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 .
Claim Status
Applicant’s amendments and remarks, filed 09/03/2025, are acknowledged.
Claims 2-4, 7, 12, 14-15, 17, 19-23, 26, 28-29, 31-43, and 45 are canceled.
Claims 1, 5-6, 9-11, 16, 18, 24-25, 27, 30, and 44 are amended.
Claims 46-48 are new.
Claims 1, 5-6, 8-11, 13, 16, 18, 24-25, 27, 30, 44, and 46-48 are pending.
Claims 24-25, 27, and 30 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 03/25/2024.
As such, claims 1, 5-6, 8-11, 13, 16, 18, 44, and 46-48 are pending examination and currently under consideration for patentability under 37 CFR 1.104.
DETAILED ACTION
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 09/03/2025 has been entered.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 09/04/2025 was filed after the mailing date of the final Office action on 03/03/2025. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Withdrawn Objections
The claim objections are withdrawn. Issues regarding minor informalities have been sufficiently addressed through amendments to the claims filed on 09/03/2025.
The specification objections are withdrawn. Issues regarding minor informalities and trademarks/names have been sufficiently addressed through amendments to the specification on 09/03/2025.
Withdrawn Rejections
Applicant’s arguments, see pages 21-22 and 24-31, filed 09/03/2025, with respect to claims 1, 3, 5-6, 8-11, 13-14, 16-18, and 44 rejected under 35 USC 112(b) as allegedly being indefinite have been fully considered and are persuasive. The issue regarding the claims comprising indefinite language have been sufficiently addressed through amendments to the claims. Further, Examiner acknowledges that claims 3, 14, and 17 are canceled thus rendering the rejection moot. As such, the rejection under 35 USC 112(b) is withdrawn.
Applicant’s arguments, see pages 37-44, filed 09/03/2025, with respect to claims 1, 3, 5-6, 8-11, 13-14, 16-18, and 44 rejected under 35 USC 112(a) as allegedly lacking of enablement have been fully considered and are persuasive. The issue regarding the specification failing to disclose that the specification is enabling for a method of modulating the expression and/or activity of MPO in all mammals with all gene editing compounds and all undifferentiated BM cells nor a method for treating, ameliorating, inhibiting or delaying the onset of any MPO-related condition or disorder, or NETosis and related conditions, in all mammals, with all gene editing compounds in any undifferentiated BM cell of said subject, any nucleic acid molecule comprising a sequence encoding said gene editing compound, any composition, or vehicle comprising said at least one gene editing compound; and (b) any undifferentiated BM cell or cell population exhibiting a modulated expression and/or activity of MPO been sufficiently addressed through amendments to the claims. Specifically, Examiner acknowledges that the base claims were amended to specifically recite specific conditions or disorders. Further, Examiner acknowledges that claims 3, 14, and 17 are canceled thus rendering the rejection moot. As such, the rejection under 35 USC 112(a) is withdrawn.
Applicant’s remarks, see pages 44-49, filed on 09/03/2025, with respect to claims 1, 3, 6, 9-11, 14, 17-18, and 44 rejected under 35 USC 102 as allegedly anticipated by Zhang et al (US 2016/0175462 A1, pub. 06/23/2016) have been fully considered and are persuasive. Examiner acknowledges that claims 3, 14, and 17 are canceled, thus rendering the rejection moot. Further, Examiner acknowledges that the claims were amended to recite reducing MPO expression and/or activity in a mammalian subject affected by or suffering from at least one MPO-related condition or disorder comprising administering an effective amount of at least one of: (a) at least one CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated BM, and (b) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting reduced or inhibited expression and/or activity of MPO which is not disclosed by Zhang et al. As such, the rejection of claims 1, 6, 9-11, 18, and 44 under 35 USC 102 is withdrawn.
Claim Objections
Claims 1, 6, and 46 are objected to because of the following informalities:
Claims 1 and 6: “CRISPER/Cas system” should read “CRISPR/Cas system”.
Claim 46 does not end with a period. Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations. See Fressola v. Manbeck, 36 USPQ2d 1211 (D.D.C. 1995).
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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, 5-6, 8-11, 13, 16, 18, 44, and 46-48 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.
Claims 1 and 10 recite “AVV” as an acronym for ANCA-associated vasculitis; however, the specification recites “AVV” and “AAV” as acronyms for this condition (see pages 58-60) and “AAV” for adeno associated vectors (see pages 24 and 25), thus it is unclear what acronym Applicant is using for ANCA-associated vasculitis. As such, the claims 1 and 10, and their dependent claims, are rejected.
