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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10-28-25 has been entered.
Claims 2-4, 8-15, 21-100 have been canceled. Claims 1, 5-7, 16-20 remain pending.
Election/Restrictions
The restriction between groups I, III, V, VII, IX was withdrawn. Groups I, III, V, VII, IX remain patentably distinct from Groups II, IV, VI, VIII, X.
Applicants elected Group I, 1, 4-7, 16-20, 34, in the reply filed on 1-17-24 with traverse, drawn to a nucleic acid that produces a hVH/chemokine receptor/hJH/CH chimeric antibody.
Claims 16 and 17 have been withdrawn because they further limit the conotoxin in the hVH/conotoxin/hJH/CH chimeric antibody of claim 5 which is not under consideration.
Claims 1, 5-7, 18-20 are under consideration but only as they relate to a nucleic acid that produces a hVH/chemokine receptor/hJH/CH chimeric antibody. The claims are NOT under consideration as they relate to a nucleic acid that produces a hVH/conotoxin/hJH/CH chimeric antibody or a hVH/tarantula toxin/hJH/CH chimeric antibody as broadly encompassed by claim 1 and enumerated in claim 5.
Claim Rejections - 35 USC § 112
Enablement
Claims 1, 5-7, 18-20 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a mouse/rat comprising a germ cell whose genome comprises a replacement of all endogenous immunoglobulin heavy chain variable (VH) gene segments and all endogenous immunoglobulin heavy chain joining (JH) gene segments with a plurality of human VH (hVH) gene segments and a plurality of human (hJH) gene segments operably linked to an endogenous heavy chain constant (CH) gene segment, wherein B-cells of the mouse/rat express a functional antibody comprising a hVH region operably linked to an endogenous CH region, does not reasonably provide enablement for a nucleic acid comprising: i) a human Ig VH gene segment, ii) an eDH gene segment comprising a nucleic acid sequence encoding a chemokine receptor; and iii) a human Ig JH gene segment, wherein the VH, eDH, and JH gene segments comprise RSSs “that allow for hVH/eDH/hJH recombination according to the 12/23 rule”. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
The rejections have been restructured in an attempt to clarify the issues.
A) The specification does not enable those of skill to determine the structure/function of the eD or the structure/function of RSSs flanking VH, eD, & JH gene segment that “allow for hVH/eD/hJH recombination according to the 12/23 rule” in claim 1.
The nucleic acid of claim 1 is drawn to a nucleic acid comprising in operable linkage:
i) a human immunoglobulin (Ig) variable heavy [chain] (VH) gene segment,
ii) an engineered DH (hDH) region comprising one or more engineered gene segments that each comprises a nucleic acid sequence encoding a non-immunoglobulin polypeptide of interest or portion thereof;
iii) a human Ig joining heavy chain (hJH) gene segment,
wherein each of the hVH gene segment, the one or more engineered gene segments, and the hJH gene segment comprising RSSs that allow for hVH/eDH/hJH recombination according to the 12/23 rule.
Scope:
Claim 1 no longer requires the engineered diversity (eD) is an Ig heavy chain diversity gene segment. The claim now appears to encompass Ig heavy and light chain eD gene segments.
Claim 1 encompasses the chemokine receptor portions of the “eD” are flanked by a 12-mer RSS on the 5’ end, the 3’ end or both; however, the specification does not disclose whether the “eD” are flanked by a 12-mer RSS on the 5’ end, the 3’ end or both. Nor does the specification disclose whether the “eD” must be flanked by a 12-mer RSS on the 5’ end, the 3’ end or both to “allow [ ] recombination according to the 12/23 rule”.
Claim 1 encompasses:
i) a homology vector for integrating multiple hVH, eD, and hJH gene segments into a mouse or rat,
ii) a nucleic acid encoding a plurality of hVH, eD, and hJH gene segments operably linked to each other and to a mouse/rat CH gene in vivo, and
iii) a nucleic acid after rearrangement in a B-cell in vivo that encodes a chimeric hVH, eD, hJH, and a mouse/rat CH protein.
The nucleic acid may be in vivo or in vitro. Claim 1 is not limited to an isolated nucleic acid sequence. The nucleic acid in vivo encompasses two or more hVH and hJH gene segments.
The nucleic acid in vivo encompasses a homology vector that results in integration anywhere in the genome of a mouse/rat or any other species of animal.
The hVH gene segment, the hJH gene segment, the engineered DH, and the mouse/rat Ig CH gene must be operably linked.
The specification does not enable making any “engineered diversity (eD) gene segment comprising a [chemokine receptor sequence] flanked by a 12-mer recombination signal sequence (RSS)” as encompassed by claim 1. Fig. 3B shows “four DNA fragments (D6-DH1116, D6-DH17613, D6-DH114619, D6-DH120126) each containing “several D6 coding sequences” (pg 122, para 263). Only one single DH segment (DH6-25) remained intact. Pg 59-73 show the sequences of D6-DH1166, D6-D17613, D6-DH114619, D6-DH120126. But it is unclear how/why they are Ig heavy or light chain D gene segments because they do not contain any sequences from an Ig heavy or light chain D gene segment. Nothing is left of any Ig heavy or light chain D gene segment in the sequences so they cannot be Ig “diversity” gene segments as claimed. To complicate matters, the specification is limited to eDH gene segments (pg 1, para 2), so the scope of eD in claim 1 is not enabled because it is greater and more expansive than an “eDH” as originally disclosed. The specification does not teach any eD light chain gene segments or compare eD heavy chain gene segments to eD light chain gene segments.
The exact structure and function of the eD and the function of the non-immunoglobulin coding sequence within the eD gene segment in context of the hVH/eD/hJH nucleic acid cannot be determined. Nor can they be determined in context of any chimeric hVH/eD/hJH/CH protein made by the nucleic acid sequence in vivo.
The specification discusses a “12/23 rule, in which gene segments flanked by an RSS with a 12bp spacer are typically joined to a gene segment flanked by a 23bp spacer” and cites Hiom and Cuomo (pg 49). However, the specification never clearly defines the rule. Cuomo says gene segments with RSSs containing “12-spacer signals” recombine with gene segments with RSSs containing “23-spacer signals”; however, Hiom and Cuomo never clearly define the metes and bounds of the “12/23 rule”. In fact, Hiom and Cuomo taught that the process is more significantly more complicated because V gene segments are only flanked on the 3’ end with one RSS (with a 12-spacer – Cuomo, pg 5683, para 2), D gene segments are flanked on both the 5’ and 3’ end with RSSs (is one a 12-spacer and the other a 23-spacer signal? – claim 1 just requires one RSS with a 12-mer), and J gene segments are only flanked on the 5’ end with one RSS (it a 23-spacer – Cuomo, pg 5683, para 2).
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Murphy (2019/0380316)
The structures/functions of VH, eD, and JH gene segments and their corresponding RSSs that comply with the teachings of Hiom and Cuomo or any “12/23 rule” are not in the claims.
The structures/functions of VH, eD, and JH gene segments and their corresponding RSSs required to comply with the teachings of Hiom and Cuomo or any “12/23 rule” cannot be determined.
This is especially true because “the 12/23 rule” has nothing to do with VH/eD/JH recombination, so it is unclear when an eD gene segment will comply with a rule that was not made for it.
To add complication, claim 1 refers to “the RSSs” of the V, D, and J segments that “allow for VH/eD/JH recombination according to the 12/23 rule”, but claim 1 does not require the V or J segments have RSSs. The phrase “the RSSs of the VH gene segment” lacks antecedent basis. The phrase “the RSSs of the [ ] JH gene segment” lacks antecedent basis. Therefore, it is unclear if applicants are attempting to say the nucleic acid claimed HAS undergone rearrangement and IS capable of expressing a chimeric protein or if it simply has the capability of being rearranged for expressing the chimeric protein.
