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 .
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 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.
Priority
The instant application, filed 06/26/2023, is a 371 filing of PCT/US2021/065813, filed 12/31/2021, and claims domestic benefit to US provisional application 63/132,852, filed 12/31/2020.
Status of Claims/Application
Applicant’s preliminary amendment of 09/30/2024 is acknowledged. Claims 2, 8, 10, 13, 16, 17, 19, 23, 25-27, 30, 31, 36, and 47-50 are amended and claims 3-7, 9, 11-12, 14-15, 18, 20-22, 28-29, 32-35, 37-46, and 51-61 are cancelled. Claims 1-2, 8, 10, 13, 16-17, 19, 23-27, 30-31, 36, and 47-50 are currently pending and are examined on the merits herein.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 09/30/2024 (2) are in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statements have been considered by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
The instant specification, filed 06/26/2023, includes the following sequences comprising 4 or more amino acids without a corresponding SEQ ID NO:
[0098]: VRER, NGAG, NGCG, NNGRRT, and NNNRRT; and
[00110] (page 35): TTTV
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – Nucleotide and/or amino acid sequences appearing in the specification are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Drawings
The drawings filed 06/26/2023 are objected to because they contain figures that are low resolution that are difficult to read. For instance, see Figs. 1, 2A-C, 11A, 11F, 11G, 11P, 11Q, 12K, 12L, 12M, 12N, 12O, 12P, 12Q, 12R, 12S, 12T, 12U, 12V, 13C, 13D, and 14A. Additionally, the box in Fig. 2B is cutting off the top and bottom of the figure text.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Specification Objection
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
The disclosure includes the following hyperlink. Non-top level domain, browser executable code is bolded for clarity.
Page 54, [00153] and page 57, [00157]: www.bd.com/documents/bd-legacy/catalogue/biosciences/DS_Human-Mouse-CD-Maker- Biosciences_CT_DE.pdf; and
Page 57, [00157]: www.bd.com/documents/bd-legacy/catalogue/biosciences/DS_Human-Mouse-CD-Maker- Biosciences_CT_DE.pdf.
Claim Rejections - 35 USC § 112(b)
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 8, 13, 17, 19, 31, and 36 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.
Claims 8, 13, 17, 19, 31, and 36 recite optional and/or preferable limitations as follows:
Claim 8, lines 3-5: “optionally wherein expression of CD34 is less than 25% as compared to the expression level of CD34 in the wild-type counterpart cell that does not harbor a modified gene encoding CD34”;
Claim 13, lines 3-7: “optionally wherein: (a) the lineage-specific cell-surface antigen is CD33, CD123, CLL-1, CD19, CD30, CD5, CD6, CD7, CD38, or BCMA; and/or (b) the hematopoietic cell, or descendant thereof, has reduced or no binding to an agent comprising a binding domain that targets the lineage-specific cell-surface antigen”;
Claim 17, lines 3-5: “optionally wherein the agent is an antibody-drug conjugate or an immune effector cell expressing a chimeric antigen receptor (CAR)”;
Claim 19, line 5: “optionally wherein the malignant cells are cancer stem cells”;
Claim 31, lines 2-4: “optionally wherein the CRISPR/Cas nuclease is a Cas9 nuclease, an spCas nuclease, an saCas nuclease, or a Cpf1 nuclease”; and
Claim 36, lines 7-8: “optionally wherein the nucleic acid encoding the gRNA of (i) and/or the RNA-guided nuclease of (ii) is an RNA, preferably an mRNA or an mRNA analog”.
The use of “optionally”, as recited in the instances above, render the claims indefinite as it is unclear if the limitations that follow, which are narrower embodiments of the preceding limitations, are part of the claimed invention or exemplary embodiments. As such, the metes and bounds of the claim are unclear.
The use of “preferably” in claim 36 also renders the claim indefinite as it is unclear if the limitations that follow, which are narrower embodiments of RNA, are a limiting feature of the claimed invention or exemplary embodiments. As such, the metes and bounds of the claim are unclear.
