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 .
DETAILED ACTION
Pursuant to a preliminary amendment, claims 1-20 and 25, filed April 25, 2023 are currently pending in the instant application.
Therefore, claims 1, 3-20 and 25 are under consideration to which the following grounds of rejection are applicable.
Priority
The present application filed April 25, 2023, is a 35 U.S.C. 371 national stage filing of International Application PCT/US2021/056471, filed October 25, 2021, which claims the benefit of US Provisional Patent Application 63105741, filed October 26, 2020.
Information Disclosure Statement
No information disclosure statement has been filed in the instant application. Applicants are reminded of their duty to disclose all information known to them to be material to the patentability as defined in 37 C.F.R. 1.56.
Claim Objections/Rejections
Claim Objection
Claims 1, 4-6, 11, 13, 15, 16 and 25 are objected to because of the following informalities: Claims 1, 4-6, 11, 13, 15, 16 and 25 recite terms such as: “PCR”, "UV”, “UDP”, “mRNA”, “bp”, “UTR”, “LNA”, “APP”, “ATG9A”, “BTG2” and ULK1”, where an abbreviation should be spelled out in the first encounter of the claims.
Appropriate correction is required.
Claim 5 is objected to because of the following informalities: Claim 5 recites the terms: “prionaldehyde” and “water-soluble carbomiidides”, where there are no such chemical agents by those names. The Examiner believes that the terms “propionaldehyde” and “water-soluble carbodiimides” might be more appropriate.
Appropriate correction is required.
Specification Objection
The disclosure is objected to because of the following informalities: the as-filed Specification, filed April 25, 2023, teaches that chemical crosslinking agents include “proionaldehyde,” which is not a chemical crosslinking agent.
Appropriate correction is required.
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.
Claims 1, 3-20 and 25 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention.
Claim 1 is indefinite for the recitation of the term “enriching microRNA (miRNA) targeted RNA molecules” such as recited in claim 1, line 1 because the term “miRNA targeted RNA molecules” is unclear with regard to what is being enriched; and whether miRNA is being enriched; whether miRNA that targets specific RNA is enriched; whether RNA molecules are being enriched; or whether the term refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 1 is indefinite for the recitation of the term “target-specific miRNA molecules” such as recited in claim 1, line 3. There is insufficient antecedent basis for the term “target-specific miRNA molecules” in the claim because claim 1, line 1 recite the term “miRNA targeted RNA molecules.” The Examiner suggests that Applicant amend claim 1, line 1 to recite, for example, “enriching target-specific miRNA molecules.”
Claims 1, 10 and 12 are indefinite for the recitation of the term “the miRNA molecules” such as recited in claim 1, line 6. There is insufficient antecedent basis for the term “the miRNA molecules” in the claim because claim 1, lines 1 and 3 recite the terms “miRNA targeted RNA molecules” and “target-specific miRNA molecules.”
Claim 1 is indefinite for the recitation of the term “enriching non-chimeric RNA molecules of interest” such as recited in claim 1, line 8 because claim 1 does not recite the presence, production and/or formation of “non-chimeric RNA molecules of interest.” Instant claim 1, line 7 recites the formation of “chimeric RNA molecules,” such that it is completely unclear where the “non-chimeric RNA molecules of interest” originate and, thus, the metes and bounds of the claim cannot be determined.
Claim 3 is indefinite for the recitation of the term “lysing cells prior to isolating” in claim 3, lines 1-2 because it is unclear as to the origin of the “cells.” Instant claim 3 depends from claim 1, wherein claim 1 does not recite the presence of cells, such that it is unclear where the cells originate and, thus, the metes and bounds of the claim cannot be determined.
Claim 8 is indefinite for the recitation of the term “contacting the complex with an Ago2 antibody” recited in claim 8, line 2 because immunoprecipitation cannot be carried out by contacting the complex just any Ago2 antibody. As indicated in the as-filed Specification, immunoprecipitation is carried out using an antibody that is specific for the Ago2 protein (paragraph [0097]); or more specifically, using anti-Ago2 antibodies (paragraph [0116]) and, thus, the metes and bounds of the claim cannot be determined.
