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 .
Applicant’s amendment filed on 07/15/2025 has been entered.
Amended claims 38, 55-56, 58-61 and new claim 93 are pending in the present application.
Accordingly, amended claims 38, 55-56, 58-61 and 93 are examined on the merits herein.
Priority
This application is a 371 of PCT/EP2017/077826, filed on 10/30/2017; and claims foreign priority to EPO EP16196860.7, filed on 11/02/2016; EPO 16196858.1, filed on 11/02/2016; PCT/EP2017/059799, filed on 04/25/2017; and EPO EP17197820.8, filed on 10/23/2017.
Since none of EPO EP16196860.7, EPO 16196858.1 and PCT/EP2017/059799 have a written support for a method for treating a human patient in need thereof, comprising the steps (a)-(c) recited in independent claim 38, claims 38, 55-56, 58-59, 61 and 93 have at best the effective filing date of 10/23/2017; while claim 60 has only the effective filing date of 10/30/2017 because none of the above cited foreign priority documents have a written support for the concept of treating a malignant hematopoietic disease refractive to treatment with anti-CD19 CAR T-cells.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
Claim Rejections - 35 USC § 112 (Lack of 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.
Amended claims 38, 55-56, 58-61 and 93 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. This is a modified rejection necessitated by Applicant’s amendment.
MPEP 2163 - 35 U.S.C. 112(a) and the first paragraph of pre-AIA 35 U.S.C. 112 require that the “specification shall contain a written description of the invention ....” This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010) (en banc). Vas-Cath Inc. v. Mahurkar, 19USPQ2d 1111 (Fed. Cir. 1991), clearly states 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.” Vas-Cath Inc. v. Mahurkar, 19USPQ2d at 1117. The specification does not “clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed” Vas-Cath Inc. v. Mahurkar, 19USPQ2d at 1116.
The instant claims encompass a method for treating a human patient in need thereof, comprising the steps of: (a) genetically engineering a human hematopoietic cell (e.g., a T cell or a hematopoietic stem cell) with a CRISPR-Cas9 nuclease and any DNA template to achieve homology-directed repair to express a non-native first isoform of CD45 or CD90 surface protein comprising an extracellular portion and comprising a substitution (e.g., a conservative or a non-conservative substitution) of a single amino acid anywhere in the extracellular loop domain portion, compared to a native second isoform of said surface protein, wherein said non-native first isoform of the surface protein is functionally tolerated, but immunologically distinguishable from the native second isoform, and wherein said substitution is made at a site that is non-conserved in mouse, rat, primate, and human homologues of said surface protein; (b) administering said engineered human hematopoietic cell to said human patient; and (c) administering an ablative agent to said human patient, wherein the ablative agent is an antibody comprising means for specifically reacting to the native second isoform but not reacting to said first isoform of the surface protein, preferably the antibody is not coupled to a toxin, wherein said cell is administered prior to or concomitant with ablation of cells expressing said second isoform of said surface protein.