Additionally, a broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claims 8, 13, 17, 19, 31, and 36 recite broad recitations followed by the term “optionally” or “preferably” which is proceeded by narrower limitations of the broader limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
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 1-2, 8, 10, 13, 16-17, 19, and 47-50 are rejected under 35 U.S.C. 103 as being unpatentable over US 2017/0326179 A1 (Mukherjee, S.) 16 Nov 2017.
US’179 teaches methods of administering an agent targeting a lineage specific cell surface antigen and a population of hematopoietic cells that are deficient in the lineage specific cell surface antigen for immunotherapy of hematological malignancies (abstract). US’179 teaches that the disclosure is based, at least in part, on the discovery that agents comprising an antigen binding fragment that binds a lineage specific cell surface antigen selectively cause cell death of cells expressing the lineage specific cell surface antigen, whereas cells that are deficient for the antigen, e.g., genetically engineered hematopoietic cells, evade cell death caused thereby (page 1, [0007]).
US’179 further teaches that the cell surface lineage specific antigen is CD19, CD20, CD11, CD123, CD56, CD34, CD14, CD33, CD66b, CD41, CD61, CD62, CD235a, CD146, CD236, LMP2, CD22, CD22, CD52, CD10, CD3/TCR, CD79/BCR, and CD26 (page 7, [0071]), indicating that the cell surface lineage specific antigen can be CD34.
US’179 teaches agent targeting treatments including antibodies, antibody-toxin conjugates, and CAR T cells (page 1, [0003]-[0004]). US’179 describes approaches to cancer immunotherapy that target certain classes of lineage specific cell surface antigens on tumor cells. For instance, the CAR T cell treatment is combined with replacement of the non-tumor cells by infusion or reinfusion of a modified population of cells that are deficient for the lineage specific cell surface antigen. Recurrence of the tumor is prevented or decreased by maintaining surveillance of the patient in vivo with the CAR T cells (page 1, [0006]).
US’179 teaches a population of hematopoietic cells deficient in the cell-surface lineage specific antigen, as well as pharmaceutical compositions comprising the hematopoietic cells mixed with a pharmaceutically acceptable carrier (page 24, [0184]; page 23, [0175]).
US’179 teaches that the hematopoietic cells are genetically engineered to be deficient in a cell surface lineage specific antigen and that, in some embodiments, the cell surface lineage specific antigen is the same as that targeted by the agent. A hematological cell is considered to be deficient in a cell surface lineage specific antigen if the hematopoietic cell has substantially reduced expression of the cell surface lineage specific antigen as compared to a naturally occurring hematopoietic cell of the same type as the genetically engineered cell. In some embodiments, the cell has no detectable expression of the antigen. The expression level of the antigen can be assessed by any means known in the art. For example, by detecting the antigen with an antigen specific antibody, flow cytometry methods, or Western blotting. In some embodiments, the expression of the antigen on the genetically engineered cell is compared to the expression on a naturally occurring hematopoietic cell. In some embodiments, the genetic engineering results in a reduction in the expression level of the cell surface lineage specific antigen by at least about 50%, 60%, 70%, 80%, 90%, 91%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% compared to a naturally occurring hematopoietic cell (page 19, [0136]-[0137]). US’179 further teaches that “deficient in the antigen” can be lower than about 40%, e.g., 30%, 20%, 15%, 10%, 5%, or lower of the expression level of the same lineage specific antigen of the naturally occurring counterpart (page 5, [0061]). In some embodiments, the hematopoietic cell is deficient in the whole endogenous gene encoding the antigen. In some embodiments the gene has been deleted. In other embodiments, the cell comprises a portion of the endogenous gene encoding the antigen and the cell expresses a truncated protein portion of the antigen (page 19, [0138]).