Accordingly, those of skill would not be able to determine when the elements “allow for hVH/eD/hJH recombination according to the 12/23 rule” as required in claim 1, and the elements described by Hiom and Cuomo for rearrangement of VH, DH, JH, and CH gene segments and their respective RSSs are missing from the claims.
The specification states the purpose of the invention is to create a diverse human immune response using numerous hVH segments that make up an immunoglobulin in the sentence bridging pg 47-48; pg 49, para 131; pg 50, last sentence; pg 54, para 150.
Chemokine receptors are described on pg 51, para 135-136, as binding chemokines.
Fig. 3A shows “de novo synthesis of 4 D6 DNA fragments”, but the starting material cannot be determined, the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined, and the function of the sequence cannot be determined.
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The description of Fig. 3A on pg 17, para 64, is of no help in this regard:
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Fig. 3B shows a vector with a single hVH gene segment, operably linked to multiple modified hDH gene segments, multiple hJH gene segments and an endogenous Ig heavy chain constant (CH) gene:
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The multiple hDH gene segments, multiple hJH gene segments, and mouse/rat Ig CH gene in Fig. 3B are missing from the claim, and the structure/function of the D6-DH chemokine receptor cannot be determined. The final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined.
Fig. 4A is a strategy for assembling a D6 chemokine decoy receptor coding sequence, but the starting material cannot be determined, the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined, and the function of the sequence cannot be determined:
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The description of Fig. 4A is of no help in this regard:
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Fig. 4B shows two additional steps for making the targeting vector, but the starting material cannot be determined, the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined, and the function of the sequence cannot be determined:
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The description of Fig. 4B is of no help in this regard:
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Fig. 5 shows a screening strategy for using “genetic material of drug resistant colonies”
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The starting material cannot be determined, and the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined. The description of Fig. 5 is of no help in this regard:
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The specification states the mouse/rat can be used to direct “binding to particular antigens [ ] for example [ ] in identifying and developing antibody-based therapeutics, which may target e.g., membrane-spanning or cytoplasmic polypeptides” or “for development of antibodies and/or antibody-based therapeutics for administration to humans” (para 2). The specification also teaches the chimeric antibody “binds a chemokine or voltage-gated sodium (Nav) channel” (para 50, 55). Paragraph 128 suggests the chimeric antibodies bind “antigens associated with low and/or poor immunogenicity” and that the “animal provide an in vivo system for identifying and developing antibodies and/or antibody-based therapeutics that bind disease targets beyond the targeting capabilities of established drug discovery technologies.” Para 242 suggests the chimeric antibody binds membrane-spanning proteins or blocks inflammatory cytokines. Para 244 suggests using the mouse/rat expressing the chimeric antibody to develop therapeutics that modulate/target cytokines/chemokines.
Para 246 (pg 118) teaches: “non-human animals described herein are used to measure the therapeutic effect of blocking or modulating β-chemokine activity (or 3-chemokine signaling, or β-chemokine mediated interactions) and the effect on gene expression as a result117 of cellular changes or the β-chemokine receptor density of cells of non-human animals as described herein. In various embodiments, a non-human animal described herein or cells isolated therefrom are exposed to a candidate therapeutic that binds a human β-chemokine polypeptide (or a portion of a human β-chemokine polypeptide) and, after a subsequent period of time, analyzed for effects on β-chemokine-dependent processes (or interactions), for example, ligand-receptor interactions or β-chemokine signaling.”
Figures 3-5 and their descriptions are too generic to determine the structure function of the eDH or the modifications required to make it capable of any rearrangement in the hVH/eDH/hJH nucleic acid of claim 1. The specification and the art do not teach what “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, or “D6-DH120126” mean in Fig.3A and 4A. The specification does not teach the starting material in Fig. 3A and 4A that contains “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, or “D6-DH120126” along with the proper “AgeI/EcoRI”, “SnaBI”, & “NotI/AscI” restriction sites. It is unclear what is being deleted after “AgeI/EcoRI”, “SnaBI”, & “NotI/AscI” restriction in Fig. 3A and 4A. The specification does not teach how the “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, and “D6-DH120126” obtained in Fig. 3A and 4A becomes an engineered D heavy chain gene segment in Fig. 3B or 5. The specification does not teach the RSSs flanking the “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, and “D6-DH120126” cassette in Fig. 3B or 5. The specification does not teach how the “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, and “D6-DH120126” cassette in Fig. 3B or 5 is “operably linked” to the human VH and JH gene segments or the mouse IgM gene segment such that rearrangement in a B-cell could occur.
The specification does not teach how to use the final chimeric hVH/eDH/hJH/mCH protein. The specification does not teach the structure/function hVH/eDH/hJH/mCH in context of “hotspots” engineered into the DH region or the defective RSSs that flank eDH coding regions and replace endogenous RSSs. The meaning, metes, and bounds of when/how RSSs for each hVH/eDH /hJH/CH gene segment allow for “hVH/eDH/hJH recombination according to the 12/23 rule” in claim 1 is unclear (see 112/2nd).
The specification does not teach how to use a chimeric antibody containing hVH/eDH-chemokine receptor/hJH/CH encoded by the nucleic acid of claim 1. The specification does not teach the purpose of expressing the chemokine receptor in context of the hVH, hDH, hJH, and CH antibody elements. It is unclear if the chimeric antibody has dual specificity, i.e. binding a chemokine via the chemokine receptor and binding an antigen via the hVH domain. It is unclear whether a hVH domain encoded by the hVH gene segment in claim 1 is functional when the nucleic acid is inserted into the genome of a mouse/rat. It is unclear whether a chemokine receptor encoded by the eDH gene segment in claim 1 is functional when the nucleic acid is inserted into the genome of a mouse/rat.
There is no evidence that a chimeric antibody encoded by the nucleic acid of claim 1 can bind a chemokine (para 50, 55) because the chemokine receptor is flanked by a hVH domain and a mCH domain (encoded by a sequence when integrated into the genome of a mouse or rat). There is no evidence that the chemokine receptor portion of the chimeric protein would be functional since its binding sites are unavailable and folded differently because of the adjacent hVH, hDH and CH domains.
There is no evidence that a chimeric antibody encoded by the nucleic acid of claim 1 can bind a chemokine (via a chemokine receptor encoded by the eDH) AND a different antigen (via a hVH domain encoded by the hVH gene segment).
The specification fails to provide adequate guidance for those of skill to use a chimeric antibody containing an internal chemokine receptor encoded by the nucleic acid of claim 1 for treatment (para 2, 128), to bind to antigens with low/poor antigenicity (para 128), to bind membrane-spanning proteins or block inflammatory cytokines (para 242), or to develop therapeutics that modulate/target cytokines/chemokines (para 244). While antibody binding assays can be envisioned and were known in the art, the specification fails to clearly set forth any chimeric antibody with an internal chemokine receptor capable of binding any chemokine. The amount of blocking/modulating β-chemokine activity and the desired effect of gene expression required for treatment as generically discussed in para 246 are not disclosed. Pg 141, para 302, generically states “when a desired immune response is achieved, splenocytes” are used to make hybridomas; however, there is no evidence that a chimeric antibody encoded by the nucleic acid of claim 1 is capable of binding a chemokine, and the desired amount of binding and immune response is not disclosed.
Given the lack of guidance in the specification taken with the art at the time of filing, it would have required those of skill undue experimentation to determine how to determine when an “eD” gene segment had been obtained or when the hVH, hJH, eD, and mouse/rat CH gene segments and their respective RSSs are “operably linked” and capable of rearrangement “according to the 12/23 rule”.
