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 .
Priority
The preliminary amendments filed 28 October 2024 are acknowledged and have been entered. Claims 38, 39, 41, 42, 44, 45, 49, 51-54, 56, 57, 60, and 61 are amended. Claims 1-37, 46-47, 55, and 62-71 have been cancelled. Claims 38-45, 48-54, and 56-61 are pending and being examined on the merits.
Information Disclosure Statement
The information disclosure statements filed 12/12/2024 and 01/27/2026 have been considered.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - The incorporation by reference paragraph required by 37 CFR 1.834(c)(1), 1.835(a)(2), or 1.835(b)(2) is missing, defective or incomplete.
Required response - Applicant must:
• Provide a substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required incorporation by reference paragraph, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Specification
The specification is objected to as failing to provide proper antecedent basis for the claimed subject matter. See 37 CFR 1.75(d)(1) and MPEP § 608.01(o). Correction of the following is required: Paragraph 0009 states that “The introduction of the LD unit to the 5' end of the guide strand can be avoided so as to avoid RNA-induced silencing complex (RISC) formation” whereas claim 61 recites that the complex of claim 60, which comprises 5 repeated LD units modifications only at the 3’ end of the guide strand, does not yield RISC formation. It is unclear whether the specification intends to state that leaving the 5’ end of the guide strand unmodified avoids RISC formation or instead preserves RISC formation. Shu (Shu et al. Chemical and Pharmaceutical Bulletin 68.2 (2020): 129-132) teaches that keeping the 5’- terminus of the guide strand unmodified is very important for formation of the RISC. Correction is required so that the specification and claims consistently state the intended effect of the modification.
The use of the term Bio-Rad, Santa Cruz, Sigma-Aldrich, Life Technologies, Invitrogen, ATCC, Ibidi, Millipore, and Bruker to name a few, which is a trade name or a mark used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term. A cursory review of the specification has revealed these trademarks or names. It would be remedial to check the specification for additional trademarks or names and amend all upon amendment.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 38, 48, and 60 are objected to because of the following informalities:
Claim 38 recites “first second, third, and fourth” and is missing a comma between first and second.
Claim 38 recites “fourth RNA oligonucleotides”. It would be remedial to amend to “fourth RNA oligonucleotide”.
Claim 48 recites “Her2”. It would be remedial to amend to the conventional nomenclature of “HER2”.
Claim 60 recites “3' ends of the guide strand”. It would be remedial to amend to “3' end of the guide strand”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
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 38-45, 48-54, and 56-61 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 38 recites “four RNA oligonucleotides selected from siRNA or shRNA”. It is unclear whether each of the for individual oligonucleotides is required to be an siRNA or shRNA, whether each arm formed by two or more strands constitutes an siRNA or shRNA, or whether the junction-forming strands merely contain sequences that become siRNA or shRNA after processing. An siRNA ordinary comprises at least a guide strand and a passenger strand forming a duplex, whereas an individual RNA oligonucleotide is a single strand. A shRNA comprised a single strand folded into a stem-loop structure. The claim does not establish how four individual RNA oligonucleotides can each be selected from siRNA or shRNA while simultaneously hybridizing with adjacent junction-forming oligonucleotides in the recited cross-pattern.
Claim 38 recites “wherein the first, second, third, and fourth peripheral oligonucleotides are partially or wholly complementary to the first RNA oligonucleotide, second RNA oligonucleotide, third RNA oligonucleotide, or fourth RNA oligonucleotides”. It is unclear whether each peripheral oligonucleotide must hybridize to a respectively numbered RNA oligonucleotide, may hybridize to any one of the four RNA oligonucleotides, or may hybridize to multiple RNA oligonucleotides.
Claim 38 recites that each peripheral oligonucleotide independently comprise a trigger, wherein the trigger can be an RNA binding protein sequence. It is unclear whether “RNA binding protein sequence” denotes a nucleic-acid sequence that binds an RNA-binding protein, a nucleic acid sequence encoding an RNA-binding protein, or the amino acid sequence of an RNA-binding protein. It is also unclear what constitutes a “target molecule” and what event that molecule is intended to trigger. Therefore, the structural boundaries of the required peripheral oligonucleotides cannot be determined with reasonable certainty.
Claim 39 recites the limitation "the Internal ribosome entry site" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 39 recites the limitation " the eukaryotic initiation factor 3" in line 2. There is insufficient antecedent basis for this limitation in the claim.
Claim 43 recites the limitation "the targeting molecule" in line 1. There is insufficient antecedent basis for this limitation in the claim.
Claim 44 recites “RNA protein binding sites”, lists types of triggers of claim 38, and depends from claim 38 which recites “RNA binding protein sequence”. It is unclear whether these recitations refer to the same features or different features.
Claim 48 recites “wherein the affibody is an antibody or portion thereof to ASPH or Her2”. An affibody is not an antibody or antibody fragment. Therefore, it is unclear whether the claim requires an affibody that binds ASPH or HER2, an antibody that binds ASPH or HER2, or an antigen-binding portion of such antibody. The recitation of “portion thereof” renders that claim indefinite as it is unclear if the “portion thereof” is referring to the affibody or the antibody; and whether or not it is limited to the binding portion of the affibody or antibody.
Claim 50 recites the limitation "the sequence AUG" in lines 1-1. There is insufficient antecedent basis for this limitation in the claim.
The term “long mRNA” in claims 53 and 54 is a relative term which renders the claim indefinite. The term “long mRNA” is not defined by the claim, 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 claim provides no munerical length, comparative standard, or other objective boundary for determining whether an mRNA is “long”.
Claim 54 recites “a 3-D tube, sheet, triangle, or hexagon”. It is unclear whether “3-D” modifies only the “tube” or if it describes the “sheet”, “triangle”, and “hexagon”.
Claim 56 recites “A method of killing a cancer cell”, but the body of the claim only requires ‘contacting a cancer cell with a RNA complex of claim 38’. It is unclear whether killing of a cancer cell is a required step or result that limits the claim or merely an intended purpose of the contacting step. If the latter, it is unclear how contacting the cell with the complex results in the killing of a cancer cell.
