DETAILED ACTION
Notice of Pre-AIA or AIA Status
1. The present application is being examined under the pre-AIA first to invent provisions.
2. Applicant’s reply filed on 5/20/2026 is acknowledged. New claim 24 has been added. Claims 1-11, 16, 18 and 20-24 are pending. Claims 12-15, 17 and 19 are canceled. Claims 1, 16 and 18 have been amended.
3. Claims 1-11, 16, 18 and 20-24 are under examination.
Objections and Rejections Withdrawn
4. The objection to the drawings filed on 7/22/2025 because they include the following reference character(s) not mentioned in the description: Fig. 4A and 4B, and Fig. 7A-7C is withdrawn in view of applicant’s amendments to the specification.
5. The objection to the specification for missing the Incorporation by Reference paragraph required by 37 CFR 1.821(c)(1) is withdrawn in view of applicant’s amendments
6. The objection to claims 16 for missing the term “the” before “MBD2” is withdrawn in view of applicant’s amendments.
Rejections Maintained
Claim Rejections - 35 USC § 112
7. 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.
8. Claims 1-11, 16, 18, 20-22 and new claim 24 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.
New claim 24 is drawn to the method of claim 1, wherein the first polypeptide and the second polypeptide each comprise a methyl-DNA-binding domain of an MBD2 protein having an amino acid sequence that is at least 98% identical to a sequence consisting of amino acid residues 29 to 115 of SEQ ID NO: 2.
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% or 98% (new claim 24) 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% or 98% 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
The response states that the specification provides a clear and sufficient description of the invention as claimed, especially when considered in view of the knowledge in the art at the time of filing. As disclosed in the specification, the invention describes and exemplifies a bifunctional polypeptide comprising a methyl-DNA-binding domain of human MBD2, an Fc region, and a flexible linker, and explicitly teaches that variants with at least 95% identity to amino acids 29-115 of SEQ ID NO:2 are within the scope of the invention and are expected to retain the ability to bind methylated DNA. For example, paragraph [0102] of the Published Application states:
Even more preferably, the methyl-DNA-binding domain or fragment or variant thereof of a polypeptide of the present invention employed in the method of the present invention shares preferably 50 %, 60%, 70%, 80% or 90%, more preferably 95% or 97%, even more preferably 98%, and most preferably 99% identity on amino acid level to the MBDs shown in Figure 1 of Ballestar and Wolffe (2001), loc. cit. and is able to bind methylated DNA.
The specification further details the structure-function relationship of the MBD2 domain, stating that "the methyl-DNA-binding domain or fragment thereof of a polypeptide of the present invention...possesses a unique alpha-helix/beta-strand sandwich structure with characteristic loops as is shown in Figure 1 of Ballestar and Wolffe, Eur. J. Biochem. 268 (2001), 1-6 and is able to bind methylated DNA," [0100], and that "the protein belonging to the MBD family or fragment thereof...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 Ballestar and Wolffe (2001), loc. cit. and is able to bind methylated DNA" [0101].
Importantly, the art as of the filing date provided a well-recognized understanding of which residues in the MBD domain are essential for methylated DNA binding. As demonstrated in the Ballestar & Wolffe (Eur J Biochem 268:1-6, 2001) review, the methyl-CpG-binding domain (MBD) is a conserved domain of about 70 residues, present in MBD2, that adopts a unique a/P- sandwich structure with characteristic loops and is able to bind a single methylated CpG pair as a monomer. Their Figure 1 and accompanying discussion make clear that the residues essential for binding methylated DNA are highly conserved across the MBD family. The authors further explain that point mutations at certain conserved residues-specifically, those marked by asterisks in Figure 1-dramatically impair or abolish methylated DNA binding. Importantly, Ballestar & Wolffe highlight that the functional integrity of the MBD domain is determined by preservation of these key amino acids, particularly a conserved arginine and tyrosine, among a handful of other residues. Thus, the field recognized as of the filing date that variants of the MBD2 MBD retaining these critical residues would be expected to retain methylated DNA binding function, while substitutions at these positions would abolish function. As Ballestar & Wolffe explicitly discloses, the essential residues are those conserved across all MBDs, particularly arginine and tyrosine, and residues forming the p-sheets and loops involved in DNA contact. Routine substitution outside these conserved positions was known in the art to be tolerated, as further discussed in the cited references. Applicant notes that residues 29-115 contains 87 residues, a 95% identity allows for no more than four (4) amino acid mutations relative to SEQ ID NO: 2, one of ordinary skill in the art would be able to readily create variants with only four or fewer amino acid residues relative to SEQ ID NO:2 and select those having the claimed properties. Claim 24 (the new claim) sets forth even more stringent structural requirement, i.e., requiring 98% sequence identity, which allows for only two (2) amino acid mutations at most, relative to the reference sequence.