Response to arguments
Applicants’ discussion of V/D/J recombination and the “12/23 rule” on pg 13-16 of the Appeal Brief filed 9-26-25 is noted but does not address this rejection.
Applicants’ discussion of the enablement rejections being inconsistent with the claims and specification and unsupported (pg 17-28) are noted, but applicants are not persuasive. The rejection is based on the literal text of the claim and the specification. It is not a question of whether the specification uses the terms “eDH” domain and 12/23 rule. The specification taken with the art fails to provide adequate guidance for those of skill to be able to determine what applicants mean by the “eD gene segment” in claim 1, how to make the nucleic acid sequence of claim 1, when the nucleic acid complies with “the 12/23 rule”, and how to use the nucleic acid of claim 1 to produce a chimeric antibody that contains a hVH domain, an eDH domain comprising one or more chemokine receptor, and endogenous CH domain, and how to use the chimeric antibody produced by the nucleic acid of claim 1.
Pg 18 of the Appeal Brief says the specification teaches how to make and use the nucleic acid claimed with a reasonable correlation to the entire scope of the claims. Applicants point to pg 92, para 165-179. Applicants’ argument is not persuasive. Para 165-168, 170-179 discuss cDNA cloning, YACs, “optimized RSSs” having 50-100% identity with a 5’ RSS in Fig. 2, none of which are in the claims. Para 169 discusses an “ACKR2 DNA sequence” encoding an extracellular portion of a human ACKR2 flanked by RSS “for recombination” with VH and JH gene segments in a “transgenic non-human animal” without disclosing the structure of the eD gene segment encoding a chemokine receptor or the structure of the RSSs required to give it the ability to rearrange with hVH and hJH gene segments and a rat/mouse CH gene to create some chimeric protein made up of a hVH domain, a chemokine receptor, and a mouse or rat CH domain.
Applicants’ discussion of VDJ rearrangement and paragraphs 179, 16, 17 on pg 19 are noted but not persuasive. The examiner is not questioning whether VDJ rearrangement exists. The specification does not provide adequate guidance to apply the teachings of Hiom or Cuomo to hVH, eD, hJH, and mouse/rat CH gene segments so those of skill would be able to determine the structure of the eD and it’s RSSs, the RSSs required for each hVH, eD, hJH, and mouse/rat CH gene segments such that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
Applicants point to paragraphs 64, 65, 68, 69, Fig. 3-4 on pg 20. These citations and figures are not persuasive. The examiner is not questioning whether VDJ rearrangement exists. The specification does not provide adequate guidance to apply the teachings of Hiom or Cuomo to hVH, eD, hJH, and mouse/rat CH gene segments so that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
Applicants argue there is nothing of record to contradict the specification (pg 23-25). Applicants’ argument is not persuasive. The rejection is based on the teachings in the specification taken with the art at the time of filing, science, logic, the Wands factors, and legal standards.
Applicants argue the rejections are erroneous because they question features not claimed (pg 25-28). Applicants’ argument is not persuasive. The nucleic acid in claim 1 is not limited to a targeting vector. The nucleic acid in claim 1 must encode a functional chimeric protein after hVH, eD, hJH, mouse/rat CH after rearrangement “according to the 12/23 rule”. But the specification does not provide adequate guidance to apply the teachings of Hiom or Cuomo to hVH, eD, hJH, and mouse/rat CH gene segments so those of skill would be able to determine the structure of the eD and it’s RSSs, the RSSs required for each hVH, eD, hJH, and mouse/rat CH gene segments such that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
Applicants argue Example 5 and para 297 show a D6 chemokine decoy sequence can replace a DH gene segment (pg 22). Applicants’ argument is not persuasive because the structure/function of the VH/eD/JH/CH gene segments and the corresponding protein after rearrangement cannot be determined.
Applicants may be attempting to argue the VH/eD/JH/CH gene segments encode an antibody, but they don’t because a D6 chemokine decoy sequence replaced the DH gene segment. Fig. 3B shows the DH gene segment is 41 kb which is a massive coding sequence that would prevent expression of any normal antibody.
Applicants argue the nucleic acid can be simply used for insertion into a mouse or rat. Applicants’ argument is not persuasive because the sole disclosed use for doing so it so express a chimeric protein in which a D6 chemokine decoy sequence has replaced a DH gene segment.
Applicants arguments fail to teach the specific structure of one eD gene segment along with its RSSs.
Applicants fail to teach the specific RSSs required for each VH/eD/JH/CH gene segment, which side they’re on, and which spacer they have such that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
B) The specification does not enable making/using the nucleic acid in the absence of being capable of operably linking to an Ig CH gene in vivo as broadly encompassed by claim 1 and required in claim 4. The specification does not enable making/using any nucleic acid comprising a “rat [or mouse Ig] heavy chain constant [CH] region” as required in claims 4 or 34 other than a mouse Ig CH gene. Claim 1 does not require the nucleic acid is capable of (or is) operably linking to a CH gene in any animal. Claims 4 and 34 are limited to the nucleic acid sequence being operably linked to a mouse or rat CH gene. The specification and the art at the time of filing are limited to humanizing the mouse or rat genome so that hVH and hJH gene segments are operably linked to endogenous CH genes in the genetically modified mouse/rat. The specification suggests making transgenic rats but does not teach the sequences of the rat heavy chain gene, the structure of the transgene required to modify the rat heavy chain gene, or the structure of the genome after modifying a rat heavy chain gene. Given the lack of guidance in the specification taken with the art at the time of filing, it would have required those of skill undue experimentation to determine how to make/use any nucleic acid comprising any “non-human immunoglobulin heavy chain constant region” as required in claim 4 or 34 other than mice.
Response to arguments
Applicants do not specifically address this rejection.
C) The specification does not enable using any “atypical chemokine receptor” as required in claim 6 other than a “hotspot”-modified extracellular domains of a D6 chemokine decoy receptor (para 273), using any number of such a chemokine receptor other than at least 4 (pg 122, para 263), or flanking the sequence encoding the atypical chemokine receptor with any RSSs other than those with suboptimal or defective function that replace encoding RSSs. As per the election, the genetic modification of the endogenous DH region is only being examined as it relates to expressing a chemokine receptor. Claim 1 encompasses any “atypical” chemokine receptor, or a D6 chemokine decoy receptor (claims 5-7). Claims 104-108 are limited to any ACKR1, 2, 3 or 4 protein. It also appears claim 1 encompasses any intracellular, transmembrane or extracellular or portions thereof. Claim 18 is limited to an extracellular portion of ACKR2. Paragraph 263, bridging pg 122-123, teaches: “A single human DH segment (i.e., Dh6-25) remained intact in a DH region engineered to contain nucleotide coding sequences corresponding to portions of an extracellular domain of a D6 decoy chemokine receptor. Immunoglobulin gene segments (e.g., DH segments) can, in some embodiments, be associated with suboptimal or defective recombination signal sequences (e.g., a heptamer and/or nonamer sequence) such that usage of such DH segments is substantially less than usage of DH segments associated with recombination signal sequences characterized as wild-type, normal and/or not defective. Thus, such DH segments (e.g. DH6-25, RSS sequences shown in Fig 2) may be left intact or deleted when engineering a DH region to contain nucleotide coding sequences that each encode a non-immunoglobulin polypeptide of interest, or portion thereof (e.g., a D6 chemokine decoy receptor).” Fig. 3B has been reviewed, but it appears applicants only inserted 4 modified extracellular D6 decoy receptor fragments into the DH region. The specification does not correlate inserting decoy receptors with inserting any wild-type receptor, D6 decoy receptors with other chemokine receptor, multiple copies with a single copy, extracellular fragments to whole chemokine receptors, extracellular fragments to intracellular or transmembrane fragments.