Claim 9 is indefinite for the recitation of the term “the contacting step” such as recited in claim 9, line 1. There is insufficient antecedent basis for the term “the contacting step” in the claim because claim 1, line 3 recites the term “contacting an RNA sample.” The Examiner suggests that Applicant amend claim 9 to recite, for example, “wherein contacting…”
Claim 9 is indefinite for the recitation of the term “the contacting step is followed converting associated RNA into libraries” such as recited in claim 9, lines 1-2 because the meaning of the claim is completely unclear. It is unclear whether “contacting” is followed by a series of reactions to covert RNA into libraries, or whether the claim refers to something else and, thus, the metes and bounds of the claim cannot be determined.
Claim 9 is indefinite for the recitation of the term “associated RNA” such as recited in claim 9, line 2. There is insufficient antecedent basis for the term “associated RNA” in the claim because claim 1, line 1, 7 and 8 recite the terms “targeted RNA molecules;” “chimeric RNA molecules;” and “non-chimeric RNA molecules of interest.” Moreover, it is completely unclear what RNA molecules are encompassed by the term “associated RNA.”
Claim 9 is indefinite for the recitation of the term “that can be subjected to high throughput sequencing to quantify association” such as recited in claim 9, lines 2-3 because the term recite a potential step that is not performed. Moreover, it is completely unclear what “association” is being referred to, how it could be quantified, and/or what that means and, thus, the metes and bounds of the claim cannot be determined.
Claims 11 and 14 are indefinite for the recitation of the term “antisense nucleic acid probes in a length between 10 bp and 100 bp” such as recited in claim 11, lines 1-2 because the as-filed Specification teaches that the antisense probes are RNA, ssDNA, or synthetic nucleic acids such as LNA probes (pg. 3, lines 1-4) (e.g., single-stranded probes). It is unclear whether all antisense probes used in the method are intended to recite double-stranded probes (e.g., 10 base pairs to X base pairs) and, thus, the metes and bounds of the claim cannot be determined.
Claim 15 is indefinite for the recitation of the term “reverse transcribing RNA molecules” such as recited in claim 15, line 2 because it is completely unclear which “RNA molecules” are reverse transcribed into cDNA because claim 15 depends from instant claim 1, wherein claim 1 recites a variety of different RNA molecules including: target-specific miRNA molecules, targeted RNA molecules, miRNA molecules, RNA sample, RNA molecules within the complex, non-chimeric RNA molecules of interest, and chimeric RNA molecules and, thus, the metes and bounds of the claim cannot be determined.
Claims 15, 17, 18 and 19 are indefinite for the recitation of the terms “the enriching step” or “the enrichment step” such as recited in claim 15, line 2. There is insufficient antecedent basis for the terms “the enriching step” or “the enrichment step” in the claims because claim 1, line 10 recites the term “enriching non-chimeric RNA molecules of interest and chimeric RNA molecule or cDNA molecules thereof” such that claim 1 does not recite an “enriching step.”
Claim 18 is indefinite for the recitation of the term “the enrichment step produces…chimeric reads out of all uniquely mapped reads” such as recited in claim 18, lines 1-2 because claim 18 depends from instant claim 1, wherein claim 1 does not recite an “enrichment step,” chimeric reads, and/or mapping reads and, thus, the metes and bounds of the claim cannot be determined.
Claim 19 is indefinite for the recitation of the term “the enrichment step increases the proportion of chimeric reads in the library” such as recited in claim 19, lines 1-2 because claim 19 depends from instant claim 1, wherein claim 1 does not recite an “enrichment step,” proportions, chimeric reads, and/or a library and, thus, the metes and bounds of the claim cannot be determined.
Claim 19 is indefinite for the recitation of the term “the library” such as recited in claim 19, line 2. There is insufficient antecedent basis for the term “the library” in the claim.
Claim 20 is indefinite for the recitation of the term “the overall chimeric read population” such as recited in claim 20, line 1. There is insufficient antecedent basis for the term “the overall chimeric read population” in the claim. Moreover, claim 20 depends from claims 1 and 19, wherein claims 1 and 19 do not recite overall chimeric read populations and/or anything to which a read population can be compared (e.g., to note an increase or decrease) and, thus, the metes and bounds of the claim cannot be determined
Claim 25 is indefinite for the recitation of the term “the Ago2” such as recited in claim 25, line 1. There is insufficient antecedent basis for the term “Ago2” in the claim because claim 1, line 4 recites the term “Ago2 proteins.”