Claim 5 recites the limitation "said gRNA" in lines 1 and 2. There is insufficient antecedent basis for this limitation in the claim.
Claims 6(i), 11(i), and 13 recite “one undifferentiated BM cell or a BM cell population”. It is unclear whether the “BM cell population” is also undifferentiated, or if the singular BM cell is solely undifferentiated.
Claims 10, 44, and 48 recite “a nucleic acid molecule encoding said Cas protein, or a nucleic acid construct comprising said nucleic acid sequence”. It is unclear if the “said nucleic acid sequence” within the nucleic acid construct is referring to the “nucleic acid molecule” mentioned prior, or if the claim is referencing a different sequence. As such, claims 10, 44, and 48, and their dependent claims are rejected.
Claim Rejections - 35 USC § 112(a) Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 6, 8-11, 13, 18, 44, and 47-48 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, as of the filing date of the application, of the specific subject matter later claimed. The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include “level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention.”
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, disclosure of drawings, or by disclosure of relevant identifying characteristics, for example, structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the Applicants were in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Claim 1 is drawn to a method of reducing the expression and/or activity of Myeloperoxidase (MPO) in a mammalian subject, the method comprising the step of administering to said subject an effective amount of at least one of: (a) at least one clustered regulatory interspaced short palindromic repeat (CRISPR)/CRISPR associated (cas) protein system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated bone marrow (BM) cell of said subject, said CRISPR/Cas system comprising at least one of: clustered regulatory interspaced short palindromic repeat (CRISPR)/CRISPR associated (cas) protein system; and (b) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting a reduced or inhibited expression and/or activity of MPO; wherein said subject is a subject affected by or suffering from at least one MPO-related condition or disorder selected from the group consisting of: Alzheimer's disease (AD), multiple sclerosis (MS), Pulmonary arterial hypertension (PAH), Antineutrophil cytoplasmic autoantibody (ANCA)-Associated Vasculitis (AVV) and ANCA-associated glomerulonephritis (AAGN).
Claim 6 is drawn to the method according to claim 1, wherein at least one of: (i) said at least one undifferentiated BM cell or undifferentiated BM cell population is at least one undifferentiated BM cell or a BM cell population transduced or transfected with said at least one said CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in said cells; (ii) the at least one undifferentiated BM cell or the undifferentiated BM cell population is of an autologous or of an allogenic source.
Claim 8 is drawn to the method according to claim 1, wherein said undifferentiated BM cell population is a BM cell population of an allogeneic subject exhibiting an inhibited or eliminated expression and/or activity of MPO.
Claim 9 is drawn to the method according to claim 1, wherein reducing the expression and/or activity of MPO comprises inhibiting or eliminating the expression and/or activity of MPO in said subject.
Claim 10 is drawn to the method according to claim 1, for treating, ameliorating, inhibiting or delaying the onset of an MPO-related condition in a mammalian subject, said method comprises the step of administering to said subject a therapeutically effective amount of at least one of: (A) at least one CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated BM cell of said subject; said CRISPR/Cas system comprising at least one of:(i) at least one CRISPR/cas protein; and at least one gRNA that targets a protospacer within the MPO gene:(ii) a nucleic acid molecule encoding said Cas protein, or a nucleic acid construct comprising said nucleic acid sequence; and a nucleic acid sequence encoding said gRNA or a nucleic acid construct comprising said nucleic acid sequence; and (iii) a composition comprising (i) or (ii); and (B) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting a reduced or inhibited expression and/or activity of MPO; wherein said MPO-related condition or disorder is selected from the group consisting of: AD, MS, PAH, AVV and AAGN.
Claim 11 is drawn to the method according to claim 10, wherein at least of: (i) said at least one undifferentiated BM cell or undifferentiated BM cell population is at least one undifferentiated BM cell or a BM cell population transduced or transfected with said at least CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in said cells; and (ii) the at least one undifferentiated BM cell or undifferentiated BM cell population is of an autologous or of an allogenic source.
Claim 13 is drawn to the method according to claim 10, wherein said at least one undifferentiated BM cell or undifferentiated BM cell population is at least one undifferentiated BM cell or a BM cell population of an allogeneic subject exhibiting an inhibited or eliminated expression and/or activity of MPO.
Claim 18 is drawn to the method according to claim 10, wherein at least one of: (a) said disorder is Alzheimer's disease (AD); (b) said disorder is multiple sclerosis (MS); and (c) said disorder is Pulmonary arterial hypertension (PAH).
