DETAILED ACTION
The amendment filed on 09/25/2025 has been entered.
Claims 1, 7, 9, 23, and 37 were amended in the claim set filed on 09/25/2025.
Applicant’s election with traverse of Group I (claims 1-3, 7-9, 11, 13, 15, 20-24, 28-30, 33, 35, 37), drawn to a method for identifying regions of genomic DNA bound to a protein, the method comprising: contacting genomic DNA with an adenine methyltransferase (A-MTase) to detect locations in the genomic DNA lacking methylated adenine residues to identify regions of genomic DNA bound to a protein. It is the Applicant's position that examination of claims of Group II and Ill would not pose an undue burden, in the reply filed on 09/25/2025 is acknowledged.
Claims 2-6, 10, 12, 14-19, 24-36 and 38-72 are canceled in the claim set filed on 09/25/2025. Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Claims 73-74 are added in the claim set filed on 09/25/2025. No new matter was added.
Claims 1, 7-9, 11, 13, 20-23, 37 and 73-74 in the claim set filed on 09/25/2025 are currently under examination.
Response to the Arguments
As necessitated by cancellation of claims 28 and 33, the 35 U.S.C. 112(b) rejections documented in the previously mailed non-final have been withdrawn.
As necessitated by amendment of claim 23 and cancellation of claim 30 the 35 U.S.C. 112(d) rejections documented in the previously mailed non-final have been withdrawn.
As necessitated by cancellation of claims 15, 24, 28-30, 33 and 35, the 35 U.S.C. 101 rejections documented in the previously mailed non-final have been withdrawn.
As necessitated by cancellation of claims 2-3, 15, 24, 28-30, 33 and 35, the 35 U.S.C. 103 rejections towards claims 2-3, 15, 24, 28-30, 33 and 35 documented in the previously mailed non-final have been withdrawn.
As necessitated by amendment, Applicant’s arguments regarding previous rejection(s) of claim(s) 1-3, 7, 11, 13, 15, 21, 23, 33 and 37 under 35 U.S.C. 103 have been fully considered and are persuasive. Applicant’s argument on Pg. 7, states that “Applicants submit that a prima facie case of obviousness has not been established as least because the combination of the cited references fails to teach or suggest each and every claim element. In addition, the primary reference teaches away from the claimed invention. Furthermore, the claimed invention provides unexpected results.” The 35 U.S.C. 103 rejections documented in the previously mailed non-final have been withdrawn in light of applicants claim amendments and arguments on Pg. 12-17. However, upon further consideration and search, new grounds of rejection are made as documented below in the 35 U.S.C. 103 rejection in this office action on Pg. 4-30.
The rejections for claims 1, 7-9, 11, 13, 20-23, 37 and 73-74 are documented below in this Final Office Action are necessitated by claim amendments filed on 09/25/2025.
Priority
This application is a 371 of PCT/US2021/025644 04/02/2021 which claims benefit of United States Provisional Application No. 63/004,361, filed on 04/02/2020.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 1, 7,11,13, 21, 23 and 37 are rejected under 35 U.S.C. 103 as being unpatentable over Shipony et al. (“Shipony”; (2020). Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature methods, 17(3), 319-327, Epub 2020 Feb 10. 2020.) in view of Drozdz et al. (“Drozdz”; Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res. 2012 Mar;40(5):2119-30.)
Shipony discloses a method for profiling the accessibility of individual chromatin fibers, a single-molecule long-read accessible chromatin mapping sequencing assay (SMAC-seq), enabling the simultaneous, high-resolution, single-molecule assessment of chromatin states at multikilobase length scales. Our strategy is based on combining the preferential methylation of open chromatin regions by DNA methyltransferases with low sequence specificity, in this case EcoGII, an N6-methyladenosine (m6A) methyltransferase, and the ability of nanopore sequencing to directly read DNA modifications. We demonstrate that aggregate SMAC-seq signals match bulk-level accessibility measurements, observe single-molecule nucleosome and transcription factor protection footprints, and quantify the correlation between chromatin states of distal genomic elements. (Abstract)
Regarding claim 1, Shipony teaches a method comprising “m6A methyltransferase EcoGII as an alternative/addition to CpG/GpC and use nanopore sequencing to generate single-molecule readouts of accessibility states over many kilobases (Fig. 1a) … enabling the generation of methylation maps for individual DNA molecules, which can then be interpreted
in terms of chromatin accessibility” (Pg. 319, Col. 2, Para. 1). m6A methyltransferase EcoGII is interpreted as an A-MTase. “enabling the generation of methylation maps…in terms of chromatin accessibility” is interpreted as A-MTase causes methylation of adenine residues at genomic sites not bound by protein and thus accessible. Nanopore sequencing is interpreted as long-read sequencing. Shipony also teaches a method comprising “To verify the specificity and efficiency of enzymatic treatments, we carried out … experiments on chromatin (Pg. 319, Col 2, last sentence; Pg. 320, Col 1, first sentence). “carried out experiments on chromatin is interpreted as contacting genomic DNA with A-MTase. Thus, Shipony teaches a method for identifying regions of genomic DNA bound to a protein, the method comprising: contacting genomic DNA with an adenine methyltransferase (A-MTase), wherein the A-MTase causes methylation of adenine residues in regions of the genomic DNA not bound to a protein.
