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 .
Election/Restrictions
The response the Restriction/Election requirement filed 12 February 2026 is acknowledged. Applicant elects, without traverse, Group I claims 122-134, drawn to a complex comprising a peptide, one or more linkers, and a segment comprising a human HLA class 1 heavy chain sequence wherein said class 1 heavy chain sequence comprises HLA-C and one or more mutations selected from a group. However, the Examiner notes that the instantly amended claims submitted in response to the Restriction/Election requirements are directed towards “wherein said human HLA class 1 heavy chain sequence comprises a synthetic HLA-E or fragment thereof” (emphasis is the Examiner’s). As such, it is unclear to what extent the election of the product of Group I reads on the instant claims except for claim 132, which recites the complex further comprising the HLA-C.
For clarity of the record, an updated restriction/election requirement appears below:
Restriction to one of the following inventions is required under 35 U.S.C. 121:
I. Claims 122-134, drawn to a complex comprising a segment comprising a peptide, one or more linkers, and a segment comprising a human HLA class 1 heavy chain sequence wherein said HLA class 1 heavy chain sequence comprises HLA-E or a fragment thereof, classified in C07K 14/70539.
II. Claims 135-137, drawn to an isolated cell encoding a nucleic acid molecule encoding the complex of claim 122, classified in C12N 5/0602, C12N 5/0647, or C12N 5/0661.
III. Claims 138-140, drawn to a method of generating an immune incompetent cell, comprising administering a nucleic acid molecule encoding the complex of claim 122, classified in C12N 15/62.
The inventions are independent or distinct, each from the other because:
Inventions I and II are directed to related compositions. The related inventions are distinct if: (1) the inventions as claimed are either not capable of use together or can have a materially different design, mode of operation, function, or effect; (2) the inventions do not overlap in scope, i.e., are mutually exclusive; and (3) the inventions as claimed are not obvious variants. See MPEP § 806.05(j). In the instant case, the inventions as claimed are distinct as a peptide composition and a cell comprising an encoding nucleic acid; and therefore the peptide and the cell comprising a nucleic acid have a materially different mode of operation, function, and effect. The peptide and the cell comprising the nucleic acid do not overlap in scope because peptides and cells comprising nucleic acids are distinct molecular structures with different compositions. Furthermore, the inventions as claimed do not encompass overlapping subject matter and there is nothing of record to show them to be obvious variants.
Inventions I and III are related as process of making and product made. The inventions are distinct if either or both of the following can be shown: (1) that the process as claimed can be used to make another and materially different product or (2) that the product as claimed can be made by another and materially different process (MPEP § 806.05(f)). In the instant case the claimed peptide can be made using in vitro translation; and further the method of administering the nucleic acid molecule could result in the production of an immunogenic human HLA peptide (e.g. administering the nucleic acid to a non-human species).
Inventions II and III are related as process of making and product made. The inventions are distinct if either or both of the following can be shown: (1) that the process as claimed can be used to make another and materially different product or (2) that the product as claimed can be made by another and materially different process (MPEP § 806.05(f)). In the instant case the claimed cell can be made by contacting the cell with the nucleic acid and performing electroporation; and further the method of administering the nucleic acid molecule could result in the production of an immunogenic cell comprising the nucleic acid (e.g. administering the nucleic acid to a non-human species).Restriction for examination purposes as indicated is proper because all the inventions listed in this action are independent or distinct for the reasons given above and there would be a serious search and/or examination burden if restriction were not required because one or more of the following reasons apply:
the species or groupings of patentably indistinct species have acquired a separate status in the art in view of their different classifications
the species or groupings of patentably indistinct species have acquired a separate status in the art due to their recognized divergent subject matter
the species or groupings of patentably indistinct species require a different field of search (e.g., searching different classes /subclasses or electronic resources, or employing different search strategies or search queries).
Applicant is advised that the reply to this requirement to be complete must include (i) an election of an invention to be examined even though the requirement may be traversed (37 CFR 1.143) and (ii) identification of the claims encompassing the elected invention.
The election of an invention may be made with or without traverse. To reserve a right to petition, the election must be made with traverse. If the reply does not distinctly and specifically point out supposed errors in the restriction requirement, the election shall be treated as an election without traverse. Traversal must be presented at the time of election in order to be considered timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are added after the election, applicant must indicate which of these claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
The examiner has required restriction between product or apparatus claims and process claims. Where applicant elects claims directed to the product/apparatus, and all product/apparatus claims are subsequently found allowable, withdrawn process claims that include all the limitations of the allowable product/apparatus claims should be considered for rejoinder. All claims directed to a nonelected process invention must include all the limitations of an allowable product/apparatus claim for that process invention to be rejoined.
In the event of rejoinder, the requirement for restriction between the product/apparatus claims and the rejoined process claims will be withdrawn, and the rejoined process claims will be fully examined for patentability in accordance with 37 CFR 1.104. Thus, to be allowable, the rejoined claims must meet all criteria for patentability including the requirements of 35 U.S.C. 101, 102, 103 and 112. Until all claims to the elected product/apparatus are found allowable, an otherwise proper restriction requirement between product/apparatus claims and process claims may be maintained. Withdrawn process claims that are not commensurate in scope with an allowable product/apparatus claim will not be rejoined. See MPEP § 821.04. Additionally, in order for rejoinder to occur, applicant is advised that the process claims should be amended during prosecution to require the limitations of the product/apparatus claims. Failure to do so may result in no rejoinder. Further, note that the prohibition against double patenting rejections of 35 U.S.C. 121 does not apply where the restriction requirement is withdrawn by the examiner before the patent issues. See MPEP § 804.01.
For the purposes of expedited prosecution, the Examiner will understand the election of Group I without traverse to read on the product as amended (a complex comprising a segment comprising a peptide, one or more linkers, and a segment comprising a human HLA class 1 heavy chain, wherein the HLA class 1 heavy chain comprises a synthetic HLA-E or a fragment thereof) because the previous restriction/election reads at least on dependent claim 132. Applicant is expected, in response to this Office Action, to make an election to the updated Restriction/Election requirement above to clarify the record.
Claims 135-140 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12 February 2026.
Regarding the election of species, Applicant elects, without traverse:
deletion of an amino acid at residue 226
the immune check point agonist CD47
a peptide sequence comprising nine amino acid residues, wherein said peptide comprises Y at the second position and L at the ninth position
Claim Status
Claims 122-140 are pending. Claims 135-140 are withdrawn as directed towards a nonelected invention, there being no allowable generic or linking claims, as described in the Restriction/Election above. Claims 122-134 are under the examination in the instant office action.
Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 124-126, 128-129, 132, and 134 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 124 is indefinite for the recitation of “wherein said peptide modulates a conformation of said human HLA class 1 heavy chain sequence”. The term “modulates” is a relative term which renders the claim indefinite. The term “modulates” is not defined by the claim, and the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear how or to what degree the peptide must “modulate” the conformation of said human HLA class 1 heavy chain sequence because no particular structure or sequence of the HLA class 1 heavy chain is required, or of the peptide, and therefore it is unclear if the modulation must of the interaction between a short peptide and the MHC binding groove or if it includes other modulations that may occur, even transiently, between two peptides that are physically linked together.
Claim 125 is indefinite for the recitation of “wherein said linker comprises a conformation configured to not block one or more killer cell immunoglobulin like receptor binding sites on said HLA class 1 heavy chain sequence”. The term “configured to not block” is not defined by the claim, and the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what the metes and bounds are of linkers that are configured to not block because it is uncertain what structures would be required for not blocking or blocking, or whether a method step of assessing blocking is required by the claim. Additionally, it is unclear if the metes bounds of the claim are met if the linker is not disclosed as blocking but binding does not occur.
Claim 126 is indefinite for the recitation of “wherein said human HLA class 1 heavy chain sequence is inhibited from eliciting a T-cell response when said complex is interrogated by one or more T cells”. The terms “is inhibited” and “is interrogated” are relative terms which render the claim indefinite. The term “inhibited” is not defined by the claim, and the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. The term “interrogated” is not defined by the claim, and the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. Each T cell has a different TCR and specificity and recognizes a different antigen, and nearly all peripheral T cells are selected to not recognize and activate to self-antigens. It is unclear if the T cell would be considered inhibited if the HLA class 1 heavy chain is wildtype but is presenting a self-antigen that is not recognized by the TCR. Additionally, it is unclear whether interrogation by a T cell simply means contact between a T-cell and the complex or whether there are additional requirements for a complex to be considered to be interrogated.
Claims 128 and 129 are indefinite for the recitation “wherein said complex further comprises one or more immune checkpoint agonists”, and wherein the immune checkpoint agonists comprise one or more checkpoint agonists selected from a list (e.g. elected species CD47). The metes and bounds of the claims are unclear because a person of ordinary skill in the art would understand the instant complex to refer to “an assembly of individual proteins” (Marsh, Joseph A., and Sarah A. Teichmann. "Structure, dynamics, assembly, and evolution of protein complexes." Annual review of biochemistry 84.1 (2015): 551-575; Abstract) and there is no evidence of record of CD47 associating in any physical manner with pMHC complexes in order to mediate the checkpoint agonist signaling; indeed, overexpression of CD47 has been shown to overcome NK-cell killing in MHC deficient cells, indicating that it acts outside of the same complex as a pMHC (Deuse, Tobias, et al. "Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients." Nature biotechnology 37.3 (2019): 252-258).
Claim 132 recites the complex of claim 122 further comprising a synthetic HLA-C or fragment thereof, wherein said human HLA-C comprises one or more mutations occurring at one or more of amino acid residues 115, 122, 128, 194,197,198, 212, 214, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 243, 245, 248, 262, or any combination thereof. The claim is indefinite because it is unclear what numbering is being used or what structure is required to identify the particular residue and whether or not there is a point mutation at the recited position. For example, regarding elected position 226, Salter, Russell D., et al. "A binding site for the T-cell co-receptor CD8 on the α3 domain of HLA-A2." Nature 345.6270 (1990): 41-46 teaches that a glutamine 226 to alanine in HLA-A2 disrupts CD8 binding to the HLA (Fig. 1b); however, this residue glutamine is at a different position in the HLA class I chain depending on which HLA class 1 sequence is referred to: in Uniprot P110321-1 “HLAC_HUMAN” this Q is at residue 250. The metes and bounds of the claim are unclear because an artisan would not be able to discern which amino acid changes constitute a mutation such as a mutation of elected species residue 226 as claimed.
Claim 132 is indefinite for the recitation of “wherein said complex further comprises a synthetic HLA-C or a fragment thereof”. It is unclear what a complex is contemplated to be because the “complex” is not defined in the specification and there are no examples in the art or the specification of a complex comprising both an HLA-E and an HLA-C heavy chain, where complex in considered to be a physical interaction as it is used in “protein complex” as in Marsh et. al., above. A person of skill in the art would not be reasonably comprised as to what types of complexes fall within the instant definition; it is uncertain how much must the different HLAs interact for the complex to be considered further comprising. Thus, the metes and the bounds of the claim are indefinite. For the purposes of expedited prosecution, the examiner will interpret “complex” to include non-physical interactions such as being comprised by the same cell as shown in Fig. 9 of the instant specification.
Dependent claims are rejected for failing to resolve the deficiency as described.
Claim Rejections - 35 USC § 112(a)- New Matter
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 132 and 134 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new matter rejection.
An embodiment of claim 132 is the complex of claim 122 further comprising a synthetic HLA-C or fragment thereof, wherein said human HLA-C comprises one or more mutations occurring at one or more of amino acid residues 115, 122, 128, 194,197,198, 212, 214, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 243, 245, 248, 262, or any combination thereof. Regarding the interpretation of complex, the instant specification does not have a special definition of complex. A person of ordinary skill in the art would understand the instant complex to refer to “an assembly of individual proteins” (Marsh, Joseph A., and Sarah A. Teichmann. "Structure, dynamics, assembly, and evolution of protein complexes." Annual review of biochemistry 84.1 (2015): 551-575; Abstract), which would mean that an HLA-E and HLA-C would have to physically interact or assemble in some way to meet the limitations of the claim; or the claim would require the HLA-E or fragment thereof and the HLA-C or fragment thereof to be fused such that they are part of the same polypeptide complex. Description of a complex comprising both HLA-E and HLA-C or fragments thereof is not found in the specification in such a way as to reasonably convey to one skilled in the art that the inventors, at the time the invention was filed, had possession of the claimed invention. Paragraph 6 describes “The complex of any one of claims 2 to 10, wherein the human HLA class 1 heavy chain sequence comprises HLA-A, HLA-B, HLA-C, or any combination thereof. In some embodiments, the human HLA class 1 heavy chain sequence comprise multiple versions of HLA-A, HLA-B, HLA-C or any combination thereof. In some embodiments, the human HLA classs 1 heavy chain sequence comprises the HLA-A, wherein the HLA-A is displaced between the HLA-B and the HLA-C”. The specification further states “In some embodiments, the human HLA class 1 heavy chain sequence comprises HLA-E or a fragment thereof, HLA-F or a fragment thereof, HLA-G or a fragment thereof, or any combination” [0064]. There is no recitation that indicates the complex comprising HLA-E complexed with another HLA.
Regarding claim 134, claim 134 is rejected for the dependency on claim 132 while failing to resolve the new matter issue as described.
Claim Rejections - 35 USC § 112(a)- Written Description
Claims 122-134 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.
