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 .
Priority
Acknowledgment is made of applicant’s claim for priority based on a provisional application filed as 62/890,542 on 08/22/2019.
All claims are given the priority date of 08/22/2019.
Application Status
Receipt is acknowledged of amendment, filed 09/12/2025. Claims 134, 137 and 139 are canceled and claim 159 was amended. Claims 130-133, 135, 136, 138 and 140-159 are currently pending.
Election/Restriction
Applicant’s election without traverse of Group I, drawn to claims 130-144, in the reply filed on 09/12/2025 is acknowledged.
Applicant’s election without traverse of Cas9 from claim 132, SEQ ID NO: 19 (from previously pending claim 134), SEQ ID NO: 10 (from previously pending claim 137) and SEQ ID NO: 2 (from previously pending claim 139), in the reply filed on 09/12/2025 is acknowledged.
Claims 145-159 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09/12/2025.
Claims 130-133, 135, 136, 138 and 140-144 are currently under examination.
Information Disclosure Statement
Receipt of acknowledgment of the information disclosure statements filed on 02/21/2022, 10/05/2023, 04/09/2025, 04/25/2024, 08/21/2024, 09/11/2024 and 01/16/2025 have been received and all references have been considered.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claim 140 is rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101). The claim is interpreted as reading on a human organism because the instant specification describes the cell is from a subject wherein the subject is a human [0004, 0011, 00109, 00117, 00126, 00134, 00144, 00146 and 00195]. Therefore, the cell reads on a human organism.
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.
Claim 138 is 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 138 recites the limitation "the guide oligonucleotide" in line 1. There is insufficient antecedent basis for this limitation in the claim. It would be remedial to amend claim 138 to depend on claim 133 which provides antecedent basis for a guide oligonucleotide.
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), 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.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], 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 138 is rejected under 35 U.S.C. 112(d) or pre-AIA 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 130 recites “(ii) a targeted endonuclease” while claim 138 recites the limitation of " the targeted endonucleases are encoded in a viral or non-viral construct". Thus, the dependent claim substitutes the endonuclease protein of the composition of claim 130 with a viral or non-viral construct encoding the endonuclease protein. Claim 138 does not include all of the limitations of the claim from which it depends. 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.
Claims 142-144 are rejected under 35 U.S.C. 112(d) or pre-AIA 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 142 relies on claim 130 but is broader in scope than claim 130. Claim 130 requires a single homology arm construct comprising a replacement sequence and a targeted endonuclease cleavage site, however claim 142 only requires a nucleic acid molecule encoding the single homology arm construct. Claims 143 and 144 rely on claim 142. 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.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 130-133, 135-136, 138, 140-142 and 144 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhu et al (Stem Cell Reports, Vol 4, pgs 1103-1111 and Supplemental Pages 1/18-18/18; 2015).
Regarding claims 130-133, Zhu teaches a composition comprising a donor plasmid (single homology arm construct of the claim), where the donor plasmid comprises the left homology region containing at least partial introns and exons of the Pdx1 coding sequence, GFP gene and then single right homology arm as well as a CRISPR cas9 endonuclease and two guide RNAs, cr1 and cr2 (Page 1108, Figure 4 and Page 1107, column 1 bridging column 2).
Regarding claim 135, Zhu teaches the donor plasmid knocks in a GFP gene and portion of a Pdx1 gene (Page 1108, Figure 4 and Page 1107, column 1 bridging column 2).
Regarding claim 136, the claim is interpreted as requiring the replacement sequence to comprise at least a portion of an intron and at least a portion of an exon of a gene of the target genome. Thus, the donor must comprise at least a portion of the introns or exons of Pdx1 gene.
Zhu teaches the donor plasmid comprises the left homology region contains at least partial introns and exons of the Pdx1 coding sequence to be inserted into the genome along with a GFP gene and a single right homology arm as well as a CRISPR cas9 endonuclease and two guide RNAs, cr1 and cr2 (Page 1108, Figure 4 and Page 1107, column 1 bridging column 2).
Regarding claim 138, Zhu teaches the donor plasmid comprises the left homology region contains at least partial introns and exons of the Pdx1 coding sequence, GFP gene and then single right homology arm as well as a plasmid encoding CRISPR cas9 endonuclease and two guide RNAs, cr1 and cr2 (Page 1108, Figure 4 and Page 1107, column 1 bridging column 2).
Regarding claim 140, Zhu teaches successful knockin reporter lines for PDX1 in differentiated hESCs (Page 1108, Column 1 bridging Column 2).
Regarding claim 141, Zhu teaches the cells were co-transfected with the donor plasmid and the Cas9/sgRNA and then kept in medium (Supplemental Page 14, Paragraphs 1-2).
Regarding claims 142 and 144, Zhu teaches the donor plasmid comprises the left homology region contains at least partial introns and exons of the Pdx1 coding sequence, GFP gene and then single right homology arm as well as a CRISPR cas9 endonuclease and two guide RNAs, cr1 and cr2 (Page 1108, Figure 4 and Page 1107, column 1 bridging column 2).
Claims 130-133, 135, 138, 140-142 and 144 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Basiri et al (Cell J. 2017; 18(4): 532-539).