Claims 4-7, 13 and 16 are indefinite insofar as they ultimately depend from claim 1.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 3, 9, 13, 15 and 17-20 are rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 3 recites (in part): “further comprising lysing cells prior to isolating the complexes” in lines 1-2 because claim 3 depends from instant claim 1, wherein claim 1 does not recite the presence of cells which can be lysed. Thus, claim 3 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 9 recites (in part): “the contacting step is followed converting associated RNA into libraries that can be subjected to high-throughput sequencing” in lines 1-2 because claim 9 depends from instant claim 1, wherein claim 1 does not recite the presence of associated RNA, sequencing devices, steps for converting, the production of libraries, etc. Thus, claim 9 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 13 recites (in part): “the non-chimeric RNA molecules of interest map to specific genes or 3’-UTR of genes” in lines 1-2 because claim 13 depends from instant claim 1, wherein claim 1 does not recite mapping of non-chimeric RNA molecules of interest and/or any specific genes or portions of genes. Thus, claim 13 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 15 and 17 recite (in part): “the enriching step” in claim 15, line 2 because claims 15 and 17 depend from instant claim 1, wherein claim 1 does not recite and “enriching step.” Thus, claims 15 and 17 are improper dependent claims for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 18 recites (in part): “wherein the enrichment step produces about 5% to about 30% chimeric reads out of all uniquely mapped reads” in lines 1-2 because claim 18 depends from instant claim 1, wherein claim 1 does not recite an enrichment step; the production of reads, and/or uniquely mapped reads. Thus, claim 18 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 19 recites (in part): “wherein the enrichment step increases the proportion of chimeric reads in the library” in lines 1-2 because claim 19 depends from instant claim 1, wherein claim 1 does not recite an enrichment step; the production of reads, any specific number or proportion of reads, and/or a library. Thus, claim 19 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 20 recites (in part): “wherein overall chimeric read population is increased by at least 20-fold” in lines 1-2 because claim 20 depends from instant claims 1 and 19, wherein claims 1 and 19 do not recite the production of reads, an overall chimeric read population and/or any specific beginning quantity of chimeric reads. Thus, claim 20 is an improper dependent claim for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
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 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.
Claims 1, 3, 4, 6-10, 12, 13, 15-17 and 19 are rejected under 35 U.S.C. 102(a1)/102(a2) as being anticipated by Hong, Hung (hereinafter “Hong”) (Thesis, The Hong Kong Polytechnic University, 2017, 1-399) as evidenced by Van Der Oost et al. (hereinafter “Van Der Oost”) (US Patent No. 9902973, issued February 27, 2018); and Fotin-Mleczek et al. (hereinafter “Fotin-Mleczek”) (US Patent No. 11078247, issued Augst 3, 2021; PCT/EP2017/060692, filed May 4, 2017).
Regarding claims 1, 4, 6-8, 10, 15 and 17, Hong teaches that the RNA Interactome Identification by Next Generation Sequencing (RIINGS) experiment starts with cells or tissues that have been disrupted into small pieces, wherein like other RNA intercome identification methods RIINGS requires crosslinking, immuno-precipitation and RNA digestion (interpreting cells and tissues as an RNA sample comprising mRNA or mRNA fragments; crosslinking; disruption produces RNA fragments; and IP as isolating, claims 1, 4, 6 and 7) (pg. 99, Section 1.6.1, first full paragraph). Hong teaches that crosslinking can be achieved by 254 nm UV light or 365 nm UV light with the assistance of 4-thiouridine (4SU) (interpreted as crosslinking with UV light can include a chemical agent 4SU, claim 4) (pg. 99, Section 1.6.1; last partial paragraph, lines 1-2), wherein it is known in the art that cells or complexes can be fixed or crosslinked using suitable fixatives and crosslinkers including: formaldehyde, glutaraldehyde, ethanol-based fixatives, methanol-based fixatives, acetone, acetic acid, osmium tetraoxide, potassium dichromate, chromic