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 Prior Rejections/Response to Arguments
RE: Rejection of claims 1, 3-5, 7-8, 10-11, 19-20, and 23 under 35 U.S.C. 102 over Gibco (Reprogramming Fibroblasts with CytoTune, 2012) as evidenced by ThermoFisher (useful numbers for cell culture) and Fujie et al (PLOS One, 2014).
Applicants amended claims to require culturing cells until the cells become TRA-1-60 positive, seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, and passage culturing the seeded TRA-1-60 positive cells.
Gibco does not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less. The rejection is therefore withdrawn.
RE: Rejection of claims 1-5, 7-11, 20, and 23 under 35 U.S.C. 103 over Fujie, et al. (PLOS One, 2014) in view of Gibco (Reprogramming Fibroblasts with CytoTune) as evidenced by ThermoFisher (useful numbers for cell culture).
Applicants amended claims to require culturing cells until the cells become TRA-1-60 positive, seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, and passage culturing the seeded TRA-1-60 positive cells.
Fujie et al does not teach culturing, seeding, or passaging cells that are TRA-1-60 positive. Gibco does not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less. The rejection is therefore withdrawn.
RE: Rejection of claims 1-11, 20, and 23 under 35 U.S.C. 103 over Fujie et al. (PLOS One, 2014) as evidenced by ThermoFisher (useful numbers for cell culture) and in view of Gibco (Reprogramming Fibroblasts with CytoTune) and Fusaki, et al (US9127256B2).
Applicants amended claims to require culturing cells until the cells become TRA-1-60 positive, seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, and passage culturing the seeded TRA-1-60 positive cells.
Fujie et al and Fusaki et al do not teach culturing, seeding, or passaging cells that are TRA-1-60 positive. Gibco does not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less. The rejection is therefore withdrawn.
RE: Rejection of claims 1-5, 7-13, 20, and 23 under 35 U.S.C. 103 over Fujie et al (PLOS One, 2014) ) as evidenced by ThermoFisher (useful numbers for cell culture) and in view of Gibco (Reprogramming Fibroblasts with CytoTune) and Willmann et al. (PLOS One, 2013)
Applicants amended claims to require culturing cells until the cells become TRA-1-60 positive, seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, and passage culturing the seeded TRA-1-60 positive cells.
Fujie et al does not teach culturing, seeding, or passaging cells that are TRA-1-60 positive. Gibco and Willmann et al do not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less. The rejection is therefore withdrawn.
RE: Rejection of claims 1-11, 14-20, 22, and 23 under 35 U.S.C. 103 over Fujie et al. (PLOS One, 2014) ) as evidenced by ThermoFisher (useful numbers for cell culture) and in view of Gibco (Reprogramming Fibroblasts with CytoTune) and Sarafian et al. (Stem Cell Research, 2018).
Applicants amended claims to require culturing cells until the cells become TRA-1-60 positive, seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, and passage culturing the seeded TRA-1-60 positive cells.
Fujie et al and Sarafian et al do not teach culturing, seeding, or passaging cells that are TRA-1-60 positive. Gibco does not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less. The rejection is therefore withdrawn.
RE: Rejection of claims 1-5, 7-11, 20, 21, and 23 under 35 U.S.C. 103 over Fujie et al. (PLOS One, 2014) as evidenced by ThermoFisher (useful numbers for cell culture) and in view of Gibco (Reprogramming Fibroblasts with CytoTune) and Tanabe et al. (WO2018155595A1).
Applicants amended claims to require culturing cells until the cells become TRA-1-60 positive, seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, and passage culturing the seeded TRA-1-60 positive cells.
Fujie et al does not teach culturing, seeding, or passaging cells that are TRA-1-60 positive. Gibco does not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less. Tanabe et al does not teach seeding TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less or passage culturing the seeded TRA-1-60 positive cells. The rejection is therefore withdrawn.
New Rejections
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.
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 1-11, 14-15, 17, 20, 22-23, 27, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Yamanaka et al (US20160122720A1) in view of Gibco (Reprogramming Fibroblasts with CytoTune, 2012).
