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 .
Status of the Claims
Claims 1-5, 7-9, and 18-20 are pending.
Claims 1-2, 5, and 18 are newly amended.
Claims 18-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 12/27/2022.
Claims 1-5 and 7-9 have been examined on their merits.
Withdrawn Objections & Rejections
The objections and rejections presented herein represent the full set of objections and rejections currently pending in the application. Any objections or rejections not specifically reiterated are hereby withdrawn. The rejections, have been maintained but modified to address the new limitations. Prior objections have been addressed by amendment.
The rejection of claims 1 and 7-8 under 35 U.S.C. 103 as unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited), Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), and Yin et al. (Nature Methods, 2014) is withdrawn to address the claims as amended.
The rejection of claims 2-4 under 35 U.S.C. 103 as unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited), Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), and Yin et al. (Nature Methods, 2014), as applied to claim 1 above, and further in view of Vallier et al. (US 20160237401 A1, 2016, previously cited) as evidenced by Thermo Fisher RPMI 1640 (Retrieved from internet 03/15/2023, previously cited) is withdrawn to address the claims as amended.
The rejection of claim 5 under 35 U.S.C. 103 as being unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019) and of Vallier et al. (US 20160237401 A1, 2016, previously cited), as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited), Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), Yin et al. (Nature Methods, 2014), and Thermo Fisher RPMI 1640 (Retrieved from internet 03/15/2023, previously cited), as applied to claims 1 and 4 above, and further in view of Higuchi et al. (PLOS ONE, 2015, previously cited) is withdrawn to address the claims as amended.
The rejection of claim 9 under 35 U.S.C. 103 as being unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited), Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), and Yin et al. (Nature Methods, 2014), as applied to claim 1 above, and further in view of Nossol et al. (Histochem Cell Biol, 2011, previously cited) is withdrawn to address the claims as amended.
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 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.
Claims 1 and 7-8 are rejected under 35 U.S.C. 103 as unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019, previously cited) and Spence et al. (Nature, 2011) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited) and Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited).
In regards to claims 1 and 7-8, Tong teaches methods for expanding and differentiating (preparing) monolayers of Lgr5+ intestinal stem cells (Abstract, p60; Fig. 1, p63) (intestinal epithelial cell progenitors (see instant specification, p15, lines 7-16).
Tong teaches that this method comprises culturing cells in ENR media, which as evidenced by Tamminen comprises EGF (Formation of organoids from hindgut cells is independent of R-spondin 1, p9). Continuing, Tong teaches that the media can be supplemented with a Wnt inhibitor and valproic acid (VPA, a Notch activator) (p67, column 2, last paragraph; Figure 5, p69).
As taught by Tong, ENR media alone is known to drive simultaneous differentiation of intestinal stem cells into multiple lineages including enterocytes, goblet cells, enteroendocrine cells, and Paneth cells differentiated from ENR media alone (p67, right column, bottom paragraph; Supp Table 3, supp p3).
Moreover, as demonstrated by Tong, culturing intestinal epithelial progenitor cells in ENR with IWP-2 (Wnt inhibitor) and VPA (Notch activator), still results in expression of markers Alpi, ChgA, Lyz1, and Muc2 (Fig. 5, p69) which Tong identifies are markers for enterocytes (Alpi), enteroendocrine (ChgA), goblet cells (Muc2), and Paneth cells (Lyz1). Therefore, the claimed cells are present in the method of Tong.
While Tong uses Wnt inhibitor IWP-2 specifically (p67, column 2, last paragraph; Figure 5, p69), as taught by Halloin, IWP-2 and Wnt-C59 are both known in the art to be suitable for inhibiting Wnt signaling in vitro (Introduction, p366), and are therefore, art recognized equivalents for the same purpose. According to MPEP 2144.06, it is prima facie obvious to substitute equivalents known for the same purpose. Moreover, a person of ordinary skill in the art would have been motivated to choose Wnt-C59 because Halloin teaches that it has greater differentiation efficiency compared to IWP-2 (p371, left column; Fig. 4, p371). Additionally, because Halloin teaches that cells can be cultured alike with IWP-2 and Wnt-C59 (p371, left column; Fig. 4, p371), it could have been done with predictable results and a reasonable expectation of success.
In regards to the types of cells used, the Lgr5+ cells as taught by Tong are derived from gut biopsies of either mouse or human intestinal crypts (Materials and Methods, p61-62). While these cells are derived from pluripotent stem cells (as evidence by Miquel, pluripotency is defined as the potential of a cell to differentiate into cells of the three germ layers: endoderm, mesoderm, and ectoderm, and that these cells give rise to any fetal or adult cell type (Mammalian Early Development, p633). Thus, as all cells ultimately derived from pluripotent stem cells, the cells of Tong are also derived from pluripotent stem cells), they derive from gut biopsies not by culturing endoderm cells differentiated in vitro from PSCs.
