DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11/21/2025 has been entered.
Claims 128, 130-139, 141-145, 148 and 151-153 are pending.
The instant application is a 371 filing of PCT/US2019/028858 filed 4/24/2019 which claims priority to provisional application 62/663,485 filed 4/27/2018. It is noted that SEQ ID NO:28 is the complement of the sequence provided in SEQ ID NO:12. Claims 138 and 145, drawn to introducing an HDM2 protein, lacks support in the provisional document and therefore have a priority date of 4/24/2019.
Response to Amendments
Applicants amendments are sufficient to overcome the previous objections as well as the rejections under 35 USC 112. New rejections are set forth below.
Claim Rejections - 35 USC § 112, second paragraph
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 128, 138 and 153 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. These are new rejections necessitated by applicants amendment.
Claim 128 recites in line 19 that the template polynucleotide is at an MOI of greater than 1000. This is unclear as this terminology is typically reserved for viral administration steps. However, there is no indication of viral vectors in claim 128. It is therefore unclear if there is a requirement of viral vectors or if the claim has a special step that uses a template polynucleotide in a manner that relates to MOI. A viral vector is not introduced until claim 132. This deficiency is true of claim 153.
On amendment, claim 138 lacks antecedent basis by reciting “the cell”. There are numerous cells in claim 128, the original cell, the pre-stimulated cell and the introduced cell. It is unclear to which cell the claim is referencing.
Claim Rejections - 35 USC § 112 ¶4 rejection
The following is a quotation of the fourth paragraph of 35 U.S.C. 112:
Subject to the [fifth paragraph of 35 U.S.C. 112 prohibiting improper multiple dependent claims], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 134 is rejected under 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 134 is not encompassed by the limitations of claim 133. Claim 134 requires that a titer or MOI that is higher than that limited in claim 133. Specifically, claim 134 has not upper limit whereas claim 133 does. .Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements. This is a new rejection necessitated by applicants’ amendment.
Claim Rejections - 35 USC § 112, first paragraph
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.
Claims 128, 130-139, 141-145, 148 and 151-153 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new rejection.
Claim 128 recites “culturing a cell to obtain a pre-stimulated cell”. The disclosure provides a single example of this in which CD34+ cells were grown in cell growth media comprising cytokines for 48 hours. The cytokines were limited to those in Table 1.
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As a second issue, the claims in part b are drawn to introducing Cas or a nucleic acid encoding thereof into a cell and a gRNA and a template polynucleotide comprising CD40LG cDNA. At issue is the recitation wherein Cas is capable of “cleaving a target locus in order to promoter insertion of a template polynucleotide within a first exon of a CD40LG gene in the cell genome” and “wherein the template poly nucelotide3 is configured such that the cDNA is inserted downstream and operably linked to an endogenous CD40LG promoter”. These steps are specifically the result of a gRNA that has a sequence that specifically delivers the Cas to a target locus within a first exon of the CD40LG gene and for directional insertion, the template has homologous arms corresponding to the 5’ and the 3’ end of the nicked site such that the sequence is inserted i.e. downstream and linked to the endogenous CD40LG promoter. Claim 139 makes reference to the gRNA required and claim 142 to the homology arm that would make the claim fully described. Claim 148 indicates the gRNA necessary to direct Cas to the CD40LG gene but does not provide the requisite components for integration as required. However, claim 151 suffers from the same deficiencies noted for claim 128 part b.
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.
Claims 128, 132, 134, 141 and 144 are rejected under 35 U.S.C. 103 as being unpatentable over Hubbard et al (Blood, 2016, pages 2513-2522) in view of Sadelain and Glavridis (WO 2019099993). This is a new rejection necessitated by applicants’ amendment.
Here, we report efficient, on-target, homology-directed repair (HDR) editing of the CD40LG locus in primary human T cells using a combination of a transcription activator-like effector nuclease–induced double-strand break and a donor template delivered by recombinant adeno-associated virus. HDR-mediated insertion of a coding sequence (green fluorescent protein or CD40L) upstream of the translation start site within exon 1 allowed transgene expression to be regulated by endogenous CD40LG promoter/enhancer elements.
The specifics are Hubbard et al teach collection of cells from an X-HIGM donor (see page 2514, col 1, last ¶). The cells were activated (pre-stimulated) and then plated at 1 x106 (see page 2514, col 2) and AAV used at an MOI of 50,000 -100,000 wherein cDNA was introduced into the cell (see figure 2).
