DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The applicant's election of species Alzheimer's disease (AD) in their reply dated 2/24/2026 is acknowledged. Claims 1-11 are pending and considered on the merits below.
Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The Information Disclosure Statements filed on 1/27/2023 and 6/17/2025 are in compliance with the provisions of 37 CFR 1.97 and have been considered. An initialed copy of the Form 1449 is enclosed herewith.
Drawings
The drawings are objected to because Figures 1-8 are blurry. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
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 1-11 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 1, the limitation (lines 4-15)“said PTMs being: ….” is indefinite because there is no conjunction (e.g. “or” or “and”) in the list of PTMs being listed. It is unclear if all of the PTM are required (i.e. “and”) or at least one of them (i.e. “or”). For examination purposes the examiner interprets at least one of them (i.e. “or”). Thus the limitation reads “…said PTMs being: PTM-1 at the amino acid M 1, PTM-2 at the amino acid K1 64, PTM-3 at the amino acid K370, PTM-4 at the amino acid L101, PTM-5 at the amino acid K120, PTM-6 at the amino acid K132, PTM-7 at the amino acid K139, PTM-8 at the amino acid K291, PTM-9 at the amino acid K357, PTM-10 at the amino acid S6, OR PTM-11 at the amino acid S33,”
Further regarding claim 1, the limitation (lines 37-43) “or wherein…” is indefinite because it is unclear what the were in clause is modifying. It could either be back to lines 26-27, or after line 36. For examination purposes the examiner interprets that it modifies the limitations of lines 26-27.
Regarding claims 8 and 11, the limitations “monoclonal/polyclonal” and “with/without”, respectively, are indefinite because it is unclear if the “/” means “and”, “or”, or “and/or”. For examination purposes the examiner interprets that the “/” means “or”.
Dependent claims follow the same reasoning.
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 1-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to an abstract idea without significantly more.
Step 2A, Prong 1: identify the abstract ideas. The “analyzing”, “assessing” and “correlating” steps are all abstract ideas as they represent mathematical equations or simple evaluations. The MPEP holds that both evaluations and mathematical calculations are abstract ideas (MPE 2106.04(a)).
Step 2A, Prong 2: has the abstract idea been integrated into a particular practical application? The claims present limitations of analysing, assessing, and correcting, but are not actual tangible method steps. No process limitations leading to any tangible actions seem to be taking place. As such, it appears there is no application, and by extension, no practical application either. Even if we assume, for the sake of argument, that analysing is an action this is an insignificant post solution activity (MPEP 2106(g)). Data gathering and/or generically applying an abstract idea have been deemed to not be integrated into a practical application, there must be a meaningful limit to the judicial exception which is claimed (MPEP 2106(f) and (g)).
Step 2B: does the claim recite any elements which are significantly more than the abstract idea? Here we look at the other elements of the claim beyond the abstract idea. There are no other elements beyond the abstract idea, thus nothing “significantly more”.
Dependent claims only further refine the abstract idea.
Claims 1-11 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a law of nature without significantly more.
Step 2A, Prong 1: identify the law of nature. The correlation is a consequence of natural processes, similar to the naturally occurring correlation found to be a law of nature by the Supreme Court in Mayo.
Step 2A, Prong 2: has the law of nature been integrated into a particular practical application? The claims present limitations of analysing, assessing, and correcting, but are not actual tangible method steps. No process limitations leading to any tangible actions seem to be taking place. As such, it appears there is no application, and by extension, no practical application either. Even if we assume, for the sake of argument, that analysing is an action this is an insignificant post solution activity (MPEP 2106(g)). Data gathering and/or generically applying an abstract idea have been deemed to not be integrated into a practical application, there must be a meaningful limit to the judicial exception which is claimed (MPEP 2106(f) and (g)).
Step 2B: does the claim recite any elements which are significantly more than the law of nature? Here we look at the other elements of the claim beyond the law of nature. There are no other elements beyond the law of nature, thus nothing “significantly more”.
