DETAILED ACTION
Applicant’s response to the restriction/election requirement received on 6/1/26 has been entered. Claims 40-54 are pending in this application. Applicant’s election with traverse of the species 2) nucleic acid encoding GLUT3 as the species of supplementation. Applicant traverses the election of species requirement by arguing that the search and examination burden to examiner all the species is not undue. This is not agreed. As set forth in the election of species requirement, there is a serious search and examination burden for the patentably distinct species because a) the species have acquired a separate status in the art due to their recognized divergent subject matter as evidenced by their distinct molecular structures with unique structural and functional properties, b) the species require a different field of search (for example, searching different classes/subclasses or electronic resources, or employing different search queries), c) the prior art applicable to one species would not likely be applicable to another invention, and d) the species are likely to raise different non-prior art issues under 35 U.S.C. 101 and/or 35 U.S.C. 112, first paragraph. Applicant’s traversal does not address these issues. As such, the traversal is not found persuasive and the election of species requirement is made FINAL.
Claims 40-54 are currently under examination based on the elected species of “nucleic acid encoding GLUT3”. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . An action on the merits follows.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 3/10/23 is in compliance with the provisions of 37 CFR 1.97 and 1.98. Accordingly, the information disclosure statement has been considered by the examiner, and an initialed and signed copy of the 1449 is attached to this action.
Claim Interpretation
The following claim interpretation of "young" iPSCs versus "old" iPSCs has been adopted based on the definitions provided in applicant's specification: "young" iPSCs are defined in the specification as being derived from young donors such as young mice up to 5 days old, or young humans up to the age 16, whereas "old" iPSCs are derived from old donors such as mice more than 1.4 years in age or humans older than 50 years of age, see the specification on page 17.
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.
Claims 40-54 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.
Claim 40 recites a method for producing induced pluripotent stem cells generated from somatic cells of aged donors (A-iPSCs), the method comprising: supplementing somatic cells of aged donors prior to the initiation of reprogramming, during reprogramming, and/or after reprogramming of the somatic cells with an effective amount of GLUT3 thereby producing A-iPSCs with at least one of DNA damage response, apoptosis response, glucose metabolism, and genomic stability levels approximating those of induced pluripotent stem cells from young donors (Y-iPSCs), wherein the supplementation is carried out by adding GLUT3 to a culture medium in which the somatic cells are maintained or by transfecting the somatic cells with a vector harboring a nucleic acid sequence encoding GLUT3. As written, claim 40 is confusing as the initial step broadly recites “supplementing somatic cells” before reprogramming, during reprogramming, and/or after reprogramming with GLUT3. The claim as written does not appear to actually include any step in which the somatic cells are in fact subjected to a step of reprogramming, unless applicant intends that the supplementation step directs the reprogramming of the somatic cells to iPSCs. As written, it is unclear whether reprogramming of the aged donor somatic cells is an active part of the method. It is further noted that during reprogramming and after reprogramming, the cells are no longer “somatic cells”, but are rather cells in a state of reprogramming, i.e. no longer somatic cells and not yet iPSC, or cells which have completed reprogramming and now are iPSC. Thus, the further recitation, “wherein the supplementation is carried out by adding GLUT3 to a culture medium in which the somatic cells are maintained or by transfecting the somatic cells with a vector harboring a nucleic acid sequence encoding GLUT3” appears to limit the method to one in which somatic cells are contacted with the nucleic acid encoding GLUT3 (the elected species) prior to any reprogramming. As such, the metes and bounds of the claims cannot be determined as it is unclear whether the method is simply a method for providing somatic cells with a nucleic acid encoding GLUT3 prior to reprogramming, or whether applicant intends the method to include both a step of reprogramming and a step of providing the nucleic acid to either the somatic cell, the cell undergoing reprogramming, or the iPSC obtained following reprogramming, or whether the applicant intends that simply providing the nucleic acid encoding GLUT3 to the somatic cell is sufficient to reprogram the somatic cell into an iPSC. Claims 41-47 and 51-52 depend on claim 40 and thus are included in this rejection.