US’179 teaches that the genetically engineered hematopoietic cells that are deficient in a cell surface lineage specific antigen can be prepared by a routine method or by a method described. In some embodiments, the engineering is performed using genome editing. As used in US’179, “genome editing” refers to a method of modifying the genome including any protein coding or noncoding nucleotide sequence of an organism to knockout expression of the target gene. In general, genome editing methods involve use of an endonuclease that is capable of cleaving the nucleic acid of the genome, for example, at a targeted nucleotide sequence. Repair of the double-stranded breaks in the genome may be repaired by introducing mutations and/or exogenous nucleic acid may be inserted into the target site (page 19, [0141]-[0143]). Cleavage of a gene region may comprise cleaving one or two strands at the location of the target sequence by a Cas enzyme. Cleavage can result in decreased transcription of a target gene. The cleavage can further comprise repairing the cleaved target polynucleotide by homologous recombination with an exogenous template polynucleotide wherein the repair results in an insertion, deletion, or substitution of the target polynucleotide. US’179 teaches that such modification results in a functionally dead gene (page 20, [0146]-[0147]; Fig. 4).
US’179 further teaches that the cells are hematopoietic cells such as hematopoietic stem cells (HSCs) that are capable of giving rise to both myeloid and lymphoid progenitor cells that further give rise to myeloid cells and lymphoid cells (page 18, [0130]). US’179 teaches that HSCs are characterized by the expression of cell surface markers, which can be used for the identification and/or isolation of HSCs and the absence of cell surface markers associated with commitment to a cell lineage (page 18, [0130]).
US’179 teaches therapeutic methods using an agent comprising an antigen binding fragment that binds a cell surface lineage specific antigen and a population of hematopoietic cells deficient in the cell surface lineage antigen. In such therapeutic methods, the agent recognizes (binds) a target cell expressing the cell surface lineage specific antigen for targeted killing. The hematopoietic cells that are deficient in the antigen allow for repopulation of a cell type that is targeted by the agent. In some embodiments, the treatment of patients can involve the following steps: (1) administering a therapeutically effective amount of an agent targeting a cell surface lineage specific antigen to the patient and (2) infusing or reinfusing the patient with hematopoietic stem cells, either autologous or allogenic, where the hematopoietic cells have reduced expression of a lineage specific disease associated antigen. US’179 teaches that the agent is an immune cell comprising a nucleic acid sequence encoding a chimeric receptor that binds the antigen (page 24, [0184]).
US’179 exemplifies the use of several gRNAs designed to hybridize to the IgC domain of CD33. Each of the gRNAs were expressed along with a Cas9 endonuclease in K562 cells. The expression of CD33 was assessed by flow cytometry and demonstrated a significant reduction in CD33 expression compared to control cells (page 32, [0261]). The CD33 deficient hematopoietic stem cells were also assessed for various characteristics, including proliferation, erythropoietic differentiation, and colony formation. CD33 deficient hematopoietic stem cells underwent differentiation and flow cytometry profiles appeared similar to control cells. the cells were also subjected to MTT assay to measure the metabolic activity of the deficient cells. As shown in Fig. 16, panel C, the CD33 deficient cells performed comparably to control cells. Finally, the ability of the cells to proliferate and form colonies of cells was observed using a microscope colony forming assay. Again, the CD33 deficient cells were able to form colonies to similar extents as the control cells. These results indicate that the CRISPR/Cas9 deletion of a portion of CD33 does not significantly impact the ability of the cells to proliferate, differentiate, or form colonies (page 32, [0262]). US’179 also teaches conditioning regimens for autologous stem cell transfer including total body irradiation (page 30, [0237]).
