DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 November 24, 2025 has been entered.
Applicant’s response and amendments received November 24, 2025 are acknowledged.
Claims 1-10, 12-45, 47, 50, 51, 56-58, 60-64, 66-75, 77-81, and 84-90 have been canceled.
Claim 11 has been amended.
Claims 11, 46, 48, 49, 52-55, 59, 65, 76, 82, 83, and 91-93 are pending in the instant application.
Claims 11, 46, 48, 49, 52-55, 59, 65, 76, 82, 83, and 91-93 are under examination in this office action as they read upon single domain antibodies that bind aggrecan and which comprise the CDR sequences of SEQ ID NOs: 32, 50, and 68. Note that as per Table A-2 in the instant specification, these CDRs were obtained from the 604F02 clone.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 11, 48, 49, 52-54, 59, 65, 76, 82, 83, and 91-93 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.
Applicant has amended independent claim 11 as part of the November 24, 2025 response to claim immunoglobulin single variable domain (ISV) polypeptides that bind to Aggrecan which are identified as comprising 3 CDRs defined by SEQ ID number OR mutants of said 3 CDRs with specific residues being marked for substitution mutagenesis, wherein it appears at least one of the three CDRs must be of exact sequence due to the newly added limitation of “wherein CDR1 is SEQ ID NO:32, CFR2 is SEQ ID NO50 and/or CDR3 is SEQ ID NO:68”. To support such breadth, the instant specification discloses the recovery of antibodies from 5 different immunized llamas as part of the working examples. Notably, no data concerning mutagenesis studies, such as wherein CDR residues are deliberately mutated typically in an attempt to increase binding affinity, appear to be disclosed. What is disclosed in Table 1.2 is that applicant recovered 5 clones as part of a “lead panel” (applicant’s words, see the paragraph immediately preceding Table 1.2) which bind an epitope labeled as “G1-IGD-G2” with clone 604F02 (i.e. the clone comprising CDRs of SEQ ID NOs:32, 50, and 68 (see particularly Table A-2)).
The guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112, § 1 "Written Description" Requirement make clear that if a claimed genus does not show actual reduction to practice for a representative number of species, then the Requirement may be alternatively met by reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the genus. See MPEP 2163. In The Regents of the University of California v. Eli Lilly (43 USPQ2d 1398-1412) 19 F. 3d 1559, the court held that disclosure of a single member of a genus (rat insulin) did not provide adequate written support for the claimed genus (all mammalian insulins). In this same case, the court also noted: “A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is. See Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen). It is only a definition of a useful result rather than a definition of what achieves that result. Many such genes may achieve that result. The description requirement of the patent statute requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming rejection because the specification does “little more than outlin [e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate."). Accordingly, naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not a description of that material.” The court has further stated that “Adequate written description requires a precise definition, such as by structure, formula, chemical name or physical properties, not a mere wish or plan for obtaining the claimed chemical invention.” Id. at 1566, 43 USPQ2d at 1404 (quoting Fiers, 984 F.2d at 1171, 25 USPQ2d at 1606). Also see Enzo-Biochem v. Gen-Probe 01-1230 (CAFC 2002). Recent court cases have emphasized the need for correlation between a well-defined structure and recited functional limitations. For example, the courts have indicated that recitation of an antibody which has specific functional properties in the absence of knowledge of the antibody sequences that give rise to said functional properties do not satisfy the requirements for written description. See for example AbbVie Deutschland GmbH v. Janssen Biotech. Inc. 759 F.3d 1285 (Fed. Cir. 2014) as well as Amgen v. Sanofi, (Fed Cir, 2017-1480. 10/5/2017). Indeed, in Amgen the court indicates that that it is improper to allow patentees to claim antibodies by describing something that is not the invention, i.e. the antigen, as knowledge of the chemical structure of an antigen does not give the required kind of structure-identifying information about the corresponding antibodies, with the antibody-antigen relationship be analogized as a search for a key on a ring with a million keys on it. As such, knowledge of where an antibody binds provides no information as to what such an antibody necessarily looks like (i.e. its primary amino acid structure). Applicant is reminded that the courts have long ruled that “Possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features.” See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895. As such, disclosure of a screening assay to test for functional properties of an antibody (such as the epitope to which a test antibody binds or the fact that it does or does not inhibit some enzymatic process) does not provide evidence of possession of the antibody itself.
