DETAILED ACTION
Continued Examination Under 37 CFR 1.114
1. A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 10/15/2025 has been entered.
Notice of Pre-AIA or AIA Status
2. The present application is being examined under the pre-AIA first to invent provisions.
3. Claims 1-11, 16, 18 and 20-23 are pending. Claims 22-23 are newly added. Claims 12-15, 17 and 19 are canceled. Claims 1 and 7 have been amended.
4. Claims 1-11, 16, 18 and 20-23 are under examination.
Information Disclosure Statement
5. The information disclosure statement filed 10/22/2025 fails to comply with 37 CFR 1.98(a)(3)(i) because it does not include a concise explanation of the relevance, as it is presently understood by the individual designated in 37 CFR 1.56(c) most knowledgeable about the content of the information, of each reference listed that is not in the English language. It has been placed in the application file, but the information referred to therein has not been considered as it pertains to Foreign Document No. 26 JP2002506183.
Objections and Rejections Withdrawn
6. All objections and rejections except those maintained below are withdrawn in view of applicant’s amendments.
Objections Maintained
Drawings
7. The drawings filed on 7/22/2025 remain objected to as failing to comply with 37 CFR 1.84(p)(5) because they include the following reference character(s) not mentioned in the description: Fig. 4A and 4B, and Fig. 7A-7C.
Although applicant amended the specification, the amendment is not entered because it is not made to the immediate prior version.
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:
8. Specific deficiency - The Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is missing or incomplete. See item 1) a) or 1) b) above.
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.
Although applicant amended the specification, the amendment is not entered because it is not made to the immediate prior version.
Claim Objections
9. Claims 16 remain objected to because of the following informalities:
Claim 16 should be amended to add the term “the” before “MBD2”.
Rejections Maintained
Claim Rejections - 35 USC § 112
10. 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.
11. Claims 1-11, 16, 18, 20-21 and new claim 22 remain/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.
“[T]he purpose of the written description requirement is to ‘ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor’s contribution to the field of art as described in the patent specification.’” Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1353-54 (Fed. Cir. 2010) (en banc) (quoting Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920 (Fed. Cir. 2004)). To satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991). See also MPEP 2163.04.
For a claim to a genus, a generic statement that defines a genus of substances by only their functional activity does not provide an adequate written description of the genus. Reagents of the University of California v. Eli Lilly, 43 USPQ2d 1398 (CAFC 1997). The recitation of a functional property alone, which must be shared by the members of the genus, is merely descriptive of what the members of the genus must be capable of doing, not of the substance and structure of the members.
“[A] sufficient description of a genus . . . requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can ‘visualize or recognize’ the members of the genus.” Ariad, 598 F.3d at 1350 (quoting Eli Lilly, 119 F.3d at 1568-69). A “representative number of species” means that those species that are adequately described are representative of the entire genus. AbbVie Deutschland GMBH v. Janssen Biotech, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (“The ’128 and ’485 patents, however, only describe species of structurally similar antibodies that were derived from Joe-9. Although the number of the described species appears high quantitatively, the described species are all of the similar type and do not qualitatively represent other types of antibodies encompassed by the genus.”). Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus to provide a "representative number” of species.
The “structural features common to the members of the genus” needed for one of skill in the art to ‘visualize or recognize’ the members of the genus takes into account the state of the art at the time of the invention.
Lastly, even if a selection procedure is disclosed that was, at the time of the invention, sufficient to enable the skilled artisan to identify antibodies with the recited functional properties, the written description provision of 35 U.S.C § 112 is severable from its enablement provision.
Independent claim 1 is drawn to a method for detecting cancer in a subject, wherein the method comprises:
(a) contacting a reagent capable of specifically binding methylated DNA with a sample obtained from the subject comprising methylated and/or unmethylated DNA, wherein the reagent has been coated on a container; wherein the reagent comprises
(i) a first polypeptide and a second polypeptide each comprising a methyl-DNA-binding domain of an MBD2 protein having an amino acid sequence that is at least 95% identical to a sequence consisting of amino acid residues 29 to 115 of SEQ ID NO: 2,
(ii) an Fc portion of an antibody; and
(iii) a flexible peptide linker,
wherein the first polypeptide and second polypeptide each have the methyl-DNA-binding domain fused to the Fc portion of an antibody through the flexible peptide linker; and the Fc portion of the antibody fused to the first polypeptide is bonded to the Fc portion of the antibody fused to the second polypeptide; the Fc portion of the antibody fused to the first polypeptide is bonded to the Fc portion of the antibody fused to the second polypeptide; and
(b) detecting the binding of the reagent to methylated DNA, thereby detecting degree of DNA methylation of promoters of one or more tumor suppressor genes, proto-oncogenes, or oncogenes in the sample, and
(c) detecting the presence or absence of cancer in the subject matter based on the degree of DNA methylation as compared to a control sample.
The claims are rejected because the specification does not adequately describe all the species encompassed by the genus of polypeptides comprising an amino acid sequences which is at least 95% identical to residues 29-115 of SEQ ID NO:2 and having a function of being capable of binding methylated DNA.
The specification discloses one species for the genus, i.e. amino acids 29-115 of SEQ ID NO:2 (a methyl-DNA-binding domain of human MBD2). The specification does not disclose any variants which are at least 95% identical to residues 29-115 of SEQ ID NO:2 and have the claimed function (being capable of binding methylated DNA). Therefore, the written description is not commensurate in scope with the claimed invention. The specification does not disclose which amino acid residues in amino acids 29-115 of SEQ ID NO:2 can be changed by deletion, addition, and/or substitution such that the resulting polypeptides still have the function of being capable of binding methylated DNA. The disclosed species, i.e. amino acids 29-115 of SEQ ID NO:2 cannot be considered a representative number of species for the genus because the genus encompasses all variants of the disclosed species. Furthermore, the specification does not disclose a correlation between a structure and a function.
The art does not disclose variants of amino acids 29-115 of SEQ ID NO:2 that can bind to methylated DNA.
