Notice of Pre-AIA or AIA Status
The examiner prosecuting the application has changed.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
This action is written in response to applicant’s correspondence received on 10/22/2025. Claims 38, 40, 44, 47-49, 87-98 are currently pending.
Detailed Action
Applicant’s response and claim amendments filed on 10/22/2025 are received and entered.
In the Response to Restriction, Applicant’s election, without traverse, of claims 38, 40, 44, and 47-49 in the reply filed on 03/19/2025 is acknowledged.
Applicant’s election of species with respect to claim 40; nucleotides 1801-1970 of SEQ ID NO: 42; with respect to claim 44 applicant’s election of; a) a first DSB is within nucleotides 1801-1970 of SEQ ID NO: 42 and a second DSB is within nucleotides 2051-2156 of SEQ ID NO: 42; and with respect to claim 47 applicant’s election of; a) SEQ ID NO: 1 and SEQ ID NO: 2; are acknowledged
Claims 48 and 49 have been withdrawn from examination in a prior office action.
Though applicants, in their response, argue that claim 1 has been amended, claim has been amended. Applicants are advised to clarify the records as to the pendency of claim 1. Claim is considered canceled. Claim 38 has been amended and new claims 97 and 98 are added in the response filed on 10/22/2025. Proper support in the specification has been acknowledged for the new claims and no new matter has been added.
Priority
Applicant claims priority to US Provisional Application 63/085,636, filed on 9/30/2020.
Any rejections/objections not repeated/presented here are withdrawn.
New Rejections
Claim Rejections - 35 USC § 102
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 38, 40, 44, and 87-98 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Cowan et al. (WO 2017/109757 A1, published 6/29/2017).
The applied reference (Cowan) has a common assignee (CRISPR Therapeutics AG) with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2) and 35 U.S.C. 102 (a)(1) as being published outside of the one year grace period provided by the effective filing date.
Regarding claim 38, Cowan teaches a method using CRISPR/Cas9 to edit the C9ORF72 gene in a human cell (see paragraph 0017 and 0215) by introducing into the cell one or more DNA endonucleases to effect one or more double-stranded breaks within or near the C9ORF72 gene or other DNA sequences that encode regulatory elements of the C9ORF72 gene that results in permanent deletion, insertion, or correction of the expanded hexanucleotide repeat within or near the C9ORF72 gene (see paragraph 0020). Furthermore, Cowan teaches editing within or near a locus of the first exon of the C9ORF72 gene (see paragraph 0023). Cowan also teaches SEQ ID NO: 2855 and 2827, which have 100% sequence identity to SEQ ID NO: 1 and 2, respectively.
Regarding claim 38, though Cowan does not directly teach SEQ ID NO: 42, SEQ ID NO: 42 of the instant application is a 2900 nucleotide fragment derived from nucleotide positions 3001-5900 of the human C9ORF72-SMCR8 complex on chromosome 9, shown below.
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Since Cowan teaches the target of gene editing as the human C9ORF72 gene, and the C9ORF72 gene comprises SEQ ID NO: 42 of the instant application, SEQ ID NO: 42 was known in the art as being a target for the treatment of amyotrophic lateral sclerosis, as taught by Cowan (see paragraph 0017).
Furthermore, Cowan teaches SEQ ID NO: 1 (T11) and SEQ ID NO: 2 (T7) as SEQ ID NO. 2855 and 2827, respectively, in its entirety. Though Cowan does not specifically disclose positions T11 and T7, the gRNA of SEQ ID NO: 2855 and 2827 will bind and direct DSBs at the exact same positions (T11 and T7) as SEQ ID NO: 1 and 2 as a result of having the exact same structure. Furthermore, the ABSS alignment of SEQ ID NO: 2855 and 2827 of Cowan and SEQ ID NO: 42 of the instant application are shown below. As evident by the results, SEQ ID NO: 2855, or SEQ ID NO: 1 of the instant application, binds to region 1864-1883 nucleotides of SEQ ID NO: 42 and SEQ ID NO: 2827, or SEQ ID NO: 2 of the instant application, binds to region 2062-2081 of SEQ ID NO: 42. Therefore, Cowan fully anticipates claim 38.