It should be pointed out that it is well established in the art that the formation of an intact antigen-binding site requires the association of the complete heavy and light chain variable regions of a given antibody, each of which consists of three different complementarity determining regions, CDR1, 2 and 3, which provide the majority of the contact residues for the binding of the antibody to its target epitope. The amino acid sequences and conformations of each of the heavy and light chain CDRs are critical in maintaining the antigen binding specificity and affinity which is characteristic of the parent immunoglobulin (Janeway et al., see entire selection, of record). It is also known that single amino acid changes in a CDR can abrogate the antigen binding function of an antibody (Rudikoff et al., see entire document, particularly the abstract and the middle of the left column of page 1982, of record). Thus, based upon the prior art, skilled artisans would reasonably understand that it is the structure of the CDRs within an antibody which gives rise to the functional property of antigen binding, the epitope to which said CDRs bind is an inherent property which appears to necessarily be present due to conservation of critical structural elements, namely the CDR sequences themselves.
In Amgen Inc. v. Sanofi, 124 USPQ2d 1354 (Fed. Cir. 2017), relying upon Ariad Pharms., Inc. v. Eli Lily & Co., 94 USPQ2d 1161 (Fed Cir. 2010), the following is noted. To show invention, a patentee must convey in its disclosure that is “had possession of the claimed subject matter as of the filing date. Demonstrating possession “requires a precise definition” of the invention. To provide this precise definition” for a claim to a genus, a patentee must disclose “a representative number of species within the scope of the genus of structural features common to the members of the genus so that one of skill in the art can visualize or recognize the member of the genus” (see Amgen at page 1358). Further, an adequate written description must contain enough information about the actual makeup of the claimed products – “a precise definition, such as structure, formula, chemic name, physical properties of other properties, of species falling with the genus sufficient to distinguish the gene from other materials”, which may be present in “functional terminology when the art has established a correlation between structure and function” (Amgen page 1361). Indeed, the courts have long ruled that “When a patent claims a genus using functional language to define a desired result, the specification must demonstrate that the applicant has made a generic invention that achieves the claimed result and do so by showing that the applicant has invented species sufficient to support a claim to the functionally-defined genus.” See Capon v. Eshhar, 418 F.3d 1349 (Fed. Cir. 2005). Also, “A sufficient description of a genus . . . requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can "visualize or recognize" the members of the genus.” See AbbVie, 759 F.3d at 1297, reiterating Eli Lilly, 119 F.3d at 1568-69. It should also be noted that the USPTO has released a Memo on the Clarification of Written Description Guidance For Claims Drawn to Antibodies and Status of 2008 Training Materials, 02/22/2018. See uspto.gov/sites/default/files/documents/amgen_22feb2018.pdf. This Memo clarifies the applicability of USPTO guidance regarding the written description requirement of 35 U.S.C. § 112(a) concerning the written description requirement for claims drawn to antibodies and states: “In view of the Amgen decision, adequate written description of a newly characterized antigen alone should not be considered adequate written description of a claimed antibody to that newly characterized antigen, even when preparation of such an antibody is routine and conventional”. Further, the courts have indicated that the enablement and written description requirements of 35 USC 112 are separable as can be seen in for example Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111.
Artisans concur with such reasoning because they know that knowledge of a given antigen provides no information concerning the sequence/structure of antibodies that bind the given antigen. For example, Edwards et al. teach that over 1,000 different antibodies to a single protein can be generated, all with different sequences spanning almost the entire heavy and light chain germline repertoire (42/49 functional heavy chain germlines and 33 of 70 V-lambda and V-kappa light chain germlines, and with extensive diversity in the HCDR3 region sequences (that are generated by VDJ germline segment recombination) as well, see entire document, of record). Similarly, Lloyd et al. teach that a large majority of VH/VL germline gene segments are used in the antibody response to an antigen, even when the antibodies were selected by antigen binding, as their sequencing studies revealed that out of 841 unselected and 5,044 selected antibodies, all but one of the 49 functional VH gene segments was observed (see entire document, of record). Goel et al. disclose the synthesis of three mAbs that bind to the same short (12-mer) peptide and found that the sequences of these antibodies which bound the same epitope exhibited diverse V gene usage indicating their independent germline origin (see entire document, of record). As such, it does not seem possible to predict the sequence/structure of an antibody that binds a given antigen as there does not appear to be any common or core structure present within all antibodies that gives rise to the function of antigen binding. Further, given data such as that of Edwards et al. indicating the diversity of sequence bound in a population of antibodies that bind to a given antigen no number of species appears to reasonably representative of the breadth of the genus of antibodies that bind the given antigen.
