DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 4-5, 7-8, 10-11, 13-17, 19-23, 25-27, 29-31, 33-35, 37-39, 41-42, 44-50, 52-55, 57-59, 61-63, 65-73, 75-77, 79-80, 82-84, 86-87, 89, 91, and 93-95 are canceled.
Claims 1-3, 6, 9, 12, 18, 24, 28, 32, 36, 40, 43, 51, 56, 60, 64, 74, 78, 81, 85, 88, 90, and 92 are pending.
Claims 2-3, 6, 28, 32, 36, 40, 43, 51, 56, 60, 64, 74, 78, 85, 88, 90, and 92 are withdrawn from consideration.
Claims 1, 9, 12, 18, 24, and 81 are examined herein.
Claims 1, 9, 12, 18, 24, and 81 are rejected.
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1, 9, 12, 18, 24, and 81 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites:
“…wherein the ISG comprises:
an amino acid sequence having at least 85% sequence identity to the amino acid sequence of SEQ ID NO: 7;
(ii) ILQQILQQQLIPCRDVVLQQHNIAHGSSQVLQQSTYQLLQQLCC QQLWQIPEQSRCQAIHNVVHAIILHQQQQQ (SEQ ID NO: 28); or
(iii) LWQIPEQSRCQAIHNVVHA (SEQ ID NO: 29)…”
However, SEQ ID NO: 28 is disclosed in the specification as a consensus alpha gliadin nrr1 sequence (Table 2 and 3), SEQ ID NO: 7 is disclosed as an ISG sequence that appears to be within the nrr1 region (with some sequence variation), and SEQ ID NO: 29 is within the ISG region of SEQ ID NO: 7 (with some sequence variation). That is, SEQ ID NO: 28 appears to be a nrr1 sequence comprising an ISG sequence. This is contradictory to the claim language that claims SEQ ID NO: 28 is comprised within an ISG sequence. Therefore, the claim is unclear and indefinite.
Claims 9, 12, 18, 24, and 81 are also rejected as a function of their dependency.
Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1, 9, 12, 24, and 81 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.
Claims 1, 9, 12, 24, and 81 are broadly drawn to introducing any one or more alterations in an ISG sequence having at least 85% identity to SEQ ID NO: 7, or the ISG sequence of SEQ ID NO: 28 or 29 to produce a modified gluten polypeptide that has reduced inflammatory potential.
Applicant describes in working examples mutating the sequence of SEQ ID NO: 29 (gld-1) by replacing a single cationic arginine (R) with a non-cationic amino acid Glutamin (Q) to produce SEQ ID NO: 31 (gld-2) (see p. 81, Table 2, and ¶0259). Applicant also describes mutating SEQ ID NO: 29 (gld-1) plus the 4 bp directly upstream the sequence of SEQ ID NO: 29 (as seen in SEQ ID NO: 28) by replacing a cationic arginine (R) and a cationic Histidine (H) each with a non-cationic amino acid Glutamin (Q) to produce SEQ ID NO: 32 (gld-3) (see p. 81, Table 2, and ¶0259). Applicant describes that these mutated sequences associated with E. coli dsDNA (example of PAMP readily available in gastrointestinal tract (spec., ¶0252)), but were unable to form ordered nanocrystalline structures with the dsDNA that promotes binding of TLR9s for TLR9 activation and amplification of an immune response (¶0252-0253). Applicant further describes gld-2 and gld-3 elicited attenuated production of interleukin-8 (an immunogenic protein) in the presence of dsDNA as compared to gld-1 (Fig. 3, ¶0262).
Applicant also describes mutating a portion of the sequence of SEQ ID NO: 28 (gld-1) that flanks SEQ ID NO:29 by replacing Cysteines (C) with Alanines (A) to produce SEQ ID NO: 30 (gld-1A) (see p. 81, Table 2, and ¶0263). Applicant describes these mutations to have reduced the dsDNA-peptide complex activity compared to the dsDNA-gld-a complex, and also elicited attenuated production of interleukin-8 in the presence of dsDNA as compared to gld-1 (¶0263, Fig. 3).