Claim 61 recites “The RNA oligonucleotide carrier of claim 60”. Claim 60 is directed to the complex of claim 38 and does not introduce a RNA nucleotide carrier, nor does claim 38. It is unclear whether claim 61 is intended to further limit the complex of claim 60 or a different carrier.
Those claims identified in the statement of rejection but not explicitly referenced in the rejection are also rejected for depending from a rejected claim but failing to remedy the indefiniteness therein.
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.
Claim 45 is 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.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Claim 45 is directed to the genus of complexes of claim 38 in which the Pro-mRNA encodes “a cancer neoantigen expressed from” any one of five tumor-associated genes: AP2S1, Survivin, CTSL, MPZL2, or LSP1. Accordingly, the claim encompasses the various tumor-specific mutant proteins and mutant epitopes that may arise from each of the five recited genes and qualify as cancer neoantigens.
The Specification teaches generally that Pro-mRNA nanostructures may translate proteins for cancer immunotherapy and states that a trigger Pro-mRNA may be translated into an immunogenic neoantigen for use in a personalized mRNA vaccine [0225]. The Specification further identifies AP2S1, Survivin, CTSL, MPZL2, and LSP1 as genes encoding representative “tumor associated antigen[s]” [0233; SEQ ID NOs: 22–28]. However, the Specification does not identify a tumor-specific mutation in any of these genes, disclose the nucleotide or amino-acid sequence of a mutant gene product, identify a mutation-derived neoepitope, or demonstrate that a peptide arising from any recited gene is processed, presented by an MHC molecule, and recognized by an immune cell. The Specification therefore describes tumor-associated antigens, but does not provide representative species of the claimed genus of cancer neoantigens.
The art establishes that a cancer neoantigen is not merely a protein associated with or overexpressed in a tumor. Rather, cancer neoantigens generally arise from tumor-specific alterations and are identified by determining whether a mutation produces a peptide that is processed, presented by an MHC molecule, and recognized by T cells. Schumacher (Schumacher et al. Science 348.6230 (2015): 69-74) teaches that only a subset of tumor mutations produces peptides having the required processing, MHC-binding, presentation, and immune-recognition properties [pg. 69–72]. Thus, identifying a gene as tumor-associated does not establish possession of the structurally and functionally distinct neoantigens that may arise from that gene.
The Specification therefore does not reasonably convey to a person of ordinary skill that Applicant possessed the claimed genus of cancer neoantigens at the time of filing. The disclosure provides neither a representative number of species within the claimed genus nor structural features common to the genus by which a person of ordinary skill could distinguish a cancer neoantigen within the scope of claim 45 from a non-mutated tumor-associated antigen or a mutated peptide that is not processed, presented, or immunogenic. Merely naming five tumor-associated genes and stating the desired result of producing a neoantigen is insufficient to demonstrate possession of the claimed genus.
Claims 56-59 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.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
Claim 56 is directed to the genus of methods of killing a cancer cell by contacting the cancer cell with any complex encompassed by claim 38. Claim 57 is directed to the genus of methods of treating cancer by administering a therapeutically effective amount of a composition comprising any complex encompassed by claim 38. Claim 58 encompasses treatment of colorectal, pancreatic, breast, ovarian, or lung cancer or melanoma, and claim 59 encompasses treatment using the complex together with any anticancer agent.
The Specification teaches generally that an RNA four-way junction may contain Pro-mRNA, disulfide modifications, targeting molecules, and siRNA or shRNA components [0232–0233]. Example 6 demonstrates that separately transfected shRNAs targeting Mcl-1 and Bcl-xL reduced protein expression and induced death of liver-cancer cells [0322–0323]. Example 7 demonstrates increased in-vitro GFP expression from an mRNA containing an enhancer sequence [0326–0328]. However, neither example employs the four-way complex of claim 38. The Specification’s proposed multifunctional nanodevice experiments concern principally a DNA-origami nanodevice and describe future optimization, testing, and “expected” tumor-killing results [0335–0352]. The Specification does not identify a representative four-way RNA complex of claim 38 that was shown to kill a cancer cell or treat cancer.
The art establishes that therapeutic activity cannot be predicted merely from the presence of RNAi, targeting, disulfide, or mRNA components. Han (WO 2019/014656) teaches that stability and intracellular release depend on the number, location, and type of crosslinkers and that an inappropriate linker length may result in an unstable construct or prevent effective intracellular release [0041–0043]. Han further teaches that added secondary structures may reduce Dicer processing [0069–0072]. Samarsky (WO 2020/065602) teaches that the efficacy of individual RNAi molecules is not assured and that sequence activity, off-target effects, stability, and intracellular delivery are recognized obstacles to successful RNAi therapy [pg. 2]. The art therefore demonstrates substantial structure-function variability among RNA sequences and nanostructures falling within the claimed genus.
The Specification does not disclose a representative number of species commensurate with the breadth of the claimed cancer-killing and cancer-treatment genera and does not identify structural features common to the claimed complexes that correlate with the recited functional results. Claim 38 encompasses complexes lacking a cancer-specific targeting molecule, a cancer-relevant siRNA or shRNA sequence, a cytotoxic or immunogenic Pro-mRNA payload, or any other limitation requiring cancer-cell killing. The disclosure of isolated shRNA activity, isolated enhancer activity, and proposed nanodevice experiments does not demonstrate possession of the much broader genus of methods employing any complex within claim 38. Accordingly, the Specification does not reasonably convey that Applicant possessed the full scope of the claims at the time of filing.
Claim 58 narrows the treatment method of claim 57 to six categories of cancer and claim 59 adds administration of an unspecified anticancer agent; however, neither identifies an operative RNA complex, anticancer agent, combination, or common structure-function relationship demonstrating possession of the claimed combination-treatment genus. Claims 58 and 59 therefore do not cure the written-description deficiency of claim 57.
