DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Response to Amendment
Applicant’s remarks and amendments filed 3/2/2026, in response to the non-final rejection mailed 12/2/2025, are acknowledged and have been fully considered.
Applicant’s amendment to the claims is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Any previous rejection or objection not mentioned herein have been withdrawn based upon Applicant’s amendments to the claims.
EXAMINER’S COMMENT
Although not indicated, it appears that claim 58 was inadvertently amended in the claim set filed 3/2/2026. In the claims filed on 8/1/2025, claim 58 was amended to recite: “or both comprise AKT or a RAS protein”. However, in the most recent version of the claims, claim 58 does not include “AKT or”. The Examiner understands that this was an inadvertent omission of the amendment submitted on 8/1/2025. A call with the Attorney of Record confirmed this was unintentional. Thus, claim 58 has been examined as inclusive of the AKT signaling pathway. Formal correction is requested in the next amendment from Applicant.
Claim 59 remains withdrawn as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 50-58, 60-61, and 63-69 are pending and have been examined on the merits.
Claim Rejections - 35 USC § 112(a) - Enablement
(Modified as necessitated by Applicant’s amendment)
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 50-58, 60-61 and 63-69 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 claims 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 test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue.” In re Angstadt, 537 F.2d 498, 504, 190 USPQ 214, 219 (CCPA 1976). Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)). The factors include, but are not limited to: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. See MPEP § 2164.01(a). The factors considered to be most relevant to the instant invention are addressed in detail below.
(A) The breadth of the claims and (B) nature of the invention:
The claims are drawn to methods of treating a cancer characterized by an aberrant signaling of one or more signal transducers, of which AKT (e.g. the AKT/PI3K signaling pathway) is the elected species that was examined.
The claimed method comprises expressing a synthetic protein circuit in a cell of a subject in need thereof, the synthetic protein circuit comprising a first polypeptide comprising a first signal transducer binding domain and a first part of a first protease domain, wherein the first signal transducer binding domain is capable of binding a first signal transducer of the cell to form a first signal transducer-bound polypeptide; a second polypeptide comprising a second signal transducer binding domain and a second part of the first protease domain, wherein the second signal transducer binding domain is capable of binding a second signal transducer of the cell to form a second signal transducer-bound polypeptide, wherein the first part of the first protease domain and the second part of the first protease domain have weak association affinity, and wherein the first part of the first protease domain and the second part of the first protease domain are capable of associating with each other to constitute a first protease capable of being in a first protease active state when the first signal transducer and the second signal transducer are in close proximity at an association location; and an effector protein comprising a first cut site the first protease in the first protease active state is capable of cutting to change the effector protein to an effector active state, or an effector inactive state, which correlates with an aberrant signaling of the first signal transducer and/or the second signal transducer, and wherein the effector protein in the effector active state, or the effector inactive state, that induces cell death in response to the aberrant signaling, thereby treating the cancer characterized by the aberrant signaling of the first signal transducer and/or the second signal transducer.
Claims 51-55 recite additional details about the synthetic protein circuit and do not further limit the cancer treated.
Claim 56 recites that the first signal transducer and/or the second signal transducer regulates cell survival, cell growth, cell proliferation, cell adhesion, cell migration, cell metabolism, cell morphology, cell differentiation, apoptosis, or any combination thereof. This is an extremely broad set of alternatives that includes a very large amount of signaling pathways.
Claim 57 recites that one or both of the signal transducers comprise “AKT, PI3K, MAPK, p44/42 MAP kinase, TYK2, p38 MAP kinase, PKC, PKA, SAPK, ELK, JNK, cJun, RAS, Raf, MEK 1/2, MEK 3/6, MEK 4/7, ZAP-70, LAT, SRC, LCK, ERK 1/2, Rsk 1, PYK2, SYK, PDK1, GSK3, FKHR, AFX, PLCy, PLCy, NF-kB, FAK, CREB, aIII33, FcsRI, BAD, p70S6K, STAT1, STAT2, STAT3, STATS, STAT6, or any combination thereof”.