acid, potassium permanganate, mercurials, picrates, formalin, paraformaldehyde, amine-reactive NHS-ester crosslinkers such as bis[sulfosuccinimidyl] suberate (BS3), etc. as evidenced by Van Der Oost (col 45, lines 16-33; and col 99, lines 48-65). Hong teaches that the targeted RNA-induced silencing complexes (RISCs) are then isolated from the crude lysate by immunoprecipitation by using anti-Argonaute antibody-conjugated magnetic beads, wherein the antibody captures the non-denatured (native) Argonaute proteins (interpreted as contacting an RNA sample with miRNA in the presence of Ago2 protein; interpreting IP as isolating RSIC as complexes; lysing prior to IP; using Ago2 antibody; and where non-chimeric molecules of interest are miRNA, claims 1, 3, 7, 8 and 10) (pg. 100, Section 1.6.1, first partial paragraph, lines 1-4). Hong teaches that after immunoprecipitation, sequential ligation of miRNA 5’-mismatch repairer and then miRNA 3’-mismatch repairer is performed because both ends of the miRNA might stick out from the Argonaute protein (interpreted as ligating miRNA molecules to the RNA molecules within the complex, claim 1) (pg. 100, Section 1.6.1, first partial paragraph, lines 4-6). Hong teaches that RNA digestion is performed to trim the RNAs protruding from the RISCs to the length sufficient for adaptor ligation (interpreting adaptor ligation as ligating miRNA molecules to the RNA molecules within the complex, claim 1) (pg. 100, Section 1.6.1, first partial paragraph, lines 9-10). Hong teaches that the Stem-Loop Adaptor (RNA) is used to connect the miRNAs and their corresponding target site to generate the chimeric sequences that represent the miRNA-target site interactions; and subsequently, the Argonaute protein is removed by digestion using proteinase K at 4℃, where this low temperature (4℃) keeps the RNA duplexes in duplex form (interpreting adaptor ligation as ligating miRNA molecules to the RNA molecules within the complex; and forming chimeric RNA molecules; and digesting Ago2 proteins before enrichment, claims 1 and 17) (pg. 100, Section 1.6.1, last partial paragraph, lines 6-10). Hong teaches that the chimeric sequence quantification assay uses a hydrolysis probe (Chimera Quanti Probe), and two primers (interpreted as enriching using probes, claim 1) (pg. 181, Section 4.11.3.1; first full paragraph). Hong teaches that the use of TargetScan, which was first developed prediction algorithm for predicting mammalian miRNA targets, wherein the algorithm seeks for seed matches at 3’ UTR of mRNA of the query organism such as humans, such that the definition of seed match is the full complementarity of miRNA positions 2 to 8 (the 7-mer seed region of miRNA) to anywhere in the 3’ UTR of candidate target mRNAs (interpreted as computationally identifying RNA molecules of interest, claim 1) (pg. 67, Section 1.4.1, first full paragraph), where it is known that 3’-UTR corresponds to mature mRNA of a gene including APP, ATG9A, BTG2 and ULK1 as evidenced by Fotin-Mleczek (col 13, lines 7-8 and 15-16; col 19, line 42; col 20, line 14; col 21, line 10; and col 48, line 47). Hong teaches a flow chart of RIINGS as shown in Figure 3.1 including: UV irradiation to crosslink the effecting Argonaute complex, which in vivo includes an Argonaute protein, a miRNA and a target RNA; ligation of Reattaching Adaptor and Stem-Loop Adaptor (RNA); a first mismatch-repairing step; a second mismatch-repairing step; generation of chimeric sequences by RT-PCR; and sequence analysis of the chimeric library by NGS (interpreted as converting RNA into libraries that can be subjected to sequencing, claim 9) (pg. 105; Figure 3.1). Figure 3.1 is shown below:
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Hong teaches that RNA duplexes are captured by Library Enrichment Beads (interpreted as enriching non-chimeric RNA and chimeric RNA, claim 1) (pg. 101, Section 1.6.1; first full paragraph, line 1). Hong teaches that a second round of ligating miRNA 5’- and 3’-mismatch repairers is performed at the 5’ and 3’ ends of miRNAs respectively and sequentially, such that these two repairers generate new ends on the mismatched ends and these newly generated ends are potentially able to match their corresponding target sequence; and the gap between the miRNA 5’ end and the Stem-Loop Adaptor (RNA) 3’end is then repaired (filled) by the ligation of some short fillers (RNA tetramers), such that during this