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
Newly submitted claims 22-23 are directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: The methods of claims 22-23, while including reprogramming steps, are ultimately differentiation methods that results in a distinctly different cell type than the elected reprogramming method.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claims 22-23 are withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
Claims 1-3 and 7-10 are under consideration in this office action.
Withdrawn Objection/Rejections
The objection to claim 1 is withdrawn. The amendments to the claim adopt the suggested correction provided in the previous office action.
The rejection of claims 1-3, 7-10, and 12, 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention, is withdrawn. The amendments to the claims overcome this rejection.
Claim Rejections - 35 USC § 103
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.
(1) Claims 1-3, 7-10 and 12, as amended, originally presented or previously presented, are rejected under 35 U.S.C. 103 as being unpatentable over Noggle et al., 2022 (US 20220073884 A1, effective filing date, 6-27-14) (ref. of record) in view of Morrell et al., 2012 (WO 2012/131387 A1) (ref. of record) in further view of Uhlin et al. (Journal of Visualized Experiments, 2017, 125).
Regarding claim 1, Noggle teaches automated methods for obtaining, generating, culturing and handling cells such as induced pluripotent stem cells (iPSCs) (abstract; [0009]). Dermal fibroblasts derived from patient tissue samples were maintained in Complete M106 media before being changed into antibiotic free M106 media. Cells were passaged using TrypLE CTS into 6 well plate and maintained in Complete M106 until reaching ideal freezing confluence. Upon reaching freezing confluence, each well was passaged using TrypLE Select CTS, pooled and resuspended in freezing medium. Three aliquots of the resuspended cell suspension were transferred into three 2D barcoded Matrix tubes (a first expansion step comprising at least one medium change having a first growth medium and at least a division of the plurality of fibroblasts into multiple vessels; and a second expansion step comprising at least one medium change having a second growth medium and at least a replating of the plurality of fibroblast cells) ([0435-0438]. The expanded plurality of fibroblast cells were cryopreserved (frozen) in Syntha-a-Freeze medium (first freezing medium) [0438]. Cells were thawed, fibroblast growth medium was added to each vial, centrifuged, supernatant was removed and the fibroblasts were resuspended in fresh media before being transferred to 12-well plates (thawing the expanded plurality of fibroblasts cells, wherein thawing the expanded plurality of fibroblast cells comprises at least one medium change and at least a replating of the thawed expanded plurality of fibroblast cells [0439].
Fibroblasts were reprogrammed by delivering a polynucleotide encoding reprogramming factors Oct4, Sox2, Klf4 and c-Myc and performing medium exchanges, thus generating a plurality of iPSC [0080; 0330; 0341]. Noggle describes using probes for human Oct4, Sox2, and KLF4 [0344]. Therefore, Noggle teaches the human gene of the reprogramming factors. After reprogramming, the generated iPSCs were expanded in 2D culture medium (Freedom media, feeder-free cell culture medium, #A14577SA) [0404] [0442] and samples were selected robotically cherry-picked based upon growth rates and well confluency levels [0426; 0444]. Cells are resuspended in Synth-a-Freeze freezing medium and stored at -80ºC before being transferred to liquid nitrogen for long term storage [0446].
Regarding claim 2, Noggle teaches the reprogramming factor refers to a developmental potential altering factor such as RNA [0080]. Regarding claim 3, the fibroblasts used by Noggle are obtained from skin biopsies [0107]. Regarding claims 8 and 9, the polynucleotide encoding a reprogramming factor is delivered to the fibroblast cells via a viral vector, including a Sendai vector [0256]. Regarding claims 10 and 12, Noggle teaches that after wells with uniform confluence values were identified, three candidate wells per sample were selected and consolidated for expansion and further quality control assays, e.g., flow cytometry analysis; gene expression assays using a panel of pluripotency marker gene (NANOG, POU5F1, LIN28, ZPF42, SOX2) [0408].
