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 .
Any rejection of record in the previous office actions not addressed herein is withdrawn. New grounds of rejection are presented herein that were not necessitated by applicant’s amendment of the claims since the office action mailed 1/27/2025. Therefore, this action is not final.
Receipt is acknowledged of an amendment, filed 6/27/2025, in which claims 1, 2, 5, 8, 12, 13, 15 and 22 were amended.
It is noted that the amendment to the claims filed on 6/27/2025 does not comply with the requirements of 37 CFR 1.121(c) because each claim was not provided with the proper status identifier. Claims 15, 18, 22 and 24 should have the status identifier “Withdrawn.” However, in the interest of compact prosecution, the amendment to the claims has been entered. Claims 1-5, 8, 11-15, 18, 22, 24, 28 and 29 are pending.
Election/Restrictions
Applicant’s election with traverse of Group I and the species BCR-ABL, chronic myeloid leukemia (CML), and SEQ ID NOS: 4 and 5 on 8/12/2024 is acknowledged.
Claims 15, 18, 22 and 24 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 8/12/2024.
Claims 1-5, 8, 11-14, 28 and 29 are under consideration.
Specification
The substitute specification filed 6/27/2025 has been entered.
The disclosure is objected to because of the following informalities: The tables at pages 34-35 are not legible.
Appropriate correction is required.
Claim Objections
Claim 1 is objected to because of the following informalities:
1. The claim contains periods after parts labeled “a” and “b.” Each claim must start with a capital letter and end with a period, and periods may not be used elsewhere in the claims except for abbreviations See MPEP § 608.01(m).
2. The phrase “the cleavage without repair” should be amended to recite “cleavage without repair” so that the word “the” is deleted. This will improve the grammar of the claim.
Appropriate correction is required.
Claim 2 is objected to because of the following informalities:
1. The phrase “method according claim 1” should be amended to recite “method according to claim 1” to improve the grammar of the claim.
2. The phrase “the cleavage without repair” should be amended to recite “cleavage without repair” so that the word “the” is deleted. This will improve the grammar of the claim.
Appropriate correction is required.
Claim 5 is objected to because of the following informalities: the recitations of “leads to the expression of fusion gene EWSR1-FLI1 or BCR-ABL” is redundant and should be deleted. Prior to that phrase, the claim lists EWSR1-FLI1 and BCR-ABL as alternatives for expression of a fusion gene. Appropriate correction is required.
Claim 8 objected to because of the following informalities:
In the reply filed 6/27/2025, claim 8 was amended to recite, “wherein the cleavage is in a genomic region other than a coding region or a regulatory region, in an intronic region, or in an intronic region of a genomic amplification other than the splice sites.” It is clear from reading the specification that the claim is intended to be drawn to “wherein the cleavage is in a genomic region other than a coding region or a regulatory region,” and “wherein the cleavage is in an intronic region, or in an intronic region of a genomic amplification other than the splice sites.” At page 16, lines 23-30 of the substitute specification filed 6/27/2025 state the following:
The target of said endonuclease may be in an intron or an exon or a noncoding sequence including promoter and 5' and 3' ends. In a preferred embodiment, the target of said endonuclease is not in a coding sequence or in a regulatory sequence. In a preferred embodiment, the target of the endonuclease or endonucleases is not in an exon or a non-coding sequence that is including a promoter, an enhancer or any other regulatory sequence. In a preferred embodiment, the target of said endonuclease is in an intron. In a more preferred embodiment, the target is in an intron sequence other than the splice sites.
Thus, from reading the specification, it is clear that the claim is not intending to exclude cleavage in an intronic region.
Throughout the disclosure two different embodiments are set forth: (1) the cells comprise a genomic rearrangement that leads to the expression of a fusion gene; and (2) the cells comprise a genomic amplification or rearrangement that leads to the induction or to the overexpression of a cancer inducing gene (e.g., original specification at page 4, lines 5-7 and 19-26). In a preliminary amendment present on the filing date of the instant application, original claim1 was amended to delete the embodiment directed to genomic amplifications. The dependent claim was not amended to be consistent.