Apart from disclosing two functionally comparable isoforms of CD90 (CD90.1 and CD90.2) that differs by a single amino acid substitution (a conservative arginine/glutamine substitution) in the extracellular loop domain of the CD90 molecule, and two functionally comparable isoforms of CD45 (CD45.1 and CD45.2) that also differ by a single amino acid substitution (a lysine/glutamic acid substitution) in the extracellular loop domain of the CD45 molecule; a DNA template encoding the introduced single amino acid substitution for CD45 or CD90 molecule; and in each case the single amino acid substitution can be detected and distinguished by a pair of specific mAbs (page 25, line 36 continues to line 17 on page 26 and Figures 1, 3 and 5); the instant disclosure fails to provide sufficient written description for other functionally tolerable isoforms of CD90 or CD45 having a substitution of a single amino acid anywhere in the extracellular loop domain portion compared to the respective native CD90 or CD45 as long as such substitution is made at a site that is non-conserved in mouse, rat, primate and human homologues, and the isoforms are immunologically distinguishable by an ablative agent which is an antibody comprising means for specifically reacting to the native second isoform but not reacting to the first isoform of the surface protein in a method for treating a human patient in need thereof as encompassed broadly by the instant claims? For example, which other specific single amino acid substitution(s) at which particular amino acid residue(s) in the extracellular loop domain portion of a native isoform of CD90 or CD45 molecule and at a site that is non-conserved in mouse, rat, primate and human homologues to be made such that the resulting non-native isoform of CD90 or CD45 molecule is still functionally tolerated and immunologically distinguishable from the native isoform of CD90 or CD45 molecule in a genetically engineered human hematopoietic cell to be used in a method for treating a human patient as encompassed broadly by the instant claims? The instant specification merely stated “[t]he insertion, deletion and/or substitution is located in the extracellular portion of said first surface protein, particularly in an extracellular loop. Mutations in extracellular loops are less likely to affect protein function” (page 8, lines 16-18). Based on the polymorphism of CD45.1 and CD45.2 isoforms, Lutteropp et al (US 2016/0144026) determined that only the mutation of the amino acid K in position 277 to E allows the anti-CD45.1 antibody to bind to the antigen and abrogates the binding of anti-CD45.2 antibody, while other mutations (e.g., N453T or V375A/E379D/S380P) in CD45.2 isoform maintain specificity for the CD45.2 antibody (Example 2). This indicates or suggests at least the unpredictability in predicting which particular mutation(s) (e.g., a single or multiple amino acid substitutions) at which particular amino acid position(s) in a CD45 molecule to be made for a desired mutation/substitution that is recognized by an existing anti-CD45.1 antibody but not by another existing anti-CD45.2 antibody, and yet the mutant CD45 isoform is still functionally tolerable.
Apart from a DNA template encoding the introduced single amino acid lysine/glutamic acid substitution for CD45.1 and CD45.2 isoforms or a single amino acid conservative arginine/glutamine substitution for CD90.1 and CD90.2 isoforms (page 14, line 37 continues to line 7 at page 15; page 25, line 36 continues to line 17 on page 26 and Figures 1, 3 and 5), the instant specification also fails to provide sufficient written description of any other DNA template to achieve homology-directed repair to genetically engineer a human hematopoietic cell to express a non-native first isoform of a surface protein of CD45 or CD90 surface protein comprising an extracellular loop domain portion with a substitution of a single amino acid in the extracellular loop domain and at a site that is non-conserved in mouse, rat, primate and human homologues compared to a native second isoform of said surface protein that results in a functionally tolerated non-native first surface protein but immunologically distinguishable from the native second isoform of the surface protein as encompassed broadly by the instant claims. For example, what are the detailed structures of the other DNA templates such that the genetically engineered human hematopoietic cell expressing a non-native first isoform of CD45 or CD90 surface protein with the recited characteristics of the instant claims?
Moreover, the instant specification is also devoid of any specific structure (means) such as the unique complementarity-determining regions (CDRs) within the VH and VL regions for any ablative antibody that specifically reacts to the native second isoform but does not react to the first isoform of the CD45 or CD90 surface protein in the treatment method as claimed broadly. Apart from the generic statement “The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen” (at page 2, line 4-5), there is no description of a specific structure in any ablative antibody that specifically reacts to the native second isoform but does not react to the first isoform of the CD45 or CD90 surface protein as required and encompassed by the instant broad claims.
Since the prior art before the effective filing date of the present application (10/23/2017) did not provide sufficient written description for the aforementioned issues as evidenced at least by the teachings of Lutteropp et al (US 2016/0144026), Poma et al (WO 2014/164693), Binder et al (Blood 108:1975-1978, 2006), Scadden et al (WO 2016/164502) and Gori et al (WO 2017/160890); it is incumbent upon the present specification to do so. Additionally, the present application also fails to provide a representative number of species for a broad genus of a genetically engineered human hematopoietic cell and an ablative antibody having the recited features to be used in a method for treating a human patient in need thereof as claimed broadly.