Claim 44 is drawn a method for inhibiting neutrophil extracellular trap (NET) activation and release (NETosis) in a mammalian subject, said method comprising the step of administering to said subject a therapeutically effective amount of at least one of: (a) at least CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated BM cell of said subject; and (b) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting a reduced or inhibited expression and/or activity of MPO, wherein said CRISPR/cas system comprising at least one of: (i) at least one CRISPR/cas protein and at least one gRNA that targets a protospacer within the MPO gene: (ii) a nucleic acid molecule encoding said Cas protein, or a nucleic acid construct comprising said nucleic acid sequence; and a nucleic acid sequence encoding said gRNA or a nucleic acid construct comprising said nucleic acid sequence; and(iii) a composition comprising (i) or (ii).
Claim 47 is drawn to the method according to claim 44, wherein said undifferentiated BM cell population is a BM cell population of an allogeneic subject exhibiting an inhibited or eliminated expression and/or activity of MPO.
Claim 48 is drawn to a method for inhibiting production of reactive oxygen species (ROS) in a mammalian subject, said method comprising the step of administering to said subject a therapeutically effective amount of at least one of: (a) at least one CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated BM cell of said subject; and (b) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting a reduced or inhibited expression and/or activity of MPO, wherein said CRISPR/cas system comprising at least one of:(i) at least one CRISPR/cas protein; and at least one gRNA that targets a protospacer within the MPO gene; (ii) a nucleic acid molecule encoding said Cas protein, or a nucleic acid construct comprising said nucleic acid sequence; and a nucleic acid sequence encoding said gRNA or a nucleic acid construct comprising said nucleic acid sequence; and(iii) a composition comprising (i) or (ii).
The specification discloses of targeting MPO in the experimental allergic encephalomyelitis (EAE) model of MS (see Example 1). The specification disclose that Lin-hematopoietic progenitors retain their hematopoietic reconstitution potential and are adequate for CRISPR-Cas9 KO experiments (see pg. 95). The specification also discloses of targeting MPO in the FAD model of Alzheimer disease (AD) (see Example 2). The specification discloses that blood samples from FAD model mice subjected to transplantation of BM cells obtained from MPO KO mice showed less peroxidase activity, confirming MPO KO hematopoietic reconstitution of MPO KO cells in these mice (see pg. 96, Figs. 3E-3F). Further, almost undetectable MPO-mRNA levels were found in BM derived from wildtype-MPO KO and 5XFAD-MPO KO mice, as compared to high levels in the controls indicating for efficient exchange of the hematopoietic population in the transplanted mice (see pg. 97, Fig. 4B). Example 3 discloses MPO knock-out using CRISPR/Cas9 technology in isolated HSCs (see pgs. 99-101). Example 4 discloses MPO knock-out using CRISPR/Cas9 technology in human cells (HEK293); specifically, discloses transfecting HEK293 cells with ribonucleoproteins (RNP) complexes containing Cas9 protein, fluorescently labeled tracrRNA and crRNA sequences that target the human MPO encoding sequences and the corresponding protospacers: T173 (denoted by SEQ ID NO: 33 and SEQ ID NO: 43, respectively), D260 (denoted by SEQ ID NO: 34 and SEQ ID NO: 44, respectively), H502 (denoted by SEQ ID NO: 35 and SEQ ID NO: 45, respectively), C319 (denoted by SEQ ID NO: 42 and SEQ ID NO: 46, respectively). The specification discloses of using the CRISPR/Cas9 system for manipulating human MPO function and levels (see Example 5). Specifically, Example 5 disclose of the following amino acid substitutions that: form conformational changes in the MPO protein or changes in protomer biosynthesis and processing – C167A, C180A, C319A, C158A, R128A, N355A; mimic human MPO deficiency substitutions – T173C, M251T, R569W, R499C, G501S; interfere with promoter heme binding – Q257A, D260A, M409A, E408A, H261A, H502A; and, interfere with proper protein glycosylation – N355A (see pg. 103). Example 6 discloses of a procedure for a clinical study highlighting hematopoietic stem cell transplantation (HSCT) combined with CRISPR-mediated gene editing. Example 7 discloses of a proposed treatment of PAH using MPO knock-out. Lastly, Example 8 discloses of a proposed treatment of crescentic glomerulonephritis (CGN) using MPO knock-out.