It would be remedial to replace the phrase “wherein the cleavage is in a genomic region other than a coding region or a regulatory region, in an intronic region, or in an intronic region of a genomic amplification other than the splice sites” with the phrase “wherein the cleavage is in an intronic region or in an intronic region other than the splice sites.” See the original specification at page 7, lines 1-3 for support.
Appropriate correction is required.
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 1-5, 8, 11-14, 28 and 29 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. This is a new rejection, which has not been necessitated by amendment.
Claim 1 recites the limitation "said fusion gene or cancer inducing gene" in part (b). There is insufficient antecedent basis for this limitation in the claim. The claim provides antecedent basis for only the fusion gene. The claim does not set forth a cancer inducing gene. The specification defines the term “cancer inducing gene” to mean “an oncogene or proto-oncogene that has the potential to cause cancer,” See page 5, lines 27-28. The term “cancer inducing gene” is broader in scope than the fusion gene set forth in the claim. It would be remedial to amend the phrase “said fusion gene or cancer inducing gene” to delete “or cancer inducing gene.”
Claims 2-5, 8, 11-14, 28 and 29 depend from claim 1 and are rejected for the same reason applied to claim 1.
Claim 11 contains the trademark/trade name TALEN. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe the material carrying out the cleaving and, accordingly, the identification/description is indefinite. It would be remedial to amend the claim to delete “(TALEN).”
Claim 11 is vague and indefinite in that the metes and bounds of the phrase “wherein the cleaving is done by an endonuclease selected from a CRISPR associated protein, a zinc-finger nuclease (ZFN) and a transcription activator-like effector nuclease (TALEN)” are unclear. The phrase is unclear in that two different types of cleaving are recited in claim 1: (a) cleaving the genome; and (b) cleaving the expression product. It is uncertain which of the two cleaving events was intended to be limited. It would be remedial to specify which cleaving event(s) are to be limited.
Claim 12 is vague and indefinite in that the metes and bounds of the phrase “wherein the cleaving is done by a Cas protein, w herein the Cas protein is selected from the group consisting of Cas9 and Cas13” are unclear. The phrase is unclear in that two different types of cleaving are recited in claim 1: (a) cleaving the genome; and (b) cleaving the expression product. It is uncertain which of the two cleaving events was intended to be limited. It would be remedial to specify which cleaving event(s) are to be limited.
Claim 14 recites the limitation "the target of said endonuclease" in lines 1-2. There is insufficient antecedent basis for this limitation in the claim. Claim 14 depends from claim 1, which requires “cleaving the genome in at least two sites,” and/or “cleaving the expression product of said fusion gene.” However, claim 1 do not explicitly or inherently limit the cleaving to cleaving by an endonuclease that recognizes a target. Other methods of cleaving were known in the art and, given the plain meaning of the term “cleaving” would be encompassed by the claim (Oike et al. Scientific Reports, Vol. 6, 22275, March 1, 2016, printed as pages 1-7, especially pages 1-2, which teaches that multiple close-proximity double strand breaks are created by carbon ion radiotherapy).
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 2 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 2 depends from claim 1 and recites, “wherein the cancer cells comprise a genomic rearrangement which leads to the expression of the rearranged gene not present in non-cancer cells, which leads to the expression of a fusion gene not present in non-cancer cells.” Claim 1 recites, “said cells comprise a genomic rearrangement which leads to the expression of a fusion gene not present in non-cancer cells.” For the rearrangement to lead to the expression of a fusion gene it must necessarily be expressed. Thus, claim 2 does not add any further limitation to claim 1. 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.