Moreover, the specification is limited to using decoy receptors with artificial “hot spots” (pg 123, para 264; Fig. 1). Paragraph 264 teaches: “Immunoglobulins participate in a cellular mechanism, termed somatic hypermutation, which produces affinity-matured antibody variants characterized by high affinity to their target. Although somatic hypermutation largely occurs within the CDRs of antibody variable regions, mutations are preferentially targeted to certain sequence motifs that are referred to as hot spots, e.g., RGYW activation-induced cytidine deaminase (AID) hotspots (see, e.g., Li, Z. et al., 2004, Genes Dev. 18:1-11; Teng, G. and F.N. Papavasiliou, 2007, Annu. Rev. Genet. 41:107-20; hereby incorporated by reference). The nucleic acid sequence of each D6 coding sequence naturally contained such hot spot sequences, however, artificial hot spots were introduced into selected D6 coding sequences to optimize the potential for somatic hypermutation during clonal selection of B cell receptors. Artificial hot spots for SHM were introduced into D6 coding sequences in silico prior to de novo synthesis. Figure 1 set forth exemplary analysis of natural and artificial hotspots employed in D6 coding sequences described herein.” The specification does not teach the absence of the artificial “hot spots” allows adequate somatic hypermutation to obtain a repertoire of hVH segments. While the term “optimized” is used, applicants fail to show any data regarding the absence of artificial “hot spots”. Therefore, “hot-spot” modification appears essential to the invention.
Finally, the specification does not enable flanking the sequence encoding the chemokine receptor with any RSSs other than a pair of exogenous RSSs that replace endogenous RSSs and cause suboptimal or defective recombination signaling. The specification clearly states the RSSs have to be “suboptimal or defective” (pg 123, line 3) to allow the engineered DH expressed the exogenous coding sequence in context of the hVH and CH to form a functional antibody that has the desired binding property (see para 263 cited above). The specification does not correlate defective RSSs to wild-type RSSs or teach that wild-type RSSs would allow functional expression of the exogenous sequence in context of a chimeric antibody.
Given the teachings in the specification taken with the lack of correlative guidance it would have required those of skill undue experimentation to make/use a nucleic acid with any engineered DH region that expresses any chemokine receptor in context of an chimeric antibody as required in claim 1 other than a eDH region comprising a single hDH gene segment and a plurality of nucleic acid sequences consisting of extracellular ACKR1, ACKR1, ACKR1, or ACKR4 coding sequences, wherein the eDH region is flanked by “suboptimal or defective” recombination sites.
Response to arguments
Applicants argue Examples 1-5 and para 297 describe using a D6 chemokine decoy receptor and replacing a hDH gene segment with a sequence encoding the D6 receptor (pg 21-23). Applicants’ argument is not persuasive for reasons set forth above.
D) The specification does not enable making/using any engineered D gene segment comprising a plurality of eD gene segments each of which encodes an atypical chemokine receptor as required in claim 18 other than an eDH gene segment that has a single human DH segment (i.e. DH6-25) and encodes a plurality of D6 coding sequences (pg 122, para 263“A single human DH segment (i.e., Dh6-25) remained intact in a DH region engineered to contain nucleotide coding sequences corresponding to portions of an extracellular domain of a D6 decoy chemokine receptor”). The specification teaches four DNA fragments containing several D6 coding sequences (Table 5). Table 5 (pg 125) describes putting the four fragments into various DH positions. The specification does not correlate the limited example of an eDH comprising a single hDH gene segment (and a plurality of sequences encoding an extracellular region of a D6 chemokine decoy receptor) to a plurality of eD gene segments as claimed. The specification does not adequately correlate the plurality of sequences encoding an extracellular region of a D6 chemokine decoy receptor to a plurality of eD gene segments each encoding an extracellular region of a D6 chemokine decoy receptor. Fig. 3B appears to show applicants only inserted 4 modified extracellular D6 decoy receptor fragments into the DH region. Accordingly, claim 18 should be limited to an engineered D gene segment that has a single human DH segment (i.e. DH6-25) and encodes a plurality of D6 coding sequences.
Response to arguments
Applicants mention claim 18 on pg 22 but this discussion does not rise to the level of an argument. The structure of the eD in the specification appears to be limited to a single human DH segment (i.e. DH6-25) and a plurality of D6 coding sequences which is not in any of the claims. The specification does not correlate this single embodiment to any other eD gene segment. The RSSs required to allow it to rearrange with hVH, hJH, and rat/mouse CH gene segments cannot be determined.
Written Description
Claims 1, 5-7, 18-20 remain 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 rejections have been restructured in an attempt to clarify the issues.
A) The specification lacks written description for the structure/function of the eD or the structure/function of RSSs flanking VH, eD, & JH gene segment that “allow for hVH/eD/hJH recombination according to the 12/23 rule” in claim 1.
The nucleic acid of claim 1 and its scope are cited above.
The specification lacks written description for any “engineered diversity (eD) gene segment comprising a [chemokine receptor sequence] flanked by a 12-mer recombination signal sequence (RSS)” as encompassed by claim 1. Fig. 3B shows “four DNA fragments (D6-DH1116, D6-DH17613, D6-DH114619, D6-DH120126) each containing “several D6 coding sequences” (pg 122, para 263). Only one single DH segment (DH6-25) remained intact. Pg 59-73 show the sequences of D6-DH1166, D6-D17613, D6-DH114619, D6-DH120126. But it is unclear how/why they are Ig heavy or light chain D gene segments because they do not contain any sequences from an Ig heavy or light chain D gene segment. Nothing is left of any Ig heavy or light chain D gene segment in the sequences so they cannot be Ig “diversity” gene segments as claimed. To complicate matters, the specification is limited to eDH gene segments (pg 1, para 2), so the scope of eD in claim 1 lacks written description because it is greater and more expansive than an “eDH” as originally disclosed. The specification does not teach any eD light chain gene segments or compare eD heavy chain gene segments to eD light chain gene segments.
The exact structure and function of the eD and the function of the non-immunoglobulin coding sequence within the eD gene segment in context of the hVH/eD/hJH nucleic acid cannot be determined. Nor can they be determined in context of any chimeric hVH/eD/hJH/CH protein made by the nucleic acid sequence in vivo.
The specification discusses a “12/23 rule, in which gene segments flanked by an RSS with a 12bp spacer are typically joined to a gene segment flanked by a 23bp spacer” and cites Hiom and Cuomo (pg 49). However, the specification never clearly defines the rule. Cuomo says gene segments with RSSs containing “12-spacer signals” recombine with gene segments with RSSs containing “23-spacer signals”; however, Hiom and Cuomo never clearly define the metes and bounds of the “12/23 rule”. In fact, Hiom and Cuomo taught that the process is more significantly more complicated because V gene segments are only flanked on the 3’ end with one RSS (with a 12-spacer – Cuomo, pg 5683, para 2), D gene segments are flanked on both the 5’ and 3’ end with RSSs (is one a 12-spacer and the other a 23-spacer signal? – claim 1 just requires one RSS with a 12-mer), and J gene segments are only flanked on the 5’ end with one RSS (it a 23-spacer – Cuomo, pg 5683, para 2) (see Fig. 1 of Murphy (2019/0380316)).
The structures/functions of VH, eD, and JH gene segments and their corresponding RSSs that comply with the teachings of Hiom and Cuomo or any “12/23 rule” are not in the claims.
The structures/functions of VH, eD, and JH gene segments and their corresponding RSSs required to comply with the teachings of Hiom and Cuomo or any “12/23 rule” cannot be determined.