Further, the specification teaches that the endothelial barrier disruption by neutrophiles was suggested to occur by the release of reactive oxygen species (ROS) (see page 5). The specification discloses the term “MPO activity” refers to at least one of MAPK and NFĸB activation, ROS production, surface integrin upregulation, and degranulation, as well as decreased apoptosis leading to enhanced inflammation in the lung (see page 45). The specification discloses by modulating and elevating the MPO levels, using the methods of the invention, the present specification further provides methods for treating conditions associated for example with ROS-deficiency and/or MPO-deficiency… the MPO-related condition that may be applicable for the methods of the invention may be associated with reduced or deficient ROS levels (see page 74).
However, the specification fails to disclose that Applicant was in possession of the large genera of methods of reducing the expression and/or activity of MPO in a mammalian subject as recited in the claims. Specifically, the specification fails to disclose that Applicant was in possession of administering an effective amount of any CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in any undifferentiated BM cell; any composition or vehicle comprising the CRISPR/Cas system; or a nucleic acid molecule encoding the CRISPR/Cas system. It is noted that the targets are not limited to MPO, but can be any molecule either upstream or downstream in the MPO protein signaling or activation. The only requirement is that the expression or activity is affected. This encompassed an extremely large genus of possible targets. Further, the specification fails to disclose administering multiple CRISPR-Cas systems.
Additionally, the specification fails to disclose that Applicant was in possession of a method of treating, ameliorating, inhibiting, or delaying the onset of any MPO-related condition or disorder in a mammalian subject. Also, the specification fails to demonstrate that Applicant was in possession of inhibiting NETosis and related conditions in any mammalian subject. Lastly, the specification fails to disclose that Applicant was in possession of the claimed method of inhibiting production of ROS.
Although the specification discloses of utilizing CRISPR-Cas9 mediated KO experiments on the BM cells of MS mice models to determine MPO levels and of AD mice models to determine peroxidase activity, MPO-mRNA and amyloid-β levels, functional behavior, inflammation activity, and APOE expression, the claims are not limited to these constructs or conditions, and are inclusive of any gRNA that targets any protospacer within the MPO gene. This indicates that there are hundreds, if not thousands, of possible compositions and disorders encompassed by the claims. Thus, the claims encompass a vast genus of CRISPR/Cas systems – MPO expression modulations that have the claimed functions. However, the specification provides limited guidance on the structure and steps required to impart the claimed function(s). Therefore, the specification does not provide adequate written description to identify the broad and variable genus of MPO reducing CRISPR/Cas systems because, inter alia, the specification does not disclose a correlation between the necessary structure of the CRISPR/Cas system-gRNA and the function(s) recited in the claims; and thus, the specification does not define the claimed genus and encompassed species, except by function. Further, the specification fails to provide method steps that result in treating, ameliorating, inhibiting, or delaying the onset of any MPO-related condition or disorder or inhibiting NETosis and related conditions in any mammalian subject. Although the term “protein” does impart some structure, the structure that is common to proteins is generally unrelated to its specific binding function; therefore, correlation is less likely for proteins than for other molecules. Accordingly, the specification does not define any structural features commonly possessed by the members of the genus, because while the description of an ability of the claimed substance may generically describe the molecules’ function, it does not describe the substance itself. A definition of function does not suffice to describe the genus because it is only an indication of what the substance does, rather than what it is; therefore, it is only a definition of a useful result rather than a definition of what achieves the result. In addition, because the genus of substances is highly variable (i.e. each substance would necessarily have a unique structure, See MPEP 2434), the generic description of the substance is insufficient to describe the genus. Further, given the highly diverse nature of proteins, particularly in binding site sequences, even one of skill in the art cannot envision the structure of a protein by only knowing its binding characteristics. Thus, the specification does not provide substantive evidence for possession of this large and variable genus, encompassing a potentially massive number of CRISPR/Cas systems and gRNA compositions and variants thereof claimed only be a functional characteristic(s) and/or partial structure.
A biomolecule sequence described only by a functional characteristic, without any known or disclosed correlation between that function and the structure of the sequence, normally is not sufficient identifying characteristics for written description purposes, even when accompanied by a method of obtaining the agent. The specification does not adequately describe the correlation between the chemical structure and function of the genus, such as structural domains or motifs that are essential and distinguish members of the genus from those excluded. Thus, the genus of peptides has no correlation between their structure and function.
