DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA . The amendment filed on 03/03/2026 has been entered. Claims 1-17 are pending in this application. Claims 5, 6, and 11-17 are withdrawn. Claims 1-4 and 7-10 are currently under examination.
Priority
This application is a 371 of PCT/US21/44587 filed on 08/05/2021 and claims benefit of US PRO 63/061,344 filed on 08/05/2020.
Note: The PRO 63/061,344 filed in the Application Data Sheet does not match the certified priority application 63/061,334.
Election/Restrictions
Applicant's election without traverse of Group I invention (claims 1-10) and species (HIF1α for species A and specific step recited in claim 4 for species B) in the reply filed on 03/03/2026 is acknowledged. Claims 5, 6, and 11-17 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention or species, there being no allowable generic or linking claim. Thus, claims 1-4 and 7-10 are currently under examination.
Information Disclosure Statement
Two information disclosure statements (IDS) filed on 04/08/2024 and 09/06/2024 have been considered.
Claim Objections
Claims 1, 2, and 7-9 are objected to because of the following informalities: In claim 1, change the incorrect recitation “biomarkers levels” (line 13) to “biomarker levels”; and insert the missing phrase “one or more” immediately before the recitation “biomarker levels” (lines 4, 13, and 16) because the “biomarker levels” would refer to all listed biomarkers without the “one or more”. In claim 2, change the incorrect recitation “, the panel further comprising one or more biomarker” (lines 1 to 2) to “, wherein the panel further comprises one or more biomarkers:” to become proper dependent claim format; delete the incorrect recitation “selected from one or more isoforms selected from” (line 2) because it contains closed transitional phrase “selected from”, which is contradictory to the preceding open-ended transitional phrase “comprises”. In claim 7, change the incorrect recitation “measurement; detecting one or more biomarkers” (lines 3 to 4) to “measurement and the change in the level of one or more biomarkers” because the “detecting” is done in the preceding claim 1; and replace the incorrect recitation “detecting of the biomarkers” (line 6) with “change in the level of one or more biomarkers” for the same reason. In claim 8, change the incorrect recitation “, an individual” (line 1) to “, wherein said individual” to become proper dependent claim format. In claim 9, change the incorrect conjunction “and” (line 3), which means that the detecting at multiple timepoints is done at the same time, to “or”. Appropriate correction is required.
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 1-4 and 7-10 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.
Claim 1 recites “a reference value” (line 14), which is not clear what the reference value is. The recitations “predicting whether said individual is likely to develop BOS” and “based on the determined change” (lines 15-16) are also confusing. The “whether” would have two scenarios: yes or no. If the predicting is “no”, the step (d) would not be needed. It is not clear what “determined change” would consider “likely to develop BOS”. Applicant is advised to insert the clause “which is a mean value from a cohort without BOS” immediately after the recitation “a reference value” (line 14); to delete the recitation “whether” (line 15); to change the recitation “is likely” (line 15) to “being likely”; and to insert the phase “that indicates increase” immediately after the recitation “change” (line 16).
Claims 2 and 8 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being incomplete for omitting essential structural cooperative relationships of elements, such omission amounting to a gap between the necessary structural connections. See MPEP § 2172.01. The omitted structural cooperative relationships are: Claim 2 recites “the panel further comprises… CASP8-associated protein 2… hypoxia-inducible factor I-alpha isoform 1… interferon-induced protein with tetratricopeptide repeats 1B… SAC3 domain-containing protein 1 isoform a”, which have been recited or encompassed by the preceding claim 1 and the “further comprises” would destroy structural relationship with claim 1. Also, claims 2 and 8 recite “one or more… and combinations thereof, in which the recitation ”more” encompasses “combinations thereof” and thus omits the structural relationship. Applicant is advised to delete the biomarkers in claim 2 that have been recited in claim 1 and to delete the ”combinations thereof”.
Claim 4 recites “predicting is further based on said lung function parameter determination”. It is not clear what lung function parameter determination would predict said individual likely to develop BOS. Applicant is advised to insert the phrase “that is worsening” at the end of the claim.
