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 .
Election/Restrictions
Applicant's election of 1) an anti-nucleolin agent including aptamer AS1411 and 2) breast cancer that is triple negative in the reply filed on 08/27/2025 is acknowledged. While traversal is not explicitly stated, the response is treated as a traversal because Applicant argues that that there is not undue burden in examining multiple species together. This is not found persuasive because the application was filed as a 371 of a PCT application. As noted in the original rejection, the alternatives lack a technical interrelationship because they do not belong to a single recognized class of compounds as required under PCT Rule 13.2.
However, upon further search and consideration the requirement for a species election of a treatment to which a breast tumor is responsive and a breast cancer subtype is withdrawn.
Status of Claims
Applicant’s amendment filed 08/27/2025 is acknowledged. Claims 1, 18, 20, and 21 have been amended. Claims 2-3 and 12-13 have been cancelled. Claims 1, 4-11, and 14-24 are pending in the instant application and the subject of this non-final office action.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or marked as considered on a provided IDS, they have not been considered.
Specification
The use of the terms including “Texas Red”, which is a trade name or a mark used in commerce, has been noted in this application. Such terms should be accompanied by the generic terminology; furthermore such terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the terms.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
The abstract of the disclosure is objected to because the amended abstract recites “CKYPB2” and “sternness”; these appear to be an OCR errors of “CRYβB2”and “stemness”, respectively. A corrected abstract of the disclosure is required and must be presented on a separate sheet, apart from any other text. See MPEP § 608.01(b).
The disclosure is objected to because of the following informalities: Brief Description of the Drawings section makes reference to colors (e.g., para [0023] discussing Fig. 13) but drawings were submitted in black and white and contain no colors.
Appropriate correction is required.
Claim Objections
Claims 1, 11, and 21 are objected to because of the following informalities:
Claim 1: The claim has an extra space between “method” and “comprising” in the third line.
Claim 11: Step (c) is missing a comma between “inhibitor” and “an”
Claims 11 and 21: The claims recite “CRYPB2” throughout; this appears to be an OCR error of “CRYβB2”. Appropriate correction is required.
Claim Notes
The genes CRYβB2 and nucleolin are also referred to in the art, respectively as at least CRYBB2 and NCL (see instant Table 4). They may be referred to by either name interchangeably herein.
Claim Interpretation
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP 2111.
Regarding claims 1, 11, and 21, “positive for CRYβB2” (claims 1 and 11) may be interpreted broadly as either in reference to the threshold of greater than a reference breast tissue sample in a bulk sample (e.g., in a Western blot) or, along with the “positive for CRYβB2 protein” of claim 21, on a per-cell basis, wherein the representative images provided in Figs. 6A and 16A (see para [0016] of the instant specification) may be used as a basis for reference.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 4-11, 14-20 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.
Regarding claims 1 and 11, the claims recite “identifying the subject as having a breast tumor that … may likely respond to…” The phrase “may likely” is renders the claim indefinite. The phrase “may likely” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention.
Namely, it is not clear what degree of likelihood would need to be required to meet the limitation. Therefore, the metes and bounds cannot be ascertained by one of ordinary skill in the art.
Claims 4-10 and 14-20 are indefinite for depending from claims 1 and 11, respectively, and not rectifying the deficiency.
Regarding claims 4-5 and 14-15, the claims recite “the breast cancer”. There is insufficient antecedent basis for this limitation in the claim. The claims upon which they depend recite “breast tumor”.
Regarding claims 7-10, the claims recite “wherein the breast tumor responds to…”. It is unclear whether the claims are intended to require a further step of administering the respective inhibitor/agent, upon which treatment the tumor responds, or whether the limitations were intended to limit only the types of each class of inhibitor/agent to which the breast tumor was identified as responsive.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 4-11, 14-24 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.