Protein chemistry is probably one of the most unpredictable areas of biotechnology. It is known in the art that the relationship between the amino acid sequence of a protein (polypeptide) and its tertiary structure (i.e. its binding activity) are not predictable. There is no recognition in the art that sequence with identity predicts biological function. It is known in the art that even single amino acid changes or differences in a protein's amino acid sequence can have dramatic effects on the protein's function. For example, conservative replacement of a single “lysine” reside at position 118 of acidic fibroblast growth factor by “glutamic acid” led to the substantial loss of heparin binding, receptor binding and biological activity of the protein (Burgess et al., J of Cell Bio. 111:2129-2138, 1990). In transforming growth factor alpha, replacement of aspartic acid at position 47 with alanine or asparagine did not affect biological activity while replacement with serine or glutamic acid sharply reduced the biological activity of the mitogen (Lazar et al. Molecular and Cellular Biology 8:1247-1252, 1988). Further, Leninger et al. (Elife. 2019, 8:e48909, pages 1-16) teaches: “a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria…changing a single amino acid (the building blocks that make up proteins) in one of the two subunits to make them minimally different from each other, dramatically modified the transporter’s structure and function”(Abstract). These references demonstrate that even a single amino acid substitution or what appears to be an inconsequential chemical modification will often dramatically affect the biological activity and characteristic of a protein. Furthermore, the specification fails to teach what deletions, truncations, substitutions and mutations of the disclosed sequence can be tolerated that will allow the protein to function as claimed.
In the absence of a representative number of species and lack of a correlation between structure and function, one of ordinary skill in the art would not be able to envision, without further experimentation variants that have the claimed function.
Mere idea or function is insufficient for written description; isolation and characterization at a minimum are required. A description of what a material does, rather than what it is, usually does not suffice. Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. Without a correlation between structure and function, the claim does little more than define the claimed invention by function. That is not sufficient to satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (“definition by function … does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is”).
It is noted that, “[r]egardless whether a compound is claimed per se or a method is claimed that entails the use of the compound, the inventor cannot lay claim to the subject matter unless he can provide a description of the compound sufficient to distinguish infringing compounds from non-infringing compounds, or infringing methods from non-infringing methods.” University of Rochester v. G.D. Searle Co., 69 USPQ2d 1886 1984 (CAFC 2004) (emphasis added).
Applicant’s Arguments
First, the specification provides sufficient identifying structural characteristics; preferred bifunctional polypeptides are disclosed in paragraphs [0072]-[0076], complete with a sequence listing, SEQ ID NO:2, and contemplated variants. Furthermore, paragraphs [0105]-[0113] and Table IV disclose "polypeptides having a lower degree of identity but having sufficient similarity so as to perform one or more of the functions performed by a polypeptide as described herein which is employed in the method of the present invention." Para. [0114]. As stated in amended claim 1, these variants all comprise a methyl DNA binding domain that share at least 95% sequence homology with residue 29 to 115 of SEQ ID NO: 2. Thus, the sequences of the claimed polypeptides may only vary up to 10% from SEQ ID NO:2. The specification also discloses the functional properties of the claimed polypeptides and functional fragments thereof: they all can bind to methylated DNA.
Second, the application discloses functional characteristics of the bifunctional polypeptides used in the claimed methods, i.e., all can bind methylated DNA. The specification teaches conservative substitutions that can best preserve the functional characteristics of the claimed bifunctional polypeptides. See paras. [0110]-[0120]. The specification further discloses how to determine whether a variant produced as disclosed has sufficient identity and similarity "so as to perform one or more of the functions performed by a polypeptide as described herein which is employed in the method of the present invention." See paras. [0109]-[0113].
Third, the application also discloses detecting cancer based on degree of DNA methylation, i.e., hypermethylation or hypomethylation ([0142]-[0145]) and provides examples tumor suppressor genes such as ICSBP and proto-oncogenes such as, e.g., bcl-2 or c-myc ([0009], [0010] and [0140])), where detection of hypermethylation and hypomethylation of which, respectively, is indicative of the presence of cancer.
Fourth, the application provides working examples on how to generate recombination methyl-CpG binding polypeptide ([0201]-[0203])) and demonstrated that method was able to detect and quantify of CpG-methylated DNA fragments, and the methylation degree indicative of cancer presence. The application discloses as a non-limiting example, coating a recombinant methyl-CpG binding polypeptide (MBD2-Fc) is onto the walls of a PCR-compatible reaction vessel to selectively capture methylated DNA fragments from a complex genomic DNA sample. After binding and washing steps, the retained DNA is directly amplified in the same tube using gene-specific PCR (standard or real-time), enabling the detection and relative quantitation of methylation at specific gene promoters. The assay is validated using DNA from various cell lines ([0210]-[0211]), primary patient samples ([0212]-[0214]), and in vitro methylated controls, demonstrating its ability to discriminate between methylated and unmethylated CpG island promoters, including ESR1, CDKN2B, ICSBP, ETV3, and DDX20 ([0215]). with results correlating closely to bisulfite sequencing data ([0218]). The application discloses that the method can be used to detect the methylation in tumor cell lines and normal cell lines, the results of which were in good concordance with previously published methylation analysis of the promoters of the respective tumor suppressor genes. [0216], Sensitivity and specificity of the claimed methods are further supported by the assay's ability to detect methylation in mixtures of normal and tumor DNA and by the reproducibility of results across a range of input DNA concentrations ([0214] and [0242]).
The working examples show that the method is robust, reproducible, and applicable to both cell lines and primary clinical samples, providing a reliable means of analyzing the methylation status of multiple gene promoters relevant to hematologic malignancies. The detailed experimental procedures-including preparation of reagents, reaction conditions, control of specificity, and data normalization-are extensively described, demonstrating possession of the invention and enabling one of ordinary skill in the art to practice the claimed method without undue experimentation. The results establish a clear relationship between methylation detected by the claimed method and gene expression, further substantiating the utility and completeness of the disclosed method.