The claimed invention as a whole is not adequately described if the claims require essential or critical elements which are not adequately described in the specification and which are not conventional in the art as of Applicants’ filing date. Possession may be shown by actual reduction to practice, clear depiction of the invention in a detailed drawing, or by describing the invention with sufficient relevant identifying characteristics such that a person skilled in the art would recognize that the inventor had possession of the claimed invention. Pfaff v. Wells Electronics, Inc., 48 USPQ2d 1641, 1646 (1998). The skilled artisan cannot envision the complete detailed structure of a representative number of species for a broad genus of a genetically engineered human hematopoietic cell and an ablative antibody having the recited features to be used in a method for treating a human patient in need thereof as claimed broadly; and therefore conception is not achieved until reduction to practice has occurred, regardless of the complexity or simplicity of the method. Adequate written description requires more than a mere statement that it is part of the invention and reference to a method of isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991). One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481, 1483.
Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 U.S.C. §112 is severable from its enablement provision (see page 1115).
Response to Arguments
Applicant’s arguments related to the above modified Lack of Written Description rejection in the Amendment filed on 07/15/2025 (pages 4-6) have been fully considered, but they are respectfully not found persuasive for the following reasons.
Once again, Applicant argued basically that the present application provides working examples with the two claimed surface proteins CD90 and CD45, as well as rational and sufficient guidance to design mutation in these surface proteins. Applicant also argued that the application discloses several methods for identifying an amino acid to be mutated in the extracellular portion in non-conserved site in mouse, rat, primate and human homologues, in particular the mutation is determined by aligning one or more several homologous sequences of different mammalian species and positioning the mutations in a non-conserved site. Applicant further cited the section titled “Design considerations” at page 27, particular lines 25-27 of the present application to show that Applicant has provided sufficient guidance for identifying an amino acid to be mutated in the claimed method. With respect to the Lutteropp reference, Applicant argued that the reference did not take into account structural considerations which can help in the rationale design of potential mutations; and by following the teachings of the present application a person of ordinary skill in the art would identify the amino acids that can be mutated in CD45 by aligning one or more several homologous sequences of different mammalian species and positioning the mutation in a non-conserved site, then the ordinary skill in the art would then predict the amino acid that can be mutated by taking into account the structural considerations so that the surface antigen variant is not recognized by the corresponding antigen binding molecule. Accordingly, the present application provides a sufficient written description of the subject matter of the present claims.
First, please refer to the above modified Lack of Written Description for details. Particularly, apart from a DNA template encoding the introduced single amino acid lysine/glutamic acid substitution for CD45.1 and CD45.2 isoforms or a single amino acid conservative arginine/glutamine substitution for CD90.1 and CD90.2 isoforms (page 14, line 37 continues to line 7 at page 15; page 25, line 36 continues to line 17 on page 26 and Figures 1, 3 and 5), the instant specification fails to provide sufficient written description of any other DNA template to achieve homology-directed repair to genetically engineer a human hematopoietic cell to express a non-native first isoform of a surface protein of CD45 or CD90 surface protein comprising an extracellular loop domain portion with a substitution of a single amino acid in the extracellular loop domain and at a site that is non-conserved in mouse, rat, primate and human homologues compared to a native second isoform of said surface protein that results in a functionally tolerated non-native first surface protein but immunologically distinguishable from the native second isoform of the surface protein as encompassed broadly by the instant claims. For example, what are the detailed structures of the other DNA templates such that the genetically engineered human hematopoietic cell expressing a non-native first isoform of CD45 or CD90 surface protein with the recited characteristics of the instant claims? Additionally, the instant specification is also devoid of any specific structure (means) such as the unique complementarity-determining regions (CDRs) within the VH and VL regions for an ablative antibody that specifically reacts to the native second isoform but does not react to the first isoform of the CD45 or CD90 surface protein in the treatment method as claimed broadly. Apart from the generic statement “The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen” (at page 2, line 4-5), there is no description of a specific structure in any ablative antibody that specifically reacts to the native second isoform but does not react to the first isoform of the CD45 or CD90 surface protein as required by the instant broad claims.
Second, once again please note that adequate written description requires more than a mere statement that it is part of the invention and reference to a method of isolating it. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016 (Fed. Cir. 1991). One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481, 1483. Ultimately, which other specific single amino acid substitution(s) at which particular amino acid residue(s) in the extracellular loop domain portion at a site that is non-conserved in mouse, rat, primate and human homologues of a native isoform of CD90 or CD45 molecule to be made such that the resulting non-native isoform of CD90 or CD45 molecule is still functionally tolerated and immunologically distinguishable from the native isoform of CD90 or CD45 molecule in a genetically engineered human hematopoietic cell to be used in a method for treating a human patient as encompassed broadly by the instant claims? Additionally, what are the specific structures (e.g., the unique complementarity-determining regions (CDRs) within the VH and VL regions) possessed by ablative antibodies that are used to discriminate a plurality of the first and second isoforms of the CD45 or CD90 surface protein as encompassed by instant broad claims?