Regarding claims 1, 4-11, 14-24, claims 1 and 11 recite “identifying the [female] subject as having a breast tumor that … may likely respond to a CDK4 inhibitor, an anti-nucleolin agent or a ribosomal RNA synthesis inhibitor” based on the relative level of CRYBB2. Claim 21 recites “administering … an effective amount of a CDK4 inhibitor, and/or an anti-nucleolin agent and/or a rRNA inhibitor when a sample … from the breast cancer tissue … is tested for nuclear and/or nucleolar expression for CRYBB2 and greater than 1% of the cell nuclei and/or nucleoli are positive for CRYBB2 protein”.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 U.S.C. 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (Fed. Cir. 1988). Wands states, on page 1404:
Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex part 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 these in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.
First, the claims are broad. Claims 1 and 11 require testing for expression of CRYBB2 protein through any means and include both increased per-cell expression or increased numbers of cells expressing CRYBB2 relative to a reference. Claim 21 requires nuclear or nucleolar expression above the 1% threshold, but may be assessed by any means. Claim 1 simply identifies the tumor as “may likely respond” to at least one of the inhibitors/agent; claims 11 and 21 administer an inhibitor/agent when the threshold is met.
It is noted that as the reference sample is not specified, claims 1 and 11 broadly comprise comparing to another breast tumor, normal breast tissue from the subject, normal breast tissue from another individual of that organism, breast tissue from any other organism, etc.
Second, the invention is in the 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).
Third, the working examples and state of the prior art show a high level of unpredictability. While it is acknowledged that the disclosure supports an interaction between nucleolin and CRYBB2 (e.g., Figs. FB and 3C), the results of NCL knock-outs were mixed (para [0155], emphasis added):
Knockout of nucleolin significantly decreased proliferation (Fig. 5A and Fig. 15B), sphere formation (Fig. 5B and Fig. 15C), and tumor size and weight (Fig. 5C and Fig. 15D) of MCF10AT1-CRY3B2 cells. Interestingly, nucleolin deficiency had a smaller effect on sphere formation by MCF10AT1-vector cells (Fig. 5B and Fig. 15C) and no effect on tumor formation by these cells (Fig. 5C and Fig. 15D). Importantly, MCF10AT1-CRY3B2 tumors that are nucleolin-deficient showed significantly lower incidence and size of lung metastases (Fig. 5D, Fig. 15E and Fig 15F). In line with these observations, the nucleolin aptamer AS-1411 inhibited the growth of CRY3B2 tumors and had no effect in tumors lacking CRY3B2 (Fig. 5E).
Further, contrary to Applicant’s claimed responsiveness being dependent on expression of increased levels of CRYBB2 protein, Soundararajan (Soundararajan S, et al. The nucleolin targeting aptamer AS1411 destabilizes Bcl-2 messenger RNA in human breast cancer cells. Cancer Res. 2008 Apr 1;68(7):2358-65.) teaches cytotoxicity of the anti-nucleolin agent AS-1411 on MCF-7 cells (Fig. 1A). Applicant has established that MCF-7 cells express minimal to no CRYBB2 protein (Fig. 4H). Thus, it is evident that there is unpredictability in whether CRYBB2 over a threshold that greater than a reasonable reference sample would be necessary to predict responsiveness to an anti-nucleolin agent, such as AS-1411.
In addition, Applicant describes treatment with a CDK4 inhibitor palbociclib, wherein palbociclib reduced tumor volume and weight to a greater degree in CRYBB2-expressing MCF10AT1 cells compared to vector-only cells (Fig. 9B) and wherein palbociclib IC50 was significantly correlated with CRYBB2 expression in TNBC cells (Fig. 9C).
Contrary to this finding, however, the disclosure teaches that, while CDK4 expression is correlated with CRYBB2 expression in African American tumors, it is uncorrelated in those of European American patients (Fig. 10B). Further, Fassl (Fassl A, et al. Increased lysosomal biomass is responsible for the resistance of triple-negative breast cancers to CDK4/6 inhibition. Sci Adv. 2020 Jun 17;6(25):eabb2210.) teaches the following subset of cell lines treated with CDK4 inhibitor palbociclib, which have been annotated according to Fig. 6A of Fassl and Fig. 4G, 4H, and 8D (see also para [0162]) of the instant disclosure:
Cell Line
Subtype
AA
CRYBB2 Expression
CDK4/6 Inhibition
MDA-175
ER+
Y
-
Independent
MCF7
ER+
-
-
Sensitive
HCC1187
TNBC
-
-
Independent
MDA468
TNBC
Y
-
Independent
HCC1937
TNBC
-
Y
Independent
HCC70
TNBC
Y
Y
Independent
MDA157
TNBC
Y
Y
Independent
HCC1806
TNBC
Y
Y
Resistant
SUM149
TNBC
unknown
Y
Resistant
As may be observed, both CDK4 inhibitor sensitive and independent cell lines are found in cell lines that express minimal to no CRYBB2, and indeed all CRYBB2-expressing cell lines that overlapped in the experiments of the instant disclosure and Fassl were either CDK4 inhibitor independent or resistant. Thus, it is evident that there is a high level of unpredictability in responsiveness to a CDK4 inhibitor, such as palbociclib, when differentiating breast cancers solely based on the level of CRYBB2 expression.