Aside from these 3 examples that mutations to a sequence 100% identical to SEQ ID NO: 29, thereby producing sequences 100% identical to instant SEQ ID NOs: 30-32, Applicant has not described any other example of any mutation that produces a modified gluten polypeptide that has reduced inflammatory potential. Aside from the upstream AA residues flanking SEQ ID NO: 29, Applicant does not describe any mutation in the upstream or downstream regions of SEQ ID NO: 28 (which spans an additional 47 AA’s upstream and 9 AA’s downstream SEQ ID NO: 29) that produces a modified gluten polypeptide that has reduced inflammatory potential, nor any mutation any mutation in the upstream or downstream regions of SEQ ID NO: 7 (which spans an additional 22 AA’s upstream and 7 AA’s downstream SEQ ID NO: 29), much less a sequence having as little as 85% sequence identity to SEQ ID NO: 7.
Claim 81 is further broadly drawn the method of claim 1, wherein the gluten polypeptide with a reduced inflammatory potential comprises one or more of: (a) a reduced ability to mediate organization of innate immune ligands into ordered nanocrystalline structures; and/or (b) a reduced ability to promote activation of Toll-Like Receptors (TLRs); , as compared to a gluten polypeptide without the one or more alterations in the ISG.
As stated above, Applicant describes two specific mutated sequences of SEQ ID NO: 29 that were unable to form ordered nanocrystalline structures with the dsDNA that promotes binding of TLR9s for TLR9 activation and amplification of an immune response (¶0252-0253). Applicant further describes 3 examples of mutated sequences that elicited attenuated production of interleukin-8 in the presence of dsDNA as compared to gld-1 (¶0262-0263, Fig. 3).
Applicant has not described any other mutation aside from the two mutated sequences that reduces organization of innate immune ligands into ordered nanocrystalline structures, nor any other mutated sequences that reduce the ability to promote activation of TLRs. Applicant has not described reduced activation of any TLR other than TLR9 as well.
The prior art fails to remedy this deficiency. There is a dearth of description in the prior art of mutations to these ISG sequences, altogether, much less mutations to these sequences that would confer reduced inflammatory potential as recited in claim 1. The prior art also fails to describe mutations to these sequences that could be expected to reduce inflammatory potential of the gliadin polypeptide. Furthermore, even years after the filing of the instant Application, Patt (Patt, Y. S., Lahat, A., David, P., Patt, C., Eyade, R., & Sharif, K. (2023). Unraveling the immunopathological landscape of celiac disease: a comprehensive review. International Journal of Molecular Sciences, 24(20), 15482.) highlights much is still unknown regarding celiac disease (CD).) Patt describes immune responses associated with celiac disease are complex, and there are still gaps in knowledge and unknown factors that contribute to the exact mechanisms and immune-pathophysiology of this immune response (abstract, p. 2, ¶1-2). Patt describes these gaps in the knowledge partially persist due to the complexity of immune responses, genetic variations, environmental influences, and their interplay in disease manifestation (p. 2, ¶2). Therefore, given the vast scope of claims 1, and the dearth of description in the art of mutations to these sequences that reduce inflammatory potential and the complexity of immune responses, the prior art does not remedy Applicant’s failure to fully describe the scope of the claims.
Because the full scope of mutations to the recited sequences that reduce inflammatory potential was unknown and unpredictable at the time of filing, and given the complexity and various factors of immune responses, Applicant could not have described the full genus of mutations in the sequences recited in claim 1 that are capable of producing a modified gluten polypeptide that has reduced inflammatory potential. Therefore, the specification fails to provide an adequate written description to support the claim of any mutation to the sequences that produces a modified gluten polypeptide that has reduced inflammatory potential. The limited examples of 3 mutant sequences at 100% sequence identity does not describe the claimed genus by virtue of example. Therefore, one of ordinary skill in the art would not have recognized the Applicant to be in possession of the claimed invention at the time the application was filed.
Response to Arguments
Applicant argues beginning on p. 12 of remarks dated 07/22/2026 the
following arguments:
Claims 13-14 are rejected on the basis that they allegedly contain an improper Markush grouping of alternatives.
To begin, the rejection is of claims 13-14, which were previously canceled in the
application. It is believed reference to claims 13-14 is an unintentional error as the Examiner's language in the rejection references claims 12 and 18, and thus Applicant's response is with respect to claims 12 and 18.
Applicant respectfully traverses the rejection and its supporting remarks. However, to facilitate prosecution, without prejudice or disclaimer, Applicant has amended the claims as described above. Specifically, SEQ ID NO: 33 was removed from claim 12 and SEQ ID NO: 34 was removed from claim 18. In view of these amendments, it is believed the Examiner's rejection is moot. Therefore, Applicant respectfully requests that the rejection be withdrawn.
