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 .
1. Claims 1 – 3, 6 – 7, 10 – 11, 13 – 17, 19, 21 – 25, 27, and 31 – 33 are pending.
Election/Restrictions
2. Applicant’s election without traverse of Group I (claims 1 – 3, 6 – 7, 10 – 11, 13 – 17, 19, and 21) in the reply filed on 09/10/2025 is acknowledged.
3. Claims 22 – 25, 27, and 31 – 33 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09/10/2025.
4. Claims 1 – 3, 6 – 7, 10 – 11, 13 – 17, 19, and 21 are under consideration.
Priority
5. This application is a National Stage entry of PCT/FI2021/050241 which claims priority to application FI202005335 filed 04/02/2020.
Information Disclosure Statement
6. The information disclosure statement (IDS) submitted on 09/30/2022 and 04/24/2024 are acknowledged. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements are being considered by the examiner.
Drawings
7. The drawings are objected to because of the following informalities: there is a description of colon in Figure 1 and 2 and the various colors cannot be distinguished from each other since the figures are in black and white.
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
Specification
8. The use of the term MammoCult, Matrigel, GrowDex, MilliQ, Ultra-Turrax, and TruSeq, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
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.
Claim Objections
9. Claim 6 is objected to because of the following informalities: in line 1, “The method of any of claim 1” should read “The method of claim 1”. Appropriate correction is required.
10. Claim 10 is objected to because of the following informalities: in line 1, “wherein storage” should read “wherein the storage”. Appropriate correction is required.
11. Claim 14 is objected to because of the following informalities: in line 1, “The method of any of claim 1” should read “The method of claim 1”. Appropriate correction is required.
Claim Interpretation
12. For the purpose of applying prior art, the limitation “at least about 10 kPa” is interpreted as at least 10 kPa because Applicant’s specification at page 15, line 35 states a minimum storage modulus of 10 kPa.
13. For the purpose of applying prior art “substantially gelled” in claim 3 in interpreted as the 3D matrix is not a fluid because Applicant’s specification at page 18, lines 11 – 14 states that “substantially gelled materials refer to materials that have fully or partial levels of elastic behavior whereas fluids not belonging to the scope of gels or substantially gelled materials do not have elastic component”.
14. For the purpose of applying prior art, “bioinert” in claim 3 is interpreted to include alginate, agarose, ovomucin, or egg white because Applicant’s specification defines “bioinert” at page 19, lines 19 – 21 and states that alginate, agarose, ovomucin, egg white or any combination thereof can be considered as bioinert at page 19, lines 30 – 31.
Claim Rejections - 35 USC § 112
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.
15. Claims 1 – 3, 6 – 7, 10 – 11, 13 – 17, 19, and 21 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 method of maintaining the presence or activity of an endogenous mammalian estrogen receptor (ER) and luminal phenotype of an ex vivo mammalian primary mammary cell or tissue comprising culturing the cell or tissue in a 3D agarose matrix with a storage modulus of at least 10 kPa, does not reasonably provide enablement for a method of maintaining the presence or activity of a mammalian ER of the claimed breadth of “other hormone responsive primary cell or tissue” by culturing in the claimed breadth of “a 3D matrix with storage modulus of at least about 10 kPa”. 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.
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). The court in Wands states: "Enablement is not precluded by the necessity for some experimentation such as routine screening. However, experimentation needed to practice the invention must not be undue experimentation. The key word is 'undue,' not 'experimentation.' " (Wands, 8 USPQ2d 1404). Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. "Whether undue experimentation is needed is not a single, simple factual determination, but rather is a conclusion reached by weighing many factual considerations." (Wands, 8 USPQ2d 1404). The factors to be considered in determining whether undue experimentation is required include: (a) the breadth of the claims, (b) the nature of the invention, (c) the state of the prior art, (d) the level or ordinary skill in the art, (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 use of the invention based on the content of the disclosure. While all of these factors are considered, a sufficient amount for a prima facie case are discussed below.
(a) The breadth of the claims: The claims broadly recite “other hormone responsive primary cell or tissue” and “3D matrix with storage modulus of at least about 10 kPa” and therefore the claims read on any hormone responsive primary cell or tissue and any 3D matrix with storage modulus of at least 10 kPa. The claims recite “maintaining the presence or activity” of a mammalian ER but also recite “other hormone responsive” cell. Thus, the claims read on any primary cell responsive to any hormone. The claims read on any 3D matrix with any storage modulus that is at least 10 kPa. Consequently, the breadth of the claims is expansive.