Scope of the claimed genus
Instant claim 122 is directed at a complex comprising any HLA-E or a fragment thereof, any segment comprising a peptide, any one or more linkers. The examiner notes that there is no definition of fragment in the instant specification, and therefore the broadest reasonable interpretation of ‘fragment’ is that is can be any amino acid of HLA-E. The peptide may be any peptide, and the one or more linkers need not be covalent or peptide linkers.
Regarding claims 123-126, the claims recite functional limitations that do not have a clear link to the structure that performs the function. For example, claim 126 recites the complex of claim 122 wherein said human class 1 heavy chain sequence is inhibited form eliciting a T-cell response when said complex is interrogated by one or more T cells. This encompasses any HLA-E or fragment thereof wherein the heavy chain sequence is inhibited, with any structure, for any reason, or in any way from eliciting a T-cell response when interrogated by one or more T cells.
Claim 127 teaches wherein the peptide is coupled to said complex by a disulfide bond, but does not limit the peptide or where on the complex the undefine peptide should be coupled with a disulfide bond.
Claims 128 and 129 teach wherein the complex further comprises one or more immune checkpoint agonists (e.g. CD47).
Claim 130 teaches wherein a linker is disposed between the peptide and a human B2-microglobulin sequence, between a human B2-microglobulin sequence and said human HLA class 1 heavy chain, or both.
Claim 131 teaches wherein a linker is at least about 90% identical to any one of SEQ ID NOs: 48-54.
Claim 132 is directed wherein the complex further comprises HLA-C or any fragment thereof. As described in the 112(b) and 112(a) new matter rejections above, it is unclear what the complex further comprising HLA-C means for how HLA-E and HLA-C or the fragments thereof must interact in order to be within the scope of the complex. Further, the HLA-C or any fragment thereof, as described for HLA-E above, does not have a definition in the specification and therefore would include any length fragment. HLA class I heavy chains have very high percent identity to one another, and almost any HLA class I heavy chain would naturally comprise a fragment of another. For example, the HLA-E and HLA-C heavy chains are shown aligned below:
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 1438.5 74.8 366 1 AASEQ2_04102026_194233
ALIGNMENTS
RESULT 1
AASEQ2_04102026_194233
Query Match 74.8%; Score 1438.5; DB 1; Length 366;
Best Local Similarity 76.3%;
Matches 271; Conservative 32; Mismatches 51; Indels 1; Gaps 1;
Qy 1 MVDGTLLLLLSEALALTQTWAGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDND 60
| |||||| ||||:||| |||::|| |:||||||||||||||||||||||||||:|
Db 4 MAPRALLLLLSGGLALTETWACSHSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSD 63
Qy 61 AASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMH 120
||||| |||||:|||| |||||||: : || ||:|| ||||||||| |||||| |
Db 64 AASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQADRVSLRNLRGYYNQSEDGSHTLQRMS 123
Qy 121 GCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAY 180
||:|||||| ||||:| |||||||: |||||||||| ||||||:::| | || |||
Db 124 GCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAY 183
Qy 181 LEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQ 240
|| |||||| :||| ||||| |||||||||||:||||||||||||||||||||||||:
Db 184 LEGTCVEWLRRYLENGKETLQRAEPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQR 243
Qy 241 DGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKPASQ 300
||| ||||||||||||||||||||||||||||:|||||||:||||| ||:|| |:|:||
Db 244 DGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSSQ 303
Qy 301 PTIPIVGIIAGL-VLLGSVVSGAVVAAVIWRKKSSGGKGGSYSKAEWSDSAQGSE 354
|||||:||:||| ||: | |||| |:: |:||||||||| |:| |:|||||:
Db 304 PTIPIMGIVAGLAVLVVLAVLGAVVTAMMCRRKSSGGKGGSCSQAACSNSAQGSD 358
Claims 133-134 are directed towards mutations in HLA-E or fragment thereof, and specific lengths and amino acid residues in the peptide comprising nine amino acids. These claims are ultimately dependent on claims 122 and 132 above and do not sufficiently limit the structure in which mutations occur for the HLA class I or the backbone of the peptide comprising amino acid residues at the selected positions. For example, the “comprising” language in claim 134 limits the peptide to any peptide nine amino acids or longer, but does not require any particular function of the peptide or place an upper limit on the length; therefore, the scope of the claims includes peptides that are not directed towards the function of the invention described in the specification, which is a linked short peptide that binds the MHC groove.
State of the Relevant Art
Synthetic HLA class I heavy chains are known in the art for multiple purposes, including both HLA-E and HLA-C containing pMHC complexes comprising peptides and linkers. For example, Gornalusse, Germán G., et al. "HLA-E-expressing pluripotent stem cells escape allogeneic responses and lysis by NK cells." Nature biotechnology 35.8 (2017): 765-772 (Of record, IDS dated 4/17/2025) teaches constructs comprising either an HLA-E single chain dimer (the heavy chain fused to B2M through a flexible GS linker), such that it can bind a normal repertoire of peptides for antigen presentation, or an HLA-E single chain trimer consisting of the heavy chain fused to a peptide derived from the signal sequence of HLA-G by a GS linker, which is a non-polymorphic peptide that inhibits NK-cell dependent lysis (p. 1 right column ¶3). Regarding HLA-C single-chain trimers, U.S. 20080219947 to Linette et. al. (Of record, IDS dated 4/17/2025) teaches single chain trimer molecules comprising an MHC antigen peptide sequence, a B2-microglobulin sequence, and a full-length MHC class I heavy chain sequence joined by linker sequences (Abstract) wherein the MHC class I heavy chain may be HLA-C [0137]. Methods of modulating the response to T cells using the single chain trimers (complexes comprising peptides, linkers, and MHC heavy chains) are also known in the art; WO 98/03552 to Hirsch et. al. (Of record, cited in IDS dated 4/17/2025) teaches methods for modulating T cell functions including suppressing T cell function in autoimmunity and transplant rejection using single-chain timers (p. 1 lines 33-30; p. 2 line 10; p. 3 lines 22-26). However, there are no fragments of the MHC class 1 heavy chains of record, especially not small fragments. Additionally, there are no complexes of record (defined as a protein-protein complex requiring the components to physically react) comprising both HLA-E and HLA-C MHC heavy chains as claimed.