This is especially true because “the 12/23 rule” has nothing to do with VH/eD/JH recombination, so it is unclear when an eD gene segment will comply with a rule that was not made for it.
To add complication, claim 1 refers to “the RSSs” of the V, D, and J segments that “allow for VH/eD/JH recombination according to the 12/23 rule”, but claim 1 does not require the V or J segments have RSSs. The phrase “the RSSs of the VH gene segment” lacks antecedent basis. The phrase “the RSSs of the [ ] JH gene segment” lacks antecedent basis. Therefore, it is unclear if applicants are attempting to say the nucleic acid claimed HAS undergone rearrangement and IS capable of expressing a chimeric protein or if it simply has the capability of being rearranged for expressing the chimeric protein.
Accordingly, those of skill would not be able to determine when the elements “allow for hVH/eD/hJH recombination according to the 12/23 rule” as required in claim 1, and the elements described by Hiom and Cuomo for rearrangement of VH, DH, JH, and CH gene segments and their respective RSSs are missing from the claims.
The specification states the purpose of the invention is to create a diverse human immune response using numerous hVH segments that make up an immunoglobulin in the sentence bridging pg 47-48; pg 49, para 131; pg 50, last sentence; pg 54, para 150.
Chemokine receptors are described on pg 51, para 135-136, as binding chemokines.
Fig. 3A (see above) shows “de novo synthesis of 4 D6 DNA fragments”, but the starting material cannot be determined, the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined, and the function of the sequence cannot be determined. The description of Fig. 3A on pg 17, para 64, is of no help in this regard:
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Fig. 3B (see above) shows a vector with a single hVH gene segment, operably linked to multiple modified hDH gene segments, multiple hJH gene segments and an endogenous Ig heavy chain constant (CH) gene. The multiple hDH gene segments, multiple hJH gene segments, and mouse/rat Ig CH gene in Fig. 3B are missing from the claim, and the structure/function of the D6-DH chemokine receptor cannot be determined. The final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined.
Fig. 4A (see above) is a strategy for assembling a D6 chemokine decoy receptor coding sequence, but the starting material cannot be determined, the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined, and the function of the sequence cannot be determined. The description of Fig. 4A is of no help in this regard:
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Fig. 4B (see above) shows two additional steps for making the targeting vector, but the starting material cannot be determined, the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined, and the function of the sequence cannot be determined. The description of Fig. 4B is of no help in this regard:
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Fig. 5 (see above) shows a screening strategy for using “genetic material of drug resistant colonies”. The starting material cannot be determined, and the final sequence required for “operable linkage” of the eD encoding a chemokine receptor with human VH and JH gene segments and mouse/rat CH gene segment capable of rearranging in a B-cell to form a hVH/chemokine receptor/mouse or rat CH chimeric protein cannot be determined. The description of Fig. 5 is of no help in this regard:
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The specification states the mouse/rat can be used to direct “binding to particular antigens [ ] for example [ ] in identifying and developing antibody-based therapeutics, which may target e.g., membrane-spanning or cytoplasmic polypeptides” or “for development of antibodies and/or antibody-based therapeutics for administration to humans” (para 2). The specification also teaches the chimeric antibody “binds a chemokine or voltage-gated sodium (Nav) channel” (para 50, 55). Paragraph 128 suggests the chimeric antibodies bind “antigens associated with low and/or poor immunogenicity” and that the “animal provide an in vivo system for identifying and developing antibodies and/or antibody-based therapeutics that bind disease targets beyond the targeting capabilities of established drug discovery technologies.” Para 242 suggests the chimeric antibody binds membrane-spanning proteins or blocks inflammatory cytokines. Para 244 suggests using the mouse/rat expressing the chimeric antibody to develop therapeutics that modulate/target cytokines/chemokines.
Para 246 (pg 118) teaches: “non-human animals described herein are used to measure the therapeutic effect of blocking or modulating β-chemokine activity (or 3-chemokine signaling, or β-chemokine mediated interactions) and the effect on gene expression as a result117 of cellular changes or the β-chemokine receptor density of cells of non-human animals as described herein. In various embodiments, a non-human animal described herein or cells isolated therefrom are exposed to a candidate therapeutic that binds a human β-chemokine polypeptide (or a portion of a human β-chemokine polypeptide) and, after a subsequent period of time, analyzed for effects on β-chemokine-dependent processes (or interactions), for example, ligand-receptor interactions or β-chemokine signaling.”
Figures 3-5 and their descriptions are too generic to determine the structure function of the eDH or the modifications required to make it capable of any rearrangement in the hVH/eDH/hJH nucleic acid of claim 1. The specification and the art do not teach what “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, or “D6-DH120126” mean in Fig.3A and 4A. The specification does not teach the starting material in Fig. 3A and 4A that contains “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, or “D6-DH120126” along with the proper “AgeI/EcoRI”, “SnaBI”, & “NotI/AscI” restriction sites. It is unclear what is being deleted after “AgeI/EcoRI”, “SnaBI”, & “NotI/AscI” restriction in Fig. 3A and 4A. The specification does not teach how the “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, and “D6-DH120126” obtained in Fig. 3A and 4A becomes an engineered D heavy chain gene segment in Fig. 3B or 5. The specification does not teach the RSSs flanking the “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, and “D6-DH120126” cassette in Fig. 3B or 5. The specification does not teach how the “D6-DH1166”, “D6-DH17613”, “D6-DH114619”, and “D6-DH120126” cassette in Fig. 3B or 5 is “operably linked” to the human VH and JH gene segments or the mouse IgM gene segment such that rearrangement in a B-cell could occur.
The specification does not teach how to use the final chimeric hVH/eDH/hJH/mCH protein. The specification does not teach the structure/function hVH/eDH/hJH/mCH in context of “hotspots” engineered into the DH region or the defective RSSs that flank eDH coding regions and replace endogenous RSSs. The meaning, metes, and bounds of when/how RSSs for each hVH/eDH /hJH/CH gene segment allow for “hVH/eDH/hJH recombination according to the 12/23 rule” in claim 1 is unclear (see 112/2nd).
The specification does not teach how to use a chimeric antibody containing hVH/eDH-chemokine receptor/hJH/CH encoded by the nucleic acid of claim 1. The specification does not teach the purpose of expressing the chemokine receptor in context of the hVH, hDH, hJH, and CH antibody elements. It is unclear if the chimeric antibody has dual specificity, i.e. binding a chemokine via the chemokine receptor and binding an antigen via the hVH domain. It is unclear whether a hVH domain encoded by the hVH gene segment in claim 1 is functional when the nucleic acid is inserted into the genome of a mouse/rat. It is unclear whether a chemokine receptor encoded by the eDH gene segment in claim 1 is functional when the nucleic acid is inserted into the genome of a mouse/rat.
There is no evidence that a chimeric antibody encoded by the nucleic acid of claim 1 can bind a chemokine (para 50, 55) because the chemokine receptor is flanked by a hVH domain and a mCH domain (encoded by a sequence when integrated into the genome of a mouse or rat). There is no evidence that the chemokine receptor portion of the chimeric protein would be functional since its binding sites are unavailable and folded differently because of the adjacent hVH, hDH and CH domains.
There is no evidence that a chimeric antibody encoded by the nucleic acid of claim 1 can bind a chemokine (via a chemokine receptor encoded by the eDH) AND a different antigen (via a hVH domain encoded by the hVH gene segment).