However, methods for differentiating intestinal epithelial cells progenitors from endoderm derived from PSCs in vitro was known in the art before the effective filing date and a person of ordinary skill in the art would have been motivated to use intestinal epithelial cells progenitors from endoderm derived from PSCs in vitro (e.g., from induced pluripotent stem cells) because tissue biopsies are invasive and would want to avoid harming patients/subjects.
Furthermore, Spence teaches specific methods of deriving intestinal epithelial progenitor cells from human induced pluripotent stem cells which involves differentiation of endoderm in vitro (Title, Abstract, p1; p4 top paragraph; Fig. 3, p11). Spence also teaches that these cells were able to differentiate into all major cell lineages of the gut including enterocytes, Goblet cells, enteroendocrine cells, and Paneth cells (p4). Therefore, a person of ordinary skill in the art could have modified the method of Tong and derive intestinal epithelial cells from endoderm derived from PSCs in vitro with predictable results and a reasonable expectation of success.
In regards to the specific animal, Tong teaches that both human and mouse intestinal epithelial cells were used in their experiments (Abstract, p60; Figure 1, p63). While it is unclear if human or mouse cells were specifically used in the experiments, in the event that Tong does not teach that the cells used the experiments were human cells specifically, a person of ordinary skill in the arts would have been motivated to choose human intestinal epithelial cells because it would be most relevant to studying or treating human disease. Furthermore, because Tong teaches that their experiments could employ both human and mouse cells (Abstract, p60; Figure 1, p63) and because, as above, Spence teaches that intestinal epithelial cells can be derived from human induced pluripotent stem cells, a person of ordinary skill in the art could have used human cells specifically with predictable results and a reasonable expectation of success.
Therefore, the teachings of Tong, Halloin, and Spence render obvious the invention as claimed.
Claims 2-4 are rejected under 35 U.S.C. 103 as unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019, previously cited) and Spence et al. (Nature, 2011) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited) and Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), as applied to claim 1 above, and further in view of Vallier et al. (US 20160237401 A1, 2016, previously cited) as evidenced by Thermo Fisher RPMI 1640 (Retrieved from internet 03/15/2023, previously cited).
In regards to claims 2-4, as discussed above, while Tong teaches that the intestinal epithelial cell progenitors are derived from biopsies, these cells are still derived from pluripotent stem cells as discussed above.
However, in as much as Applicant intends to imply an induced pluripotent stem cell (as suggested in claims 2-4 which are methods for inducing pluripotent stem cells), a person of ordinary skill in the arts would have been motivated to modify the method of Tong and derive human pluripotent intestinal epithelial cells from induced hPSCs because, as taught by Vallier, numerous cultured hESCs lines are publicly available from repositories (paragraph [0033]), and using cell lines would eliminate the need to invasively take biopsy samples from humans. Furthermore, because Vallier teaches that stem cell lines are readily available, and teaches methods for inducing human pluripotent intestinal epithelial cells from hESCs or hiPSCs to form endoderm (Fig. 4; paragraph [0025]) discussed in depth below), it could have been done with predictable results and a reasonable expectation of success.
Additionally, methodologically, for derivation of intestinal epithelial progenitors, Vallier teaches that this method comprises culturing hPSCs through definitive endoderm to hindgut endoderm that can further differentiate into intestinal epithelium which can be patterned to hindgut endoderm that can differentiate into intestinal epithelium (paragraph [0025]; Fig. 4).
In regard to claims 2-3, Vallier also teaches that the method comprises culturing endoderm in media comprising R-spondin and EGF supplemented with B27 (which itself comprises insulin) (paragraph [0222]).
Additionally, Vallier teaches that definitive endoderm can be induced by culturing cells in RMPI medium supplemented with Activin A (paragraph [0066]). As evidenced by Thermo Fisher RPMI 1640, RPMI medium requires supplementation, and usually with 10% FBS (Using RPMI, second page). Therefore, Vallier suggests that media conditions comprise FBS.
Furthermore, Vallier teaches that the hPSCs can be either hESCs and hiPSCs (paragraph [0219]).
A person of ordinary skill in the art would have been motivated to utilize the method of Vallier for derivation of human pluripotent stem cells because Vallier indicates that the method is useful for the in vitro production of endoderm cells for research and therapeutic applications and can establish heterogeneous populations of cells (paragraph [0011]), which addresses the issue of inconsistencies in cell populations by other methods (paragraph [0002]). Furthermore, because Vallier teaches methods for differentiation of endoderm cells from human pluripotent stem cells, as discussed above, it could have been done with predictable results and a reasonable expectation of success.