The instant claimed antibody products do not recite conventional antibodies that have six CDRs as discussed above but are immunoglobulin single variable domains, a class of antibodies derived from camelid heavy chain antibodies (VHH) which are distinct in that they comprise only a single polypeptide chain, and thus only have 3 CDRs which are responsible for antigen binding (see page 30 of the instant specification). However, the majority of antigen contacts are still found within the CDRs (Ghahroudi et al., see entire document, of record), and thus it is the structures of the CDRs which give rise to the function of antigen binding. As briefly discussed above, example 1 of the instant specification discloses the immunization of 5 llamas with a human aggrecan construct, and the recovery of numerous clones. Importantly, in addition to sequencing, applicant functionally tested such clones and found that they bound distinct epitopes on the immunizing antigen, a result which is not unexpected. Table 1.2 discloses the following:
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Five clones were recovered that bind “G1-IGD-G2” (also referred to as “GIG binders” elsewhere in the specification), specifically 113A01, 601D02, 601E09, 604F02, and 604G01. As evidenced by Table A-2 in the specification, the CDR sequences of these five different clones are often quite different, especially in CDR3.
The specification also discloses on page 98
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Note that it is completely unclear how the information of section 1.4 was generated since as per Table 1.2 there are 5 “GIG” binders and the CDR3 of 113A01 is “SPRVGS” and the CDR3 of 601D02 is “ARIPVRTYTSEWNY” as clearly set forth in the sequences of Table A-2. The specification does not appear to provide any data concerning clonal families (e.g.an initial sequence than mutates via somatic hypermutation with parsimony used to define parental from progeny sequences) and based upon the quite disparate CDR3 sequences it does not appear that such a relationship is possible. This is because unlike CDRs1 and 2 which are germline encoded, CDR3 is always assembled via V(D)J recombination in an error-prone manner which serves to increase sequence diversity (see for example Janeway et al., particularly sections 3-10 to 3-18) and there does not appear to be any reasonable way all of the identified “GIG” binders appear to be derivatives of one another vial clonal descent (similar, but not exactly like “Joe9” and its multitudinous mutated progeny in the AbbVie case) given the relatively extreme CDR3 sequence diversity, with CDRs 1 and 2 also showing higher levels of diversity than that asserted in section 1.4 copied above, albeit to a lesser extent. As such it is not clear why tables 1.4A-C show data for some, but not all disclosed “GIG” binders. Further, no mutagenesis appears to have been performed and as such Figures 1.4A-C appear to just be an alignment with the “wildtype sequence” being that recovered from 604F02 and the “mutations” simply being a composite list of other amino acids at various locations from an unspecified subset of “GIG” binders.
Based upon the information in Figure 1.4A-C it appears that applicant believes that significant sequence alterations beyond that recovered in any one clone can be made without impacting antigen binding. To put it another way, independent claim 11 allows for selection of specific CDR amino acids that were never isolated together in a single clone. Again, applicant has not clearly demonstrated any clonal descent for the sequences in question, and it is known in the art that even a change as small as a single CDR residue can abrogate binding as evidenced by Rudikoff (of record, see entire document). Additionally, it is known that mutations in antigen binding interactions cannot be assumed to be additive as a mutation that is permissible in one background may not retain function in a different background and this issue becomes significantly more complex as the number of mutations rises (Mateu et al., see entire document particularly the abstract as well as Winkler et al., see entire document, and Clark et al., see entire document, particularly the “combination mutants” and “Discussion” sections, all of record). Thus randomly combining mutations observed in different clones to be permissive for binding does not ensure that the resulting combination will maintain the function of antigen binding. Thus while the specification does disclose more clones than just 604F02 which bind “GIG” (see again Tables 1.2 and A-2) applicant’s assertions that individual mutations from clones can be combined to generate new sequences not recovered as part of the screening process and not experimentally validated as maintaining binding as part of a mutagenesis study does appear to be sufficiently correlated with the requirements of such a new structure to have the function of binding aggrecan as set forth in the claims based upon the teachings of the prior art with regard to the non-linearity of combining mutations involved in antigen binding interactions.
