant transcription machinery and synthetic or recombinant steroid metabolism machinery.
Claim Rejections - 35 USC § 112
14. Claims 6, 8-15 and 18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a cell free test kit comprising: (i) a non-ligand bound synthetic or recombinant steroid hormone receptor; (ii) a synthetic or recombinant nucleic acid comprising a response element that is capable of being bound by the receptor-ligand complex; (iii) a transcription-based reporter construct operably linked to the nucleic acid response element; and (iv) a nuclear or cell extract that provides transcription machinery, and steroid metabolism machinery, does not reasonably provide enablement for a cell free test kit comprising: (i) a non-ligand bound synthetic or recombinant steroid hormone receptor; (ii) a synthetic or recombinant nucleic acid comprising a response element that is capable of being bound by the receptor-ligand complex; (iii) a transcription-based reporter construct operably linked to the nucleic acid response element; and (iv) a synthetic or recombinant transcription machinery, and/or a synthetic or recombinant steroid metabolism machinery. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Wands states at page 1404,
''Factors to be considered in determining whether a disclosure would
require undue experimentation have been summarized by the board in Ex
parte Forman. They include (1) the quantity of experimentation necessary,
(2) the amount of direction or guidance presented, (3) the presence or
absence of working examples, (4) the nature of the invention, (5) the state
of the prior art, (6) the relative skill of those in the art, (7) the predictability
or unpredictability of the art, and (8) the breadth of the claims.''
The nature of the invention
Claim 1 is drawn to a cell free test kit for screening a test sample for presence of a ligand, which ligand is capable of forming a complex with a steroid hormone receptor and binding to a nucleic acid response element, the test kit comprising:
(i) a non-ligand bound synthetic or recombinant steroid hormone receptor that is capable of forming a receptor-ligand complex with a ligand from the test sample;
(ii) a synthetic or recombinant nucleic acid comprising a response element that is capable of being bound by the receptor-ligand complex;
(iii) a transcription-based reporter construct operably linked to the nucleic acid response element; and
(iv) zero, one, two, or all three, or all four of a synthetic or recombinant steroid hormone receptor cofactor, synthetic or recombinant transcription machinery, and synthetic or recombinant steroid metabolism machinery,
wherein a relative amount of the steroid hormone reporter to the nucleic acid response element in the test kit is x:1, where x is the amount of steroid hormone receptor and is defined as [0.2 <x<20], and wherein the test kit does not comprise a cell lysate.
The nature of the inventions is in vitro steroid metabolism and in vitro transcription.
The invention is in a class of invention, which the CAFC has characterized as ''the unpredictable arts such as chemistry and biology.'' Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
The breadth of the claims
The specification defines the term "steroid metabolism machinery" as any enzyme or non- enzyme cofactor, and includes combinations of enzyme and non-enzyme cofactors, sufficient to convert a ligand from a physiologically inactive form to a physiologically active form or from a physiologically active form to a more physiologically active form, or from a physiologically active form to a less physiologically active form, or from a physiologically active form to a physiologically inactive form (page 25, lines 10-15). The specification does not disclose any recombinant or synthetic steroid metabolism machinery.
Steroid metabolism machinery isn’t a single enzyme. It is a multi-enzyme pathway including cytochrome P450s, reductases, dehydrogenases, cofactors membrane context. Each steroid requires different enzymes and cofactors.
The specification does not define the term “synthetic or recombinant transcription machinery”. The specification discloses that transcription machinery is provided by a cell-free extract and/or in a recombinant or synthetic form (page 29, last paragraph). The specification does not disclose any recombinant or synthetic transcription machinery. To get transcription one would need RNA polymerase II, general transcription factors, mediators, and chromatin context.
The breadth of the claim is enormous.
Quantity of experimentation
The quantity of experimentation is extremely large in view of the breadth of the claims and unpredictability of the art.
The unpredictability of the art and the state of the prior art
Although individual steroid-metabolizing enzymes have been made recombinantly in the art, however, making reconstituted multi-enzyme systems for using in the claimed method are technically demanding because it requires careful balancing of multiple enzymes and cofactors, etc. Zhang et al. (Chinese J of Catalysis 2022, 43: 1749-1760) discloses that although the construction of a cell‐free multienzyme system is highly flexible and adaptable, it is challenging to make all enzymatic reactions act in concert (abstract). Zhang et al. teaches that with the increasing number of enzymes involved, the complexity of a cell‐free system would increase exponentially, and unexpected interactions among the reaction entities may occur, leading to difficulties in the construction of a synthetic route with reaction compatibility and optimized catalytic performance (page 1749, column 1).