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Regarding claim 40, Cowan discloses the target as the C9ORF72 gene, specifically the hexanucleotide repeat expansion (HRE). Furthermore, Cowan discloses targeting other DNA sequences that encode regulatory elements (such as exons) (see paragraph 0017). As C9ORF72 gene comprises SEQ ID NO:42 to its entirety, Cowan teaches the region of the C9ORF72 gene including nucleotides 1801-1970. Furthermore, Cowan teaches SEQ ID NO: 2855, which shown above, targets regions 1864-1883 of SEQ ID NO: 42.
Regarding claim 44 Cowan teaches SEQ ID NO: 2855 and 2827 which will target the same positions as SEQ ID NO: 1 and 2 (T11 and T7), between nucleotides 1801-1970 and 2051-2156. This is supported by the ABSS alignment of SEQ ID NO: 2855 and 2827 of Cowan with SEQ ID NO: 42 of the instant application, shown above. Cowan also teaches delivering to a cell one or more DNA endonucleases to affect one or more single-strand breaks or one or more double strand breaks (see paragraph 0018).
Regarding claim 87, Cowan teaches where in some embodiments, the one or more gRNAs are single-molecule guide RNA (sgRNAs) (see paragraph 0051).
Regarding claim 88, Cowan teaches where the guide RNA can be expressed from the same DNA, or can be delivered as an RNA. The RNA can be chemically modified to alter or improve its half-life, or decrease the likelihood or degree of immune response (see paragraph 0468).
Regarding claim 89, Cowan teaches in further alternative embodiments, the DNA endonuclease may be delivered as one or more polypeptides, either alone or pre-complexed with one or more guide RNAs, or one or more crRNA together with a tracrRNA (see paragraph 0448).
Regarding claim 90, Cowan teaches in some embodiments, Cas9 or Cpf1 mRNA, gRNA, and donor template are either each formulated separately into lipid nanoparticles or all co-formulated into a lipid nanoparticle (see paragraph 0068).
Regarding claim 91 and 92, Cowan teaches where Cas9 or Cpf1 mRNA is formulated into a lipid nanoparticle, and both the gRNA and donor template are delivered to the cell by a viral vector. In some embodiments, the viral vector is an AAV vector (see paragraph 0467).
Regarding claim 93, Cowan teaches where for delivery, AAV vector serotypes can be matched to target cell types. In Table 2 (see paragraph 0464), Cowan teaches AAV9 can be used to target liver, lung, and skeletal muscle cells.
Regarding claim 94, Cowan teaches in the brief description of sequence listings, SEQ ID NO: 1-6148 are 20bp spacer sequences for targeting the C9ORF72 gene with a S. pyogenes Cas9 endonuclease (see paragraph 0082).
Regarding claim 95, Cowan teaches in some embodiments, options to deliver the Cas9 nuclease can be as a DNA plasmid, as a mRNA, or as a protein (see paragraph 0467).
Regarding claim 96, Cowan teaches in another method, method 7, the present disclosure provides a method wherein the editing step comprises introducing into the iPSC one or more DNA endonucleases to effect one or more SSBs or DSBs within or near the C9ORF72 gene or other DNA sequences that encode regulatory elements of the C9ORF72 gene that results in permanent deletion, insertion, or correction of the expanded hexanucleotide repeat within or near the C9ORF72 gene. A deletion of the hexanucleotide repeats in iPSC cells due to the method of presenting an endonuclease would result in a reduction of hexanucleotide repeat containing transcripts when compared to cells that do not have the method introduced.
Regarding claim 97, Cowan teaches claim 3 and 7, which is an ex vivo method for treating a patient with ALS or FTLD comprising of introducing DNA endonucleases to effect one or more single-stranded breaks or double-stranded breaks within or near the C9ORF72 gene that results in permanent deletion, insertion, or correction of the expanded hexanucleotide repeat within or near the C9ORF72 gene or other DNA sequences that encode regulatory elements of the C9ORF72 gene.
Regarding claim 98, Cowan discloses claim 28 and 29, wherein the present invention provides an in vivo method for treating a patient with ALS comprising the step of editing within or near the C9ORF72 gene in a cell of a patient or other DNA sequences that encode regulatory elements of the C9ORF72 gene. Claim 29 of Cowan teaches wherein the editing step comprises introducing into the cell one or more DNA endonucleases to the C9ORF72 gene.