Noggle fails to teach transferring the plurality of fibroblast cells to a reprogramming medium comprising a vitamin C derivative, as recited in claim 1. While Noggle teaches transferring the plurality of fibroblast cells to a vessel comprising a 2D culture medium, Noggle fails to teach that the vessel also comprises an extracellular protein matrix comprising a laminin matrix.
However, regarding the vitamin C derivative, Morrell teaches the use of late out-growth endothelial progenitor cells (L-EPCs) as a cellular substrate for the generation of induced pluripotent stem cells (iPSCs) (Abstract). Several improvements in the efficiency of iPSC generation have been reported since their inception and vitamin C has been shown to increase the reprogramming efficiency of skin fibroblasts to varying degrees (e.g., p. 1, line 32 to p. 2, line 4). Reprogramming promoting agents, such as methylation and deacetylation inhibitors, modified RNAs, valproic acid and vitamin C may be used to increase reprogramming efficiency further (e.g., p. 16, lines 32-35).
With respect to the extracellular protein matrix comprising a laminin matrix, Uhlin describes a protocol to generate hiPS cells from fibroblasts. Uhlin teaches that utilizing the defined recombinant laminin 521 matrix in combination with xeno-free and defined media formulations reduces variability and allows for consistent generation of hiPS cells (abstract). Uhlin uses the extracellular matrix comprising a laminin matrix in the transduced fibroblast expansion step (step 2.3).
Accordingly, it would have been obvious to one of ordinary skill in the art at the effective filing date of the claimed invention to combine the teachings of Noggle regarding a method of reprogramming fibroblast cells with the teachings of Morrell regarding the use of reprogramming-promoting agents such as Vitamin C, to arrive at the invention as claimed. One would have been motivated to combine Noggle with Morrell since Morrell taught that the addition of vitamin C improves and increases reprogramming efficiency and thus, iPSC generation. A person of ordinary skill would have had a reasonable expectation of success since Morrell teaches incorporating Vitamin C in a method of reprogramming cells to generate iPSCs.
Similarly, it would have been obvious to expand the fibroblast cells using an extracellular matrix comprising a laminin matrix since the prior art taught that incorporating laminin matrix in combination with a xeno-free, defined medium in a protocol for reprogramming fibroblast cells generated hiPS cells consistently while reducing variation, as taught by Uhlin. Therefore, one of ordinary skill in the art would have been motivated to modify Noggle’s method of reprogramming cells by including a laminin matrix as taught in Uhlin’s protocol, to arrive at an improved method of generating hiPS cells.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made, especially in the absence of evidence to the contrary.
(2) Claims 1-3, 7-10 and 12, as amended, originally presented, or previously presented are rejected under 35 U.S.C. 103 as being unpatentable over Noggle et al., 2022 (US 20220073884 A1, effective filing date, 6-27-14) (ref. of record) in view of Morrell et al., 2012 (WO 2012/131387 A1) (ref. of record) in further view of Couchman (Couchman et al. JCB 96:177-182, 1983).
Regarding claim 1, Noggle teaches automated methods for obtaining, generating, culturing and handling cells such as induced pluripotent stem cells (iPSCs) (abstract; [0009]). Dermal fibroblasts derived from patient tissue samples were maintained in Complete M106 media before being changed into antibiotic free M106 media. Cells were passaged using TrypLE CTS into 6 well plate and maintained in Complete M106 until reaching ideal freezing confluence. Upon reaching freezing confluence, each well was passaged using TrypLE Select CTS, pooled and resuspended in freezing medium. Three aliquots of the resuspended cell suspension were transferred into three 2D barcoded Matrix tubes (a first expansion step comprising at least one medium change having a first growth medium and at least a division of the plurality of fibroblasts into multiple vessels; and a second expansion step comprising at least one medium change having a second growth medium and at least a replating of the plurality of fibroblast cells) ([0435-0438]. The expanded plurality of fibroblast cells were cryopreserved (frozen) in Syntha-a-Freeze medium (first freezing medium) [0438]. Cells were thawed, fibroblast growth medium was added to each vial, centrifuged, supernatant was removed and the fibroblasts were resuspended in fresh media before being transferred to 12-well plates (thawing the expanded plurality of fibroblasts cells, wherein thawing the expanded plurality of fibroblast cells comprises at least one medium change and at least a replating of the thawed expanded plurality of fibroblast cells [0439].
