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 .
Application Status
Applicant’s remarks, Declaration under 37 CFR 1.130(a), and amendments to the claims filed June 24, 2026 are acknowledged. Claims 1-2, 7, 26-28, 32-33, and 36 were amended, and claim 31 was cancelled. Claims 1-2, 4, 6-7, 10-12, 26-30, 32-36 are pending and under examination.
Priority
Applicant's priority claims to provisional Application No. 63/226,210 are acknowledged. The effective filing date of the claims under examination is July 28, 2021.
Evaluation of Declaration under 37 C.F.R. § 1.130(a)
Regarding MPEP 717.01(a)(1)(A), the disclosure of Guan (Hao et al., 8 February 2021, Developmental Cell, 56, pg. 341-355, and Supplemental Information) applied in the rejections of the prior action, and referred to in the Declaration as “the Hao reference,” is subject to the exceptions of 35 U.S.C. 102(b)(1)(A).
Regarding MPEP 717.01(a)(1)(C)-(D), the Declaration is timely presented according to MPEP 717.01(f), and satisfies the formal requirements described in MPEP 717.01(c). Regarding MPEP 717.01(a)(1)(B), Declarant Jun-Lin Guan unequivocally states that they, along with co-inventor Mingang Hao, invented the subject matter disclosed in Guan et al. (para. 3). Declarant Jun-Lin Guan also states that the additionally named authors did not contribute to the subject matter of the present application (paras. 4-9). The Declaration provides both an unequivocal statement from the joint inventor, and a reasonable explanation as to the presence of additional authors as described in MPEP 2155.01. Examiner finds the Declaration filed June 24, 2026 sufficient to disqualify the content of Guan as prior art under the provisions of 35 U.S.C. 102(b)(1)(A).
Withdrawn Rejections
Applicant’s amendments to claims are sufficient to overcome the § 112(b) rejections raised in the prior action. These rejections are withdrawn, accordingly.
As stated directly above, the Declaration is sufficient to disqualify the content of Guan (Hao et al., 8 February 2021, Developmental Cell, 56, pg. 341-355, and Supplemental Information) as prior art. The § 102 and § 103 rejections raised over Guan, Guan in view of Huynh, Guan in view of Huynh and GPP, Guan and Huynh in further view of Garrett, and Hao in view of Guan are withdrawn, accordingly. The amendments to claims 1 and 26 to recite a “method of treating breast cancer” are sufficient to overcome the § 102 and § 103 rejections raised in the prior action over Hao as evidenced by Guan, Hao in view of Swiatnicki, and Hao in view of Huynh and GPP. None of the prior art cited in the previous action provides a method of treating breast cancer as instantly claimed. All prior art rejections raised in the previous action are withdrawn, accordingly.
Applicant’s response has been thoroughly reviewed, but is not persuasive to place the claims in condition for allowance for the reasons that follow. Any rejection or objection not reiterated herein has been overcome by amendment.
Claim Objections
Claim 28 is objected to because of the following informalities:
Claim 28 recites “wherein the HER2-positive breast cell cancer is in a subject.” This phrase contains a clear typographical error, and should be amended to recite “wherein the HER2-positive breast cancer cell
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 26-30 and 32-36 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention. The rejections below are new and necessitated by Applicant’s amendments to the claims.
Claim 26 recites “the HER2-positive breast cancer cell.” The claim does not previously explicitly recite such a cell. The claim recites “treating breast cancer” and “a HER2-positive breast cell,” but these phrases do not set forth that the cell is cancerous so as to provide sufficient antecedent basis for “the HER2-positive breast cancer cell.” The term lacks sufficient antecedent basis in the claim, accordingly.
Claims 27-30, and 32-36 are rejected for depending from claim 26 and failing to remedy the indefiniteness. Claim 26 will be interpreted hereinafter as reciting “a HER2-positive breast cancer cell.”
Response to Remarks – 35 USC § 112(b)
Applicant submits that the amendments to the claims address the § 112(b) rejections raised in the prior action. Examiner agrees that the amendments to claims resolve the § 112(b) rejections raised in the prior action. However, the amendments also introduce new grounds of rejection for the claims above.