In view of the foregoing, it is clear Cowan anticipates claims 38, 40, 44, and 87-98.
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.
Claims 47 is rejected under 35 U.S.C. 103 as being obvious over Cowan et al. (WO 2017/109757 A1, published 6/29/2017) in view of Nakanishi et al. (Highly multiple guide RNA expression units of CRISPR/Cas9 were completely stable using cosmid amplification in a novel polygonal structure, J Gene Med., Volume 21, Issue 11, published 2019).
The applied reference (Cowan) has a common assignee (CRISPR Therapeutics AG) with the instant application. Based upon the earlier effectively filed date of the reference, it constitutes prior art under 35 U.S.C. 102(a)(2) and 35 U.S.C. 102 (a)(1) as being published outside of the one year grace period provided by the effective filing date.
Regarding the method of claim 38, which claim 47 depends on, Cowan teaches a method using CRISPR/Cas9 to edit the C9ORF72 gene in a human cell (see paragraph 0018) by introducing into the cell one or more DNA endonucleases to effect one or more double-stranded breaks within or near the C9ORF72 gene or other DNA sequences that encode regulatory elements of the C9ORF72 gene that results in permanent deletion, insertion, or correction of the expanded hexanucleotide repeat within or near the C9ORF72 gene (see paragraph 0020). Furthermore, Cowan teaches editing within or near a locus of the first exon of the C9ORF72 gene (see paragraph 0023). Cowan also teaches SEQ ID NO: 2855 and 2827, which have 100% sequence identity to SEQ ID NO: 1 and 2, respectively, and targets nucleotides 1801-1970 and 2051-2156 of SEQ ID NO: 42.
Regarding claim 47, Cowan teaches SEQ ID NO: 2855 which corresponds with 100% identity to SEQ ID NO: 1 and SEQ ID NO: 3385 or SEQ ID NO: 2848 which has 100% identity with SEQ ID NO: 6 and SEQ ID NO: 8 of the instant application, respectively.
Cowan does not teach the use of one or more gRNAs comprising of a pair of gRNAs and further comprising of a second pair (four or more gRNAs total).
Regarding claim 47, Nakanishi teaches simultaneous expression of multiplex guide RNA and Cas9/Cas9 derivative is attractive for the efficient knockout of genes and a safe double-nicking strategy (see background). Multiple gRNA expression is often desired for several reasons. First, the simultaneous modification of several loci/genes in the same cell is useful in basic research fields and can be valuable for genome editing therapy. Genome of cancer cells usually contain multiple mutated genes, which accelerate abnormal growth. Therefore, simultaneous disruption of multiple genes is desired to stop the develop and growth of cancer. Second, although single cleavage in the cell genome is immediately repaired by the end-joining mechanism, two simultaneous cleavages in one target gene achieves efficient gene knockout via irreversible deletion. Third, the strategy of double nicking using Cas9 nickase, a mutated Cas9 introducing a nick instead of a cleavage, drastically increases cleavage specificity and reduces off target activity, which contributes to safety (see introduction). This strategy requires two gRNA for one cleavage and multiple cleavages in one target gene guarantees disruption even if cleavage efficiency is low (see introduction). Nakanishi further teaches a method of Four-guide Tandem where four gRNA-expressing units are specifically connected to produce an array, cloned into a closmid, show that up to 16 multiple gRNA-expressing units were stably amplified (see introduction and discussion).
It would have been obvious, to one with ordinary skill in the art, to combine the teachings of Cowan and Nakanishi to arrive at the claimed invention of a CRISPR editing system comprising of two pairs of gRNAs (four total), before the effective filing date.
One would have expected a reasonable chance of success as Nakanishi teaches that up to 16 multiplex gRNA-expressing units were stably amplified, indicating that eight simultaneous double-nicking cleavages are possible (see discussion). Furthermore, Nakanishi showed multiple gRNAs were able to disrupt target gene expression at multiple sites using HEK293T cells expressing the target HBV X gene. Nakanishi teaches Fig. 5B which shows as the intensity of the bands of 4g, 8g, and 12g decreased, the number of guides increased, which might suggest that the additional multiple guides can disrupt targets more efficiently (see section 3.4).