Fibroblasts were reprogrammed by delivering a polynucleotide encoding reprogramming factors Oct4, Sox2, Klf4 and c-Myc and performing medium exchanges, thus generating a plurality of iPSC [0080; 0330; 0341]. Noggle describes using probes for human Oct4, Sox2, and KLF4 [0344]. Therefore, Noggle teaches the human gene of the reprogramming factors. After reprogramming, the generated iPSCs were expanded in 2D culture medium (Freedom media, feeder-free cell culture medium, #A14577SA) [0404] [0442] and samples were selected robotically cherry-picked based upon growth rates and well confluency levels [0426; 0444]. Cells are resuspended in Synth-a-Freeze freezing medium and stored at -80ºC before being transferred to liquid nitrogen for long term storage [0446].
Regarding claim 2, Noggle teaches the reprogramming factor refers to a developmental potential altering factor such as RNA [0080]. Regarding claim 3, the fibroblasts used by Noggle are obtained from skin biopsies [0107]. Regarding claims 8 and 9, the polynucleotide encoding a reprogramming factor is delivered to the fibroblast cells via a viral vector, including a Sendai vector [0256]. Regarding claims 10 and 12, Noggle teaches that after wells with uniform confluence values were identified, three candidate wells per sample were selected and consolidated for expansion and further quality control assays, e.g., flow cytometry analysis; gene expression assays using a panel of pluripotency marker gene (NANOG, POU5F1, LIN28, ZPF42, SOX2) [0408].
Noggle fails to teach transferring the plurality of fibroblast cells to a reprogramming medium comprising a vitamin C derivative, as recited in claim 1. While Noggle teaches transferring the plurality of fibroblast cells to a vessel comprising a 2D culture medium, Noggle fails to teach that the vessel also comprises an extracellular protein matrix comprising a laminin matrix.
However, regarding the vitamin C derivative, Morrell teaches the use of late out-growth endothelial progenitor cells (L-EPCs) as a cellular substrate for the generation of induced pluripotent stem cells (iPSCs) (Abstract). Several improvements in the efficiency of iPSC generation have been reported since their inception and vitamin C has been shown to increase the reprogramming efficiency of skin fibroblasts to varying degrees (e.g., p. 1, line 32 to p. 2, line 4). Reprogramming promoting agents, such as methylation and deacetylation inhibitors, modified RNAs, valproic acid and vitamin C may be used to increase reprogramming efficiency further (e.g., p. 16, lines 32-35).
With respect to the extracellular protein matrix comprising a laminin matrix, four decades before the effective filing date, Couchman teaches that human fibroblast cultured on laminin substrate show cell spreading with formation of focal adhesions and microfilament bundles. Couchman teaches that such cell spreading is a prerequisite for fibroblast proliferation and further teaches that fibroblast cultured on laminin substrate facilitated fibroblast proliferation (paragraph bridging pp. 177-178; p. 80 col 1 last paragraph; Figure 7; and p. 182, col 2, last paragraph).
Accordingly, it would have been obvious to one of ordinary skill in the art at the effective filing date of the claimed invention to combine the teachings of Noggle regarding a method of reprogramming fibroblast cells with the teachings of Morrell regarding the use of reprogramming-promoting agents such as Vitamin C, to arrive at the invention as claimed. One would have been motivated to combine Noggle with Morrell since Morrell taught that the addition of vitamin C improves and increases reprogramming efficiency and thus, iPSC generation. A person of ordinary skill would have had a reasonable expectation of success since Morrell teaches incorporating Vitamin C in a method of reprogramming cells to generate iPSCs.