The amended claims are directed to high sequence identity- i.e., 95% -to SEQ ID NO:2, which comprises only 87 amino acids. The claimed polypeptides possess only 5% variability, i.e., at most only four (4)-amino acid difference. The application provides guidance on introducing this variability while preserving its function (i.e., the ability to bind methylated DNA), for example, in paragraph [0097] of the as-filed application. The application further discloses the structure function correlation for the claimed polypeptides, see paragraph [0100]-[0101]:
Preferably, the methyl-DNA-binding domain or fragment thereof of a polypeptide of the present invention which is employed in the method of the present invention possesses a unique alpha-helix/beta-strand sandwich structure with characteristic loops as is shown in Figure 1 of Ballester and Wolffe, Eur. J. Biochem. 268 (2001), 1-6 and is able to bind methylated DNA. More preferably, the protein belonging to the MBD family or fragment thereof of a polypeptide of the present invention which is employed in the method of the present invention comprises at least 50, more preferably at least 60, even more preferably at least 70 or at least 80 amino acid residues of the MBDs shown in Figure 1 of Ballester and Wolffe (2001), loc. cit. and is able to bind methylated DNA.
Furthermore, Applicant notes that it is not necessary to provide working examples of every polypeptide having at least 95% sequence identity to SEQ ID NO:2. The mere absence of a specific description of certain embodiments or aspects of a claimed invention in the specification does not, by itself, constitute a lack of adequate written description. Rather, the test is whether the Applicant has conveyed, with reasonable clarity to those skilled in the art, that he or she was in possession of the invention at the time of filing. Vas-Cath Inc. v. Mahurkar, 935 F.2d 1555, 1563-64 (Fed. Cir. 1991). Given the high level of skill in the art-and the principle that the number of species required to form a representative number varies inversely with the level of skill-those of ordinary skill would consider Applicant to have been in possession of the breadth of polypeptides recited in the claimed methods, based on the information and examples provided in the application.
In summary, the specification discloses sufficient identifying structural characteristics for the claimed genus, which is narrowly drawn to polypeptides comprising a methyl DNA binding domain with high sequence identity (i.e., over 95%) to amino acid residues 29 to 115 of SEQ ID NO: 2, and that function to detect cancer based on methylation patterns of tumor suppressor genes or oncogenes. Further, the specification provides guidance on how to generate variants within the genus, how to confirm that such variants exhibit the claimed activity, and includes working examples demonstrating how to practice the invention (e.g., Example 1). In view of this disclosure, one of ordinary skill in the art would have understood that Applicant was in possession of the claimed genus at the time of filing. Accordingly, Applicant respectfully requests that the written description rejection be withdrawn.
Response to Arguments
Applicant’s arguments have been carefully considered but are not persuasive. The claims are rejected because the specification does not adequately describe all the species encompassed by the genus of variants, i.e. first and second polypeptides which comprise an amino acid sequences that is at least 95% identical to residues 29-115 of SEQ ID NO:2 and have a function of capable of binding methylated DNA (emphasis added). Although one of ordinary skill in the art can envision all the variants having an amino acid sequences that is at least 95% identical to residues 29-115 of SEQ ID NO:2, one cannot envision without further testing the members which have the claimed function (capable of binding methylated DNA). Even if a selection procedure is disclosed that was, at the time of the invention, sufficient to enable the skilled artisan to identify the variant with the recited functional properties, the written description provision of 35 U.S.C § 112 is severable from its enablement provision.
Contrary to applicant’s assertion, paragraphs [0072]-[0076], [0097], [0105]-[0114], [0110]-[0120], ([0201]-[0203]), Table IV and Example I do not disclose any polypeptides which have an amino acid sequence that is at least 95% identical to residues 29-115 of SEQ ID NO:2 and can bind methylated DNA (emphasis added), other than residues 29-115 of SEQ ID NO:2 (a methyl-DNA-binding domain of human MBD2). Ballester and Wolffe (Eur. J. Biochem. 2001, 268: 1-6, submitted by applicant in the reply) does not disclose any variants which have an amino acid sequence that is at least 95% identical to residues 29-115 of SEQ ID NO:2 and can bind methylated DNA. Although human MeCP2 and human MBD2 share lower than 95% homology and can bind methylated DNA, this does not indicate that any variants of human MBD2 which share at least 95% sequence homology can bind methylated DNA. Rutz et al. (Eur J Immunol, 2004, 34:2541-2550 submitted by applicant in the reply) discloses that mutation analysis demonstrated that replacement of D32 and Y34 with alanine abolishes MBD-1 mediated DNA binding (page 2544, column 2, para 2).
The disclosed species, i.e. amino acids 29-115 of SEQ ID NO:2 cannot be considered a representative number of species for the genus of variants because the variants differ from the disclosed species by 1-4 amino acid insertion, deletion and/or substitution. There is no teaching regarding which 5% of the amino acids can vary from amino acids 29-115 of SEQ ID NO:2 and still result in a polypeptide that binds methylated DNA. Further, there is no disclosed or art-recognized correlation between any structure other than amino acids 29-115 of SEQ ID NO:2 and the claimed function.
Applicant’s arguments of conservative substitutions are not persuasive. Leninger et al. (Elife. 2019, 8:e48909, pages 1-16) teaches: “a single conservative mutation introduced into an SMR dimer is sufficient to change the resting conformation and function in bacteria…changing a single amino acid (the building blocks that make up proteins) in one of the two subunits to make them minimally different from each other, dramatically modified the transporter’s structure and function”(Abstract). The reference demonstrates that even a single amino acid substitution or what appears to be an inconsequential chemical modification will often dramatically affect the biological activity and characteristic of a protein.
In the absence of a representee number of species and absence of a correlation between structure and function, given the unpredictability of protein chemistry, one of ordinary skill in the art would not consider that applicant was in possession of the claimed genus.
For the foregoing reasons, the rejection is maintained.
Claim Rejections - 35 USC § 103
12. The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) 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.
13. Claims 1-11, 16, 20 and new claims 22- 23 remain/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Shia (WO 02/101353A2, pub. date 12/19/2001), in view of Bauer et al (US 2003/0104523A1, pub. date: 6/5/2003), Jones et al (Journal of Chromatography A, 1995, 707: 3-22), and further in view of Hendrich et al (Mol. Cell Biol., 1998, 18(11): 6538-6547).
