DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Claims 19-24, 26-37 are pending in the application. Claims 33-37 are withdrawn. Claims 19-24 and 26-32 are currently under examination.
This office action is in response to the amendment filed on 2/9/2026.
All previous rejection not reiterated in this office action are withdrawn.
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 19-24 and 26-32 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.
Regarding claim 19, the recitation of “determining the expression levels of the one or more proteins by quantifying the mRNA levels corresponding to the protein using quantitative PCR techniques wherein detection is accomplished with an enzyme linked immunosorbent assay (ELISA)” renders the claim indefinite because it is unclear whether the expression is determined by qPCR, ELISA, or both. It is also unclear how the ELISA may be performed using RNA sample that is obtained from synovial fluid because RNA sample does not have protein.
Dependent claims 20-24 are rejected for same reason because they depend on claim 19 but does not remedy this indefiniteness.
Regarding claim 26, the claim recites “wherein determining the expression of the one or more proteins in the sample is accomplished with an enzyme linked immunosorbent assay” which means the detection using protein, rather than RNA. It is thus unclear how RNA samples may be used to perform ELISA.
Dependent claims 27-32 are rejected for same reason because they depend on claim 26 but does not remedy the indefiniteness.
Response to Arguments
Applicant argues that claim 19 is amended by removing the paragraph break between “determining the expression level” and “wherein detection is accomplished with an enzyme linked immunosorbent assay” to make it clear that the detection methodology without requiring both techniques to be performed simultaneously.
The above argument is not persuasive because there is no “and” “or” between two detection method. Moreover, Applicant has not clarify how an RNA sample may be used to detect protein using enzyme linked immunosorbent assay.
Regarding claim 26, Applicant does not clarify how an RNA sample may be used to detect protein using enzyme linked immunosorbent assay either.
Therefore, the rejection are still considered proper and thus maintained.
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 19-24 and 26-32 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more. The claim(s) (19 and 26) recite(s) “comparing the expression of the one or more proteins comprising alpha defensin-1 with a reference expression of the corresponding one or more proteins comprising alpha defensin-1 in a reference synovial fluid from a plurality of individuals confirmed to not have joint infection and inflammation,” and “diagnosing the subject as having bacterial infection when the expression of the one or more proteins is at least two fold greater than the reference expression, or diagnosing the subject as having aseptic inflammation when the expression is not at least two fold greater than the reference protein,” which is a mental process in the abstract idea grouping. An ordinary skilled in the art looking at both sets of expression data will meet this limitation. The diagnosis step may also be performed in human mind by looking at both expression level. This judicial exception is not integrated into a practical application in claims 19-24 because the only additional step is “detecting the expression of one or more protein in the sample,” which is mere data gathering step that is highly general and does not impose a meaningful limitation for the abstract idea. Claims 26-32 recites an additional step of “informing a treatment provider of the results of the comparison,” which is also an extra-solution activity that does not impose further limitation to the abstract idea. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims do not recite additional steps to integrate the abstract idea to a practical application. Therefore, claims 19-24 and 26-32 are not eligible under 101.
The above rejection has been rewritten to address the amendment.
Response to Arguments
Applicant argues that amended claim 19 now recites a “diagnosing” step which is not a mental process of comparing information but rather a specific diagnostic method that produces an actionable clinical diagnosis, and the method apply the discovery that alpha defensin-1 expression level differ between bacterial infection and aseptic inflammation to make a specific diagnosis that determines the appropriate treatment pathway. Applicant asserts the diagnostic methods provide a concrete technological improvement in the field of clinical diagnostics. The claimed invention enables clinicians to distinguish between bacterial infection and aseptic inflammation in joint samples where conventional analysis shows similar white blood cell infiltration. Applicant asserts that the two fold expression threshold recited in the amended claims represents a specific, quantitative diagnostic criterion derived from experimental evidence, and the claimed method are not well-understood, routine or conventional.