To get transcription one would need RNA polymerase II, general transcription factors, mediators, and chromatin context, which are provided in the art by nuclear extract. The art does not disclose a fully defined cell-free transcription system based, response-element-driven, cell-free hormone receptor assay as claimed. Swank et al. (PNAS, 2019, 116(13): 5892-5901) disclose “Gene-regulatory networks (GRNs) are of central importance in both native and engineered systems. They integrate, compute, and transduce input signals, leading to specific changes in gene expression. Many components contribute to the function of GRNs, and transcription factors and their interaction with promoters are core players. Due to the complexity of even a single transcription factor promoter interaction, it has proven difficult to quantitatively study these systems in vitro or in vivo. Although the development of new technologies is steadily enabling progress in this area, our understanding of GRNs remains limited, as exemplified by our inability to predict in vivo gene-expression levels in essentially any organism and the difficulty associated with de novo engineering of GRNs.” (page 5899, column 1). Swank et al. discloses “As engineered systems become more complex, it will become increasingly important that a large number of standardized characterized components become available. It will be equally important to develop a comprehensive mechanistic understanding of these components and systems to allow parts to be standardized and rationally assembled without requiring extensive trial-and-error cycles or large screens, which may not be feasible for large systems. As work progresses on cellular subsystems such as gene regulation, DNA replication, ribosome biogenesis, metabolic networks, and membrane and protein superstructures, it will be intriguing to contemplate whether it may be possible to integrate these individual systems to create a synthetic cell or cell-like mimic.” (page 5900, column 2).
Furthermore, making a recombinant bioactive enzyme is conventional. However, making a synthetic bioactive enzyme is not as easy because it requires proper folding of the synthesized enzyme. Multi-domain enzymes were impractical and membrane proteins were essentially inaccessible. Many enzymes required cellular chaperones for folding.
Working examples and guidance in the specification
The specification discloses that a cell-free extract provides transcription and/or translation machinery as well as the steroid metabolism machinery (page 36, lines 29-30 and page 37-38). The specification uses nuclear or cell-free extract as the transcription and/or translation machinery in working examples (Example 1, pages 57, line 4 and 64).
The specification does not disclose any recombinant or synthetic transcription machinery and does not disclose any recombinant or synthetic steroid metabolism machinery.
The specification does not provide any guidance on making such recombinant or synthetic machinery.
Level of skill in the art
The level of skill in the art is deemed to be high.
Conclusion
Thus given the broad claims in an art whose nature is identified as unpredictable, the unpredictability of the art, the large quantity of research required to define these unpredictable variables, the lack of guidance provided in the specification, the absence of a working example on making recombinant or synthetic machinery and the negative teachings in the prior art balanced only against the high skill level in the art, it is the position of the examiner that it would require undue experimentation for one of ordinary skill in the art to perform the method as broadly claimed.
Claim Rejections - 35 USC § 103
15. 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.
16. Claims 6, 9, 13-15 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Klein-Hitpass et al. (Cell, 1990, 60, 247-257), in view of Poletti et al. (Gene, 1992, 114: 51-58), and McDonnell (US 5,506,102, date of patent: 4/9/1996, PTO-892 dated 5/5/2023).
For this rejection, part (iv) of claim 6 is interpreted as zero of a synthetic or recombinant steroid hormone receptor cofactor, synthetic or recombinant transcription machinery, and synthetic or recombinant steroid metabolism machinery (emphasis added).
Regarding claims 6 and 13, Klein-Hitpass et al. teaches an in vitro transcription assay which uses the following reagents:
purified chicken progesterone aporeceptor cPR (cPRA or cPRB) (instant part (i), a non-ligand bound steroid hormone receptor that is capable of forming a receptor-ligand complex with progesterone from a test sample);
a template (a nucleic acid) comprising progesterone response element (PREs) upstream of a G-free cassette (a reporter) (page 254, last para) (instant parts (ii) and (iii));
wherein the assay used 100 ng template and different amounts of cPR (e.g. 0.72, 3.2 pmol) (page 255, column 1, para 3 and page 249, last para). The amount of 0.72 and 3.2 pmol of cPRa (molecular weight of cPRa is about 80 KDa) corresponds to approximately 57.6 and 256 ng, respectively. This will give a ratio of cPRA to template of 0.576 and 2.56, respectively (which meets the limitation of 0.2≤x≤20).
Regarding claim 9, Klein-Hitpass et al. teaches that a promoter is linked to the a G-free cassette (reporter) (page 255, para 1).
Klein-Hitpass does not teach that cPRA is a recombinant cPRA. Klein-Hitpass does not teach a kit comprising the above reagents.
Poletti teaches recombinant production of cPRA in yeast (title). The produced cPRA is biologically active since it activates transcription of a co-transformed reporter gene containing its responsive element, and the activation is progesterone dependent (abstract and Fig. 7). The induced expression level of cPRA is five to seven times higher than that found in the chicken oviduct cytosol (page 54, column 2, para 1).
McDonell teaches that assay kits can be constructed and used to discover steroid antagonist ligands in a drug discover effort (column 10, lines 4-7).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have purified cPRA from yeast in view of Poletti et al. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success because Poletti et al. teaches recombinant production of bioactive cPRA in yeast and has shown the induced expression level of cPRA is five to seven times higher than that found in the chicken oviduct cytosol (page 54, column 2, para 1). Note that Klein-Hitpass purified cPRA from chicken oviduct cytosol.