The instantly examined claims have been examined on the elected species wherein at least one of the signal transducers or both comprises AKT, which is encompassed by claim 58 (see the Explanation above regarding the interpretation of claim 58).
The amended claims are drawn to treating disease is “a cancer”, which is, of note, an extremely broad genus of diseases, having a multitude of different types of cancers as well as distinct subtypes and genetic variants.
Claims 60 and 61 recite that wherein the disease or disorder is characterized by an aberrant signaling of the first signal transducer, and by both the first and second transducers. These do not practically limit the subject population or treatment modality. Further, these claims still have a large breadth in that many possible pathways and interactions can be involved.
Claims 63-64 involved administering a prodrug such as 5-fluorocytosine (5-FC) or ganciclovir. However, it is unclear from the claim how such prodrug administration relates to the methods for expressing a synthetic protein circuit that uses a protease to activate an effector protein that is capable of changing a state of the cell. Specific recitation of the effector protein targeting a molecule that affects the prodrug (i.e. expression cytosine deaminase for 5-fluorocytosine) is not present in the claim (see [0009] of the specification). Limitations from the specification are not read into the claims, and thus the breadth of the method and the expressed protein circuit is not significantly narrowed by claims 63-64.
Claims 65-69 recite additional limitations regarding expressing the synthetic protein circuit which involved administering a nucleic acid encoding the synthetic protein circuit. However, such methods pertain only to the delivery step(s) of the synthetic protein circuit and does not practically limit the intended result of thereby treating a disease or disorder characterized by the aberrant signaling of the first signal transducer and/or the second signal transducer, as required by claim 50. The specification of a genetic delivery mechanism does not further limit the subject patient population, nor the full breadth of a disease or disorder.
In regards to the full breadth of the claimed treatments, the specification describes the term "treatment" as referring to “an intervention made in response to a disease, disorder or physiological condition manifested by a patient. The aim of treatment may include, but is not limited to, one or more of the alleviation or prevention of symptoms, slowing or stopping the progression or worsening of a disease, disorder, or condition and the remission of the disease, disorder or condition. The terms "treat" and "treatment" include, for example, therapeutic treatments, prophylactic treatments, and applications in which one reduces the risk that a subject will develop a disorder or other risk factor” ([0083]). Thus, when considering the full scope of the claimed treatment methods, the claims encompass any intervention, prophylactic treatments, and/or applications for reducing the risk that a subject will develop the disorder or other risk factor. Therefore the scope of the invention encompasses treating any cancer (a solid tumor, carcinoma, sarcoma, lymphoma, leukemia, et cetera.) with aberrant Akt signaling, pertaining to any of the PI3K (phosphatidylinositol 3-kinase) and Akt (protein kinase B) signaling pathway.
The full scope of the claimed invention is so broad as to encompass treatments of a vast number of different cancer types having a large number of possible cellular signaling aberrations, including but not only limited to those involving any possible mutation in AKT and any dysfunction in the PI3K-AKT signaling pathways and its regulators (e.g. any part of this complex pathway).
(C) The state of the prior art and (E) the predictability or unpredictability of the art:
When considering the level of predictability and knowledge in the art, the following references were considered due to their similar subject matter and/or relevance to instantly claimed methods of manipulating cellular signaling pathways, including the AKT pathway, to treat diseases and disorders, including cancers.