The above argument has been fully considered but deemed unpersuasive. As discussed in the above rejection, the added step of making a diagnosis based on the expression level of the biomarker is also a mental step, which may be performed in human mind based on the comparison of the protein expression level. MPEP2106.05(g) has listed examples of activities that the courts have found to be insignificant extra-solution activity, including determining the level of biomarker in blood, to be used in a diagnosis. The diagnosis step merely states the outcome of the determining step, wherein a 2-fold increase of an unknown biomarker (the claim recites the expression of one or more protein is at least two fold greater without specifying which one or more protein) in synovial fluid indicates bacterial infection, and less than 2-fold changes indicates aseptic inflammation. It does not include additional elements that are sufficient to amount to significantly more than the judicial exception. Therefore, the rejection is still considered proper and thus maintained.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 19, 20, 22-24 and 26-32 is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Paulsen (IDS), in view of Kacena. This rejection is rewritten to address the amendment.
Paulsen et al. teach a combination comprises protein isolated from a synovial membrane, and antibody configured specifically detect the expression of DEFA1 (HNP1) and lactoferrin (LTF) (see page 372, bridging paragraph of 1st and 2nd col. and Table 2). Paulsen et al. teach said protein are detected in healthy, septic arthritis (PA), osteoarthritis (OA) and rheumatoid arthritis (RA) (see Table 2). Paulsen et al. also teach measuring other proteins such as HBD-1-6, CAP37 and LL37 in synovial membrane of healthy, OA, PA and RA individuals using RT-PCR technique (see Figure 1 and legend). Paulsen et al. teach the purpose of the study is to identify and characterize antimicrobial peptides released by human synovial membrane in healthy and diseased individual (see page 370, 1st col., 2nd paragraph). Paulsen et al. teach neutrophils expressing alpha defensin 1-3 are increased in number in pyogenic synovial membrane (Figure 3 and legend), indicating alpha defensin (HNP1) would be increased in synovial fluid. Paulsen et al. teach only a few HNP1-3 positive cells were seen in RA samples and OA samples (page 373, 1st col., 2nd and 3rd paragraph).
Paulsen does not teach detecting alpha defensin using enzyme linked immunosorbent assay (ELISA) technique, and making a diagnosis of the subject having bacterial infection or aseptic inflammation based on the expression of alpha defensin-1 in the synovial fluid from a patient having joint inflammation.
Kacena disclose obtaining a synovial fluid sample from a subject having temporomandibular disorder (TMD), and healthy control, determining expression of TNFα, IL-1β, IL-6, IL-8 and IFN-γ in the sample (page 259, 1st col., 2nd paragraph, and Tables 1-5). Tables 1-5 listed amount of the cytokines from both healthy control and TMD patients, so that values from both groups are compared. Kacena teaches the detection method is ELISA (Tables 1-7, 8th col). Kacena teaches a variety of medical therapies could be used to target the inflammation cascade, including proinflammatory cytokine inhibitors such as TNF receptors, receptor antagonists (IL-1ra), and inhibitory cytokines IL-10 (page 263, 2nd col., 2nd paragraph). A treatment provider reading this article is informed of the result of the comparison of the measured cytokines, and will provide treatment to those with increased expression of proinflammatory cytokine markers.