Dependent claims only further refine the law of nature.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
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) 1-6 and 10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tramutola et al. (J Alzheimers Dis. 2016 ; 52(1): 359–371, provided on the IDS on 1/27/2023) in view of Meek et al. (Cold Spring Harb Perspect Biol 2009;00:a000950, provided on the IDS on 6/17/2025).
Regarding claim 1, Tramutola describes an in vitro or ex vivo method for the diagnosis or prognosis of a neurodegenerative disease (abstract), the method comprising the steps of:
a) analysing a biofluid sample for the presence of post-translation modifications (PTMs) in the region of amino acids 1-371 of the p53 protein (U-p53) (page 3 “cortex samples” and page 5 “activation of p53, which results from multiple PTMs, we focused our attention on two different PTMs”), said PTMs (page 14 “ Figure 1. p53 protein levels and post-translational modifications: p53 phosphorylation at Ser-20 (1)(ph.), acetylation at Lys382 (K382)”),
wherein the presence of at least two PTMs is indicative of a cognitive unimpaired subject (CU) (page 14 “p53 phosphorylation at Ser-20 (1)(ph.), acetylation at Lys382 (K382)”), and
b) assessing the presence of PTMs as indicative of the occurrence or the risk of development of a neurological disease, said neurodegenerative disease being selected from Mild Cognitive Impairment (MCI), Alzheimer's disease (AD), Fronto-temporal dementia (FTD), Lewi's Body (LB), and vascular dementia (VD) (page 3 “hypothesize that p53 and its regulatory network in DS brain, is active prior to and after the development of AD pathology”), and
c) correlating the PTMs assessed in step b) with those identifying the corresponding neurodegenerative disease, wherein the presence of at least two PTMs indicative of a prognosis of cognitive decline to AD (page 5 “To investigate the activation of p53, which results from multiple PTMs, we focused our attention on two different PTMs, phosphorylation and acetylation. Both phosphorylation at Ser20 and acetylation of at Lys382 residues within the C-terminal region of p53, are a determinant of its activity [28]. The p-(Ser20)p53 /p53 ratio, which represents the majority of nuclear p53 protein and weakens the interaction of p53 with MDM2, was significantly increased in DS/AD vs. DS (~2 fold increase, *p<0.05) and DS/AD vs. CTRO (~ 150% increase, *p<0.05) (Figure 1, A.1). Similarly, the levels of acetyl-p53 at Lys382 (K382)/p53 were increased in DS/AD vs. DS (~100% increase, *p<0,05). This increase was not statistically significant, in DS/AD vs. CTRO (Figure 1, A.2).”)
OR wherein said in vitro or ex vivo method is for differentiating Alzheimer's disease, from other neurodegenerative diseases, wherein in step b) the assessment of following criteria are indicative of AD:
- a sequence variability in terms of length within the region of amino acids 1-271, said variability including a truncation within the same region, and
- the presence of at least two PTMs selected from PTM-1, PTM-3, PTM-4, PTM-5, and PTM-6, in a residual amount of untruncated sequence.
However Tramutola is silent to PTM-1 at the amino acid M 1, PTM-2 at the amino acid K1 64, PTM-3 at the amino acid K370, PTM-4 at the amino acid L101, PTM-5 at the amino acid K120, PTM-6 at the amino acid K132, PTM-7 at the amino acid K139, PTM-8 at the amino acid K291, PTM-9 at the amino acid K357, PTM-10 at the amino acid S6, OR PTM-11 at the amino acid S33; and assessing the presence of: - at least two PTMs selected from PTM-1, PTM-3, PTM-4, PTM-5, PTM-6, PTM-9, and PTM-10, and - at least one PTM selected from PTM-2, PTM-7, PTM-8, and PTM-11; and - the presence of at least two PTMs selected from PTM-4, PTM-5, and PTM-9 is indicative of a prognosis of cognitive decline to AD of an asymptomatic subject; the presence of at least two PTMs selected from PTM-1, PTM-3, PTM-5, PTM-6, and PTM-10 is indicative of MCI with a prognosis of cognitive decline to AD.