It is noted that the instant rejection is based on two separate issues:
(i) absence of an enabling disclosure of maintaining the presence or activity of a mammalian ER in any hormone responsive cell;
(ii) absence of an enabling disclosure for maintaining the presence or activity of a mammalian ER by culturing in any 3D matrix with a storage modules of at least 10 kPa.
(b) The nature of the invention: The nature of the invention is maintaining the presence of activity of a mammalian ER and maintaining the luminal phenotype in an ex vivo cultured mammalian primary mammary cell or tissue in a 3D matrix. (page 1, lines 5 – 19).
(c) The state of the prior art:
Regarding issue (i) of absence of an enabling disclosure of maintaining the presence or activity of a mammalian ER in any hormone responsive cell, the state of the prior art teaches that a hormone responsive fibroblast cell line maintains ER expression in 3D culture where ERα is expressed at higher levels after 7 days of 3D culture relative to 2D culture (Montani, Claudia, et al. Toxicology and applied pharmacology 280.3 (2014): 421-433; page 427, left col. para. 2; Figure 5). The prior art teaches ER was activated to a greater extent in 3D culture relative to 2D culture at 1 nM estradiol suggesting a better response to estradiol when cells are in 3D (Montani, Claudia, et al. Toxicology and applied pharmacology 280.3 (2014): 421-433; page 427, right col. para. 1; Figure 6A). The state of the prior art teaches that prostate tumor explants and breast tumor explants cultured on a gelatin sponge platform maintain expression of and activity of androgen receptor and estrogen receptor, respectively (Centenera, Margaret M., et al. Molecular oncology 12.9 (2018): 1608-1622: page 1609, right col. para. 4 – 5; Figure 1A and D; page 1612, right col. para. 2; page 1614, left col. para. 1 and right col. last para.). Thus the state of the prior art teaches that 3D culture of hormone responsive cells maintains ER presence and activity. However, the prior art does not appear to provide evidence that a 3D matrix with a storage modulus of at least 10 kPa maintains ER expression/activity.
Regarding issue (ii) of absence of an enabling disclosure for maintaining the presence or activity of a mammalian ER by culturing in any 3D matrix with a storage modules of at least 10 kPa, the state of the art teaches that culturing human breast cancer cells on Matrigel or collagen maintains some ERβ expression but culturing on tissue culture plastic increases ERβ expression (Neubauer, Hans, et al. Oncology reports 21.2 (2009): 475-481: page 477, left col.; Figure 3 and Figure 4A). However, culturing breast cancer cells on a matrix of laminin-111 does not maintain ER expression and instead completely represses ERβ expression (Neubauer, Hans, et al. Oncology reports 21.2 (2009): 475-481: page 478, left col.; Figure 4). The state of the prior art teaches that estrogen induction of the progesterone receptor in breast cancer cells occurred on matrixes of fibronectin or collagen I but not on laminin (Woodward, Terry L., et. al. Endocrinology 141.8 (2000): 2814-2821: Abstract; Figure 6; page 2818, left col. para. 2; page 2820, left col. para. 2). The prior art teaches that laminin reduces estrogen response element-mediated transcription despite not affecting ER content (Woodward, Terry L., et. al. Endocrinology 141.8 (2000): 2814-2821: page 2818, right col. para. 2; page 2819, left col.). Thus, the state of the prior art teaches that Matrigel and collagen maintain ER expression. However, the state of the prior art does not appear to provide any evidence that agarose with a storage modulus of at least 10 kPa maintains ER expression/activity.
(d) The level skill in the art:
The level of skill in the art of 3D cell culture in a matrix with specific storage modulus is high, as an artisan in this art needs specialized knowledge such as a postgraduate degree (Ph.D. and/or M.D.) given the complex nature of the chemical composition of cell culture matrices and the mechanical properties of such matrices. An artisan in the area of 3D cell culturing would have experience in culturing primary mammary cells and mammary cell lines in 3D matrices.
Determining the mechanical properties of a 3D matrix that maintains ER expression in a hormone responsive cell is not routine. There is no way to target only modulation of ER expression/activity in a cell cultured in a 3D matrix. Further, the ER acts in concert with other pathways, which may affect ER expression/activity.
