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 .
The claims dated 2/26/2026 are under consideration.
The amendments and arguments presented in the papers filed 2/26/2026 ("Remarks”) have been thoroughly considered. The issues raised in the Office action dated 1/6/2026 listed below have been reconsidered as indicated.
a) The rejections of claims 1-11, 14-20 and 31-32 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, are withdrawn.
b) The rejections of claim(s) 1-11, 14-20 and 31-32 under 35 U.S.C. 103 as being unpatentable over Lipsky (WO 2020/102043 A1) are withdrawn in view of the amendments to the claims.
The Examiner’s responses to the Remarks regarding issues not listed above are detailed below in this Office action.
New and modified grounds of rejection necessitated by amendment are detailed below and this action is made FINAL.
Priority
The present application is a continuation of PCT/US2023/013173, filed 2/15/2023. Priority is recognized.
Drawings
High resolution copies of the drawings may be accessed via PAIR/Patent Center Retrieval using the Supplemental Content tab.
Claim Interpretation
Parts (b) and (d) of claim 1 are interpreted as requiring the performance of at least one of (i), (ii) and (iii).
Regarding claim 5, the claim recites “systemic data”. The term “systemic” is interpreted view of para. 239 of the original specification as referring to expression values derived from the “circulation”.
Regarding claim 11, the term “endotype” is understood to encompass a subtype of a disease defined by an underlying biological mechanism or pathways.
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 44-46 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.
The following are new rejections necessitated by the amendments to the claims.
Regarding new claim 44, the claim states “the first patient is determined to have systemic lupus erythematosus (SLE) based at least in part on the first endotype”. Based on the use of the passive voice, it is unclear if the claim requires an active method step of “determining the first patient is systemic lupus erythematosus (SLE) based at least in part on the first endotype”.
Claims 45-46 depend from claim 44 and are rejected for the same reason.
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.
Claim(s) 1-7, 10-11, 14, 31-32 and 44-46 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Panousis (Ann Rheum Dis. 2019. 78:1079-1089 and Supplementary Data).
Regarding claims 1 and 10, Panousis teaches obtaining “first biological” samples and “second biological” samples from groups such as inactive disease SLE patients, low disease activity SLE patients and active disease SLE patients (Supplementary Table S1), as encompassed by present steps (a) and (c).
Panousis teaches assaying the samples through RNA sequencing (p. 1080, RNA sequencing, mapping, quantifications and quality control), as encompassed by present steps (b) and (d), and thus generates a “first data set” and a “second data set”. The assaying through RNA sequencing results in transcriptomic RNA sequencing data.
Panousis teaches processing of the RNA sequencing data between groups to “define a signature” that indicates “a first lupus endotype”, e.g., inactive disease SLE endotype, low disease activity SLE endotype and active disease SLE endotype, as encompassed by step (e).
The analysis of Panousis evaluates a “first lupus endotype” e.g., inactive disease SLE endotype, that is different from a “second lupus endotype”, e.g., low disease activity SLE endotype or active disease SLE endotype.
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The RNA sequencing of Panousis includes “at least 32 genes that are part of oxidative phosphorylation pathway” based on the sequencing of bulk RNA, and includes:
The highlighted genes include those recited in claim 1.
It is noted that the recited genes are not part of any “lupus endotype” as the claim only describes them as being part of data obtained in the assaying steps.
Regarding claim 2, Panousis teaches SLE patient groups such as inactive disease SLE patients, low disease activity SLE patients and active disease SLE patients (Supplementary Table S1), which are different endotypes that respond to different treatments.
Regarding claim 3, Panousis teaches SLE patient groups such as inactive disease SLE patients, low disease activity SLE patients and active disease SLE patients (Supplementary Table S1), which are different endotypes that correlate with different treatment groups (Supplementary Table S1).
Regarding claim 4, Panousis teaches SLE patient groups such as inactive disease SLE patients, low disease activity SLE patients and active disease SLE patients (Supplementary Table S1), which are different endotypes that respond differently to a treatment.
