DETAILED CORRESPONDENCE
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 papers filed January 29, 2026. Currently, claims 1-30 are pending. Claims 3, 4, 6-8, 15-16, 27-30 have been withdrawn as drawn to non-elected subject matter.
Election/Restrictions
Applicant's election without traverse of Group 1 and the single gene COL14A1, Claims 1-2, 5, 9-14, 17-26, in the paper filed January 29, 2026 is acknowledged.
The Election of species directed to a particular treatment agent has been withdrawn in view of further consideration.
The requirement is still deemed proper and is therefore made FINAL.
Priority
This application claims priority to provisional 63/283,359 file November 26, 2021.
Drawings
The drawings are acceptable.
Information Disclosure Statement
The listing of references in the specification is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609 A(1) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
The specification has a list of references on pages 106-107.
Requirement for Information
Applicant and the assignee of this application are required under 37 CFR 1.105 to provide the following information that the examiner has determined is reasonably necessary to the examination of this application.
The Orange reference used in this office action was authored, in part, by the inventor of this application, namely Dana Orange. The examiner requires further information in order to make further determinations about the patentability of the instant claims. In response to this requirement, please provide answers to each of the following interrogatories eliciting factual information:
The Orange reference cites Supplementary Figure, namely Fig. S10, S13. The examiner requests copies of all of the Supplementary Figures discussed in Orange.
The applicant is reminded that the reply to this requirement must be made with candor and good faith under 37 CFR 1.56. Where the applicant does not have or cannot readily obtain an item of required information, a statement that the item is unknown or cannot be readily obtained may be accepted as a complete reply to the requirement for that item.
This requirement is an attachment of the enclosed Office action. A complete reply to the enclosed Office action must include a complete reply to this requirement. The time period for reply to this requirement coincides with the time period for reply to the enclosed Office action.
Claim Objections
Claims 2 is objected to under 37 CFR 1.75(c), as being of improper dependent form for failing to further limit the subject matter of a previous claim. Applicant is required to cancel the claim(s), or amend the claim(s) to place the claim(s) in proper dependent form, or rewrite the claim(s) in independent form. Claim 2 recites an inherent property of the AC3 marker, namely elected COL14A1 gene. Claim 2 does not require any further narrowing limitations.
Improper Markush Rejection
Claims 1-2, 5, 9-14, 17-26 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
A Markush claim contains an “improper Markush grouping” if:
(1) the species of the Markush group do not share a “single structural similarity,” or (2) the species do not share a common use. Members of a Markush group share a “single structural similarity” when they belong to the same recognized physical or chemical class or to the same art-recognized class. Members of a Markush group share a common use when they are disclosed in the specification or known in the art to be functionally equivalent. See MPEP § 2117.
Here each species is considered to each of the AC3 biomarker genes listed in Table 10-11 and AC2 markers listed in Table 7.
The recited alternative species in the groups set forth here do not share a single structural similarity, as each different gene that could be detected is itself located in a separate region of the genome and has its own structure. The genes recited in the instant claims, do not share a single structural similarity since each consists of a different nucleotide sequence with different expression patterns. The only structural similarity present is that all detected positions are part of nucleic acid molecules. The fact that the markers comprise nucleotides per se does not support a conclusion that they have a common single structural similarity because the structure of comprising a nucleotide alone is not essential to the common activity of being correlated with RA flare or increased RA disease activity. Accordingly, while the different markers are asserted to have the property of being expressed in RA flare or increased RA disease activity, they do not share a single structural similarity.
MPEP 2117 (II)(A) provides the following guidance as to what constitutes a physical, chemical, or art recognized class:
A recognized physical class, a recognized chemical class, or an art-recognized class is a class wherein “there is an expectation from the knowledge in the art that members of the class will behave in the same way in the context of the claimed invention. In other words, each member could be substituted one for the other, with the expectation that the same intended result would be achieved”
The recited genes do not belong to a recognized chemical class because there is no expectation from the knowledge in the art that the genes will behave in the same manner and can be substituted for one another with the same intended result achieved. In other words, there is no expectation from the knowledge in the art that each of the recited genes would function in the same way in the claimed method; it is only in the context of this specification that it was disclosed that all members of this group may behave in the same way in the context of the claimed invention. Further there is no evidence of record to establish that it is clear from their very nature that each of the recited genes possess the common property of being associated with RA flare or increased RA disease activity.
