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 .
This action is in response to the amendment filed 07/07/2025, in which claims 5, 7-10, 12, 14-16, 19, 22 and 23 were amended and claims 24-28 were added. Claims 5-12, 14-16 and 19-28 are currently pending.
Applicant’s arguments have been thoroughly reviewed, but are not persuasive for the
reasons that follow. Any rejection and objections not reiterated in this action have been
withdrawn. This action is FINAL.
Election/Restrictions
Applicant’s election without traverse of Group II in the reply filed on 03/14/2025 is acknowledged.
Claims 7-12 and 14-23 were previously improper multiple dependent claims not further treated on the merits in the prior action. In the amendment filed 7/7/2025, the claims have been amended to be proper dependent claims. Thus, they have not been further treated on the merits.
Claims 5-12 and 14-28 are under consideration.
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55. Applicant's claim for priority based on the foreign applications filed as EP 20157371.4 on 02/14/2020, EP 19191840.8 on 08/14/2019 and EP 19162150.7 on 03/12/2019.
All claims are given the priority date of 03/12/2019.
Response to Amendments - Drawings Objections
The previous objection to the drawings has been withdrawn in view of the replacement drawings submitted on 07/07/2025.
Claim Objections
Claim 16 is objected to because of the following informalities: claim 16 recites “The composition for the use according to any one of claims 12”. The claim should be amended to recite “The composition for the use according to claim 12”.
Appropriate correction is required.
Response to Amendment - Claim Objections
The previous objections to claims 5-12, 14 and 19-23 has been withdrawn in view of Applicant’s amendments to the claims filed on 07/07/2025.
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 10-12, 14-16, 20-23, 27 and 28 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 composition comprising a CRISPR system, wherein the CRISPR system comprises: a guide RNA and the polynucleotide according to claim 5 (wherein claim 5 recites “A polynucleotide encoding a Streptococcus pyogenes Cas9 (SpCas9) protein comprising or consisting of:(i) a polypeptide with an amino acid sequence according to SEQ ID NO: 1 wherein the arginine at position 63 and the glutamine at position 768 are each replaced by alanine; or (ii) a polypeptide with an amino acid sequence having at least 90% sequence identity to the amino acid sequence according to SEQ ID NO: 1, wherein the residue corresponding to the arginine at position 63 of SEQ ID NO: 1 and the residue corresponding to the glutamine at position 768 of SEQ ID NO: 1 are each replaced by alanine, and wherein said polypeptide has enhanced specificity compared to a polypeptide with the amino acid sequence according to SEQ ID NO: 1”), does not reasonably provide enablement for a composition comprising a CRISPR complex, wherein the CRISPR complex comprising: a guide RNA and the polynucleotide according to claim 5, or for treating a disease base on one or more mutations and inheritable such as the disease is Cystic fibrosis. 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, necessitated by the amendment filed 7/7/2025.
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:
The claims are drawn to a polynucleotide composition comprising (i) a polypeptide with an amino acid sequence according to SEQ ID NO: 1 wherein the arginine at position 63 and the glutamine at position 768 are each replaced by alanine; or (ii) a polypeptide with an amino acid sequence having at least 90% sequence identity to the amino acid sequence according to SEQ ID NO: 1, wherein the residue corresponding to the arginine at position 63 of SEQ ID NO: 1 and the residue corresponding to the glutamine at position 768 of SEQ ID NO: 1 are each replaced by alanine, and wherein said polypeptide has enhanced specificity compared to a polypeptide with the amino acid sequence according to SEQ ID NO: 1. Dependent claims 10-12, 20 and 24-26 further limits the claims where the polynucleotide forms a complex with a guide RNA. Dependent claims 14-16 and 21-23, 27 and 28 further limits the CRISPR system, comprising the polynucleotide and guide RNA, for the treatment of a disease wherein the disease includes one or more mutations and the disease is inheritable, where the elected disease is cystic fibrosis.