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have placed all the reagents of Klein-Hitpass (i.e. purified aporeceptor cPR (cPRA or cPRB) and the template comprising progesterone response element (PREs) upstream of a G-free cassette) in a kit format in view of McDonell. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success because McDonell teaches that assay kits can be constructed (column 10, lines 4-7) and placing assay components (reagents) in a kit was conventional.
Regarding claim 14, a ligand is not a component of the kit. It is recited in the preamble which is considered as intended use. Furthermore, the cPR is capable of forming a receptor ligand complex with progesterone (a ligand) from the test sample.
Regarding claim 15, a test sample is not a component of the kit. It is recited in the preamble which is considered as intended use.
Regarding claim 18, the printed matter (instructions for using the kit) is not given patentable weight, see MPEP §2112.01 and In re Ngai, 367 F.3d 1336 (Fed. Cir.2004).
MPEP §2112.01 III states “Where the only difference between a prior art product and a claimed product is printed matter that is not functionally related to the product, the content of the printed matter will not distinguish the claimed product from the prior art. In re Ngai, 367 F.3d 1336, 1339, 70 USPQ2d 1862, 1864 (Fed. Cir. 2004) (Claim at issue was a kit requiring instructions and a buffer agent. The Federal Circuit held that the claim was anticipated by a prior art reference that taught a kit that included instructions and a buffer agent, even though the content of the instructions differed, explaining "[i]f we were to adopt [applicant’s] position, anyone could continue patenting a product indefinitely provided that they add a new instruction sheet to the product."). See also In re Gulack, 703 F.2d 1381, 1385-86, 217 USPQ 401, 404 (Fed. Cir. 1983)”.
Note that the kit does not comprise a cell lysate.
Moreover, Klein-Hitpass used HeLa nuclear extract (40-60ul of protein) for cell-free in vitro transcription. Nuclear extract is different from a cell lysate. A cell lysate is made by directly lysing intact cells and as such it contains cytosolic proteins, membrane fragments, chaperones and metabolites. A nuclear extract is a fractionated preparation enriched specifically for nuclear proteins.
17. Claims 6, 8-15 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Klein-Hitpass et al. (Cell, 1990, 60, 247-257), in view of Poletti et al. (Gene, 1992, 114: 51-58), and McDonnell (US 5,506,102, date of patent: 4/9/1996, PTO-892 dated 5/5/2023), and further in view of Fernandez-Millan et al (RNA, September 2017, 23(12):1788-1795).
The teachings of Klein-Hitpass, Poletti and McDonnell have been set forth above as they apply to claims 6, 9, 13-15 and 18.
Regarding claims 10-12, Klein-Hitpass does not teach the promoter driven by progesterone response elements is linked to a nucleic acid sequence encoding an RNA aptamer such as iSpinach which is capable of binding to DFHBI. However, these deficiencies are made up for in the teachings of McDonell.
Fernandez-Millan et al teaches that fluorogenic RNA aptamers are short nucleic acids able to specifically interact with small molecules and strongly enhance their fluorescence upon complex formation. Among the different systems recently introduced, Spinach, an aptamer forming a fluorescent complex with the 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI, a GFP mimicking dye that is nontoxic, bio-orthogonal and cell permeable), is one of the most promising, the best characterized and most widely used (abstract and page 1788, column 2). Fernandez-Millan et al teaches that iSpinach is an improved version of the aptamer, endowed with an increased folding efficiency and thermal stability (abstract). Fernandez-Millan et al teaches that similarly to fluorescent proteins, fluorescent RNAs have a wide application spectrum, e.g., live-cell gene expression imaging, biosensing of proteins, nucleic acids or even metabolites (page 1788, column 1).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have linked the nucleic acid response element PREs to a light-up RNA aptamer such as iSpinach in view of Fernandez-Millan. One of ordinary skill in the art would have been motivated to do so because Fernandez-Millan et al teaches that similarly to fluorescent proteins, fluorescent RNAs have a wide application spectrum, e.g., biosensing of proteins, nucleic acids or even metabolites (page 1788, column 1), and Spinach, an aptamer forming a fluorescent complex with DFHBI is one of the most promising, the best characterized and most widely used (abstract and page 1788, column 2). One of ordinary skill in the art would have had a reasonable expectation of success because Fernandez-Millan et al teaches that similarly to fluorescent proteins, fluorescent RNAs have a wide application spectrum, e.g., live-cell gene expression imaging, biosensing of proteins, nucleic acids or even metabolites (page 1788, column 1).
Conclusion
18. No claims are allowed.
19. Any inquiry concerning this communication or earlier communications from the examiner should be directed to HONG SANG whose telephone number is (571)272-8145. The examiner can normally be reached Monday-Friday 8am-5pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Janet Epps-Smith can be reached on 5712720757. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/HONG SANG/Primary Examiner, Art Unit 1643