Yamanaka et al teaches a method of producing iPS cells from human dermal fibroblasts comprising steps of (i) introducing reprogramming factors into somatic cells; (ii) culturing the cells obtained in step (i) for more than 11 days and not more than 29 days; (iii) sorting TRA-1-60 positive cells from the cells obtained in step (ii); (iv) culturing the TRA-1-60 positive cells sorted in step (iii); (v) transferring a colony obtained in step (iv) to another culture vessel; and (vi) culturing the cells obtained in step (v) thereby obtaining iPS cells (See abstract and ¶0019). Yamanaka et al discloses performing steps (i) and (iv) at 37° C (See ¶0079). The transduction step of Yamanaka et all comprises mixing viruses comprising reprogramming factors and exposing the viruses to HDF cells in a culture medium comprising 10% FBS (See ¶0094). Post transduction, the cells are replated onto feeder cells (See ¶0094). In step (v), single colonies can be separately picked up and subcultured in a separate vessel or a plurality of colonies can be picked up and transferred together in another culture vessel and cultured in bulk (See ¶0088). Additionally, the cells obtained in step (v) are preferably subcultured 10 times or more. Step (iv) can be performed by culturing the TRA-1-60 positive cells in a bFGF-containing culture medium for primate ES cell (See ¶0083). The reprogramming factor can be in the form of a protein, DNA, or RNA (See ¶0070-0072). And can be introduced into a somatic cell using a viral vector, plasmid, artificial chromosome, lipofection, or liposome microinjection (See ¶0071-0072). In embodiments where a viral vector is used the viral vector can include a retrovirus, lentivirus, adenovirus, adeno associated virus, or a Sendai virus.
Regarding claims 1-4: Yamanaka et al discloses a method of producing iPS cells comprising the following steps:
introducing reprogramming factors into somatic cells;
culturing the cells obtained in step (i) for more than 11 days and not more than 29 days;
sorting TRA-1-60 positive cells from the cells obtained in step (ii);
culturing the TRA-1-60 positive cells sorted in step (iii);
transferring a colony obtained in step (iv) to another culture vessel; and
culturing the cells obtained in step (v) thereby obtaining iPS cells.
Yamanaka et al therefore discloses a method for manufacturing pluripotent stem cells comprising step (i) which reads on a step of introducing reprogramming factors into cells. Step (iii) of Yamanaka et al teaches sorting TRA-160 positive cells obtained in step (ii) thus, step (ii) reads on culturing the cells into which the reprogramming factor is introduced, until the cells become TRA-1-60 positive. Steps (iii) and (v) of Yamanaka et al read on seeding the TRA-1-60 positive cells. Yamanaka et al further discloses the cells obtained in step (v) are preferably subcultured 10 times or more which reads on passage culturing the seeded TRA-1-60 positive cells.
Yamanaka et al does not teach seeding the TRA-1-60 positive cells at a concentration of 1.25x103 cells/cm2 or less, 0.25x103 cells/cm2 or less, a density where 11 or more of the seeded cells do not come in contact with each other, or 5% or less confluency.
Gibco teaches a method of producing iPSCs. In a troubleshooting guide, Gibco teaches if there are too many colonies on the plate, the number of cells plated after transduction should be decreased (See Sec. Troubleshooting).
Given that Yamanaka et al teaches a method of producing iPSCs comprising a step of transducing cells with reprogramming factors (i.e. step (i)) and Gibco teaches the number of cells plated after transduction can be decreased if too many colonies form on the plate, it would have been prima facie obvious, before the effective filing date, to optimize the seeding density of the TRA-1-60 positive cells of Yamanaka et al, and arrive at the claimed seeding densities, in order to optimize the number of colonies produced. Where the general conditions of a claim are disclosed in the prior art it is not inventive to discover the optimum or workable ranges by routine experimentation. See MPEP2144.05(II).
Regarding claim 5: Following the discussion of claim 1 above, Yamanaka et al discloses the reprogramming factor can be RNA.
Regarding claim 6: Following the discussion of claim 1 above, Yamanaka et al discloses the reprogramming factors can be introduced into somatic cells using lipofection.
Regarding claims 7 and 8: Following the discussion of claim 1 above, Yamanaka et al discloses the reprogramming factor can be introduced into cells using a viral vector such as a Sendai virus.
Yamanaka et al does not disclose using a viral vector that is temperature-sensitive in which stability of a viral nucleic acid decreases at a certain temperature or higher.
Gibco discloses instructions for reprogramming fibroblasts using the CytoTune iPS reprogramming kit. The CytoTune kit comprises Sendai virus (SeV) based vectors capable of expressing Oct4, Sox2, Klf3, and c-Myc (See Sec. Introduction, last paragraph). The CytoTune SeV vectors comprise a c-Myc expressing vector with a functional temperature sensitivity mutations that allow the host cell to be cleared of vectors and reprogramming factor genes by incubating cells at 38-39°C for 5 days (See Sec. Introduction, 3rd paragraph, and pg. 10, Step 4. Note).