Breadth of the claims:
The claims encompass: the treatment of any disease (elected cystic fibrosis) using the composition comprising a SpCas9 protein where the sequence comprising mutations at R63A and Q768A to enhance specificity of the Cas9 protein. 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 the CRISPR cas system comprising both the polynucleotide encoding the SpCas9 protein with the two specific modifications for enhanced specificity as well as comprising a guide RNA for the purpose for therapeutic applications for an animal or human patient (Page 15, Paragraph 2). The specification does teach that additional experimental steps, such as whole genome sequencing or double stranded break capture are highly beneficial for defining the ideal sgRNA that can be considered safe for therapeutic applications (Page 79, Paragraph 2). The specification does not teach that the guide RNA complexes with the target nucleic acid encoding a protein but instead the guide RNA complexes with the Cas9 protein (Page 66, Paragraph 2).
The working examples of the instant specification teaches the enhanced specificity of the specific mutations of the SpCas9 sequence including the R63A and Q768A mutations for administration to a cell. Working example one is drawn to the construction of the experiments such as, DNA handling, RNA in vitro transcription, Cas9 protein purification, preparation of substrates for electrophoretic mobility shift assays, in vivo activity of Cas9 in HaCat and MCF7 cell lines and bacterial survival assay (Pages 59-63). Working examples two through six are drawn to the materials and methods wherein these examples teach the Cas9 protein and guide RNA complex interaction with the target DNA (Pages 63-70). Working examples seven and eight are drawn to the materials and methods for the construction of human cell cultures and transfection of the cell cultures. However, the working examples do not provide any examples or experimentation of therapeutically administration of the composition for treating cystic fibrosis or any other disease.
Predictability and state of the art:
The claimed invention is directed to using a CRISPR system for gene therapy to treat disease, such as cystic fibrosis. However, at the time of the filing, CRISPR systems for successful gene therapy to treat cystic fibrosis has not been completed and therefore, there are issues of enablement for their use in the claimed method.
The prior art, Cox et al (Nature Medicine Vol. 21 No. 2, pgs. 121-131; 2015), teaches that although genome editing is a very exciting opportunity to treating complex disease it is still unpredictable due to limitations of the CRISPR systems and the complexity of certain diseases (Page 129, Column 1 bridging column 2). Cox teaches further work to enable precise gene correction in post-mitotic cells such as neurons is critical to developing therapeutic strategies (Page 128, Column 1). Cox teaches delivery of nuclease proteins, specifically microbially derived Cas9, exposure of the proteins can cause immune reactions (Page 129, Column 1). Cox teaches despite valid therapeutic hypotheses and strong efforts in drug development, there have been only a limited number of successes in using small molecules to treat diseases with strong genetic contributions (Page 121, Column 1).
Although post filing art, Maule et al (Int. J. Mol. Sci. 21, 3903, pgs. 1-13; 2020) teaches that patient-derived cells are often used to test the efficacy of a treatment for a given mutation, however, considering the high number of CFTR variants associated with CF, it is very difficult to cover the entire mutation repertoire in homozygous cellular models (Page 7, Paragraph 5). Maule teaches CRISPR-Cas mediated sequence cleavage was successfully used in CF to repair splicing mutations, accounting for about 10% of CF cases where the production of aberrant mRNA transcripts impairs the expression of CFTR (Page 5, Paragraph 4). Maule envisions that although it is on the forefront of being able to successfully accomplish treating cystic fibrosis using CRISPR Cas systems, it is not yet achieved and therefore would not have been achieved at the time of filing (Page 4, Paragraph 2 and Page 8, Paragraph 1).