MPEP 2117 (II) further states the following:
Where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the compounds do not appear to be members of a recognized physical or chemical class or members of an art-recognized class, the members are considered to share a "single structural similarity" and common use when the alternatively usable compounds share a substantial structural feature that is essential to a common use. Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
The recited alternative species do not share a substantial common structure just because they all have a sugar phosphate backbone. The sugar phosphate backbone of a nucleic acid chain is not considered to be a substantial common structural feature to the group of genes being claimed because it is shared by ALL nucleic acids. Further, the fact that the genes all have a sugar phosphate backbone does not support a conclusion that they have a common single structural similarity because the structure of comprising a sugar phosphate backbone alone is not essential to the asserted common use of being associated with RA flare or increased RA disease activity.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Following this analysis, the claims are rejected as containing an improper Markush grouping.
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.
Claims 1-2, 5, 9-14, 17-26 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter.
35 U.S.C. § 101 requires that to be patent-eligible, an invention (1) must be directed to one of the four statutory categories, and (2) must not be wholly directed to subject matter encompassing a judicially recognized exception. M.P.E.P. § 2106. Regarding judicial exceptions, “[p]henomena of nature, though just discovered, mental processes, and abstract intellectual concepts are not patentable, as they are the basic tools of scientific and technological work.” Gottschalk v. Benson, 409 U.S. 63, 67 (1972); see also M.P.E.P. § 2106, part II.
Based upon consideration of the claims as a whole, as well as consideration of elements/steps recited in addition to the judicial exception, the present claims fail to meet the elements required for patent eligibility.
Question 1
The claimed invention is directed to a process that involves a natural principle and a judicial exception.
Question 2A Prong I
The claims are taken to be directed to an abstract idea, a law of nature and a natural phenomenon.
Claim 1 is directed to “a method for monitoring and predicting a RA flare or increased RA disease activity in a patient”.
Claim 13 is also directed to a method “for predicting or treating an impending RA flare” by detecting increased amounts of a AC3 marker, namely elected COL14A1, comparing the amount of the marker to a control and administering a therapeutically effective amount “if” the marker is increased relative to a control.
Claim 26 is directed to a method of treating a patient having an impending RA flare or increased RA disease by selecting a patient who has been diagnosed as having increased amounts of markers as compared to a control and administering a therapeutically effective amount of disease modifying agents prior to the onset of RA.
Claim 1 is directed to a process that involves the judicial exceptions of an abstract idea (i.e. the abstract steps of “monitoring and predicting a RA flare or increased RA disease activity in a patient” and an “increased amount of the AC3 marker”) and a law of nature/natural phenomenon (i.e. the natural correlation between the expression of elected COL14A1 and a RA flare or increased RA disease activity in a patient). Claims 5 and 17 are further directed to a natural correlation of an increased amount of the AC3 marker, namely elected COL14A1 and an RA flare in about one week or about 5-7 days.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception for the reasons that follow.
Herein, claim 1 involves the patent-ineligible concept of an abstract process. Claim 1 requires monitoring and predicting a RA flare or increased RA disease activity in a patient. Neither the specification nor the claims set forth a limiting definition for "monitoring” or “predicting” and the claims do not set forth how "monitoring” or “predicting” is accomplished. As broadly recited the "monitoring” or “predicting” may be accomplished mentally by thinking about a subject’s expression of elected COL14A1 and "monitoring” or “predicting” a RA flare or increased RA disease activity in a patient. Thus, the determining step constitutes an abstract process idea.
Claims 1 and 13 further recite a comparison between the expression level, namely increased amounts of the AC3” that is deemed an abstract idea (see MPEP 2106.04(a)(2)(III)(A); • claims to “comparing BRCA sequences and determining the existence of alterations,” where the claims cover any way of comparing BRCA sequences such that the comparison steps can practically be performed in the human mind, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 763, 113 USPQ2d 1241, 1246 (Fed. Cir. 2014)).
A correlation that preexists in the human is an unpatentable phenomenon. The association between expression of elected COL14A1 and a RA flare or increased RA disease activity in a patient is a law of nature/natural phenomenon. The wherein clause which tells users of the process to predict a RA flare or increased RA disease activity in a patient in the sample, amounts to no more than an "instruction to apply the natural law". This wherein clause is no more than a mental step. Even if the step requires something more such as to verbalize the discovery of the natural law, this mere verbalization is not an application of the law of nature to a new and useful end. The wherein clause does not require the process user to do anything in light of the correlation. The wherein clause fails to provide the “practical assurance” sought by the Prometheus Court that the “process is more than a drafting effort designed to monopolize the law of nature itself.”
Question 2A Prong II
The exception is not integrated into a practical application of the exception. The claims do not recite any additional elements that integrate the exception into a practical application of the exception. While the claim recites isolating a blood sample and evaluating blood sample for expression or quantitatively increased amounts of elected COL1A2, this is not an integration of the exception into a practical application. Instead, these elements are data gathering required to perform the method. Thus, the claim is “directed to” the exception.