Regarding claims 1 and 23, Shia teaches a method for detecting abnormal methylation of a nucleic acid molecule, comprising determining a methylation pattern of a nucleic acid molecule in a biological sample from a subject, and comparing the methylation pattern of the nucleic acid molecule to a control (page 5, last para and page 6, first para), wherein the methylation pattern of a nucleic acid molecule is determined using a methylated nucleic acid binding protein (MBP), or simply a methylated nucleic acid binding domain thereof (page 4, lines 15-20, page 17, lines 23-24), wherein the nucleic acid molecule is DNA, genomic DNA (claims 17-19), wherein the MBP is MBD2 (claim 24). Shia teaches exposing the nucleic acid molecule to a methylated nucleic acid binding protein (claim 17). Shia et al teach that MBPs can be linked to a detectable label including an affinity molecule, a magnetic bead, or a microbead (claim 60). Shia et al. teaches a method of detection cancer by detecting DNA methylation in a biological sample from a subject, and comparing it to a control (page 5, last para and page 30).
Regarding claims 2 and 3, Shia teaches that the level of methylation of a nucleic acid can be determined by methylation-specific PCR (page 2, line 16).
Regarding claim 4, Shia teaches that the nucleic acid molecule is DNA, genomic DNA (claims 17-19).
Regarding claim 5, Shia teaches that the level of methylation of a nucleic acid can be determined by sequencing of bisulfite-modified DNA (page 2, line 16)
Regarding claim 7, Shia teaches determining a methylation pattern of a nucleic acid molecule in a biological sample from a subject (page 5, last para and page 6, first para), wherein the biological sample is a biological fluid or tissue (page 11, last para)
Regarding claims 8 and 9, Shia teaches that the subject is suspected to have hypo- or hypermethylated gene loci (page 29, para 2). Hypermethylation has been observed in cancers, particularly at the promoter regions of genetic loci, where it is believed to cause silencing of gene expression from the locus (page 29, para 2).
Regarding new claim 22, Shia teaches that the biological fluid is serum, plasma, urine (page 12, para 1).
Shia et al. does not teach that MBPs including MBD2 are fused to Fc via a flexible peptide linker and is coated on a container. Shia, et al. does not teach that the MBD2 is human MBD2.
Bauer et al teach methods of making a fusion protein comprising a TLR polypeptide or a fragment thereof fused to an Fc fragment of an antibody, wherein the TLR polypeptide may be a mouse or human TLR7, TLR8 or TLR9 extracellular domain, (see paragraphs [0050], [0104], Figure 27, Examples 22-24 and claim 66). The extracellular domain of the TLR polypeptide includes a methyl-CpG binding (MBD) motif (see paragraph [0024], [0031], [0038], [0046], [0119] and [0120]). Bauer et al teach that the Fc fragment portion of the fusion protein is useful for attaching the TLR polypeptide to a substrate or for providing a target for detecting the presence of the TLR polypeptide (see paragraph [0050]), the substrate is multiwell plate or a column ([0049] and [0190]) (which meets the limitation “a container”). Bauer et al disclose that the TLR polypeptide can also be fused with an Fc fragment of an antibody with a specific cleavage site at or near the junction between the TLR polypeptide and the Fc fragment, wherein the specific cleavage site is a flexible peptide linker (see paragraph [0050] and Example 22).
Jones et al. discloses that the affinity tags on the desired fusion protein can be used to anchor the protein to surfaces allowing them to be directly adapted for quantitative in vitro assays, without need for additional modification, and this allows rapid screening of biological activity for potential agonists or antagonists of a specific affinity interaction (see page 14, column 1, paragraph 2). Jones also discloses that a receptor can be fused to an Fc tag, immobilized on a column via the Fc tag, and used to screen for ligands that bind to the receptor (page 14).
Hendrich et al. teaches the amino acid sequence of human MBD2 (see abstract and page 6539, column 1), which comprises amino acids 29-115 of instant SEQ ID NO:2, see sequence alignment below:
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It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have combined the teachings of Shia, Bauer and Jones to make a fusion protein comprising a methylated DNA binding domain of a MBP such as MBD2 fused to a Fc via a flexible peptide linker and further immobilize the fusion protein to a solid support for detecting methylated DNA. One would have been motivated to do so because Shia et al teach that MBPs including MBD2 or simply their methylated nucleic acid binding domains are useful for detecting methylated DNAs, and can be linked to a detectable label including an affinity molecule (claims 17 and 60), Bauer et al teach that the Fc fragment portion of the fusion protein is useful for attaching the TLR polypeptide to a substrate or for providing a target for detecting the presence of the TLR polypeptide (see paragraph [0050]), and Jones also discloses that a receptor can be fused to an Fc tag, immobilized on a column via the Fc tag, and used to screen for ligands that bind to the receptor (page 14). One of ordinary skill in the art would have had a reasonable expectation of success because methods of making a fusion protein comprising a polypeptide fused to a Fc region via a flexible peptide linker and immobilizing the fusion protein to a solid support were conventional at the time the instant invention was made as evidenced by Bauer and Jones.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have combined the teachings of the cited references to make a fusion protein comprising a human MBD2 or the methyl-DNA-binding domain thereof linked to Fc via a flexible peptide linker further in view of Hendrich. One would have been motivated to use human MBD2 for purpose of detecting human methylated DNAs in human samples. One of ordinary skill in the art would have had a reasonable expectation of success because human MBD2 protein sequence was known in the art as shown by Hendrich and methods of making fusion proteins comprising a functional binding domain of a protein and Fc were conventional at the time the instant invention was made as evidenced by Bauer and Jones.
The fusion protein comprising a methylated nucleic acid binding domain of a human MBD2 linked to a Fc via a flexible peptide linker is expected to form a dimer due to spontaneous Fc dimerization. The dimer would have two binding sites for methylated nucleic acid.