Claim 45 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for Pro-mRNA sequences that encodes for known cancer neoantigens expressed from a tumor associated gene selected from: AP2S1, Survivin, CTSL, MPZL2, and LSP2, does not reasonably provide enablement for all cancer neoantigens. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Nature of the invention. Claim 45 concerns an RNA nanostructure in which a Pro-mRNA encodes a functional cancer neoantigen arising from one of five tumor-associated genes. Practicing the invention requires identification of a tumor-specific alteration and a resulting peptide that is generated by antigen processing, presented by an appropriate MHC molecule, and capable of immune recognition. The invention therefore involves mutation identification, RNA design, protein expression, antigen processing, MHC binding and presentation, and immunology.
Breadth of the claim. Claim 45 encompasses any cancer neoantigen expressed from AP2S1, Survivin, CTSL, MPZL2, or LSP1. The claim is not limited to a particular mutation, mutant nucleotide sequence, mutant amino-acid sequence, epitope, MHC allele, cancer type, patient population, or demonstrated immune response. It therefore encompasses the numerous actual and potential mutations within each gene and the numerous peptides that may be produced, processed, and presented from the resulting mutant proteins.
Guidance from the Specification. The Specification states that Pro-mRNA may be translated into an immunogenic neoantigen and identifies the five recited genes as sources of tumor-associated antigens [0225, 0233]. However, the Specification does not disclose a tumor-specific mutation, a mutant sequence, a neoepitope, an MHC restriction, an antigen-processing analysis, an MHC-binding result, or an immune-recognition result for any of the five genes. The Specification therefore does not provide a working example or selection criteria by which a skilled artisan could identify which species within the broad claimed genus are operative cancer neoantigens.
State of the art. The art establishes that neoantigen identification is patient-, mutation-, and MHC-dependent. Schumacher teaches that a mutation must produce an altered peptide that is generated through cellular processing, binds an appropriate MHC molecule, is presented on the cell surface, and is recognized by the immune system. Only a subset of tumor mutations produces such peptides [pg. 69–72]. The state of the art therefore does not permit a skilled artisan to predict a functional neoantigen merely from the identity of its source gene.
Experimentation required. To practice the full scope of the claim, a skilled artisan would need to identify tumor-specific alterations in each recited gene; determine the corresponding mutant protein and candidate peptide sequences; predict or measure proteasomal processing; evaluate MHC binding and presentation across relevant MHC alleles; and test immune recognition. Because the Specification provides no representative operative species or reliable selection criteria, these steps would need to be repeated for the numerous mutations, epitopes, MHC alleles, and patient populations encompassed by the claim. The required experimentation constitutes extensive screening rather than routine optimization.
Considering the complex nature of neoantigen biology, the breadth of the claimed genus, the limited guidance and absence of working examples in the Specification, the unpredictability recognized in the art, and the substantial amount of screening required, a person of ordinary skill could not make and use the full scope of claim 45 without undue experimentation.
Claim 48 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for certain full-length antibodies or affibodies, does not reasonably provide enablement for the full scope of the claimed “portion thereof”. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Nature of the invention. Claim 48 recites that the affibody is “an antibody or portion thereof to ASPH or Her2.” The claimed portion must function as a targeting molecule in the RNA-oligonucleotide complex and therefore must retain sufficient structure to bind ASPH or HER2 after incorporation into or conjugation with the complex. Successful practice requires identification of a protein portion that retains proper folding, an operative target-binding surface, sufficient affinity and specificity, compatibility with oligonucleotide conjugation, and accessibility to the target on a cell surface.
Breadth of the claim. The phrase “portion thereof” is not limited to an antigen-binding fragment, a variable region, a complementarity-determining region, an affibody domain retaining all three alpha helices, a particular amino-acid sequence, a minimum length, a minimum binding affinity, or a defined conjugation site. The claim therefore encompasses portions of varying lengths and structures derived from any antibody or affibody directed to either ASPH or HER2. Under this scope, the claim covers not only conventional Fab, F(ab′)₂, scFv, and other recognized antigen-binding fragments, but also undefined truncations, deletions, domains, and subdomains whose ability to retain target binding cannot be determined from the claim.
Guidance from the Specification. The Specification teaches that an antibody fragment may comprise an antigen-binding site of an intact antibody and thereby retain the ability to bind antigen [0117]. The Specification also identifies ABY-025 as a particular HER2-binding affibody [0118] and teaches that antibodies, fusion proteins, fragments, scFvs, or aptamers may selectively bind ASPH [0202]. However, the Specification does not identify a particular portion of ABY-025 that retains HER2 binding, identify any portion of an ASPH-binding affibody, provide a sequence for such a portion, or disclose minimum structural requirements for retaining ASPH or HER2 binding. The general statement that a targeting molecule may be “an affibody or portion thereof to ASPH, Her2” states the desired result but does not teach which portions achieve that result [0233].
State of the art. The state of the art established that conventional antibody fragments, such as Fab, F(ab′)₂, and scFv fragments, may retain antigen binding when the necessary variable domains and complementarity-determining regions are preserved. The art also established that an affibody is a structurally distinct, small alpha-helical binding scaffold rather than an immunoglobulin fragment. Whether a particular deletion or truncated portion retains binding depends on preservation of the binding surface, folding of the remaining scaffold, the location of the target-contacting residues, and the manner in which the portion is conjugated to the delivery complex. The art therefore does not support a conclusion that arbitrary portions of an antibody or affibody predictably retain ASPH or HER2 binding.
Experimentation required. To determine which portions fall within the operative scope of claim 48, a skilled artisan would need to produce numerous truncations, deletions, domains, or subdomains; assess whether each candidate folds properly; test ASPH or HER2 binding affinity and specificity; conjugate each candidate to an oligonucleotide component; and retest binding, junction assembly, cellular targeting, and uptake. Because the Specification provides no sequence, minimum domain, conserved structural boundary, affinity threshold, or representative operative “portion,” the artisan could not identify the claimed portions from the disclosure alone. Instead, the scope of operative portions would have to be discovered through repeated construction and functional screening.
Considering the functional and structural complexity of antigen-binding proteins, the unrestricted breadth of “portion thereof,” the limited guidance provided by the Specification, the absence of a working example or representative operative portion, the unpredictability of retaining binding following truncation and conjugation, and the amount of testing required, the Specification does not enable the full scope of claim 48 without undue experimentation. The Specification may enable conventional antigen-binding antibody fragments and the complete ABY-025 HER2 affibody, but it does not enable the full genus of unspecified portions encompassed by the claim.