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 1-5, 8, 11-14, 28 and 29 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 a method of eliminating cancer cells in vitro, wherein said cells comprise a genomic rearrangement which leads to the expression of a fusion gene not present in non-cancer cells, said method comprising: (a) cleaving the genome in at least two sites, said cleavage leading to either a deletion, an inversion, a frameshift, cleavage without repair and/or an insertion in the genome of said cancer cells, and/or (b) cleaving the expression product of said fusion gene or cancer inducing gene in at least one site, wherein the expression product is RNA, does not reasonably provide enablement for the methods to be carried out in vivo or for the purpose of treating a subject afflicted with cancer, including chronic myeloid leukemia (CML), except for the prior art applied below, which embodiment does not find support in the disclosure of this application. 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 and use the invention commensurate in scope with these claims. This is a new rejection.
Enablement is considered in view of the Wands factors (MPEP 2164.01(A)). These include: the breadth of the claims, the nature of the invention, the state of the prior art, the level of one of ordinary skill, the level of predictability in the art, the amount of direction provided by the inventor, the existence of working examples, and the quantity of experimentation needed to make or use the invention. All of the Wands factors have been considered with regard to the instant claims, with the most relevant factors discussed below.
Nature of the invention: Claim 1 and its dependent claims are drawn to a method for eliminating cancer cells. The method comprises “a. cleaving the genome in at least two sites, said cleavage leading to either a deletion, an inversion, a frameshift, the cleavage without repair and/or an insertion in the genome of said cancer cells, and/or b. cleaving the expression product of said fusion gene or cancer inducing gene in at least one site, wherein the expression product is RNA.” Dependent claim 3 requires the cleavage of the genome to lead to “a deletion, an inversion, a frameshift, the cleavage without repair or any combination thereof.” Claim 4 limits the method to one comprising cleavage in two sites, or in three sites or in four sites. Claim 5 limits the genomic rearrangement to BCR-ABL (elected species). Claim 8 limits the method to cleavage in an intronic region or in an intronic region of a genomic amplification other than the splice sites. Claim 11 depends from claim 1 and requires the cleaving to be done by an endonuclease selected from a CRISPR associated protein, a zinc-finger nuclease (ZFN) and a transcription activator-like effector nuclease (TALEN). Claim 12 depends from claim 1 and requires the cleaving to be done by a Cas9 or Cas13 protein. Claim 13 depends from claim 1and requires the use of at least one or two guide RNA to target the cleaving of the genome. Claim 14 depends from claim 1 and requires a target of an endonuclease to be in an intron of a fusion gene present in cancer cells and absent in non-cancer cells and wherein said target is not patient-specific. Claim 28 depends from claim 1 and requires the method to treat a subject with chronic myeloid leukemia (CML). Claim 29 depends from claim 1 and requires the method to treat a subject afflicted with cancer. The nature of the invention is complex in that the cleavage must result in elimination of cancer cells in vitro or in vivo, including for the purpose of treating cancer, or more specifically CML.
Breadth of the claims: The nature of the invention is broad in the cancer cells can be present in any environment that is in vitro or in vivo. The nature of the invention is broad in that the cleaving can occur by an act, such as radiation-induced cleavage, chemical-induced cleavage, DNAzyme, Ribozyme, siRNA, or nuclease-mediated cleavage. The claims broadly encompass the cleavage of any two sites in the genome. The claims broadly encompass the cleavage of any number of sites greater than two with no upper limit on the number of cleavage events. While the cancer cell has a translocation, the cleavage does not need to involve the translocation. Additionally, the claims broadly encompass the treatment of any type of cancer where the method of claim 1 is performed on any cancer cells in any environment that is in vitro or in vivo. The complex nature of the subject matter of this invention is greatly exacerbated by the breadth of the claims.
Guidance of the specification and existence of working examples: The specification envisions directing cleavage to a genomic rearrangement, where the genomic rearrangement is cancer causing (e.g., page 4, lines 16-29). The specification envisions limiting genomic modifications to cancer cells, leading to irreversible damage and death of cancer cells without impacting normal cells (e.g., page 4, lines 16-29).
The specification defines the term “cleaving,” “cleave” or “cleavage” to mean “both DNA chains or strands are cut when it is referred to the genome, which is double stranded DNA.” See page 5, lines 6-7. When the term is referred to a DNA or RNA molecule that is single-stranded, it means that only one chain or strand is cut. See page 5, lines 9-10.