Meek describes that p53 protein is modified by as many as 50 individual PTMs (page 4 “The main p53 targets of MDM2-mediated ubiquitylation are the six carboxy-terminal lysines (K370, K372, K373, K381, K382, and K386)”). Furthermore, Meek describes that p53 PTMs include: phosphorylation at S6 (i.e., PTM-10); phosphorylation at S33 (PTM-11); ubiquitylation at K101 (PTM-4), K120 (PTM-5), K132 (PTM-6), K139 (PTM-7), K164 (PTM-2), K291 (PTM-8) and/or K370 (PTM-3) (see Figure 1 at page 3). Additionally, Meek suggests that p53 is an integral component of numerous cellular signaling pathways, including those that regulate apoptosis, cell cycle arrest, mitosis, and cellular metabolism, and is a crucial determinant of cell fate in response to genotoxic and other forms of stress (page 1). This suggests motivation to analyze the specific PTM as this would be a crucial determinant of cell fate in response to genotoxic and other forms of stress.
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was filed to analyze the specific PTMs in the method of Tramutola as suggested by Meek because would be a crucial determinant of cell fate in response to genotoxic and other forms of stress.
Regarding claim 2, the combination described above describes the in vitro or ex vivo method of claim 1, wherein: - the post-translation modification PTM-1 has a group CO-CH3 branched to the amino acid M1 of the p53 protein; - the post-translation modification PTM-2 has a group CO-CH3 branched to the amino acid K164 of the p53 protein; - the post-translation modification PTM-3 has a group CO-CH3 branched to the amino acid K370 of the p53 protein; - the post-translation modification PTM-4 has a ubiquitination site [GG] branched at the amino acid K101 of the p53 protein; - the post-translation modification PTM-5 has a ubiquitination site [GG] branched at the amino acid K120 of the p53 protein; - the post-translation modification PTM-6 has a ubiquitination site [GG] branched at the amino acid K132 of the p53 protein;- the post-translation modification PTM-7 has a ubiquitination site [GG] branched at the amino acid K139 of the p53 protein;- the post-translation modification PTM-8 has a ubiquitination site [GG] branched at the amino acid K291 of the p53 protein;- the post-translation modification PTM-9 has a ubiquitination site [GG] branched at the amino acid K357 of the p53 protein;- the post-translation modification PTM-10 has phosphorylation at the amino acid S6 of the p53 protein;- the post-translation modification PTM-11 has phosphorylation at the amino acid S33 of the p53 protein (Meek: page 3 “Figure 1. Posttranslational modification of human p53. The figure is updated from Anderson and Appella (Anderson and Appella 2009). The principal functional domains of p53 are shown together with the sites of modification and their potential modifying and demodifying enzymes.”
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Regarding claim 3, the combination described above describes the in vitro or ex vivo method of claim 1, said in vitro or ex vivo method being for differentiating Alzheimer's disease, from other neurodegenerative diseases, wherein in step b) the assessment of following criteria are indicative of AD: - a sequence variability in terms of length within the region of amino acids 1-271, said variability including a truncation within the same region, and - the presence of all PTM-1, PTM-3, PTM-4, PTM-5, and PTM-6 (Meek: page 4 “The main p53 targets of MDM2-mediated ubiquitylation are the six carboxy-terminal lysines (K370, K372, K373, K381, K382, and K386)”).
Regarding claim 4, the combination described above describes the in vitro or ex vivo method of claim 1, wherein the presence of all PTM-4, PTM-5, and PTM-9 is indicative of a prognosis of cognitive decline to AD of an asymptomatic subject (Meek: page 4 “The main p53 targets of MDM2-mediated ubiquitylation are the six carboxy-terminal lysines (K370, K372, K373, K381, K382, and K386)”).