Regarding claim 1, Shipony teaches a method comprising “all bases at 1-bp resolution” (Supp. Fig. 4 and 5 legends) and “m6A-only, 1 bp resolution” (Supp. Fig. 4 and 5). Shipony also teaches a method comprising “Nuclei were then treated with EcoGII” (Pg. 328, Methods-GM12878 SMAC-seq experiments, para. 1) Thus, Shipony teaches a method comprising a single enzyme that is a (m6A-MTase) and detect locations in the genomic DNA lacking methylated adenine residues to identify at single nucleotide resolution regions.
Regarding claim 1, Shipony suggests that “EcoGII’s methylation efficiency is more difficult to estimate as fully methylated templates are known to be difficult to sequence … the limited number of observed reads exhibited ~50% methylation levels. We hypothesize these rates are underestimates, as biochemical reports suggest ≥50% methylation of gDNA after 5 min, increasing to ≥85% after an hour” (Pg. 320 col. 2- Pg. 321 col. 1).
Shipony does not explicitly teach the limitations of claim, wherein the m6A-MTase is Hia5.
Drozdz discloses “…Products of the hin1523, hia5 and nma1821 genes modify adenine residues to N(6)-methyladenine, both in vitro and in vivo. All of these enzymes catalyzed extensive DNA methylation; most notably the Hia5 protein caused the methylation of 61% of the adenines in λ DNA. Kinetic analysis of oligonucleotide methylation suggests that all adenine residues in DNA, with the possible exception of poly(A)-tracts, constitute substrates for the Hia5 and Hin1523 enzymes. Their potential 'sequence specificity' could be summarized as AB or BA (where B = C, G or T)…” (Abstract)
Regarding claim 1, Drozdz teaches a method wherein “The observed high level of adenine methylation strongly suggested that the Hia5… enzymes have minimal sequence specificity” (Pg. 2125-2126,Sequence preferences of MTases, Para. 1). Drozdz teaches that “These results were the first indication of the massive DNA methylation catalyzed by the Hia5… Corroborating evidence was obtained using an HPLC DNA methylation assay to evaluate the base composition of λ DNA methylated with Hia5 in vitro. This analysis revealed that as much as 61% of the adenine residues were converted to m6A.” (Pg. 2128, col. 2 para. 2). Lastly, Drozdz teaches that “Sequence searches with the Hia5 sequence against a non-redundant database (NCBI) revealed many closely related proteins, suggesting that there may exist more DNA : m6A MTases with similar properties, i.e. extremely relaxed substrate specificity” (Pg. 2129, col. 1, Para. 5) and “the discovery of a group of DNA:m6 A MTases with extremely relaxed substrate specificity has significance due to their potential as tools in molecular biology research” (Pg. 2129, col. 2, Para. 3).
Shipony and Drozdz are both considered to be analogous to the claimed invention because they are in the same field of non-specific m6A methyltransferases as a molecular biology tool. Therefore, it would have been obvious to someone of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of methylating adenine residues in regions of the genome not bound by proteins using the nonspecific m6A-methyltransferase EcoGII as taught by Shipony to incorporate the method wherein the nonspecific m6A-methyltransferase is Hia5 of as taught by Drozdz in order to yield a predictable result of identifying regions of genomic DNA bound to a protein and accessible unbound DNA regions with similar bp resolution. A person of ordinary skill in the art would have had a reasonable expectation of success in modifying the non-specific m6A methyltransferase to Hia5 from EcoGII to methylate adenine residues in regions of the genomic DNA not bound to a protein to gain high, 1-bp resolution information on nucleosome positioning, chromatin architecture and accessibility and regulatory states, because both enzymes are non-specific and can produce high levels of adenine methylation.