Although US’179 does not exemplify CD34 as the cell surface lineage specific antigen, it would have been prima facie obvious prior to the effective filing date of the claimed invention to select CD34 as the cell surface lineage specific antigen based on the disclosure of US’179 as a whole. It would have been obvious to use CD34 as the antigen as US’179 considers CD34 as a potential antigen; thus, an ordinarily skilled artisan would have had a reasonable expectation of success. This conclusion of obviousness is further supported by KSR(E) obvious to try. As discussed in detail above, US’179 considers CD34 as a specific antigen among a finite number of identified predictable potential solutions to the recognized need or problem (page 7, [0071]). One of ordinary skill in the art would have been able to pursue the known potential solutions with a reasonable expectation of success in both preparing a genetically engineered hematopoietic cell with a modified CD34 gene, preparing compositions thereof, and using the compositions with targeting agents to treat hematopoietic malignancies as disclosed by US’179.
Regarding claim 10, as discussed in detail above, US’179 teaches complete deletion of the cell surface lineage specific antigen gene and discloses embodiments in which the cells have no detectable expression of the antigen. In these embodiments, there would not be binding to an agent comprising an anti-CD34 binding domain or a CD34 epitope as CD34 would not be expressed on the cell; thereby meeting the limitations of claim 10 (a) and (b).
Additionally, it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to modify CD34 in the hematopoietic cell such that the antigen binding fragment of a specific agent does not bind to it based on the disclosure of US’179. An ordinarily skilled artisan would have been motivated to ensure that the agent does not bind the hematopoietic cell as US’179 teaches that cells that are deficient for the antigen targeted evade cell death caused by the agent comprising the antigen binding fragment (page 1, [0007]).
Regarding claim 13, US’179 teaches additional linage specific cell surface antigens that can be modified including CD33, CD123, CD19, CD30, CD5, CD6, CD7, and CD38 (pages 6-7, [0070]). US’179 also exemplifies CD33 as an antigen (page 27, Example 1), and teaches hematopoietic stem cells expressing both CD33 and CD34 (Table 6, page 28).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to modify the hematopoietic cell taught by US’179 by further modifying an additional antigen disclosed by US’179. It would have been obvious to further modify an additional antigen as US’179 teaches additional antigens that can be modified and also demonstrates the presence of these additional antigens on hematopoietic cells. Thus, an ordinarily skilled artisan would have had a reasonable expectation of success.
Regarding claim 49, as discussed in detail above, US’179 teaches a genetically engineered hematopoietic stem cell comprising a modification in the gene encoding CD34 and does not express an endogenous CD34 protein. While US’179 does not exemplify cells with modifications in a gene encoding CD34, and; therefore does not conclusively demonstrate that the cell would be functionally indistinguishable from a naturally occurring cell, US’179 does provide a reasonable expectation that the cell would be functionally indistinguishable when gRNA is used to modify the CD34 gene. For instance, as discussed in detail above, US’179 exemplifies CD33 deficient hematopoietic stem cells using gRNA and demonstrates that the CRISPR/Cas deletion of a portion of CD33 did not significantly impact the ability of the cells to proliferate, differentiate, or form colonies (page 32, [0262]). Based on this demonstration, one of ordinary skill in the art would have reasonably expected that using CRISPR/Cas deletion of a portion of an antigen disclosed, including CD34, could be performed providing for a functionally indistinguishable cell and cells that are capable of engraftment, particularly using methods disclosed by US’179 which include, for example, the use of conditioning regimens.
Additionally, the claimed functions would flow naturally from following the suggestions of the prior art in which the CD34 gene is modified in the HSCs. MPEP 2145 II. states “The fact that appellant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious.” The MPEP section further states “The recitation of an additional advantage associated with doing what the prior art suggests does not lend patentability to an otherwise unpatentable invention.”
Claims 23-27, 30-31, and 36 are rejected under 35 U.S.C. 103 as being unpatentable over US 2017/0326179 A1 (Mukherjee, S.) 16 Nov 2017 in view of US 9,834,791 B2 (Zhang, F., et al) 05 Dec 2017.
The teachings of US’179 are as discussed in detail above.
