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 .
Status of Application, Amendments, And/Or Claims
The Applicants amendments/remarks received 12/30/2025 are acknowledged. Claims 66, 100-101 and 103-105 are amended; claims 2-3, 5-18, 20-25, 27-28, 30-42, 44-48, 51-57, 59-61, 63-65 and 68-98 are canceled; claim 106 is new; claims 1, 4, 19, 26, 29, 43, 49-50, 58, 62, 66-67 and 99-106 are pending; claims 1, 4, 19, 26, 29, 43, 49-50, 58 and 62 are withdrawn; claims 66-67 and 99-106 have been examined on the merits.
Drawings
The color replacement sheets received 12/30/2026 are accepted. Applicant has addressed all the concerns raised in the previous Office action; however, as Applicant notes in the petition to accept colored drawings received 12/30/2025, for many of the figures, comprising fluorescent images of stained cells, etc., the only practical medium by which to disclose the subject matter is by colored drawings. Examiner concurs that Figs. 1BA, 1BB, 2A, 2B, 3B-C, 3H, 4F, 4H, 5AA, 5AB, 5B, 5D, 6C, 7C, 7F, 8E-F, 9C, 9E, 11A, 11G-H, 12D, 13C-D and 13F-G require color drawings or images.
Claim Objections
The objection to claims 66-67, 100-101 and 103-105 as set forth at pp. 5-6 of the previous Office Action, is withdrawn in view of the amendment of the claims.
Claim Rejections - 35 USC § 101
The rejection of claims 66-67 and 99-105 under 35 U.S.C. § 101, as set forth at pp. 6-8 of the previous Office Action, is withdrawn in view of the amendment of the claims.
Claim Rejections - 35 USC § 112
The rejection of claims 66-67 and 99-105 under 35 U.S.C. § 112(b), as set forth at pp. 8-9 of the previous Office Action, is withdrawn in view of the amendment of the claims.
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.
Claim 100 is 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 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.
Claim 100 recites the in vitro assay of claim 99, wherein the SS18-SSX fusion protein has the amino acid sequence set forth in SEQ ID NO: 225 or SEQ ID NO: 226. SEQ ID NO: 226 does not recite an amino acid sequence; hence, Applicant is not in possession of the claimed method of claim 100.
NOTE: SEQ ID NO: 226 is the nucleic acid sequence encoding the amino acid sequence of SEQ ID NO: 225; hence, deleting “or SEQ ID NO: 226” would overcome this rejection without any diminishment of the scope of claim 100.
Claim Rejections - 35 USC § 103
The rejection of claims 66-67 and 99-105 under 35 U.S.C. § 103(a) over Kadoch et al., US 2014/0288162 (US Patent Document cite AB, IDS, 6/20/2023; herein “Kadoch”) in view of Valencia et al., 2019 (cite U, PTO-892, 10/1/2025; herein “Valencia”) as set forth at pp. 9-13 of the previous Office Action, is withdrawn in view of the amendment of the claims.
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 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 66-67 and 99-105 are rejected under 35 U.S.C. 103 as being unpatentable over Kadoch et al., US 2014/0288162 (US Patent Document cite AB, IDS, 6/20/2023; herein “Kadoch”) in view of Kato et al., 2002 (cite U, attached PTO-892; herein “Kato”) and Valencia et al., 2019 (cite U, PTO-892, 10/1/2025; herein “Valencia”).
Kadoch teaches methods for screening for therapeutics to treat synovial sarcoma (Abst.; [0005], [0008], [0025], [0062], [0073-78]; claims 32 and 35) wherein the screen is an in vitro screen designed to detect the binding of a candidate agent to an SS18-SSX fusion protein or an SS18-SSX fusion protein in a BAF complex ([0062], [0073-78]; claims 32 and 35), wherein the screen can comprise an in vitro assay comprising mixing SS18-SSX fusion protein, other protein(s), such as the BAF complex, and a candidate test agent and detecting that the candidate test agent decreases binding of the SS18-SSX fusion protein to the other protein(s) ([0073], claim 32).
Kadoch discloses that the SS18-SSX fusion protein is produced by a translocation event associated with human synovial sarcoma, t(X;18) (pl 1.2;q11.2), which fuses the SS18 gene on chromosome 18 to one of three closely related genes - SSX1, SSX2, or SSX4 - on the X chromosome, resulting in an in-frame fusion protein in which the eight C-terminal amino acids of SS18 are replaced with 78 amino acids from the SSX C-terminus [0004]. Kadoch discloses that the pathogenicity of the SS18-SSX fusion protein, produced by the synovial sarcoma associated translocation event, involves the eviction or ejection of BAF47 (also known as SMARCB1) from the chromatin-binding complex ([0008], [0014], [0062]. Kadoch discloses that SS18-SSX1, SS18-SSX2 and SS18-SSX4 eject BAF47 from the complex, while SS18-SSX3 and SS18-SSX5 do not [0134] and that this ejection of BAF47 is dependent on the presence of basic residues in the C-terminus of the SSX1, SSX2 or SSX4 part of the fusion protein (Figs. 5A-H and 12A-B; [0132-134]; [0014]; [0021-23]).