Kwon et al. (US PGPub 20200010513) is drawn to a nucleic acid molecule encoding a fusion protein, wherein the nucleic acid molecule comprises: (a) a first nucleic acid sequence encoding a transmembrane domain linked to a first biosensor, wherein said first biosensor is a first molecule capable of interacting with a second molecule to form part of a first inducible interaction module, and wherein said first biosensor is linked to the transmembrane domain such that the first biosensor is located intracellularly upon expression of the fusion protein in a cell; (b) a second nucleic acid sequence encoding an effector-activating module, wherein the effector-activating module comprises: (i) a nucleic acid sequence encoding a first part of a protease, wherein said first part of the protease is capable of interacting with a second part of said protease to form an active form of said protease; or (ii) a nucleic acid sequence encoding a second biosensor, wherein said second biosensor is a first molecule capable of interacting with a second molecule to form part of a second inducible interaction module; (c) a third nucleic acid sequence encoding a third biosensor comprising a protease cleavage site, wherein the protease cleavage site is sterically occluded in the absence of a stimulus for said third biosensor and wherein the protease cleavage site becomes accessible in the presence of said stimulus; and (d) a fourth nucleic acid sequence encoding an effector molecule ([0001]; claim 1). Kwon also claims methods for inducing intracellular signaling, as well as methods for monitoring intracellular signaling ([0001]; [0116]-[0119]; [0129]-[0134]; claims 14 and 15). The methods discussed in Kwon using the fusion proteins and cells taught therein includes improved methods for inducing and/or monitoring intracellular signaling events, such as the previously described “BLITZ” system, the “iTango or iTango2” system, or the “Cal-Light” system (see [0039] and [0136]). Examples 2-3 of Kwon describes various implementations of the system using the inducible protease with these reporter systems for monitoring gene expression ([0188]-[0200]; Fig. 1).
Kwon does not demonstrate nor teach any methods for treating a disease or disorder (including any intervention for alleviating or preventing a disease or disorder) arising from aberrant signal. Kwon hypothesizes using the system to improve control of gene editing ([0061]; [0068]; Fig. 21), however no practical implementation is taught. Further, there is no reduction to practice or practical embodiment of a treatment that would amount to an enabling disclosure.
Juillerat et al. (US PGPub 20170073423) discloses methods to engineer T cell for immunotherapy. In the method taught in Juillerat, T cells are engineered in order to be activated by a combination of input signals and involves chimeric antigen receptors able to redirect immune cell specificity and reactivity toward a selected target exploiting the ligand-binding domain properties ([0001]). Juillerat teaches cells obtained by the claimed method, in particular T-cells, comprising said chimeric antigen receptors for use in cancer treatments (Abstract).
In one embodiment, Juillerat teaches a split protease system using multiple CARs and a split protease that is reconstituted by the interacting of one or more binding domains of signaling proteins ([0018]; [0096]; FIGs 9 and 10). One such system is described as: “The simultaneous presence of three tumor cell ligands will activate the CARs. The intracellular domain of the first CAR comprehends the protease target sequence and the signaling protein. The intracellular domains of the second and third CARs are constituted by the two complementary split protease domains. Each CAR independently is not activated by the presence of the single tumor ligand cell; the activation derives from the co-localization of three CARs dues to the presence of the three tumor ligand cells. The co-localization of three CARs allows their activation through the reconstitution of the full active protease which could cleave the protease target sequence and cause the release of the signaling protein” ([0018]).
Although not exactly the same as the methods of the instant claim, the signaling platform taught in Juillerat also pertains to multiple fusion proteins having a split protease system that responds to multiple inputs to activate a transcription factor. Juillerat states that an “isolated cell according to the invention or cell line derived from said isolated cell can be used in the manufacture of a medicament for treatment of a cancer, viral infection or autoimmune disease in a patient in need thereof.” ([0134]).
However, no practical embodiments of such a treatment are demonstrated of such a treatment modality. Juillerat demonstrates that engineered T-cells can be produced in which a CAR-regulated engineered CARMA1 protein recruits different proteins forming a multi-protein complexes that activates two different signaling cascade: NF-κB and c-Jun N-terminal kinase in order to control T-cell activation (see Example 1, [0191]-[0195]). Other examples in Juillerat pertain to control of CAR with the environmental condition of hypoxia (Examples 3-6). However Juillerat does not provide an enabling disclosure for a treatment of a cancer or other disease using as split protease system as in the instant invention.
Regarding potential treatments, Juillerat states that “Timing of administration is within the judgment of managing physician and depends on the clinical condition of the patient. The cells or population of cells may be obtained from any source, such as a blood bank or a donor. While individual needs vary, determination of optimal ranges of effective amounts of a given cell type for a particular disease or conditions within the skill of the art. An effective amount means an amount which provides a therapeutic or prophylactic benefit. The dosage administrated will be dependent upon the age, health and weight of the recipient, kind of concurrent treatment, if any, frequency of treatment and the nature of the effect desired” ([0143]).
