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 .
DETAILED ACTION
This application is in response to the papers filed on May 5, 2026. Pursuant to the amendment filed on claims 1, 3, 5-7, 11, 13, 15, 22, 28, 31, 37, 38, 43, 45, 46, 54-56, and 58 are currently pending of which claims 2, 4, 8-10, 12, 14, 16-21, 23-27, 29-30, 32-36, 39-42, 44, 47-53, 57, and 59-63 have been cancelled and claim 54 has been amended.
Applicant’s election without traverse of the invention of Group I, claims 1, 3, 5-7, 11, 13, 15, 22, 28, drawn to a method of genetically modifying a cell from a subject with a Recombination-Activating Gene 2 (RAG2) deficiency, in the reply filed on May 5, 2026 in response to the restriction requirement filed on March 5, 2026 is acknowledged.
Claims 31, 37, 38, 43, 45, 46, 54-56, and 58 are withdrawn from further consideration by the Examiner, pursuant to 37 CFR 1.142(b), as being drawn to non-elected inventions, there being no allowable generic or linking claim. Reinstatement of claims drawn to non-elected inventions will be withdrawn during prosecution. The requirement for restriction between Groups I-IV is maintained for reasons of record, and hereby made FINAL. Applicant timely responded to the restriction (election) requirement in the Paper filed on May 5, 2026.
Therefore, claims 1, 3, 5-7, 11, 13, 15, 22, and 28 are currently under examination to which the following grounds of rejection are applicable.
Priority
The present application is a 35 U.S.C. 371 national stage filing of the International Application No. PCT/US2022/071549, filed on April 5, 2022. Applicant’s claim for the benefit of a prior-filed parent provisional application 63/170,935 filed on April 5, 2021 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged.
Thus, the earliest possible priority for the instant application is April 5, 2021.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on May 5, 2026 was filed. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892 or an official IDS, they have not been considered.
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.
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, 5-6, 11, 13, 22, and 28 are rejected under 35 U.S.C. 103 as being unpatentable over Tran et al. (Cell reports 28.13 (2019): 3510-3522) in view of Gallo et al. (U.S. Patent No. 8,012,714 B2) as evidenced by Shinkai et al. (Cell 68.5 (1992): 855-867).
Claim 1 is directed to a method of genetically modifying a cell from a subject with a Recombination-Activating Gene 2 (RAG2) deficiency, the method comprising: introducing into a cell isolated from the subject a single guide RNA (sgRNA) targeting the RAG2 gene, an RNA-guided nuclease, and a homologous donor template comprising a RAG2 cDNA comprising a nucleotide sequence having at least 80% identity to SEQ ID NO:5 or SEQ ID NO:6, flanked by a first and a second RAG2 homology region; wherein: the sgRNA binds to the nuclease and directs it to a target sequence within the RAG2 gene, whereupon the nuclease cleaves the gene at the target sequence, and wherein: the cDNA is integrated by homology directed recombination (HDR) at the site of the cleaved RAG2 gene, such that the cDNA is expressed under the control of the endogenous RAG2 promoter, thereby providing functional RAG2 protein product in the cell.
Tran teaches the repair of RAG2 knockout with CRISPR Cas9 “To repair the disrupted Rag2 allele, we electroporated Sca1+ HSPCs with RNPs containing both sgRNAs and, 30 min later, infected them with AAV-DJ vectors carrying the wild-type Rag2 (AAV-DJ-Rag2) donor template. Three days after targeting, the efficiency of HR-mediated repair in the Rag2 locus was assessed by PCR, using the primer sets indicated in Figure 6A… Sanger sequencing confirmed the successful repair of the mutant (Neo-disrupted) Rag2 allele (Figure 6F).” (p 3516).
In reference to instant SEQ ID NO: 6, Gallo teaches a codon-optimized RAG-2 polynucleotide [SEQ ID NO:3], that translates into the wild-type polypeptide sequence (col 41; Example 1). A sequence alignment between instant SEQ ID NO: 6 and Gallo SEQ ID NO: 3 has a similarity of around 83% as seen below (full alignment provided in the previous Office Action).