(e) The level of predictability in the art:
Regarding issue (i) of absence of an enabling disclosure of maintaining the presence or activity of a mammalian ER in any hormone responsive cell, maintaining ER expression/activity in any hormone responsive cell within the scope of the claim is not predictable. For example, the state of the art teaches that culturing human breast cancer cells on Matrigel or collagen maintains ERβ expression but culturing breast cancer cells on a matrix of laminin-111 does not maintain ER expression and instead completely represses ERβ expression (Neubauer, Hans, et al. Oncology reports 21.2 (2009): 475-481: page 478, left col.; Figure 4). Thus, it is unpredictable whether ER expression will be maintained for a given hormone responsive cell when cultured on different matrices.
Regarding issue (ii) of absence of an enabling disclosure for maintaining the presence or activity of a mammalian ER by culturing in any 3D matrix with a storage modules of at least 10 kPa, the use of any other 3D matrix within the scope of the claim is not predictable. For example, the state of the art teaches that the stiffness of freshly isolated breast tumors is between 0.1 and 5 kPa and a smaller contribution of rigidities between 5 and 25 kPa while decellularized tissues have three regions of stiffness of 0.52 kPa, 5 – 10 kPa and 15 – 25 kPa (Medina, Scott H., et al. Biomaterials 202 (2019): 1-11 which is cited on the IDS filed 04/24/2024: page 4, right col. para. 3; Figure 1). Thus, it is unpredictable whether a 3D matrix of decellularized tissue that supported in vivo breast tumor cell growth would maintain ER expression at stiffness of at least 10 kPa in in vitro culture. The predictability of any 3D matrix with a storage modulus of at least 10 kPa to maintain ER expression/activity encompassed by the instant claim would be low given that the stiffness of a primary tumor varies but is primarily less than 10 kPa and the corresponding decellularized matrix also varies in stiffness but is primarily less than 10 kPa.
(f) The amount of direction provided by the inventor:
The specification shows that human primary breast cells cultured in agarose with a storage modulus of at least 10 kPa maintains luminal phenotype and maintains functional estrogen signaling compared to other matrices with a storage modulus less than 10 kPa. Therefore, there is a nexus between these results and the maintenance of ER activity and luminal phenotype, but not to the full scope of the method as claimed.
(g) The existence of working examples:
The specification shows that culturing primary human mammary cells in an agarose matrix where the concentration of agarose greater than 20 mg/mL yields a storage modulus of at least 10 kPa maintains ER expression and luminal phenotype (page 33, lines 9 – 23; Figure 4A – B; page 34, lines 1 - 25). The specification does not provide any additional examples or guidance on how to culture other hormone responsive cells on any other matrix with a storage modulus of at least 10 kPa to maintain ER expression/activity and luminal phenotype.
Thus, the specification provides sufficient teachings only for the enablement for culturing primary mammary cells in a 3D agarose matrix with a storage modulus of at least 10 kPa to maintain ER expression/activity and luminal phenotype. The specification teaches that no other 3D matrix tested with a storage modulus less than 10 kPa maintained ER expression/activity in any other hormone responsive primary cell. The prior art provides no compensatory guidance, since culturing the same cell on different matrices leads to different effects on the maintenance of ER expression, it would require undue experimentation to practice the invention as broadly claimed.
(h) The quantity of experimentation needed to make use of the invention based on the content of the disclosure:
The amount of experimentation would be undue because it would require determining which primary hormone responsive cells when cultured in a given 3D matrix with storage modulus of at least 10 kPa would yield ER expression/activity and luminal phenotype. Since, as discussed above, it is not routine to determine the mechanical properties of a 3D matrix that maintains ER expression in a hormone responsive cell, knowing only that primary mammary cells when cultured in 30 mg/mL agarose maintain ER expression/activity would mean that significant experimentation would be required to determine which other hormone responsive cells could be cultured in a 3D matrix with a storage modulus of at least 10 kPa to maintain ER expression/activity and what composition of 3D matrix yields the recited storage modulus and allows culturing of cells. This is because one cannot extrapolate between the working example in the specification and culturing the other cells and 3D matrices claimed and since there is little guidance with respect to culturing any other hormone responsive primary cells in a 3D matrix. Thus, the full scope of claim 1 is not enabled by the disclosure.
Claim 7: are they in possession of the genus of: stress pathway inducing compounds or epigenetic pathway modulating compounds (that optionally influence H3K27 methylation; what about the inhibitors also recited in that claim?