ligation process, the 3’ end of the miRNAs is also extended, finally reaches and then passes the restriction enzyme cleavage site on the “Re-attaching Adaptor”; and after these ligation steps, the chimeric sequences are generated (pg. 101, Section 1.6.1; first full paragraph, lines 1-9). Hong teaches that the chimeric sequences can be eluted by the restriction enzyme BanI because the Reattaching Adaptor includes a BanI cutting site; and finally, the chimeras are recovered through reverse transcription, PCR and NGS (interpreted as enriching cDNA; PCR; and sequencing the PCR products, claims 1 and 15) (pg. 101, Section 1.6.1; last full paragraph, lines 1-3). Hong teaches that the stem-loop adaptor has to be ligated to the 3' end of the miRNA target as shown in the scheme of RIINGS (Figure 3.1), such that this adaptor effectively extends the 3' end of the miRNA target and flips it over and backward, and positions the 3' end of the “miRNA target” and the 5' end of the miRNA in a head-to-tail manner with a gap in between; and the loop of the adaptor conceals a probe-binding site because it is in fact the binding site of a specific probe, wherein this binding site facilitates the quantification of valid cDNA by means of qPCR or digital PCR in a library prepared by RIINGS (interpreted as enriching with probes, claim 1) (pg. 126, Section 4.6; last partial paragraph; and pg. 127, first partial paragraph). Hong teaches that the miRanda algorithm is also commonly used for predicting target sites of miRNAs; and uses criteria similar to those of TargetScan, and was initially built for predicting miRNA target sites in fly and humans, wherein it first aligns miRNAs (the whole sequence of each miRNA) to the 3’ UTR of target mRNAs to recognize highly complementary sequences (interpreted as computationally identifying RNA molecules of interest, claim 1) (pg. 68, Section 1.4.3, first partial paragraph).
Regarding claim 9, Hong teaches a flow chart of RIINGS as shown in Figure 3.1 including:
UV irradiation to crosslink the effecting Argonaute complex, which in vivo includes an Argonaute protein, a miRNA and a target RNA; ligation of Reattaching Adaptor and Stem-Loop Adaptor (RNA); a first mismatch-repairing step; a second mismatch-repairing step; generation of chimeric sequences by RT-PCR; and sequence analysis of the chimeric library by NGS (interpreted as converting RNA into libraries that can be subjected to sequencing, claim 9) (pg. 105; Figure 3.1).
Regarding claims 12 and 16, Hong teaches that the hydrolysis probe has the structure of Figure 4.11.3, which comprises miRNA, target RNA target site, stem-loop adaptor and sequencing adaptors (interpreted as comprising RNA; and 100% complementary to miRNA, claims 12 and 16) (pg. 180, Figure 4.11.3). Figure 4.11.3 is shown below:
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Regarding claim 13, Hong teaches that the use of TargetScan, which was first developed prediction algorithm for predicting mammalian miRNA targets, wherein the algorithm seeks for seed matches at 3’ UTR of mRNA of the query organism such as humans, such that the definition of seed match is the full complementarity of miRNA positions 2 to 8 (the 7-mer seed region of miRNA) to anywhere in the 3’ UTR of candidate target mRNAs (interpreted as mapping to specific genes or 3’-UTR of genes, claim 13) (pg. 67, Section 1.4.1, first full paragraph). Hong teaches that the miRanda algorithm is also commonly used for predicting target sites of miRNAs; and uses criteria similar to those of TargetScan, and was initially built for predicting miRNA target sites in fly and humans, wherein it first aligns miRNAs (the whole sequence of each miRNA) to the 3’ UTR of target mRNAs to recognize highly complementary sequences (interpreted as mapping to specific genes or 3’-UTR of genes, claim 13) (pg. 68, Section 1.4.3, first partial paragraph).
Regarding claim 19, Hong teaches that unlike CLASH, Mapping RNA interactome in vivo (MARIO) is a method that requires the insertion of a biotinylated short linker between the two interacting RNAs in RNA chimera construction, such that the chimeras can thus be enriched from the sample by this biotinylated short linker (Figure 1.5.5), wherein the chimera enrichment is a very distinctive advantage of MARIO (interpreted as enrichment increases the proportion of chimeric reads in the library, claim 19) (pg. 88, Section 1.5.6, first full paragraph).