Regarding the complex comprising any peptides, there are specific motifs that are known for MHC binding in the art, but the MHC-presented peptides can be difficult to predict. Although not prior art, Perez, Marta AS, et al. "Structural prediction of peptide–MHC binding modes." Computational Peptide Science: Methods and Protocols (2022): 245-282 teaches “Although intensively studied for decades, ligand-protein docking remains largely an unsolved problem [80,81,82,83] […] The knowledge of the nature of interactions between a peptide and an MHC protein (see section “The structure of the pMHC complex”), notably for MHC class I, can be used to facilitate the docking of peptides, despite the fact that their number of degrees of freedom makes them intractable by standard docking approaches”. Perez et. al. further teaches “The predictive ability of standard small molecule/protein ligand software drops if the number of internal degrees of freedom (DoF) of the ligand is larger than 10. However, the number of DoF of 8 to 11-mer peptides largely surpasses this limit, making standard docking software inadequate for the peptide-MHC system” (Section 4.4 Incremental Peptide Reconstruction ¶1). Perez et. al. teaches that although some predictive approaches have a “satisfactory” predictive ability in re-docking, there is room for improvement and the number of complexes tested remains small compared to the genus of MHC allotypes and peptide sequences.
Summary of Species disclosed in the original specification
Regarding HLA complexes, the instant specification teaches 44 specific sequences of either single chain dimers and trimers, or synthetic HLAs (Table A p. 16). SEQ ID NOs: 1-6 are single chain trimers comprising two different HLA-binding peptides (GILGFVFTL and SYRPGTVAL), beta-2 microglobulin, and 3 different alleles (one for SEQ ID NOs: 5 and 6; one for SEQ ID NOs: 1, 3, and 4; and one for SEQ ID NO: 2) of HLA-C as shown below:
CLUSTAL O(1.2.4) multiple sequence alignment
EMBOSS_002 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_001 HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDG 60
EMBOSS_003 HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDG 60
****** *:************:****************** * ******:*********
EMBOSS_002 ETQKYKRQAQADRVSLRNLRGYYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_001 ETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKD 120
EMBOSS_003 ETRKVKAHSQTHRVDLGTLRGYYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKD 120
**:* * ::*:.**.* .********* ****:*** ***:* * *:****.* ******
EMBOSS_002 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_001 YIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRT 180
EMBOSS_003 YIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRT 180
****:********** *** *::* ***:.*****************************:
EMBOSS_002 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_001 DAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_003 DAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
: ****:*** :************.***********************************
EMBOSS_002 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH------------ 288
EMBOSS_001 KWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEENLYFQGHHHHHH-------------- 286
EMBOSS_003 KWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEPSSQPTIPIVGIIAGLVLFGAVITGAV 300
******************:***** :**** ** .
EMBOSS_002 --------------------------------------- 288
EMBOSS_001 --------------------------------------- 286
EMBOSS_003 VAAVMWRRKSSDRKGGSYSQAASSDSAQGSDVSLTACKV 339
SEQ ID NO: 7 is a single chain dimer comprising a beta-2 microglobulin and the same HLA-C heavy chain as SEQ ID NO: 2. SEQ ID NOs: 8-13 comprise a the same 9 amino acid peptide linked to B2M. SEQ ID NOs: 14-41 are different synthetic HLAs comprising a peptide “GILGFVFTL” “SYRPGTVAL” or “RYRPGTVAL” linked to a synthetic HLA sequence, alignment shown below:
CLUSTAL O(1.2.4) multiple sequence alignment
EMBOSS_001 HSMRYFFTSVSRPGRGEPRFIAVGYVDDTQFVRFDSDAASQRMEPRAPWIEQEGPEYWDG 60
EMBOSS_002 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_003 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_004 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_005 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_006 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_007 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_008 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_009 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_010 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_011 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_014 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_017 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_020 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_023 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_026 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_027 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_029 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_012 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_015 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_018 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_021 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_024 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_025 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_013 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_016 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_019 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_022 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
EMBOSS_028 HSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSDAASPRGEPRAPWVEQEGPEYWDR 60
****** *:************:****************** * ******:*********
EMBOSS_001 ETRKVKAHSQTHRVDLGTLRGAYNQSEAGSHTVQRMYGCDVGSDWRFLRGYHQYAYDGKD 120
EMBOSS_002 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_003 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_004 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_005 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_006 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_007 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_008 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_009 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_010 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_011 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_014 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_017 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_020 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_023 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_026 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_027 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_029 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_012 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_015 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_018 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_021 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_024 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_025 ETQKYKRQAQADRVSLRNLRGAYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_013 ETQKYKRQAQADRVSLRNLRGCYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_016 ETQKYKRQAQADRVSLRNLRGCYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_019 ETQKYKRQAQADRVSLRNLRGCYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_022 ETQKYKRQAQADRVSLRNLRGCYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
EMBOSS_028 ETQKYKRQAQADRVSLRNLRGCYNQSEDGSHTLQRMSGCDLGPDGRLLRGYDQSAYDGKD 120
**:* * ::*:.**.* .***.***** ****:*** ***:* * *:****.* ******
EMBOSS_001 YIALKEDLRSWTAADMAAQTTKHKWEAAHVAEQLRAYLEGTCVEWLRRYLENGKETLQRT 180
EMBOSS_002 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_003 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_004 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_005 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_006 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_007 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_008 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_009 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_010 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_011 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_014 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_017 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_020 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_023 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_026 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_027 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_029 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_012 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_015 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_018 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_021 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_024 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_025 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_013 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_016 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_019 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_022 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
EMBOSS_028 YIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAYLEGTCVEWLRRYLENGKETLQRA 180
****:********** *** *::* ***:.*****************************:
EMBOSS_001 DAPKTHMTHHAVSDHEATLRCWALSFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_002 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_003 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_004 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_005 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_006 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_007 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_008 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_009 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_010 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_011 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_014 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_017 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_020 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_023 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_026 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_027 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_029 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTQDTELVETRPAGDGTFQ 240
EMBOSS_012 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_015 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_018 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_021 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_024 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_025 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_013 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_016 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_019 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_022 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
EMBOSS_028 EPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQRDGEDQTAKTELVETRPAGDGTFQ 240
: ****:*** :************.****************** .***************
EMBOSS_001 KWAAVVVPSGQEQRYTCHVQHEGLPKPLTLRWEENLYFQGHHHHHH-- 286
EMBOSS_002 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_003 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_004 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_005 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_006 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_007 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_008 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_009 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_010 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_011 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_014 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_017 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_020 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_023 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_026 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_027 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_029 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_012 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_015 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_018 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_021 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_024 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_025 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_013 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_016 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_019 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_022 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
EMBOSS_028 KWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSENLYFQGHHHHHH 288
******************:***** :**** ** . : : ****
Most of these HLAs appear to be HLA-C, though they are not clearly labeled and there is high identity between the HLA class I heavy chains so it is uncertain; SEQ ID NO: 14 is identified as HLA-A. There does not appear to be any sequences encompassing the elected species of mutation, a deletion at position 226; the only mutation at position 226 appears to be a Q>A substitution. There are no species of HLA-E whatsoever, or any working examples of fragments of any HLA class I heavy chain.