The claims also assert that responsiveness to an rRNA synthesis inhibitor may be predicted when CRYBB2 expression over a threshold is found. However, the disclosure describes only that dysregulation of major signaling pathways like p53 and pRb altered activity of the RNA Pol I (para [0031]) and that NCL was first identified in ribosomal RNA processing (para [0060]). However, as the disclosure further states, NCL is a multifunctional nucleocytoplasmic protein involved in numerous processes (para [0060]), and it is not clear—absent any data, of which there was none identified in the disclosure—what relationship CRYBB2 would display with rRNA synthesis.
Indeed, Drygin (Drygin D., et al. Targeting RNA polymerase I with an oral small molecule CX-5461 inhibits ribosomal RNA synthesis and solid tumor growth. Cancer Res. 2011 Feb 15;71(4):1418-30.) teaches treating with the rRNA synthesis inhibitor CX-5461 and at least the cell lines MDA-175-VII, SUM 149 PT, and MCF-7 (entire document, e.g., Fig. 4). Drygin teaches that CRYBB2-expressing SUM 149 PT has an intermediate EC50 to the two other cell lines that lack at least strong CRYBB2 expression (Fig. 4A; see also the table above). While it is noted that some of these cell lines may be derivatives of the cell lines noted above, absent information to the contrary, the artisan would expect the expression to be approximately similar if CRYBB2 plays an important role in stemness, tumorigenesis, and metastasis as described in the instant specification (para [0006]). Thus, combined with the previous unpredictability of NCL, from which the claimed to rRNA (synthesis) inhibitors appears to stem, and the further in view of the apparent lack of relationship between CRYBB2 expression and relative effectiveness in breast cancer cell lines, there is a high degree of unpredictability in determining responsiveness to an rRNA synthesis inhibitor when CRYBB2 expression is greater than a threshold.
Taken together, while there are working examples of treating tumors from a limited number of genetic backgrounds and some direction provided by the inventor, the diversity of responses to each of the three treatments in the art from a greater number of genetic backgrounds combined with the CRYBB2 expression information provided from the instant disclosure indicates a high degree of unpredictability in the claimed relationship. Balanced only against the high level of skill in the art, it is held that the amount of experimentation required to use the invention would be undue.
Claims 1, 4-11, and 14-24 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.
Regarding claims 1, 4-11, 14-24, claims 1 and 11 recite “identifying the [female] subject as having a breast tumor that … may likely respond to a CDK4 inhibitor, an anti-nucleolin agent or a ribosomal RNA synthesis inhibitor” based on the relative level of CRYBB2. Claim 21 recites “administering … an effective amount of a CDK4 inhibitor, and/or an anti-nucleolin agent and/or a rRNA inhibitor when a sample … from the breast cancer tissue … is tested for nuclear and/or nucleolar expression for CRYBB2 and greater than 1% of the cell nuclei and/or nucleoli are positive for CRYBB2 protein”.
However, the Applicant’s disclosure lacks sufficient detail to demonstrate possession of the full scope of the invention, as required under 112(a).
As discussed in the enablement rejection above, the disclosure provides examples of treating with the anti-nucleolin aptamer AS-1411 and further describes CRISPR/Cas9 depletion of nucleolin (e.g., para [0025]). However, these are not a sufficiently representative number of species to represent the entire genus of all possible anti-nucleolin agents (e.g., NCL-binding peptides/pseudopeptides and anti-NCL antibodies), which may preferentially target, for example, either the nuclear or the cytoplasmic located NCL, resulting in markedly different outcomes.
