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 .
Claims 1, 2, 4-8, 10-12, 31, 37, 38, 43, 47, 70, 109, 140 and 153 are pending in the application.
This office action is in response to the amendment filed on 6/27/2025.
All previous rejection not reiterated in this office action are withdrawn.
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 1, 2, 4-8, 10-12, 31, 37, 38, 43, 47, 70, 109, 140, 146 and 153 are rejected 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. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection is rewritten to address the amendment.
The written description requirement is set forth by 35 U.S.C. 112, first paragraph which states that the: “specification shall contain a written description of the invention. . .[emphasis added].” The written description requirement has been well established and characterized in the case law. A specification must convey to one of skill in the art that “as of the filing date sought, [the inventor] was in possession of the invention.” See Vas Cath v. Mahurkar 935 F.2d 1555, 1560 19 USPQ2d 1111, 1117 (Fed. Cir. 1991). Applicant may show that he is in “possession” of the invention claimed by describing the invention with all of its claimed limitations “by such descriptive means as words, structures, figures, diagrams, formulas, etc., that fully set forth the claimed invention.” See Lockwood v. American Airlines Inc. 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997).
In analyzing whether the written description requirement is met, it is first determined whether a representative number of species have been described by their complete structure. Next, it is determined whether a representative number of species have been sufficiently described by other relevant identifying characteristics. The amended claim 1 recites “wherein the Cas9 domain comprises a R461I substitution in the amino acid sequence of SEQ ID NO: 9, or a corresponding substitution in any of the amino acid sequences provided in SEQ ID NO: 10-262” and has the function of recognize a non-canonical PAM sequence.” The claimed Cas9 domain in claim 1 thus encompasses a large genus of polypeptides that have mutation(s) at R461I, and other variant sequences at other position(s) (90% sequence homology to SEQ ID NO: 9 means up to 137 amino acid difference). Example 1 describes beneficial mutations conferring Cas9 activity on noncanonical PAM mapped to a S. pyogenes wild type sequence including 122, 137, 182, 62, 294, 409, 480, 543, 660, 694, 1219, 1329 (paragraph [00349]), and mapping of said mutations to Cas9 protein from other species, SEQ ID NO: 10-12. The specification teaches alignment of a total of 250 Cas9 sequences may be obtained following alignment parameters as given in the above example and disclosed in WO2017/070633. The specification states “additional suitable Cas9 sequences in which amino acid residues homologous to residues 51, 86, 261, 274, 331, 341, 388, 40, 435, 461, 510, 522, 548, 593, 653, 712, 715, 72, 77, 798, 811, 839, 847, 955, 967, 991, 1139, 1199, 1227, 1229, 1296, 1318 can be identified by known methods,” citing Supplementary Table S2 and Supplementary Figure S2 of Fonfara et al. In example 4, the specification describes identification of point mutations A262T, K294R, S409I and M694I, E480K, E543D and E1219V (paragraphs [0420]-[0421]) that results in expanded PAM recognition, and confirmed by PAM depletion assay, transcriptional activation, and base editing in mammalian cells. The function of expanded PAM recognition compared to wild type Cas9 appears to be related to specific mutations at position A262T, K294R, S409I and M694I, E480K, E543D and E1219V. There is no teaching from the specification that relates to noncanonical PAM recognition to Cas9 variants at position R461I of SEQ ID NO: 9, or corresponding amino acid residues in other amino acid sequences sharing 90% sequence identity to SEQ ID NO:9. The specification thus fails to describe a Cas9 domain has the recited mutation(s) that has the function of recognizing noncanonical PAM, or other identifying characteristics for the claimed Cas9 domain having the recited mutation. The structure and functional relationship is missing.