The specific examples focus on HLA proteins SYNC4-1 (SEQ ID NO: 18), SYNA1-1 (SEQ ID NO: 14), SYNC5-1 (SEQ ID NO: 19), SYNC6-1 (SEQ ID NO: 20), SCTC1-1 (SEQ ID NO: 4) (Example 9 starting on p. 95). Regarding disulfide bonds, the specification prophetically recites “The cysteine present in the HLA-C07 domain as described in Example 9 is mutated to another amino acid, potentially reducing or ablating the possibility or mis-paired disulfides forming and thus improving protein expression. Other mutations may be introduced to improve expression and/or refolding as measured by techniques described herein” (Example 10, [0264]). The specification teaches there is a physical interaction between SYNC4-1 and KIR2DL2 based on melting curves [0266-0269]. The specification prophetically recites investigating the ability of soluble synthetic HLA proteins to evade the immune systems and states “When compared to controls, soluble HLA proteins harboring specific mutations are less reactive with the receptors on immune cells, resulting in increased killing of the wild type mammalian cells”. There is no guidance about which mutations have which functions, or about any other particular peptides or HLA complexes.
Are the species representative of a genus?
MPEP § 2163 states that a “representative number of species” means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus.
Applicant describes 42 complexes or portions of complexes comprising a peptide, linkers, and an HLA class I heavy chain; as described above, there are no fragments of the class I heavy chains. Only 3 peptides, all of which consist of 9 amino acids, are described. Some of them vary only in the presence or absence of a signal peptide. There is only one example of a mutation at position 226. There are no examples of a complex comprising more than one HLA heavy chain or fragment thereof. There are no examples of the complex comprising additional checkpoint agonists. There is no functional data or species of complex meeting the functional limitations of claims 124-126, for example which species do not elicit a T-cell response.
Identifying characteristics and structure/function correlation
In the absence of a representative number of species, the written description requirement for a claimed genus may be satisfied 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 claimed genus. To meet this requirement in the instant case, the specification must describe structural features that the skilled artisan as of the effective filing date would have expected to convey the claimed binding activity.
The instant specification does not give guidance about the structure/function correlation between the undefined peptide, the linkers, and the HLA class I heavy chain or fragment thereof. There are no teachings about the requirements of the fragment. There are no teachings about which linkers function in which manner, or what length is preferred for each linker. The specification teaches a structure/function relationship between anchor residues of the peptide and particular HLA class I alleles (Example 1), but those limitations are not required by the majority of the claims because the independent claim does not require the peptide to have an MHC-binding ability or function. Additionally, there are no teachings about the structure/function relationship with HLA-E peptide anchor residues. As described in the art section above, it would not have been predictable a priori which peptides of any sequence and length would interact with HLA-E except for those with known experimental data as taught in the art. Further, because it is not clear what applicant means by complex, the structure/function relationship between the different polypeptides claimed and their functional relationships is uncertain, and there are no teachings or guidance on what these complexes further comprising additional pMHCs or checkpoint agonists would look like.
Summary
A genus of species is not present in the instant specification or prior art that would demonstrate a structure/activity relationship would be for the complex comprising any HLA class I heavy chain comprising HLA-E or a fragment thereof and comprising any generic peptide and linker. There is a lack of an appropriate number of species with identical or alternative amino acids in the HLA-E heavy chain, the peptide, and the linkers to determine which residues are essential for function of the invention to comprise a fragment, or to meet the structural and functional limitations of the dependent claims. One of skill in the art would reasonably conclude that the applicant was not in possession of the genus of substitutions and deletions of the polypeptide of claim 122 at the time of filing. Regarding claims 123-134 the claims are ultimately dependent on the rejected claim 122 without narrowing the claimed subject matter and thus are also rejected.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 122-125, and 130-131 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by WO2012145384 to Russell et. al. published 26 October 2012 as evidenced by Yanaka, Saeko, et al. "Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex." Journal of Biological Chemistry 289.35 (2014): 24680-24690; Spahr, Chris, et al. "High-resolution mass spectrometry confirms the presence of a hydroxyproline (Hyp) post-translational modification in the GGGGP linker of an Fc-fusion protein." MAbs. Vol. 9. No. 5. Taylor & Francis, 2017.
Regarding claim 122, Russell et. al. teaches a single chain fusion of an HLA class I protein wherein the peptide antigen is covalently linked with a G4S linker to the single chain fusion HLA class I protein “trimeric construct” comprising an HLA class 1 heavy chain, HLA-E and beta-2 microglobulin (B2M) ([0048], Fig. 3B).
Regarding claim 123, the peptide is designed to occupy the binding cleft of the single chain fusion HLA class I protein (reads on coupled to one or more HLA binding groove).
Regarding claim 124, Russell et. al. teaches that the peptide is designed to occupy the binding cleft; as evidenced by Yanaka et. al., peptides that occupy the binding cleft cause the HLA to go through a conformational fluctuation that increases thermostability and results in them being more tightly packed towards the peptide (Abstract, Fig. 8, Fig. 9, Fig. 11): “In solution, pHLAs predominantly form a bound peptide-independent conformation that would be similar to the crystal structure except that they form a peptide-dependent dehydrated minor conformation at the peptide binding domain” (p. 24687 right column-24688-left column, emphasis is the Examiner’s).
Regarding claim 125, Russell et. al. is silent as to whether the G4S linker is protease resistant. As evidenced by Spahr et al.: “Flexible and protease resistant (G4S)n linkers are used extensively in protein engineering to connect various protein domains” (Abstract); therefore, the G4S linker in Fig. 3B reads on “linker configured to resist proteolytic cleavage”. Regarding “linker comprises a conformation configured to not block one or more killer cell immunoglobulin like receptor binding sites on said human HLA class 1 heavy chain sequence”, Russell discloses that due to expression of the HLA-E single chain trimer “the cells are able to escape NK cell-mediated killing and elicit minimal or no immune response in the recipient after transplantation” (See [00053-00054], [00057], [00094]). This reads on configured not to block the killer cell Ig-like receptor binding sites because an artisan would understand that if the binding sites were blocked an NK cell would activate the ‘missing self’ signal as described by Russell and it would fail to suppress the NK cell killing.
Regarding claim 130, Russell et. al. teaches a linker is disposed between both the peptide and a B2M sequence and a B2M sequence and the HLA class I heavy chain sequence (See Fig. 3B).
Regarding claim 131, Russel et. al. teaches a linker (G4S)3 (Fig. 3B) which is 100% identical to SEQ ID NO: 48.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 127 and 133 are rejected under 35 U.S.C. 103 as being unpatentable over WO2012145384 to Russell et. al published 26 October 2012 as applied to claim 122 above, and further in view of Truscott, Steven M., et al. "Human major histocompatibility complex (MHC) class I molecules with disulfide traps secure disease-related antigenic peptides and exclude competitor peptides." Journal of Biological Chemistry 283.12 (2008): 7480-7490.