Therefore, it is evident from the teachings of Juillerat that for any given desired signaling transducer target (i.e. AKT as in the elected species of the instant invention) a great deal of optimization must go into designing and implementing a cellular-based treatment. Although Juillerat states that determination of optimal ranges of effective amounts of a given cell type for a particular disease or conditions is within the skill of the art, it also indicates that such treatments could be to any number of diseases amongst a vast variety of patient populations, and a great amount of other factors (i.e. age, health and weight of the recipient) must also be considered. Thus, there does not appear to be any enabling methods taught in Juillerat et al. for which one could apply to treatments with cells having the instantly claimed synthetic protein circuit.
Wintgens et al. (2019. “Monitoring activities of receptor tyrosine kinases using a universal adapter in genetically encoded split TEV assays”. Cellular and Molecular Life Sciences, 76:1185–1199) pertains to using a split TEV technique to robustly monitor the dynamic recruitment of both naturally occurring full-length adapters and artificial adapters of receptor tyrosine kinases (RTKs) (Abstract, Fig. 1). Wintgens teaches that the RTK split TEV recruitment assays could qualify for high-throughput screening approaches, suggesting that the artificial adapter taught therein may be used as universal adapter in cell-based profiling assays within pharmacological intervention studies (Abstract, Fig. 5). Wintgens suggests that using the split TEV recruitment assay and integrating the universal SH2(GRB2) adapter may represent a promising approach to build a technology platform to assess RTK activities in early drug discovery to finally improve compound selectivity (pg. 1198, left col). However, the techniques taught in Wintgens appear to be limited to reporter assays and monitoring cell signaling events with the split protease. There is no enabling disclosure of using such components to treat a disease or disorder characterized by the aberrant signaling of a first signal transducer and/or second signal transducer.
Gao et al. ("Programmable protein circuits in living cells." Science 361.6408 (21 Sep 2018): 1252-1258, on IDS filed 3/11/2024), which is authored by inventors of the instant invention, teaches engineered viral proteases that function as composable protein components, which can together implement a broad variety of circuit-level functions in mammalian cells using a system termed CHOMP (circuits of hacked orthogonal modular proteases) (Abstract, Fig. 1). Gao et al. teaches the specific application of a circuit that induces cell death in response to upstream activators of the Ras oncogene (Abstract, Fig. 4). Gao thus teaches using a CHOMP circuit engineered to detect and kill in response to upstream activators of Ras through a process of rational iterative design optimization (pg. 6, 1st and 2nd columns). Gao speculates that by one can envision smart therapeutics or sentinels based on CHOMP circuits (pg 6, last paragraph).
However, it is clear that the process of designing implementing and testing such a circuit involves a large amount of design considerations and experimentation for any one target. Thus, Gao does not provide an enabling disclosure that amounts to applying a synthetic protein circuit for the actual treatment (i.e. prevention or treatment) of any disease or disorder (including the vast number and variants of possible cancers). Gao also does not particularly discuss the elected species of an AKT signaling transducer.
Nicholson et al. (2002. "The protein kinase B/Akt signaling pathway in human malignancy". Cellular Signalling. 14 (5): 381–395) is a review article discussing the mechanisms and consequences of PKB/AKT activation in cancer (i.e. human malignancy). Nicholson teaches that “AKT” (or Protein Kinase B) in mammals comprises three highly homologous members known as PKBa (Akt1), PKBb (Akt2), and PKBg (Akt3), and is activated in cells exposed to diverse stimuli such as hormones, growth factors, and extracellular matrix components (Abstract, Fig. 1). The activation of AKT is downstream of phosphoinositide 3-kinase (PI-3K) and requires the secondary messenger phosphatidylinositol-3,4,5-trisphosphate (PIP3) (Abstract; Fig. 2). Table 1 of Nicholson discloses a number of known AKT substrates at that time (Table 1, page 386), demonstrating the complexity of signaling downstream of AKT. Nicholson teaches that the AKT signaling pathway affects many components of cells, including cell growth and cell survival (Fig. 3), and cell cycle progression (Fig. 4). From the teachings and figures of Nicholson it is evident that modulation of the AKT pathway will affect many cellular targets and may have large-scale consequences throughout the cell (see Section 5. Cellular process regulated by PKB/Akt, starting on pg. 385).