Regarding claims 10, 11 and 20, because the fusion protein suggested by the cited references has the same structure as claimed reagent as such would have the claimed properties (i.e. can detect methylated DNA in a sample of less than 5, or 10 ng of genomic DNA, the capacity to bind to methylated DNA is dependent on salt concentration). The office does not have the facilities and resources to provide the factual evidence needed in order to establish that the product of the prior art is not the same as the claimed product. In the absence of evidence to the contrary, the burden is on the applicant to prove that the claimed product is different from that taught by the prior art and to establish patentable differences. See In re Best 562F.2d 1252, 195 USPQ 430 (CCPA 1977) and Ex parte Gray 10 USPQ 2d 1922 (PTO Bd. Pat. App. & Int. 1989).
Regarding claim 1: detecting DNA methylation of promoters of one or more tumor suppressor genes, proto-oncogenes or oncogenes, Shia et al. teaches detecting DNA methylation in a patient sample, which would necessarily detect one or more tumor suppressor genes, proto-oncogenes or oncogenes.
14. Claims 1-11, 16, 20-21 and new claims 22-23 remain/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Shia (WO 02/101353A2, pub. date 12/19/2001), in view of Bauer et al (US 2003/0104523A1, pub. date: 6/5/2003), Jones et al (Journal of Chromatography A, 1995, 707: 3-22), and Hendrich et al (Mol. Cell Biol., 1998, 18(11): 6538-6547), further in view of Levenson et al. (US 2004/0137474A1, pub. date: 7/15/2004).
The teachings of Shia, Bauer and Hendrich have been set forth above as they apply to claims 1-11, 16, 20 and 22- 23.
Regarding claim 21, Shia, Bauer and Hendrich do not teach detecting cancer by detecting abnormal DNA methylation in one or more gens including CDKN2B (also known as p15).
Levenson et al. teaches a method of characterizing cancer, comprising: a) providing a biological sample from a subject, said biological sample comprising genomic DNA; b) detecting the presence or absence of DNA methylation in one or more genes to generate a methylation profile for said subject; and c) comparing said methylation profile to one or more standard methylation profiles, wherein said standard methylation profiles are selected from the group consisting of methylation profiles of non-cancerous samples and methylation profiles of cancerous samples, wherein the one or more genes include p15 (CDKN2B), thereby characterizing cancer in said subject.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have modified the method of Shia, Bauer and Jones discussed above to detect cancer by detecting abnormal DNA methylation in one or more genes including p15 in view of Levenson. One would have been motivated to do so because Levenson et al. teaches a method of characterizing cancer comprising detecting DNA methylation in one or more genes including p15. One of ordinary skill in the art would have had a reasonable expectation of success because the abnormal DNA methylation of p15 has been used to detect cancer as shown by Levenson.
Applicant’s Arguments
Shia does not teach coating the methyl binding reagent on a container, let alone teaching that the methyl binding agent is a Fc-MBD protein. Hendrich, Bauer nor Jones, even mentions cancer detection. Toll-like receptors (TLRs) are not methyl-binding proteins, as established by well-published literature, in fact, they bind to unmethylated DNA. For example, Ishii and Akira's review article, "TLR Ignores Methylated RNA?" (Immunity, Vol. 23, Issue 2, August 2005, pp. 111-113; copy attached), discloses that TLRs do not recognize methylated nucleic acids but recognizes unmethylated CpG motifs in DNA (see page 111: "Overall, these new data strongly suggest that TLR3, TLR7, and TLR8 recognize 'unmethylated RNA,' similar to TLR9 recognition of unmethylated CpG motifs in DNA," col. 2, second paragraph). Further, the article confirms that methylated CpG motifs actually silences TLR9 activity: "CpG methylation of DNA silences TLR9-mediated innate immune recognition" (abstract). This finding is also corroborated by additional published literature, Rutz et all, (Eur. J. Immunol. 2004. 34: 2541-2550), which states that "Here, we demonstrate that TLR9 binds directly and sequence specifically to single-stranded unmethylated CpG-DNA containing a phosphodiester backbone." Thus, the published art cast serious doubt on Bauer's claim that TLR as disclosed therein contains a MBD, which allows binding to methylated DNA. There is absolutely no motivation to combine the Shia and Bauer to reach the claimed invention of a methyl-CpG binding domain fused to an Fc fragment. Thus, the claims are not obvious in view of the cited references.
Levenson was cited for teaching a method of characterizing cancer, comprising: a) providing a biological sample from a subject, said biological sample comprising genomic DNA; b) detecting the presence or absence of DNA methylation in one or more genes to generate a methylation profile for said subject; and c) comparing said methylation profile to one or more standard methylation profiles, wherein said standard methylation profiles are selected from the group consisting of methylation profiles of non-cancerous samples and methylation profiles of cancerous samples, wherein the one or more genes include p15 (CDKN2B), thereby characterizing cancer in said subject. Levenson also did not teach or suggest the use of a reagent comprising two polypeptides, each containing a methyl-DNA-binding domain from an MBD2 protein that is at least 95% identical to amino acid residues 29 to 115 of SEQ ID NO: 2 and fused to the Fc portion of an antibody through the flexible peptide linker. As such, the combination of the five references does not render the claims obvious.
The claimed invention has achieved commercial success, as evidenced by its licensing by New England Biolabs (NEB) and its implementation in EpiMark® Methylated DNA Enrichment Kit. Many researchers have used this NEB kit, which use the dimeric MBD2-Fc fusion construct for high-affinity capture of methylated DNA and for cancer detection and monitoring:
For example, Chemi et al. Nature Cancer, 2022, previously submitted to the USPTO, discloses using the EpiMark® Methylated DNA Enrichment Kit (which contains the claimed MBD-Fc fusion construct) for detection of small cell lung cancers (see, p1266, col. 2, the section entitled "T7-MBD-seq library preparation and NGS").
See also, Richarson et al., Med_Rxiv 2025, also previously submitted to the USPTO, discloses using EpiMark® Methylated DNA Enrichment Kit for monitoring Ewing Sarcoma (section 4.4 entitled "4.4 T7-MBD-seq library preparation").