Claim Rejections - 35 USC § 112
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.
16. Claim 7 is 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.
The instant claim is drawn to a stress pathway inducing compound, an epigenetic pathway modulating compound that optionally influences H3K27 methylation, an inhibitor of EZH2. Thus, the claims are broadly drawn to any compound or molecule that induces any factor of any stress pathway pathway, any compound or molecule that modulates any factor in any epigenetic pathway, and any compound or molecule that inhibits EZH2. Therefore, the claims are considered genus claims that encompass a wide array of compounds. The claims encompass any agent that induces any stress pathway, any compound that modulates any epigenetic pathway, and any inhibitor of EZH2, which are not described by their function, structure or relation thereto. The genus for the inducing factors, the genus for modulating factors, and the genus for the inhibitor is highly variant, inclusive to numerous structural variants because a significant number of structural differences between genus members is permitted.
For a stress pathway inducing compound, the specification describes only anisomycin but also states “any other p38 inducing compounds” (page 12, lines 26 – 33; page 35, lines 5 - 7). For an epigenetic pathway modulating compound and EZH2 inhibitor, the specification describes only GSK-126 as an inhibitor of EZH2 (page 8, lines 29 – 33; page 11, lines 27 – 29; page 12, lines 16 – 28; page 35, lines 14 – 15). The specification does not disclose the diverse genus for each of the agents that induce, modulate, or inhibit. The specification does not place any structure, chemical or functional limitations on the embraced by genus an agent which induces a stress pathway, an agent which modulates an epigenetic pathway, or an EZH2 inhibitor. The recitation of “compound’ and “inhibitor’ does not convey a common structure or function and is not so defined in the specification. In sum, the specification and the claims do not provide any guidance on the structure of an agent which induces a stress pathway, modulates an epigenetic pathway, and an EZH2 inhibitor.
The MPEP states that written description for a genus can be achieved by a representative number of species within a broad generic. It is unquestionable that the claims are broad generics, with respect to all of the potential species of agents and inhibitor that may exhibit one, all, of or any of the claimed activity. The possible variations of compounds are limitless with potentially thousands of compounds that may exhibit the claimed activities. The purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter claimed by them. A patent specification must describe an invention and do so in sufficient detail that one skilled in the art can clearly conclude that the inventor invented the claimed invention. Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations," and by using "such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention."
The specification lacks sufficient variety of species of compounds to reflect this variance in the genus since the specification does not provide any examples of such a genus of compounds. Accordingly, the specification fails to provide adequate written description for the genus of “a stress pathway inducing compound”, “an epigenetic pathway modulating compound”, and “an inhibitor of the methyltransferase EZH2” and does not reasonably convey to one skilled in the relevant art that the inventors, at the time the application was filed had possession of the entire scope of the claimed invention. Moreover, the specification neither describes the complete structure of a representative number of species, nor describes a representative number of species in terms of partial structure and relevant identifying characteristics. Absent of such teachings and guidance as to the structure and function of these compounds, the specification does not describe the claimed compound and inhibitor in such full, clear, concise and exact terms so as to indicate that Applicant had possession of these agents/inhibitor at the time of filing of the present application. Thus, the written description requirement has not been satisfied.
Claim Rejections - 35 USC § 112
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.
17. Claims 1 – 3, 6 – 7, 10 – 11, 13 – 17, 19, and 21 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.
18. Regarding claim 1, it is unclear if “at least about 10 kPa” means the storage modulus is at least 10 kPa or is about 10 kPa (inclusive of values less than 10 kPa). Recitation of “at least” sets a lower limit, while recitation of “about” contradicts the lower limit of “at least”. Claims 2 – 3, 6 – 7, 10 – 11, and 13 – 14 are also rejected as they depend from claim 1 and do not clarify the grounds of rejection.
19. Regarding claim 1, it is unclear what “primary cells of an ex vivo mammary cell or tissue culture” means. It is unclear if this recitation refers to cells taken from in vivo mammary cells and established for growth in tissue culture or refers to mammary tissue taken from a subject and placed directly into culture. The specification defines “ex vivo” at page 22, line 35, but also states that “the ex vivo culture of the present invention is an in vitro culture” using components of an organism including “cells, tissues, cell lines” that have been isolated from their usual biological surroundings (page 22, lines 36 – 37 and page 23, lines 1 – 3). For the purpose of applying prior art, “primary cells of an ex vivo mammary cell or tissue culture” is interpreted as an explant of mammary tissue taken from a subject in accordance with Figure 1 of Applicant’s disclosure.