Similarly, Hendrich & Bird (Mol. Cell. Biol. 18:6538-6547, 1998) describes the family of mammalian MBD proteins, including MBD2, and provide the primary sequence and alignment of the MBD domains. They confirm that MBD2 binds specifically to methylated DNA in vitro and in vivo (see Abstract and Fig. 1). The authors further demonstrate that the MBD domains are highly conserved, and that DNA binding function is a property of this well-defined region, which is structurally and functionally characterized by these conserved residues.
Taken together, the combination of the explicit disclosure of the MBD2 sequence and its structure-function relationship in the application, the detailed discussion of sequence conservation, permissible variation, and critical residues in Ballestar & Wolffe (2001) and Hendrich & Bird (1998), and the well-established methods for routine verification of binding activity, would have led a person of skill in the art to understand that the inventors were in possession of the claimed genus of polypeptides-those having at least 95% identity to SEQ ID NO:2, provided the key binding determinants are retained. There is no requirement to provide individual working examples of every conceivable variant when the field recognized, as of the filing date, which residues are essential and which can be conservatively substituted without loss of function. Therefore, the written description is commensurate in scope with the claimed invention, and withdrawal of the rejection is respectfully requested.
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% or 98% 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% or 98T 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, in particular capable of detecting less than 10 ng methylated DNA in a sample). 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.
The specification does not disclose any polypeptides which have an amino acid sequence that is at least 95% or 98% 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).
Ballestar and Wolffe (Eur. J. Biochem. 2001, 268: 1-6) does not disclose any variants which have an amino acid sequence that is at least 95% or 98% identical to residues 29-115 of SEQ ID NO:2 and can bind methylated DNA. Fig. 1 of Ballestar and Wolffe is sequence alignment of the MBD of human MeCP2, MBD1, MBD2, MBD3, Xenopus MBD3 and human MBD4. In Fig. 1, the five amino acids which are essential for binding to methylated DNA are indicated by an asterisk. Although Ballestar and Wolffe support that these five residues are important for binding, it does not support that other residues can all be altered without affecting binding. Ballestar and Wolffe disclose “The lack of ability to recognize methylated DNA by MBD3 is somehow surprising considering the high similarity to MBD2b”. MBD1 contains 4 of the 5 essential amino acids (Fig. 1) bind to methylated DNA (page 3 1st column). However, MBD3 contains 4 of the 5 essential amino acids (Fig. 1) do not bind to methylated DNA (page 3 1st column), indicating other residues also affect binding. Similarly, Hendrich & Bird (Mol. Cell. Biol. 18:6538-6547, 1998) discloses that MBD2, MBD3 and MBD4 all contain the methylated-CpG binding domain, MBD2 and MBD4 bind to methyl-CpG in vitro and in vivo, however, MBD3 does not bind methylated DNA in vivo and in vitro (abstract). Ballestar and Wolffe further discloses that attempts to find any sequence specificity in the binding of MBDs to DNA have been unsuccessful to date (page 3, last para).
Before the effective filing date of the instant invention, there was no evidencing proving that all other residues can be changed without affecting binding. Some residues do not contact the binding partner directly but help maintain the protein’s three-dimensional structure, other residues could destabilize the fold and indirectly reduce binding. Furthermore, individual mutations may show little effect, but combinations of mutation can significantly impair binding. Therefore, it is unpredictable which amino acids in 29-115 of SEQ ID NO:2 can be changed by addition, deletion and/or substitution without affecting binding. 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.
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% or 2% 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. 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
9. 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.
10. Claims 1-11, 16, 20, 22, amended claim 18 and new claim 24 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, 23, amended claim 18, and new claim 24, 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).
Regarding the above claims, 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. Regarding claim 16, 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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351
1160
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70
1011
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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.