As discussed above, US’179 teaches genetically engineered hematopoietic cells, including hematopoietic stem cells, that are deficient in a cell surface lineage specific antigen, including CD34, can be prepared by a routine method or by a method described.
US’179 further teaches the use of CRISPR/Cas9 systems (page 20, [0143]). US’179 utilizes the CRISPR/Cas9 system that hybridizes with a target sequence in a lineage specific antigen polynucleotide, where the CRISPR/Cas9 nuclease and an engineered crRNA/tracrRNA, or single guide RNA. CRISPR/Cas9 complex can bind to the antigen polynucleotide and allow the cleavage of the antigen polynucleotide thereby modifying the polynucleotide (page 20, [0145]). The guide RNAs taught by US’179 can be designed such that the gRNA directs binding of the Cas9-gRNA complexes to a pre-determined cleavage site (target site) in a genome. The cleavage sites may be chosen to release a fragment that contains a region of unknown sequence, or a region containing a SNP, nucleotide insertion, deletion, or rearrangement (page 20, [0146]).
The gRNA, or CRISPR guide sequence, is a nucleic acid comprising a sequence that determines the specificity of a Cas DNA binding protein of a CRISPR/Cas system. The gRNA hybridizes to, either complementary to, partially or completely, a target nucleic acid sequence in the genome of a host cell. The gRNA may be between 15-25, 18-22, or 19-21 nucleotides in length (page 20, [0148]). In addition to the sequence that binds to a target nucleic acid, the gRNA can also comprise a scaffold sequence. Expression of a gRNA encoding both a sequence complementary to a target nucleic acid and scaffold sequence has the dual function of hybridizing to the target nucleic acid and recruiting the endonuclease to the target nucleic acid which results in site specific CRISPR activity. Such a gRNA may be referred to as a single guide RNA (sgRNA) (page 20, [0149]). In other embodiments, the gRNA sequence does not comprise a scaffold sequence and the scaffold sequence is expressed as a separate transcript. In such embodiments, the gRNA sequence further comprises an additional sequence that is complementary to a portion of the scaffold sequence and functions in binding the scaffold sequence and recruiting the endonuclease to the target nucleic acid (page 20, [0151]).
US’179 teaches that genetically engineering a cell comprises introducing a Cas endonuclease into the cell. In some embodiments, the Cas endonuclease and the nucleic acid encoding the gRNA are provided on the same nucleic acid, e.g., a vector. In some embodiments they are provided on different vectors. Additionally, or alternatively, the Cas endonuclease may be provided or introduced into the cell in protein form (page 21, [0154]). US’179 also exemplifies the application of the CRISPR-Cas9 system in targeting CD33 and CD45 (page 27).
US’179; however, does not disclose that the gRNA comprises a targeting domain comprising a sequence selected from the group consisting of instant SEQ ID NOs: 11-15 or the instantly claimed formats of the gRNA.
US’791 provides methods and compositions useful in targeting a payload to, or editing, a target nucleic acid, where a governing gRNA molecule is used to target, a Cas9 molecule, or a Cas9 molecule/gRNA complex (abstract).
US’791 teaches that the CRISPR/Cas system has been adapted for genome editing in eukaryotic cells and that the introduction of site specific double strand breaks allows for target sequence alterations through one of two endogenous DNA repair mechanisms- either non-homologous end-joining (NHEJ) or homology-directed repair (HDR). US’791 discloses methods and compositions, e.g., a Cas9 molecule complexed with a gRNA molecule, that can be used to target a specific location in a target DNA (col. 1, lines 55-63).
US’791 teaches a unimolecular, or chimeric, gRNA comprising, preferably from 5’ to 3’: a targeting domain comprising 15-20 nucleotides which is complementary to a target nucleic acid; a first complementarity domain; a linking domain; a second complementarity domain, which is complementary to the first complementarity domain; a proximal domain; and an optional tail domain (col. 31, lines 24-34).