As discussed in the section addressing the 35 USC § 112 rejection above, the claimed method of using the dimeric reagent as claimed increases binding avidity for methylated DNA and enables capture and enrichment of methylated DNA from complex samples, therefore enabling sensitive, specific, and robust detection of cancer-associated DNA methylation. This uniquely engineered reagent is not suggested by the prior art. The examples in the patent disclosure establish a clear and reliable correlation between methylation detected by the claimed method and the presence of cancer, providing unexpected diagnostic utility and addressing a long-felt need for non-invasive, accurate cancer diagnostics.
The Examiner argues that the showing of unexpected results and commercial success is not commensurate in scope with the claimed invention. Specifically, the Examiner asserts that Applicant only provided results for a single reagent comprising a first and second polypeptide, each containing residues 29-115 of SEQIDNO:2 fused to Fc via a flexible peptide linker consisting of residues 116-129 of SEQIDNO:2. The claims, however, encompass reagents comprising a first and second polypeptide, each comprising an amino acid sequence having at least 90% or 95% identity to residues 29-115 of SEQIDNO:2 fused to Fc via any flexible peptide linker. The Examiner contends that Applicant has not shown results across the entire scope of the claims.
In response, MPP§716.03 states that arguments of commercial success can be used to rebut a finding of obviousness under 35U.S.C.§103 if a nexus-a connection-can be established between the commercial success and the claimed invention, rather than with unclaimed features or extraneous factors such as advertising or market trends. There is no requirement that the commercial product must embody every conceivable variation within the scope of the claims, nor must the claims be limited only to the commercial embodiment.
In the present case, while the commercial product uses a specific linker (residues 116-129 of SEQ ID NO :2), one of ordinary skill in the art would understand that various flexible linkers may also be used without materially affecting the functionality of the fusion protein. Furthermore, as discussed in the response to the written description rejection, the high sequence identity permitted by the claims ensures that variants falling within the claimed scope would retain similar structure and function, and therefore would also be expected to exhibit the same or similar unexpected results. Accordingly, there exists a strong nexus between the claimed features and the commercial success. These unexpected results and the demonstrated commercial success support that the claimed invention is not obvious.
In view of the foregoing, the rejection under 35 U.S.C. § 103(a) is improper. The cited references do not teach, suggest, or enable the claimed method, nor do they provide any motivation to select and combine the prior art in the manner required by the claims. Furthermore, the secondary considerations of commercial success, copying, and unexpected results strongly support the nonobviousness of the claimed invention. As such, withdrawal of the obviousness rejection is thus respectfully requested.
Response to Arguments
Applicant’s arguments have been carefully considered but are not persuasive. Shia et al teach that MBPs including MBD2 or simply their methylated nucleic acid binding domains are useful for detecting methylated DNAs, and can be linked to a detectable label including an affinity molecule (claims 17 and 60), Bauer et al teaches methods of making a fusion protein comprising an extracellular domain of a TLR polypeptide fused to an Fc fragment, wherein the TLR polypeptide may be a mouse or human TLR7, TLR8 or TLR9, (see paragraphs [0050], [0104], Figure 27, Examples 22-24 and claim 66). The extracellular domain of the TLR polypeptide includes a methyl-CpG binding (MBD) motif (see paragraph [0024], [0031], [0038], [0046], [0119] and [0120]). Bauer et al teach that the Fc fragment portion of the fusion protein is useful for attaching the TLR polypeptide to a substrate such as a multiwell plate or a column (see ([0049], [0050]), and [0190]) (which meets the limitation “a container”). Bauer et al disclose that the TLR polypeptide can also be fused with an Fc fragment of an antibody with a flexible peptide linker (see paragraph [0050] and Example 22).
Jones et al. discloses that the affinity tags on the desired fusion protein can be used to anchor the protein to surfaces allowing them to be directly adapted for quantitative in vitro assays, without need for additional modification, and this allows rapid screening of biological activity for potential agonists or antagonists of a specific affinity interaction (see page 14, column 1, paragraph 2). Jones also discloses that a receptor can be fused to an Fc tag, immobilized on a column via the Fc tag, and used to screen for ligands that bind to the receptor (page 14).
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have combined the teachings of Shia, Bauer and Jones to make a fusion protein comprising a methylated DNA binding domain of a MBP such as MBD2 fused to a Fc via a flexible peptide linker and further immobilize the fusion protein to a solid support for detecting methylated DNA. One would have been motivated to do so because Shia et al teach that MBPs including MBD2 or simply their methylated nucleic acid binding domains are useful for detecting methylated DNAs, and can be linked to a detectable label including an affinity molecule (claims 17 and 60), Bauer et al teach that the Fc fragment portion of the fusion protein is useful for attaching the TLR polypeptide to a substrate (see paragraph [0050]), and Jones also discloses that a receptor can be fused to an Fc tag, immobilized on a column via the Fc tag, and used to screen for ligands that bind to the receptor (page 14). One of ordinary skill in the art would have had a reasonable expectation of success because methods of making a fusion protein comprising a polypeptide fused to a Fc region via a flexible peptide linker and immobilizing the fusion protein to a solid support were conventional at the time the instant invention was made as evidenced by Bauer and Jones.
Applicant’s arguments that the TLP polypeptides bind to unmethylated DNA are not persuasive. The following teachings of Bauer are still relevant to the claimed invention: (i) the Fc fragment is useful for attaching an extracellular domain of a TLP polypeptide to a substrate such as a multiwell plate or a column (see ([0049], [0050]), and [0190]), (ii) the TLR polypeptide can be fused with an Fc fragment with a flexible peptide linker (see paragraph [0050] and Example 22).
Applicant’s arguments regarding long-felt need are not persuasive.
MEPE 716.04 [R-2] states that establishing long-felt need requires objective evidence that an art recognized problem existed in the art for a long period of time without solution. The relevance of long-felt need and the failure of others to the issue of obviousness depends on several factors. First, the need must have been a persistent one that was recognized by those of ordinary skill in the art. Second, the long-felt need must not have been satisfied by another before the invention. Third, the invention must in fact satisfy the long-felt need.
In the instant case, a method of detecting cancer by detecting abnormal DNA methylation using a methylated nucleic acid binding protein including MBD2 was taught by Shia. Cottrell et al. (Nucleic Acids Research, Jan 13, 2004, 32(1):e10) teaches a method of detecting methylated DNA. The method is capable of detecting as little as 30 or 60 pg of methylated DNA, and can detect a highly significant methylation difference between normal colon and colon adenocarcinomas (abstract). Therefore, the long-felt need has been satisfied by another before the invention.