The specification envisions using nucleases, such as zinc finger nucleases (ZFN), transcription activator-like effector nucleases (TALEN), and CRISPR related proteins, such as Cas9 to cleave the genome in at least 2 sites, at least 10 sites, or at least 100 sites (e.g., page 6, lines 22-28). The specification envisions cleaving at two sites in a translocation to create an inversion that leads to the death of the cancer cells due to the lack of a fusion protein being produced or preventing a cancer inducing gene from being expressed (e.g., page 8. lines 14-18). The specification envisions using a pair of guide RNAs (gRNA) that target a genomic rearrangement present in the cancer cell (e.g., paragraph bridging pages 18-19). The specification discloses preferred pairs of gRNA (e.g., pages 19-23). The specification envisions targeting a number of different translocations in different types of cancers (e.g., pages 8-13). The specification envisions using Cas13 to cleave RNA of the fusion gene (e.g., page 15).
The working examples teach the design of a pair of sgRNAs targeting introns 3 of EWSR1 and intron 8 of FLI1 (e.g., page 29, lines 10-23; Fig. 1a; Table 2). The specification states, “The design of the sgRNAs in intronic regions guaranteed no modification of the wild type EWSR1 and FLI1 proteins in non-tumour cells because any indel generated by the NHEJ repair of the on-target introns in wild type (WT) genes will be removed in the mRNA.” The working examples demonstrate the ability of the two guide RNAs to direct deletion in model cell lines in vitro (e.g., page 35). The in vitro deletion significantly suppressed cell proliferation as compared to controls (e.g., page 36). Analysis of the in vitro modified cells did not identify any off-target effects by karyotype, array comparative genomic hybridization (aCGH) or next-generation sequencing of 19 genomic regions with the highest homology to the target site (e.g., paragraph bridging pages 36-37). The gene deletion strategy was tested in xenografted tumors in nude mice over 28 days (i.e., human tumors placed into immune compromised mice) (e.g., page 37). The CRISPR editing resulted in reduced tumor growth (e.g., pages 37 and 42).
The working examples teach the design of four pairs of sgRNAs targeting BCR intron 8 and ABL intron 1 (e.g., page 43, lines 1-4; Fig. 11a; Table 2). The pairs of sgRNA were tested for the ability to create a gene deletion of 133.9 kb of genomic BCR-ABL1 DNA (e.g., page 43, lines 4-11). Upon testing in human patient-derived cells, it was confirmed that targeted deletion resulted in a reduction in proliferation, and colony formation with increased apoptosis as compared to control cells (e.g., page 43, lines 8-18). The same cells were placed into athymic mice (i.e., human cells placed into immune compromised mice), and adenoviral delivery of both targeting sgRNAs and Cas9 was tested (e.g., page 43, lines 19-28). Editing resulted in lower tumor volumes over time (e.g., page 43, lines 19-28).
The working examples of the specification tested a series of crRNAs with Cas13 protein for the ability to silence EWSR-FLI1 and BCR-ABL mRNA expression in cell lines (e.g., paragraph bridging pages 43-44; page 44). Growth was suppressed and apoptosis was increased in the cultured cell lines treated with the CRISPR-Cas13 system (e.g., page 44, lines 15-25). Mice bearing xenografts were treated with repeated intratumoral injections of the CRISPR-Cas13 system delivered by adenoviral vectors (e.g., paragraph bridging pages 44-45). The treatment resulted in reduced tumor volume and lower mortality (e.g., paragraph bridging pages 44-45).