One would be motivated to combine the teachings as Cowan teaches the method of editing a C9ORF72 gene in a human cell is to reduce or delete the hexanucleotide repeat which is a known factor in ALS. Cowan aims to disrupt this by targeting the repeats or regulatory elements of the C9ORF72 gene such as exon 1a. Nakanishi shows that by using a multiplex gRNA system with gRNA pairs (up to 8 pairs), one could create multiple nicks in a region of the C9ORF72 gene that would allow for a more efficient gene knockout (see introduction). This is because Nakanishi teaches single cleavage in the cell genome is immediately repaired by the end-joining mechanism, two simultaneous cleavages in one target gene achieves efficient gene knockout via irreversible deletion. Therefore, the combination of the two arts would allow one to better delete regions of the C9ORF72 gene in order to eliminate or reduce the number of hexanucleotide repeat expansions.
Response to Applicant’s Arguments
Regarding claims 38, 40, 44, 47, and 87-96 being rejected under 35 U.S.C. 103 as being unpatentable over Mueller et al. (WO 2018/208972 A1), Cowan et al. (US 20210260219 A1), and Jensen et al. (US 2016/0108396 A1), applicant argues that Cowan is disqualified as prior art under the 35 U.S.C. 102(b)(2)(C) exception as Cowan and the instant application are deemed to have been owned or subject to an obligation of assignment to the same person, i.e. CRISPR Therapeutics AG.
Applicant’s arguments are found persuasive, however, are still moot as Cowan (WO 2017/109757 A1, published 6/29/2017) qualifies as 102(a)(1) prior art and discloses the limitations of the invention as described above. Furthermore, applicant argues Cowan discloses 18807 gRNA sequences that can target the C9ORF72 gene, therefore the Examiner’s motivation of picking and choosing these two sequences out of 18807 gRNA sequences is unsubstantiated by any reasoning and rational underpinning other than the knowledge gleaned from the Applicant’s claims. Examiner disagrees as Cowan discloses in paragraph 0082 that SEQ ID NOs: 1-6148 are specifically 20 bp spacer sequences for targeting the C9ORF72 gene with a S. pyogenes Cas9 endonuclease. Based off the claim language and specification of the instant specification, Cowan teaches the structural limitations of the claimed invention, the inherent binding sites associated with the disclosed gRNA sequences, and the target gene without secondary sources. As a result of the information disclosed in Cowan and the publication date of the WO document, Cowan qualifies as anticipatory art and obviousness analysis is not required.
Maintained Rejections
Claim Rejections - 35 USC § 112
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 38, 40, 44, 47, 87-96, and 98 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 the claimed method of editing out Exon 1a of the C9ORF72 gene in a human cell in vitro, does not reasonably provide enablement for the method of editing a C9ORF72 gene in a human cell through the deletion of exon 1a in vivo. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to utilize the invention commensurate in scope with these claims.
Scope of enablement
The factors to be considered in determining whether a disclosure would require undue experimentation include: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the specification; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 8 USPQ2d, 1400 (CAFC 1988) and MPEP 2164.01.
The breadth of the claims: The claims 38, 40, 44, 47 and 87-96 and 98 all address “A method for editing a C90RF72 gene in a human cell by gene editing (claim 38)…”. Looking for guidance in the specifications, applicant states “the present application provides materials and methods for treating a patient with Amyotrophic Lateral Sclerosis (ALS)”. As the claim currently recites a “human” gene, the BRI for this statement for utility and therapeutic effect would be that the applicant intends to claim treatment of ALS in affected individuals, wherein said individuals are humans.
The nature of the invention: The invention as instantly claimed encompasses a method of editing a C90RF72 gene in a human cell in vitro and in vivo by gene editing, comprising delivering to the cell one or more CRISPR systems comprising one or more guide ribonucleic acids (gRNAs) and one or more Cas9 endonucleases that effect double-stranded breaks (DSBs) within a region of the C90RF72 gene that causes a permanent deletion of the hexanucleotide repeat of the C90RF72 gene. In ¶23 applicant further describes “In some embodiments, the methods described herein comprise introducing into the cell a guide ribonucleic acid (gRNA), and wherein the DNA endonucleases is a Cas9 or Cpf1 endonuclease that effect a single double-strand breaks (DSBs) within the transcription start site of exon 1a of the C9ORF72 gene that renders the transcription start site to be non-functional.”