Claim Rejections - 35 USC § 112(a) – Enablement
Claims 1-2, 4, 6-7, 10-12, 26-30, and 32-36 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention. The rejections that follow are new and necessitated by Applicant’s amendments to the claims.
The test of enablement is whether one skilled in the art could make or use the claimed invention from the disclosures in the specification coupled with information known in the art without undue experimentation (United States v. Telectronics Inc., 857 F.2d 778, 785, 8 USPQ2d 1217, 1223 (Fed. Cir. 1988)). Whether undue experimentation is needed is not based upon a single factor, but rather is a conclusion reached by weighing many factors. These factors were outlined in In re Wands, 858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988), and the most relevant factors are indicated below:
Nature of the Invention and Breadth of the Claims
Claims 1-2, 4, 6-7, 10, 26, 28-30, 32-33, and 36 encompass methods of “treating breast cancer,” wherein the methods comprise administering to a HER2-positive breast cancer cell, e.g., a HER2-positive breast cancer cell in a subject (see claims 2 and 28), an effective amount of an agent that inhibits a nucleic acid encoding FIP200, wherein the agent is a gene editing agent (CRISPR-Cas system, TALEN, or ZFN, see claims 4, 29, and 36), shRNA (see claims 6 and 30 for specific shRNAs), and/or siRNA targeting a nucleic acid encoding FIP200. The methods recite that small extracellular vesicle (sEV) release is stimulated by the administration step, which thereby reduces expression of HER2 on a plasma membrane of the HER2-positive breast cancer cell.
“Treating breast cancer” is interpreted hereinafter as alleviating or abrogating HER2-positive breast cancer and/or symptoms of HER2-positive breast cancer, based on the scope of “treating” described in the specification (pg. 12), and given that the recited cell to which the agent is administered is HER2-positive. HER2-positive breast cancer cells are interpreted as breast cancer cells considered HER2-positive according to the ASCO/CAP guidelines accepted in the art. Accordingly, enablement of the claims requires that one of ordinary skill in the art be able to treat HER2-positive breast cancer, by administering to a HER2-positive breast cancer cell, e.g., a HER2-positive breast cancer cell in a subject, any, or a specifically recited gene editing agent, shRNA, and/or siRNA targeting FIP200, which stimulates release of sEVs comprising HER2 from the cell’s plasma membrane, without undue experimentation.
Guidance in the Specification
As stated in the prior actions, based on the art, the endogenous levels of HER2 in HeLa cells and MCF-7 cells do not appear to meet the criteria to be considered HER2-positive. However, the specification overexpresses HER2 in HeLa and MCF-7 cells, which is considered sufficient to mimic the cellular physiology of a HER2-positive state. Accordingly, MCF-7 cells with overexpression of HER2, as well as MMTV-Neu mice, and the tumor cells derived therefrom, are HER2-positive breast cancer models disclosed in the specification (Fry, pg. 4, para. 2; Fry, et al. 2017, Int J Cancer, 140(3) 495-503). HeLa cells with overexpression of HER2, while not a breast cancer cell line, are suitable for modeling aspects of cellular physiology under HER2-positive conditions. A summary of the findings from these models is included below:
The specification describes Cre recombinase-mediated knock-out of FIP200 in the mammary epithelium of MMTV-Neu mice (hereinafter designated cKO mice)(pg. 21, lines 13-16). cKO mice express far less FIP200, but more p62, an indicator of autophagy inhibition (Fig. 1B, 1E bottom panels, 1G). The specification also discloses knock-in of a mutant FIP200-4A allele in cKO mice (hereinafter designated cKI mice) which limits autophagy induction (pg. 21, lines 16-20, Fig. 1E bottom panels). The specification demonstrates that cKO and cKI mice have longer tumor free survival (Fig. 1A), normal mammary structures (Fig. 1C-D), and decreased tumor cell proliferation (as indicated by Ki-67 staining, Fig. 1E top panels). It is concluded that FIP200 ablation (cKO) or blocking FIP200-mediated autophagy (cKI) abolishes mammary tumorigenesis in MMTV-Neu mice (pg. 21, lines 28-30). The specification also demonstrates that MMTV-Neu mammary tumor derived cells with FIP200 knockout (Fip200 -/- tumor cells) have decreased tumor cell proliferation and migration compared to mammary tumor derived cells with intact FIP200 (Fip200 +/+ tumor cells) (Fig. 8A-B). Accordingly, syngeneic FVB mice implanted with Fip200 -/- tumor cells had longer tumor free survival (Fig. 2C) and decreased tumor cell proliferation (Fig. 2D-E) compared to mice implanted with Fip200 +/+ tumor cells. The specification also discloses that Fip200 -/- tumor cells have significantly reduced metastatic activity (Fig. 16B-C).