Nicholson also teaches a number of mechanisms in which the PKB/AKT pathway is involved in human cancers (pgs. 384-385), including activating mutations of PKB/AKT, increased activity of upstream AKT regulators, such as PIK3, and loss of function of PIK3-AKT suppressors such as the well-studied tumor suppressor PTEN (see section 4. PKB/Akt in human cancer). Nicholson teaches multiple pathways in which AKT promotes cancer progression, as activated AKT drives cell growth and proliferation, and inhibits cell death pathways (of which many cancer therapies are planned to target) (see pgs. 386-390; Table 1).
In regards to the complexity of targeting the PIK3-AKT pathway, Nicholson postulates that “It seems likely that cellular context will play a role, with PKB/Akt substrates subserving distinct functions in different cell types. Moreover, many of the proteins and downstream cellular processes thought to be modulated by PKB/Akt are subject to simultaneous regulation by other signaling pathways. The response of cells to PKB/Akt activation may therefore be dependent upon the levels of activity of these other signals, a situation that may be particularly important during tumour progression”. Thus, in order to target a desired treatment or outcome, one must consider the multitude of points of regulation and feedback involved in such signaling pathways. The complexity of even a signaling pathway in a cell must be considered in regards to its interactions with components of related pathways.
To further illustrate the complexity involved in modulation of the PIK3/AKT pathway in particular (although such complexity is expected in all cellular signaling pathways), Georgescu MM (December 2010 "PTEN Tumor Suppressor Network in PI3K-Akt Pathway Control". Genes & Cancer. 1 (12): 1170–1177) is herein cited. Georgescu is a review that discusses the PI3K-Akt pathway, a major survival pathway activated in cancer, and efforts to develop targeted therapies, which have not been fully successful, mainly because of extensive internal intrapathway or external interpathway negative feedback loops or because of networking between pathway suppressors (Abstract). Georgescu discusses the multiple roles of PTEN in regards to inhibiting the pathway, relevant to cancer progression, and teaches that PTEN constitutes the main node of the inhibitory network (Abstract). To further complicate these matters, Georgescu teaches that PTEN is a highly regulated tumor suppressor that behaves differently in different types of tumors and teaches the existence of redundant coexisting PTEN inactivating mutations and PI3K-activating mutations in certain cancers (pg 1172, col 1- col 2). Figure 1 of Georgescu demonstrates the complexity of linear and nonlinear signaling through the PI3K-Akt pathway, as well as other pathways involved in cell growth (i.e. the mTOR and Ras/ERK pathways). Georgescu discusses a number of known PTEN-interacting proteins and how they may influence PTEN’s tumor suppression role (see Fig. 3 and pages 1172- 1174).
Regarding the scope of the claimed therapeutic treatments for cancer, it is noted that no method for treating all cancers is known and the likelihood of one therapeutic method being effective for the full claimed scope of any cancer is low. Song et al. (“Cancer classification in the genomic era: five contemporary problems” Human Genomics (2015) 9:27, DOI 10.1186/s40246-015-0049-8) discusses the vast biological diversity of human cancers (Abstract), and states that there are at least 200 types of cancer, organized primarily by organ location, although with some exceptions (see page 2, left col, “How many cancer types are there?”). The review further discusses that the organ-centric system is further stratified, most often by the known cell type of origin within the organ and further each of the major types can have multiple sub-types of cancer (pg. 2, left col). The review concludes that “The usefulness of classification ultimately rests on increased prognostic power or more precisely targeted therapies” (pg 7, left col). Thus, it is evident from Song et al. that there exists a great amount of diversity among the types of cancers, including a large amount of heterogeneity and differences in cell signaling pathways (see e.g. the discussion on page 4 regarding heterogeneity among samples). From Song one can also conclude that a great amount of unpredictability exists among known cancer subtypes and that the field is moving towards personalized or targeted treatment methods.