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 1-4 and 7-10 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon or a product of nature without significantly more. The 2019 Revised Patent Subject Matter Eligibility Guidance (issued January 7, 2019)” (https://www.govinfo.gov/content/pkg/FR-2019-01-07/pdf/2018-28282.pdf) and “October 2019 Update: Subject Matter Eligibility (issued October 17, 2019)” (https://www.uspto.gov/sites/default/files/documents/peg_oct_2019_update.pdf), are followed here. The claim is directed to a statutory category, e.g., a process (Step 1: YES). The claim is then analyzed in Step 2A (Prong one) to determine whether it is directed to any judicial exception. The claims 1-4 and 7-10 recite a method comprising detecting one or more biomarker levels in a biomarker panel, the biomarker panel comprising: Hypoxia-Inducible Factor 1-alpha (HlF1α), Caspase 8 Associated Protein 2 (CASP8AP2)… in a biological sample obtained from an individual who has undergone a hematopoietic stem cell transplant (HSCT); determining a change in one or more biomarker levels relative to a reference value which is a mean value from a cohort without BOS; predicting said individual being likely to develop BOS based on the determined change that indicates increase in the biomarker levels in the biomarker panel; and administering a therapy effective for treatment of BOS to the individual predicted to be likely to develop BOS. The claimed process encompass a mental process of looking up a chart and comparing the level of, for example, HIF1α and lung function between individuals who have undergone a hematopoietic stem cell transplant with or without bronchiolitis obliterans syndrome (BOS); arbitrarily selecting a cutoff value to differentiate the individual with BOS from the individual without BOS according to HIF1α level and lung function; and observing the outcome of the individual without BOS or with undiagnosed BOS after a routine therapy. Accordingly, the claim is directed to at least one exception (Step 2A, prong one: YES). The claim is then analyzed in Step 2A (Prong two) and is deemed that this judicial exception is not integrated into a practical application because there is no indication that the detecting, determining, and predicting steps change the administering step in any marked way. Instead, the individuals who have undergone a hematopoietic stem cell transplant with undiagnosed or without bronchiolitis obliterans syndrome (BOS) would be routinely monitored and given medication. Thus, the claimed process as a whole does not display markedly different characteristics compared to the closest naturally occurring process. Accordingly, the Step 2A (Prong two) is NO because this judicial exception is not integrated into a practical application. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because prior to applicant’s invention and at the time of filing the application, the detecting of biomarkers, correlating of HIF1α level and lung function to BOS, and administering of a therapy to treat BOS were well-understood, routine and conventional in the field, as evidenced by the references under the 102 and 103 rejection below. The recitation of specific medication or timepoint for detecting does not affect this analysis, because it was also well-understood, routine and conventional. Thus, the claimed method, when recited at this high level of generality, does not meaningfully limit the claim, and the claim as a whole does not amount to significantly more than each “natural phenomenon” by itself (Step 2B: NO). The claim does not qualify as eligible subject matter.
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.
Claims 1, 3, 4, 7, and 8 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ditschkowski et al. (Bone Marrow Transplantation 48, 1224-1229, 2013, hereinafter referred to as Ditschkowski ‘2013).
With regard to structural limitations “a method comprising detecting one or more biomarker levels in a biomarker panel, the biomarker panel comprising: Hypoxia-Inducible Factor 1-alpha (HlF1α) in a biological sample (or blood) obtained from an individual who has undergone a hematopoietic stem cell transplant (HSCT); determining a change in one or more biomarker levels relative to a reference value which is a mean value from a cohort without BOS; predicting said individual being likely to develop BOS based on the determined change that indicates increase in the biomarker levels in the biomarker panel (or further comprising determining a lung function parameter and predicting based on said lung function parameter determination that is worsening; or providing a risk assessment based on the lung function and change in the level of biomarker); and administering a therapy (or montelukast or azithromycin) effective for treatment of BOS to the individual predicted to be likely to develop BOS” (claims 1, 3, 4, 7, and 8):
Ditschkowski ‘2013 disclosed that among 982 patients after myeloablative hematopoietic stem cell transplantation (SCT) between January 2000 and October 2010, 68 were diagnosed with Bronchiolitis obliterans (BO). The median onset of BO was 18 months post-transplant. The mean exhaled nitric oxide (NO) concentrations were lower in BO-patients than in stem cell recipients without BO or healthy controls. Hypoxia-inducible factor 1 alpha (HIF-1α) was significantly elevated in BO as compared with healthy controls or GVHD-patients without lung involvement. Adult patients, who underwent myeloablative allogenic hematopoietic SCT between January 2000 and October 2010 and survived more than 100 days post-transplant were evaluated. Pulmonary function tests (PFTs) were performed routinely every 6 months after transplantation and additionally out-of-band in symptomatic patients with non-resolving symptoms like exertional dyspnea and dry cough. BO treatment was standardized and consisted of inhaled beta mimetics and steroids, increase in the dosage of systemic immunosuppressive treatment (calcineurin inhibitors, corticosteroids, mycophenolate), medication with montelukast and azithromycin, occasional administration of systemic beta agonists and supportive ant-infectious therapy/prophylaxis. HIF-1α mRNA levels were measured in blood samples of 40 patients with advanced BO, 20 patients with moderate and severe chronic GVHD without BO and 10 healthy controls. Online assessment of the exhaled NO was performed in a cohort of 45 patients with manifest BO, 30 hematopoietic SCT-recipients without BO (22 with chronic GVHD, 8 without chronic GVHD) and 25 healthy controls (page 1224, Abstract; right col., para. 3; page 1225, left col. para. 1 to 3). As HIF-1α is a key regulator in the cellular adaptation to hypoxia it can be suggested that HIF-1 accumulates during initial BO manifestation consecutively leading to enhanced tissue fibrosis and further aggravation of BO (page 1228, left col., para. 1).
