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 the Claims
Claim 12 has been withdraw as being directed to a non-elected invention. Claims 9-10 have been withdrawn as being directed to a non-elected species. Claims 1-8, 11 and 14-21 are under examination at this time.
Claim Objections
Claim 1 is objected to because of the following informalities: For consistency, claim 1 should recite IFNγ instead of IFNG. Appropriate correction is required.
Withdrawn Rejections
The rejection of claim 13 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, has been withdrawn in view of the cancelation of claim 13.
The rejection of claims 1-8 and 11 under 35 U.S.C. 102(a)(1) as being anticipated by Lee et al. (WO 2020/096984; May 14, 2020) has been withdrawn in view of applicant’s amendments to claim 1 to recite CD74, IFNG, CX3CR1 and TAP2.
New Rejections Necessitated by Amendment
Claim Rejections - 35 USC § 112
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 14 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 1 recites that expression levels of C3AR1 and at least one of CD74, IFNγ, CX3CR1 and TAP2 are measured. Claim 14, which depends from claim 1, recites that expression levels of each of C3AR1, CD74, IFNy, CD177, S100A9, CX3CR1, and TAP2 are measured. CD177 and S100A9 are not recited in claim 1. Claim 14 broadened the scope of claim 1 instead of narrowing the scope.
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.
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.
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.
Claim(s) 1-8, 11, 15-17 and 21 are rejected under 35 U.S.C. 103 as being unpatentable over Lee et al. (WO 2020/096984; May 14, 2020) and further in view of Cazalis et al. (Critical Care, 2013, 17:R287) and Friggeri et al. (Critical Care, 2016, 20:204).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
Lee et al. teaches a method of diagnosing sepsis in a subject including detecting or measuring expression of the set of at least six genes in a sample from a subject, wherein the subject is diagnosed with sepsis when expression of a panel of genes including CCR1, C3AR1, C9orf95, BATF, C9orf103, GNA15, CD177, CD63, EMR1, FCERIG, FES, PLAC8, and/or SEPHS2 is increased compared to a control (see, for example, page 2, lines 26- 29).
Cazalis et al. measured the expression of 5 genes (CD74, HLA-DRA, HLA-DMB, HLA-DMA, and CIITA) in septic shock patients. Cazalis et al. found that among mRNA markers, the best prognostic value was obtained for CD74 and that decreased CD74 mRNA expression significantly predicts 28-day mortality after septic shock (see, for example, the abstract).
Friggeri et al. teaches that chemokine (C-X3-C motif) receptor 1 (CX3CR1) was identified as the most differentially expressed gene between survivors and non-survivors in two independent cohorts of septic shock patients and was proposed as a marker of sepsis-induced immunosuppression. Friggeri et al. found that decreased CX3CR1 mRNA expression at D1 was associated with high D7 mortality, while decreased expression at D3 was associated with increased D28 mortality (see, for example, the abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods taught by Lee et al. and include other known biomarkers of sepsis such as CX3CR1 and CD74. One would have been motivated to do so and there would have been a reasonable expectation of success given the teachings of Cazalis et al. and Friggeri et al. Further, including additional biomarkers for sepsis would allow for a more accurate prediction of sepsis.
For claims 2-5, Lee et al. teaches measuring “the expression of at least one gene selected from the following genes” GNLY, S100A9, ADGRE3, CD177, CX3CR1, IFIH1, OAS2, and OAS3. CD177 is gene that encodes a molecule involved in the innate immune system (as defined in the instant specification).
For claim 6, Lee et al. teaches that the sample can be a blood sample (see page 10, lines 33-37).
For claims 7 and 8, Lee et al. teaches that determining the level expression in either a qualitative, semi-quantitative, or quantitative manner is done by detection of nucleic acid molecules (e.g., DNA, RNA, and/or mRNA) or proteins. Exemplary methods include microarray analysis, PCR (such as RT-PCR, real-time PCR, or qRT-PCR), Northern blot, Western blot, ELISA, and mass spectrometry (see page 10, lines 29-32 and page 21, line 3 to page 22, line 14).
For claim 11, Lee et al. teaches comparing the expression level of the panel of genes to control genes, such as one or more housekeeping or internal control genes (see page 2, lines 26-29 and page 13, line 36 to page 14, line 4 and page 16, lines 7-12).
For claim 15, Lee et al. teaches that gene expression of C3AR1 is increased compared to a control (see, for example, page 2, lines 26- 29).