Third, the present application also fails to provide a representative number of species for a broad genus of a genetically engineered human hematopoietic cell and an ablative antibody having the recited features to be used in a method for treating a human patient in need thereof as claimed broadly.
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.
Amended claims 38, 55-56, 58-61 and 93 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. This is a modified rejection necessitated by Applicant’s amendment.
Currently amended independent claim 38 recites the limitation “wherein the ablative agent is an antibody comprising means for specifically reacting to the native second isoform but not reacting to said first isoform of the surface protein” invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The disclosure is devoid of any specific structure for an antibody such as the unique complementarity-determining regions (CDRs) within the VH and VL regions for specifically reacting to the native second isoform but not reacting to the first isoform of the surface protein. Apart from the generic statement “The variable regions of the heavy and light chains contain a binding domain that interacts with an antigen” (at page 2, line 4-5), there is no description of a specific structure in an antibody that specifically reacting to the native second isoform but not reacting to the first isoform of the surface protein. Therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Response to Arguments
Applicant’s arguments related to the above modified 35 U.S.C. 112(b) rejection in the Amendment filed on 07/15/2025 (page 7, first paragraph) have been fully considered, but they are respectfully not found persuasive for the following reasons.
Applicant argued that the application describes an example commercially available antibody that reacts to the native mouse CD45.2, but not the engineered CD45.1. Accordingly, one of ordinary skill in the art would recognize which antibodies that could bind the native isoform as claimed.
At best the specification describes the single pair of commercially available antibodies that recognize either CD45.2 or the CD45.1 isoform of the mouse CD45 surface molecule as described in the Lutteropp reference (Example 2). However, the instant claims are not necessarily limited to the use of this single pair of commercially available antibodies. Particularly, independent claim 38 recites the limitation “a non-native first isoform of CD45 or CD90 surface protein comprising an extracellular loop domain portion and comprising a substitution of a single amino acid in the extracellular loop domain compared to a native second isoform of said surface protein…wherein said substitution is made at a site that is non-conserved in mouse, rat, primate, and human homologues of said surface protein”. What are the specific structures or “means” (e.g., the unique complementarity-determining regions (CDRs) within the VH and VL regions) possessed by ablative antibodies that are used to discriminate a plurality of the first and second isoforms of the CD45 surface protein as encompassed by instant broad claims?
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.
Amended claims 38, 55-56, 58-59, 61 and 93 are rejected under 35 U.S.C. 103 as being unpatentable over Lutteropp et al (US 2016/0144026) in view of Scadden et al (WO 2016/164502) and Wulf et al (Haematologica 91:886-894, 2006). This is a modified rejection necessitated by Applicant’s amendment, particularly to accommodate the rejection of new claim 93.
The instant claims are drawn to a method for treating a human patient in need thereof, comprising the steps of: (a) genetically engineering a human hematopoietic cell (e.g., a T cell or a hematopoietic stem cell) with a CRISPR-Cas9 nuclease and a DNA template to achieve homology-directed repair to express a non-native first isoform of CD45 or CD90 surface protein comprising an extracellular portion and comprising a substitution of a single amino acid in the extracellular loop domain portion, compared to a native second isoform of said surface protein, wherein said non-native first isoform of the surface protein is functionally tolerated, but immunologically distinguishable from the native second isoform, and wherein said substitution is made at a site that is non-conserved in mouse, rat, primate, and human homologues of said surface protein; (b) administering said engineered human hematopoietic cell to said human patient; and (c) administering an ablative agent to said human patient, wherein the ablative agent is an antibody comprising means for specifically reacting to the native second isoform but not reacting to said first isoform of the surface protein, preferably the antibody is not coupled to a toxin, wherein said cell is administered prior to or concomitant with ablation of cells expressing said second isoform of said surface protein.