The knowledge from prior art does not remedy the deficiency from the specification. Neither disclosure from WO2017/070633 and Fonfara teaches mutation(s) at claimed sites R461I alone or in combination with other mutation (as recited in claims 2, 4-8, 10-12, 31 and 153) of SEQ ID NO: 9, or corresponding positions to sequences having 90% homology to SEQ ID NO: 9. Carsten teaches some of the mutations at specific sites such as 461, 777 in Cas9 domain. However, there is no teaching from Carsten indicates such mutation(s) is related to noncanonical PAM recognition. The function of Cas9 having mutation(s) R461I alone or in combination with position 51, 86, 261, 274, 331, 341, 388, 40, 435, 461, 510, 522, 548, 593, 653, 712, 715, 72, 77, 798, 811, 839, 847, 955, 967, 991, 1139, 1199, 1227, 1229, 1296, 1318 of SEQ ID NO: 9 as recited in claims as 2, 4-8, 10-12, 31 and 153, or corresponding positions to sequences having 90% homology to SEQ ID NO: 9 is thus unpredictable. A skilled artisan cannot immediately envision the structure of the claimed genus of Cas9 domain that can recognize noncanonical PAM sequence. Therefore, the specification lack sufficient description for the claimed genus of Cas9 domain to demonstrate that Applicant has possession of claimed invention at the time the application was filed.
Dependent claims requires all limitation of claim 1, which are not sufficiently described by the present specification for same reason discussed above.
Response to Arguments
Applicant asserts that the specification provides ample written description and guidance to serve as basis and support for the scope of amended claims. Applicant states that a large number of exemplary Cas9 homologs are disclosed in the application including SEQ ID NO: 9-262, some of which has 90% sequence identity with SEQ ID NO: 9 (SEQ ID NO: 97, 101-105). Applicant asserts that a person in the art would understand that a wide range of sequence variation can be tolerated in a Cas9 protein without altering its activity or function. Applicant states SEQ ID NO: 217, 219-221, having approximately 48% sequence identity with SEQ ID NO: 9 but are known to function as Cas9 proteins. Applicant asserts that the amended claims now requires a substitution at R461I, which the application teaches is capable of recognizing a target nucleic acid sequence that does not comprise the canonical 5’-NGG-3’ end.
The above arguments have been fully considered but deemed unpersuasive. As discussed in the above rejection, the amend claim 1 recites “wherein the Cas9 domain comprises a R461I substitution in the amino acid sequence of SEQ ID NO: 9, or a corresponding substitution in any of the amino acid sequences provided in SEQ ID NO: 10-262” and has the function of recognize a non-canonical PAM sequence.” The claimed Cas9 domain in claim 1 thus encompasses a large genus of polypeptides that have mutation(s) at R461I, and other variant sequences at other position(s) (90% sequence homology to SEQ ID NO: 9 means up to 137 amino acid difference), which need to have the function of recognizing non-canonical sequences. The description of a number of natural occurring Cas9 sequences having SEQ ID NO: 9-262 and has Cas9 function does not equate to the description of non-natural occurring Cas9 sequences that only recognizes non-canonical sequences. A review of the specification does not show that R461I alone or in combination with recited mutation in claims 2, 4-8, 10-12, 31 and 153 would make Cas9 to recognize non-canonical PAM sequence. Rather, example 1 demonstrates mutation at 122, 137, 182, 62, 294, 409, 480, 543, 660, 694, 1219, 1329 in SEQ ID NO: 9 has the claimed function. (paragraph [00349]). Therefore, for reason discussed in previous rejection and rewritten above, this rejection is still considered proper and thus maintained.
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, 2, 4-8, 10-12, 31, 37, 38, 43, 47, 70, 109, 140, 146 and 153 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 ground of rejection necessitated by amendment.
Regarding claim 1, the recitation of “a corresponding substitution in any of the amino acid sequences provided in SEQ ID NO: 10-262” renders the claim indefinite because it is unclear whether the “corresponding substitution” is referring a substitution of R to I at the corresponding position (to 461 in SEQ ID NO:9) in SEQ ID NO: 10-262, or a substitution of R amino acid to an amino acid corresponding to I, such as R461A, R461L, R461M or R61V as disclosed in paragraph [00151] of the specification.
Dependent claims 2, 4-8, 10-12, 31, 37, 38, 43, 47, 70, 109, 140, 146 and 153 are rejected for same reason because they depend on claim 1 but fails to clarify the indefiniteness.
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 37 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 37 recites the Cas9 domain exhibits activity on a target sequence having 3’ end that is not directly adjacent to the canonical NGG PAM sequence or does not comprise canonical NGG PAM sequence, which is same limitation as the Cas9 protein recognizes a non-canonical PAM sequence as recited in claim 1, thus fails to further limit 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. This is a new ground rejection necessitated by amendment.
Conclusion
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.
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/CELINE X QIAN/ Primary Examiner, Art Unit 1637