Given that Yamanaka et al discloses a method of producing iPSCs using a SeV and Gibco discloses a SeV comprising c-Myc which has a temperature sensitive mutation that allows the host cells to be cleared of the SeV and c-Myc by culturing the cells at 38-39°C (reads on certain temperature) for 5 days, it would have been prima facie obvious to modify the method of Yamanaka et al to use the temperature sensitive SeV of Gibco. One would have been motivated to use the SeV of Gibco in the method of Yamanaka et al because the SeV of Gibco comprises a mutation that allows the host cell to be cleared of vectors and reprogramming factors by incubating the cells at 38-39° C. There is a reasonable expectation of success because Yamanaka discloses a reprogramming method comprising a SeV and Gibco discloses a SeV for reprogramming cells.
Regarding claim 9: Following the discussion of claims 1, 7, and 8 above, Yamanaka et al discloses the reprogramming factor can be introduced into cells using a viral vector such as a Sendai virus. Gibco teaches using a SeV comprising c-Myc which has a temperature sensitive mutation that allows the host cells to be cleared of the SeV and c-Myc. It would have been prima facie obvious to modify the method of Yamanaka et al to use the SeV of Gibco (See rejection of claim 8 above). Furthermore, it would have been prima facie obvious to not include viruses that do not include the temperature sensitive mutation of in the modified method of Yamanaka et al and Gibco because viruses which do not comprise the temperature sensitive mutation would not have been cleared from the cells.
Regarding claims 10 and 11: Following the discussion of claims 1, 7, and 8 above, Yamanaka et al discloses the reprogramming factor can be introduced into cells using a viral vector such as a Sendai virus. The reprogramming method of Yamanaka et al comprises introducing reprogramming factors to cells at 37° C and culturing for 11-29 days which reads on wherein after the reprogramming factor is introduced, the cells are cultured at a temperature lower than the certain temperature for at least two days.
Gibco teaches using a SeV comprising c-Myc which has a temperature sensitive mutation that allows the host cells to be cleared of the SeV and c-Myc by incubating cells at 38-39°C (reads on certain temperature) for 5 days. It would have been prima facie obvious to modify the method of Yamanaka et al to use the SeV of Gibco (See rejection of claim 8 above). Furthermore, it would have been prima facie obvious to perform the 38-39° C incubation step after any of steps (iii-vi) of Yamanaka et al which reads on after the cells are cultured at the temperature lower than the certain temperature, the cells are passaged and cultured at the certain temperature or higher. One would have been motivated to perform the 38-39° incubation step after any of steps (iii-vi) of Yamanaka at all because the cells of steps iii-vi express TRA-1-60 indicating they have been reprogrammed and a person of ordinary skill in the art would have not removed the reprogramming factors prior to the cells being reprogrammed. There is a reasonable expectation of success because Gibco teaches the SeV can be cleared from host cells by increasing the temperature.
Regarding claims 14, 15, 17, and 22: Following the discussion of claim 1 above, Yamanaka discloses in step (v), a plurality of colonies (reads on cells derived from different single cells into which the reprogramming factor is introduced) can be picked up and transferred together in another culture vessel and cultured in bulk which reads on the cells into which the reprogramming factor is introduced are separated/recovered from an incubator, and at least some of the separated cells are mixed and seeded.
Regarding claim 20: Following the discussion of claim 1 above, Yamanaka et al discloses replating the cells into which the reprogramming factor is introduced onto feeder cells. Cells cultured on feeder cells will necessarily be adherent. Therefore, Yamanaka et al discloses an adherent culture.
Regarding claim 23: Following the discussion of claim 1 above, Yamanaka et al discloses reprogramming human dermal fibroblasts.
Regarding claim 27: Following the discussion of claim 1 above, Yamanaka et al discloses the sorted TRA-1-60 positive cells can be cultured in a bFGF-containing culture medium for primate ES cells which reads on the TRA-1-60 positive cells are seeded in a culture medium suitable for culturing iPS cells.
Regarding claim 29: Following the discussion of claim 1 above, Yamanaka et al discloses reprogramming HDF cells in culture medium comprising 10% FBS then replating the cells onto feeder cells after the cells have been transduced. Thus, the reprogramming factor of Yamanaka et al is introduced in a culture absent of feeder cells.