It would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the Tran method of utilizing CRISPR-Cas9 gene editing technologies to repair the RAG2 gene with a cDNA version that encodes a functional RAG2 protein, in particular a cDNA version that is codon optimized such as the sequence provided by Gallo. There is a reasonable expectation that by including this sequence version, or rather any cDNA comprising a codon optimized RAG2 gene, that there would be a similar outcome of gene repair via HDR.
Regarding claim 5, dependent to claim 1, the rejection to claim 1 is applied herein as the cell is a hematopoietic stem and progenitor cell (HSPC).
Regarding claim 6, dependent on claim 1, the instant Specification states, “As shown in FIG. 1C, the RAG2 gene comprises two initial “exons” that comprise 5′ UTRs but do not comprise any coding sequence. The coding sequence is entirely present in what is labeled “exon 3.” However, as exon 3 is the first exon to comprise a coding sequence, it is also at times referred to as exon 1.
Tran states, “Rag2 knockout mice had previously been generated by inserting a TK-Neo-pA cassette into the coding sequence of exon 2 of the Rag2 gene (Shinkai et al., 1992). We designed two sgRNAs targeting the TK-Neo-pA cassette, termed sg1 and sg2 hereafter (Figure 6A). However, Shinkai et al. reference which produces this knockout mice, describes the RAG-2 protein as being encoded within a single exon that was targeted for editing with the PMC1NeopA cassette as depicted in Shinkai Fig. 1 (p 856, col 1). Therefore, it can be seen that Tran teaches wherein the target sequence of the sgRNA is within exon 3 of the RAG2 gene or exon 1 of the coding sequence, and wherein the RAG2 cDNA comprises exon 3 of the RAG2 gene as described above in the claim 1 rejection with the cDNA provided by Gallo.
Regarding claim 11, dependent on claim 1, Tran teaches wherein the RNA-guided nuclease is Cas9 (abstract).
Regarding 13, dependent on claim 1, Tran teaches wherein the sgRNA and the RNA-guided nuclease are introduced into the cell as a ribonucleoprotein (RNP) (p 3516, col 1; Fig. 6B).
Regarding claim 22, dependent on claim 1, Tran teaches the homologous donor template is introduced into the cells using a recombinant adeno-associated virus (rAA V) serotype 6 vector (p 3512, col 2, par 3).
Regarding claim 28, dependent on claim 1, Tran teaches wherein the RAG2 deficiency is a severe combined immunodeficiency (SCID) based on using a mice model that has SCID due to having a double knockout of RAG2 (p 3510, col 2).
Claims 1, 3 are rejected under 35 U.S.C. 103 as being unpatentable over Tran et al. (Cell reports 28.13 (2019): 3510-3522) in view of Gallo et al. (U.S. Patent No. 8,012,714 B2) as applied to claim 1 above, and further in view of Conway et al. (US 9,616,090 B2).
Regarding claim 1, the disclosure of Tran in view of Gallo is applied as in the 103 rejections above, the content of which is incorporated above, in its entirety.
Regarding claim 3, dependent on claim 1, Tran teaches the cell type as HSPC as opposed to the claimed iPSC.
Conway teaches genome engineering in iPSC particularly targeted integration of a functional SCID-related genes (e.g., IL2RG, RAG1 and/or RAG2 gene) by using CRISPR-Cas9 nuclease system (abstract, col 9, ln 40-44; claim 9; col 5, ln 8-12).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the effective filing date to have modified the method taught by Tran in view of Gallo to substitute the HSPCs with iPSCs as taught by Conway based on teaching engineering iPSC with a nuclease system to target SCID related genes, e.g. RAG2. Therefore, there is a reasonable expectation of success that such cell type would similarly be engineered to target Rag2 gene, and furthermore motivation to do so since Conway teaches this cell type can be used to target the Rag2 gene.
Claims 1, 7 are rejected under 35 U.S.C. 103 as being unpatentable over Tran et al. (Cell reports 28.13 (2019): 3510-3522) in view of Gallo et al. (U.S. Patent No. 8,012,714 B2) as applied to claim 1 above, and further in view of Musunuru et al. (US 10,208,319 B2).
Regarding claim 1, the disclosure of Tran in view of Gallo is applied as in the 103 rejections above, the content of which is incorporated above, in its entirety.