The state of the prior art: Practicing gene editing methods in vivo have potential challenges. Cox, D., Platt, R. & Zhang, F. Therapeutic genome editing: prospects and challenges. Nat Med 21, 121–131 (2015) states “CRISPR-Cas systems have demonstrated the ability to effectively edit cell lines, but they are often unreliable in editing primary cells, certain tissues, and in patient's bodies. Furthermore, in general, the editing efficiency in vivo is much lower than in vitro. The reasons for this phenomenon are largely attributed to the lack of efficient delivery methods for Cas endonucleases…” ”In sum, every approach (for delivery) has some advantages and disadvantages (Table 1) and the success of CRISPR-based clinical applications will largely depend on the further development of suitable carriers for delivering the CRISPR components, often requiring huge consortium efforts and long-term studies.”
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Another challenge of in vivo gene editing the amount of genome modification in a target cell population required to create a therapeutic effect differs depending on the disease, where the efficacy of most editing treatments will be improved with increased editing rates. Since NHEJ-mediated DSB repair is active in most cell types and is relatively efficiency, the primary challenge to date has been to increase the efficiency of HDR. So far, applications of HDR in genome editing have been limited primarily to dividing cells because of the selective expression of HDR machinery during cell division and its downregulation in slowly cycling or post-mitotic cells. Cell cycle regulation can now by somewhat bypassed for slowly cycling cell types through stimulation of mitosis with pharmacologic agents ex vivo. However, truly post-mitotic cells are unlikely to be amendable to such manipulation, limiting the applicability of this strategy (see section titled ‘Increasing efficacy of gene correction’ of Cox).
At the time of filing, the method of delivering a CRISPR system to an in vivo model either through iPSCs or AAVs in order to target the C9ORF72 gene for a therapeutic effect was not well established. According to Dong et al. (Knock in of hexanucleotide repeat expansion in the C9ORF72 gene induces ALS in rats, Animal Model and Experimental Medicine, Volume 3, Issue 3, pgs. 237-244, published 8/7/2020), the development of animal models expressing the ALS phenotype was being established, however, offers no insight into administering CRISPR systems to treat said phenotype. This is further supported by in Cowan et al., where Cowan discloses in vivo testing of CRISPR Cas9 systems in a mouse model with either a normal or extended hexanucleotide repeat complement. However, both the Tg line 112 mice and the control line 8 mice are viable, fertile, and did not develop any locomotor or cognitive phenotype by 16 months of age (see paragraph 0750). Cowan also only recited that gRNAs will be tested in mice models but offers no further disclosure on experimental results. While there is established prior art showing CRISPR/Cas9 targeting the SOD1 gene in mice models for the treatment of ALS, such as Gaj et al. (In vivo genome editing improves motor function and extends survival in a mouse model of ALS, Science Advances, Volume 3, Issue 12, published 2017), targeting the C9ORF72 gene in animal models yielded no results, in 2020, absent evidence to the contrary. As a result, the state of the prior art is unpredictable to whether one could administer a CRISPR system to target C9ORF72 to an in vivo model would yield a therapeutic effect.
Furthermore, in Morrice et al. (Animal models of amyotrophic lateral sclerosis: a comparison of model validity, Neural Regeneration Research, Volume 13, Issue 12, pgs. 2050-2054, published 12/2018), it is stated that mice are the most common species used to model ALS. However, to date, therapeutics that have been developed in mouse gene models have failed to translate to effective interventions in humans, challenging the use of these models for therapeutic screening (see introduction). Even in a post filing date art, Bonifacino et al. (Nearly 30 Years of Animal Models to Study Amyotrophic Lateral Sclerosis: A Historical Overview and Future Perspectives, Int. J. of Mol. Sci., Volume 22, Issue 22, published 11/12/2021) discloses different animal models used to study ALS. However, Bonifacino states “there is no doubts that the models here summarized have been playing a key role in unravelling the myriad of cellular and molecular determinants that are involved in ALS and its progression, and in showing the multifactorial and non-cell autonomous nature of this disease. With regards to mammal models, especially rodents, it is evident that none fully recapitulate the characteristics of the human disease…As for the predictive potential, interspecies and intraspecies variation could certainly play a major role in complicating the interpretation of the results and making their translation to the clinic not so straightforward. As a matter of fact, the very many therapies showing beneficial effects in animal studies fail to significantly impact the disease progression in humans” (see section 13. Translational Burdens and Usefulness of In Vivo ALS Models).