The teachings of Shipony and Drozdz are documented above in the rejection of claim 1 under 35 U.S.C. 103. Claims 7, 11, 13, 21, 23 and 37 depends on claim 1.
Regarding claim 7, Shipony teaches a method comprising "GM12878 cells were washed … resuspended in … nuclei lysis buffer… Nuclei were then centrifuged, resuspended in … wash buffer…and centrifuged again … Finally, nuclei were resuspended in … reaction buffer ... Nuclei were then treated with EcoGII by adding 200 U of EcoGII (NEB) and SAM …" (Pg. 328, GM12878 SMAC-seq experiments, Para. 1). GM12878 cells are interpreted as containing genomic DNA. Thus, Shipony and Drozdz teach a method wherein the contacting comprises contacting isolated genomic DNA with the A-MTase.
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Regarding claim 11, Shipony teaches a method wherein at least 1 kb of genomic DNA was sequenced as shown in supplementary figure 73 below. (Supp. Fig. 73, Measurement of chromatin accessibility around transcription start sites using m6A-SMAC-seq human GM12878 cells.). With regard to supplementary figure 73, 500 bases in the plus and minus direction is interpreted as 1 kb. Thus, Shipony and Drozdz teach a method wherein the sequencing is conducted on a stretch of genomic DNA that is at least 1 kilobase (kb) long or at least 3 kb long.
Regarding claim 13, Shipony teaches a method comprising “Nanopore sequencing” (Pg. 328, SMAC-seq analysis. Para. 1). Thus, Shipony and Drozdz teach a method wherein the sequencing comprises translocating the genomic DNA through a nanopore.
Regarding claim 21, Shipony teaches a method comprising “GM12878 human lymphoblastoid cell lines” (Pg. 328, GM12878 cell culture, Para. 1). Thus, Shipony and Drozdz teach a method wherein the genomic DNA is from a mammalian cell.
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Regarding claim 23, Shipony teaches a method wherein “sacCer3 reference genome” (Document Pg 10, Methods, Col. 1 Nanopore base calling, Para.1). SacCer3 is interpreted as a normal yeast cell. Shipony teaches a method further comprising “We use the m6A methyltransferase EcoGII as an alternative/addition to CpG/GpC and use nanopore sequencing to generate single-molecule readouts of accessibility states over many kilobases (Fig. 1a). Nanopore sequencing allows direct detection of these modifications, enabling the generation of methylation maps for individual DNA molecules, which can then be interpreted in terms of chromatin accessibility. The addition of an m6A signal associated with accessible chromatin…" (Pg. 319, Col. 2, Para. 1-2; Figure 1). Mapped accessible and inaccessible regions to the A-MTase are shown in Figure 1. (Figure1; see m6A and accessibility footprint in Figure 1a and comparisons to SMAC-seq in 1h below). Shipony also teaches a method comprising "generated low-coverage SMAC-seq data for human GM12878 cells using only EcoGII and examined aggregate ‘m6ASMAC’ profiles around CTCF sites, open chromatin regions and TSSs. (Pg. 326, Discussion, Para.4; Suppl. Figures 71-73). GM12878 cells are interpreted as human lymphoblastoid cells often used as a reference/normal cells. Thus, Shipony and Drozdz teach a method
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wherein the cell is a normal cell and the method further comprises generating a chromatin accessibility map for the region of genomic DNA sequenced, wherein the map indicates regions of chromatin not bound to the protein and hence accessible to the A-MTase and regions of the chromatin bound to the protein and hence inaccessible to the A-MTase.
Regarding claim 37, Shipony teaches a method wherein “We recovered the expected features of chromatin accessibility (strong nucleosome positioning…” (Pg. 326, Discussion, Para. 4). “Nucleosomes” reads on histones and DNA. Shipony teaches a method comprising “transcription factor” (Pg. 319, Col. 1, Para. 2). “transcription factor” reads on a transcriptional repressor or a transcriptional activator. Thus, Shipony and Drozdz teach a method wherein the protein comprises nucleosomes, a transcriptional repressor, or a transcriptional activator.