Predictability and state of the art: One would have recognized the unpredictability of creating two cleavage events (double-strand breaks, DSBs), such as by using two nucleases, to eliminate cancer cells. Although the specification asserts that targeting the nucleases to introns will not modify the wild type genes, one would have recognized that creating double strand breaks in introns to two different genes can lead to cancer-causing chromosomal translocations. Babin et al (iScience, Vol. 5, pages 19-29, and pages 1/18-18/18 pages of Supplemental Information, July 27, 2017) state the following at page 21, 1st paragraph of text:
The consistent advances in programmable nuclease technology, including ZFNs (zinc-finger nucleases), TALENs (transcription activator-like effector nucleases), and CRISPR/Cas9 RNA-guided nucleases, facilitates easier and more precise genome editing. Particularly, we and others have shown that introduction of DNA double-strand breaks (DSBs) at patient translocation breakpoints enables specific oncogenic translocation formation (Brunet et al., 2009; Piganeau et al., 2013; Choi and Meyerson, 2014; Ghezraoui et al., 2014; Torres et al., 2014).
Babin et al demonstrate that the creation of two double strand breaks in introns of wild type cells results in a de novo translocation and growth advantage after culture without IL-3, whereas only a single cleavage event did not allow for the growth advantage (e.g., page 21, last full paragraph; page 27, 1st paragraph). Thus, one would have recognized the unpredictability in applying the claimed method in vivo where cancer cells are mixed with wild type cells capable of being converted to translocation-containing cells. Additionally, one would have recognized the danger in creating double-strand breaks elsewhere in the genome, including the coding region of wild type genes, and at much larger numbers.
The instant specification acknowledges that that the intracellular delivery of therapeutic molecules is challenging and their tumor specificity is an important motivating factor for developing new therapies, which highlights the importance of specificity (e.g., substitute specification at page 2, lines 20-21). The post-filing art teaches that challenged to applying gene editing to cancer therapy remain, including off-target effects leading to potentially harmful mutations, delivery challenges causing low efficiency, low editing efficiency for larger or more complex mutations, and challenging large-scale genomic edits leading to errors or rearrangements (Atalor et al. International Research Journal of Oncology, Vol. 8, No. 2, pages 179-192, 2025; e.g., section 3.1, pages 183-184). Atalor et al teach that for safe and successful clinical translation, programmable chromosome engineering must overcome the following obstacles: (i) chromosomal off-target effects, (ii) risks of genomic instability, (iii) immune reactions to editing machinery, and (iv) ethical and regulatory issues (e.g., section 5, pages 187-188). For example, Atalor teach that programmable chromosome engineering (PCE) to fix BCR-ABL translocations in leukemia models have occasionally resulted in inadvertent deletion of neighboring genes, which may jeopardize the effectiveness of the treatment (e.g., paragraph bridging pages 188-189). Similarly, the prior art recognizes that challenges to translating the use of CRISPR-Cas13 to therapy include delivery challenges and side effects (Granados-Riveron et al. Cancer Research, Vol. 78, No. 15, pages 4107-4113, July 31, 2018; e.g., page 4109, paragraph bridging columns). Accordingly, translation of gene editing of cells in vitro to in vivo and therapeutic applications was underdeveloped and unpredictable.
One would have recognized the unpredictability of translating results from human tumors implanted into immune compromised mice. The art teaches challenges due to immune reactions to the editing machinery (Atalor et al. 2025; e.g., section 5, pages 187-188). Mice lacking an immune system cannot adequately address this issue. Morgan (Molecular Therapy, Vol. 20, No. 5, pages 882-884, May 2012) state the following at the third column of page 882:
Although the mouse has been the paradigm for understanding human immunology, as Barrett and Melenhorst pointed out in a Commentary in Molecular Therapy last year, human cell and gene therapy researchers need to be careful not to get caught in a “mousetrap.”1 Any study in immunodeficient mice must consider several factors when attempting to extrapolate findings to humans. First and foremost is that the study subject (e.g., an NSG mouse) is a genetically uniform organism that is born and raised in a sterile environment. The clean environment should not be viewed as an irrelevant consequence of animal-handling requirements, because it can have dramatic consequences on experimental outcomes. For example, Paulos and colleagues16 demonstrated that microbial translocation from the gut augments the function of adoptively transferred T cells, suggesting that differences in the extent to which a given mouse room is “clean” could have an impact on experimental results.