MPEP § 2163.03(V) states:
While there is a presumption that an adequate written description of the claimed invention is present in the specification as filed, In re Wertheim, 541 F.2d 257, 262, 191 USPQ 90, 96 (CCPA 1976), a question as to whether a specification provides an adequate written description may arise in the context of an original claim. An original claim may lack written description support when (1) the claim defines the invention in functional language specifying a desired result but the disclosure fails to sufficiently identify how the function is performed or the result is achieved or (2) a broad genus claim is presented but the disclosure only describes a narrow species with no evidence that the genus is contemplated. See Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1349-50 (Fed. Cir. 2010) (en banc). The written description requirement is not necessarily met when the claim language appears in ipsis verbis in the specification. "Even if a claim is supported by the specification, the language of the specification, to the extent possible, must describe the claimed invention so that one skilled in the art can recognize what is claimed. The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement. “Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 968, 63 USPQ2d 1609, 1616 (Fed. Cir. 2002).
Applicant has not shown possession of a representative number of species of methods of reducing the expression and/or activity of Myeloperoxidase (MPO) in a mammalian subject, the method comprises the step of administering to said subject an effective amount of at least one of: (a) at least one CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated bone marrow (BM) cell of said subject; and (b) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting a reduced or inhibited expression and/or activity of MPO. Even more so, Applicant has not shown possession of a representative number of species of treating, ameliorating, inhibiting or delaying the onset of an MPO-related condition or disorder or NETosis related condition in a mammalian subject, the method comprises the step of administering to said subject a therapeutically effective amount of at least one of: (a) at least one CRISPR/Cas system that inhibits or reduces the expression and/or activity of MPO in at least one undifferentiated BM cell of said subject; and (b) at least one undifferentiated BM cell or undifferentiated BM cell population exhibiting a reduced or inhibited expression and/or activity of MPO, said CRISPR/cas system comprises at least one of: (i) at least one CRISPR/cas protein, or any nucleic acid molecule encoding said Cas protein; and (ii) at least one nucleic acid sequence comprising at least one gRNA that targets a protospacer within the MPO gene, or any nucleic acid sequence encoding said gRNA; or any composition or vehicle comprising at least one of (i) and (ii).
The disclosure of only one or two species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us]." See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) ("[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.") (MPEP 2163).
The instant claims do not fully describe the required method, or present any form of specific threshold or other standards that would allow the method to achieve the required function. Accordingly, the specification also does not provide adequate written description to identify the broad genus of CRISPR/Cas systems and MPO-related conditions or disorders, claimed only be a function characteristic(s) and not structures per se, because inter alia, it does not describe a sufficient number and/or a sufficient variety of representative species to reflect the breadth and variation within the claimed genus. Consequently, based on the lack of information within the specification, there is evidence that a representative number and a representative variety of the numerous proteins and gRNAs had not yet been identified and thus, the specification represents little more than a wish for possession. Therefore, one of skill in the art would not conclude that Applicant was in possession of the broad and highly variable genus of CRISPR/Cas systems claimed only by a partial structure and functional characteristic(s). Thus the method described by the instant specification encompasses an overly broad genus, and there is no correlation between the steps of the method, the structure of the CRISPR/Cas systems, and the functional outcome.
As stated above, Applicant has not demonstrated possession of the overly broad genus of methods of reducing the expression and/or activity of MPO comprising administering a CRISPR/Cas system. For example, Ma et al. (ACS Appl. Mater. Interfaces 2022, 14, 6358−6369; previously submitted in Office Action mailed 05/30/2024) disclose of biomimetic, pH-responsive metal organic framework (MOF) nanoparticles to deliver carbon nanodots (C-dot) nanozyme and CRISPR/Cas9 system for site-specific treatment of ulcerative colitis (UC) (see Abstract). In this system, C-dots and CD98 CRISPR/Cas9 plasmid were successfully encapsulated into MOF carrier by a one-pot approach and then camouflaged with macrophage membrane (see Abstract). Cas9 plasmids with two different CD98-targeting gRNAs were constructed on the basis of plasmid pX458 (see pg. 6361, left column). Ma et al. disclose that MPO activity could reflect the degree of neutrophil infiltration at inflammatory sites, could be used for evaluating the severity of UC (see pg. 6366, left column). After inducing dextran sulfate sodium (DSS), MPO activity was increased while treatment with the CRISPR/Cas system decreased the MPO activity; indicating that neutrophil infiltration was decreased and the severity of UC was mitigated (see pg. 6366, left column).