Claims 1-17, 20, 22-23, 27, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Yamanaka et al (US20160122720A1) in view of Gibco (Reprogramming Fibroblasts with CytoTune, 2012) and Willmann et al (PLOS One, 2013).
The teachings of Yamanaka et al and Gibco are set forth above.
Yamanaka et al and Gibco render claims 1-11, 14-15, 17, 20, 22-23, 27, and 29 obvious.
Regarding claim 12 : Following the discussion of claim 1 above, Yamanaka et al. discloses a method of producing iPSCs fibroblasts comprising passaging steps.
Yamanaka et al. does not disclose a method in which stem cells or colonies of pluripotent stem cells are not isolated.
Willmann et al., teaches that fully reprogrammed cells are highly proliferative and escape cellular senescence allowing them to outgrow non-pluripotent and partially reprogrammed cells during culture expansion without the need of clonal selection (See abstract). Furthermore, Willmann et al., teaches there are no significant differences in pluripotency markers, gene expression profiles, and differentiation potential between clonally derived iPSCs and iPSCs derived from bulk cultures after a few passages (See abstract).
Given that Yamanaka et al discloses a method of producing iPSCs which include passaging the cells and Willman discloses iPSCs derived from bulk passaging of cultures are not significantly different from cells derived from clonal selection (reads on isolating colonies of iPSCs), it would have been prima facie obvious to modify the method of Yamanaka et al. to include bulk passaging of cells as taught by Willman et al. rather than including a colony picking step. One would be motivated to make this change because Willman et al discloses iPSCs produced through bulk culture passaging are not significantly different from cells produced by clonal selection. There would be a reasonable expectation of success because Willman teaches iPSCs outgrow non-pluripotent cells in culture without the need of clonal selection.
Regarding claims 13 and 16: Following the discussion of claim 1 above, Yamanaka et al. discloses a method of producing iPSCs from fibroblasts. The method of Yamanaka et al. comprises picking colonies and passaging the picked colonies which reads on the cells are cloned.
Yamanaka et al. does not disclose a culturing method wherein the cells into which the reprogramming factor is introduced are not cloned.
Willmann et al., teaches that fully reprogrammed cells are highly proliferative and escape cellular senescence allowing them to outgrow non-pluripotent and partially reprogrammed cells during culture expansion without the need of clonal selection (See abstract). Furthermore, Willmann et al., teaches there are no significant differences in pluripotency markers, gene expression profiles, and differentiation potential between clonally derived iPSCs and iPSCs derived from bulk cultures after a few passages (See abstract).
Given that Yamanaka et al discloses a method of producing iPSCs which include passaging the cells and Willman discloses iPSCs derived from bulk passaging of cultures (reads on the cells are not cloned) are not significantly different from cells derived from clonal selection (reads on the cells are cloned), it would have been prima facie obvious to modify the method of Yamanaka et al. to include bulk passaging of cells (reads on not picking up a plurality of colonies) as taught by Willman et al. rather than including a colony picking step. One would be motivated to make this change because Willman et al discloses iPSCs produced through bulk culture passaging are not significantly different from cells produced by clonal selection. There would be a reasonable expectation of success because Willman teaches iPSCs outgrow non-pluripotent cells in culture without the need of clonal selection.
Claims 1-11, 14-15, 17-20, 22-23, 27, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Yamanaka et al (US20160122720A1) in view of Gibco (Reprogramming Fibroblasts with CytoTune, 2012) and Sarafian et al (Stem Cell Research, 2018).
The teachings of Yamanaka et al and Gibco are set forth above.
Yamanaka et al and Gibco render claims 1-11, 14-15, 17, 20, 22-23, 27, and 29 obvious.
Claim 18 and 19 cryopreserving cells: Following the discussion of claim 1 above, Yamanaka et al. discloses a method of producing iPSCs from fibroblasts
Yamanaka et al. does not disclose all the cells or all separated cells are cryopreserved as pluripotent stem cells.
Sarafian et, al. teaches methods of producing and monitoring cell line identity for large quantities of human induced pluripotent stem cells (See abstract). The method of Sarafian et al. includes reprogramming erythroblasts and culturing the cells. Colonies with hiPSC morphology are then pooled and cultured in a 6-well dish. The cells are then cryopreserved (reads on all the cells are cryopreserved) in 9 vials which are used as a SEED BANK (See Fig. 1). One vial is expanded and further cryopreserved (reads on all separated cells are cryopreserved) as 9 vials to constitute a MASTER BANK. Cells from the Master bank are further expanded to constitute a Working bank from which quality control tests can be performed (See Fig. 1). Performing quality control testing is important for cell identification of iPSC cell lines, because iPSC-based research often involves long term culturing, expansion, and differentiation and iPSC cell lines are commonly shared among researchers (See introduction).