With respect to Claims 13 and 26, the administering step is both generic in nature and conditional. The claim does not require any administering step “if” the marker is not increased compared to a control. Further, the administration of a “disease-modifying agent” is generic in nature and is not a particular treatment. Disease-modifying may be any treatment for any disease.
Accordingly, the claims are directed to judicial exceptions.
Question 2B
The second step of Alice involves determining whether the remaining elements, either in isolation or combination with the other non patent ineligible elements, are sufficient to “’transform the nature of the claim’ into a patent eligible application” Alice, 134 S. Ct. at 2355 (quoting Mayo, 132 S. Ct. at 1297).
The claims are not sufficiently defined to provide a method which is significantly more from a statement of a natural principle for at least these reasons:
The claims do not include applying the judicial exception, or by use of, a particular machine. The claims do not tie the steps to a “particular machine" and therefore do not meet the machine or transformation test on these grounds. The use of machines generally does not impose a meaningful limit on claim scope.
The claims also do not add a specific limitation other than what is well-understood, routine and conventional in the field. The measuring expression of elected COL14A1 is mere data gathering step that amounts to extra solution activity to the judicial exception. It merely tells the users of the method to determine the expression of biomarkers of a sample without further specification as to how the sample should be analyzed. The claim does not recite a new, innovative method for such determination. The determining step essentially tells users to determine the markers through whatever known processes they wish to use.
The step of determining the expression levels was well known in the art at the time the invention was made. The prior art teaches that expression analysis using commercially available biochips and arrays that comprise the claimed genes. The steps are recited at a high level of generality. The claim merely instructs a scientist to use any expression analysis assay. The claim does not require the use of any particular non-conventional reagents. When recited at this high level of generality, there is no meaningful limitation that distinguishes this step from well understood, routine and conventional activities engaged in by scientists prior to applicant’s invention and at the time the application was filed.
Additionally, the teachings in the specification demonstrate the well understood, routine, conventional nature of additional elements because it teaches that the additional elements were well known.
Further it is noted that the courts have recognized the following laboratory techniques as well-understood, routine, conventional activity in the life science arts when they are claimed in a merely generic manner (e.g., at a high level of generality) or as insignificant extra-solution activity.
Analyzing DNA to provide sequence information or detect allelic variants, Genetic Techs., 818 F.3d at 1377; 118 USPQ2d at 1546;
Amplifying and sequencing nucleic acid sequences, University of Utah Research Foundation v. Ambry Genetics, 774 F.3d 755, 764, 113 USPQ2d 1241, 1247 (Fed. Cir. 2014)
For these reasons the claims are rejected under section 101 as being directed to non-statutory subject matter.
Claim Rejections - 35 USC § 112- Second Paragraph
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.
Claims 1-2, 5, 9-14, 17-26 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 pre-AIA the applicant regards as the invention.
A) The claim refers to tables. MPEP 2173.05(s) states:
Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table “is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience.” Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993) (citations omitted).
Claim 1 recites Table 10, 11, and 7. Claim 10 recites table 12 and 13. Claim 13 recites Table 10-11, 7. Claim 26 recites Claims 10-12 and 7. Appropriate correction is required.
B) The claims are indefinite. It is not clear how the recited preamble is intended to breathe life and meaning into the claim. The preamble of Claim 1 is directed to an method for monitoring and predicting a RA flare or increased RA disease activity in a patient. However, the claim only provides for detecting in a blood sample increased amounts of one or more AC3 markers. The claim provides a “wherein” clause but this statement does not add any additional method steps and it’s not clear what is required by the limitation. Thus, it is not clear if applicant intends to cover any method for isolating a blood sample and evaluating the sample for expression or quantitatively increased amounts of one or more AC3 markers, or if the method is intended to somehow require more to accomplish the goal set forth in the preamble. If the claim requires something more, it is unclear what additional active process step the method requires and it appears that the claims are incomplete. The claims fail to provide any active steps that clearly accomplish the goal set for the by the preamble of the claims. The wherein clause is not an active method step.
C) Claim 1 requires “increased amounts of the AC3 markers predicts an impending RA flare” because increased is a relative term and it is not clear what it is increased relative to. Claims 2, 5, 9-14, 17-26 are similarly indefinite over the language of “increased amounts”. Clarification is required.
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.
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 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.
Claim(s) 1-2, 5, 9, 12, 13-14, 18-25 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Baker et al. (J. of Autoimmunity, Vol. 105, No. 102298, 2019) as evidenced by GEO (GSE122612, July 12, 2019).
Baker teaches methods of isolating blood samples and evaluating the blood sample for expression or increased amounts of one or more ACE3 markers provided in Table 8, including elected COL1A2. Baker teaches isolating circulating CD4+ T cells from whole blood in 44 patients with RA in remission before DMARD cessation. Total RNA extraction was performed and mRNA was sequenced using Illumina NextSeq 500 (limitations of Claim 11).