Claim 41 depends on claim 40 and is further indefinite in that the claim recites further comprising reducing expression of GPX2 or GSS by “supplementing the A-iPSC with an effective amount of GLUT3”. However, as discussed above, independent claim 40 does not appear to include a step of reprogramming where an iPSC has been produced and further recites that it is the somatic cell that is supplemented with the nucleic acid encoding GLUT3. Thus, it is unclear how the additional supplementation step recited in step 41 fits into the method of claim 40. Further, considering that claim 40 recites of providing the nucleic acid encoding GLUT3 to the somatic cell, it is unclear whether claim 41 is intended as a second provision of the nucleic acid to an iPSC generated from the somatic cell which has already been transfected/transduced with the nucleic acid encoding GLUT3.
Claim 42 depends on claim 40 and is further confusing as claim 40 recites the effects of the supplementation with the nucleic acid encoding GLUT3 to A-iPSCs, where various protein levels and functional activities in the A-iPSC are “restored” or “reduced”. However, since claim 40 provides the somatic cell with the nucleic acid encoding GLUT3, any iPSC obtained from that modified somatic cell that have already been exposed to GLUT3 such that it is unclear how any of the protein levels or functional activities in the A-iPSC have been changed. Claim 43 depends on claim 42 and is thus included in this rejection.
Claims 43-45 are further indefinite as they are drawn to an iPSC produced by the method of claim 40 which is recited having being deficient in GLUT3 prior to the GLUT3 supplementation. However, as discussed above, claim 40 does not appear to provide method steps which generate an iPSC and further recites that the somatic cell is supplemented with the nucleic acid encoding GLUT3 such that any iPSC derived from the modified somatic cell would have always been in the presence of the nucleic acid encoding GLUT3.
Claim 47 is further indefinite in the recitation, “wherein the reprogramming of the somatic cells is carried out with pluripotency factors ….”. As discussed above, claim 40, upon which claim 47 depends, does not actually include a step of reprogramming, such that it is unclear to which step of reprogramming claim 47 is referring to.
Independent claim 48 is indefinite in that it is unclear how the term “iPSC” differs from an “A-iPSC” or a “Y-iPSC”. The specification differentiates between young and old iPSCs and does not provide a definition of what type of cells is encompassed by “iPSC”. Generally, the state of the art refers to any reprogramming pluripotent stem cell as an “iPSC”. Thus, this term appears to be the broader term which encompasses both “A-iPSC” and “Y-iPSC”. Thus, its use in the claim as an alternative to either the “A-iPSC” or “Y-iPSC” is confusing such that the metes and bounds of this cell types cannot be determined. Claims 49-50 depend on claim 48 and thus are included in this rejection.
Claim 51 is further indefinite in the recitation, “An iPSC or A-iPSC produced by the method of claim 44”. Claim 44 is drawn to an A-iPSC product and not to a method. Further, claim 51 is definite for the same reasons set forth for claim 48 above in regards to “iPSC” vs “A-iPSC” and “Y-iPSC”. Claim 52 depends on claim 51 and is therefore included in this rejection.
Independent claim 53 is indefinite in that it recites a product which is an “iPSC” derived from a somatic cell of an aged donor (A-iPSC). Thus, it would appear that applicant is in fact claiming an A-iPSC not an iPSC. However, lines 5 and 6 refer to an “iPSC” and not an “A-iPSC” such that it is unclear what type of cell comprises the vector encoding GLUT3. Claim 54 depends on claim 53 and thus is included in this rejection.
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 40-54 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 1) a method of producing induced pluripotent stem cells from aged donors (A-iPSCs) comprising reprogramming skin fibroblasts from aged donors with at least the Yamanaka factors OCT4, SOX2, KLF4, and MYC to generate A-iPSC, followed by transfection/transduction of the A-iPSC with an expression vector comprising a nucleic acid encoding GLUT3, wherein prior to transfection/transduction, the A-iPSC exhibit a defect in DNA damage response, a defect in glucose metabolism, a deficit in ROS, and excessive glutathione-mediated H202 scavenging activity compared to embryonic stem cells (ESCs) or induced pluripotent stem cells from young donors (Y-iPSCs), and wherein expression of GLUT3 in the A-iPSCs substantially restores the DNA damage response, glucose metabolism, ROS pathway, and glutathione-mediated H202 scavenging activity to levels substantially the same as those of Y-iPSC or ESC, and 2) an A-iPSC transfected/transduced with an expression vector encoding GLUT3 made by the method of 1), does not reasonably provide enablement for practice of the claimed methods where the somatic cell is any somatic cell, where the somatic cell has not been reprogrammed to A-iPSC prior to transfection with an expression vector encoding GLUT2, and where the resulting A-iPSC, prior to transfection, does not exhibit any deficits compared to a Y-iPSC. 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 or use the invention commensurate in scope with these claims.