As evidenced by all of the references cited above, there is an extremely high level of unpredictability in cancer treatments and in the regulation of biological pathways. The complexity of the cellular signaling pathways involved, coupled with the difficulty in accomplishing cellular gene editing for treating any one disease, indicates that many studies and optimization must go into applying a synthetic gene circuit, such as the split TEV protease inducible systems taught in Kwon or Wintgens, for treating a disease or disorder.
Since methods for artificially manipulating gene expression in order to specifically treat a disease or disorder characterized by the aberrant signaling of a first signal transducer and/or a second signal transducer remains largely unsolved, when at least one of the signal transducers is AKT, means for using the claimed synthetic protein circuit to treat any cancer as claimed is highly unpredictable.
(D) The relative skill of those in the art:
The relative skill of those in the art is high, as evidenced from the references discussed above. However, as demonstrated in the cited art, there is enormous complexity involved in the PI3K/AKT signaling pathways (and even larger complexity when considering the full breadth of claim 50 as pertaining to any cell signaling aberration). When considering the nearly infinite combination of mutations which could be involved in any given cancer, one skilled in the art seeking to perform a treatment according to the instant claims would turn to the specification for additional guidance in seeking to practice the instant invention.
(F) The amount of direction or guidance presented and (G) the existence of working examples:
The specification has provided guidance and general discussion regarding applying a synthetic protein circuit (such as one using a split protease system) when using the circuit to treat a disorder or disease characterized by the aberrant signaling of a first signal transducer and/or a second signal transducer. The specification states that expressing the protein circuit can comprise administering one or more nucleic acids encoding the synthetic protein circuit, such as any of the nucleic acids described herein (including those of claims 65-69) ([0152]).
The specification states that: “In some embodiments, aberrant signaling of the one or more signal transducers is a direct or indirect cause of a symptom of the disease or disorder. In some embodiments of the methods provided herein, treatment reduces the aberrant signaling of the one or more signal transducers. In some embodiments of the methods provided herein, treatment reduces the induces the death of cells comprising the aberrant signaling of the one or more signal transducers. In some embodiments of the methods provided herein, treatment reduces the induces or prevents an immune response versus cells comprising the aberrant signaling of the one or more signal transducers. In some embodiments, treatment of the disease or disorder comprises the action of the agent of interest as described herein.” ([0154]). None of the teachings in the instant disclosure address the severe complexity of manipulating cellular signaling pathways, such as the multi-pronged PI3K-AKT pathway as described in the prior art.
Further, only two working examples are presented in the instant disclosure. Example 1 pertains to a synthetic protein circuit wherein the synthetic circuit exploits the recruitment of Ras binding domain (RBD) to the plasma membrane by active Ras. An RBD domain was fused to each half of split TEV protease such that increased Ras activity causes both TEV components to translocate to the plasma membrane, increasing the local concentration of both protease halves, and thereby increasing the concentration of reconstituted protease through weak residual affinity between the two halves (see [0245]). Flow cytometry analysis of the TEV protease-activated reporter demonstrated the detection of active Ras (constitutively active Ras was compared to wildtype Ras) through membrane translocation and reconstitution of split TEV protease (FIGS. 2B-2C). However, this only pertains to detecting Ras activity in cell cultures and does not suggest or teach a method for treating or preventing a disease.
Example 2 provides further validation for the enrichment through translocation synthetic protein circuit design concept described herein by showing that it can detect non-protein signal transducers as well as proteinaceous signal transducers ([0246]). A synthetic protein circuit was designed where the input is PI3P (produced by transfecting a PI3 kinase) and the signal transducer binding domain is PH. Versions of the circuit with constitutive localization of the iTEV reporter to the membrane (FIG. 4A), as well as a circuit where the reporter is conditionally translocated to the membrane through a PH domain (FIG. 4B) were validated. The results demonstrate that an improvement in the dynamic range was observed when the reporter was conditionally translocated to the membrane through the PH domain (FIG. 4B and [0246]). However this does not amount to treatment or prevention of a disease or disorder.