Lutteropp et al disclosed a combination immunotherapy for disease in an individual, including but not restricted to cancer, comprising: i) an antigen-recognizing receptor, which recognizes an antigen present on target cells, but also on at least one hematopoietic cell type of said individual, and ii) hematopoietic cells resistant to recognition of said antigen by said antigen-recognizing receptor to reduce the side-effects of the antigen-recognizing receptor (Abstract; and Summary of the Invention). Lutteropp et al taught the utilization of a group of antigens as potential targets for immunotherapy (e.g., CD19, CD20, CD45 and others) that are present on at least one hematopoietic cell type, and therefore are not suitable targets for immunotherapies currently known in the art; and the hematopoietic cells resistant to recognition of the antigen-recognizing receptor express a naturally occurring version (natural polymorphism) of said antigen or the hematopoietic cells resistant to recognition of the antigen-recognizing receptor are genetically modified to express an altered version of said antigen (paragraphs [0015], [0025], [0044], [0053] and [0059]). Fig. 1 below is a schematic representation of a preferred embodiment in which the antigen-recognizing receptor is exemplified by chimeric antigen receptors (CAR) be expressed on the surface of an immune effector cells and the hematopoietic cells are resistant to recognition of the same antigen by the antigen-recognizing receptor.
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Lutteropp et al stated specifically “The antigen-recognizing receptor may be a soluble receptor or may be expressed on the cell membrane of an immune effector cell” (paragraph [0038]); “Said hematopoietic cells may be hematopoietic stem cells or hematopoietic progenitor cells” (paragraph [0039]); and “Said immune effector cells expressing said antigen-recognizing receptor may be autologous or allogeneic transplants. Said hematopoietic cells resistant to recognition of said antigen by said antigen-recognizing receptor may be autologous or allogenic transplants” (paragraphs [0042]-[0043]). Lutteropp et al specifically taught that the hematopoietic cells resistant to recognition of the antigen by the antigen-recognizing receptor may have a deviation in said antigen, thereby altering the epitope recognized by said antigen-recognizing receptor; and said deviation in CD20 antigen of said hematopoietic cells may be the amino acid substitution alanine to serine at position 170 and/or proline to serine at position 172 of the CD20 antigen with the human wild type CD20 sequence of SEQ ID NO: 3 (paragraphs [0045]-[0046]; and Example 1); and the deviation/modification is within the extracellular domain of the antigen and such modification does not alter or affect the natural function of the hematopoietic cells in an individual (functionally tolerated) (paragraph [0059]). Lutteropp et al disclosed that CD20 is expressed on healthy B cells, melanoma cell and CD20 positive malignant hematopoietic cell such as a lymphoma cell, a chronic lymphoid leukemia cell or an acute lymphoid leukemia cell (paragraphs [052] and [0121]). Lutteropp et al also stated explicitly “Genetic modification of genomic DNA of cells such as hematopoietic cells, for example hematopoietic stem cells can be performed via methods well known in the art. The genetic modification may be performed by introduction of designer nucleases such as ZFN, TALEN or CRISPR/Cas into hematopoietic cells. Designer nucleases can be used to introduce double strand breaks at specific locations of the genomic DNA of a cell, which may induce error prone repair mechanisms such as non-homologous end joining in the cell that leads to insertions or deletions at said location of the genomic DNA. Said location may be part of the genomic sequence encoding for said antigen and leads to the absence of said antigen on said cells….The designer nuclease may be applied together with a template DNA in order to exploit the cellular repair mechanism of homologous recombination, that leads to inclusion of the genomic sequence of the template DNA at the site of the strand break introduced by the designer nuclease. In one embodiment of the invention a designer nuclease specific for the genomic sequence of CD20 is applied to hematopoietic cells such as hematopoietic stem cells, together with a template DNA that is largely homologous to the CD20 genomic sequence but contains one or more sequence alterations” (paragraph [0054]). Lutteropp et al also taught the hematopoietic cells resistant to recognition of the antigen by the antigen-recognizing receptor may be administered at the same time or at a time point prior to or after the antigen recognizing receptor or the