Regarding claim 7, Tran teaches “We designed two sgRNAs targeting the TK-Neo-pA cassette, termed sg1 and sg2 hereafter (Figure 6A). Both sgRNAs showed high editing activity, based on T7EI assays, after electroporation of the sgRNAs within RNPs into Sca1+ HSPCs isolated from Rag2 /mice (Figure 6B).” (p 3516, col 1).
Tran in view of Gallo does not teach wherein the sgRNA comprises a nucleotide sequence complementary to a sequence selected from the group consisting of SEQ ID NO: 1, SEQ ID NO:2, SEQ ID NO:3, or SEQ ID NO:4.
Musunuru teaches guide RNA sequences that are useful in targeting the RAG2 gene, and moreover a method for altering a target severe combined immunodeficiency (SCID)-associated polynucleotide sequence in a cell comprising contacting the SCID-associated polynucleotide sequence with a CRISPR-Cas9 nuclease system (par 0004). In particular, Musunuru teaches sgRNAs listed as SEQ ID NOs: 4703 & 4781 that are 100% identical to instant SEQ ID NOs: 3 & 4 (provided with this Office Action).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the effective filing date to have modified the method taught by Tran in view of Gallo to incorporate the sgRNAs that target RAG2 as taught by Musunuru because it would have been obvious to substitute one known element for another to obtain predictable results. Substituting the claimed sgRNAs as taught by Tran for the sgRNAs of Musunuru would have led to predictable results with a reasonable expectation of success because Musunuru et al. teaches the use of these sgRNAs in particularly targeting the RAG2 gene for treating SCID, and additionally Tran teaching the targeting of RAG2 for treating SCID similarly with other sgRNAs. Therefore, the substitution of the targeting sgRNAs would be an obvious step.
Claims 1, 15 are rejected under 35 U.S.C. 103 as being unpatentable over Tran et al. (Cell reports 28.13 (2019): 3510-3522) in view of Gallo et al. (U.S. Patent No. 8,012,714 B2) as applied to claim 1 above, and further in view of Wilson et al. (US 9,719,106 B2).
Regarding claim 1, the disclosure of Tran in view of Gallo is applied as in the 103 rejections above, the content of which is incorporated above, in its entirety.
Regarding claim 15, Tran in view of Gallo teaches a codon-optimized RAG-2 polynucleotide [SEQ ID NO:3], that translates into the wild-type polypeptide sequence (col 41; Example 1). A sequence alignment between instant SEQ ID NO: 6 and Gallo SEQ ID NO: 3 has a similarity of around 83%.
Tran in view of Gallo does not teach wherein the RAG2 cDNA comprises a nucleotide sequence having at least 85%, 90%, 95%, 96%, 97%, 98%, 99% or more identity to SEQ ID NO:5 or SEQ ID NO:6.
Wilson teaches a codon optimization method based on the knowledge of codon usage bias which refers to frequency differences in the occurrence of synonymous codons in coding DNA within an organism. The reference acknowledges this is well-known in the art and provides a conventional codon frequency for humans in Table 2 (p 9, par 1). Wilson states, “Since the early published work in this area, a variety of different algorithms have been described for modifying coding sequences for expression in different bacterial and eukaryotic host cell species.”(col 1, ln 42-59; col 6, ln 15-25).
It would have been prima facie obvious for one of ordinary skill in the art at the time of the invention to to modify the known coding sequence for RAG2 because Tran teaches wherein codon optimization can be used for this sequence, and moreover Wilson teaching the practice of synonymous codon optimization for select organisms, e.g. humans, in addition to acknowledging the practice as being well-known in the art. In respect to instant SEQ ID NOs: 5 and 6, wherein the RAG2 cDNA comprises a nucleotide sequence having at least 85% similarity, it would be obvious to optimize expression of the RAG2 cDNA by codon optimizing the sequence, and moreover the codon optimized cDNA template is considered an obvious variant of the wild-type sequence for improving outcomes related to using the template for treating SCID.
Conclusion
Claims 1, 3, 5-7, 11, 13, 15, 22, and 28 are rejected. No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MICHAEL A RIGA whose telephone number is (571)270-0984. The examiner can normally be reached Monday-Friday (8AM-6PM).
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/MICHAEL ANGELO RIGA/Examiner, Art Unit 1634
/TERESA E KNIGHT/Primary Examiner, Art Unit 1634
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