As such, the instant specification discloses a limited number of species which are correlated with the function of binding aggrecan, yet the breath of structures encompassed by the instant claims is much broader than the constructs identified in the examples disclosed by applicant and such broadened subject matter is not reasonably expected to maintain the function of binding aggrecan as discussed above. Therefore, in view of the facts that the full length VHH/ISV constructs disclosed by applicant are not representative of the breadth of structures encompassed by the instant claims and the fact that no correlation between structure and the function of antigen binding appears to be disclosed except for VHH/ISV which comprise three defined CDRs which are known to bind the same epitope within aggrecan, skilled artisans would reasonably conclude that applicants were not in possession of the genus of recited ISVD at the time the instant application was filed.
Applicant's arguments filed June 3, 2025 have been fully considered but they are not persuasive. Applicant argues that claim 35 was previously not rejected but only objected to and that the limitations of claim 35 have been incorporated into independent claim 11, and thus applicant believes all grounds of rejection should be withdrawn.
This argument has been considered and is not persuasive. The prior office action contains a typographical error in that claim 46, which is limited to 3 exact CDR sequences was indicated as rejected, while claim 35 which recites the same three sequences joined by “and/or” such that a little as one (rather than all three) fully defined sequences needs to be present was indicated as being objected to, which is the opposite of what should have been communicated. Note that a reasonable reading of the body of the rejection setting forth what concepts are problematic, such as the lack of reciting three fully defined CDR sequences in the absence of supporting experimental mutagenesis data, would reasonably have identified such a logical discrepancy. As such applicant’s remarks do not rebut the premise set forth in the rejection that CDR mutagenesis covering biological sequences not experimentally known to actually bind (i.e. combining mutations from unrelated clones in the hope that they will maintain the function of antigen binding) would not reasonably be accepted by artisans as evidence that the breadth of structures encompassed by the instant claims necessarily has the recited, and therefore required, functional properties. Indeed, given that the art teaches that combining mutations has nonlinear (i.e. non-additive) impacts on binding activity as discussed above and the claims allow for biological sequences not recovered via screening or mutagenesis studies that were experimentally validated to have the function of binding aggrecan, artisans would reasonably conclude that applicant was not in possession of the full breadth of independent combinatorial sequence mutations within the CDRs that maintain antigen binding function at the time of filing.
Claims 11, 48, 49, 52-54, 59, 65, 76, 82, 83, and 91-93 are 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 aggrecan binding single variable domains comprising the three CDRs of SEQ ID NOs:32, 50, and 68 respectively, does not reasonably provide enablement for more. 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 use the invention commensurate in scope with these claims.
Applicant has claimed immunoglobulin single variable domains (ISV), a special type of antibody that comprises only three CDRs rather than the six found in conventional antibodies having an antigen binding domain made from a paired heavy and light chain, that bind aggrecan, an antigen predominantly found in cartilage. In independent claim 11, such ISV are partially defined by CDR sequence. Specifically, as presently constructed claim 11 recites three fully defined CDR sequences (i.e. SEQ ID NOs:32, 50, and 68) that may or may not be mutated at various positions defined relative to the recited SEQ ID numbers, with the proviso that at least one of the CDRs is fully defined per the penultimate “wherein” clause. The specification discloses immunizing llamas with aggrecan followed by recovery and sequencing of lead clones (example 1). No experimental data concerning CDR mutagenesis appears to be disclosed in the instant specification.
It is well established in the art that the formation of an intact antigen-binding site requires the association of the complete heavy and light chain variable regions of a given antibody, each of which consists of three different complementarity determining regions, CDR1, 2 and 3, which provide the majority of the contact residues for the binding of the antibody to its target epitope. The amino acid sequences and conformations of each of the heavy and light chain CDRs are critical in maintaining the antigen binding specificity and affinity which is characteristic of the parent immunoglobulin (Janeway et al., see entire selection, of record). It is also known that single amino acid changes in a CDR can abrogate the antigen binding function of an antibody (Rudikoff et al., see entire document, particularly the abstract and the middle of the left column of page 1982, of record). Thus, based upon the prior art, skilled artisans would reasonably understand that it is the structure of the CDRs within an antibody which gives rise to the functional property of antigen binding, the epitope to which said CDRs bind is an inherent property which appears to necessarily be present due to conservation of critical structural elements, namely the CDR sequences themselves.