Additionally, Yan et al. (Sci. Adv. 7, eabj0624 (2021); previously submitted in Office Action mailed 05/30/2024) disclose of a CRISPR-Cas9 prodrug nanosystem (termed NanoProCas9) that combines the targeted delivery and the conditional activation of CRISPR-Cas9 for the precision therapy of inflammatory bowel disease (see Abstract). NanoProCas9 is composed of (i) cationic poly(β-amino ester)(PBAE) capable of complexing plasmid DNA encoding destabilized Cas9 (dsCas9) nuclease, (ii) a layer of biomimetic cell membrane coated on PBAE/plasmid nanocomplexes for the targeted delivery of PBAE/dsCas9 complexes, and (iii) the stimuli-responsive precursory molecules anchored on the exofacial membrane (see Abstract). Similarly to the teachings of Ma et al. above, Yan et al. found that MPO activity was highly elevated in the colon of mice in the colitis group and was markedly decreased in the NanoProCas9-treated group (see pg. 8, left column; Fig. 5F).
Colamartino et al (Blood 142 (2023) 7120) developed a gene therapy approach to PAH in which autologous hematopoietic stem cells (HSCs) will undergo gene editing using CRISPR/Cas9 to achieve bi-allelic disruption of the MPO gene (see entire document). These MPO-knock-out HSCs will then be autologous transplanted; that autologous transplantation of hematopoietic stem and progenitor cells (HSPC) in which the MPO gene is disrupted is expected to prevent progression of PAH due to the essential role of neutrophil MPO activity on disease development (see 3rd paragraph). Colamartino et al identified a sgRNA that leads to high frequency disruption of MPO in primary human CD34+ HSPC, leading to efficient elimination of MPO protein in the resultant neutrophils; that sequence was assessed for genome-wide off-target and showed no detectable locus, validating it as a lead candidate for safe gene editing strategy (see 4th paragraph). Colamartino et al validated in an in vitro neutrophil differentiation model the functional efficiency of the knock-out; MPO KO differentiated cells exhibit reduced NETosis and absence of MPO protein (see 5th paragraph). An optimized gene editing protocol for HSC was optimized and showed consistent allelic disruption over 80%; the edited cells retain hematopoietic potential and showed no skewing in the generated lineages in an in vitro colony forming assay (see 5th paragraph).
Lastly, Jerke et al (Kidney International (2025) 108, 145–149) disclose of a CRISPR-Cas9 mediated proteinase 3 (PR3) autoantigen deletion as a treatment strategy for anti-neutrophil cytoplasmic autoantibody-associated vasculitis (ANCA-AAVs) (see title and entire document). Jerke et al disclose that ANCA-AAVs are life-threatening systemic autoimmune diseases wherein patients lose tolerance to either PR3 or MPO and consequently develop PR3-ANCA or MPO-ANCA (see pg. 145, right col.). Jerke et al disclose of a ribonucleoprotein (RNP) complex of Cas9 protein and a PR3-specific single guide-RNA was transfected into human CD34+ HSPC by electroporation (see Abstract). Figures 1(g) and 1(h) demonstrate that the CRISPR/Cas complex disrupted PR3 protein but did not impact the intracellular ROS producti8on and degranulation of MPO indicating that PR3 is dispensable for a variety of neutrophil defense responses and for constitutive apoptosis that is pivotal to inflammation resolution (see pg. 147, right col.). Jerke et al found that PR3 gene editing strongly reduced PR3-ANCA binding to and activation of neutrophils – a central vascular injury mechanism in AAV (see pg. 149, left col.). Jerke et al disclose that AAV is suited for a gene editing approach because the disease features autoimmunity to a single autoantigen such as PR3 and MPO (see pg. 147, left col).
As such, the art indicates there are known species of methods of reducing the expression and/or activity of MPO comprising administering a CRISPR/Cas system that is structurally different than the compounds disclosed in the instant application.
In Amgen Inc. v. Sanofi, 124 USPQ2d 1354 (Fed. Cir. 2017), relying upon Ariad Pharms., Inc. v. Eli Lily & Co., 94 USPQ2d 1161 (Fed Cir. 2010), it is noted that to show invention, a patentee must convey in its disclosure that is “had possession of the claimed subject matter as of the filing date. Demonstrating possession “requires a precise definition” of the invention. To provide this precise definition” for a claim to a genus, a patentee must disclose “a representative number of species within the scope of the genus of structural features common to the members of the genus so that one of skill in the art can visualize or recognize the member of the genus” (see Amgen at page 1358). Also, it is not enough for the specification to show how to make and use the invention, i.e., to enable it (see Amgen at page 1361). An adequate written description must contain enough information about the actual makeup of the claimed products — “a precise definition, such as structure, formula, chemic name, physical properties of other properties, of species falling with the genus sufficient to distinguish the gene from other materials”, which may be present in “functional terminology when the art has established a correlation between structure and function” (Amgen page 1361). Most significant to the present case, the Court held that "knowledge of the chemical structure of an antigen [does not give] the required kind of structure-identifying information about the corresponding antibodies" (Amgen at 1361). The idea that written description of an antibody can be satisfied by the disclosure of a newly-characterized antigen “flouts basic legal principles of the written description requirement” as it “allows patentees to claim antibodies by describing something that is not the invention, i.e., the antigen... And Congress has not created a special written description requirement for antibodies” (Amgen at page 1362).