The specification fails to provide adequate guidance for those of skill to use a chimeric antibody containing an internal chemokine receptor encoded by the nucleic acid of claim 1 for treatment (para 2, 128), to bind to antigens with low/poor antigenicity (para 128), to bind membrane-spanning proteins or block inflammatory cytokines (para 242), or to develop therapeutics that modulate/target cytokines/chemokines (para 244). While antibody binding assays can be envisioned and were known in the art, the specification fails to clearly set forth any chimeric antibody with an internal chemokine receptor capable of binding any chemokine. The amount of blocking/modulating β-chemokine activity and the desired effect of gene expression required for treatment as generically discussed in para 246 are not disclosed. Pg 141, para 302, generically states “when a desired immune response is achieved, splenocytes” are used to make hybridomas; however, there is no evidence that a chimeric antibody encoded by the nucleic acid of claim 1 is capable of binding a chemokine, and the desired amount of binding and immune response is not disclosed.
Accordingly, the specification lacks written description for when an “eD” gene segment had been obtained or when the hVH, hJH, eD, and mouse/rat CH gene segments and their respective RSSs are “operably linked” and capable of rearrangement “according to the 12/23 rule”.
Response to arguments
Applicants’ discussion of V/D/J recombination and the “12/23 rule” on pg 29-35 of the Appeal Brief filed 9-26-25 is noted but is not persuasive for reasons set forth above. The rejection is based on the literal text of the claim and the specification. It is not a question of whether the specification uses the terms “eDH” domain and 12/23 rule. The specification taken with the art fails to adequately describe what applicants mean by the “eD gene segment” in claim 1, how to make the nucleic acid sequence of claim 1, when the nucleic acid complies with “the 12/23 rule”, and how to use the nucleic acid of claim 1 to produce a chimeric antibody that contains a hVH domain, an eDH domain comprising one or more chemokine receptor, and endogenous CH domain, and how to use the chimeric antibody produced by the nucleic acid of claim 1.
Applicants point to pg 92, para 165-179. Applicants’ argument is not persuasive. Para 165-168, 170-179 discuss cDNA cloning, YACs, “optimized RSSs” having 50-100% identity with a 5’ RSS in Fig. 2, none of which are in the claims. Para 169 discusses an “ACKR2 DNA sequence” encoding an extracellular portion of a human ACKR2 flanked by RSS “for recombination” with VH and JH gene segments in a “transgenic non-human animal” without disclosing the structure of the eD gene segment encoding a chemokine receptor or the structure of the RSSs required to give it the ability to rearrange with hVH and hJH gene segments and a rat/mouse CH gene to create some chimeric protein made up of a hVH domain, a chemokine receptor, and a mouse or rat CH domain.
Applicants’ discussion of paragraphs 129, 169 on pg 32-33 is noted but not persuasive. The examiner is not questioning whether applicants contemplated an eD gene segment comprising RSSs and an atypical chemokine receptor. The specification does not adequately describe how to apply the teachings of Hiom or Cuomo to hVH, eD, hJH, and mouse/rat CH gene segments so those of skill would be able to determine the structure of the eD and it’s RSSs, the RSSs required for each hVH, eD, hJH, and mouse/rat CH gene segments such that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
Applicants point to paragraphs 64, 65, 68, 69, Fig. 3-4 on pg 34. These citations and figures are not persuasive. The examiner is not questioning whether VDJ rearrangement exists. The specification does not provide adequate guidance to apply the teachings of Hiom or Cuomo to hVH, eD, hJH, and mouse/rat CH gene segments so that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
Applicants argue the rejection fails to provide sufficient evidence to satisfy the burden required to make the rejection (pg 35-42). Applicants’ argument is not persuasive. The rejection is based on the teachings in the specification taken with the art at the time of filing, science, logic, and the legal standards for Written Description.
Applicants arguments on pg 35-42 fail to teach the specific structure of one eD gene segment along with its RSSs.
Applicants arguments on pg 35-42 fail to teach the specific RSSs required for each VH/eD/JH/CH gene segment, which side they’re on, and which spacer they have such that “operable linkage” or VH/eD/JH recombination according to the 12/23 rule” would occur.
Applicants argue Example 5 and para 297 show a D6 chemokine decoy sequence can replace a DH gene segment (pg 35-42). Applicants’ argument is not persuasive because the structure/function of the VH/eD/JH/CH gene segments and the corresponding protein after rearrangement cannot be determined.
Applicants may be attempting to argue the VH/eD/JH/CH gene segments encode an antibody, but they don’t because a D6 chemokine decoy sequence replaced the DH gene segment. Fig. 3B shows the DH gene segment is 41 kb which is a massive coding sequence that would prevent expression of any normal antibody.
Applicants argue the nucleic acid can be simply used for insertion into a mouse or rat. Applicants’ argument is not persuasive because the sole disclosed use for doing so it so express a chimeric protein in which a D6 chemokine decoy sequence has replaced a DH gene segment.
B) The specification lacks written description for the nucleic acid in the absence of being capable of operably linking to an Ig CH gene in vivo as broadly encompassed by claim 1 and required in claim 4. The specification lacks written description for any nucleic acid comprising a “rat [or mouse Ig] heavy chain constant [CH] region” as required in claims 4 or 34 other than a mouse Ig CH gene. Claim 1 does not require the nucleic acid is capable of (or is) operably linking to a CH gene in any animal. Claims 4 and 34 are limited to the nucleic acid sequence being operably linked to a mouse or rat CH gene. The specification and the art at the time of filing are limited to humanizing the mouse or rat genome so that hVH and hJH gene segments are operably linked to endogenous CH genes in the genetically modified mouse/rat. The specification suggests making transgenic rats but does not teach the sequences of the rat heavy chain gene, the structure of the transgene required to modify the rat heavy chain gene, or the structure of the genome after modifying a rat heavy chain gene. Accordingly, the specification lacks written description for any nucleic acid comprising any “non-human immunoglobulin heavy chain constant region” as required in claim 4 or 34 other than mice.
Response to arguments
Applicants do not specifically address this rejection.
C) The specification lacks written description for any “atypical chemokine receptor” as required in claim 6 other than a “hotspot”-modified extracellular domains of a D6 chemokine decoy receptor (para 273), using any number of such a chemokine receptor other than at least 4 (pg 122, para 263), or flanking the sequence encoding the atypical chemokine receptor with any RSSs other than those with suboptimal or defective function that replace encoding RSSs. As per the election, the genetic modification of the endogenous DH region is only being examined as it relates to expressing a chemokine receptor. Claim 1 encompasses any “atypical” chemokine receptor, or a D6 chemokine decoy receptor (claims 5-7). Claims 104-108 are limited to any ACKR1, 2, 3 or 4 protein. It also appears claim 1 encompasses any intracellular, transmembrane or extracellular or portions thereof. Claim 18 is limited to an extracellular portion of ACKR2. Paragraph 263, bridging pg 122-123, teaches: “A single human DH segment (i.e., Dh6-25) remained intact in a DH region engineered to contain nucleotide coding sequences corresponding to portions of an extracellular domain of a D6 decoy chemokine receptor. Immunoglobulin gene segments (e.g., DH segments) can, in some embodiments, be associated with suboptimal or defective recombination signal sequences (e.g., a heptamer and/or nonamer sequence) such that usage of such DH segments is substantially less than usage of DH segments associated with recombination signal sequences characterized as wild-type, normal and/or not defective. Thus, such DH segments (e.g. DH6-25, RSS sequences shown in Fig 2) may be left intact or deleted when engineering a DH region to contain nucleotide coding sequences that each encode a non-immunoglobulin polypeptide of interest, or portion thereof (e.g., a D6 chemokine decoy receptor).” Fig. 3B has been reviewed, but it appears applicants only inserted 4 modified extracellular D6 decoy receptor fragments into the DH region. The specification does not correlate inserting decoy receptors with inserting any wild-type receptor, D6 decoy receptors with other chemokine receptor, multiple copies with a single copy, extracellular fragments to whole chemokine receptors, extracellular fragments to intracellular or transmembrane fragments.