US’791 teaches that methods for selection and validation of target sequences, as well as off-target analyses, are described in the art. Additionally, software tools can be used to optimize the choice of gRNA within a user’s target sequence, e.g., to minimize total off-target activity across the genome. Each possible gRNA is ranked and the top ranked gRNAs represent those that are likely to have the greatest on-target and the least off-target cleavage. Other functions, e.g., automated reagent design for CRISPR construction, primer design for the on-target Surveyor assay, and primer design for high-throughput detection and quantification of off-target cleavage via next-gen sequencing can also be included in the tool. Candidate gRNA molecules can be evaluated by art-known methods or as described in US’791 (col. 58, lines 3-37).
US’791 teaches exemplary cells that can be manipulated and genes that can be modulated in table VII, starting on col. 150. The cells include lymphocytes T cells, and hematopoietic stem cells (col. 151, Table VII-9 and VII-10) and the proposed genes include CD34 (col. 152, Table VII-13).
US’791 further teaches that modified nucleosides and nucleotides can be present in the nucleic acids, particularly the gRNA (col. 213, lines 33-41). In some embodiments, the modified nucleotides can exhibit a reduced innate immune response when introduced into a population of cells (col. 214, lines 25-42). US’791 teaches modifications including modification of one or more nucleotides with phosphorothioate (col. 215, lines 45-57) or 2’-O-methyl moieties (col. 220, lines 60-64).
It would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to modify the methods and compositions of US’179 by targeting the CD34 gene in hematopoietic cells, including hematopoietic stem cells, based on the disclosure of US’179 as a whole. It would have further been obvious to use the methods disclosed by US’179 and US’791 and optimization that was routine in the art to identify an optimal targeting sequence for the gRNA for targeting the CD34 gene, arriving at the instantly claimed targeting sequences of SEQ ID NOs: 11-15.
It would have been obvious to target CD34 with the gRNA as US’179 considers CD34 as a potential antigen for targeting with the gRNA and CRIPSR/Cas system; thus, an ordinarily skilled artisan would have had a reasonable expectation of success. This conclusion of obviousness is further supported by KSR(E) obvious to try. As discussed in detail above, US’179 considers CD34 as a specific antigen among a finite number of identified predictable potential solutions to the recognized need or problem (page 7, [0071]). One of ordinary skill in the art would have been able to pursue the known potential solutions with a reasonable expectation of success in both preparing a genetically engineered hematopoietic cell with a modified CD34 gene, preparing compositions thereof, and using the compositions with targeting agents to treat hematopoietic malignancies as disclosed by US’179.
Additionally, both US’179 and US’791 teach the inclusion of a targeting domain in the gRNA and teach that the targeting domain is a sequence that determines the specificity of a Cas DNA binding protein of a CRISPR/Cas system and both references teach an approximate length of the targeting domain. The teachings of US’791 demonstrate that methods of selecting and validating targeting sequences is routine in the art and that software tools also exist that can be used to optimize the choice of gRNA within the target sequence to minimize off target activity across the genome. As such, it would have been obvious to an ordinarily skilled artisan to identify the optimal targeting sequence for use in the gRNA and the CRISPR/Cas system for targeting the CD34 gene. MPEP 2144.05 (II) A. states "’[W]here 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.’ In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)” and "It is a settled principle of law that a mere carrying forward of an original patented conception involving only change of form, proportions, or degree, or the substitution of equivalents doing the same thing as the original invention, by substantially the same means, is not such an invention as will sustain a patent, even though the changes of the kind may produce better results than prior inventions."). See also KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007)”.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to AUDREY L BUTTICE whose telephone number is (571)270-5049. The examiner can normally be reached M-Th 8:00-4:00.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Joanne Hama can be reached on 571-272-2911. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/AUDREY L BUTTICE/Examiner, Art Unit 1647
/SCARLETT Y GOON/Supervisory Patent Examiner
Art Unit 1693
Prosecution Insights