Abbvie v. Centocor (Fed. Cir. 2014) is also relevant to the instant claims. In Abbvie, the Court held that a disclosure of many different antibodies was not enough to support the genus of all neutralizing antibodies because the disclosed antibodies were very closely related to each other in structure and were not representative of the full diversity of the genus. The Court further noted that functionally defined genus claims can be inherently vulnerable to invalidity challenge for lack of written description support especially in technology fields that are highly unpredictable where it is difficult to establish a correlation between structure and function for the whole genus or to predict what would be covered by the functionally claimed genus.
The instant case has many similarities to AbbVie above. First, the claims clearly attempt to define the genus of compounds by the functions of reducing the expression and/or activity of MPO. As noted by AbbVie above, functionally defined genus claims can be inherently vulnerable to invalidity challenge for lack of written description. Second, there is no information in the specification based upon which one of skill in the art would conclude that the disclosed species for which applicant has identified as having the recited functions would be representative of the entire genus. The specification discloses no structure to correlate with the function. Therefore, the specification provides insufficient written description to support the genus encompassed by the claim.
Furthermore, regardless whether a compound is claimed per se or a method is claimed that entails the use of the compound, the inventor cannot lay claim to that subject matter unless he can provide a description of the compound sufficient to distinguish infringing compounds from non-infringing compounds, or infringing methods from non-infringing methods. Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920-23, 69 USPQ2d 1886, 1890-93 (Fed. Cir. 2004).
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.)
Further, the skilled artisan cannot envision the detailed chemical structure of the encompassed CRISPR/Cas systems, regardless of the complexity or simplicity of the method of isolation. Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. The nucleic acid and/or protein itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (CAFC 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. In Fiddes v. Baird, 30 USPQ2d 1481, 1483, claims directed to mammalian FGF's were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence.
Finally, University of California v. Eli Lilly and Co., 43 USPQ2d 1398, 1404. 1405 held that: ... To fulfill the written description requirement, a patent specification must describe an invention and does so in sufficient detail that one skilled in the art can clearly conclude that "the inventor invented the claimed invention." Lockwood v. American Airlines Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (1997); In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) (" [T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using “such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2d 1966.
Furthermore, regardless whether a compound is claimed per se or a method is claimed that entails the use of the compound, the inventor cannot lay claim to that subject matter unless he can provide a description of the compound sufficient to distinguish infringing compounds from non-infringing compounds, or infringing methods from non-infringing methods. Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920-23, 69 USPQ2d 1886, 1890-93 (Fed. Cir. 2004).
Regarding the encompassed proteins and peptides, protein chemistry is one of the most unpredictable areas of biotechnology. This unpredictability prevents prediction of the effects that a given number or location of mutation will have on a protein (such as TNF or a cytokine) as taught by Skolnick et al. (Trends Biotechnol. 2000 Jan;18(1):34-9; previously submitted in Office Action mailed 05/30/2024), sequence-based methods for predicting protein function are inadequate because of the multifunctional nature of proteins (see e.g. abstract). Further, just knowing the structure of the protein is also insufficient for prediction of functional sites (see e.g. abstract). Sequence to function methods cannot specifically identify complexities for proteins, such as gain and loss of function during evolution, or multiple functions possible within a cell (see e.g. page 34, right column). Skolnick advocates determining the structure of the protein, then identifying the functionally important residues since using the chemical structure to identify functional sites is more in line with how a protein actually works (see e.g. page 34, right column).
The sensitivity of proteins to alterations of even a single amino acid in a sequence are exemplified by Burgess et al. (J. Cell Biol. 111:2129-2138, 1990; previously submitted in Office Action mailed 05/30/2024) who teach that replacement of a single lysine residue at position 118 of acidic fibroblast growth factor by glutamic acid led to the substantial loss of heparin binding, receptor binding and biological activity of the protein and by Lazar et al. (Mol. Cell. Biol., 8:1247-1252, 1988; previously submitted in Office Action mailed 05/30/2024) who teach that in transforming growth factor alpha, replacement of aspartic acid at position 47 with alanine or asparagine did not affect biological activity while replacement with serine or glutamic acid sharply reduced the biological activity of the mitogen. These references demonstrate that even a single amino acid substitution will often dramatically affect the biological activity and characteristics of a protein.