immune effector cells expressing the antigen recognizing receptor; preferably hematopoietic cells resistant to recognition of said antigen by said antigen-recognizing receptor are administered before treatment with immune effectors expressing the antigen recognizing receptor of the invention, and thereby a partial or complete reconstitution of the blood system could be achieved (paragraph [0064]). In example 1, Lutteropp et al utilized the CRISPR-Cas9 system to target CD20 wild type gene in the human Raji cell line (paragraph [0119]). In example 2, Lutteropp et al also determined that the mutation of the amino acid K at position 277 in the extracellular domain to E (via a single nucleotide change at position 943 in the CD45 gene from A to G) allows the anti-CD45.1 antibody to bind to the antigen and abrogates the binding of anti-CD45.2 antibody, while other mutations (e.g., N453T or V375A/E379D/S380P) in CD45.2 isoform maintain specificity for the CD45.2 antibody; and taught that it is possible to use the anti-CD45.2 antibody to generate an anti-CD45.2 recognizing CAR that would be “blind” to the K position 277 to E mutation, or vice versa to use the anti-CD45.1 antibody to generate an anti-CD45.1 recognizing CAR that would be “blind” to the K in position 277 (paragraphs [0122]-[0123]; Figs. 5-6). Lutteropp et al also noted that the current first line treatment for most hematopoietic cancers involves the administration of chemotherapeutic agents, radiation therapy or a combination thereof; and in many cases such therapies are combined with or followed by hematopoietic stem cell transfer (HSCT), where the graft versus leukemia (GVL) effect mediated by donor derived lymphocytes, especially T cells, can lead to the eradication cancer cells that survived the pre-conditioning chemo or radiotherapies and result in complete remission. The desired GvL effect is only achieved in allogeneic HSCT, which at the same time is often accompanied by the occurrence of graft versus host disease (GvHD), a serious and sometimes fatal complication (paragraph [0004]).
Lutteropp et al did not teach explicitly using at least an ablative anti-CD45 antibody (with or without coupled/conjugated to a toxin) in their disclosed treatment method, and the substitution of a single amino acid in the extracellular loop domain portion of a non-native first isoform of CD45 surface protein is made at a site that is non-conserved in mouse, rat, primate, and human homologues of said surface protein.
Before the effective filing date of the present application (10/23/2017), Scadden et al already taught the use of an antibody-toxin conjugate targeting cell surface markers such as the CD34, CD45 or CD117 receptors for effectively conditioning a subject’s tissues prior to engraftment or transplant (e.g., a hematopoietic stem cell transplant) (see at least the Abstract; Summary of the Invention and Figure 33). Scadden et al stated “[t]he invention disclosed herein are directed to methods of selectively depleting or ablating an endogenous hematopoietic stem cell (HSC) or progenitor population in a target tissue of a subject, the methods comprising administering to the subject an effective amount (e.g., 1.5 mg/kg) of an agent coupled to a toxin; wherein the agent selectively binds to CD45 and the toxin is internalized by the endogenous HSC or progenitor cell population, thereby depleting or ablating the endogenous HSC or progenitor cell population in the target tissue” (page 3, line 31 continues to line 5 on page 4); “In some embodiments, the subject has, suffers from or it otherwise affected by a malignancy” (page 14, lines 28-29); “For example, in certain embodiments the subject suffers from a malignancy selected from the group consisting of hematologic cancers (e.g., leukemia, lymphoma, multiple myeloma and myelodysplastic syndrome) and neuroblastoma” (page 15, lines 3-6); and “In certain aspects, the subject is a mammal (e.g., the subject is a human)” (page 15, line 18). Scadden et al also taught clearly that CD45 receptor is a unique and ubiquitous membrane glycomembrane that is expressed on almost all hematopoietic cells (page 33, lines 25-26).
Additionally, Wulf et al also disclosed the CD45 rat monoclonal IgG2b antibodies YTH24.5 and YTH54.12 that act synergistically to produce cytolysis of normal lymphocytes and have been safely given to patients in conditioning regimens for allogeneic stem cell transplantation; and they demonstrated that these CD45 antibodies have lytic activity against NK and T lymphoma cells via complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC), are effective in a preclinical tumor model, and may be candidates for immunotherapeutic approaches for the treatment of human NK and T lymphoma (see at least Abstract).