Examiner’s Response:
In view of Applicant’s amendments, the Improper Markush Grouping rejection has been withdrawn.
Applicant argues beginning on p. 13 of remarks dated 07/22/2026 the
following arguments:
III. Claim Rejections - 35 U.S.C. § 112(b)
Claims 1, 9, 12, 18, 24, and 81 are rejected under 35 U.S.C. 112(b) as allegedly being indefinite. The Examiner states "SEQ ID NO: 28 is disclosed in the specification as a consensus alpha gliadin nrrl sequence" and "That is, SEQ ID NO: 28 appears to be a nrrl sequence comprising an ISG sequence. This is contradictory to the claim language that claims SEQ ID NO: 28 is comprised within an ISG sequence. Therefore, the claim is unclear and indefinite" (See Office Action dated April 22, 2026, page 6).
Applicant respectfully traverses the rejection and its supporting remarks. With respect to SEQ ID NO: 28 and the ISG language, the instant specification as filed states: "In some embodiments, the ISG comprises the amino acid sequence ILQQILQQQLIPCRDVVLQQHNIAHGSSQVLQQSTYQLLQQLCCQQLWQIPEQSRCQAIH NVVHAIILHQQQQQ (SEQ ID NO: 28)." See paragraph [0014] of the specification as filed, emphasis added. The specification as filed clearly indicates that SEQ ID NO: 28 is an ISG sequence. This aligns with the language of the claims (e.g. claim 1), which recites "...wherein the ISG comprises...SEQ ID NO: 28" (emphasis added). As such, Applicant contends that the claim language is clear and definite. Applicant respectfully requests that the rejection be withdrawn.
With respect to claim 81, the Examiner states "It is unclear if each of (a)- (e) are required, or if only at least one of (a)- (e) is required for the limitations of the claim to be met" (See Office Action dated April 22, 2026, page 7). Applicant respectfully traverses the rejection and its supporting remarks. However, to facilitate prosecution, without prejudice or disclaimer, the Applicant has amended the claims as described herein. Specifically, the claims have been amended to remove the original options (a), (b), and (e), and the amendment clarifies that one or more of the relabeled (a) and/or (b) is required. Applicant contends that the claims as amended are clear and definite.
Applicant thus respectfully requests that the rejection be withdrawn.
Examiner’s Response:
Regarding the 112(b) issue in claim 1, the rejection is maintained because the referenced paragraph also states in the first sentence:
“[0014] In some embodiments of any of the methods provided herein, the ISG is present in a non- repetitive region 1 (NRR1) of the gluten polypeptide.”
Then further in paragraph 0014 the specification proceeds to state:
“In some embodiments, the ISG comprises the amino acid sequence ILQQILQQQLIPCRDVVLQQHNIAHGSSQVLQQSTYQLLQQLCCQQLWQIPEQSRCQAIHNVVHAIILHQQQQQ (SEQ ID NO: 28).”
Additionally, SEQ ID NO: 28 in Table 3 is titled “CONS-AGLD-NRR1”, which appears to stand for consensus alpha gliadin NRR1. Table 3 also describes SEQ ID NO: 7 as A/B GLIADIN A-I ISG (i.e. an ISG sequence) which is within SEQ ID NO: 28 from positions 25-72 with some variation, and SEQ ID NO: 29 is a smaller section within the ISG region defined by SEQ ID NO: 7, spanning positions 47-65 of SEQ ID NO: 28.
Based on the specification and a review of the sequences, SEQ ID NO: 28 appears to be an NRR1 sequence comprising an ISG sequence, and not an ISG sequence itself. Although the specification uses the language “the ISG comprises the amino acid sequence…. (SEQ ID NO: 28)” in the latter citation, it also says the ISG is present in a non- repetitive region 1 (NRR1) of the gluten polypeptide which appears to be consistent with the labeling and sequence of SEQ ID NO: 28. For this reason, Applicant’s argument is not persuasive and the 112(b) rejection is maintained.
Specifically regarding the 112(b) rejection made to claim 81, this rejection has been withdrawn in view of Applicant’s amendments.