Regarding claims 5, 6 and 7, Panousis teaches the sample is blood (p. 1080, Experimental design and patient characteristics), which produces “systemic data”.
Regarding claim 11, Panousis teaches the “first gene expression data” comprises RNA expression levels from RNA sequencing data as described above. This data is able to classify a third patient between two or more lupus endotypes. It is noted the claim does not require an active step of “classifying a third patient”.
Regarding claim 14, Panousis teaches “classifying” third patients by validating trained classifiers (p. 1080, Disease classification).
Regarding claims 31 and 32, Panousis teaches the groups include patients that have not been given DMARDs or a biologic (Supplementary Table S1).
Regarding claims 44-46, Panousis teaches patients are determined to have a type of SLE based the “first endotype” or classifier (p. 1080, Disease classification). The endotypes include “Type 1 SLE”, which is the active disease group having an average SLEDAI of 8.7 and “Type 2 SLE”, which is the inactive disease or low disease activity, having average SLEDAI scores of 0.0 and 2.9, respectively (Supplementary Table S1).
Claim Rejections - 35 USC § 103
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.
Claim(s) 1, 8-10 and 15-20 are rejected under 35 U.S.C. 103 as being unpatentable over Panousis (Ann Rheum Dis. 2019. 78:1079-1089 and Supplementary Data) and Lipsky (WO 2020/102043 A1).
The following are new rejections necessitated by the amendments to the claims.
Regarding claims 1 and 10, Panousis teaches obtaining “first biological” samples and “second biological” samples from groups such as inactive disease SLE patients, low disease activity SLE patients and active disease SLE patients (Supplementary Table S1), as encompassed by present steps (a) and (c).
Panousis teaches assaying the samples through RNA sequencing (p. 1080, RNA sequencing, mapping, quantifications and quality control), as encompassed by present steps (b) and (d), and thus generates a “first data set” and a “second data set”. The assaying through RNA sequencing results in transcriptomic RNA sequencing data.
Panousis teaches processing of the RNA sequencing data between groups to “define a signature” that indicates “a first lupus endotype”, e.g., inactive disease SLE endotype, low disease activity SLE endotype and active disease SLE endotype, as encompassed by step (e).
The analysis of Panousis evaluates a “first lupus endotype” e.g., inactive disease SLE endotype, that is different from a “second lupus endotype”, e.g., low disease activity SLE endotype or active disease SLE endotype.
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The RNA sequencing of Panousis includes “at least 32 genes that are part of oxidative phosphorylation pathway” based on the sequencing of bulk RNA, and includes:
The highlighted genes include those recited in claim 1.
It is noted that the recited genes are not part of any “lupus endotype” as the claim only describes them as being part of data obtained in the assaying steps.
Panousis does not teach the additional elements specific to claims 8 and 9 and 15-20.
Regarding claims 8-9, Lipsky teaches the samples include synovial/local samples (para. 1666) or blood/systemic samples (para. 29, 67).
It would have been obvious to substitute the blood samples of Panousis with the synovial samples of Lipsky because synovial represents a localized sample. Further, Lipsky teaches blood and synovial and alternative samples that are relevant to the analysis of SLE.
Regarding claim 15, Lipsky teaches selecting and administering an appropriate treatment to a patient based on phenotype (para. 15, 114 and 866).
Regarding claims 16-20, Lipsky teaches patients that are administered parenteral drugs, such as inhibitors, gene targeted drugs or monoclonal antibodies (para. 114). See para. 15, 415, 1106 and 1193.
It would have been prima facie obvious to the ordinary artisan at the time of invention to have modified the method of Panousis by trying to identify and administer appropriate treatments based on the type of SLE a patient is determined to have.
Conclusion
No claims allowed.
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 JOSEPH G DAUNER whose telephone number is (571)270-3574. The examiner can normally be reached 7 am EST to 4:30 EST with second Fridays Off.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng Winston Shen can be reached at 5712723157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JOSEPH G. DAUNER/Primary Examiner, Art Unit 1682