It would have been obvious to an ordinary skilled in the art that Paulsen et al. was attempt to identify and characterize proteins that is released from synovial membrane and identified DEFA1 and LTF are among those present in synovial membrane. Based on the anatomy of a joint, it would have been obvious that proteins will be released into synovial fluid depending on synovial membrane permeability, which may be affected by joint diseases of inflammation and/or infection. The ordinary skilled in the art would thus be motivated to detect what protein(s) are present in synovial fluid in healthy and diseased individual (such as PA, OA and RA) for studying the pathogenesis of joint disease, and identifying effective therapy. Drawing synovial fluid from joint and isolating protein or mRNA is routinely carried out by an ordinary skilled in the art at the time of filing as evidenced by the teaching of Kacena. The ordinary skilled in the art would recognize that detecting a protein expression may be carried out by either immunochemistry (ELISA, for example, taught by Kacena) or mRNA as demonstrated by Paulsen et al. The ordinary skilled in the art reading Paulsen reference would recognize that alpha defensin 1 (HNP1-3) is increased in PA synovial membrane because the increased presence of granulocytes, but not in inflammation condition as in RA and OA. Such finding indicates the difference in HNP1-3 expression exists between bacterial infection and aseptic inflammation when compared with healthy individual and/or each other, and alpha defensin may be used as a biomarker to differentiate/diagnose bacterial infection from aseptic inflammation. The ordinary skilled in the art would have reasonable expectation of obtaining synovial fluid from a subject having inflammation or infection and determining the expression of DEFA1 using ELISA technique following combined teaching from Paulsen and Kacena. Therefore, the claimed invention of claims 19 would have been prima facie obvious to an ordinary skilled in the art at the time the invention was made.
Regarding claim 20, since the claim does not specify which protein is at least two fold greater than the reference expression, increased expression of HBD2 is at least two fold in OA and PA samples compared to healthy sample (see page 371, Figure 1 and legend, specially lane 3).
Regarding claims 22 and 23, Kacena discloses measuring IL-1β, IL-6, IL-8 in synovial fluid sample (Tables 2-4).
Regarding claim 24, the expression of interleukin-1 receptor antagonist (IL-1ra) is also measured from the synovial sample (Table 6).
Regarding claim 26, since there is no teaching from the specification defining the limitation of “multiple points a single time point corresponding to the peak inflammation as determined by clinical symptoms,” obtaining RNA samples from patient sample taught by Paulsen meets this limitation.
Regarding claim 27, Kacena place the expression data in a Table format that indicates whether the expression is greater or not greater than the reference sample. Since the specification does not provide limiting definition of an indicator, the presentation of the amount of cytokines in the table format meets this claim limitation.
Regarding claim 28, the expression of TNFα, IL-1β, IL-6, IL-8 and IFN-γ in the sample is more than two fold greater than the healthy control (Tables 1-5).
Regarding claim 29, Paulsen teaches measuring alpha defensin 1 protein expression (Figure 3 and legend).
Regarding claim 30, the expression of interleukin-1 receptor antagonist (IL-1ra) is also measured from the synovial sample (Table 6).
Regarding claims 31 and 32, Kacena discloses measuring IL-1β, IL-6, IL-8 in synovial fluid sample (Tables 2-4).
Claim 21 is rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Paulsen and Kacena, as applied to claim 19, 20, 22-24, 26-32 above, and further in view of Pufe (Arthritis & Rheumatism, 2003, Vol. 48, No. 3, pages 660-667).
The teaching of Paulsen and Kacena has been discussed above. However, neither reference teaches measuring vascular endothelial growth factor (VEGF) from synovial sample.
Pufe teaches pleiotrophin (PTN) expression in normal adult synovial membranes and cartilage is barely detectable, but elevated in synovial tissues from rheumatoid arthritis (RA) patients. Pufe teaches PTN is also found in endothelial cells of blood vessel, and stimulated proliferation of human synoviocytes and monocyte cell, and synthesis of VEGF (Figure 2 and legend, Figure 6 and legend, and Figure 7 and legend). Pufe teaches only a few endothelial cells are present in normal synovium, but increased number of endothelial cells are present in RA synovium (Figure 3 and legend). Pufe teaches chronic inflammation is characterized by the production of various cytokines including TNF, interleukins 1 and 6 and VEGF (page 665, 2nd col., 1st paragraph, lines 1-4). Pufe also teaches vascularization is observed in RA (page 666, 1st col., 1st paragraph).