For claims 16, 17 and 21, Lee et al. teaches that when expression is altered compared to a control, one or more antibiotics are administered to the subject. In some examples, the subject does not exhibit symptoms of sepsis (for example, is pre-symptomatic or pre-clinical for sepsis) (see page 4, lines 13-15). Exemplary antibiotics include ceftriaxone, azithromycin, ciprofloxacin, vancomycin, aztreonam, moxifloxacin, nafcillin, daptomycin, meropenem, ceftazidime, cefotaxime, cefepime, piperacillin-tazobactam, ampicillin-sulbactam, imipenem/cilastatin, levofloxacin), clindamycin, and combinations of two or more thereof (see page 33, lines 9-16).
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
Claim(s) 18-20 are rejected under 35 U.S.C. 103 as being unpatentable over Lee et al. (WO 2020/096984; May 14, 2020) and further in view of Cazalis et al. (Critical Care, 2013, 17:R287) and Friggeri et al. (Critical Care, 2016, 20:204) as applied to claims 1-8, 11, 15-17 and 21 above, and further in view of Hutchins et al. (Trends Mol Med., 2014, 20(4): 224–233) and Annane (Annals of Intensive Care, 2011,1:7).
The instant claims are directed to the method of claim 1, wherein if the patient is immunosuppressed, the immunomodulatory treatment is an immunostimulant treatment, and if the patient has an inflammatory state, the immunomodulatory treatment is an anti-inflammatory treatment.
The teachings of Lee et al., Cazalis et al. and Friggeri et al. are outline above and incorporated herein. Lee et al., Cazalis et al. and Friggeri et al. do not teach claims 18-20. However, Hutchins et al. teaches the use of cytokines such as IL-7, IL-15, GM-CSF as well as co-inhibitory molecule blockade, such as anti-PD-1 and anti-BTLA, for treating sustained sepsis in immune suppressed patients. Annane teaches that septic shock is characterized by uncontrolled systemic inflammation that contributes to the progression of organ failures and eventually death. There is now ample evidence that the inability of the host to mount an appropriate hypothalamic-pituitary and adrenal axis response plays a major in overwhelming systemic inflammation during infections. Annane further teaches the use of anti-inflammatory agents such as glucocorticoids for treating systemic inflammation (septic shock) in patients.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the methods taught by Lee et al. and administer an immunostimulant such as IL-7 or IL-15 if the patient is immunosuppressed (see Hutchins et al.) or administer anti-inflammatory treatment if the patient has an inflammatory state. One would have been motivated to do so and there would have been a reasonable expectation of success given the teachings of Hutchins et al. regarding the relationship between immunosuppression and sepsis and treatments and give the teachings of Annane regarding the relationship between inflammation and sepsis and treatments.
Thus, the invention as a whole was clearly prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention.
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. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); 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); 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) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1-8 and 11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3 and 8-12 of copending Application No. 18/880056 (reference application).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
The copending claims are directed to an in vitro or ex vivo method for determining the risk of death of a subject infected with a respiratory virus, comprising a step of measuring the expression level of the CD74 gene in a biological sample from said subject, where the method further comprises measuring the expression of one or more other additional genes in the biological sample from the subject, said genes being involved in host response and being selected from ADGRE3, ARL14EP, BPGM, C3AR1, CCNB1IP1, CD274, CD3D, CIITA, CTLA4, CX3CR1, GNLY, IFNG, IL10, IL1RN, IL7R, IP10/CXCL10, MDC1, OAS2, S100A9 and combinations thereof in the biological sample from the subject. The expression level of CD74 is compared to a predetermined threshold value (copending claim 3).
Copending claims 1, 3 and 12 teach instant claims 1-5.
Copending claim 8 teaches instant claim 6.
Copending claim 9 teaches instant claim 7.
Copending claim 10 teaches instant claim 8.
Copending claim 11 teaches instant claim 11.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-8 and 11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 7, 8, 10 and 11 of copending Application No. 18/880034 (reference application).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
The copending claims are directed to an in vitro or ex vivo method for determining the risk of death of a subject infected with a respiratory virus, said method comprising the following steps: a) measuring the expression level of the ADGRE3 gene in a biological sample from said subject, b) comparing the expression level of the ADGRE3 gene measured in step a) with a predetermined reference value. The method further comprises a step of measuring the expression of at least one other additional gene selected from C3AR1, CD177, OAS2, CIITA, IL-10, IL1R2, CD74, TDRD9 and combinations thereof in the biological sample from said subject.
Copending claims 1 and 5 teach instant claims 1-5.
Copending claim 8 teaches instant claim 6.
Copending claim 7 teaches instant claim 7.