11. Claims 1-11, 16, 20-21, 22, amended claim 18 and new claim 24 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, 22- 23, amended claim 18 and new claim 24.
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
The response states that The references fail to provide a reasonable expectation of success for the claimed method. Shia generically discusses the correlation between DNA methylation (hypo- and hypermethylation) and cancer. Shia discloses using labeled methyl binding agent to detect the methylation pattern in genomic DNA samples. Shia does not teach (1) coating the methyl binding reagent on a container, (2) that the methyl binding agent is a MBD2 protein fused to an Fc portion of an antibody, nor (3) a reagent comprising an Fe portion fused to an MBD2 protein for binding methylated DNA in a sample obtained from a subject for detecting cancer. Hendrich, Bauer nor Jones, even mentions cancer detection. TLRs are not methyl-binding proteins, as established by well-published literature, in fact, they bind to unmethylated DNA. As previously presented in the Office Action Response filed October 15, 2025, Ishii and Akira's review article, "TLR Ignores Methylated RNA?" (Immunity, Vol. 23, Issue 2, August 2005, pp. 111-113), 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). These findings are 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." Rutz et al. explicitly describe this as "a putative CpG-DNA binding domain homologous to that described for methyl-CpG-DNA binding proteins," not as a functional or canonical MBD.
Applicant submits that the MBD2 binds double stranded, symmetrical methylated CpG DNA with high affinity and specificity, however, TLR9's "MBD-like" region was shown by Rutz et al. to participate in binding single-stranded unmethylated CpG DNA, not methylated DNA. Mutation of the TLR9 D535 and Y537 residues (homologous to MBD1 D32/Y34) abolished CpG DNA binding, but this is a distinct activity-TLR9 does not bind methylated CpG DNA (Rutz et al. 2004, p. 2544, Fig. 4). Furthermore, The "MBD-like" region in TLR9, while sharing a superficial motif, is embedded in a much larger TLR9 extracellular domain and is not associated with the same chromatin or methylation-dependent gene silencing mechanisms as the MBD2 protein (Rutz et al. 2004, p. 2546). And finally, TLR9, was shown to bind unmethylated CpG DNA at endosomal pH, and its "MBD-like" region is essential for this, but not for methylated DNA binding. In fact, methylation of the CpG motif in the DNA abolishes TLR9 binding (Rutz et al. 2004, Fig. 3A, 3E).
Thus, Applicant submits that TLR9 is not the same as the canonical, functional MBD domain in MBD2. TLR9's "MBD-like" region is a structural motif with partial sequence similarity, but it is not functionally equivalent: it binds unmethylated CpG DNA and is not capable of binding methylated DNA in the way that MBD2's MBD does. The prior art makes clear that the two domains are mechanistically and functionally distinct, and that knowledge of one does not provide a reasonable expectation of success for substituting or combining their activities. Thus, Applicant submits that there is no reasonable expectation of success for the method as recited in amended claim 1.
Applicant respectfully submits that the Examiner's rationale for combining Shia, Bauer, Jones, and Hendrich relies on impermissible hindsight. The Office Action reconstructs the intention by selectively combining disparate elements from the cited reference, but none of Shia, Bauer, Jones, and Hendrich, alone or together, teach or suggest using MBD2 protein fused to an Fc portion of an antibody for detecting cancer via methylated DNA presence in the sample as claimed, nor do they anticipate the detection of methylated DNA as demonstrated in the Published Application Examples.
The Office Action's reliance on general statements such as "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" (OA, p. 23) is not supported by the actual disclosures of the cited references. Specifically, Shia evaluates methods for detecting DNA methylation using methylated nucleic acid binding proteins (MBPs)-including MBD2-but teaches only the use of MBPs labeled with a detectable tag for hybridization or capture, not fusion to Fc or use in a dimeric format for high-avidity solid-phase capture, nor any method for cancer detection involving such constructs. Bauer describes Fc fusions of TLRs, which are pattern- recognition receptors that bind unmethylated CpG DNA as part of innate immune signaling; Bauer does not disclose the use of MBD2, nor does it suggest using any MBD domain as a fusion partner in an Fc construct for capturing methylated DNA, and in fact, the TLR-Fc fusions are designed for recognizing unmethylated, not methylated, DNA. Jones discusses affinity tags generally for protein purification and immobilization, but does not address MBD2, methylated DNA binding, or cancer diagnostics. Hendrich & Bird provides the sequence and function of MBD family proteins, including MBD2, but does not describe Fc fusions, immobilization, or any diagnostic method, let alone one for cancer detection.