The limitations of the utility of tumor xenograft models go beyond the tumor itself and are restricted by the biology of the mouse. Not to belabor a point that has been made many times in other reviews, I will only briefly mention that tumor xenograft models utilize a cancer-treatment model that is based on an animal that, in comparison to humans, is significantly smaller, has a much higher metabolic rate, is inbred, and has a short life span. These differences cannot be overcome. In addition, whereas most human tumors take years to grow, tumor xenografts are transplantable tumors designed to grow to treatment size in weeks, not years. The tumor line chosen to be transplanted is probably one of the most significant reasons for failure of xenotransplantation data to be translated to human clinical results. Monogenic human tumor cell lines are almost exclusively used, and it is now well established that tumor cell lines can bear little resemblance to primary cancers. For an example, one can look at the work in glioblastoma—detailed analysis of genomic stability and gene expression changes revealed considerable differences when primary tumors were compared with established cell lines.17
Thus, it would be unpredictable to extrapolate the short-term results from human tumor xenografts into immune compromised mice to treat tumors in their native environment in animals with competent immune systems and where the genomic DNA of the tumor and host are from the same species of organism.
Amount of experimentation necessary: The quantity of experimentation necessary to carry out the full scope claimed invention is high, as the skilled artisan could not rely on the prior art or the present specification to teach how to make and use the claimed methods. With any method of cleaving one would have to determine how to deliver the given reagent for cleaving (e.g., nucleic acid encoding nucleases) to the appropriate target cells with specificity and efficiency, and how to get sufficient expression to induce at least some therapeutic effect while avoiding the introduction of cancer-causing chromosomal translocations, deletions, etc. in the non-target cells. Since neither the prior art nor the specification provides the answers to all of these questions, it would require a large quantity of trial and error experimentation by the skilled artisan to do so.
In view of the breadth of the claims and the lack of guidance provided by the specification as well as the unpredictability of the art, the skilled artisan would have required an undue amount of experimentation to make and/or use the claimed invention. Therefore, claims 1-5, 8, 11-14, 28 and 29 are not considered to be fully enabled by the instant disclosure.
Response to Arguments - 35 USC § 112
The previous rejection of claims 2, 5, 8, 12 and 13 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, has been withdrawn in view of Applicant’s amendment to the claims in the reply filed 6/27/2025.
The previous rejections of claims 1-5, 8, 11-14, and 28-29 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 (pages 7-10 of the action mailed 1/27/2025), and as failing to comply with the enablement requirement (pages 10-14 of the action mailed 1/27/2025) have been withdrawn in view of Applicant’s amendment to the claims in the reply filed 6/27/2025. The claims were amended to limit the cleaved expression product to RNA.
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 1-3 and 5 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kim et al (Leukemia, Vol. 27, pages 1650-1658, 2013; see the entire reference). This is a new rejection.
Regarding claims 1, 2 and 5, BCR-ABL leukemic cells comprise a genomic rearrangement that leads to the expression of the rearranged BCR-ABL gene not present in non-cancer cells, which leads to the expression of a fusion gene not present in non-cancer cells (e.g., page 1650, left column; page 1651, Cell culture, DNAzyme transfection and drug administration; pages 1652-1653, Cleavage of ABL transcripts reduced ABL expression and cell viability). Kim et al teach a method of eliminating BCR-ABL leukemic cells, comprising cleaving the RNA expression product of the BRC-ABL fusion gene in at least one site with a DNAzyme (e.g., Title; Abstract; pages 1652-1653, Cleavage of ABL transcripts reduced ABL expression and cell viability).
Claim 3 recites, “wherein cleaving the genome leads to a deletion, an inversion, a frameshift, the cleavage without repair or any combination thereof.” This phrase only further limits part (a) of claim 1 and does not limit the cleaving to cleaving the genome. The claim is readable on cleaving the genome and/or cleaving the expression product of said fusion gene.