It would have been obvious for an ordinary skilled artisan before the effective filing date of the present application to modify the teachings of Lutteropp et al by also utilizing at least the anti-CD45.2 antibody (with or without a toxin conjugate) to target and selectively deplete/abrogate native or endogenous CD45-positive cancers such as lymphoma and leukemia in their disclosed combined immunotherapy method, wherein the anti-CD45.2 antibody does not bind to administered genetically modified hematopoietic cell expressing the CD45 isoform with the single amino acid substitution at residue 277 in the extracellular domain (K is substituted by E via a single nucleotide change at position 943 in the CD45 gene from A to G, and the resulting CD45 isoform is only recognized by anti-CD45.1 antibody), in light of the teachings of Scadden et al and Wulf et al as presented above.
An ordinary skilled artisan would have been motivated to carry out the above modification because Scadden et al already taught successfully the use of an antibody-toxin conjugate targeting the cell surface marker CD45 for selectively depleting or ablating an endogenous hematopoietic stem cell (HSC) or progenitor population in a subject suffering from a hematologic cancer such as leukemia, lymphoma, multiple myeloma and myelodysplastic syndrome, with CD45 is ubiquitously expressed on all hematopoietic cells; while Wulf et al demonstrated that the CD45 rat monoclonal IgG2b antibodies YTH24.5 and YTH54.12 (without toxin conjugates) have lytic activity against NK and T lymphoma cells via complement-dependent cytotoxicity (CDC) and antibody-dependent cell-mediated cytotoxicity (ADCC). Additionally, the primary Lutteropp et al taught explicitly that the antigen-recognizing receptor may be a soluble receptor or may be expressed on the cell membrane of an immune effector cell. Moreover, since the substitution of a single amino acid in the CD45 surface protein of the present application (see instant specification at page 25, line 36 continues to line 17 on page 26; and Figure 5) is the same as that described by Lutteropp et al, such amino acid substitution is in the extracellular loop domain portion of the CD45 surface molecule and is made at a site that is non-conserved in mouse, rat, primate, and human homologues.
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Lutteropp et al, Scadden et al and Wulf et al; coupled with a high level of skill of an ordinary skilled artisan in the relevant art.
The modified method resulting from the combined teachings of Lutteropp et al, Scadden et al and Wulf et al is indistinguishable and encompassed by the presently claimed invention because it has the same method steps and starting materials [e.g., using the CRISPR/Cas9 system along with a template DNA containing the alteration for genetically engineering human hematopoietic cells and anti-CD45.2 antibody (with or without a toxin conjugate) to target and selectively deplete/abrogate native or endogenous CD45-positive cancers such as lymphoma and leukemia, wherein the anti-CD45.2 antibody does not bind to administered genetically modified hematopoietic cell expressing the CD45 isoform with the single amino acid substitution at residue 277 in the extracellular domain (K is substituted by E via a single nucleotide change at position 943 in the CD45 gene from A to G), and the resulting CD45 isoform is only recognized by anti-CD45.1 antibody].
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Claim 60 is rejected under 35 U.S.C. 103 as being unpatentable over Lutteropp et al (US 2016/0144026) in view of Scadden et al (WO 2016/164502) and Wulf et al (Haematologica 91:886-894, 2006) as applied to claims 38, 55-56, 58-59, 61 and 93 above, and further in view of Lee et al (Blood 128(22):218; http://doi.org/10.1182/blood.V128.22.218.218, 4 pages; 2016).
The combined teachings of Lutteropp et al, Scadden et al and Wulf et al were presented above. However, none of the cited references teach explicitly to treat a malignant hematopoietic disease refractive to treatment with anti-CD19 CAR T-cells.
Before the effective filing date of the present application (10/30/2017), Lee already taught that relapse rates among complete responders to CD19 CAR therapy occur in nearly half of patients in the first year, and they reported outcomes from completed clinical trial of 53 children and young adults with relapsed refractory pre-B acute lymphoblastic leukemia (ALL) or lymphoma with a median follow up of 18.7 months (page 2, first paragraph). They found that long-term outcomes following CD19 CAR T cell therapy for B-ALL are superior in patients receiving a Fludarabine/Cyclophosphamide preparative regimen and post-CAR hematopoietic stem cell transplantation (Figs. 1-2).