The claims, as discussed above in the rejection of the claims for indefiniteness under 35 U.S.C. 112(b), appear to recite a method with a single method of providing somatic cells from aged donors with a nucleic acid encoding GLUT3 in order to produce A-iPSC which expression and functional characteristics closer to those observed in Y-iPSC. The claims, as written, do not actually include an active step of reprogramming the somatic cell to become an A-iPSC. Certain claims further appear to indicate that A-iPSC are produced and then transfected with a nucleic acid encoding GLUT3 in order to restore or reduce various protein expression levels or functional activities in the A-iPSC such that they resemble ESC or Y-iPSC. The claims further read broadly on the transfection or reprogramming of any aged somatic cell.
The specification provides a more specific disclosure of aged somatic cells which are reprogrammed into aged-iPSC (A-iPSC), and which in some cases exhibit various deficits in protein expression such as reduced expression of GLUT3, reduced expression of glutathione, reduced ROS levels, and excessive O2 consumption compared to young-iPSCs (Y-iPSCs). The specification discloses that expression of GLU3 in A-iPSC with these defects results in an A-iPSC with the characteristics of a Y-iPSC. The specification provides a number of working examples which primarily involve the effects of the transfection of A-iPSCs with a vector encoding Z-SCAN, not GLUT3, but does provide an example where A-iPSCs are transfected with an expression vector encoding GLUT3. All of the working examples generated A-iPSCs from skin fibroblasts derived from aged or young mouse or human donors, where the fibroblasts are cultured in the presence of the Yamanaka factors OCT4, SOX2, KLF4, and MYC under conditions which promote reprogramming resulting in A-iPSCs. The specification discloses, however, that only certain A-iPSCs derived from certain strains of mice, or that A-iPSCs from certain individuals and not others, exhibit different characteristics than Y-iPSCs, including differences in the expression of GLUT3 and glutathione, and difference in glucose metabolism, oxygen consumption, ROS pathway activity, and DNA repair pathway activity. The working example demonstrates that in A-iPSCs with these particular deficits, transfection with an expression vector encoding GLUT3 is capable of reversing the deficits such that the A-iPSCs exhibit GLUT3 and glutathione expression, glucose metabolism, oxygen consumption, ROS pathway activity, and DNA repair pathway activity similar to that seen in ESCs or Y-iPSCs. The working examples, however, are limited to A-iPSCs obtained from aged skin fibroblasts, and even starting with these specific donor cells teaches that not all skin fibroblast somatic cells reprogram into A-iPSCs with deficits that can be repaired by GLUT3 expression. Further, neither the specification nor the working examples teach that any other aged somatic cell type produces A-iPSCs with these particular deficits, particularly low GLUT3 expression, that are amendable to repair by heterologous GLUT3 expression in the cell. In addition, neither the specification nor the working examples teach or demonstrate that GLUT3 expression in any somatic cell, in the absence of the Yamanaka factors or any other reprogramming factors, can induce reprogramming into an iPSC.