Hong does not specifically exemplify the crosslinking agents as recited in claim 5 (claim 5); antisense nucleic acid probes having a length between 10 bp and 100 bp (claim 11); antisense nucleic acid probes having a length between 10 bp and 5000 bp (claim 14); where the enrichment step produces about 5% to 30% chimeric reads out of all uniquely mapped reads (claim 18); where the overall chimeric read population is increased 20-fold (claim 20); and where the Ago2 protein includes a gene selected from APP, ATG9A, BET2 and ULK1 (claim 25).
Hong meets all the limitations of the claims and, therefore, anticipates the claimed invention.
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 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 may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
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 1, 3-20 and 25 are rejected under 35 U.S.C. 103 as being unpatentable over Hong, Hung (hereinafter “Hong”) (Thesis, The Hong Kong Polytechnic University, 2017, 1-399) in view of Xu et. al. (hereinafter “Xu”) (RNA Biology, 2017, 14(2), 259-274) as evidenced by Van Der Oost et al. (hereinafter “Van Der Oost”) (US Patent No. 9902973, issued February 27, 2018); and Fotin-Mleczek et al. (hereinafter “Fotin-Mleczek”) (US Patent No. 11078247, issued Augst 3, 2021; PCT/EP2017/060692, filed May 4, 2017).
The teachings of Hong as applied to claims 1, 3, 4, 6-10, 12, 13, 15-17 and 19 are described supra.
Hong does not specifically exemplify crosslinking agents as recited in claim 5 (claim 5); antisense nucleic acid probes having a length between 10 bp and 100 bp (claim 11); antisense nucleic acid probes having a length between 10 bp and 5000 bp (claim 14); where the enrichment step produces about 5% to 30% chimeric reads out of all uniquely mapped reads (claim 18); where the overall chimeric read population is increased 20-fold (claim 20); and where the Ago2 protein includes a gene selected from APP, ATG9A, BET2 and ULK1 (claim 25).
Regarding claims 5, 11, 14, 18, 20 and 25, Xu teaches high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (CLIP), wherein the isolated Argonaute protein (Ago) binding sites are analyzed computationally to infer the possible microRNA(s) that could have been responsible for tethering Ago to those binding sites (pg. 259, col 2, first partial paragraph, lines 4-9). Xu teaches that a crosslinking and ligation approach termed CLASH was reported in which crosslinked miRNA-target sequence are ligated to generate chimeras for sequencing, wherein the method should overcome the ambiguity in assigning the Ago- bound sequence to the microRNA responsible for recruiting the target gene to the RISC complex, where a drawback of the method is its relatively low efficiency of chimera generation and capture (pg. 259, col 2, last partial paragraph, lines 14-20; and pg. 260, col 1, first partial paragraph, line 1). Xu teaches that TargetLink is used for identifying target genes directly bound by a specific microRNA, wherein TargetLink involves crosslinking microRNA and its target genes in intact live cells by UV illumination, and cell lysates containing the crosslinked microRNA-Argonaute-mRNA ternary complexes were prepared and subjected to affinity purification using locked nucleic acid (LNA) as the capture probe to pull down complementary microRNA and its crosslinked target genes (interpreted as anti-sense nucleic acid probes; pull down; LNA; inherently produces 5% to 30% chimeric reads; and inherently increases reads by at least 20-fold, claims 11, 14, 18 and 20) (pg. 260, col 1; second full paragraph, lines 1-8). Xu teaches that TargetLink is based on the principles of RNA photo-crosslinking and antisense purification of crosslinked RNA complexes, wherein because microRNAs are only ~22 nt long, locked nucleic acid (LNA) was applied as the affinity probe to pull down microRNA and associated protein complexes, wherein LNA oligonucleotides bind to complementary RNA with very high affinity and specificity to yield remarkably stable LNA/RNA duplexes, and antisense LNA oligonucleotides as short as 8-mer have been successfully used to knock down miRNA (interpreted as anti-sense nucleic acid probes between 10-100 or 10-5000 bp; and LNA, claims 11 and 14) (pg. 260, col 2; first full paragraph, lines 1-9). Xu teaches that the resulting file containing the unique mapped reads reflected the distribution of affinity purified RNA fragments across the transcriptome, and it was used for detecting the enrichment of sequences resulting from LNA affinity purification (interpreted as increases in chimeric reads, claims 18 and 20) (pg. 261, col 1, last partial paragraph; and pg. 262, col 1, first partial paragraph). Xu teaches that the LNA affinity probe selectively pulled down more transcripts in UV crosslinked samples through the crosslinked ternary complexes containing miR-21/Ago/targets (pg. 262, col 2, first partial paragraph).