The teachings of Russell et. al. in regards to claim 122 are in the 102 rejection above.
Russell et. al. does not teach the complex wherein said peptide is coupled to said complex by a disulfide bond.
This deficiency is resolved by Truscott et. al.
Truscott et. al. teaches single-chain HLA trimeric complexes and methods of engineering coupling of the MHC-displayed peptide to the MHC by engineering a disulfide bond to trap peptide into the binding groove of MHC class I molecules expressed as a single-chain trimers (SCTs) (Abstract, Fig. 1A). Truscott et. al. teaches that the HLA-I SCTs with disulfide-bond trapped peptides prevented dissociation of the linker-attached peptides and lowered the amount of SCT molecules with an open peptide binding groove (Fig. 5). Truscott et. al. teaches “It is important to note that incorporation of the disulfide trap into the SCT appears to further increase the kinetics of assembly and folding, likely reflecting the improved C-terminal peptide anchoring” (Discussion ¶5); “Each of these novel applications and many other likely ones, require SCTs to be stably expressed and highly resistant to exogenous peptide binding. Thus for all future SCT applications incorporation of disulfide traps should be a consideration” (Discussion ¶7).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to design a disulfide-trap version of the SCT HLA-E peptide of Russel et. al. by introducing cysteine mutations into the HLA class I heavy chain and the C-terminus of the peptide linker of the peptide as taught by Truscott et. al. in order to benefit from the increased stability and stable expression resistant to exogenous peptide binding as taught by Truscott et. al. This would result in a complex comprising an HLA-E heavy chain with cysteine mutation at position 84 of the HLA class I compared to the endogenous HLA-E peptide. This would have a reasonable expectation of success because Truscott et. al. teaches a method that allows for disulfide-trapping across multiple peptides and HLA alleles, and an artisan would be able to design the disulfide trap given the particular peptide and SCT.
Claims 126 and 132 are rejected under 35 U.S.C. 103 as being unpatentable over WO2012145384 to Russell et. al published 26 October 2012 as applied to claim 122 above, and further in view of WO 02077030 to Jakobsen et. al. published 3 October 2002 (Of record, IDS dated 4/17/2025).
The teachings of Russell et. al. in regards to claim 122 are in the 102 rejection above.
Claim interpretation: As described in the 112(b) and 112(a) rejections above, the scope of the claims is indefinite and the entire scope of the claims has not been described by the application. It is unclear and not described what interactions would constitute the HLA-C or fragment thereof or the checkpoint agonist being “further comprised” by the complex if it is not a physical interaction as defined for protein complexes in the art, described above. Additionally, as described in the written description rejection above, applicant does not demonstrate possession of any polypeptide comprising any fragment of the HLA-E and HLA-C heavy chains. For the purposes of expedited prosecution, the Examiner notes that, as HLA class I heavy chains have very high percent identity to one another, almost any HLA class I heavy chain would naturally comprise a fragment of another. For example, the HLA-E and HLA-C heavy chains are shown aligned below:
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 1438.5 74.8 366 1 AASEQ2_04102026_194233
ALIGNMENTS
RESULT 1
AASEQ2_04102026_194233
Query Match 74.8%; Score 1438.5; DB 1; Length 366;
Best Local Similarity 76.3%;
Matches 271; Conservative 32; Mismatches 51; Indels 1; Gaps 1;
Qy 1 MVDGTLLLLLSEALALTQTWAGSHSLKYFHTSVSRPGRGEPRFISVGYVDDTQFVRFDND 60
| |||||| ||||:||| |||::|| |:||||||||||||||||||||||||||:|
Db 4 MAPRALLLLLSGGLALTETWACSHSMRYFDTAVSRPGRGEPRFISVGYVDDTQFVRFDSD 63
Qy 61 AASPRMVPRAPWMEQEGSEYWDRETRSARDTAQIFRVNLRTLRGYYNQSEAGSHTLQWMH 120
||||| |||||:|||| |||||||: : || ||:|| ||||||||| |||||| |
Db 64 AASPRGEPRAPWVEQEGPEYWDRETQKYKRQAQADRVSLRNLRGYYNQSEDGSHTLQRMS 123
Qy 121 GCELGPDGRFLRGYEQFAYDGKDYLTLNEDLRSWTAVDTAAQISEQKSNDASEAEHQRAY 180
||:|||||| ||||:| |||||||: |||||||||| ||||||:::| | || |||
Db 124 GCDLGPDGRLLRGYDQSAYDGKDYIALNEDLRSWTAADTAAQITQRKLEAARAAEQLRAY 183
Qy 181 LEDTCVEWLHKYLEKGKETLLHLEPPKTHVTHHPISDHEATLRCWALGFYPAEITLTWQQ 240
|| |||||| :||| ||||| |||||||||||:||||||||||||||||||||||||:
Db 184 LEGTCVEWLRRYLENGKETLQRAEPPKTHVTHHPLSDHEATLRCWALGFYPAEITLTWQR 243
Qy 241 DGEGHTQDTELVETRPAGDGTFQKWAAVVVPSGEEQRYTCHVQHEGLPEPVTLRWKPASQ 300
||| ||||||||||||||||||||||||||||:|||||||:||||| ||:|| |:|:||
Db 244 DGEDQTQDTELVETRPAGDGTFQKWAAVVVPSGQEQRYTCHMQHEGLQEPLTLSWEPSSQ 303
Qy 301 PTIPIVGIIAGL-VLLGSVVSGAVVAAVIWRKKSSGGKGGSYSKAEWSDSAQGSE 354
|||||:||:||| ||: | |||| |:: |:||||||||| |:| |:|||||:
Db 304 PTIPIMGIVAGLAVLVVLAVLGAVVTAMMCRRKSSGGKGGSCSQAACSNSAQGSD 358
Further, for the purposes of expedited prosecution, as described in the 112(b) rejection above, because it cannot be discerned what the Applicant means by complex, the Examiner will interpret the definition of “complex” to include a cell comprising the components as shown in Fig. 9 of the application.
In regards to claims 126 and 132, Russell et. al. further teaches that the chain is selected from the group consisting of HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, and HLA-G [00054]. Russell et. al. teaches “Any immune effects of the single chain fusion HLA class I protein expressing B2M-I- cells can be studied by various means. For example, B2M-I- cells expressing a SC fusion HLA class I protein can be differentiated into antigen-presenting dendritic cells (iDCs). Suppression of NK cell-mediated lysis can be measured by chromium release assays after incubating iDCs with normal human NK cells and NKL cell lines. A variety of controls (untransduced B2M-/- iDCs, B2M+/+ iDCs, the 721.221 class I-negative cell line, and anti-receptor and anti-HLA antibodies) can be used to establish the specificity of the interactions. Additional characterization can be done with Elispot assays by incubating the cells with T cells” [00053]; “In certain embodiments, the differentiated cell further expresses a single chain fusion HLA class I protein. In general, each cell type can be analyzed for HLA class I protein expression, reactivity with human T cells and NK cells, appropriate differentiation markers, and xenotransplantation in immunodeficient mice to examine in vivo developmental potential” [00069]; “Thus, B2M-I- cells or B2M-I- cells expressing a single chain fusion HLA class I protein presenting a predetermined peptide antigen provide additional advantages in that they do not present these auto-antigens and can avoid autoimmune rejection and prevent a relapse of diabetes after transplantation” [00076]. Russell et. al. further teaches that the cells can be engineered to comprise more than one single chain fusion HLA protein ([00034], [00054], [00057]).