Regarding claim 5, the combination described above describes the in vitro or ex vivo method of claim 1, wherein the presence of all PTM-1, PTM-3, PTM-5, PTM-6, and PTM-10 is indicative of MCI with a prognosis of cognitive decline to AD (Tramutola: page 7 “our results suggest that p53 is transcriptionally active in the presence of AD pathology in DS, suggesting that molecular cascades associated with apoptosis are induced in the neurodegenerative process affecting DS individuals.”).
Regarding claim 6, the combination described above describes the in vitro or ex vivo method of claim 1, wherein said biofluid is blood, plasma, serum, saliva, urine, neuronal cells, preferably blood, in particular, plasma (Tramutola: page 3 “frontal cortex samples” are neuronal cells).
Regarding claim 10, the combination described above describes the in vitro or ex vivo method of claim 1, wherein a diagnostic kit is used for implementing the method, the kit comprising a reagent set to perform the immunoprecipitation including an antibody, the digestion of the protein, elution buffer to precipitate the protein captured by the antibody, and an injection buffer (Tramutola: page 4 “Western Blot For Western blot, 30 μg of proteins were separated by 12% SDS– PAGE using Criterion Gel TGX Stain free (Bio-Rad) and blotted onto a nitrocellulose membrane (Bio-Rad, Hercules, CA, USA). Before blotting, the gel image was used to obtain total protein load to normalize blot analysis. Membranes were blocked for 1h and 30 min with 3% bovine serum albumin in T-TBS at room temperature and then incubated with primary anti-body. The following antibodies were used: p53 (Human, 1:1000) and Acetyl-p53 (1:1000) from Millipore (Boston, MA, USA), from Abcam (Cambridge, MA, USA), Caspase-3 (1:500), p53 (Mouse, 1:1000), p-p53 (1:1000), Sirt1 and 2 (1:1000), Hsp70 (1:1000), Hsp27 (1:1000), PARP1 (1:1000), Bax (1:1000), PCG1alpha (1:1000), Mdm-2 (1:1000) from Santa Cruz Biotechnology (Santa Cruz, CA, USA). The membranes were incubated for 1 h at room temperature with secondary antibody horseradish peroxidase-conjugated anti-rabbit, anti-mouse or anti-goat IgG (1:5000; Sigma–Aldrich, St Louis, MO, USA). Membranes were developed with the Clarity Western ECL Substrate (Bio-Rad) acquired with ChemiDoc XP (Bio-Rad) and analyzed using Image Lab software (Bio-Rad). Immunoprecipitation Briefly, 100 μg of protein extracts were dissolved in RIA buffer (10mM Tris, pH 7.6; 140mM NaCl; 0.5% NP40 including protease inhibitors) and then incubated with 1 μg of primary antibody at 4°C overnight. Immunocomplexes were collected by using protein A/G beads (Santa Cruz, CA, USA) for 2 h at 4°C. Immunoprecipitated protein was recovered by resuspending the pellets in reducing SDS buffers and subjected to electrophoresis on 12% gels followed by western blot analysis.”).
Claim(s) 7-9 and 11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Tramutola et al. (J Alzheimers Dis. 2016 ; 52(1): 359–371, provided on the IDS on 1/27/2023) in view of Meek et al. (Cold Spring Harb Perspect Biol 2009;00:a000950, provided on the IDS on 6/17/2025) in further view of Cristoni et al. (Expert Review of Proteomics, 1(4), 469–483, provided on the IDS on 6/17/2025).