These two working examples demonstrate that with two different signaling pathways, the claimed system having a first signal transducer binding domain and second signal transducer binding domain coupled to a first and second part of a protease such that the protease in an active state is capable of cutting an effector protein to create an active effector (or inactive effector state) is capable of being expressed in cells and can be used to detect activation of these targeted pathway (either RAS activity or increased PI3P, related to the PI3K-AKT pathway).
The specification does not provide sufficient guidance for treating cancer using the synthetic protein circuit. There is no reduction to practice or practical demonstration of a method for treating cancer in the instant specification. The instant disclosure does not demonstrate any method in which the synthetic protein circuit is applied in such a way that cells in vivo or ex vivo are successfully transformed to express all of the necessary components, such that an aberrant signaling pathway activates the claimed circuit precisely to cause cell death as claimed, in only the desired tissue type.
As discussed above, this would require not only the specific means for targeting the signaling pathway, but also highly specific gene transfection (or infection) along with means to limit the induced apoptosis to only desired cell types (and thus not cause additional side effects or unwanted damage in non-targeted tissues). How such results are to be practically achieved with the synthetic protein circuit is not extensively discussed nor demonstrated by a reduction to practice in the instant disclosure. There is no evidence of using the circuit as claimed to induce cell death in any cell type in the instant disclosure, much less suitable evidence of applying this method to tumors (e.g. in the complex and heterogenic tumor environment).
(H) The quantity of experimentation necessary:
Considering the state of the art of synthetic cellular circuits (as discussed by Kwon et al., Juillerat et al., Gao et al., and Wintgens et al.), the extremely high unpredictability in the art of modulating cellular signaling pathways (as evidenced for the PTEN and PI3K-AKT pathways in Nicholson et al. and Georgescu), the large amount of variation among cancer types (see Song et al.), and the lack of guidance provided in the specification, one of ordinary skill in the art would be burdened with a great amount of undue experimentation to practice the full scope of the invention, which includes treating any cancer having aberrant activation of a signaling transduction pathway, when one of the signal transducers comprises AKT (or RAS).
When considering the vast scope of the claimed method, this is an incredibly large number of cancers, among a great number of types and subtypes, with a great number of varying subject populations and a very large number of different genetic factors involved. The instant specification does not provide sufficient enablement for methods to target and manipulate any signaling pathway using a synthetic protein circuit to treat (i.e. prevent, treat, or lessen symptoms) cancer as instantly claimed.
When considering the additional limitations of the dependent claims, as explained for claim 50, none of the dependent claims are supported by the disclosure to enable one skilled in the art to use the invention as claimed. The dependent claims all require the desired result of treating a cancer characterized by the aberrant signaling of the first signal transducer and/or the second signal transducer. The dependent claims do not narrow the possible subject population or specify further means for accomplishing the goal.
Claim 58 limits the first and or second signal transducer in the circuit to AKT or a component of the RAS signaling pathway, however this still encompasses a large number of cancers and various subtypes. Further, although the specification details examples using these pathways for the activation of a protease-based circuit, this is not considered enablement for the treatment of cancers.
It is therefore the Examiner’s position that one skilled in the art could not practice the invention commensurate in the scope of the claims without undue experimentation.
Claims 50-58, 60-61, and 63-69 are rejected under 35 U.S.C. § 112(a) for failing to comply with the enablement requirement.
Response to Arguments
Applicant's arguments filed 3/2/2026 regarding the rejection of claims 50-58, 60-61, and 63-69 have been fully considered but they are not persuasive.
Applicant’s amendments to claim 50 recite that the method is for therapeutically treating cancer and that the method involves the indirect or direct activation of a cell death pathway. Applicant argues that the method can be used for therapeutically treating cancer, with no specific limitations regarding the type of cancer or requiring any specific genetic features, instead the claims encompass cancer with any aberrant signaling.
Applicant respectfully traverses the enablement rejection on the grounds that the claimed invention is fully enabled in view of the specification and knowledge of one of skill in the art. However, Applicant’s argument and the disclosure of the instant application is found not sufficiently enabling for the entire breadth of the claimed treatments for practically any cancer.