Regarding claim 3, BCR-ABL leukemic cells comprise a genomic rearrangement that leads to the expression of the rearranged BCR-ABL gene not present in non-cancer cells, which leads to the expression of a fusion gene not present in non-cancer cells (e.g., page 1650, left column; page 1651, Cell culture, DNAzyme transfection and drug administration; pages 1652-1653, Cleavage of ABL transcripts reduced ABL expression and cell viability). Kim et al teach a method of eliminating BCR-ABL leukemic cells, comprising cleaving the RNA expression product of the BRC-ABL fusion gene in at least one site with a DNAzyme (e.g., Title; Abstract; pages 1652-1653, Cleavage of ABL transcripts reduced ABL expression and cell viability).
Claims 1-3, 5, 28 and 29 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Hadwiger et al (US Patent No. 7,994,307 B2; see the entire reference).
Regarding claims 1, 2, 5, 28 and 29, Hadwiger et al teach the Philadelphia chromosome (Ph) is generated by a reciprocal translocation between the long arms of Chromosome 9 and Chromosome 22 in almost all patients with chronic myelogenous leukemia (CML), where the translocation leads to the formation of an oncogenic Bcr-Abl fusion gene from which the Bcr-Abl fusion protein is expressed (e.g., paragraph bridging columns 1-2). Hadwiger et al teach that the breakpoint of the Bcr-Abl translocation is a leukemia-specific sequence, which makes it an ideal target for therapeutic RNAi approach (e.g., column 2, lines 14-40). Hadwiger et al teach a method of treating CML currently being treated with a cytotoxic agent, such as imatinib mesylate, comprising administering a composition that includes an iRNA agent that targets the mRNA encoding a Bcr-Abl fusion protein for cleavage (e.g., column 3, lines 1-15; paragraph bridging columns 8-9; column 20, line 33 to column 21, line 35).
Claim 3 recites, “wherein cleaving the genome leads to a deletion, an inversion, a frameshift, the cleavage without repair or any combination thereof.” This phrase only further limits part (a) of claim 1 and does not limit the cleaving to cleaving the genome. The claim is readable on cleaving the genome and/or cleaving the expression product of said fusion gene.
Regarding claim 3, Hadwiger t al teach the Philadelphia chromosome (Ph) is generated by a reciprocal translocation between the long arms of Chromosome 9 and Chromosome 22 in almost all patients with chronic myelogenous leukemia (CML), where the translocation leads to the formation of an oncogenic Bcr-Abl fusion gene from which the Bcr-Abl fusion protein is expressed (e.g., paragraph bridging columns 1-2). Hadwiger et al teach that the breakpoint of the Bcr-Abl translocation is a leukemia-specific sequence, which makes it an ideal target for therapeutic RNAi approach (e.g., column 2, lines 14-40). Hadwiger et al teach a method of treating CML currently being treated with a cytotoxic agent, such as imatinib mesylate, comprising administering a composition that includes an iRNA agent that targets the mRNA encoding a Bcr-Abl fusion protein for cleavage (e.g., column 3, lines 1-15; paragraph bridging columns 8-9; column 20, line 33 to column 21, line 35).
Claims 1-4, 8, 11 and 14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Piganeau et al (Genome Research, Vol. 23, pages 1182-1193, 2013; see the entire reference).
Regarding claims 1-4, Piganeau et al teach cleaving the genome in two sites in patient-derived SUDHL-1 cells carrying a t(2;5)(p23;q35) translocation, where the cells express a NPM1-ALK fusion gene from der(5) (e.g., page 1188, Reversion of the NPM1-ALK translocation; Fig. 3B; Fig. 4; Supplementary Figure 6). Piganeau et al teach that the cleavage results in reversal of the translocation with an insertion “tag” remaining relative to the wild type chromosome (e.g., page 1188, Reversion of the NPM1-ALK translocation; Fig. 4).
Regarding claim 8, Piganeau et al teach the method where the first site is cleaved by TALNPM, which targets NPM1 intron 4, and the second site is cleaved by TALALK, which targets ALK intron 16 (e.g., page 1186, left column, 1st full paragraph; page 1188, Reversion of the NPM1-ALK translocation; Fig. 3B; Fig. 4; Supplementary Figure 6).