Claims 56-59 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of killing a cancer cell and treating cancer in a subject in need thereof comprising administering a multi-functional nucleic acid nanodevice, does not reasonably provide enablement for the method using the complex as claimed. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Nature of the invention. Claims 56–59 concern cancer-cell killing and cancer treatment using multifunctional RNA nanostructures. Successful practice requires an operative RNA payload, assembly and stability of the four-way complex, delivery to the relevant cell or tissue, cellular uptake, endosomal escape or cytosolic delivery, release or accessibility of the active RNA component, interaction with the appropriate intracellular machinery, and production of a cytotoxic or therapeutic effect. The claimed invention therefore combines RNA nanotechnology, RNA interference or mRNA expression, intracellular delivery, molecular targeting, pharmacology, and cancer biology.
Breadth of the claims. Claims 56 and 57 encompass use of any complex within claim 38, including its numerous alternatives for the four central RNA oligonucleotides and four peripheral trigger oligonucleotides. The claims do not require a cancer-relevant target sequence, an active cytotoxic payload, a cancer-specific targeting ligand, receptor expression by the cancer cell, successful intracellular release, or any particular dose or formulation. Claim 58 extends the treatment genus across colorectal, pancreatic, breast, ovarian, and lung cancers and melanoma. Claim 59 further encompasses combinations with any anticancer agent. The claims therefore cover a large number of structurally and biologically distinct complexes, cancers, subjects, doses, routes, formulations, and combination therapies.
Guidance from the Specification. The Specification provides general descriptions of four-way RNA structures and their possible Pro-mRNA, siRNA, shRNA, targeting, enhancer, and disulfide components [0232–0233]. Example 6 demonstrates cancer-cell death following transfection with separate Mcl-1 and Bcl-xL shRNAs, but does not employ the complex of claim 38 [0322–0323]. Example 7 demonstrates increased in-vitro GFP expression from enhancer-containing RNA, but does not demonstrate cancer-cell killing or treatment [0326–0328]. The proposed multifunctional nanodevice studies describe future optimization and expected results and principally employ a DNA-origami nanodevice rather than the claimed four-way RNA complex [0335–0352]. The Specification thus provides no working example demonstrating that a complex within claim 38 kills a cancer cell or treats cancer and provides no generally applicable criteria for selecting an operative complex for each claimed cancer.
State of the art. The art shows that therapeutic performance is not predictable from the mere inclusion of RNAi and delivery components. Han teaches that nanostructure stability and intracellular release depend on the number, type, position, and length of crosslinking elements, with inappropriate designs producing instability or ineffective release [0041–0043]. Han also teaches that added secondary structure may reduce Dicer processing [0069–0072]. Samarsky recognizes that individual RNAi molecules are not predictably effective and that sequence efficacy, off-target activity, stability, and delivery present significant obstacles [pg. 2]. The state of the art therefore supplies general techniques but does not allow a skilled artisan to predict which of the broadly claimed combinations will reach the appropriate cancer cell, release a functional payload, and produce the claimed therapeutic result.
Experimentation required. A skilled artisan would need to design and screen numerous siRNA, shRNA, or Pro-mRNA sequences; assemble and characterize each nanostructure; optimize the number and placement of disulfide units; select and validate a targeting ligand; test serum stability, cellular uptake, endosomal escape, cytosolic release, RNA processing, target knockdown or protein expression, cancer-cell killing, toxicity, biodistribution, dose, and route of administration; and repeat this work for the biologically distinct cancers and combination therapies encompassed by claims 56–59. The Specification itself recognizes the need to tune antibody loading, peptide locks, disulfide-unit loading, RNA-cargo ratios, delivery, and gene-knockdown efficacy and to screen for potent constructs [0338–0351]. The required work is therefore a substantial research program, not routine optimization of disclosed operative embodiments.
Considering the complex nature of the invention, the breadth of the claimed structural and therapeutic alternatives, the absence of a working example using the claimed four-way complex, the limited guidance concerning operative species, the unpredictability shown by the art, and the extensive experimentation necessary to identify effective constructs and treatment conditions, the Specification does not enable a person of ordinary skill to practice the full scope of claims 56–59 without undue experimentation. Claims 56–59 therefore fail to comply with the enablement requirement of 35 U.S.C. 112(a).
Claim 58 narrows the cancer to six categories but does not provide the missing operative complex or treatment guidance for any one of them. Claim 59 adds an unspecified anticancer agent, which increases rather than resolves the experimentation needed to identify an effective and tolerable combination. Accordingly, none of the limitations of claims 58–59 cures the enablement deficiency.
Claim 61 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for preparation of LD-modified siRNA complexes having the structural arrangement recited in claim 60, does not reasonably provide enablement for the full scope of complexes defined in claim 61 by the functional limitation that the complex “does not yield RNA-induced silencing complex (RISC) formation.” The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Nature of the invention. Claim 61 concerns a linear-disulfide-modified siRNA having five repeated linear-disulfide units at the 5′ end of the passenger strand and five repeated linear-disulfide units at the 3′ end of the guide strand, wherein the complex does not yield RISC formation. Practicing the claimed invention requires control over intracellular disulfide reduction, siRNA duplex processing, strand selection, guide-strand loading, and formation or activity of the RNA-induced silencing complex.
Breadth of the claim. Claim 61 is not limited to a particular siRNA sequence, duplex length, thermodynamic asymmetry, linker chemistry beyond the broadly recited linear-disulfide modification, target, cell type, intracellular reducing condition, degree of modification removal, or assay for determining RISC formation. It therefore encompasses diverse siRNA duplexes for which strand selection, modification removal, and RISC loading may differ substantially.