Response to Arguments
Applicant' s arguments filed 09/25/2025 (Pg.12-13) with respect to claim 1-5, 7, 19-21, 25 and 26 have been considered but are moot because the arguments filed 09/25/2025 do not apply to the new grounds of rejections. To clarify some instances argued in the response filed 09/25/20205 see responses to each argument made by Applicant below:
Applicants’ argument: “Shipony does not teach or suggest a method for identifying at single nucleotide resolution regions of genomic DNA bound to a protein. Shipony does not teach or suggest a method that uses a single enzyme. Rather, Shipony teaches away from using a single enzyme. Shipony does not teach or suggest the use of Hia5, which the inventors have shown to provide unexpected results.” (Pg. 8)
Response: Applicant' s arguments have been fully considered and found unpersuasive in light of the new grounds of rejection because Shipony does teach or suggest a method for identifying at single nucleotide resolution regions of genomic DNA bound to a protein (Supp. Fig. 4 and 5 legends). Shipony does teach or suggest a method that uses a single enzyme (Supp. Fig. 4 and 5; Pg. 328, Methods-GM12878 SMAC-seq experiments, para. 1). Shipony does teach the use of m6A methyltransferase, EcoGII, which is a homolog of Hia5, which the ordinary artisan would expect similar results when the method is performed with non-specific m6A methyltransferase. The new grounds of rejection teach the non-specific m6A methyltransferase, Hia5, as a useful molecular tool for high levels of methylation of adenine residues.
Applicants’ argument: “Fig. 1D of the application shows that Hia5 was significantly more efficient at methylating genomic DNA as compared to EcoGII, Btr1921V, EcoGI, and Hin1523.” (Pg. 11)
Response: Applicant' s arguments have been fully considered and found unpersuasive in light of the new grounds of rejection because Fig. 1D of the instant application does not appear to show that Hia5 was significantly more efficient than EcoGII. Fig. 1D and Fig 1F(top) do appear to show that Hia5 and EcoGII have comparable efficiency, as would be expected since Hia5 and EcoGII are homologous non-specific m6A methyltransferases.
Applicants’ argument: “Figure S2 in the Science publication shows that Hia5 is at least 100-fold more efficient than all other m6A-MTases in this class of enzymes.” (Pg. 11)
Response: Applicant' s arguments have been fully considered and found unpersuasive in light of the new grounds of rejection. Furthermore, Figure S2 as indicated in the Remarks filed 09/25/2025 would not convince the ordinary artisan that Hia5 is subject to consistently be at a higher efficiency for m6A methylation. For many reasons, enzymes are very particular from the point of how each enzyme is designed (presence or absence of tag), prepared (extraction and purification), the timing it which it took to prepare, temperature, buffer conditions, storage conditions, the assay conditions, as well as the exact method and timing to perform each step from preparation to execution all make a difference in enzyme involved assays. While Hia5 appears to be at higher efficiency than EcoGII in FigureS2 provided in the remarks, enough data has not been provided to support the conclusion. Furthermore, the new grounds of rejection provide that it would be obvious to modify the non-specific m6A methyltransferase to incorporate Hia5 as it is also a non-specific m6A methyltransferase that produces high levels of adenine methylation.
Claims 8-9 are rejected under 35 U.S.C. 103 as being unpatentable over Shipony et al. (“Shipony”; (2020). Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature methods, 17(3), 319-327.) in view of Drozdz et al. (“Drozdz”; Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res. 2012 Mar;40(5):2119-30) as applied to claim 1, and further in view of Vogel et al. (“Vogel”; (2007). Detection of in vivo protein–DNA interactions using DamID in mammalian cells. Nature protocols, 2(6), 1467-1478.).
The teachings of Shipony and Drozdz are documented above in the rejection of claims 1, 7,11,13, 21, 23 and 37 under 35 U.S.C. 103. Claims 8 and 9 depend on claim 1. Claim 9 depends on claim 8. Shipony does not explicitly teach the limitations of claims 8 and 9.
Vogel discloses DamID, an alternative technique to map genome-wide occupancy of interaction sites in vivo, that bypasses these limitations. DamID is based on the expression of a fusion protein consisting of a protein of interest and DNA adenine methyltransferase (Dam). This leads to methylation of adenines near sites where the protein of interest interacts with the DNA. These methylated sequences are subsequently amplified by a methylation-specific PCR protocol and identified by hybridization to microarrays. Using DamID, genome-wide maps of the binding of DNA-interacting proteins in mammalian cells can be constructed efficiently. Depending on the strategy used for expression of the Dam-fusion proteins, genome-wide binding maps can be obtained in as little as 2 weeks. (Abstract)
Regarding claim 8, Vogel teaches a method wherein “Stable cell lines and lentivirus transductions… are the preferred methods” and “For DamID, transfected/transduced cells are cultured …, cells expressing Dam” (Pg. 1469, Experimental design, Para. 2-3). “Cells expressing Dam” is interpreted as contact cell with genomic DNA. Thus, Shipony, Drozdz and Vogel teach a method wherein the contacting comprises contacting a cell comprising the genomic DNA.