Regarding claims 130-133, Basiri teaches a composition for RNA guided gene targeting with a single homology arm donor plasmid in the MIN6 cell line comprising (i) a single homology arm construct comprising a GFP sequence and a targeted endonuclease cleavage site (sgPdx1 target); and (ii) a targeted endonuclease (Cas9/sgPdx1), wherein the GFP sequence comprises at least one nucleotide difference compared to a target genome and wherein the target genome comprises a sequence homologous to the targeted endonuclease cleavage site (Page 536, Figure 1). Basiri teaches a donor plasmid (pKI-Pdx1) that harbored a single homology region specific to the mouse Pdx1 locus and a GFP CDS wherein the targeted insertion of GFP sequence into the Pdx1 locus results in GFP expression (Page 535, Column 1 bridging Column 2).
Regarding claim 135, Basiri teaches the insertion of the GFP gene (Page 536, Figure 1).
Regarding claim 138, Basiri teaches a plasmid comprising a circular donor DNA that contained a single 318bp homology arm in combination with Cas9n and a single sgRNA (Page 533, Column 1, Paragraph 3 and Column 2, Paragraph 2). Basiri teaches the plasmid (pKI-Pdx1) that harbored a single homology region specific to the mouse Pdx1 locus and a GFP CDS wherein the targeted insertion of GFP sequence into the Pdx1 locus results in GFP expression (Page 535, Column 1 bridging Column 2). Basiri teaches the Cas9n/sgPdx1 is expressed within the plasmid comprising the single homology arm construct wherein the Pdx1-specific sgRNA is capable of targeting 157bp upstream of the Pdx1 CDS (Page 533, Column 2).
Regarding claim 140, Basiri teaches RNA guided gene targeting with a single homology arm donor plasmid in the MIN6 cell line (Page 536, Figure 1).
Regarding claim 141, in view of the instant specification, the term "pharmaceutically acceptable carrier" refers to a substance that aids the administration of an agent (e.g., DNA nuclease, etc.) to a cell, an organism, or a subject [00199]. Therefore, the claim is interpreted that the pharmaceutically acceptable buffer or excipient for the use of the plasmid to a cell.
Basiri teaches MIN6 cells comprising the plasmid comprising the single homology arm construct, Cas9/Cas9n and guide RNA within medium or phosphate-buffered saline (Page 533, Column 2).
Regarding claim 142, Basiri teaches pKI-Pdx1 (GenBank accession number: KU341331; the GenBank accession number is the nucleic acid sequence encoding the single homology arm construct), harbored a 318 bp fragment from the Pdxtr1 5´ untranslated region and upstream sequences were used as the single homology arm donor (Page 533, Column 2).
Regarding claim 144, Basiri teaches a plasmid comprising a circular donor DNA that contained a single 318bp homology arm in combination with Cas9n and a single sgRNA (Page 533, Column 1, Paragraph 3 and Column 2, Paragraph 2). Basiri teaches the plasmid (pKI-Pdx1) that harbored a single homology region specific to the mouse Pdx1 locus and a GFP CDS wherein the targeted insertion of GFP sequence into the Pdx1 locus results in GFP expression (Page 535, Column 1 bridging Column 2). Basiri teaches the Cas9n/sgPdx1 is expressed within the plasmid comprising the single homology arm construct wherein the Pdx1-specific sgRNA is capable of targeting 157bp upstream of the Pdx1 CDS (Page 533, Column 2).
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.
Claim 143 is rejected under 35 U.S.C. 103 as being unpatentable over Zhu et al (Stem Cell Reports, Vol 4, pgs 1103-1111; 2015) in view of Guo et al (WO 2017/214615 A1).
The teachings of Zhu are described above and applied as before.
Zhu does not teach the plasmid containing the guide oligonucleotide, the targeted endonuclease and the donor construct on one single plasmid.
Guo teaches the gRNA and donor nucleic acids are introduced to a target cell encoded on the same vector, such as a plasmid, to ensure that a host cell will have both components, rather than requiring a host cell to be transformed by two different vectors [40]. Guo teaches that this greatly increases the efficiency of successful transformations over approaches in which gRNA and donor are encoded on separate molecules [40].
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the teachings of Zhu to include the gRNA and donor nucleic acids are introduced to a target cell encoded on the same vector, such as a plasmid as taught by Guo because Zhu teaches it is within the ordinary skill in the art to use a composition comprising a donor plasmid (single homology arm construct of the claim), where the donor plasmid comprises the left homology region containing at least partial introns and exons of the Pdx1 coding sequence, GFP gene and then single right homology arm as well as a CRISPR cas9 endonuclease and two guide RNAs, cr1 and cr2 and Guo teaches the gRNA and donor nucleic acids are introduced to a target cell encoded on the same vector, such as a plasmid, to ensure that a host cell will have both components, rather than requiring a host cell to be transformed by two different vectors.
One would have been motivated to make such a modification in order to receive the expected benefit of ensuring all necessary components are delivered to the target cell as well as increased efficiency of successful transformations as taught by Guo.
Conclusion
No claims are allowed.
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/ALEXANDRA ROSE LIPPOLIS/Examiner, Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637