Guidance from the Specification. The Specification asserts that linear-disulfide units can be positioned to avoid RISC formation, but does not provide a working example measuring RISC assembly or guide-strand loading for the configuration recited in claims 60 and 61. The Specification also does not identify sequence characteristics, duplex properties, linker structures, intracellular conditions, or test results demonstrating when the recited configuration will prevent RISC formation. The disclosure therefore supplies the desired result, but not sufficient guidance for consistently achieving that result across the scope of the claim.
State of the art. The art demonstrates that substantially the same modification arrangement does not necessarily prevent RNAi activity. Shu teaches that an siRNA containing five masked amino units at the 5′ end of the passenger strand and five masked amino units at the 3′ end of the guide strand, while leaving the functionally important 5′ end of the guide strand unmodified, and reports approximately 60% target-gene knockdown [p. 131, Fig. 4]. Thus, the recited placement of five units on each strand does not itself predict an absence of RISC formation.
Experimentation required. A skilled artisan would need to construct siRNAs having different sequences and duplex properties, determine the extent and kinetics of intracellular disulfide reduction, and directly measure guide-strand loading, RISC assembly, target cleavage, or gene silencing for each construct. Because the Specification provides no operative example or generally applicable selection criterion, this testing would need to be repeated across the range of sequences, targets, cell types, and intracellular conditions encompassed by claim 61. In view of art showing gene knockdown from substantially the same modification arrangement, such testing would be necessary to discover which, if any, embodiments produce the claimed absence of RISC formation.
Considering the complex and sequence-dependent nature of RISC formation, the breadth of claim 61, the absence of working examples or meaningful selection criteria, the contrary results reported in the art, and the amount of empirical testing required, the Specification does not enable the full scope of claim 61 without undue experimentation. Claim 61 therefore fails to comply with the enablement requirement of 35 U.S.C. 112(a).
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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 38 and 43 are rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”).
Regarding claim 38, Han teaches multivalent oligonucleotide-junction delivery complexes formed from RNA oligonucleotides and used for simultaneous delivery of multiple functional cargos [abstract]. Han expressly teaches that “[m]ulti-way junctions can be formed by multiple oligonucleotides” and that a four-way junction having multiple double-stranded arms can be formed by four oligonucleotides [0039]. The component oligonucleotides partially complement one another to form the double-stranded arms [0039–0040]. Han also teaches a junction having a four-way core and a two-way junction attached to each arm, with the peripheral end of each two-way junction attached to an siRNA cargo or a cell-targeting delivery ligand [0065; Figs. 9, 17–18]. Han further teaches single-stranded anchor strands attached to junction oligonucleotides and complementary anchor-pairing strands comprising or carrying siRNA, RNA aptamer, drug, antibody, or delivery-ligand cargos [0049–0055]. Han teaches that many small molecules and macromolecules can be conjugated to either or both of the anchor strand and the anchor pairing strand due to very versatile oligonucleotide attachment chemistry, including but not limited to amine-NHS ester conjugation, thiol conjugation [0049]. Thus, Han teaches the claimed four-way cross-pattern and four peripheral oligonucleotide components that hybridize to respective junction arms and carry independently selected functional triggers. Han additionally teaches that the trigger or cargo may be an siRNA, RNA aptamer, drug, antibody, delivery ligand, or disulfide-containing component [0049–0057]. Han teaches that thiol modification may be used “to form disulfide linkages” [0057], that disulfide-containing crosslinkers stabilize the junction during delivery and are cleaved in the reducing cytosol [0043, 0047], and that one or more arms may carry delivery ligands for targeted delivery [0050, 0064–0065]. Han therefore teaches the alternatives of a disulfide-modified sequence and a target molecule.
Han does not expressly characterize each of the four central RNA oligonucleotides as an siRNA or shRNA.
Samarsky teaches multivalent nanostructures in which the structural oligonucleotide components themselves contain gene-targeting portions and are assembled through complementary interactions [pg. 2]. Samarsky teaches a four-component structure in which adjacent oligonucleotides hybridize through complementary terminal segments to form a closed structure and each oligonucleotide contains a target-complementary segment [pp. 16–17, Figs. 3 and 5A]. Samarsky explains that the structure disassembles in the biological environment to yield functional siRNAs [pp. 15–17, Figs. 2–5B]. Samarsky expressly teaches that a four-component structure can “disassemble into four different siRNAs” [p. 16, Fig. 4]. Samarsky also teaches that a targeting or delivery moiety, such as GalNAc, may be attached to each oligonucleotide building block [pp. 16–19, Figs. 3 and 5A].
Regarding claim 43, Samarsky expressly teaches that the target or delivery moiety may be “GalNAc, Cholesterol, etc.” and may be attached to different component oligonucleotides or to each oligonucleotide building block [pp. 16–17, Figs. 2, 3, and 5A; p. 19].
It would have been obvious to a person of ordinary skill before the effective filing date to use Samarsky’s siRNA-forming (or shRNA-forming) oligonucleotide components as the component RNA strands of Han’s four-way junction. Both references concern multivalent, self-assembled oligonucleotide structures that use complementary hybridization to carry multiple RNA-interference cargos into cells. The substitution would have predictably allowed the structural oligonucleotides themselves to provide RNA-interference activity upon intracellular disassembly, thereby increasing cargo density and reducing the need for separate inert structural strands. A skilled artisan therefore would have had a reason and a reasonable expectation of success in making the claimed complex because Han expressly identifies simultaneous delivery of multiple siRNAs as an objective [0035, 0043, 0054], while Samarsky supplies the known method of forming the nanostructure from oligonucleotides that become functional siRNAs after disassembly [pp. 15–19].
Claims 39, 41-42, 44, and 49–53 are rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”), as applied to claim 38, and further in view of Foot et al. (WO 2021/053405; hereinafter “Foot”) and Kozak (Nucleic Acids Research 15:8125–8148 (1987).
The teachings of Han and Samarsky is discussed above as applied to claim 38 and similarly apply to claim 39, 41-42, 44, and 49–53.