Regarding claim 9, Vogel teaches a method wherein “After transfection, cells are selected for stable genomic integration of the Dam-expressing vector using selective media” (Pg. 1469, Experimental design, Para. 1). Vogel teaches a method wherein “Stable cell lines and lentivirus transductions… are the preferred methods” and “For DamID, transfected/ transduced cells are cultured …, cells expressing Dam” (Pg. 1469, Experimental design, Para. 2-3). Thus, Shipony, Drozdz and Vogel teach a method wherein the contacting comprises introducing into the cell a nucleic acid encoding the A-MTase or wherein the A-MTase is fused to a cell penetrating peptide that renders the A-MTase plasma membrane permeable.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of methylating adenine residues in regions of the genome not bound by proteins as taught by Shipony and Drozdz to incorporate the method of contacting a cell comprising the genomic DNA with the m6A-MTase and introducing into the cell a nucleic acid into encoding the m6A-MTase as taught by Vogel to have yielded the predictable result of identifying regions of genomic DNA bound to a protein and accessible unbound DNA regions. It would be obvious to the ordinary artisan to in include contact a cell comprising the genomic DNA with the A-MTase and introduce nucleic acids encoding the A-MTase into the cell of Vogel to the method of adenine methylation of unbound genomic DNA regions with the reasonable expectation of a identifying chromatin accessible and inaccessible regions in genomic DNA from cells.
Response to Arguments
Applicant's arguments filed 09/25/2025 do not apply to the new grounds of rejections. See response to arguments against claim 1 above. Note, claims 8-9 depend on claim 1 and not claim 54 as recited on Pg. 14 of the Remarks filed 09/29/2024.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Shipony et al. (“Shipony”; (2020). Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature methods, 17(3), 319-327.) in view of Drozdz et al. (“Drozdz”; Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res. 2012 Mar;40(5):2119-30) as applied to claim 1, and further in view of Flusberg et al. (“Flusberg”; (2010). Direct detection of DNA methylation during single-molecule, real-time sequencing. Nature methods, 7(6), 461-465.).
The teachings of Shipony and Drozdz are documented above in the rejection of claims 1, 7,11,13, 21, 23 and 37 under 35 U.S.C. 103. Claim 20 depends on claim 1. Shipony does not explicitly teach the limitations of claim 20.
Flusberg discloses direct detection of DNA methylation, without bisulfite conversion, through single-molecule, real-time (SMRT) sequencing. In SMRT sequencing, DNA polymerases catalyze the incorporation of fluorescently labeled nucleotides into complementary nucleic acid strands. The arrival times and durations of the resulting fluorescence pulses yield information about polymerase kinetics and allow direct detection of modified nucleotides in the DNA template, including N6-methyladenine, 5-methylcytosine and 5-hydroxymethylcytosine. Measurement of polymerase kinetics is an intrinsic part of SMRT sequencing and does not adversely affect determination of primary DNA sequence. The various modifications affect polymerase kinetics differently, allowing discrimination between them. We used these kinetic signatures to identify adenine methylation in genomic samples and found that, in combination with circular consensus sequencing, they can enable single-molecule identification of epigenetic modifications with base-pair resolution. This method is amenable to long read lengths and will likely enable mapping of methylation patterns in even highly repetitive genomic regions. (Abstract)
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Regarding claim 20, Flusberg teaches a method wherein “In SMRT DNA sequencing, polymerase kinetics are measured alongside primary sequence determination…We showed that mA… in a DNA template alter incorporation kinetics …” (See Figure 1 below) and “By enabling repeated interrogation of individual molecules, circular consensus sequencing allows base-pair resolution and single-molecule sensitivity for detection of mA (Pg. 465, Discussion, Para. 1). Thus, Shipony, Drozdz and Flusberg teach a method wherein the sequencing comprises single molecule real-time (SMRT) circular consensus sequencing (CCS).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of methylating adenine residues in regions of the genome not bound by proteins as taught by Shipony and Drozdz to incorporate the method comprising single molecule real-time (SMRT) circular consensus sequencing as taught by Flusberg to have yielded the predictable result of identifying regions of genomic DNA bound to a protein and accessible unbound DNA regions. It would be obvious to the ordinary artisan to in include single molecule real-time (SMRT) circular consensus sequencing of Flusberg to the method of adenine methylation of unbound genomic DNA regions with the reasonable expectation of a identifying chromatin accessible and inaccessible regions in genomic DNA from cells. Doing so would enable single-molecule identification of epigenetic modifications with base-pair resolution.