Accordingly, it would have been obvious before the effective filing date of the present application to modify the combined teachings of Lutteropp et al, Scadden et al and Wulf et al by also treating patients with malignant hematopoietic disease refractive to treatment with anti-CD19 CAR T-cells, in light of the teachings of Lee et al as presented above.
An ordinary skill in the art would have been motivated to carry out the above modification because Lee already taught that relapse rates among complete responders to CD19 CAR therapy occur in nearly half of patients in the first year and reported that long-term outcomes following CD19 CAR T cell therapy for B-ALL are superior in patients receiving a Fludarabine/Cyclophosphamide preparative regimen and post-CAR hematopoietic stem cell transplantation; and such patients would further benefit from the combined immunotherapy method of Lutteropp et al and Scadden et al from the reduction of the side-effects of the antigen-recognizing receptor (e.g., CD19-CAR T-cells or toxic anti-CD19 antibody) and the hematopoietic cells resistant to recognition of the antigen by the antigen-recognizing receptor may be administered at the same time or at a time point prior to the antigen recognizing receptor or the immune effector cells expressing the antigen recognizing receptor to attain a sooner partial or complete reconstitution of the blood system.
An ordinary skilled artisan would have a reasonable expectation of success in light of the teachings of Lutteropp et al, Scadden et al, Wulf et al and Lee et al; coupled with a high level of skill of an ordinary skilled artisan in the relevant art.
The modified method resulting from the combined teachings of Lutteropp et al, Scadden et al, Wulf et al and Lee et al is indistinguishable and encompassed by the presently claimed invention because it has the same method steps and starting materials.
Therefore, the claimed invention as a whole was prima facie obvious in the absence of evidence to the contrary.
Response to Arguments
Applicant’s arguments related to the above modified 103 rejections in the Amendment filed on 07/15/2025 (pages 7-9) have been fully considered, but they are respectfully not found persuasive for the following reasons.
Once again, Applicant argued that although Lutteropp et al proposed the use of a template DNA, for knock-in gene editing in paragraph [0054], the examples considered as proof of the concept disclosed in this patent application do not show at least one way of performing the invention. Applicant also argued that all examples in the Lutteropp reference were performed in cell lines and without any example of gene editing in primary hematopoietic cell, and gene-editing in primary cells is known to be more challenging due to reduced transfectability and chromatin accessibility. Thus, the use of specific gene editing to modify hematopoietic cells in Lutteropp et al remains speculative, and it should be appreciated that a technical problem of the claimed method was to provide a method enabling to introduce point mutations in primary cells while maintaining cell viability and expected cell function in a manner sufficiently efficient to transplant correctly edited cells into a patient. Applicant further argued that in view of the low efficiency of knock-out gene editing of CD20 and CD45 in cell lines shown in the Lutteropp reference (only up to 15% or 2% respectively), it was unexpected to succeed to introduce precisely targeted single nucleotide polymorphism in CD45 and CD90 primary hematopoietic cell with high efficiency (Conversion to CD90.1: 24% (Figure 4); conversion to CD45.1: 20% (Figure 5)) as shown by the present application. Applicant also argued that given the data provided by the Lutteropp reference showing the low efficiency of deleting surface antigen by knockout gene editing method in cell lines would have discouraged the person skilled in the art from attempting to modify primary cells to introduce a point mutation in a surface antigen, especially for a therapeutic use where a sufficient number of functional engineered cells are required to be transplanted into a patient. Applicant further argued that none of cited prior art documents disclose the gene editing of surface antigens such as CD45 and CD90 in a cell to render such cell resistant to depleting agent; and in view of the data provided in Lutteropp et al with a low efficiency of gene editing in cell lines and in hematopoietic cells as disclosed in Gori, Saltzman, and Gregory previously cited by the Examiner, the person of skill in the art would not have a reasonable expectation of success to introduce precisely targeted single nucleotide polymorphism in CD45 and CD90 primary hematopoietic cell in a manner sufficiently effective to preserve the natural function of the antigen and to make the edited gene resistant to antibody, and to effectively achieved the therapeutic effect in the claimed immunotherapeutic approach. With