Applicant argues beginning on p. 13 of remarks dated 07/22/2026 the
following arguments:
IV. Claim Rejections - 35 U.S.C. § 112(d)
Claims 12 and 18 are rejected under 35 U.S.C. 112(d) as allegedly being of improper dependent form for failing to further limit the subject matter on which they depend. Specifically, the Examiner states, "Claim 12 depends from claim 1 and requires the ISG comprises the amino acid sequence selected from the group consisting of SEQ ID NO: 28, SEQ ID NO: 29, and SEQ ID NO: 33. Unlike the other sequence identifiers, SEQ ID NO: 33 was not previously recited as an ISG sequence to be mutated/ altered in claim 1. By including SEQ ID NO: 33 in the group in claim 12, the scope of claim 12 is broadened rather than further limited, thus is of improper dependent form for failing to further limit the subject matter." Regarding claim 18, the Examiner states, "Similarly, claim 18 includes SEQ ID NO: 34 which is a mutated sequence of SEQ ID NO: 33 and is therefore rejected for the same reasons above" (See Office Action dated April 22, 2026, pages 7-8).
Applicant respectfully traverses the rejection and its supporting remarks. However, to facilitate prosecution, without prejudice or disclaimer, the Applicant has amended the claims as described herein. Specifically, the claims have been amended to remove SEQ ID NOs: 33 and 34 from claims 12 and 18, respectively. In view of these amendments, it is believed the Examiner's rejection is moot. Therefore, Applicant respectfully requests that the rejection be withdrawn.
Examiner’s Response:
In view of Applicant’s amendments, the 112(d) rejection has been withdrawn.
Applicant argues beginning on p. 14 of remarks dated 07/22/2026 the
following arguments:
V. Claim Rejections - 35 U.S.C. § 112(a)
Claims 1, 9, 12, 24, and 81 are rejected under 35 U.S.C. 112(a) for allegedly failing to comply with the written description requirement. Specifically, the Examiner states, "Aside from these 3 examples that mutations to a sequence 100% identical to SEQ ID NO: 29, thereby producing sequences 100% identical to instant SEQ ID NOs: 30-32, Applicant has not described any other example of any mutation that produces a modified gluten polypeptide that has reduced inflammatory potential" (See Office Action dated April 22, 2026, page 10).
Applicant respectfully traverses the rejection and its supporting remarks. Applicant respectfully contends that the application as filed, in combination with the ordinary knowledge and skill in the art, establishes a relationship between gliadin peptide structure and their ability to form nanocrystalline structures with DNA. Indeed, paragraph [0258] of the specification as filed states:
"Mutations were designed based on the physiochemical properties
necessary for the proper formation of the correct nanocrystalline
structures of peptide and dsDNA that can activate TLRs"
Paragraph [0267] of the specification as filed further states:
"single mutations could disrupt the immune activity of the original
consensus sequence gld-1, as shown in FIG. 3.
The altered immunogenicity of mutated gld-1 peptides from the wild-type gld- 1 peptide is caused by disruptions in the formation of ordered complexes between the wild-type gld-1 peptide fragment and nucleic acids (e.g., dsDNA), as a specific range of values for the inter-nucleic acid spacing is necessary for the identified immune activation. As a result, mutations that diminished the capacity for these organized complexes to assemble also decreased markers of immune activation. It was also demonstrated that reducing the positive charge of the CFGP, as well as affecting its steric bulk properties, could lead to an attenuation of CFGP-induced immune activity".
It would be clear to one of skill in the art that at least these sections of the specification convey that changing the structure of gliadin peptides affects the ability of gliadin peptides to form nanocrystalline structures with DNA. The specification as filed then proceeds to list mutations that can reduce the peptides' immunomodulation capabilities. The list provided by the Applicant is considerably more than three examples; the list following paragraph [0267] of the specification is a substantial summary of mutation approaches, each rooted in the structure- functional rationale identified by the Applicant as described above. One of skill in the art would recognize that this information clearly directs the production of specific types of mutations to produce a modified gluten polypeptide that has reduced inflammatory potential.
Further to this point, the Examiner notes, "Applicant describes these mutations to have reduced the dsDNA-peptide complex activity compared to the dsDNA-gld-a complex, and also elicited attenuated production of interleukin-8 in the presence of dsDNA as compared to gld-1" (See Office Action dated April 22, 2026, pages 9-10). Here the Examiner acknowledges that disrupting the binding of dsDNA is important to attenuation of the immune response. When combined with the list provided by the Applicant in paragraph [0267] of the specification as filed, this disclosure demonstrates that the Applicant was in possession of mutations defined by their effect on dsDNA-peptide complex formation, supported by a clear structure-function rationale and validated by representative examples from multiple categories of the disclosed mutation approaches.