Doudna et al (Science 348, 1477-1481; 2015) teaches the CRISPR-Cas proteins function in complex with mature CRISPR RNAs (crRNAs) to identify and cleave complementary target sequences in foreign nucleic acids (Page 1481, Column 1). Doudna teaches the Cas9 enzyme cleaves DNA at sites defined by the 20-nucleotide (nt) guide segment within crRNAs, together with a trans-activating crRNA (tracrRNA) that forms a crRNA:tracrRNA hybrid structure capable of Cas9 association and once assembled on target DNA, the Cas9 HNH and RuvC nuclease domains cleave the double-stranded DNA (dsDNA) sequence within the strands that are complementary and noncomplementary to the guide RNA segment, respectively (Page 1481, Column 1). Doudna teaches that the Cas9 binds to targets by recognizing a PAM sequence and searching the adjacent DNA for complementarity to the 10- to 12-nt “seed” sequence at the 3′ end of the guide RNA segment (Page 1481, Column 2). Doudna teaches that the crystal structures of Cas9 bound to sgRNA and a target DNA strand, with or without a partial PAM-containing nontarget strand, show the entire 20-nt guide RNA segment engaged in an A-form helical interaction with the target DNA strand (Page 1481, Column 2).
At the time of filing as well as currently there exists no teachings in the art for the successful treatment of cystic fibrosis using a CRISPR system. Further as the art teaches above, cystic fibrosis in its pathogenesis and onset is complex and there are no successful treatments to date.
Amount of experimentation necessary:
In order to practice the claimed invention, an immense amount of experimentation would be required, as the skilled artisan could not rely on the prior art or the present specification to teach how to make and use the claimed method. With any form of the claimed gene therapy, one would have to determine how to treat cystic fibrosis using the CRISPR system comprising the mutated SpCas9 protein, with the specific mutations listed, along with a guide RNA with specificity and efficiency, and how to get sufficient expression to induce at least some therapeutic effect for the treatment of cystic fibrosis, as claimed.
As set forth above, there are significant challenges to treating cystic fibrosis with CRISPR systems. The molecular and genetic etiology of cystic fibrosis remains large, complex and not fully understood at the time of the filing. There remain significant issues of enablement regarding the successful treatment of cystic fibrosis as well as the unpredictability of the CRISPR system for treating diseases.
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. Therefore, it would require immense amount of unpredictable experimentation to practice the claimed invention with success with one specific type of vector, disease and route of administration not guaranteeing success with any other.
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 10-12, 14-16, 20-23, 27 and 28 are not considered to be fully enabled by the instant disclosure.
Response to Amendment - Claim Rejections - 35 USC § 112d
The previous rejection of claims 5 and 6 under 35 U.S.C 112d, 4th paragraph, is withdrawn in view of Applicant’s amendments filed on 07/07/2025.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 9 is rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101). This is a new rejection, necessitated by the amendment filed 7/7/2025.
Claim 9 is rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101). Claim 9 recites “A host cell comprising the polynucleotide according to claim 5”. While claims immediately considered on merits recite a composition, the specification describes the CRISPR cas system the purpose for therapeutic applications for an animal or human patient (Page 15, Paragraph 2 and Page 51 bridging Page 52). Accordingly, when the claimed CRISPR system is delivered to a human subject, cells of the subject will comprise the CRISPR system claimed. Therefore, the claims would encompass cells in a human organism and the human organism itself.
Amending the claim to an isolated cell or a cell in vitro (as supported by Page 16, Paragraph 1 of the disclosure) will be remedial.
Claim Rejections - 35 USC § 103
Applicant’s arguments, see Pages 8-10, filed on 07/07/2025, with respect to claims 5 and 6 have been fully considered and are persuasive. The previous rejection of claims 5 and 6 under 35 U.S.C 103 as being unpatentable over Liu et al (WO 2019/051419 A1; Provisional priority to 62/555,873 filed on 09/08/2017; Cited in a prior office action) in view of Joung et al (US 2017/0058271 A1) has been withdrawn.
Conclusion
Claims 5-8, 19 and 24-26 are allowable.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ALEXANDRA ROSE LIPPOLIS whose telephone number is (703)756-5450. The examiner can normally be reached Monday-Friday, 8:00am to 5:00pm EST.
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/ALEXANDRA ROSE LIPPOLIS/ Examiner, Art Unit 1637
/Jennifer Dunston/ Supervisory Patent Examiner, Art Unit 1637
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