Foot teaches compositions containing cargo molecules attached to elements that improve the function of the cargo molecules in the body of a subject [abstract]. Foot teaches attaching compacted RNA cargos, including mRNA, siRNA, and shRNA, to a nucleic-acid nanoparticle [pp. 2–3, Summary]. Foot teaches that multiple RNA molecules may be attached to the same nanoparticle and that the different mRNAs may encode different polypeptides [p. 2]. Foot further teaches that an mRNA cargo may include a 5′ cap, 5′ UTR, coding sequence, 3′ UTR, and poly(A) tail [p. 27, discussion of Fig. 2], and that elongated polyadenylated tails can increase mRNA stability [pp. 30–31]. Foot therefore teaches the claimed Pro-mRNA cargo and its conventional translational elements.
Regarding claims 39 and 41-42, Han and Samarsky do not teach wherein the trigger is an -enhancer sequence which is the Internal ribosome entry site (IRES) or wherein the enhancer sequence is configured to initiate Pro-mRNA sequence translation. Han and Samarsky do not teach wherein the enhancer sequence and Pro-mRNA sequence are contiguous. Foot teaches that the nanoparticle may contain “an internal ribosome entry site” that recruits translation machinery or translation-initiation factors to the mRNA [p. 32]. Foot further depicts a nanoparticle having an IRES-based ribosome-recruitment functionality that “enhances translation of the mRNA molecule” [p. 33, Fig. 12]. Foot therefore teaches an IRES enhancer configured to initiate or enhance translation of a Pro-mRNA sequence. Foot’s IRES is a cis-acting RNA element that recruits the translation machinery to the associated mRNA [pp. 32–33, Fig. 12]. It would have been obvious to place the IRES contiguously with the mRNA coding sequence because that was the conventional arrangement by which an IRES directs internal initiation on the associated transcript. Doing so would have predictably ensured that ribosome recruitment by the IRES initiated translation of the intended Pro-mRNA rather than a separate RNA molecule.
Regarding claim 44, Han and Samarsky do not teach wherein there are two independent Pro-mRNA sequences contiguous with RNA protein binding sites and enhancers, two disulfide-modified peripheral oligonucleotides, and two target molecules. Foot teaches compositions containing multiple RNA molecules, including different mRNAs encoding different polypeptides, attached to a nucleic-acid nanoparticle [p. 2]. Han teaches that a junction having two or more arms may carry two or more different RNA cargos [0043], that the same or different cargos may be loaded on different arms [0049], and that one or more arms may carry delivery ligands [0064–0065]. Han also teaches disulfide-modified or disulfide-crosslinked arms [0043, 0057]. It would have been obvious to provide two mRNA cargos, two disulfide-modified peripheral components, and two targeting molecules on different arms because Han expressly teaches independent loading of multiple cargos and ligands and Foot teaches use of multiple mRNAs on the same nanoparticle. The arrangement would have predictably provided simultaneous delivery and expression of two mRNA cargos with multivalent targeting.
Regarding claims 49-52, Han and Samarsky do not teach wherein the Pro-mRNA sequence comprises a Kozak sequence of AUG, wherein the Pro-mRNA sequence comprises a poly A tail, and wherein the Pro-mRNA sequence comprises an open reading frame (ORF). Foot teaches the conventional mRNA architecture comprising a 5′ cap, 5′ UTR, coding sequence, 3′ UTR, and poly(A) tail [p. 27, Fig. 2]. The disclosed coding sequence is an open reading frame, and Foot teaches elongation of the polyadenylated tail to increase mRNA stability [pp. 30–31]. Foot teaches an mRNA coding sequence and conventional translational elements [p. 27, Fig. 2].
Kozak teaches the vertebrate translation-initiation consensus surrounding the AUG initiation codon and identifies AUG as the initiation codon within the Kozak context [pp. 8125–8132]. The commonly recognized consensus is GCCRCCAUGG, where AUG is the translation-initiation codon.
It would have been obvious to include these conventional elements in the Pro-mRNA cargo because Foot teaches that they support stability and expression of an mRNA therapeutic. It would have been obvious to provide Foot’s coding sequence with an AUG initiation codon in a Kozak context because this was the conventional arrangement for efficient initiation of translation from a eukaryotic mRNA. The claimed requirement that the “Kozak sequence comprises the sequence AUG” therefore would have been a routine and predictable implementation of Foot’s expressed mRNA cargo.
Regarding claim 53, Han and Samarsky do not teach wherein the Pro-mRNA sequence comprises a long mRNA strand and a plurality of RNA staple strands. Foot teaches compacted mRNA molecules and explains that RNA origami permits an RNA molecule to assemble into a selected shape [pp. 28–30, Figs. 8–9]. Foot further teaches that additional nucleic-acid packing components may hybridize with the RNA through base pairing and that such components “may be described as staples or pins” [p. 30]. Foot therefore teaches a long mRNA strand and a plurality of complementary RNA staple strands used to fold the mRNA into a compacted configuration. It would have been obvious to incorporate Foot’s mRNA, IRES, translation-enhancing, poly(A), open-reading-frame, and RNA-staple teachings into the junction of Han and Samarsky because all three references concern programmable RNA nanostructures for intracellular delivery of functional nucleic-acid cargos. Foot expressly identifies increased stability, controlled expression, and improved translation as benefits of the additional elements [pp. 28–33]. A skilled artisan would have reasonably expected the known elements to perform the same functions when attached to the known multi-way RNA junction.
Claim 40 is rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”), as applied to claim 38, and further in view of Foot et al. (WO 2021/053405; hereinafter “Foot”), and Sun et al. (Nucleic Acids Research 41:7512–7521 (2013), hereinafter “Sun”).
The teachings of Han and Samarsky are discussed above as applied to claim 38 and similarly apply to claim 40. Han and Samarsky do not teach wherein the RNA binding protein sequence comprises a sequence to bind to the eukaryotic initiation factor 3 (elF3) protein binding complex.
Foot teaches an IRES sequence that recruits translation machinery or translation-initiation factors to an associated mRNA [p. 32] and enhances translation [p. 33, Fig. 12], but Foot does not expressly identify eIF3 as the recruited factor. Sun teaches that the hepatitis-C-virus IRES binds eIF3 and that mutations in the RNA-binding motif of eIF3a weaken “eIF3 binding to the HCV IRES” and suppress IRES-dependent translation [Abstract; pp. 7512–7513, 7518–7520]. See the PubMed record.