Thus, these teachings of Ditschkowski ‘2013 anticipate Applicant’s claims 1, 3, 4, 7, and 8.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4 and 7-10 are rejected under 35 U.S.C. 103 as being unpatentable over Ditschkowski et al. (Bone Marrow Transplantation 48, 1224-1229, 2013, hereinafter referred to as Ditschkowski ‘2013) in view of Ladak et al. (J Heart Lung Transplant 35:550–559, 2016, hereinafter referred to as Ladak ‘2016), Lorenzen et al. (American Journal of Transplantation 11: 2221–2227, 2011, hereinafter referred to as Lorenzen ‘2011), and Haider et al. (J. of Cardiovasc. Trans. Res. 3:89–102, 2010, hereinafter referred to as Haider ‘2010). Claims 1, 3, 4, 7, and 8 are rejected here because they have been rejected by the primary reference under 102 above. The above disclosure of Ditschkowski ‘2013 is incorporated in its entirety here.
Ditschkowski ‘2013 did not explicitly disclose the limitations “Caspase 8 Associated Protein 2 (CASP8AP2) (or further comprising complement C3 biomarker)”, “detecting is carried out at a timepoint selected from 14 days post-HSCT, 30 days post-HSCT, 60 days post-HSCT, or 100 days post-HSCT”, and “said individual is a pediatric patient”, required by claims 1, 2, 9, and 10.
Ladak ‘2016 disclosed that acute cellular rejection (ACR) is one of the major alloimmune-dependent risk factors responsible for the development of bronchiolitis obliterans syndrome (BOS). Lymphocytic bronchitis and pulmonary infections are also likely to be precursors of BOS. The non-alloimmune factors implicated in graft injury include primary graft dysfunction and result mainly from ischemia-reperfusion injury. miR-210 was elucidated as an important marker for discriminating between stable transplant patients and patients at risk for rejection (page 551, left col., para. 2; right col., para. 1; page 554, right col., para. 2).
Lorenzen ‘2011 disclosed that the miR-10b and miR-210 were downregulated and miR-10a upregulated in patients with acute rejection compared to controls. Only miR-210 differed between patients with acute rejection when compared to stable transplant patients with urinary tract infection or transplant patients before/after rejection. Low miR-210 levels were associated with higher decline in GFR 1 year after transplantation (page 2221, Abstract).