Although the combined references of Hong and Xu do not specifically teach that crosslink agents include formalin, formaldehyde, etc., Hong does teach that crosslinking can be achieved by 254 nm UV light or 365 nm UV light with the assistance of 4-thiouridine (4SU), where it is known in the art that cells or complexes can be fixed or crosslinked using suitable fixatives and crosslinkers including: formaldehyde, glutaraldehyde, ethanol-based fixatives, methanol-based fixatives, acetone, acetic acid, osmium tetraoxide, potassium dichromate, chromic acid, potassium permanganate, mercurials, picrates, formalin, paraformaldehyde, amine-reactive NHS-ester crosslinkers such as bis[sulfosuccinimidyl] suberate (BS3), etc. as evidenced by Van Der Oost; and Xu does teach high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (CLIP); a crosslinking and ligation approach (CLASH); and crosslinking microRNA and its target genes in intact live cells by UV illumination, such that one of ordinary skill in the art would clearly recognize that a variety of crosslinking agents can be used in a crosslinking reaction including the chemical agents such as formalin, formaldehyde, etc.
Although the combined references of Hong and Xu do not specifically exemplify Ago2 includes a gene selected from APP, ATG9A, BTG2 and ULK1, Hong does teach that the use of TargetScan, which was first developed prediction algorithm for predicting mammalian miRNA targets, wherein the algorithm seeks for seed matches at 3’ UTR of mRNA of the query organism such as humans, such that the definition of seed match is the full complementarity of miRNA positions 2 to 8 (the 7-mer seed region of miRNA) to anywhere in the 3’ UTR of candidate target mRNAs, where it is known that 3’-UTR corresponds to mature mRNA of a gene including APP, ATG9A, BTG2 and ULK1 as evidenced by Fotin-Mleczek; and Xu does teach reads mapped to a candidate miR-21 target gene MKNK2; and the identification of miR-21 target genes using deep sequencing data, such that one of ordinary skill in the art would clearly recognize that any specific gene of interest including the 3’ UTR of any candidate target mRNAs can be selected and/or investigated using the methods taught supra including for the identification of miR target genes bound to specific miRNA such as APP, ATG9A, BTG2 and ULK1.
“It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose.... [T]he idea of combining them flows logically from their having been individually taught in the prior art.” In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980). Moreover, it is prima facie obvious to combine prior art elements according to known methods to yield predictable results; the court held that, "…a conclusion that a claim would have been obvious is that all the claimed elements were known in the prior art and one skilled in the art could have combined the elements as claimed by known methods with no change in their respective functions, and the combination would have yielded nothing more than predictable results to one of ordinary skill in the art. KSR International Co. v. Teleflex Inc., 550 U.S. ___, ___, 82 USPQ2d 1385, 1395 (2007); Sakraida v. AG Pro, Inc., 425 U.S. 273, 282, 189 USPQ 449, 453 (1976); Anderson’s-Black Rock, Inc. v. Pavement Salvage Co., 396 U.S. 57, 62-63, 163 USPQ 673, 675 (1969); Great Atlantic & P. Tea Co. v. Supermarket Equipment Corp., 340 U.S. 147, 152, 87 USPQ 303, 306 (1950)”. Therefore, in view of the benefits of identifying target genes directly bound by a specific microRNA as exemplified by Xu, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the method of identifying the entire interactome of microRNA in a specific cell type or tissue using the RINGS method as disclosed by Hong to include the TargetLink method of antisense purification of crosslinked RNA complexes using antisense nucleic acids as taught by Xu with a reasonable expectation of success in efficiently identifying the target set of a specific microRNA in intact cells; in enhancing the generation of microRNA-target RNA chimeras from all interacting pairs during library preparation; and/or in obtaining a file of uniquely mapped reads reflecting the distribution of affinity purified RNA fragments across the transcriptome.
Thus, in view of the foregoing, the claimed invention, as a whole, would have been obvious to one of ordinary skill in the art at the time the invention was made. Therefore, the claims are properly
rejected under 35 USC §103(a) as obvious over the art.
Conclusion
Claims 1, 3-20 and 25 are rejected.
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/AMY M BUNKER/Primary Examiner, Art Unit 1684