20. Regarding claim 3, recitation of the alternatives of 3D matrix is substantially gelled or 3D medium is bioinert or 3D matrix is bioinert of any mammalian primary cell or tissue in any 3D matrix with storage modulus of at least about 10 kPa of claim 1 (from which claim 3 depends) has too many alternatives resulting in too many possible combinations of cells, matrix, and media that makes the claim unclear.
21. Regarding claim 7, it is unclear what “a stress pathway inducing compound or method” refer to. The specification does not define “stress pathway inducing compound” but states that such compounds “include but are not limited to anisomycin or any other p38 inducing compounds”. It is unclear if “method” refers to a method of culturing with a stress pathway inducing compound or a method of mechanically inducing stress. For the purpose of applying prior art, “stress pathway inducing compound” is being interpreted as any compound that negatively affects cell growth.
22. Regarding claim 7, recitation of the alternatives of compounds and method any mammalian primary cell or tissue in any 3D matrix with storage modulus of at least about 10 kPa of claim 1 (from which claim 7 depends) has too many alternatives resulting in too many possible combinations of cells, matrix, and media that makes the claim unclear.
23. Regarding claim 11, the phrase “preferably” renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
24. Regarding claim 13, it is unclear how “a cell from a cell line” is a primary cell because claim 1 recites “culturing a mammalian primary mammary cell” and “primary cell” and a cell from a cell line is not a primary cell.
25. Regarding claim 13, recitation of the alternatives of cells of any mammalian primary cell or tissue in any 3D matrix with storage modulus of at least about 10 kPa of claim 1 (from which claim 13 depends) has too many alternatives resulting in too many possible combinations of cells, matrix, and media that makes the claim unclear.
26. Claim 14 recites the limitation "the prostate" in line 3 and 5. There is insufficient antecedent basis for this limitation in the claim.
27. Regarding claim 15, it is unclear if “at least about 10 kPa” means the storage modulus is at least 10 kPa or is about 10 kPa (inclusive of values less than 10 kPa). Recitation of “at least” sets a lower limit, while recitation of “about” contradicts the lower limit of “at least”. Claims 16 – 17, 19, and 21 are also rejected as they depend from claim 15 and do not clarify the grounds of rejection.
28. Regarding claim 15, it is unclear what is meant by “luminal epithelial phenotype and/or luminal epithelial cell identity” and if the method requires that the “mammalian primary cell” have a luminal epithelial phenotype and/or luminal epithelial cell identity prior to culturing in a 3D matrix. The specification does not define luminal epithelial phenotype or luminal cell identity. For the purpose of applying prior art, “luminal epithelial phenotype” is interpreted as the cell expresses one of notch, CK8, or CK18 based on the specification at page 14, lines 21 – 33.
29. Regarding claim 17, the phrase “preferably” renders the claim indefinite because it is unclear whether the limitation(s) following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
30. Regarding claim 19, it is unclear how “a cell from a cell line” is a primary cell because claim 15 recites “culturing a mammalian primary mammary cell” and “primary cell” and a cell from a cell line is not a primary cell.
31. Regarding claim 21, it is unclear what “a gene expression profile associated with a luminal phenotype, and/or the lack of a gene expression profile associated with a basal phenotype” means regarding which genes are required to be expressed/not expressed to be considered as associated with a luminal phenotype or basal phenotype. The specification teaches gene expression profiling is the measurement of the expression of one or more genes, even hundreds or several thousands of genes at once (page 13, lines 13 – 32) but does not teach what genes correspond to which phenotype.
32. Regarding claim 21, recitation of the alternatives to characterize any mammalian primary cell in any 3D matrix with storage modulus of at least about 10 kPa of claim 15 (from which claim 21 depends) has too many alternatives resulting in too many possible combinations of cells, matrix, and media that makes the claim unclear.
Claim Rejections - 35 USC § 112
33. Claim 1 is rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of mammalian primary cell or tissue or other hormone responsive primary cell or tissue is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the cells do not belong to the same art-recognized class of expressing estrogen receptor or are responsive to estrogen. I
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
34. Claim(s) 1 – 3, 6 – 7, 10 – 11, 13 – 17, 19, and 21 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fridriksdottir (Fridriksdottir, Agla J., et al. Nature communications 6.1 (2015): 8786), hereinafter Fridriksdottir which is cited on the IDS filed 04/24/2024 in view of Kinder (Kinder, David H., et. al. Cancer letters 205.1 (2004): 49-53.), hereinafter Kinder in view of Roberts (Roberts, Justine J., et al. Journal of Biomedical Materials Research Part B: Applied Biomaterials 99.1 (2011): 158-169.), hereinafter Roberts.