Analysis of GSE112612 demonstrates COL14A1 was analyzed and five samples were found to have expression of COL14A1.
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Baker teaches each of the active method steps. The wherein clause in Claim 1 is a statement of inherent property. The claim does not require the artisan perform any step to meet the wherein clause. Claims 2, 5, 12, 17 are also an inherent property and does not require any step be performed.
With regard to Claims 13, 18-25, none of the patients were diagnosed with an impending RNA flare, thus, no administration is required.
Claim(s) 1-2, 5, 9, 12, 13-14, 18-25 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Orange et al. (N. Engl. J. Med. Vol. 383, No. 3, pages 218-228, July 2020).
Orange teaches RNA identification of PRIME cells predicting rheumatoid arthritis flares. Orange teaches detecting in a blood sample increased amount of COL14A1 as predictive of a RA flare or increased RA activity. Orange teaches RNA-seq analysis of fingerstick blood specimens identified 2613 genes that were differentially expressed at the time of a flare as compared with baseline (limitation of Claim 9). Supplementary Appendix 2 lists COL14A1 as one of the genes.
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With respect to Claim 2, Orange teaches cells that expressed surface markers of synovial fibroblasts were detectable by flow cytometry in blood from patients with rheumatoid arthritis. CD45−CD31−PDPN+ cells were more common in blood from 19 additional patients with rheumatoid arthritis than in blood from healthy controls.
With respect to Claims 5, 12 and 17, Supplemental table 6 provides the list of genes that had increased expression in blood 1 week before a flare and decreased expression during a flare (Figure 4B, Fig S13 and Suppl 6).
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With regard to Claims 13, 18-25, for the patients that were not diagnosed with an impending RNA flare, thus, no administration is required.
Claim(s) 1-2, 5, 9, 11-12, 13-14, 18-26 is/are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Darnell et al. (WO2021/243177, priority May 29, 2020).
The applied reference has a common inventor and assignee 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). This rejection under 35 U.S.C. 102(a)(2) might be overcome by: (1) a showing under 37 CFR 1.130(a) that the subject matter disclosed in the reference was obtained directly or indirectly from the inventor or a joint inventor of this application and is thus not prior art in accordance with 35 U.S.C. 102(b)(2)(A); (2) a showing under 37 CFR 1.130(b) of a prior public disclosure under 35 U.S.C. 102(b)(2)(B) if the same invention is not being claimed; or (3) a statement pursuant to 35 U.S.C. 102(b)(2)(C) establishing that, not later than the effective filing date of the claimed invention, the subject matter disclosed in the reference and the claimed invention were either owned by the same person or subject to an obligation of assignment to the same person or subject to a joint research agreement.
Darnell teaches markers and cellular antecedents of RA flares. Darnell teaches elected COL14A1 is a marker that is useful for monitoring or predicting RA flare in a blood sample from a patient (para 17, for example). Darnell teaches the ACE3 genes are expressed in PRIME cells (flow sorted CD45-/CD31-/PDPN+ cells) (para 45). Darnell teaches the markers are increased about 1 week prior to an RA flare (para 97). Darnell teaches the analysis if performed by RNAseq (para 137).
Darnell teaches the patient, once diagnosed, may be treated with a therapeutically effective amount of one or more disease modifying agents for treating RA (para 19). Darnell teaches the same list claims in Claims 18-25 including Humira (para 27).
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the "right to exclude" granted by a patent and to prevent possible harassment by multiple assignees. See In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970);and, In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the conflicting application or patent is shown to be commonly owned with this application. See 37 CFR 1.130(b).
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 1-2, 5, 8-14, 17-26 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 7-8, 11, 13-14, 20-26 of copending Application No. 17/928,513 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each. Applicant elected COL14A1 in ‘090 but the claim encompasses COL14A1 of elected ‘513. The same genes are recited in each of the cases and thus anticipate each other. In the event the claims are limited to particular genes or exclude the gene elected/allowed in the conflicting application, the rejection will be reconsidered.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims allowable.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Stephenson et al. (Nature Communications, Vol. 9, No. 791, 2018) teaches single-cell RNA seq of rheumatoid arthritis synovial tissue using low cost microfluidic instrumentation. Stephenson teaches increase in expression of COL1A2 but does not teach the expression in blood or to predict a flare.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JEANINE ANNE GOLDBERG whose telephone number is (571)272-0743. The examiner can normally be reached Monday-Friday 6am-3:30pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Wu-Cheng (Winston) Shen can be reached on (571) 272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JEANINE A GOLDBERG/Primary Examiner, Art Unit 1682
April 24, 2026
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