Although Kadoch recites an in vitro assay comprising mixing SS18-SSX fusion protein, other protein(s), such as the BAF complex, and a candidate test agent and detecting that the candidate test agent decreases binding of the SS18-SSX fusion protein to the other protein(s), Kadoch does not specifically disclose that the other protein(s) can be nucleosomes. However, a person of ordinary skill in the art at the time of filing would have found it obvious to modify Kadoch’s screening method to comprise detecting candidate agents which decrease the binding of the SS18-SSX fusion protein to the acidic patch of nucleosomes in view of the disclosures of Kato and Valencia.
Kato discloses that SYT-SSX fusion proteins, i.e., SS18-SSX fusion proteins, bind to core histones and nucleosomes via the SSX C-terminal portion of the fusion protein; thus, interfering with the function of normal SWI/SNF complexes, i.e., BAF complexes comprising BAF47, by directly inhibiting their chromatin remodeling activities (Abst.).
Valencia discloses that mSWI/SNF complexes, i.e. BAF complexes, bind to chromatin via the direct binding of the C-terminal domain of BAF47, i.e., SMARCB1, to the nucleosome acidic patch (Abst.).
Thus, a person of ordinary skill in the art at the time of filing would have found it obvious that the SS18-SSX fusion proteins eject BAF47 from the complexes due to the SS18-SSX fusion proteins outcompeting BAF47 for binding to the nucleosome acidic patch.
Hence, a person of ordinary skill in the art at the time of filing would have found it obvious to modify the screening method of Kadoch to comprise mixing SS18-SSX fusion proteins or BAF complexes comprising SS18-SSX fusion proteins with nucleosomes, adding test agents to the mixture and determining whether the test agent is able to decrease the binding of the SS18-SSX fusion protein to the nucleosome acidic patch with a reasonable expectation of success because Kadoch teaches that SS18-SSX fusion proteins function pathologically by evicting BAF47 from BAF chromatin binding complexes, i.e., SWI/SNF complexes, Kato teaches that SS18-SSX fusion proteins bind to nucleosomes and histones and Valencia teaches that BAF47 binds chromatin by direct binding to the acidic patch of nucleosomes; therefore, claims 66-67 and 99-105 are prima facie obvious.
Regarding claims 67 and 99-103, Kadoch teaches that the SS18-SSX fusion protein can comprise human SS18-SSX1, SS18-SSX2 and SS18-SSX4 comprising the full 78 aa SSX peptide (Figs. 5A-H and 12A-B; [0132-134]; [0014]; [0021-23]); therefore, claims 67 and 99-103 are prima facie obvious.
Regarding claim 104, Kadoch discloses that the screen can be of the SS18-SSX fusion in the BAF complex ([0062], [0073-78]); therefore, claim 104 is prima facie obvious.
Regarding claim 105, Valencia uses human nucleosomes (isolated from 293T cells, etc.); hence, a person of ordinary skill in the art at the time of filing would have found it obvious that the nucleosome comprises H2A protein comprising E56, E64, D90, E91, E92 and/or E113 of human H2A and/or H2B protein comprising E105 and/or E113 of human H2B; therefore, claim 105 is prima facie obvious.
Response to Arguments
Applicant's arguments filed 12/30/2025 have been fully considered but they are not persuasive. Arguments of the Applicant’s Response on pp. 14-18 regarding the objections to the drawings and claims and rejections under 35 U.S.C. §§ 101, 112(b) and 103 are moot as the rejections have been withdrawn.
Regarding the rejection of claims 66-67 and 99-105 under 35 U.S.C. § 103 over Kadoch in view of Valencia, Applicant argues that “Kadoch does not disclose an in vitro screen designed to detect the binding of a candidate agent to an SS18-SSX fusion protein” (Remarks, p. 17). This is incorrect. See Kadoch [0073-74] and claims 32 and 35.
All limitations of the amended claims are addressed in the rejection set forth above.
Allowable Subject Matter
Claim 106 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
Conclusion
No claims are allowed; claim 106 is objected to.
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 Trent R Clarke whose telephone number is (571)272-2904. The examiner can normally be reached M-F 10-7 MST.
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/TRENT R CLARKE/ Examiner, Art Unit 1651
/DAVID W BERKE-SCHLESSEL/ Primary Examiner, Art Unit 1651
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