It would have been obvious to select an established eIF3-binding IRES as Foot’s translation-enhancing IRES because Foot expressly invites use of an IRES to recruit translation-initiation factors, and Sun identifies eIF3 binding as a known mechanism of IRES-mediated initiation. Selection of the eIF3-binding IRES would have predictably recruited the eIF3 complex and promoted translation of the associated Pro-mRNA.
Claims 45 and 56-59 are rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”), as applied to claim 38, and further in view of Foot et al. (WO 2021/053405; hereinafter “Foot”), Chang et al. (US 2020/0385734; hereinafter “Chang”) and Ciesielski et al. (Cancer Immunology, Immunotherapy 59:1211–1221 (2010); hereinafter “Ciesielski”).
The teachings of Han and Samarsky are discussed above as applied to claim 38 and similarly apply to claims 45 and 56-59.
Regarding claim 45, Han and Samarsky do not teach wherein the Pro-mRNA sequence encodes for a cancer neoantigen expressed from a tumor associated gene selected from: AP2S1, Survivin, CTSL, MPZL2, and LSP1.
Foot teaches that the mRNA cargo may encode a polypeptide and that mRNA-containing nanoparticles may be used for cancer therapy [pp. 2, 21–27, and 31–33]. Chang teaches RNA nanostructures carrying tumor-specific antigens, tumor-associated antigens, or cancer vaccines [0149–0156]. Chang further teaches that an RNA nanostructure loaded with tumor-specific peptide antigens elicits antitumor immunity and kills cancer cells [0163]. Ciesielski, however, expressly teaches that “Survivin is a tumor-associated antigen with significant potential as a cancer vaccine target” and identifies Survivin-derived epitopes that elicit cytotoxic-T-cell and T-helper responses [p. 1211, Abstract; pp. 1211–1214]. It would have been obvious to encode Survivin or a Survivin-derived tumor-antigen sequence in Foot’s mRNA cargo and deliver that cargo on the RNA junction of Han and Samarsky. Chang supplies an express reason to load tumor antigens on an immunostimulatory RNA nanostructure, while Ciesielski identifies Survivin as a known cancer-vaccine target. Encoding the antigen in mRNA rather than attaching the preformed peptide would have been a predictable alternative expressly contemplated by Foot’s mRNA-delivery platform.
This rejection treats “cancer neoantigen expressed from a tumor associated gene” according to the apparent usage in the claim and Specification, which identifies ordinary tumor-associated genes rather than a particular tumor-specific mutation. If “neoantigen” is construed narrowly as requiring a mutation-specific neoepitope, the present §112(a) rejection remains applicable.
Regarding claim 56, Han and Samarsky do not teach a method of killing a cancer cell with the complex as taught and suggested by Han and Samarsky. Han teaches multi-way oligonucleotide junctions carrying multiple siRNAs directed to tumor-promoting targets and specifically teaches a junction carrying STAT3-siRNA and HDAC8-siRNA for treating acute myeloid leukemia [0054]. Chang teaches that an RNA nanostructure loaded with tumor-specific antigens elicits antitumor immunity and “eventually kills cancer cells” [0163]. Chang further defines a therapeutically effective amount for cancer as an amount that may reduce the number of cancer cells, reduce tumor size, inhibit tumor growth, or kill existing cancer cells [0257]. It would have been obvious to contact a cancer cell with the RNA junction of Han and Samarsky because both references teach intracellular delivery of functional siRNAs, and Chang expressly teaches use of RNA nanostructures to kill cancer cells.
Regarding claim 57, Han and Samarsky do not teach method of treating cancer in a subject in need thereof comprising administering to the subject a therapeutically effective amount of a composition comprising the complex as taught and suggested by Han and Samarsky. Chang teaches “a method of treating cancer in a subject” by administering a therapeutically effective amount of an RNA-nanostructure composition [0294]. Chang also teaches administering an RNA-nanostructure complex or composition to treat a disease or disorder and expressly identifies cancer [0330–0332]. It would have been obvious to use the multivalent RNA junction of Han and Samarsky in Chang’s treatment method because Han already teaches therapeutic treatment with multi-siRNA junctions [0054], and Chang supplies the known administration and cancer-treatment use.
Regarding claim 58, Han and Samarsky do not teach wherein the cancer is a colorectal cancer, pancreatic cancer, breast cancer, ovarian cancer, lung cancer or melanoma. Chang expressly identifies pancreatic, ovarian, breast, colorectal, and lung cancers and melanoma among the cancers treatable using its RNA-nanostructure compositions [0205–0207, 0260, 0294]. Therefore, selection of any one of the expressly listed cancers would have been obvious.
Regarding claim 59, Han and Samarsky do not teach further administering to the subject a therapeutically effective amount of at least one anti-cancer agent. Chang teaches RNA-nanostructure treatment in combination with at least one therapeutic agent [0200–0204] and teaches that the therapeutic agent may be a chemotherapeutic drug, including doxorubicin [0155–0157, 0325–0328]. It would have been obvious to administer the known anticancer agent with the RNA complex because Chang teaches the combination to provide complementary antitumor activity.
Claim 48 is rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”), as applied to claims 38 and 43, and further in view of Foot et al. (WO 2021/053405; hereinafter “Foot”) and Daugherty et al. (US 2012/0244154; “Daugherty”).
The teachings of Han and Samarsky are discussed above as applied to claims 38 and 43 and similarly apply to claim 48. Han and Samarsky do not teach wherein the affibody is an antibody or portion thereof to ASPH or Her2.
Han teaches attachment of antibodies and cell-targeting ligands to oligonucleotide junctions [0055, 0064]. Foot likewise teaches target-cell ligands and identifies HER2 as a cancer-associated molecular marker [pp. 25–27]. Neither reference expressly identifies the claimed antibody or portion directed to HER2. Daugherty teaches antigen-binding domains derived from full-length antibodies, Fab fragments, F(ab′)₂ fragments, single-chain antibodies, and single-chain variable fragments [0149–0150]. Daugherty expressly identifies HER2/neu as a target [0035, 0037; Table 1] and identifies Herceptin/trastuzumab as an exemplary antibody source directed to HER2 [0149–0152; Table 2].