Response to Arguments
Applicant's arguments filed 09/25/2025 do not apply to the new grounds of rejections. See response to arguments against claim 1 above. Note, claim 20 depends on claim 1 and not claim 54 as recited on Pg. 14 of the Remarks filed 09/29/2024.
Claims 22 and 73-74 are rejected under 35 U.S.C. 103 as being unpatentable over Shipony et al. (“Shipony”; (2020). Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature methods, 17(3), 319-327.) in view of Drozdz et al. (“Drozdz”; Novel non-specific DNA adenine methyltransferases. Nucleic Acids Res. 2012 Mar;40(5):2119-30) as applied to claim 1, and further in view of Xie et al. (“Xie”; (2018). N6-methyladenine DNA modification in glioblastoma. Cell, 175(5), 1228-1243.).
The teachings of Shipony and Drozdz are documented above in the rejection of claims 1, 7,11,13, 21, 23 and 37 under 35 U.S.C. 103. Claims 22 and 73 depend on claim 1. Claim 74 depend on claim 73, which depends on claim 1. Shipony does not explicitly teach the limitations of claim 22, 73 and 74.
Xie discloses N6-methyladenine DNA modifications are enriched in human glioblastoma, and targeting regulators of this modification can inhibit cancer growth by altering heterochromatin landscapes and downregulating oncogenic programs.
Regarding claim 22, Xie teaches a method wherein “we elucidated the function of N6-mA in human glioblastoma. N6-mA levels were elevated in tumor relative to normal brain tissues and in GSCs compared with normal human astrocytes” (Pg1240, Discussion, Para. 1). Thus, Shipony, Drozdz and Xie teach a method wherein the genomic DNA is from a cancer cell.
Regarding claims 73 and 74, Xie teaches a method wherein “we elucidated the function of N6-mA in human glioblastoma. N6-mA levels were elevated in tumor relative to normal brain tissues and in GSCs compared with normal human astrocytes” (Pg1240, Discussion, Para. 1). Glioblastoma is interpreted as a tumor that originates from astrocytes. Astrocytes are interpreted as glial cells. Thus, Shipony, Drozdz and Xie teach a method wherein the genomic DNA is from a human cell; and wherein test cell are epithelial cells, white blood cells, glial cells, osteoblasts, or chondrocytes
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of methylating adenine residues in regions of the genome not bound by proteins and generating a chromatin accessibility map of genomic DNA in eukaryotic cells as taught by Shipony and Drozdz to incorporate a method comprising human cancer cells originating from glial cells as taught by Xie to have yielded the predictable result of identifying regions of genomic DNA bound to a protein and accessible unbound DNA regions in a cancer cell. It would be obvious to the ordinary artisan to include a cancer cell of Xie to the method of adenine methylation of unbound genomic DNA regions with the reasonable expectation of a identifying chromatin accessible and inaccessible regions in genomic DNA from cancer cells and furthermore glial derived cancer cells. Doing so would increase the resolution of chromatin accessibility mapping in the likely aberrant epigenetic landscape of cancer cells such as those comprised in glioblastoma to further understand the genomic landscape and transcriptional regulatory factors playing a role in the disease.
Response to Arguments
Applicant's arguments filed 09/25/2025 do not apply to the new grounds of rejections. See response to arguments against claim 1 above. Note, claim 22 depends on claim 1 and not claim 54 as recited on Pg. 15 of the Remarks filed 09/29/2024.
Conclusion of Response to Arguments
In view of the amendments, new grounds of rejections and above responses to arguments are documented in this Final Office Action. No claims are in condition for allowance.
Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KENDRA R VANN-OJUEKAIYE whose telephone number is (571)270-7529. The examiner can normally be reached M-F 9:00 AM- 5:00 PM.
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/KENDRA R VANN-OJUEKAIYE/Examiner, Art Unit 1682 /WU CHENG W SHEN/Supervisory Patent Examiner, Art Unit 1682