Applicant’s arguments of unexpected results and commercial success are not persuasive because the showing of unexpected results and commercial success is not commensurate in scope with claimed invention.
MPEP 716.02(d) states “Whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support."
MPEP 716.03(a) states “Objective evidence of nonobviousness including commercial success must be commensurate in scope with the claims. In re Tiffin, 448 F.2d 791, 171 USPQ 294 (CCPA 1971) (evidence showing commercial success of thermoplastic foam "cups" used in vending machines was not commensurate in scope with claims directed to thermoplastic foam "containers" broadly). In order to be commensurate in scope with the claims, the commercial success must be due to claimed features, and not due to unclaimed features. Joy Technologies Inc. v. Manbeck, 751 F. Supp. 225, 229, 17 USPQ2d 1257, 1260 (D.D.C. 1990), aff’d, 959 F.2d 226, 228, 22 USPQ2d 1153, 1156 (Fed. Cir. 1992) (Features responsible for commercial success were recited only in allowed dependent claims, and therefore the evidence of commercial success was not commensurate in scope with the broad claims at issue.).
In the instant case, applicant only showed results for a single reagent which comprises a first and second polypeptide each comprising residues 29-115 of SEQ ID NO:2 fused to Fc via a flexible peptide linker consisting of residues 116-129 of SEQ ID NO:2. The claims encompass using a reagent which comprises a first and second polypeptide each comprising an amino acid sequence having at least 95% identity to residues 29-115 of SEQ ID NO:2 fused to Fc via any flexible peptide linker. Applicant has not shown results for the entire scope of the claims.
There is no evidence establishing a nexus between the binding property of amino acid residues 29-115 of SEQ ID NO:2 and the binding property of polypeptides having at least 95% sequence identity to amino acid residues 29-115 of SEQ ID NO:2. Rutz et al. (Eur J Immunol, 2004, 34:2541-2550 submitted by applicant in the reply) discloses that mutation analysis demonstrated that replacement of D32 and Y34 with alanine abolishes MBD-1 mediated DNA binding (page 2544, column 2, para 2).
Moreover, there is no evidence establishing a nexus between the effect of a flexible peptide linker comprising 116-129 of SEQ ID NO:2 (AAADPIEGRGGGGG) and other peptide linkers having a different length and amino acid sequence.
Double Patenting
15. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the claims at issue are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); and In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on a nonstatutory double patenting ground provided the reference application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP §§ 706.02(l)(1) - 706.02(l)(3) for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/forms/. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to http://www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
16. Claims 1-11, 16, 18, 20-21 and new claim 22-23 remain/are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 9,249,464, in view of Levenson et al. (US 2004/0137474A1, pub. date: 7/15/2004).
Claims 1-16 of U.S. Patent No. 9,249,464 disclose an in vitro method for detecting methylated DNA comprising: (a) contacting a polypeptide that is capable of specifically binding methylated DNA with a sample comprising methylated and/or unmethylated DNA, wherein said polypeptide has been coated on a container; and b) detecting the binding of said polypeptide to methylated DNA, wherein said polypeptide has been selected from the group consisting of: (i) MBD2; (ii) a fragment of the polypeptide of (i), wherein said fragment is capable of binding methylated DNA; and wherein said polypeptide is fused to an Fc-portion of an antibody through a flexible linker comprising amino acids 116 to 129 of SEQ ID NO:2,
wherein step (b) comprises restriction enzyme digestion, bisulfite sequencing, pyrosequencing, Southern Blot, or PCR,
wherein the method further comprising step (c) analyzing the methylated DNA and analyzing said methylated DNA comprises sequencing,
wherein said container is coated directly or indirectly with said polypeptide,
wherein said sample is from a subject, wherein said subject is suspected to have hypo-and/or hypermethylated gene loci, and said hypo-and/or hypermethylated gene loci are indicative of a cancer, tumor or metastasis,
wherein the methylated DNA is less than about 10 ng,
wherein MBD2 is human MBD2, and MBD2 comprises amino acids 29 to 115 of SEQ ID NO:2.
The amino acid sequence of SEQ ID NO:2 is 100% identical to instant SEQ ID NO:2.
The claims of the patent do not teach detecting cancer by detecting abnormal DNA methylation in one or more genes including CDKN2B gene (also known as p15 or INK4B).
The teachings of Levenson have been set forth above.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have used the method of the patent to detect cancer and detect abnormal DNA methylation in one or more genes including p15 in view of Levenson. One would have been motivated to do so because Levenson et al. teaches a method of characterizing cancer comprising detecting DNA methylation in one or more genes including p15. One of ordinary skill in the art would have had a reasonable expectation of success because the abnormal DNA methylation of p15 has been used in the art to detect cancer as shown by Levenson.
17. Claims 1-11, 16, 18, 20-21 and new claim 22-23 remain/are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-16 of U.S. Patent No. 10,487,351, in view of Levenson et al. (US 2004/0137474A1, pub. date: 7/15/2004).
Claims 1-16 of U.S. Patent No. 10,487,351 disclose a method for detecting methylated DNA comprising: contacting a reagent capable of specifically binding methylated DNA with a sample comprising methylated and/or unmethylated DNA, wherein the reagent has been coated on a container; wherein the reagent comprises (i) (a) a first polypeptide and a second polypeptide each comprising amino acids 116-129 of SEQ ID NO:2 (which is the methyl-DNA-binding domain of human MBD2 as evidenced by Figure 7), and (ii) an Fc portion of an antibody; wherein both the first and the second polypeptides are fused to the Fc portion of the antibody through a flexible peptide linker; (b) detecting the binding of the reagent to methylated DNA, wherein less than about 10 ng, 5 ng of methylated DNA is detected in (b), wherein the binding of the reagent to methylated DNA is dependent on the degree of methylation, and on salt concentration,
wherein step (b) comprises restriction enzyme digestion, bisulfite sequencing, pyrosequencing, Southern Blot, or PCR,
wherein the method further comprising step (c) analyzing the methylated DNA, and analyzing the methylated DNA comprises sequencing,
wherein the container is coated directly or indirectly with the reagent,
the sample is from a subject, the subject is suspected to have hypo- and/or hypermethylated gene loci, the hypo- and/or hypermethylated gene loci are indicative of a cancer, tumor or metastasis,
the methyl DNA binding domain comprises amino acids 29 to 115 of SEQ ID NO:2.