It would have been obvious to use Daugherty’s known HER2-binding antibody or antigen-binding fragment as Han’s cell-targeting ligand because Han expressly teaches attaching an antibody or delivery ligand to the junction for targeted cellular delivery. HER2 was a known tumor-associated surface target, and use of a HER2 antibody or binding fragment would have predictably directed the complex to HER2-expressing cancer cells.
Claim 54 is rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”) and Foot et al. (WO 2021/053405; hereinafter “Foot”), as applied to claims 38, 49, and 53, and further in view of Torelli et al. (Scientific Reports 8:6989 (2018); hereinafter “Torelli”), and Chang et al. (US 2020/0385734; hereinafter “Chang”).
The teachings of Han, Samarsky and Foot are discussed above as applied to claims 38 49 and 53 and similarly apply to claim 54. Han, Samarsky and Foot do not teach wherein the portions of the long mRNA strand are partially complementary to each of the plurality of RNA staple strands such that the Pro-mRNA folds into a shape selected from a 3-D tube, sheet, triangle, or hexagon.
Foot teaches a long RNA molecule compacted by complementary nucleic-acid staples or pins [pp. 28–30, Figs. 8–10]. Torelli teaches “a biologically inert and uniquely addressable RNA origami scaffold” that self-assembles into a nanoribbon using seven staple strands [p. 1, Abstract]. Torelli teaches that the complementary staples hybridize to and fold a 212-nucleotide RNA scaffold [pp. 2–3, Fig. 1]. Torelli further identifies prior RNA-origami structures including hexagonal lattices, a six-helix bundled RNA-origami tube, and triangular RNA-DNA hybrid origami structures [pp. 1–2]. Chang independently teaches that programmable RNA nanostructures may be formed into a rectangle, diamond, tetrahedron, triangle, or another desired shape by selecting a sequence that causes self-assembly through complementary pairing [0144–0145].
It would have been obvious to design the long mRNA and complementary staples of Foot to fold into a tube, sheet or ribbon, triangle, or hexagonal structure because Torelli and Chang teach that these were known programmable RNA-origami geometries. The selection of a particular known shape would have been an ordinary design choice based on desired compactness, surface area, or cargo presentation, with a reasonable expectation that complementary RNA staples would fold the scaffold into the programmed shape..
Claims 60 and 61 are rejected under 35 U.S.C. 103 as being unpatentable over Han et al. (WO 2019/014656; hereinafter “Han”) in view of Samarsky et al. (WO 2020/065602; hereinafter “Samarsky”) as applied to claim 38 and further in view of Shu et al. (Chemical and Pharmaceutical Bulletin 68:129–132 (2020); hereinafter “Shu”) and Foot et al. (WO 2021/053405; hereinafter “Foot”).
The teachings of Han and Samarsky are discussed above as applied to claims 38 and similarly apply to claims 60 and 61. Han and Samarsky do not teach wherein the disulfide modified sequence comprises a linear disulfide (LD) - modified siRNA further comprising 5 repeated LD units introduced at the 5' end of a passenger strand and the 3' ends of the guide strand where the complex does not yield RNA-induced silencing complex (RISC) formation.
Regarding claim 60, Han teaches use of thiol modifications and disulfide linkages on oligonucleotide-junction components to enhance stability and permit intracellular release [0043, 0047, 0057]. Shu teaches a repeatable linear proamino unit containing a biocleavable disulfide group and explains that five repeats were selected because ten repeats produced undesirable micelle formation [p. 129, right column; Table 1]. Shu teaches the 5PR-b siRNA arrangement having the proamino units attached to “the 3′ terminus of the guide strand and the 5′ terminus of the passenger strand” while leaving the RISC-important 5′ terminus of the guide strand unmodified [p. 131, left column; Table 1(b)]. The five-repeat 5PR-b construct produced approximately 60% knockdown at 1 μM and approximately 55% knockdown at 100 nM [p. 131, right column; Fig. 4]. It would have been obvious to use Shu’s five-repeat disulfide-containing units on an siRNA carried by the junction of Han and Samarsky because Han expressly teaches disulfide modification for extracellular stability and intracellular activation, while Shu teaches the specific number and terminal placement of disulfide-containing units that improves cellular uptake and retains siRNA activity. A skilled artisan would have selected five repeats and the 5′ passenger/3′-guide arrangement with a reasonable expectation of improved uptake and intracellular reduction.
Regarding claim 61, Shu’s isolated 5PR-b siRNA retains gene-silencing activity and therefore does not, standing alone, teach the claimed absence of RISC formation [p. 131, Fig. 4]. Han, however, teaches the structural condition that inhibits RNAi processing and loading. Han reports that RNA substrates having additional secondary structure adjacent to the guide-strand 5′ end “showed no cleavage of the guide strand” [0071; Fig. 1]. Han concludes that attached RNA secondary structures may compromise enzymatic processing and “RNAi loading” [0072]. Foot teaches that activity of an RNA cargo may desirably be inhibited in one cell type and permitted in another, thereby reducing activity in off-target cells [pp. 31–33]. Foot further teaches regulating RNA-cargo activity through structural nucleic-acid components and environmentally responsive release [pp. 27–34]. It would have been obvious to maintain Han’s inhibitory secondary structure around Shu’s disulfide-modified siRNA while the siRNA remained assembled in the delivery complex, thereby preventing processing and RISC loading before the desired intracellular or cell-specific activation event. Foot supplies an express reason for doing so: preventing premature or off-target RNA activity while permitting activity under the intended cellular conditions. Han teaches the predictable mechanism—additional secondary structure causing no guide-strand cleavage and compromised RNAi loading—and Shu supplies the claimed five-unit terminal modification pattern. The resulting assembled complex would not yield RISC formation before disassembly or activation. Claim 61 therefore would have been obvious.
Conclusion
No claims allowed.
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/TIFFANY NICOLE GROOMS/Examiner, Art Unit 1637
Prosecution Insights