Therefore, the combined teachings of Tong, Halloin, Spence, and Vallier renders obvious the invention as claimed.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019, previously cited) and Spence et al. (Nature, 2011) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited) and Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), as applied to claims 1 and 4 above, and further in view of Higuchi et al. (PLOS ONE, 2015, previously cited).
In regards to claim 5, as discussed above, Tong teaches that the human pluripotent intestinal epithelial cells were obtained from gut biopsy (Figure 1, p63). As above, Vallier teaches that human pluripotent intestinal epithelial may be derived from hESCs or iPSCs (paragraph [0219]). While Vallier also teaches that hESCs or iPSCs may derive from fibroblasts (paragraph [0034]), Vallier does not explicitly teach where the fibroblasts may be derived.
However, Higuchi teaches that fibroblasts are the principal stromal cells that exist in whole organs (Background, p1). Higuchi also teaches that compared to fibroblasts from other parts of the body, gastrointestinal fibroblasts are distinguished by their gene expression patterns (Introduction, p1; Figure 2, p8). A person of ordinary skill in the arts would have been motivated to modify the method of Tong, as suggested by Vallier, and use fibroblasts derived from intestinal tissues specifically because their gene expression profiles suggest that they are especially suited for an intestinal niche and would therefore be more ideal for differentiation into intestinal cell types. Furthermore, because Higuchi indicates that human fibroblasts can readily be obtained from intestinal tissue (Isolation and primary culture of fibroblasts, p3) and because as taught by Vallier, it is known in the art that iPSCs can be derived from fibroblasts, it could have been done with predictable results and a reasonable expectation of success.
Therefore, the combined teachings of Tong, Halloin, Spence, Vallier, and Higuchi renders the invention unpatentable as claimed.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Tong et al. (Biomaterials, 2018, previously cited) in view of Halloin et al. (Stem Cell Reports, 2019, previously cited) and Spence et al. (Nature, 2011) as evidenced by Tamminen et al. (PLOS ONE, 2015, previously cited) and Miquel et al. (Stem Cell Rev and Rep, 2010, previously cited), as applied to claim 1 above, and further in view of Nossol et al. (Histochem Cell Biol, 2011, previously cited).
In regards to claim 9, Tong teaches the cells cultured in a transwell system (see Fig. 1), and does not explicitly teach that the human pluripotent intestinal epithelial cells were exposed to air.
However, Nossol teaches that the specific function of the epithelium, as a critical barrier between the intestinal lumen and the organism’s internal microenvironment, is reflected by permanent maintenance of intercellular junctions and cellular polarity (Abstract, p103). Nossol continues that the intestinal epithelial cells are responsible for absorption of nutritional components, facing mechanical stress and changing oxygen supplementation via blood stream, and that oxygen itself can regulate the barrier and the absorptive function of the epithelium (Abstract, p103). To more accurately recapitulate the in vivo environment, Nossol devised a method that exposes intestinal epithelial cells to an oxygen enriched air-liquid interface, in vitro (ALI culture) (Abstract, p103). Compared to other methods, Nossol teaches that the ALI culture resulted in a significant increase in cell number, epithelial cell layer thickness, and expression and apical localization of the microvilli-associated protein villin (Abstract, p103). Nossol also teaches that functional analysis of protein uptake and degradation by epithelial cells cultured by this method demonstrates that the ALI system provides the necessary oxygen supply needed by cells (Abstract, p103). Moreover. Nossol teaches that the ALI system directly affects morphological differentiation and functional properties of intestinal cells in vitro (Abstract, p103).
Therefore, a person of ordinary skill in the arts would have been motivated to modify the method of Tong and add a step of exposing the human pluripotent intestinal epithelial cells because it would improve cell numbers, differentiation, and provide the oxygen needed to most accurately recapitulate an in vivo setting. Furthermore, because Nossol provides specific methods for culturing intestinal epithelial cells in air-liquid interface culture (Materials and methods, p104) and Tong and Nossol are in the same technical field of culturing intestinal epithelial cells, it could have been done with predictable results and a reasonable expectation of success.
Therefore, the combined teachings of Tong, Halloin, Spence, and Nossol renders the invention unpatentable as claimed.
Response to Arguments
Applicant argues that Tong does not teach a step of obtaining human intestinal epithelial progenitors by culturing endoderm cells differentiated from hPSCs as in amended claim 1 (Remarks, p6).
Applicant’s arguments filed 01/09/2026 have been fully considered but are not found persuasive.
As discussed above, while the intestinal epithelial progenitors as taught by Tong derive from tissue biopsies, methods for differentiating intestinal epithelial cells progenitors from endoderm derived from PSCs in vitro was known in the art before the effective filing date, and a person of ordinary skill in the art would have been motivated to use intestinal epithelial cells progenitors from endoderm derived from PSCs in vitro (e.g., from induced pluripotent stem cells) because tissue biopsies are invasive and would want to avoid harming patients/subjects.