Regarding claim 11, Piganeau et al teach the method where the cleaving is done by transcription activator-like effector nucleases, TALNPM and TALALK (e.g., page 1186, left column, 1st full paragraph; page 1188, Reversion of the NPM1-ALK translocation; Fig. 3B; Fig. 4; Supplementary Figure 6).
Regarding claim 14, Piganeau et al teach the targets of the nucleases, TALNPM and TALALK, are in an intron of a fusion gene present in cancer cells containing the translocation, where the translocation is not present in non-cancer cells (e.g., paragraph bridging pages 1182-1183; page 1186, left column, 1st full paragraph; page 1188, Reversion of the NPM1-ALK translocation; Fig. 3B; Fig. 4; Supplementary Figure 6). Piganeau et al teach that the process was also carried out on another ALCL patient-derived cell line, and also obtained revertant breakpoint junctions with small insertions (e.g., page 1188, Reversion of the NPM1-ALK translocation), indicating that the targets of TALNPM and TALALK are not patient-specific.
Response to Arguments - 35 USC § 102
Applicant’s arguments, see pages 10-14, filed 6/27/2025, with respect to the rejection of claims 1-5 and 11-13 under 35 U.S.C. 102(a)(1) as being anticipated by García-Tuñón et al (2017) have been fully considered and are persuasive. The previous rejection of claims 1-5 and 11-13 has been withdrawn.
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.
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.
Claim(s) 12 and 13 are rejected under 35 U.S.C. 103 as being unpatentable over Piganeau et al (Genome Research, Vol. 23, pages 1182-1193, 2013; see the entire reference) in view of Babin et al (iScience, Vol. 5, pages 19-29, and pages 1/18-18/18 pages of Supplemental Information, July 27, 2017; see the entire reference).
The teachings of Piganeau et al are described above and applied as before.
Piganeau et al do not teach the method where the cleavage of the genome in at least two sites is done by a Cas9 protein and at least one guide RNA.
Babin et al state, “The consistent advances in programmable nuclease technology, including ZFNs (zinc-finger nucleases), TALENs (transcription activator-like effector nucleases), and CRISPR/Cas9 RNA-guided nucleases, facilitates easier and more precise genome editing.” See page 21, 1st full paragraph of text. Babin et al note that Piganeau et al. 2013 has shown that introduction of DNA double-strand breaks (DSBs) at patient translocation breakpoints enables specific oncogenic translocation formation (e.g., page 21, 1st full paragraph of text). Babin et al teach the use of CRISPR/Cas9 technology to induce specific chromosomal translocations, specifically by targeting Cas9 to murine Npm1 intron 4 and Alk intron 19 to induce concomitant DSBs and NPM1-ALK1 translocation (e.g., page 21). Babin et al teach that the sgRNAs were designed using the CRISPOR designer tool available online (e.g., Supplementary Information, page 14/18, 1st full paragraph).
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 method of reversing a NPM1-ALK1 translocation of Piganeau et al to substitute each TALEN with a Cas9 protein directed by a guide RNA to the same target, because Babin et al teach that TALENs or CRISPR/Cas9 RNA-guided nucleases can be used for genomic rearrangements. One would have had a reasonable expectation of success in making such a substitution, because Babin et al demonstrate that CRISPR-Cas9 RNA-guided nucleases can create the same type of translocation, and an online program can be used to predictably design guide RNA. One would have made such a substitution in order to receive the predictable result of using a type of nuclease suitable for reversing a genomic rearrangement.
Response to Arguments - 35 USC § 103
Applicant’s arguments, see pages 14-18, filed 6/27/2025, with respect to the rejections under 35 U.S.C. 103 based on the application of the García-Tuñón et al (2017) reference and others have been fully considered and are persuasive. The previous rejections of have been withdrawn.
Conclusion
No claim is allowed.
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Jennifer Dunston
Supervisory Patent Examiner
Art Unit 1637
/Jennifer Dunston/Supervisory Patent Examiner, Art Unit 1637
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