Copending claim 10 teaches instant claim 8.
Copending claim 11 teaches instant claim 11.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-8 and 11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 5, 7-8 and 10-11 of copending Application No. 18/880053 (reference application).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
The copending claims are directed to an in vitro or ex vivo method for determining the risk of death of a subject infected with a respiratory virus, said method comprising the following steps: a) measuring the expression level of the OAS2 gene in a biological sample from said subject, b) comparing the expression level measured in step a) with a predetermined reference value. The method further comprises a step of measuring the expression of at least one other additional gene selected from C3AR1, CD177, ADGRE3, CIITA, IL-10, IL1R2, CD74, TDRD9 and combinations thereof in the biological sample from said subject.
Copending claims 1 and 5 teach instant claims 1-5.
Copending claim 8 teaches instant claim 6.
Copending claim 7 teaches instant claim 7.
Copending claim 10 teaches instant claim 8.
Copending claim 11 teaches instant claim 11.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-8 and 11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 6, 7, 8 and 11 of copending Application No. 18/014814 (reference application).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
The copending claims are directed to an in vitro or ex vivo method for determining the risk of incidence of a healthcare-associated infection, comprising a step of measuring the expression of CIITA in a biological sample from the patient. The method further comprises a step of measuring the expression of at least one other additional gene selected from GNLY, S100A9, C3AR1, ADGRE3, CD177, CX3CR1, OAS2, CCNB1IP1, IL10, IL1RN, IL1R2, IFNG, TNF, ARL14EP, TAP2, GATA3, MDC1, TDRD9, BPGM, CD3D, CD274, CTLA4, CD74, IL7R, ZAP70, HP.
Copending claims 1 and 3 teach instant claims 1-5.
Copending claim 6 teaches instant claim 6.
Copending claim 7 teaches instant claim 7.
Copending claim 8 teaches instant claim 8.
Copending claim 11 teaches instant claim 11.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-8 and 11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 4, 6, 7, 8 and 11 of copending Application No. 18/014885 (reference application).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
The copending claims are directed to an in vitro or ex vivo method for determining the risk of incidence of a healthcare-associated infection in a patient, comprising a step of measuring the expression of CD177 in a biological sample from said patient. The method further comprises a step of measuring the expression of at least one other additional gene selected from GNLY, S100A9, C3AR1, ADGRE3, TAP2, CX3CR1, OAS2, CCNB1IP1, IL10, IL1RN, IL1R2, IFNG, TNF, ARL14EP, CIITA, GATA3, MDC1, TDRD9, BPGM, CD3D, CD274, CTLA4, CD74, IL7R, ZAP70, HP.
Copending claims 1, 3 and 4 teach instant claims 1-5.
Copending claim 6 teaches instant claim 6.
Copending claim 7 teaches instant claim 7.
Copending claim 8 teaches instant claim 8.
Copending claim 11 teaches instant claim 11.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claims 1-8 and 11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 3, 4, 6, 7, 8 and 11 of copending Application No. 18/014878 (reference application).
The instant claims are directed to an in vitro or ex vivo method for determining the risk of complication in a patient, the method comprising:
(a) measuring the expression of C3AR1 and at least one gene selected from the group consisting of CD74, IFNG, CX3CR1, and TAP2 in a biological sample from said patient; and
(b) determining the risk of complication based on a comparison of the measured expression levels to predetermined reference values,
wherein the complication is a healthcare-associated infection.
The copending claims are directed to an in vitro or ex vivo method for determining the risk of incidence of a healthcare-associated infection in a patient, comprising a step of measuring the expression of TAP2 in a biological sample from said patient. The method further comprises a step of measuring the expression of at least one other additional gene selected from GNLY, S100A9, C3AR1, ADGRE3, CD177, CX3CR1, OAS2, CCNB1IP1, IL10, IL1RN, IL1R2, IFNG, TNF, ARL14EP, CIITA, GATA3, MDC1, TDRD9, BPGM, CD3D, CD274, CTLA4, CD74, IL7R, ZAP70, HP.
Copending claims 1, 3 and 4 teach instant claims 1-5.
Copending claim 6 teaches instant claim 6.
Copending claim 7 teaches instant claim 7.
Copending claim 8 teaches instant claim 8.
Copending claim 11 teaches instant claim 11.
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claim is 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 Nicole Kinsey White whose telephone number is (571)272-9943. The examiner can normally be reached M to Th 6:30 am to 6:00 pm.
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/NICOLE KINSEY WHITE/Primary Examiner, Art Unit 1672