Examiner notes the following: I) cKO and cKI mice were compared to litter mate controls, including controls heterozygous for FIP200 knockout (pg. 21, lines 20-25), and II) FIP200 ablation or blockade was present throughout the lifetime of cKO and cKI mice, and already present in Fip200 -/- tumor cells when they were implanted in syngeneic FVB mice. Regarding I, all control mice, including those heterozygous for FIP200 knockout developed tumors (pg. 21, lines 20-25). Regarding II, as the specification states, it is evident that genetic ablation of FIP200 or FIP200-mediated autophagy “abolishes mammary tumorigenesis,” i.e., it substantially prevents the process of tumorigenesis.
The specification also demonstrates that MCF-7 and HeLa cells overexpressing HER2 (“GFP-HER2”) with FIP200 or ATG13 knockout accumulate intracellular HER2 (Figs. 10-11). The specification shows that HER2 is localized to endosomes in FIP200 or ATG13 knockout HeLa cells, rather than on the cell surface (Fig. 4C; Fig. 13A). Thus, autophagy blockade alters cellular trafficking of HER2, which contributes to reduced HER2 levels on the cell surface of HER2-overexpressing cells (pg. 26, lines 13-15). The specification also defines the mechanism through which trafficking is altered in HER2-overexpressing, autophagy defective cells. The specification demonstrates that cKO and cKI mammary epithelial cells from MMTV-Neu mice, Fip200-/- tumor cells, and HeLa cells overexpressing HER2 have more HER2 colocalized within intraluminal vesicles (ILVs) compared to controls (Fig. 5A-D). ILVs, which form in multivesicular bodies (MVBs), are released from cells through exocytosis as cargo-bearing small extracellular vesicles (sEVs)(pg. 3, lines 11-22 and pg. 27, lines 6-9). Indeed, the specification demonstrates that sEVs collected from Fip200-/- tumor cells, and HeLa cells with FIP200 or ATG13 knockout are enriched with HER2 protein (Fig. 6). The specification also shows that the quantity of sEVs released from autophagy deficient cells is increased (Fig. 6G).
Thus, HER2-positive tumor cells with FIP200 or ATG13 knockout have altered trafficking of intracellular HER2; HER2 accumulates in intraluminal vesicles (ILVs), and is released in sEVs at higher levels than from cells with intact FIP200 or ATG13 (Example 6; pg. 27-28). Increased HER2 release in sEVs reduces the amount of HER2 on the surface. This mechanism correlates with decreased tumor cell proliferation and increased tumor free survival in cKO MMTV-Neu mice, and the decreased tumorigenic and metastatic potential of Fip200 -/- tumor cells. However, the specification does not directly determine the consequences of increased sEV biogenesis, or HER2-comprising sEVs, on HER2-positive breast cancer in any subject.
Taken together, the specification demonstrates prevention of HER2-positive breast cancer tumorigenesis in MMTV-Neu mouse subjects by ablating the DNA encoding FIP200 with a gene editing agent (Cre recombinase-mediated knockout or knock in of a defective FIP200 allele), wherein the ablation is present throughout the lifetime of the subject, and prior to the onset of tumorigenesis. Using cell lines which mimic a HER2-positive state, the specification appears to provide some level of predictability for prevention of HER2-positive breast cancer tumorigenesis in MMTV-Neu mouse subjects using a separate gene editing agent (CRISPR-Cas) to ablate the DNA encoding FIP200, wherein the ablation is present throughout the lifetime of the subject, and prior to the onset of tumorigenesis.