It would have been obvious to an ordinary skilled in the art to include vascular angiogenesis factors including PTN and VEGF when evaluating synovial fluid from patient has joint inflammation based on the combined teaching from Paulsen, Kracena and Pufe. The ordinary skilled in the art would include VEGF because Pufe demonstrated that VEGF production would have been increased in at least the endothelial cells present in synovium in RA patient due to increased PTN expression. The ordinary skilled in the art would have reasonable expectation of success to detect at least DEFA1 and VEGF in synovial fluid because detection method are known in prior art and routinely practiced as evidenced by the teaching from Paulsen, Kracena and Pufe. Therefore, the claimed invention of claim 21 would have been prima facie obvious to an ordinary skilled in the art at the time the invention was made.
Response to Arguments
Applicant argues that Paulsen does not teach using differential expression level of alpha defensin-1 as a quantitative diagnostic marker to distinguish between bacterial infection and aseptic inflammation. Applicant argues that Paulsen reports qualitative observations about the presence of various peptides but does not teach measuring expression levels, comparing those to a reference because Paulsen states its objective was “to determine the expression and production of antimicrobial peptides by healthy and inflamed human synovial membranes. Applicant argues that Paulsen’s detection of HNP1-3 in granulocytes/neutrophils in the synovial membrane is distinct from the claimed method which analyze synovial fluid samples. Applicant argues that Kacena does not teach detecting alpha defensin but other cytokines from synovial fluid. Applicant asserts that combined teaching from Paulsen and Kacena does not teach differential expression of alpha defensin-1 expression in synovial fluid can diagnose whether joint inflammation caused by bacterial infection or aseptic inflammation, which is taught by instant application in Example 2.
The above argument has been fully considered but deemed unpersuasive. As discussed in the above rejection, based on the anatomy of a joint, it would have been obvious that proteins will be released into synovial fluid depending on synovial membrane permeability, which may be affected by joint diseases of inflammation and/or infection. The ordinary skilled in the art would thus be motivated to detect what protein(s) are present in synovial fluid in healthy and diseased individual (such as PA, OA and RA) for studying the pathogenesis of joint disease, and identifying effective therapy. Drawing synovial fluid from joint and isolating protein or mRNA for quantitative analysis (Table 2) is routinely carried out by an ordinary skilled in the art at the time of filing as evidenced by the teaching of Kacena. Replacing the qualitative detection taught by Paulsen with the quantitative measurements taught by Kacena would have been routine experimentation rather than method of innovation. With regard to the argument directed to Paulsen does not teach a diagnostic method, it is not persuasive because it is apparent that alpha defensin is increased in synovial membrane of bacterial infection as compared to healthy individual and patient having OA and RA, which suggests it may be used as a diagnostic marker. Contrary to Applicant’s assertion, there is no teaching or suggestion in the specification, example 2, that 2 fold increase in alpha defensin-1 in the synovial fluid is a threshold for quantitative diagnostic differentiation between aseptic inflammation and bacterial infection. Rather, example 2 just lists a number of genes that are differentially expressed in synovial fluid of patients that are known to having septic and aseptic inflammation. There is no quantitative measurement between the comparison of bacterial infection vs. healthy individual not have joint infection and confirmed not have joint inflammation. Moreover, the measurement of example 2 is using RNA sample detected from microarray analysis, not at protein expression. The ordinary skilled in the art at the time of filing would recognize that mRNA level does not always correlates with protein level in a tissue sample. As such, the recited 2 fold difference in alpha defensin expression (for providing the diagnosis) is not an unexpected result, but rather an prediction based on the microarray data as presented in the present specification. Therefore, for reason discussed in previous office action and set forth above, this rejection is still considered proper and thus maintained.
Conclusion
THIS ACTION IS MADE FINAL. 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 CELINE X QIAN whose telephone number is (571)272-0777. The examiner can normally be reached M-F (8-4:00).
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/CELINE X QIAN/ Primary Examiner, Art Unit 1637
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