At the time of filing, the art teaches that the type of donor cell affects the properties of induced pluripotent stem cells obtained using the Yamanaka factors. Kim et al. teaches that there are substantial epigenetic differences between iPSCs derived from different donor somatic cells generated using the Yamanaka factors Oct4, Sox2, Klf4, and c-Myc, and that while in general iPSC are similar to ESC, in practice, iPSCs obtained from various tissue harbor significant functional and molecular differences likely resulting from differences in DNA methylation (Kim et al. (2010) Nature, Vol. 16(7313):285-290, author manuscript see page 2). Kim et al. 2011 further demonstrated substantial differences in gene expression between iPSCs obtained from cord blood vs iPSC derived from keratinocytes (Kim et al. (2011) Nat. Biotech., Vol. 29(12), 1117-1119, author manuscript see pages 2-3). Thus, the prior art at the time of filing clearly teaches and demonstrates substantial differences between iPSCs obtained using the Yamanaka factors from somatic cells from different tissues. Further, in regards to iPSC obtained from fibroblasts and in particular aged versus young fibroblasts, the prior art at the time of filing had looked at potential differences between iPSC obtained from old versus young donors and did not report notable differences. Miller et al., for example, teaches that somatic cells such as fibroblasts from aged donors exhibit certain age-associated features including shorter telomere length, decrease in mitochondrial fitness, increased expression of senescence markers, impaired DNA damage response, changes in nuclear morphology abnormalities and loss of heterochromatin markers (Miller et al. (2013) Cell Stem Cell., Vol. 13(6), 691-705, pages 2-4). Miller et al. tested fibroblasts from young human donors (age 11) and old human donors (ages 71-96) and compared various age-associated markers between the two, demonstrating that old donor fibroblasts exhibit measurable age-associated markers (Miller et al., page 4). Miller et al. then reprogrammed the young or old fibroblasts by transducing the fibroblasts with sendai viruses expressing the Yamanaka factors Oct4, Sox2, Kilf4, and c-Myc resulting in the generation of iPSCs from both the young and old donor fibroblasts (Miller et al., page 4). Miller et al. teaches that reprogramming of the old donor fibroblasts resulted in a loss of age-associated markers in the iPSCs, thus “re-setting” the phenotypic age of the old-iPSCs to resemble young iPSCs (Miller et al., pages 4 and 18- Figure 1). In particular, Miller et al. observed that the iPSCs derived from old fibroblasts displayed minimal levels of DNA damage or mtROS, and further exhibited a loss of age-related marker expression, where DNA damage was measured by H2AX immunocytochemistry, and mtROS was measured by level of MitoSOX (Miller et al., page 18). Thus, Miller et al., like the instant specification, shows that not all aged-iPSCs derived from fibroblasts have deficits in DNA damage or ROS, and appear to be the same as Y-iPSC. Thus, as a whole, the prior art teaches differences in iPSCs obtained from different tissue sources, such that the skilled artisan would not have been able to predict whether any iPSC derived from any somatic tissue would resemble iPSCs derived from skin fibroblasts. Further, based on the teachings of the prior art that aged-iPSC and young-iPSCs obtained from fibroblasts appear to be similar, particular in terms of ROS and DNA damage repair, and the teachings of the specification that not all aged-iPSC obtained from skin fibroblasts treated with the Yamanaka factors exhibits the deficits as claimed, the skilled artisan would not be able to predict which aged-iPSCs would be amendable to supplementation with a nucleic acid encoding GLUT3 without prior testing of at least GLUT3 expression, ROS function, and DNA damage repair.
Therefore, based on the state of the prior art at the time of filing which demonstrated structural and functional differences in iPSCs obtained from different somatic tissues, the teachings in that prior art and in the specification that not all aged-iPSC obtained from skin fibroblasts exhibits deficits compared to young-iPSCs or ESCs, the limitation of the working examples to the amelioration of deficits in aged-iPSCs obtained from aged skin fibroblasts where the A-iPSCs had been determined to exhibit specific deficits, using a nucleic acid encoding GLUT3, and the breadth of the claims, it would have required undue experimentation to practice the full scope of the invention as claimed.
No claims are allowed.
Any inquiry concerning this communication from the examiner should be directed to Anne Marie S. Wehbé, Ph.D., whose telephone number is (571) 272-0737. If the examiner is not available, the examiner’s supervisor, Maria Leavitt, can be reached at (571) 272-1085. For all official communications, the technology center fax number is (571) 273-8300. Please note that all official communications and responses sent by fax must be directed to the technology center fax number. For informal, non-official communications only, the examiner’s direct fax number is (571) 273-0737. For any inquiry of a general nature, please call (571) 272-0547.
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Dr. A.M.S. Wehbé
/ANNE MARIE S WEHBE/Primary Examiner, Art Unit 1634
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