Haider ‘2010 disclosed that cytoprotective effects of multiple cycles of brief ischemia/reperfusion involved hypoxia-regulated miRs expression downstream of HIF-1α with special emphasis on miR-210. Inhibition of HIF-1α or that of miR-210 abrogated the cytoprotective effects of ischemic preconditioning. In vitro data on miR-210 which were supported by in vivo studies in a rat model of acute myocardial infarction showed predominantly improved stem cell survival postengraftment. Notably, induction of miR-210 occurred as early as 4 h after exposure to hypoxia and persisted for 24 h above baseline levels. Moreover, miR-210 inhibition was associated with increased apoptosis of endothelial cells. A functional link between HIF-1α and miR-210 has also been reported in cancer cells for antiapoptotic effects. Four possible target genes including CASP8AP2, tumor necrosis factor receptor super family 1a, DNA fragmentation factor-β, and lymphotoxin A showed more than twofold upregulated expression in miR-210 knockdown cells. ischemic preconditioning-induced survival signaling in stem cells signifies mechanistic participation of miRs in cytoprotection afforded by ischemic preconditioning via FLASH/CASP8AP2 suppression (page 93, left col., para. 1; right col., para. 1 to 2; page 94, left col., para. 1). Antiapoptotic strategies such as gene modification for interleukin 1 (IL-1) expression, use of receptor antagonist, depletion of host C3 complement, and prevention of the humoral immune response by treating host with anti-CD154 before and after cell transplantation have been successfully used for cytoprotection (page 90, right col., para. 2).,
Thus, it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was filed to substitute or to combine the HIF1α biomarker as taught by Ditschkowski ‘2013 with CASP8AP2 and/or complement C3 biomarkers in view of Ladak ‘2016, Lorenzen ‘2011, and Haider ‘2010 to predict or to identify a subject or a pediatric patient likely to develop bronchiolitis obliterans syndrome (BOS) after hematopoietic stem cell transplantation for anti-BOS, anti-inflammatory, and/or anti-infection treatments because (a) bone marrow transplant is practiced for treating adult or children leukemia; and BOS is observed 100 days post-transplantation, and (b) BOS is associated with acute graft rejection, which is associated with apoptosis, downregulation of miR-210, and upregulation of C3 complement; and decrease or knockdown of miR-210 increases the level of CASP8AP2, described above. Thus, one of skill in the art would have a reasonable expectation that by substituting or by combining the HIF1α biomarker as taught by Ditschkowski ‘2013 with CASP8AP2 and/or complement C3 biomarkers in view of Ladak ‘2016, Lorenzen ‘2011, and Haider ‘2010 to predict or to identify a subject or a pediatric patient likely to develop bronchiolitis obliterans syndrome (BOS) after hematopoietic stem cell transplantatio, one would achieve Applicant’s claims 1-4 and 7-10. "Exemplary rationales that may support a conclusion of obviousness include: (B) Simple substitution of one known element for another to obtain predictable results". See MPEP § 2143 [R-01.2024] [I]. "[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). See MPEP § 2144.05 [R-01.2024] [II.A].
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 1-3, and 8-10 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 4, 5, 8-10, and 17 of copending Application No. 18/859,287 (APPLICANT: Children's Hospital Medical Center, claims set of 10/23/2024). Although the claims at issue are not identical, they are not patentably distinct from each other because Appl ‘287 claims “A method for identifying an individual at risk for developing bronchiolitis obliterans syndrome (BOS) after hematopoietic stem cell transplant (HSCT), comprising (a) detecting one or more biomarker (or isoform thereof) selected from: integrin-linked protein kinase (ILK), Kelch-like protein S (KLHLS), kinesin-like protein 22 (KID), SAC3 domain-containing protein 1 (SAC3D1), RRP12-like protein (PRP12), manganese transporting protein, ATPase13A1 (ATP13A1), sorting nexin 8 (SNX8), and caspase 8 associated protein 2 (CASP8AP2, or FLASH), Interferon Induced Protein with Tetratricopeptide Repeats 1 (IFIT1), MTUS2 (microtubule associated tumor suppressor candidate 2), Factor I, Vitronectin, C1 inhibitor, Plasma protease C1 inhibitor precursor, complement component 1q (C1q)… Factor B, and combinations thereof; (b) quantifying a level of said one or more biomarkers detected in (a); and (c) comparing said level of said one or biomarkers to a control value (or a level of said biomarker in said individual prior to HSCT); wherein a deviation in a level of said one or more biomarkers from said control value indicates said individual at risk for developing BOS (or wherein n an increase in said biomarker or where IFIT1 is increased as compared to said control value, said individual is diagnosed as likely to develop BOS and is treated for BOS; or wherein said individual is diagnosed as likely to develop BOS, and is administered an agent selected from a beta blocker, and antihyperlipidemic-HMG CoA reductase inhibitor (statin), a macrolide antibiotic, an anthracycline conjugate, a small molecule elastase inhibitor, an angiogenesis inhibitor, a tetracycline antibiotic, a mucolytic, a matrix metalloprotease inhibitor, and combinations thereof)” (claims 1, 2, 5, 8, and 17), and “wherein said detecting of step (a) is carried out at a time point selected from day 14 post-transplant, day 30 post-transplant, day 60 posttransplant, and day 100 post-transplant; or wherein said biomarker is detected in a biological sample obtained from said individual (or selected from a plasma sample, serum sample, blood sample, bronchoalveolar lavage fluid (BALF) sample, and combinations thereof)” (claims 4, 9, and 10), encompassing or overlapping with claims 1-3, and 8-10 of this Application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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/YIH-HORNG SHIAO/ Primary Examiner, Art Unit 1691
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