The amino acid sequence of SEQ ID NO:2 is 100% identical to instant SEQ ID NO:2.
The claims of the patent do not teach detecting cancer by detecting abnormal DNA methylation in one or more genes including CDKN2B gene (also known as p15 or INK4B).
The teachings of Levenson have been set forth above.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have used the method of the patent to detect cancer by detecting abnormal DNA methylation in one or more genes including p15 in view of Levenson. One would have been motivated to do so because the claims of the patent teach detecting cancer by detecting hypo- and/or hypermethylated gene loci, and Levenson et al. teaches a method of characterizing cancer comprising detecting DNA methylation in one or more genes including p15. One of ordinary skill in the art would have had a reasonable expectation of success because the abnormal DNA methylation of p15 has been used in the art to detect cancer as shown by Levenson.
18. Claims 1-11, 16, 18, 20-21 and new claim 22-23 remain/are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 9,074,013, in view of Shia (WO 02/101353 A2, Pub. Date 12/19/2001) and Levenson et al. (US 2004/0137474A1, pub. date: 7/15/2004).
Claims 1-8 of U.S. Patent No. 9,074,013 disclose a bifunctional polypeptide comprising an Fc portion of an antibody, a short flexible peptide linker, and a DNA-binding domain of an MBD2 protein, wherein the short flexible peptide linker comprises amino acids 116 to 129 of SEQ ID NO:2, and a composition comprising the bifunctional polypeptide, wherein the bifunctional polypeptide is capable of enriching methylated DNA from less than 10 ng of genomic DNA, the MBD2 protein is a human MBD2 protein, The amino acid sequence of SEQ ID NO:2 is 100% identical to instant SEQ ID NO:2.
The claims of the patent do not disclose a method of detecting methylated DNA using the bifunctional polypeptide and detecting cancer based on detecting abnormal DNA methylation of one or more genes including p15 as compared to a control sample.
The teachings of Shia and Levenson have been describe above.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have used the reagent of the patent for detecting cancer by detecting abnormal methylated DNA in one or more gens including p15 in view of Shia and Levenson. One would have been motivated to do so with a reasonable expectation of success because the claims of the patent disclose that the reagent is for binding methylated DNA, Shia teaches that methylated nucleic acid binding protein (MBP) including MBD2 can be used in a method of detecting methylated genomic DNA and cancer, and Levenson teaches detecting cancer by detecting abnormal DNA methylation of one or more genes including p15.
19. Claims 1-11, 16, 18, 20-21 and new claim 22-23 remain/are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-12 of U.S. Patent No. 9,873,919, in view of Shia (WO 02/101353 A2, Pub. Date 12/19/2001) and Levenson et al. (US 2004/0137474A1, pub. date: 7/15/2004).
Claims 1-12 of U.S. Patent No. 9,873,919 disclose a reagent for binding methylated DNA comprising: a first polypeptide and a second polypeptide each comprising: (i) a methyl-DNA-binding domain of an MBD2 protein; and (ii) an Fc portion of an antibody, wherein the first polypeptide and second polypeptide each have the methyl-DNA-binding domain of the MBD2 protein fused to the Fc portion of an antibody through a flexible peptide linker and the Fc portion of an antibody of the first polypeptide is bonded to the Fc portion of an antibody of the second polypeptide; wherein the methyl-DNA-binding domain of the first polypeptide and the methyl-DNA-binding domain of the second polypeptide forms a bivalent binding site for methylated DNA; and the flexible peptide linker of the first polypeptide and the second polypeptide comprise amino acids 116 to 129 of SEQ ID NO: 2, wherein the capacity to bind to methylated DNA is dependent on the degree of methylation, on salt concentration, the MBD2 protein is a human MBD2 protein, the reagent is capable of enriching methylated DNA in a sample of less than 10 ng, 5 ng or 1 ng of genomic DNA, the reagent is coupled to the bead by the Fc portion of an antibody of the first polypeptide bonded to the Fc portion of an antibody of the second polypeptide. The amino acid sequence of SEQ ID NO:2 is 100% identical to instant SEQ ID NO:2.
The claims of the patent do not disclose a method of detecting methylated DNA using the bifunctional polypeptide and detecting cancer based on detecting abnormal DNA methylation of one or more genes including p15 as compared to a control sample.
The teachings of Shia and Levenson have been describe above.
It would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to have used the reagent of the patent for detecting cancer by detecting abnormal methylated DNA in one or more gens including p15 in view of Shia and Levenson. One would have been motivated to do so with a reasonable expectation of success because the claims of the patent disclose that the reagent is for binding methylated DNA, Shia teaches that methylated nucleic acid binding protein (MBP) including MBD2 can be used in a method of detecting methylated genomic DNA and cancer, and Levenson teaches detecting cancer by detecting abnormal DNA methylation of one or more genes including p15.
All NSDP rejections are maintained in view of applicant’s request that the rejections be held in abeyance until the claims are found otherwise allowable.
New Grounds of Objection
Specification
20. The amendment to the specification filed on 10/15/2025 is objected to because it is not made to the immediate prior version (filed on 7/22/2025). Accordingly, the amendment to the specification is not entered.
37 CFR 1.125(c) requires a substitute specification filed under 37 CFR 1.125(a) or (b) be submitted in clean form without markings. A marked-up copy of the substitute specification showing all the changes relative to the immediate prior version of the specification of record must also be submitted (MPEP 608.01(q).
Claim Objections
21. Claim 1 is objected to for a typographical error. In line 12, the term “used” should be “fused”.
Conclusion
22. No claims are allowed.
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/HONG SANG/Primary Examiner, Art Unit 1643