Russell et. al. does not explicitly teach the complex wherein said human HLA class 1 heavy chain sequence is inhibited from eliciting a T-cell response when said complex is interrogated by one or more T cells (claim 126). Russell et. al. does not teach the complex of claim 122 wherein said complex further comprises a synthetic HLA-C or fragment thereof, wherein said human HLA-C comprises one or more mutations occurring at one or more amino acid residues including elected species position 226 compared to an endogenous HLA of the same type.
This deficiency is resolved by Jakobsen et. al. Jakobsen et. al. teaches a complex comprising a B2M linked to a peptide and an HLA class I heavy chain used to inhibit the activity of T cells against a cell presenting MHC molecules of the selected MHC type, the method comprising causing the cell to present modified molecules of the selected MHC type whose binding to CD8 or CD4 is inhibited (Abstract); “The inhibition of CD8 or CD4 binding to Class I HLA or Class II HLA molecules respectively may be achieved by providing mutant Class I HLA or Class II HLA molecules in which substitution, deletion and/or insertion mutations cause the binding of CD8 or CD4 respectively to be inhibited” (p. 12 lines 21-25); “For example, in Salter et al (Nature 345: 41-46, 1990), 48 separate single point substitution mutants of the ɑ1, ɑ2 & ɑ3 domains of HLA-A2.1 were produced […] three clusters of amino acids in the ɑ3 domain of HLA-A2 were identified that were particularly important for CD8 binding. Cluster I is amino acids 221-223, 227, 229, & 232 […]” (p. 14 lines 23-29). Jakobsen et. al. teaches the mutation 226Q>A that prevents CD8 binding (Table 1).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to 1) co-express single chain HLA-E and HLA-C in the same cell to benefit from reduced rejection by expressing one or more single chain HLAs as taught by Russell et. al. and 2) to introduce the mutation Q>A at position 226 as taught by Jakobsen et. al. into the HLA-C allele in order to make a non-T cell reactive HLA as taught by Jakobsen et. al. useful in the transplant cell of Russell et. al. This would have a reasonable expectation of success because HLA class Is are highly conserved in the CD8 binding region and a person of ordinary skill in the art would be able to modify the cell to express the desired subclasses of HLA most helpful for avoiding tumor rejection based on the donor and recipient cells.
Claim 134 is rejected under 35 U.S.C. 103 as being unpatentable over WO2012145384 to Russell et. al published 26 October 2012 in view of WO 02077030 to Jakobsen et. al. published 3 October 2002 (Of record, IDS 4/17/2025) as applied to claim 132 above, and in further view of Walters, Lucy C., et. al. "Detailed and atypical HLA‐E peptide binding motifs revealed by a novel peptide exchange binding assay." European journal of immunology 50.12 (2020): 2075-2091 published 27 July 2020.
The teachings of Russell et. al. and Jakobsen et. al. in regards to claim 132 are in the 103 rejection above. Russell et. al. in view of Jakobsen et. al. does not teach wherein the peptide comprises an amino acid comprising nine amino acid residues, in N-terminus to C-terminus an amino acid residue elected species Y at a second position and an amino acid residue elected species L at a ninth position of said amino acid sequence.
This deficiency is resolved by Walters et. al.
Walters et. al. teaches that HLA-E preferably accommodates a signal peptide comprising residues 3-11 of MHC class Ia leader sequences (p. 2075 ¶1). Walters et. al. teaches that non-VL9 sequence-diverse peptides that bind HLA-E have been identified in diverse immunological settings including self-derived peptides from proteins in the context of defective antigen processing, cellular stress, or autoimmune disease (p. 2076 left column, ¶1). Walters et. al. teaches that the canonical HLA-E binding sequence is 9 residues. Walters et. al. teaches a UV peptide exchange ELISA-based assay for identifying HLA-E binding peptides (Fig. 1). Walters et. al. teaches: “To further probe the tolerability of the primary anchor B and F pockets of the HLA-E binding groove, we synthesized VL9- and Mtb44-based peptide variants and screened these primary anchor mutant peptides in the peptide exchange ELISA assay (Fig. 7). A number of Mtb44 and VL9 variant peptides supported HLA-E binding despite the presence of non-canonical primary anchor residues such as a Thr, Ile, Gln, Tyr, Trp, Phe, or positively charged Lys at position 2 of VL9. Notably, the hierarchy of relative binding of position 2 anchor residue mutations differed on the Mtb44 and VL9 peptide panel backgrounds, indicating other positions along these nonamers operate synergistically with position 2 substitutions to determine overall peptide binding affinity” (p. 2086 right column, emphasis is the Examiner’s). Walters et. al. teaches that Leu at position 9 is the canonical HLA-E binding motif (p. 2079 left column ¶1).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to design an HLA-E binding peptide using known HLA-E anchor residue canonical Leu at position 9 and non-canonical Tyr at position 2 in order to benefit from high-affinity HLA-E binding peptide to make a single chain trimer as taught by Russell et. al. in view of Jakobsen et. al. with a peptide that binds in the binding groove of HLA-E as taught by Walters. This would have a reasonable expectation of success because Walters et. al. teaches motifs and particular sequences comprising these residues that bind to HLA-E and Russell et. al. teaches the HLA-E single chain trimer comprising an HLA-E binding peptide.
Claims 122 and 128-129 are rejected under 35 U.S.C. 103 as being unpatentable over WO 2021072302 to Johannesson et. al. effectively filed 10 October 2019 and Deuse T, et. al. Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients. Nat Biotechnol. 2019 Mar;37(3):252-258. doi: 10.1038/s41587-019-0016-3. Epub 2019 Feb 18; as evidenced by WO2012145384 to Russell et. al. published 26 October 2012.
Claim interpretation: As described in the 112(b) rejection above, it cannot be discerned what applicant means by “complex” if it does not mean physical interaction between the components as in an art-know “protein complex”. For the purposes of expedited prosecution, “complex” will be interpreted to include “cell” as shown in Fig. 9 of the instant application.