Moreover, the specification is limited to using decoy receptors with artificial “hot spots” (pg 123, para 264; Fig. 1). Paragraph 264 teaches: “Immunoglobulins participate in a cellular mechanism, termed somatic hypermutation, which produces affinity-matured antibody variants characterized by high affinity to their target. Although somatic hypermutation largely occurs within the CDRs of antibody variable regions, mutations are preferentially targeted to certain sequence motifs that are referred to as hot spots, e.g., RGYW activation-induced cytidine deaminase (AID) hotspots (see, e.g., Li, Z. et al., 2004, Genes Dev. 18:1-11; Teng, G. and F.N. Papavasiliou, 2007, Annu. Rev. Genet. 41:107-20; hereby incorporated by reference). The nucleic acid sequence of each D6 coding sequence naturally contained such hot spot sequences, however, artificial hot spots were introduced into selected D6 coding sequences to optimize the potential for somatic hypermutation during clonal selection of B cell receptors. Artificial hot spots for SHM were introduced into D6 coding sequences in silico prior to de novo synthesis. Figure 1 set forth exemplary analysis of natural and artificial hotspots employed in D6 coding sequences described herein.” The specification does not teach the absence of the artificial “hot spots” allows adequate somatic hypermutation to obtain a repertoire of hVH segments. While the term “optimized” is used, applicants fail to show any data regarding the absence of artificial “hot spots”. Therefore, “hot-spot” modification appears essential to the invention.
Finally, the specification lacks written description for flanking the sequence encoding the chemokine receptor with any RSSs other than a pair of exogenous RSSs that replace endogenous RSSs and cause suboptimal or defective recombination signaling. The specification clearly states the RSSs have to be “suboptimal or defective” (pg 123, line 3) to allow the engineered DH expressed the exogenous coding sequence in context of the hVH and CH to form a functional antibody that has the desired binding property (see para 263 cited above). The specification does not correlate defective RSSs to wild-type RSSs or teach that wild-type RSSs would allow functional expression of the exogenous sequence in context of a chimeric antibody.
Accordingly, the specification lacks written description for a nucleic acid with any engineered DH region that expresses any chemokine receptor in context of an chimeric antibody as required in claim 1 other than a eDH region comprising a single hDH gene segment and a plurality of nucleic acid sequences consisting of extracellular ACKR1, ACKR1, ACKR1, or ACKR4 coding sequences, wherein the eDH region is flanked by “suboptimal or defective” recombination sites.
Response to arguments
Applicants argue Examples 1-5 and para 297 describe using a D6 chemokine decoy receptor and replacing a hDH gene segment with a sequence encoding the D6 receptor (pg 35-42). Applicants’ argument is not persuasive for reasons set forth above.
D) The specification lacks written description for any engineered D gene segment comprising a plurality of eD gene segments each of which encodes an atypical chemokine receptor as required in claim 18 other than an eDH gene segment that has a single human DH segment (i.e. DH6-25) and encodes a plurality of D6 coding sequences (pg 122, para 263“A single human DH segment (i.e., Dh6-25) remained intact in a DH region engineered to contain nucleotide coding sequences corresponding to portions of an extracellular domain of a D6 decoy chemokine receptor”). The specification teaches four DNA fragments containing several D6 coding sequences (Table 5). Table 5 (pg 125) describes putting the four fragments into various DH positions. The specification does not correlate the limited example of an eDH comprising a single hDH gene segment (and a plurality of sequences encoding an extracellular region of a D6 chemokine decoy receptor) to a plurality of eD gene segments as claimed. The specification does not adequately correlate the plurality of sequences encoding an extracellular region of a D6 chemokine decoy receptor to a plurality of eD gene segments each encoding an extracellular region of a D6 chemokine decoy receptor. Fig. 3B appears to show applicants only inserted 4 modified extracellular D6 decoy receptor fragments into the DH region. Accordingly, claim 18 should be limited to an engineered D gene segment that has a single human DH segment (i.e. DH6-25) and encodes a plurality of D6 coding sequences.
Response to arguments
Applicants arguments are not persuasive. The structure of the eD in the specification appears to be limited to a single human DH segment (i.e. DH6-25) and a plurality of D6 coding sequences which is not in any of the claims. The specification does not correlate this single embodiment to any other eD gene segment. The RSSs required to allow it to rearrange with hVH, hJH, and rat/mouse CH gene segments cannot be determined.
Indefiniteness
Claims 1, 5-7, 18-20 remain 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 pre-AIA the applicant regards as the invention.
i) The structure/function of the nucleic acid and the operable linkage of the hVH, hJH, eDH, and mouse/rat CH gene segments and the structure/function of RSSs flanking VH, eD, & JH gene segment that “allow for hVH/eDH/hJH recombination according to the 12/23 rule” in claim 1 cannot be determined. The claim is incomplete because reference to the rule forces those of skill to look up the rule. The claim must be self-contained so that the rule is set forth. This is similar to incorporating a list into a claim by reference to a Table in the specification. The claim cannot be clear by reference a Table; the claim must clearly set forth the elements in the table in the claim itself. In this case, claim 1 cannot merely incorporate the rule into claim 1 by reference; the claim must clearly set forth the rule.
The specification discusses a “12/23 rule, in which gene segments flanked by an RSS with a 12bp spacer are typically joined to a gene segment flanked by a 23bp spacer” and cites Hiom and Cuomo (pg 49). However, the specification never clearly defines the rule. Hiom and Cuomo say gene segments with RSSs containing “12-spacer signals” recombine with gene segments with RSSs containing “23-spacer signals”; however, Hiom and Cuomo never clearly define the metes and bounds of the “12/23 rule”. It is clear from the Hiom and Cuomo that the process is complicated and involves V gene segments that are only flanked on the 3’ end with one RSS (with a 12-spacer – Cuomo, pg 5683, para 2), D gene segments flanked on both the 5’ and 3’ end with RSSs (is one a 12-spacer and the other a 23-spacer signal? – claim 1 just requires one RSS with a 12-mer), and J gene segments flanked on the 5’ end with one RSS (it a 23-spacer – Cuomo, pg 5683, para 2).
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Murphy (2019/0380316)
The structures/functions of VH, eD, and JH gene segments and their corresponding RSSs that comply with that “rule” are not disclosed. Accordingly, those of skill would not be able to determine when the elements “allow for hVH/eDH/hJH recombination according to the 12/23 rule” as required in claim 1.
More confusing is the fact that “the 12/23 rule” has nothing to do with VH/eD/JH recombination, so it is unclear when an eD gene segment will comply with a rule which it has nothing to do with.
To add complication, claim 1 refers to “the RSSs” of the V, D, and J segments that “allow for VH/eD/JH recombination according to the 12/23 rule”, but claim 1 does not require the V or J segments have RSSs. The phrase “the RSSs of the VH gene segment” lacks antecedent basis. The phrase “the RSSs of the [ ] JH gene segment” lacks antecedent basis. Therefore, it is unclear if applicants are attempting to say the nucleic acid claimed HAS undergone rearrangement and IS capable of expressing a chimeric protein or if it simply has the capability of being rearranged for expressing the chimeric protein.
It is also unclear if the nucleic acid is in the genome of a genetically modified mouse/rat or if it the vector used to make the mouse/rat. It is unclear when the elements are “in operable linkage” because the function of the nucleic acid is unclear. If the nucleic acid is in vivo and is intended to encode a chimeric protein, then the metes and bounds of the structures/functions protein cannot be determined.
Those of skill would not be able to determine when the hVH, hJH, eD, and mouse/rat CH gene segments and their respective RSSs are “operably linked” and capable of rearrangement “according to the 12/23 rule”.