It is clear that the state of the prior art shows that even In vivo models struggle to characterize the progression and mechanisms of ALS with regards to humans.
The level of one of ordinary skill; a person having ordinary skill in the art would be able to design guide RNAs, and then create an AAV or a recombinant expression vector which contains those RNAs as well as mRNA encoding the SpCas9 polypeptide. Given the C90RF72 gene sequence as well as the location of the hexanucleotide repeat of the C90RF72 gene, a person having ordinary skill in the art could design a CRISPR systems comprising one or more guide ribonucleic acids (gRNAs) and one or more site-directed deoxyribonucleic acid (DNA) endonucleases, and wherein the one or more site-directed DNA endonucleases are Cas9 endonucleases that effect double-stranded breaks (DSBs) within a region of the C90RF72 gene that causes a permanent deletion of the hexanucleotide repeat of the C90RF72 gene. Treating a person with this designed CRISPR system, however, is exponentially more complicated for the reasons stated above including the need for development of tissue specific delivery, more specific and less immunogenic delivery vectors, reduction of off-target effects, and enhanced control over editing outcomes, improving both the accuracy and precision of genome editing.
The level of predictability in the art; due to the need for development of tissue specific delivery, more specific and less immunogenic delivery vectors, reduction of off-target effects, and enhanced control over editing outcomes, the predictability of side effects of treatment in vivo is still extremely low, as reviewed in Cox et. al. in 2015, as well as Pacesa et. al. in 2024. Relying on the DSB repair mechanism can be problematic. According to Cox et. al. in 2015 “The efficiency of NHEJ and HDR mediated DSB repair varies significantly by cell type and cell state, NHEJ is most of the time more active than HDR. This difference in activity makes treating diseases that require gene correction or insertion of a gene more challenging than those requiring gene inactivation. NHEJ is thought to be active throughout the cell cycle and has been observed in a variety of cell types, including dividing and post-mitotic cells. Therefore, NHEJ may be used to facilitate high levels of gene disruption in target cell populations. In contrast, HDR acts primarily during S/G2 phase, and is therefore largely restricted to cells that are actively dividing, limiting treatments that require precise genome modifications to mitotic cells.”
The amount of direction provided by the inventor; The specification gives, largely, information about gRNA design (location) to target the G4C2 hexanucleotide repeat (¶14-17, 26-48, and Fig2,3,), the Cas9 sequence (mostly SpCas9 polypeptide, or a recombinant expression vector comprising a nucleotide sequence encoding the SpCas9 polypeptide or SluCas9)(¶43-49 and Fig 10-11) and the viral vector is an adeno-associated viral (AAV) vector (¶43-50).
The existence of working examples; fig 4, 5, 6 and 8 example 1 ¶53-59 summarize the data of examples 1-3 (¶ 231-262 and tables 3-5) which come from in vitro or ex-vivo cell studies done on cell lines and iPSCs with various (49) pairs of gRNAs. The data shows the extent (%) of knockdown of mRNA transcripts containing Exon 1a (which include the G4C2 hexanucleotide repeat in the C90RF72 gene).
Furthermore, in the prior art of Cowan (WO 2017/109757 A1, published 6/29/2017), which follows a similar method of gene editing using a CRISPR/Cas9 system, Cowan discloses a mouse model containing the human C9ORF72 gene with either a normal hexanucleotide repeat complement or an expanded hexanucleotide repeat. However, Cowan only discloses gRNAs will be tested in animals to assess their ability to alter the hexanucleotide repeat expansion in C9ORF72 and produce phenotypic changes, but provided no evidence if there was any success in altering the repeat expansion or recording any phenotypic changes (see paragraph 0752).
The quantity of experimentation needed to make or use the invention based on the content of the disclosure; overall the entire application is directed to in vitro or ex-vivo cells and may be enabling for the excision of the G4C2 hexanucleotide repeat in Exon1a of the C90RF72 gene in a human cell by gene editing. There are many obvious hurdles as well as unknown complications, as discussed above, before the application could be enabling for treatment through the modification of a human C9ORF72 gene in vivo.