Furthermore, Spence teaches specific methods of deriving intestinal epithelial progenitor cells from human induced pluripotent stem cells which involves differentiation of endoderm in vitro (Title, Abstract, p1; p4 top paragraph; Fig. 3, p11). Spence also teaches that these cells were able to differentiate into all major cell lineages of the gut including enterocytes, Goblet cells, enteroendocrine cells, and Paneth cells (p4). Therefore, a person of ordinary skill in the art could have modified the method of Tong and derive intestinal epithelial cells from endoderm derived from PSCs in vitro with predictable results and a reasonable expectation of success.
Therefore, in response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Applicant argues that the instant invention is a single medium comprising EGF, a Wnt inhibitor, and a Notch activator that yields a population including enterocytes, goblet cells, enteroendocrine cells, and Paneth cells (Remarks, p7). However, Applicant argues that Tong expressly uses different cocktails for obtaining different specific lineages (e.g., IWP-2 + VPA for enterocytes) and therefore, teaches away from the claimed invention (Remarks, p7).
Applicant also argues that Yin further explains that Wnt inhibition with IWP-2 preferentially induced Alpi expression and completely abolished Lyz1 expression, Wnt signaling being required for Paneth cell differentiation (Remarks, p7-8). Applicant further argues that the Office’s reliance on the fact that ENR-alone induces the differentiation of these cells is misplaced because it contains neither the Wnt inhibitor nor the Notch activator as required by claim 1 (Remarks, p8).
Applicant’s arguments filed 01/09/2026 have been fully considered but are not found persuasive.
As discussed above, as taught by Tong, ENR media alone is known to drive simultaneous differentiation of intestinal stem cells into multiple lineages including enterocytes, goblet cells, enteroendocrine cells, and Paneth cells differentiated from ENR media alone (p67, right column, bottom paragraph; Supp Table 3, supp p3).
Moreover, as demonstrated by Tong, culturing intestinal epithelial progenitor cells in ENR with IWP-2 (Wnt inhibitor) and VPA (Notch activator), still results in expression of markers Alpi, ChgA, Lyz1, and Muc2 (Fig. 5, p69) which Tong identifies are markers for enterocytes (Alpi), enteroendocrine (ChgA), goblet cells (Muc2), and Paneth cells (Lyz1).
Therefore, the claimed cells are present in the method of Tong.
In regards to the different cocktails, as taught by Tong, these different cocktails only elevate specific markers (and therefore, enrich or bias the proportions of intestinal cellular lineage cells as compared to ENR alone, see Supp Table 3), but the claims do not require specific percentages or proportions of intestinal lineage cells.
Therefore, the ENR + IWP2 + VPA medium of Tong still results in enterocytes, goblet cells, enteroendocrine cells, and Paneth cells as claimed.
In regards to Yin, the reference agrees with the findings of Tong. Specifically, as evidenced by Yin, “+IV” conditions (with a Wnt inhibitor and Notch activator) with ENR still result in expression of all of Alpi, Muc2, ChgA, and Lyz1 (Fig. 3b, p109). Therefore, a person of ordinary skill in the art would have recognized that Yin’s statement that “Wnt inhibition with IWP-2 preferentially induced Alpi expression, with modestly elevated Muc2 and Chga expression and completely abolished expression and completely abolished Lyz1 and Lgr5” (p109) is not literal, but rather refers to relative decreased expression compared to other markers, but that there are still some Paneth cells (even if in small numbers) in this population.
In regards to Applicant’s assertions that Tong is “teaching away” from the claimed invention, see MPEP 2123(II), preferred embodiments do not constitute a teaching away from a broader disclosure or nonpreferred embodiments. In re Susi, 440 F.2d 442, 169 USPQ 423 (CCPA 1971). Furthermore, ‘[t]he prior art’s mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed...." In re Fulton, 391 F.3d 1195, 1201, 73 USPQ2d 1141, 1146 (Fed. Cir. 2004).
In the instant case, Tong does not criticize, discredit, or otherwise discourage the solution claimed and indeed, as discussed above, the method of Tong still produces all of the claimed cells.
Applicant argues that none of Halloin, Vallier, Nossol, Higuchi, Thermo Fisher RPMI 1640 cures the cited deficiency (Remarks, p7).
Applicant’s arguments filed 01/09/2026 have been fully considered but are not found persuasive because Tong is not deficient for the reasons discussed above.
Applicant requests rejoinder (Remarks, p8).
Applicant’s request it noted, but is premature because the claims are still prima facie obvious as discussed above.
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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/JOSEPH PAUL MIANO/Examiner, Art Unit 1631
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