Given that Yamanaka et al. and Sarafian et al. both disclose methods of producing iPSCs and Sarafian et al further discloses methods of performing quality control testing on iPSC lines, it would have been prima facie obvious to modify the method of Yamanaka et al. to include the quality control steps of Sarafian, which includes cryopreserving the cells as iPSCs. The motivation to add the quality control steps of Sarafian to the method of Yamanaka et al., would be to expand the cells in order to provide stocks from which quality control testing could be performed because Sarafian et al. teaches quality control is important for cell line identification. There is a reasonable expectation of success because both methods are culturing iPSCs.
Claims 1-11, 14-15, 17, 20-23, 27, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Yamanaka et al (US20160122720A1) in view of Gibco (Reprogramming Fibroblasts with CytoTune, 2012) and Tanabe et al (Wo2018155595A1).
The teachings of Yamanaka et al and Gibco are set forth above.
Yamanaka et al and Gibco render claims 1-11, 14-15, 17, 20, 22-23, 27, and 29 obvious.
Regarding claim 21: Following the discussion of claim 1 above, Yamanaka et al. teaches a method of producing iPSCs by introducing reprogramming factors into fibroblasts. The reprogramming factors can be introduced to the cells using a SeV. The culturing method of Yamanaka et al. comprises culturing the cells on feeder cells.
Yamanaka et al. does not teach a suspension culture.
Tanabe et al. teaches a method for producing pluripotent stem cells. In example 3 of the first embodiment, Tanabe et al. discloses seeding fibroblasts in a suspended gel medium (reads on a suspension culture) and adding Sendai virus expressing the reprogramming factors OCT3/4, SOX2, KLF4, and c-MYC 24 hours after the cells are seeded. The tube was cultured for 23 days and gel medium was added to the tube every 48 hours.
Given that Yamanaka et al. and Tanabe et al. both teach methods of producing iPSCs from fibroblasts which comprise introducing a Sendai virus into the fibroblasts, it would have been prima facie obvious to substitute the culturing method of Yamanaka et al, which comprises culturing in a liquid media on feeder cells, for the culturing method of Tanabe et al. which comprises culturing in a suspension gel media. Substitution of one element for another known in the field, wherein the result of the substitution would have been predictable is considered to be obvious. See KSR International Co. V Teleflex Inc 82 USPQ2d 1385 (US2007) at page 1395.
Claims 1-11, 14-15, 17, 20, 22-23, and 27-29 are rejected under 35 U.S.C. 103 as being unpatentable over Yamanaka et al (US20160122720A1) in view of Gibco (Reprogramming Fibroblasts with CytoTune, 2012) and Abcam (Cell culture guidelines, 2013).
The teachings of Yamanaka et al and Gibco are set forth above.
Yamanaka et al and Gibco render claims 1-11, 14-15, 17, 20, 22-23, 27, and 29 obvious.
Regarding claim 28: Following the discussion of claim 1 above, Yamanaka et al discloses passage culturing TRA-1-60 positive cells and preferably subculturing the cells 10 times.
Yamanaka et al does not disclose culturing the cells to 60-80% confluent and passaging the cells at a concentration of 0.25x104 cells/cm2 or less.
Abcam teaches general guidelines for culturing cells. Abcam teaches cells should be split when they are approximately 80? Confluent because they will still be in the log phase of growth and will require sub-culturing. If the cells become over confluent, they will begin to die off. (See Sec. 6. Splitting).
Given that Yamanaka discloses passage culturing cells (reads on subculturing) and Abcam teaches cells should be subcultured when they reach 80% confluency to maintain the cells in log phase of growth and prevent dying, it would have been prima facie obvious to culture the cells of Yamanaka et al until they become 80% confluent. One would have been motivated to culture the cells of Yamanaka et al until they become 80% confluent because Abcam teaches cells at 80% confluency are still in the log phase of growth and should be subcultured to prevent cell death. There is a reasonable expectation of success because Abcam teaches general cell culture guidelines which are known in the art.
Conclusion
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/MARISOL ANN O'NEILL/Examiner, Art Unit 1633
/ALLISON M FOX/Primary Examiner, Art Unit 1633