Similarly, it would have been obvious to expand the fibroblast cells in the first and/or second fibroblast expansion steps taught by Noggle by culturing the fibroblasts on an extracellular matrix comprising a laminin matrix, taught by Couchman to arrive at the limitations of the claims. One would have a reasonable expectation of success in expanding the fibroblast on laminin because Couchman teaches that such expansion cultures were successfully being done for 4 decades. Therefore, one of ordinary skill in the art would have been motivated to modify Noggle’s expansion step(s) to include a laminin matrix as taught in Couchman’s protocol, because laminin matrix allows for requisite fibroblast cell spreading and facilitates fibroblast proliferation, as taught by Couchman.
Therefore, the invention as a whole was prima facie obvious to one of ordinary skill in the art at the time the invention was made, especially in the absence of evidence to the contrary.
Response to Arguments
Applicant's arguments filed 12/15/2025 have been fully considered but they are not persuasive.
Applicant traverses the 103 rejection, Noggle in view of Morrel and Uhlin. Applicant submits that Uhlin only applies laminin once, beginning at post-infection day 7 and solely during iPSC expression. In contrast, Uhlin does not discloses or suggest using laminin during fibroblast expansion. Applicant submits that the claims overcome the indefiniteness rejection and now clearly recite two uses of laminin and Uhlin only uses it once.
In response, Applicant’s argument is not found persuasive because Applicant is not giving the claims their broadest reasonable interpretation. Examiner acknowledges that the amendments clarify the claims and the amendments clarify the expanding of a plurality of iPSC in the wherein clause that is recited in that step. The second expansion step is recited in a “wherein” clause as well. Regarding “wherein” clauses, the MPEP § 2111.04 states:
Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure. However, examples of claim language, although not exhaustive, that may raise a question as to the limiting effect of the language in a claim are:
(A) “adapted to” or “adapted for” clauses;
(B) “wherein” clauses; and
(C) “whereby” clauses.
Since the second expansion step is part of a “wherein” cause, as is the first expansion step, these first and second expansion are questionably limiting to the active step stating “expanding the plurality of fibroblasts”, given its broadest reasonable interpretation. The first and second expansion steps being present in a wherein clause would not be considered active steps in the methods and therefore would need to be considered as descriptive to the outcome of the active step “expanding the plurality of fibroblast cells”. This active step does not describe any other outcome, other than expanding the plurality of fibroblast cells. As such, any means that would result in expansion of the plurality of fibroblast cells, regardless of whether there is an expansion on laminin of the fibroblast, would meet the limitations the active expanding the plurality of fibroblast cells because expansion (i.e. growing more fibroblasts) is all that is required. As such, given the broadest reasonable interpretation of the claims, Uhlin is not required to teach expansion of the fibroblast on laminin because it is not necessarily required to achieve the active step of expanding as claimed and Noggle already teaches the active step of “expanding a plurality of fibroblast cells”. Thus the rejection of record still renders obvious the limitations of the claims because the active steps of the method are taught by combined cited prior art, given that the wherein clauses do not necessarily further limit the claims.
Applicant traverses the 103 rejection with Noggle in view of Morrel, and Couchman. Applicant submits Couchman predates the development of human iPSC technology and is directed solely to characterizing fibroblast behavior on laminin substrate. Examiner’s position assumes that because laminin enhances fibroblast adhesion and proliferation, it would inherently be beneficial to a reprogramming method. Applicant submits that proliferative conditions exhibit reduced capacity to transition towards iPSC. Applicant refers to Gupta et al stating, there is “an inverse correlation between the proliferation rate of somatic cells [e.g. fibroblasts] and reprogramming efficiency” and that enhanced growth factor signaling “limiting the ability to induce pluripotency in human somatic fibroblasts”. Laminin’s established role in promoting fibroblast proliferation would therefore be counterproductive during reprogramming expansion and early stages of reprogramming, which is expected to undermine rather than facilitate the ability of these somatic cells to respond to reprogramming factors.