Further, as discussed above in the enablement rejection, the disclosure provides no working examples of a treatment with an rRNA (synthesis) inhibitor in CRYBB2-expressing cells. The described relationship between NCL and rRNA synthesis, discussed above, is not sufficient to establish that the Applicant had possession of determining responsiveness to rRNA synthesis inhibitors at the time of filing in an unpredictable art.
Thus, contrary to the breadth of the claimed invention, the disclosure does not provide written support necessary for all determining that a breast tumor will be likely responsive to all anti-nucleolin agents or any rRNA (synthesis) inhibitors based on a CRYBB2 expression level greater than a threshold.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1 and 4-10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception without significantly more. The claim(s) recite(s) abstract ideas and natural phenomena. This judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
The following three inquiries are used to determine whether a claim is drawn to patent-eligible subject matter:
Step 1. Is the claim directed to a process, machine, manufacture, or composition of matter?
Yes, the claims are directed to a process/method.
Step 2A, prong 1. Does the claim recite a law of nature, a natural phenomenon, or an abstract idea (recognized judicial exceptions)?
The claims recite a method for identifying (claims 1 and dependents) or treating (claims 11 and dependents) a breast tumor responsive to one of three classes of inhibitors/agents when the breast tumor is identified as CRYBB2 positive and the level of expression of CRYBB2 is greater than the level of expression in a reference sample. Said identifying directs the claim to the correlation between the relative expression levels of CRYBB2 in the tumor sample and the responsiveness of the breast tumor to the classes of inhibitors/agents, i.e., a natural phenomenon. See MPEP 2106.04(b)(I).
The comparison of levels and identification of a greater level likewise encompass abstract ideas, including mathematical calculations (including those that may be done by the human mind) and mental processes (i.e., observations, evaluations, and judgments). For example, the levels may be compared by subtracting the two values and/or the practitioner may simply make a judgement based on the values to determine which is the greater number. Thus, the claims are also directed to an abstract idea. See MPEP 2106.04(a)(2).
Step 2A, prong 2. Is the judicial exception(s) integrated into a practical application?
No, steps (b) and (c) of claim 1 encompass natural phenomenon and/or abstract ideas. The “testing” of step (a) is generically recited, and therefore is insignificantly extra-solution activity required to acquire data to practice the judicial exception. See MPEP 2106.04(d)(I) and 2105.05(g). It is noted that determining a level of a biomarker by any means is well-understood; see MPEP 2106.05(d)(II). In particular, testing for a level of a protein relative to a reference is routine and conventional within the art; Gown (Gown AM. Current issues in ER and HER2 testing by IHC in breast cancer. Mod Pathol. 2008 May;21 Suppl 2:S8-S15) teaches ER and HER2 IHC of breast cancer tissues, and that guidelines for doing so have been established by the American Society for Clinical Oncologists and the College of American Pathologists (entire document, e.g., Abstract).
Dependent claims 5-10 recite limitations directed to the breast tumors or the subject, thus limiting the data on which the judicial exceptions are practiced. This is not sufficient to integrate the claim into a practical application. See MPEP 2106.04(d)(I) and 2105.05(g).
Step 2B. Does the claim amount to significantly more?
Regardless of any novelty of the correlation between CRYBB2 and the targets of the inhibitors/agent, as described in MPEP 2106.05(I), “an inventive concept ‘cannot be furnished by the unpatentable law of nature (or natural phenomenon or abstract idea) itself.’” As discussed in the previous step analysis, the other elements of the claim merely encompass other judicial exceptions or are directed to acquiring (or in dependent claims limiting) the data to which the judicial exception(s) are applied. Thus, these claims fail to amount to significantly more.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMMA R HOPPE whose telephone number is (703)756-5550. The examiner can normally be reached Mon - Fri 11:00 am - 7:00 pm.
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/EMMA R HOPPE/
Examiner, Art Unit 1683
/NANCY J LEITH/Primary Examiner, Art Unit 1636