The specification does not provide predictability for treating established HER2-positive breast cancer, or inhibiting metastasis of HER2-positive breast cancer cells, in any breast tissues, including breast tissue in a subject. In the experiments detailed in the specification, FIP200 ablation or blockade was present throughout the lifetime of cKO and cKI mice, or already present in the Fip200 -/- tumor cells implanted in syngeneic FVB mice. The specification also does not provide predictability for treating HER2-positive breast cancer, or inhibiting metastasis of HER2-positive breast cells, in any breast tissue using therapeutic agents which knockdown FIP200. While the specification discloses shRNAs targeting FIP200 (pg. 29), the shRNAs were not administered to a subject having HER2-positive breast cancer, or to any breast cancer cell line overexpressing HER2. Furthermore, MMTV-Neu mice heterozygous for FIP200 knockout still develop tumors, even though they presumably have reduced levels of FIP200 relative to mice having both intact FIP200 alleles.
State of the Art
Hao teaches the opposite effects of the instant application (Hao and Guan, 2018, Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 4386; of record). Specifically, Hao teaches that “inhibiting autophagy by deletion of Fip200 or Atg13 using Crispr-Cas9 led to increased migration and partial EMT for MMTV-Neu cells,” whereas “re-expression of ectopic FIP200” rescued the effects of gene knockout. Hao’s “analysis of TCGA database showed that… in Her2+ BCa population specifically, higher expression of FIP200 correlated with better patient survival, suggesting a differential function of FIP200.” Hao speculates that “Her2 may promote tumor development and/or progression… by reducing FIP200 expression to inhibit autophagy.” Kim teaches that EMT is a key step towards metastatic dissemination of breast cancer (Kim, pg. 3; Kim and Koo, 2023, Biomedicines 2023, 11, 618, p. 1-19; of record). Thus, Hao as evidenced by Kim, teaches that administering a therapeutic agent that inhibits a nucleic acid encoding FIP200 (i.e., CRISPR-Cas9 to FIP200) or inhibits FIP200-mediated autophagy (i.e., CRISPR-Cas9 to FIP200 or ATG13), exacerbates HER2-positive breast cancer and its potential for metastasis, in a model substantially identical to that of the instant application.
Similarly, Vega-Rubin-de-Celis teaches that loss of BECN1, an essential autophagy gene downstream of the ULK1 complex, is found in ~30% of human breast cancers, and results in increased mammary tumorigenesis in mice models (pg. 4176; Vega-Rubin-de-Celis, 2018, PNAS, 115(16) p. 4176-4181; of record). Using MMTV-Neu mouse models of HER2-positive breast cancer, Vega-Rubin-de-Celis demonstrates that homozygous knock in of an autophagy-inducing allele of BECN1 prevents mammary tumorigenesis and prolongs tumor-free survival (Fig. 2). Vega-Rubin-de-Celis also demonstrates that administration of an autophagy-inducing peptide, Tat-Beclin 1, to mice with established HER2-positive tumors decreased the rate of tumor progression as effectively as a clinically approved treatment for HER2-positive breast cancer (“BT-474-VH2 xenografts… receive daily i.p. administration when their tumor volume reached 200 um3”, pg. 4179, right col.; Fig. 4). Thus, like Hao, Vega-Rubin-de-Celis shows that autophagy inhibition may have a detrimental effect in subjects with HER2-positive breast cancer.
Taken together, Hao and Vega-Rubin-de-Celis provide significant unpredictability regarding the therapeutic potential of inhibiting a nucleic acid encoding FIP200 or inhibiting FIP200-mediated autophagy generally. Vega-Rubin-de-Celis does provide predictability for treating established HER2-positive breast cancer by administering an autophagy inducing peptide, Tat-Beclin 1, to a subject. However, this treatment has the alternative effect to that which is instantly claimed, again, suggesting significant unpredictability for the instantly claimed methods.