Regarding claim 1 and 15, Fridriksdottir teaches culturing estrogen receptor-positive primary mammalian mammary luminal cells (page 9, right col. last para.). Fridriksdottir does not teach culturing the primary cells in a 3D matrix with storage modulus of at least 10 kPa. However, Fridriksdottir teaches the cells lose the ER protein in culture but the addition of TGFβ inhibitors (TGFβR2i) recapitulated ER expression and induced the expression of luminal cell transcription factors (page 5, left col. para. 2; page 4, left col. and right col.; Figure 3 – 4). Fridriksdottir teaches failure of culturing ER-positive HBECs is caused by both lack of growth and loss of ER expression under conditions otherwise favoring propagation of luminal epithelial cells (page 4, left col. and right col. para. 1).
Regarding claim 2, Fridriksdottir teaches the primary mammary cells are human (page 9, right col. para. 2).
Regarding claim 6, Fridriksdottir teaches exposing the culture to TGFβ inhibitors SB431542 and RepSox (page 4, right col. para. 2).
Regarding claim 13 and 19, Fridriksdottir teaches the cells are non-tumor cells obtained from normal breast biopsies (page 9, right col. para. 2).
Regarding claim 21, Fridriksdottir teaches in Table 1 – 2 and Figure 2 that luminal ER-positive cells were characterized by CK8/18, lack of p63, lack of CK14, and a gene expression profile associated with a luminal phenotype and lack of a gene expression profile of a basal phenotype.
Fridriksdottir does not teach “a 3D matrix with storage modulus of at least about 10 kPa” of claim 1 and 15 or “the 3D matrix is substantially gelled, and/or the 3D medium and/or matrix is bioinert” of claim 3 and 16 or culturing in the presence of a stress pathway inducing compound of claim 7 or the storage modulus is “achieved by using external mechanical compression” of claim 10 or “agarose” of claim 11 and 17 or “chondrocyte” of claim 14. However, Fridriksdottir teaches that in spite of the fact that there are multiple protocols for enrichment, long-term cultivation and clonal growth of human breast epithelial cells (HBECs), none of them are able to support the growth of ER-positive HBECs (page 7, left col. last para.). Fridriksdottir teaches that in an attempt to overcome the loss of receptor expression, ER has been ectopically introduced into breast cell lines but these cells show growth inhibition instead of responding to estrogen as expected (page 2, left col. para. 2). Fridriksdottir teaches most of our current knowledge of ER expression, regulation and action comes from breast carcinoma cell lines, whose relation to ER-positive normal breast cells at best remains elusive (page 2, left col. para. 2). Fridriksdottir teaches in culture medium that allowed luminal cells to be maintained after passaging, endogenous ER expression disappeared (page 2, left col. para. 1). Fridriksdottir teaches knowledge about how to turn on and off the ER expression in non-malignant breast epithelial cells may offer an alternative to selective ER modulators in prevention of breast cancer in women with elevated risk of disease; a reproducible source of normal human ER-positive HBECs will represent a first step towards a physiological, cell-based screen for environmental estrogenic activity and susceptibility of normal cells to breast cancer; and the protocol may serve to test the functional role of single-nucleotide polymorphisms associated with increased risk of breast cancer (page 9, left col. last para. and right col. para. 1).
Regarding “a 3D matrix with storage modulus of at least about 10 kPa” of claim 1 and 15 “substantially gelled” and “bioinert” of claim 3 and 16 and “agarose” of claim 11 and 17, Kinder teaches culturing estrogen positive breast cancer cells in a 3D format within an agarose matrix (“3D matrix” of claim 1 and 15 and “agarose of claim 11 and 17) and the agarose was refrigerated to allow the agarose to gel (the 3D matrix is substantially gelled, and/or the 3D medium and/or matrix is bioinert” of claim 3 and 16) (Abstract; page 49, right col.; page 50, left col. para. 3). Kinder teaches resuspending the cells in 0.5% agarose and plating the suspension on 1% agarose (page 50, left col. para. 3).