Further, Miosge (Proc Natl Acad Sci U S A. 2015 Sep 15;112(37):E5189-98; previously submitted in Office Action mailed 05/30/2024) teach that Short of mutational studies of all possible amino acid substitutions for a protein, coupled with comprehensive functional assays, the sheer number and diversity of missense mutations that are possible for proteins means that their functional importance must presently be addressed primarily by computational inference (see e.g. page E5189, left column). However, in a study examining some of these methods, Miosge shows that there is potential for incorrect calling of mutations (see e.g. page E5196, left column, top paragraph). The authors conclude that the discordance between predicted and actual effect of missense mutations creates the potential for many false conclusions in clinical settings where sequencing is performed to detect disease-causing mutations (see e.g. page E5195, right column, last paragraph). The findings in their study show underscore the importance of interpreting variation by direct experimental measurement of the consequences of a candidate mutation, using as sensitive and specific an assay as possible (see e.g. page E5197, left column, top paragraph). Additionally, Bork (Genome Research, 2000,10:398-400; previously submitted in Office Action mailed 05/30/2024) clearly teaches the pitfalls associated with comparative sequence analysis for predicting protein function because of the known error margins for high-throughput computational methods. Bork specifically teaches that computational sequence analysis is far from perfect, despite the fact that sequencing itself is highly automated and accurate (p. 398, column 1). One of the reasons for the inaccuracy is that the quality of data in public sequence databases is still insufficient. This is particularly true for data on protein function. Protein function is context dependent, and both molecular and cellular aspects have to be considered (p. 398, column 2). Conclusions from the comparison analysis are often stretched with regard to protein products (p. 398, column 3). Further, although gene annotation via sequence database searches is already a routine job, even here the error rate is considerable (p. 399, column 2). Most features predicted with an accuracy of greater than 70% are of structural nature and, at best, only indirectly imply a certain functionality (see legend for table 1, page 399). As more sequences are added and as errors accumulate and propagate it becomes more difficult to infer correct function from the many possibilities revealed by database search (p. 399, paragraph bridging columns 2 and 3). The reference finally cautions that although the current methods seem to capture important features and explain general trends, 30% of those features are missing or predicted wrongly. This has to be kept in mind when processing the results further (p. 400, paragraph bridging cols 1 and 2).
One key issue is the prediction of protein function based on sequence similarity, which could be one way to identify the functional proteins that are useful in the instant claims. Kulmanov et al. (Bioinformatics, 34(4), 2018, 660–668; previously submitted in Office Action mailed 05/30/2024), teach that there are key challenges for protein function prediction methods (see e.g. page 661, left column). These challenges arise from the difficulty identifying and accounting for the complex relationship between protein sequence structure and function (see e.g. page 661, left column). Despite significant progress in the past years in protein structure prediction, it still requires large efforts to predict protein structure with sufficient quality to be useful in function prediction (see e.g. page 661, left column). Another challenge is that proteins do not function in isolation. In particular higher level physiological functions that go beyond simple molecular interactions will require other proteins and cannot usually be predicted by considering a single protein in isolation (see e.g. page 661, left column). Due to these challenges it is not obvious what kinds of features should be used to predict the functions of a protein and whether they can be generated efficiently for a large number of proteins, such as the vast genus of proteins and peptides that may be encompassed by the instant claims (see e.g. page 661, left column).
The state of the art regarding the structure-function correlation cannot be relied upon because functional characteristics of any peptide/protein are determined by its structure as evidenced by Greenspan et al. 1999 (Defining epitopes: It's not as easy as it seems; Nature Biotechnology, 17:936-937; previously submitted in Office Action mailed 05/30/2024). Greenspan et al. teach that as little as one substitution of an amino acid (e.g. alanine) in a sequence results in unpredictable changes in the 3-dimenstional structure of the new peptide sequence which, in turn, results in changes in the functional activity such as binding affinity of the peptide sequence (page 936, 1st column). Greenspan et al. teach that contribution of each residue (i.e. each amino acid) cannot be estimated with any confidence if the replacement affects the properties of the free form of the molecule (page 936, 3rd column).
Given not only the teachings of Skolnick et al., Lazar et al., Burgess et al., and Greenspan et al., but also the limitations and pitfalls of using computational sequence ana