Finally, regarding the therapeutic potential of the mechanism through which FIP200 reduces HER2 levels in HER2-positive breast cancer cells, as stated in the previous actions, the art teaches that release of EVs from breast cancer cells is associated with increased drug-resistance (Ciravolo, et al., 2010, J Cell Physiology; Marleau, et al., 2012, Journal of Translational Medicine; of record), poor prognosis, and allows transfer of proteins involved in metastatic processes and cell proliferation to recipient cells (Rontogianni, et al., 2019, Communications Biology; Dong, et al., 2020, Cell Death and Disease; of record). Regarding HER2-comprising EVs specifically, Rontogianni teaches that HER2 is released in EVs of HER2-positive breast cancer cells in its active form (Rontogianni, Fig. 4B and pg. 6, left column). Finally, Huang teaches that treatment of HER2-positive breast cancer cell lines with HER2-comprising exosomes 1) stimulates tumor cell proliferation and 2) inhibits Herceptin activity (Ming Bo Huang. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6352; of record). Based on the art, it is highly unpredictable that a method stimulating release of sEVs, particularly those comprising HER2, would treat HER2-positive breast cancer or inhibit its metastasis in a subject.
Experimentation Required and Level of Skill in the Art
In order to practice the invention, a large amount of highly predictable experimentation would be required. To treat HER2-positive breast cancer with the agents encompassed by the claims, one would need to prepare HER2-positive breast cancer models and/or identify a cohort of subjects with HER2-positive breast cancer, wherein inhibiting a nucleic acid encoding FIP200 would treat the HER2-positive breast cancer. Based on the art, it is unclear that a skilled artisan could even identify suitable models or subjects for the method given I) that therapeutic agents encompassed by the claims appear to have opposing effects on mammary tumorigenesis even when administered to the same model of HER2-positive breast cancer (see the disparate effects described in the instant application and Hao, or the instant application and Vega-Rubin-de-Celis in MMTV-Neu mice), II) the resulting lack of a consensus in the art as to whether autophagy has a tumor-promoting or tumor-preventing role in HER2-positive breast cancer, and III) the significant possibility that altered HER2 trafficking resulting from FIP200 knockout or inhibition would promote the release of tumor-promoting, HER2-bearing sEVs.
Even if one skilled in the art identified a suitable model or cohort of subjects, they would need to identify appropriate agents, design the administration protocol for each agent, determine the appropriate criteria for determining whether the outcomes were achieved, and then determine whether the agents actually treat the HER2-positive breast cancers. Although the level of skill in the art is high, and the design and testing of therapeutic agents encompassed by the claims is well within the purview of the ordinarily skilled artisan, because it is not evident that an ordinarily skilled artisan could even identify models or subjects that would be treated by the claimed methods, or agents encompassed by the claims that would result in treatment of HER2-positive breast cancer, such experimentation is undue.
Conclusion
Taking into consideration the factors outlined above, including the nature of the invention, the breadth of the claims, the guidance provided in the specification, and the lack of consensus in the art regarding the breast cancer-promoting or breast cancer-preventing properties of FIP200 or FIP200-mediated autophagy, it is the conclusion that undue experimentation would be required to make and use the invention as claimed.
Additional Dependent Claims
Claims 11-12, 27, and 34-35 do not further limit the claims so as to resolve the enablement issues raised above, and are rejected for at least the reasons above.
Regarding claims 11-12, and 34-35, neither the specification nor prior art provide predictability for treating HER2-positive breast cancer by combining a first agent targeting FIP200 encompassed by the claims, which as described above could not reasonably be predicted to treat HER2-positive breast cancer, with a generic or specifically recited second agent. It is not evident that the skilled artisan could reasonably predict which of the combinations would result in “treating breast cancer,” given that the first agent’s role or therapeutic potential in breast cancer is uncertain as described above.
Regarding claim 27, isolating one or more sEVs released from the HER2-positive breast cancer cell does not remedy the issues described above related to the lack of predictability for treating HER2-positive breast cancer with the recited agents which inhibit a nucleic acid encoding FIP200.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new 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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/JENNA L PERSONS/
Examiner, Art Unit 1637
/Soren Harward/Primary Examiner, TC 1600
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