Regarding claim 7, the combination described above describes the in vitro or ex vivo method of claim 1, wherein in the step a), the p53 protein is captured in a biofluid sample by performing the following sub-steps of: (i) providing a biofluid sample;(ii) performing protein immunoprecipitation by an antibody that binds a p53 protein (Tramutola: page 3 “Brain tissue (Frontal Cortex) “ and page 4 “The following antibodies were used: p53 (Human, 1:1000) and Acetyl-p53 (1:1000) from Millipore (Boston, MA, USA), from Abcam (Cambridge, MA, USA), Caspase-3 (1:500), p53 (Mouse, 1:1000), p-p53 (1:1000), Sirt1 and 2 (1:1000), Hsp70 (1:1000), Hsp27 (1:1000), PARP1 (1:1000), Bax (1:1000), PCG1alpha (1:1000), Mdm-2 (1:1000”).
However is silent to (iii) performing protein fragmentation by trypsin and the step b) is performed by HPLC- mass spectrometry, Peptide Mass Fingerprint and Database Search.
Cristoni describes performing protein fragmentation by trypsin (page 472) and Peptide Mass Fingerprint and Database Search (page 470). Cristoni further suggests that these techniques provide an increased reliability in identification (page 471 and 472), suggesting motivation to incorporate them into protein analysis.
Therefore it would have been obvious for one skilled in the art at the time the invention was filed to incorporate performing protein fragmentation by trypsin and HPLC- mass spectrometry, Peptide Mass Fingerprint and Database Search into the method of the combination as suggested by Cristoni because this would allow for an increased reliability in identification.
Regarding claim 8, the combination described above describes the in vitro or ex vivo method of claim 7, wherein the immunoprecipitation of sub-step (ii) is performed with a monoclonal/polyclonal antibody that binds to a p53 peptide, where preferably, said monoclonal antibody is the antibody 2D3A8 (Tramutola: page 4 “The following antibodies were used: p53 (Human, 1:1000) and Acetyl-p53 (1:1000) from Millipore (Boston, MA, USA), from Abcam (Cambridge, MA, USA), Caspase-3 (1:500), p53 (Mouse, 1:1000), p-p53 (1:1000), Sirt1 and 2 (1:1000), Hsp70 (1:1000), Hsp27 (1:1000), PARP1 (1:1000), Bax (1:1000), PCG1alpha (1:1000), Mdm-2 (1:1000)”).
Regarding claim 9, the combination described above describes the in vitro or ex vivo method of claim 7, wherein the biological sample of step a) is subjected to protein plasma depletion by HPLC or chromatographic columns or chemical treatment, before performing the step (ii) (Tramutola: pages3-4 “Brain tissue (Frontal Cortex) from human and mouse samples were homogenized by sonication in RIPA buffer (pH 7.4) containing 50 mMTris-HCl (pH 7.4), 150 mMNaCl, 1% NP-40, 0.25 % sodium deoxycholate,1mM EDTA, 0,1% SDS, 1mM PMSF, 1mM NaF and 1 mM Na3VO4. was centrifuged at 14,000 ×g for 30 min to remove cellular debris. The supernatant was extracted to determine the total protein concentration by the BCA method (Pierce, Rockford, IL).”).
Regarding claim 11, the combination described above describes the method of claim 10, however is silent to wherein the protein is digested using a protease, wherein the protease comprises trypsin with/without Lys C.
Cristoni describes performing protein fragmentation by trypsin (page 472). Cristoni further suggests that techniques provide increased reliability in identification (page 471 and 472), suggesting motivation to incorporate them into protein analysis.
Therefore it would have been obvious for one skilled in the art at the time the invention was filed to incorporate digesting using a protease, wherein the protease comprises trypsin with/without Lys C into the method of the combination as suggested by Cristoni because this would allow for an increased reliability in identification.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to EMILY R BERKELEY whose telephone number is (571)272-9831. The examiner can normally be reached M-Th 9-6.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lyle Alexander can be reached at (571) 272-1254. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LYLE ALEXANDER/Supervisory Patent Examiner, Art Unit 1797
/EMILY R. BERKELEY/
Examiner
Art Unit 1796
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