As set forth above, the instant claimed antibody products are not conventional antibodies that have six CDRs but are immunoglobulin single variable domains, a class of antibodies derived from camelid heavy chain antibodies (VHH) which are distinct in that they comprise only a single polypeptide chain, and thus only have 3 CDRs which are responsible for antigen binding (see page 30 of the instant specification). However, the majority of antigen contacts are still found within the CDRs (Ghahroudi et al., see entire document, of record), and thus it is the structures of the CDRs which give rise to the function of antigen binding. Working example 1 of the instant specification discloses the immunization of 5 llamas with a human aggrecan construct, and the recovery of numerous clones. Importantly, in addition to sequencing, applicant functionally tested such clones and found that they bound distinct epitopes on the immunizing antigen, a result which is not unexpected. Table 1.2 discloses the following:
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Five clones were recovered that bind “G1-IGD-G2” (also referred to as “GIG binders” elsewhere in the specification), specifically 113A01, 601D02, 601E09, 604F02, and 604G01. As evidenced by Table A-2 in the specification, the CDR sequences of these five different clones are often quite different, especially in CDR3.
The specification also discloses on page 98
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Note that it is completely unclear how the information of section 1.4 was generated since as per Table 1.2 there are 5 “GIG” binders and the CDR3 of 113A01 is “SPRVGS” and the CDR3 of 601D02 is “ARIPVRTYTSEWNY” as clearly set forth in the sequences of Table A-2. The specification does not appear to provide any data concerning clonal families (e.g.an initial sequence than mutates via somatic hypermutation with parsimony used to define parental from progeny sequences) and based upon the quite disparate CDR3 sequences it does not appear that such a relationship is possible. This is because unlike CDRs1 and 2 which are germline encoded, CDR3 is always assembled via V(D)J recombination in an error-prone manner which serves to increase sequence diversity (see for example Janeway et al., particularly sections 3-10 to 3-18) and there does not appear to be any reasonable way all of the identified “GIG” binders appear to be derivatives of one another vial clonal descent given the relatively extreme CDR3 sequence diversity, with CDRs 1 and 2 also showing higher levels of diversity than that asserted in section 1.4 copied above, albeit to a lesser extent. As such it is not clear why tables 1.4A-C show data for some, but not all disclosed “GIG” binders. Further, no mutagenesis appears to have been performed and as such Figures 1.4A-C appear to just be an alignment with the “wildtype sequence” being that recovered from 604F02 and the “mutations” simply being a composite list of other amino acids at various locations from an unspecified subset of “GIG” binders.
Based upon the information in Figure 1.4A-C it appears that applicant believes that significant sequence alterations beyond that recovered in any one clone can be made without impacting antigen binding. To put it another way, independent claim 11 allows for selection of specific CDR amino acids that were never isolated together in a single clone. Again, applicant has not clearly demonstrated any clonal descent for the sequences in question, and it is known in the art that even a change as small as a single CDR residue can abrogate binding as evidenced by Rudikoff (of record, see entire document). Additionally, it is known that mutations in antigen binding interactions cannot be assumed to be additive as a mutation that is permissible in one background may not retain function in a different background and this issue becomes significantly more complex as the number of mutations rises (Mateu et al., see entire document particularly the abstract as well as Winkler et al., see entire document, and Clark et al., see entire document, particularly the “combination mutants” and “Discussion” sections, all of record). Thus randomly combining mutations observed in different clones to be permissive for binding does not ensure that the resulting combination will maintain the function of antigen binding and thus it reasonably appears that artisans would need to engage in additional unpredictable basic science trial and error research and experimentation to make and use that which has been presently claimed. For the sake of clarity it should be stated that while making a recombinant polypeptide of any specifically defined sequence using the tools and techniques of recombinant molecular biology is routine, the presence of desired biological activities, such as binding to aggrecan, cannot be reasonably assumed to be present in the absence of actual reduction to practice.
Therefore, in view of the breadth of the claimed invention, the guidance and direction of the instant specification, and the teachings of the art, artisans would not be able to make the full breadth of the claimed polypeptides and be assured of their ability to bind aggrecan such that they can be used in the absence of additional unpredictable research and experimentation. It should be pointed out that the specification does not appear to disclose any reasonable use of ISV that do not have the functional activity of binding aggrecan.
Claim Objections
Claims 46 and 55 are objected to as being dependent upon a rejected independent claim, but would be allowable if rewritten in independent form including all of the limitations of the independent claim and any intervening claims. It should be noted that SEQ ID NOs:13 and 118 as recited in claim 55 are full length VHH sequences and thus the CDR sequences found within these longer sequences are of exact sequence.
No claims are allowable.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Michael Szperka whose telephone number is (571)272-2934. The examiner can normally be reached Monday-Friday 8:30-5:00.
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Michael Szperka
Primary Examiner
Art Unit 1641
/MICHAEL SZPERKA/ Primary Examiner, Art Unit 1644