Regarding claim 7, Kinder teaches culturing cells in the 3D agarose matrix with etodolac which caused necrosis and apoptosis (page 50, left col. para. 3; page 52, right col. para. 1; page 53, left col. para. 2; Figure 2 – 3).
Regarding “chondrocytes” of claim 14, Kinder teaches the breast cells were grown in agarose using the same method as for chondrocytes (page 49, right col.; page 50, left col. para. 3). Roberts
Kinder does not teach a storage modulus of 10 kPa of claim 1 and 15 or the storage modulus is “achieved by using external mechanical compression” of claim 10. However, Kinder teaches growing the cells in 3D resembles the 3D growth patterns found in cancerous tumors (page 49, right col.; page 52, left col. para. 2). Kinder teaches cells in 3D treated with the drug etodolac were adversely affected at concentrations below that necessary to see an effect in monolayer (page 49, right col. last para.; page 50, left col. para. 1 and 3 and right col. para. 1). Kinder teaches the method circumvents the growth characteristics of monolayer cultures by allowing 3D growth habits and longer experiment times which seems ideal for studying compounds or drugs that are slow to demonstrate their effects (page 53, left col. para. 4). One would have been motivated to combine the teachings of Fridriksdottir and Kinder because both teach methods for better understanding of breast cells.
Regarding a 3D matrix with storage modulus of at least about 10 kPa” of claim 1 and 15 and the storage modulus is “achieved by using external mechanical compression” of claim 10, Roberts teaches a 1% agarose hydrogel with storage modulus of 14.7 – 112 kPa depending on the frequency during compression (Table I). Roberts teaches agarose hydrogels of 1% that were immersed in PBS at room temperature on a compression tester and compression testing was performed at 5% strain per 50 milliseconds to measure the storage modulus (page 160, left col. para. 2 and right col. para. 3 – 4; page 161, right col. last para.; page 162, left col. para. 1). Roberts teaches hydrogels are attractive biomaterials for numerous medical applications (page 158, left col. para. 1). Roberts teaches hydrogels recapitulate the 3D environment of native tissue and are particularly attractive for cartilage tissue engineering because they maintain the rounded chondrocyte morphology (page 158, left col. para. 1). Roberts teaches in Table 1 that as the percentage of agarose increases, the storage modulus increases at a given frequency. As Kinder teaches cells in a 3D matrix of 1.5% agarose (page 50, left col. para. 3) and Roberts teaches 1% agarose has a minimal storage modulus of 14.7 kPa in Table 1, the agarose of Kinder has a storage modulus of at least 10 kPa.
It would have been obvious prior to the effective filing date of the invention as claimed for the person of ordinary skill in the art to combine the teachings of Fridriksdottir regarding a method of culturing mammalian primary mammary cells to maintain ER expression with the teachings of Kinder regarding culturing breast cells in a 3D matrix of agarose of 1.5% agarose with the teachings of Roberts regarding 1% agarose has a storage modulus of 14.7 – 112 kPa to arrive at the claimed method comprising culturing a mammalian primary mammary cell or tissue in a 3D matrix with storage modulus of at least 10 kPa. One would have been motivated to combine the teachings of Fridriksdottir, Kinder, and Roberts in a method of culturing primary mammary cells to recapitulate in vivo growth as Fridriksdottir teaches knowledge about how to turn on and off the ER expression in non-malignant breast epithelial cells may offer an alternative to selective ER modulators in prevention of breast cancer in women with elevated risk of disease; a reproducible source of normal human ER-positive HBECs will represent a first step towards a physiological, cell-based screen for environmental estrogenic activity and susceptibility of normal cells to breast cancer; and the protocol may serve to test the functional role of single-nucleotide polymorphisms associated with increased risk of breast cancer and Kinder teaches growing the cells in 3D resembles the 3D growth patterns found in cancerous tumors and Roberts teaches hydrogels recapitulate the 3D environment of native tissue. One would have a reasonable expectation of success in combining the teachings as Fridriksdottir teaches the cells lose the ER protein in culture but the addition of TGFβ inhibitors (TGFβR2i) recapitulated ER expression and Kinder teaches the method circumvents the growth characteristics of monolayer cultures by allowing 3D growth habits and longer experiment times which seems ideal for studying compounds or drugs that are slow to demonstrate their effect.
Conclusion
No claims allowed.
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/Z.M.B./Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632