Response to arguments
Applicants point to MPEP 2173.002 and case law, Hiom, and Cuomo. Applicants’ arguments are not persuasive. Claim is incomplete because reference to the rule forces those of skill to look up the rule - the claim must be self-contained. Claim 1 cannot merely incorporate the rule into claim 1 by reference; the claim must clearly set forth the rule.
There is no plain meaning for the 12/23 rule in the specification or in Hiom or Cuomo.
The 12/23 rule applies to VH, DH, JH, CH gene segment rearrangement; it does not apply to “eD” gene segments as claimed.
The combination of RSSs with 12 or 23 spacer, the presence of one or two RSSs, and their location on the 5’ or 3’ end described by Hiom and Cuomo are certainly missing from claim 1. The requirements for successful recombination have not been taught in the specification or examples for the hVH, eD, hJH, and mouse/rat CH gene segments in claim 1. Therefore, the structures and functions for operable linkage of the segments according to the 12/23 rule cannot be determined.
ii) The metes and bounds of RSSs in claim 1 are unclear. It is unclear whether they are limited to sequences having the well-known function of recombinase recognition sites (e.g. loxP, FLP) or if RSSs have some other function. RSSs are discussed in paragraph 131, but the structure/function of RSSs is not defined. The specification discusses making the RSSs defective; however, it is unclear whether RSSs must be defective in context of the invention, especially in context of RSSs “capable of allow[ing] for hVH/eDH/hJH recombination according to the 12/23 rule” as required in claim 1. Accordingly, the structure/function of the eDH region and eDH gene segments cannot be determined.
Response to arguments
Applicants argue those of skill would know the plain meaning of RSSs. Applicants’ argument is not persuasive. The argument, the specification, and Cuomo do not define the metes and bounds of RSSs.
Applicants argue Cuomo taught “RSSs consist of conserved heptamer and nonamer motifs separated by a nonconserved spacer region of either 12 or 23 bp”. Applicants’ argument is not persuasive. The RSSs with 12 or 23 bp spacers are specific to being on one side or the other or both of VH, DH, JH gene segments, but the only RSS required in claim 1 is in the DH gene segment. The claim is missing anything about RSSs with certain spacers being associated with VH, DH, or JH gene segments, whether one or two RSSs exist for each gene segment, or whether the RSSs are on 5’, 3’, or 5’ and 3’ ends.
The phrase “the RSS” within the phrase “the RSS of each of the VH gene segment” and “JH gene segment” in the last 3 lines of claim 1 lacks antecedent basis.
iii) The metes and bounds of an atypical chemokine receptor (ACKR) in claim 6 cannot be determined. Chemokine receptors were well-known; however, it is unclear when such a receptor crosses a line and becomes “atypical”. The phrase is not defined by the specification or the art at the time of filing. Ulvmar (Exp. Cell Res., 2011, Vol. 317, pg 556-568) described such receptors as cell surface receptors with 7 transmembrane domains structurally homologous to chemokine G-protein coupled receptors (GPCRs) but fail to induce “classical” signaling and downstream cellular responses characteristics for GPCRs (abstract) and because Ulvmar provides examples of such “atypical” chemokine receptors. However, Ulvmar does not teach how much homology to GPCRs is required to define the metes and bounds of “atypical” chemokine receptors. Ulvmar does not teach the metes and bounds of what are “classical” (vs “non-classical”) signaling so those of skill could draw a line when chemokine receptors have “failed to induce classical signaling”. Ulvmar does not teach the downstream cellular responses “characteristic” for GPCRs so those of skill could draw a line when chemokine receptors have “failed to induce” the desired cellular responses. It is unclear whether the phrase refers to GPCRs that exhibit the “full spectrum of features characteristic of ACRs” (pg 557, col. 2, 1st full para of Ulvmar) or whether the phrase refers to only proteins having “non-characteristic features” or to proteins having a “partial spectrum” of characteristics. Regardless, the metes and bounds of the “full spectrum”, partial spectrum” or other “characteristics” that define GPCRs or “atypical” chemokine receptors is not defined by Ulvmar. Those of skill would be able to use Ulvmar as a starting point for a general description of proteins that may be considered “atypical chemokine receptors” and for examples; however, those of skill would NOT be able to use Ulvmar to define the metes and bounds of “atypical” chemokine receptors. Accordingly, those of skill would not be able to determine when they were infringing on the claim.
Response to arguments
Applicants argue ACKRs were well-known as described by Ulvmar as being “structured as a heptaspanning membrane receptor having homology to a GPCR, and to function, not as a G-protein coupled receptor, but instead as a chemokine internalizer” (pg 45 of the Appeal Brief). Applicants’ argument is not persuasive. The specification certainly doesn’t use that definition. And the meaning of a “heptaspanning membrane receptor” cannot be determined; the amount of homology to a GPCR cannot be determined; the meaning of a “chemokine internalizer” cannot be determined.
The specification and Ulvmar do not define the metes and bounds of a chemokine receptor that makes is atypical. The specification and Ulvmar do not define the specific structure/function of an ACKR. There is no “plain meaning” for when a chemokine receptor is “atypical”.
iii) The structure/function of the engineered D (eD) region comprising 5 or more engineered gene segments in claim 18 lacks antecedent basis and is indefinite. The claim requires the eD region encodes an extracellular region of a D6 chemokine decoy receptor. However, the specification is limited to an “eDH” region comprising one hDH gene segment and a plurality of extracellular D6 chemokine decoy receptor sequences. It is unclear how the eDH coding region can or would contain a plurality of eDH gene segments when the D6 decoy sequences are the only thing present with more than one copy. The metes and bounds of a D6 decoy receptor are also unclear. Chemokine receptors were known; however, it is unclear when such a receptor crosses the line to be considered a “decoy”. The phrases are not defined in the specification or the art at the time of filing. Furthermore, it is unclear whether the “recombination signal sequences” (RSSs) in claim 1 are related to the eD regions. Accordingly, the structure/function of the eD region in claim 18 cannot be determined.
Response to arguments
Applicants point to Ulvmar who described D6 chemokine decoy receptors on pg 559-560. Applicants’ argument is not persuasive. The specification and Ulvmar do not define the metes and bounds of a chemokine receptor that makes is a “decoy”. The specification and Ulvmar do not define the specific structure/function of a decoy D6 CKR. There is no “plain meaning” for when a chemokine receptor is a “decoy” or a D6 chemokine receptor.
None of applicants’ arguments point to a well-known, plain meaning for D6 chemokine decoy receptor.
iv) It is unclear whether an eD region “comprises 25 eD gene segments that each independently comprises a non-Ig nucleic acid that encodes an extracellular portion of a D6 receptor” in claim 19. The structure/function of the 25 eD gene segments cannot be determined, and it cannot be determined how they further limit the eD region of claim 18.
Response to arguments
Applicants mention this rejection at the bottom of pg 46 but do not specifically clarify the structure of 23 eD gene segments encoding an extracellular portion of a D6 receptor or how they further limit the eD of claim 18.
v) It is unclear when a eD gene segment in claim 1 can “include 25 eD gene segments” that each encode “an extracellular portion of a D6 receptor” that are SEQ ID NO: 1, 3, 5…49 in claim 20. It is unclear how the SEQ ID NOs correlate to the structure/function of the 25 nucleotides in claim 19 or how they further limit the DH region of claim 18. It is unclear if the SEQ ID NOs represent the “eD” or the “eD” plus two flanking RSSs (one with a 12-mer spacer and one with a 23-mer spacer?).
Response to arguments
Applicants do not address this rejection.
Conclusion
No claim is allowed.
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Michael C. Wilson
/MICHAEL C WILSON/
Primary Examiner, Art Unit 1638
Prosecution Insights