With respect to claim 81 specifically, the Examiner states "Applicant has not described any example of (a), (b), or (e)" (See Office Action dated April 22, 2026, page 11). As described above, to facilitate prosecution, without prejudice or disclaimer, Applicant has amended claim 81 as described herein. Specifically, claim 81 has been amended to remove (a), (b), and (e) from the claim. As such, it is believed that the Examiner's rejection with respect to claim 81 should be moot.
Overall, Applicant contends that the specification as filed clearly establishes a structure- function relationship with respect to gliadin peptide structure and their ability to form nanocrystalline structures with DNA, provides clear guidance on how to disrupt that structure to produce peptides with reduced inflammatory potential, and verifies that guidance with concrete representative examples. This would be clear to one of skill in the art in conjunction with the ordinary knowledge and skill in the art. As such, one of skill would readily recognize that Applicant was in possession of that which is claimed at the time the application was filed. Applicant respectfully requests that the rejection be withdrawn.
Examiner’s Response:
A modified rejection under 112(a) has been made in view of Applicant’s amendments to claim 81. However, Applicant has not described any mutation to any region of SEQ ID NO: 28 except for the region spanned by SEQ ID NO: 29 and the few AA residues flanking the 5’ region of SEQ ID NO: 29. Applicant has not described any mutation to a sequence with as little as 85% sequence identity to SEQ ID NO: 7 either. Moreover, Applicant has not described the vast genus of mutations as claimed in claim 1 that can confer reduced inflammatory potential, as well as the specified traits in amended claim 81. While paragraph 0267 describes mutations that can be made, only a few mutations in a very small region of SEQ ID NO: 29 (which is within SEQ ID NO: 28) are actually reduced to practice. These few mutations in the small region in SEQ ID NO: 29 do not describe the full genus of any mutation(s) over a much larger sequence of SEQ ID NO: 28 or in SEQ ID NO: 7 which can have as little as 85% sequence identity that can confer reduced inflammatory potential by virtue of example. For this reason, the 112(a) rejection is maintained and Applicant’s arguments are not found persuasive.
Closest Prior Art
Claims 1, 9, 12, 18, 24, and 81 appear to be free of the prior art.
Regarding claims 1, 9, 12, 18, 24, and 81, the closest prior art is Jouanin (Jouanin, A., Schaart, J. G., Boyd, L. A., Cockram, J., Leigh, F. J., Bates, R., ... & Smulders, M. J. (2019). Outlook for coeliac disease patients: towards bread wheat with hypoimmunogenic gluten by gene editing of α-and γ-gliadin gene families. BMC plant biology, 19(1), 333.). Jouanin teaches using CRISPR/Cas9 to introduce mutations into α-gliadin protein sequences either upstream the coeliac disease (CD) epitopes or within the CD epitopes that are located in the repetitive domain of the polypeptide for the purpose of inducing in- or out- of frame mutations that produce gliadin-knockouts or non-immunogenic gliadins (p. 2, ¶3, Fig. 1). However, Jouanin does not teach, suggest, or otherwise render obvious introducing one or more alterations in: i. an amino acid sequence having at least 85% sequence identity to SEQ ID NO: 7, ii. SEQ ID NO: 28, or iii. SEQ ID NO: 29 to produce a gluten polypeptide with a reduced inflammatory potential. This is because the instant sequence identifiers appear to be located within the first non-repetitive domain (also termed nrr1, nr1, non-repetitive region 1, n-terminal non-repetitive domain, or unique domain 1) which is downstream the regions targeted by Jouanin, and Jouanin does not teach, suggest, or otherwise render obvious mutating the claimed sequences to reduce the inflammatory potential of the α-gliadin protein.
Conclusion and Inquiries
No claims are allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA N STOCKDALE whose telephone number is (703)756-5395. The examiner can normally be reached M-F 8:30-5:00 CT.
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JESSICA N. STOCKDALE
Examiner
Art Unit 1663
/JESSICA NICOLE STOCKDALE/ Examiner, Art Unit 1663
/CHARLES LOGSDON/ Primary Examiner, Art Unit 1662