Applicant argues that that the cited art, including Kwon et al. (US PGPub 20200010513,
"Kwon"), Juillerat et al. (US PGPub 20170073423, "Juillerat"), Wintgens et al. (2019), Nicholson et al. (2002), and Georgescu (2010) does not teach nor contemplate the claimed therapeutic method and therefore the citations are not relevant to the state of the art of "methods of therapeutically treating a cancer" as presently recited in the independent claim (see pgs 7-9 of the remarks). This argument is unpersuasive, as the references are cited for all of the reasons explained above, and as previously stated. These references are provided as relevant examples concerning the general state of the art, and to establish the large amount of unpredictability in the art of treating cancers, including using genetic techniques to manipulate cells. This is pertinent to the instant claims, as they are also, ultimately drawn to treating cancer. As discussed by the applicant on pages 8 and 9, the cited references establish the state of the art and the known issues within studying gene-based therapies for cancer treatments, including particularly modulating the intercellular signaling pathways, and the unpredictability in doing so.
Applicant submits that the Nicholson and Georgescu references are discussed to highlight the complexity of cancer signaling pathways, like the elected AKT, and to establish that the targeting said pathways is highly unpredictable and has stymied targeted therapies.
Thus, Applicant submits that the method as presently recited overcomes these challenges. However, there is no convincing evidence on the record, or demonstrated by a reduction to practice, that the instantly disclosed invention has overcome these challenges. The only relevant working example for aberrant AKT activity is the sensor for activation of the PI3K pathway, an indirect measurement of AKT, as demonstrated in Example 2 of the specification. As discussed above, Figure 1 of Georgescu demonstrates the complexity of linear and nonlinear signaling through the PI3K-Akt pathway, as well as other pathways involved in cell growth (i.e. the mTOR and Ras/ERK pathways). The PI3P sensor demonstrated in the instant example can be activated by aberrant signaling upstream that doesn’t necessarily involve AKT (e.g. the receptor tyrosine kinases “RTK”, which are regulated by growth factor signaling, see Fig 1 of Georgescu).
There is no direct application of the claimed invention for inducing cell death in any cell type, much less for the treatment of a cancer cell within a tumor environment. MPEP § 2164.08 establishes that the enablement must be in scope with the claims, and that “The courts have repeatedly held that "the specification must teach those skilled in the art how to make and use the full scope of the claimed invention without ‘undue experimentation’" or that any experimentation must be "reasonable". See Amgen Inc. et al. v. Sanofi et al., 598 U.S. 594, 2023 USPQ2d 602 (2023);”
In this case the amount of experimentation appears to be an undue burden as for each and every type of cancer and subtypes within different tissues, a synthetic circuit would have to be engineered, tested, delivered, and optimized. Such optimization for achieving cell death in vitro with immortal cancer cells lines may be reasonable, but the claims are drawn to therapeutically treating cancer, which would also necessitate the delivery of the genetic factors in a subject, which would require a large amount of optimization beyond that which is routine in the art.
Applicant’s arguments concerning the state of the art, on pgs 10-12, establishes that there may exist an enabling disclosure for a method of inducing cell death in a cell that has aberrant signaling of the RAS or PI3K pathways, using a synthetic protein circuit sensor as described herein, due to the guidance of the specification and the teachings of the cited Gao et al. (2018).
However, this is not commensurate with the claimed scope of therapeutically treating any cancer. Inducing cell death in cells with aberrant RAS or AKT pathways is not equivalent to the treatment of cancer. Therefore, because of the high amount of unpredictability and the very large amount of experimentation and optimization that would have to be done in order to employ the disclosed invention for any and all types of cancer having aberrant signaling, the disclosure is not found fully enabling for the entire scope of the claims and the rejection is maintained.
Conclusion
Applicant's amendment necessitated the new and modified ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/A.T.M./Examiner, Art Unit 1655
/ANAND U DESAI/Supervisory Patent Examiner, Art Unit 1655
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