CD40LG[GFP.39UTR] and CD40LG[GFP.WPRE] gene-editing templates
were modified with a 2A-linked CD40L cDNA directly
downstream of GFP (Figure 2A).
The cDNA was inserted into exon 1 (see figure 2 and page 2515, col 1) using Talen.
A TALEN pair was designed targeting the 59-untranslated region (59UTR)
in exon 1 of CD40LG (Figure 1A).
Sadelain and Glavridis teach use of a nuclease that is either TALEN nuclease or CRISPR/CAS with gRNA for introducing a modification of CD40L at endogenous exon 1. Sadelain teaches use of heterologous nucleic acids that are cDNA. The claim as amended refers to “a CD40LG cDNA”. Hence at least a portion of CD40LG is integrated into the genome.
Hence, the art teaches that TALEN and Cas can be used interchangeably to introduce CD40LG into a cell genome especially at exon 1.
Based on such teachings, it would have prima facie been obvious to one of ordinary skill in the art at the time the invention was made to use Cas/gRNA as taught by Sadelain in the methods of Hubbard et al. Such a modification would have resulted in a method encompassed by claim 128. As noted above: 1) Hubbard teaches editing CD40LG using Talen and otherwise the step of claim 128; 2) Sadelain and Glavridis teach use of Cas9. Thus, a person of ordinary skill in the art, absent evidence to the contrary, would have reasonably expected that the interchanging of nucleases to work efficiently in modulating CD40LG.
A WPRE is included (see page 2515, col 2). Binding is tested (see page 2517, col 1) in cells plus and minus CD40LG in vivo as well (see page 2519, col 1-2).
Claims 130, 131, 133, 135-138 and 145 are rejected under 35 U.S.C. 103 as being unpatentable over Hubbard et al (Blood, 2016, pages 2513-2522) in view of Sadelain and Glavridis (WO 2019099993) as applied to claims 128, 132, 134, 141 and 144 above, and further in view of Gori et al (US 20200263206), Brooks et al (US 20190247517), Patterson (U.S. 20190269730), and Ihry et al (US 20180245065).This is a new rejection necessitated by applicants’ amendment.
Missing from the teachings above are the concentration of RNP as recited in claims 130-131. As well, an MOI of 1000-5000, a treatment with i.e. IL6 for 2-3 days to pre-stimulate the cells as recited in claims 135-137 and 145 and introduction of HDM2 into the cell as recited in claim 138. These doses and complexes recited in the claims are results variable conditions which can be altered and used at different doses and modes. In Patterson, RNP are used to deliver Cas9 into cell lines to genetically engineer the cell. RNP are delivered at about 200 ug/ml (specifically it is at 300 ug/mL, see ¶0133 as recited in i.e. claims 130 and 131) are used to deliver Cas. Brooks teaches that AAV doses at 2500 provides transduction efficiencies of hepatocytes for gene editing.
Ihry et al teach use of HDM2 a TP53 inhibitor in genome editing steps that enhancement of the gene editing (see e.g. abstract, ¶0196 and 300).
Gori et al teach pre-treatment of cells for 3 days with SCF, TPO, FL and IL (see ¶0372)
These adjustments demonstrate the flexibility of the art and the range of MOI, RNP and pre-stimulation known in the art. It would have been predictable to substitute known components of known methods shown to work. One would pre-stimulate cells to increase metabolic activity and increase transduction. The RNP concentration taught by Patterson provides valuable technique information for the methods of Hubbard in view of Sadelain. Modulating MOI is a well-known part of the art and is a prime consideration of results effective variables. The modifications are known and would be expected to provide improved editing.
Response to Arguments
Applicants argue that the instant method is not taught by the combination of references. However, the reasoning is unclear. Hubbard provides the basic mechanics of gene editing CD40LG wherein Sadelain directs one to use Cas. Together the basis of the method is achieved wherein Hubbard teaches cell density and AAV MOI. It is not clear what aspect of the invention is missing from the rejection as newly set forth as applicants assertions are not provided with details as to what is lacking. Those secondary references found deficient have been amended.
Conclusion
Claims 139, 142, 143, 148 and 151-153 appear to be free of the art.
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/MARIA MARVICH/Primary Examiner, Art Unit 1631