In response, Applicant is not considering the broadest reasonable interpretation of the claims and is reading limitations into the claims that are not required. First, as discussed above in the rejection with Noggle in view of Morrel and Uhlin, the expanding iPSC on laminin is within a wherein clause and is not the active method steps for reasons discussed above. As such, any means that expand the iPSC and result ultimately in reprogramming cells from expanding fibroblast will meet the limitations of the claims. Second, there is nothing in the claims recite or imply that the fibroblasts expanding step continue to be present in fibroblast expansion conditions such as the laminin when it is placed in the reprogramming conditions of the active reprogramming step. To this point, the claims, although now optional, explicitly recite steps of freezing and thawing steps that require a medium change and that medium change does not require proliferative fibroblast conditions and/or laminin. As such, the breadth of the claims encompasses expanding fibroblasts as taught by Couchman and placing the in freezing and thawing conditions prior to reprogramming and then proceed to reprogramming conditions as taught by Noggle. So while the art of Gupta and Applicant’s assertion suggest that using the fibroblast proliferative conditions with laminin would be counter to reprogramming in such conditions, the claims do not requires reprogramming under laminin culture and fibroblast proliferation conditions. As such, there is nothing that teaches away from first proliferating fibroblasts as taught by Couchman, then freezing and thawing in non-proliferative conditions following by reprogramming in non-proliferative conditions as taught by Noggle. As such, Applicant’s argument is not found persuasive.
Applicant submits that if laminin use during fibroblast expansion truly carried a reasonable expectation of improving reprogramming outcomes, such usage would logically appear in the seminal Takahashi and Yamanaka protocols or in Uhlin. This uniform exclusion of laminin during fibroblast expansion directly contradicts the Examiner’s position that adding laminin would have been routine or carried a reasonable expectation of success.
In response, Takahashi and Yamanaka protocol are not relevant as they are not part of the instant rejection. Since they have not been provided as evidence, Examiner cannot evaluate whether these protocols use laminin or proliferate fibroblasts. Even if Takahashi and Yamanaka protocols are silent or did not report using laminin in expanding of fibroblast, as suggested is also the fact pattern in Uhlin, silence is not fact based evidence of teaching away. One cannot know the rationale for their design choice unless such rationale is positive stated. As such, suggesting that laminin was left out due to a lack of reasonable expectation of success is speculation not based on scientific fact. Thus this argument is not persuasive in demonstrating a contradiction of routine optimization or reasonable expectation of success in applying Couchman to Noggle and Morrel.
Applicant submits a person of ordinary skill in the art would not maintain fibroblasts in a proliferation enhancing environment, if the goal is to have an efficient reprogramming method.
In response, Applicant is reading limitations into the claims that are not required. The claims do not recite that the fibroblast are “maintained” in proliferation enhancing condition. To the contrary, the claims further require placing them in freezing condition and then thawing conditions, albeit optional now by amendment, before placing them in reprogramming conditions. Even with the freezing and thawing steps were removed, there is nothing in the claim that states that the fibroblasts would be maintained in proliferation enhancing conditions when being placed in reprogramming conditions. As such, such maintaining is not required. One of ordinary skill in the art would understand how to take the cells out of proliferative conditions, at a minimum by washing the cells, and then placing them in reprogramming condition, with a reasonable expectation of success. Further, it is noted that the claims also do not require or imply anything regarding “an efficient reprogramming method”. The claims only recite, “A method of reprogramming”. As such, there is requirement of any particular efficiency for a reasonable expectation of success. Couchman provides a method of proliferating fibroblast that has a reasonable expectation of success. Noggle provides a method of freezing and thawing expanded fibroblast that have a reasonable expectation of success as well as a predictable means of reprogramming the thawed fibroblast. As such, Applicant’s argument is not found persuasive.
No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARCIA STEPHENS NOBLE whose telephone number is (571)272-5545. The examiner can normally be reached M-F 9-5:30.
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MARCIA S. NOBLE
Primary Examiner
Art Unit 1632
/MARCIA S NOBLE/ Primary Examiner, Art Unit 1632