Johannesson et. al. teaches modified stem cells that express immune evasion genes including one or more from a group including CD47 and HLA-E single chain trimers [0045]. Johannesson et. al. teaches that a CHO-cell line co-expressing CD55, CD46, and HLA-E single chain trimer inhibited NK cell degranulation in PBMC co-culture (Fig. 10, Example VIII)
As evidenced by Russell et. al., HLA-E single chain trimers are complexes comprising a segment comprising a peptide linked to B2M and an HLA-E heavy chain (Fig. 3B); See 102 rejection above.
Deuse et. al. teaches that one way to overcome manufacturing limitations for patient specific tissue and organ repair strategies is allogeneic cell or tissue products, which is limited by the immune response against histo incompatible cells (Abstract). Deuse et. al. teaches that hypo-immune cells are made by inactivating MHC class I and II and by overexpressing CD47. Deuse et. al. teaches that CD47 expression was sufficient to overcome the innate immune reaction to transplanted cells in vitro and in vivo (Fig. 2, Fig. 3).
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to express CD47 and HLA-E single chain trimers in an allogeneic cell for transplant or cell therapy to evade the immune system as taught by Johannesson et. al. in order to benefit from the immune evasion from CD47 overexpression taught by Deuse et. al. and the immune evasion from HLA-E expression taught by Johanesson et. al. This would have a reasonable expectation of success because Johannesson et. al. explicitly suggests combinations of HLA-E single chain trimers and additional immune evasion genes and Deuse et. al. teaches that CD47 overexpression on its own is sufficient to ablate any detectable immune response against B2M knockout cells.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 122-127 and 130-134 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 222-244 of copending Application No. 18858247 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims of the '247 application anticipate the instant claims as evidenced by Yanaka, Saeko, et al. "Peptide-dependent conformational fluctuation determines the stability of the human leukocyte antigen class I complex." Journal of Biological Chemistry 289.35 (2014): 24680-24690 and Spahr, Chris, et al. "High-resolution mass spectrometry confirms the presence of a hydroxyproline (Hyp) post-translational modification in the GGGGP linker of an Fc-fusion protein." MAbs. Vol. 9. No. 5. Taylor & Francis, 2017.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Copending application ‘247 teaches a construct comprising one or more targeting moieties (reads on peptide), one or more MHC regions (reads on fragment of HLA class I heavy chain HLA-E; because there is no special definition for fragment the HLA fragment may be any size, and all class I HLA heavy chains comprises at least a fragment 100% identical to HLA-E), wherein at least on of said one or more MHC regions comprise a CD8 binding site, and one or more linker regions.
Regarding claims 123-124, claim 232 teaches the one or more targeting moieties comprises a peptide of SEQ ID NOs: 158-174, which are MHC binding nonamers that would bind to the MHC groove and modulated its conformation as evidenced by Yanaka, Saeko, et al.
Regarding claim 125, claim 236 teaches a linker disposed between the targeting moiety and the MHC region (reads on linker between the peptide and the HLA class I heavy chain) and claim 233 teaches the linker region is sequence SEQ ID NOs: 175-186; these are GS linkers which are resistant to protease cleavage as evidenced by Spahr, Chris, et al.
Regarding claim 126, claim 225 teaches wherein the construct elicits inhibited activation of a T cell when bound to the T cell.
Regarding claim 127, claim 229 teaches a disulfide staple (reads on disulfide bond) between an HLA-C residue (class I heavy chain) and the targeting moiety (reads on peptide).
Regarding claim 130, claim 236 teaches a linker disposed between the targeting moiety and the MHC region (reads on linker between the peptide and the HLA class I heavy chain).
Regarding claim 131, claim 233 teaches the linker region is sequence SEQ ID NOs: 175-186; SEQ ID NO: 179 is 100% identical to instant SEQ ID NO: 48, for example.
Regarding claim 132, claims 228 and 229 teach that the CD8 binding site or the MHC regions comprise particular HLA-C residues (reads on a fragment of HLA-C).
Regarding claims 133 and 134, claim 228 teaches a mutation at the Q226 residue of HLA-C: this reads on a mutations in both the HLA-C and the HLA-E fragment as in claims 133 and 134 because HLA-C and HLA-E are identical at residue Q226 for wildtype and therefore this would constitute a mutation in either fragment.
Claims 128-129 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 222-244 of copending Application No. 18858247 (reference application) as applied to claim 122 above, in further view of Johannesson et. al. effectively filed 10 October 2019 and Deuse T, et. al. Hypoimmunogenic derivatives of induced pluripotent stem cells evade immune rejection in fully immunocompetent allogeneic recipients. Nat Biotechnol. 2019 Mar;37(3):252-258. doi: 10.1038/s41587-019-0016-3. Epub 2019 Feb 18; as evidenced by WO2012145384 to Russell et. al. published 26 October 2012.
Claim interpretation: As described in the 112(b) above, the complex comprising is unclear because it is uncertain what is required for the checkpoint agonist to be in the complex with the peptide/linker/HLA-E heavy chain. For the purposes of expedited prosecution, “complex” will be interpreted to include a cell comprising both components as shown in Fig. 9; additionally, HLA-E will be considered to comprise a fragment of HLA-C.
The teachings of ‘247 are in regards to claim 122 are in the NSDP rejection above.
‘247 claim 244 further teaches a hypo-immunogenic cell comprising the construct of claim 243.
‘247 does not teach wherein the complex further comprises a checkpoint agonist. This deficiency is resolved by Johannesson et. al. and Deuse et. al.
The teachings of Johannesson et. al. and Deuse et. al. are in the 103 rejection above and are incorporated by reference herein. Briefly, Johannesson et. al. teaches a cell comprising an HLA-E single chain trimer and additional checkpoint agonists selected from a group including CD47. Deuse et. al. teaches that expression of CD47 protects cells against innate immune response and NK cell killing in B2M knockout cells.
It would have been obvious for a person of ordinary skill in the art, before the effective filing date, to express the construct of ‘247 which is designed to make a hypo-immunogenic cell as claimed in claim 244 with the CD47 overexpression as taught by Johannesson et. al. and Deuse et. al. to benefit from the decreased immunogenicity of overexpressing a single chain trimer and an additional checkpoint agonist such as CD47. This would have a predictable effect because the claims of ‘247 and Johannesson et. al. are all directed at overexpression of modified HLAs and immune checkpoint agonists to make a more universal genetically modified cell for tissue or cell therapy and a person of ordinary skill in the art would anticipate at least an additive protective effect of the constructs as taught by Johannesson et. al.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Kathleen CunningChen whose telephone number is (703)756-1359. The examiner can normally be reached Monday - Friday 11-8:30 ET.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gregory Emch can be reached at (571) 272-8149. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/KATHLEEN CUNNINGCHEN/ Examiner, Art Unit 1646
/GREGORY S EMCH/ Supervisory Patent Examiner, Art Unit 1678
Prosecution Insights