Response to Arguments
Applicant’s arguments filed on 10/22/2025 have been fully considered but they are found not persuasive. Please note that MPEP 2107 states guidelines for the utility requirement. Here, the understood utility of the invention, to one with ordinary skill in the art, is the editing of a C9ORF72 gene in a human cell, resulting in a therapeutic effect as a result of the gene editing, wherein the therapeutic effect is reducing hexanucleotide repeats associated with ALS both in vitro and in vivo.
Applicant argues that in Cox et al., the editing efficiency in vivo is much lower than in vitro due to the lack of efficiency delivery methods for Cas endonucleases, exhibiting that in vivo CRISPR gene editing is enabled albeit at a much lower rate. However, for the scope of enablement, the intended utility of treating ALS, which is disclosed in “a method for editing a C9ORF72 gene in a human cell” and the instant specification, is not enabled. Cox directly states the unpredictable nature of gene editing in vivo still exist, such as whether the amount of genome modification in a target cell population required to create a therapeutic effect differs depending on the disease.
Furthermore, applicant argues that the instant specification provides working examples and convincing data from cell studies done on ALS patient-derived induced pluripotent stem cell (iPSC) lines, demonstrating the extent of knockdown of hexanucleotide repeat using the claimed gRNA pairs. According to MPEP 2164.02, section II titled ‘Correlation: In vitro/In vivo’, an in vitro or in vivo animal model constitutes a working example if that example correlates with a disclosed or claimed method invention. However, even with such evidence, the examiner must weigh the evidence for and against correlation and decide whether one skilled in the art would accept the model as reasonably correlating to the condition. In re Brana, 51 F.3d 1560, 1566, 34 USPQ2d 1436, 1441 (Fed. Cir. 1955), a USPTO decision was reversed based on the finding that in vitro data did not support in vivo applications.
Applicant further argues iPSC represents an art acknowledged in vitro or ex vivo model for studying ALS, however, no evidence is provided by the applicant to suggest such a statement. In Bonifacino et al., there is no mention of iPSCs as an in vitro model to study ALS, and furthermore, simply knocking the gene down in a cell line does not represent the complete, or even partial, mechanisms of a disease. In the prior art, Dong discloses a generated rat model that can be used to study ALS but administers no treatment. Cowan further discloses a mice model that have the hexanucleotide repeats but said model had no phenotypic differences to the control and no experimental results targeting the C9ORF72 gene in mice were provided by Cowan. Furthermore, Morrice discloses, to date, therapeutics that have been developed in mouse gene models have failed to translate to effective interventions in humans, challenging the use of these models for therapeutic screening (see introduction). As written and absent evidence to the contrary, it is uncertain how a method of editing a C9ORF72 gene in a human cell and delivering said method with the intentions of a therapeutic effect would be enabled for an in vivo subject, including a human.
Applicant further argues if they are required to wait until an animal naturally develops this specific disease before testing the effectiveness of the claimed CIRPSR systems against ALS in vivo, there would be no effective way to test compounds in vivo on a large scale. Based off the disclosed prior art of Cowan, Cowan teaches where a mouse model containing the human C9ORF72 gene with either a normal hexanucleotide repeat complement or an expanded hexanucleotide repeat was generated by Jackson Laboratory (see paragraph 0750). Therefore, the existence of a genetically engineered in vivo model was known in the art, at the time of the effective filing date. However, Cowan only states that gRNAs will be tested in animals to assess their ability to alter the hexanucleotide repeat expansion in C9ORF72 and produce phenotypic changes, but provides no evidence on whether the CRISPR system could successfully alter the target gene. This adds to the unpredictable nature of gene editing in vivo for the treatment of ALS.
While the use of CRISPR systems to edit a C9ORF72 gene in a human cell in vitro and ex vivo has been well established and is enabled, based off the evidence provided above and in the instant specification, it is still clear there is a highly unpredictable nature of in vivo gene editing, to where one cannot make the statement that an in vitro or ex vivo model of gene editing for the treatment of ALS would have similar intended effects on a broad range of in vivo subjects, such as a human or animal model, absent evidence to the contrary.
The rejection is maintained.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID YU whose telephone number is (571)272-1118. The examiner can normally be reached Monday-Friday 7:30 am -5 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram Shukla can be reached at 571-272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/D.T.Y./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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