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. See, EpiMark® Methylated DNA Enrichment Kit | NEB ("The MBD-Fc technology is licensed exclusively to New England Biolabs from Sequenom, Inc."). Many researchers have used this NEB kit, which include 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, https://www.nature.com/articles/s43018- 022-00415-9, 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"). Chemi et al. demonstrated that the NEB EpiMark® Kit-enabled workflow permitted not only highly sensitive SCLC detection from cfDNA but also reliable molecular subtyping, including subtypes not previously accessible via noninvasive sampling. The classifier could distinguish between ASCL1, NEURODI, and double-negative SCLC subtypes, supporting personalized medicine applications.
Conway et al., Nature Communications, (2024) 15:3292, using cfDNA methylation data obtained via the T7-MBD-seq method and the NEB EpiMark® Kit, was able to successfully classify and predict tissue-of-origin (TOO) in Cancers of Unknown Primary (CUP). The resulting system achieved TOO accuracy of 96.8% and sensitivity of 84.6%-results that were not predictable from the prior art and reflect a nonobvious synergy between the enrichment technology and the classifier development pipeline. Conway et al., available at https://www.nature.com /articles/s41467-024-47195-7, is attached to this paper.
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").
Conway et al. (2024) and Chemi et al. (2022) and Richarson provide compelling evidence that the use of the NEB EpiMark® Methylated DNA Enrichment Kit for cfDNA methylation profiling achieves robust, clinically actionable cancer detection and subtyping. The integration of enrichment-based methylation capture with downstream advanced processes, allows sensitive and specific detection of cancer types and subtypes from cfDNA was not suggested or enabled by the prior art.
Furthermore, the metrics reported, for example in both Nature Communications (Conway et al.) and Nature Cancer articles (Chemi et al.) -tens of thousands of accesses, dozens of citations, and substantial altmetric scores-underscore not only the scientific but also the commercial impact and interest generated by these methods. The clinical and research communities have rapidly adopted and referenced these cfDNA methylation workflows, indicating that the methods have achieved significant commercial success and third-party adoption. Such success is a direct reflection of the claimed invention's technical advantages over prior art and its practical utility.
The success of the method in detecting and subtyping cancer with high sensitivity, including in early-stage or low tumor fraction samples, was not predictable from prior art. The robust performance in challenging clinical scenarios, such as CUP or minimal residual disease, demonstrates unexpected results attributable to the inventive combination of enrichment, sequencing, and machine learning-not merely the use of a known reagent.
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 SEQ ID NO:2 fused to Fc via a flexible peptide linker consisting of residues 116-129 of SEQ ID NO:2. The claims, however, encompass reagents comprising 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. The Examiner contends that Applicant has not shown results across the entire scope of the claims.
In response, MPEP § 716.03 states that arguments of commercial success can be used to rebut a finding of obviousness under 35 U.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.
Applicant submits that the claims are narrowly tailored and commensurate with the demonstrated commercial success. As discussed above, residues 29-115 contain 87 residues; a 95% identity permits no more than four (4) amino acid mutations relative to SEQ ID NO: 2, and claim 24 (the new claim) permits no more than two (2) amino acid mutations relative to the reference sequence as claimed. One of ordinary skill in the art would be able to readily create variants with only four, two, or fewer amino acid residues relative to residues 29-115 of SEQ ID NO: 2 and select those having the claimed properties. It is unreasonable-and it is not the law to require commercial success to be demonstrated for every single species covered by the claim. Instead, nonobviousness is supported if there is an established nexus between the commercial success and the claimed features. Such a nexus exists here: detecting methylated DNA in cancer using a fusion protein with a polypeptide having extremely high structural similarity to amino acid residues 29 to 115 of SEQ ID NO: 2, an Fc portion of an antibody, and a flexible 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 as claimed.
Likewise, 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 demonstrated 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.
MPEP 2145 states: One cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., Inc., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Where a rejection of a claim is based on two or more references, a reply that is limited to what a subset of the applied references teaches or fails to teach, or that fails to address the combined teaching of the applied references may be considered to be an argument that attacks the reference(s) individually. Where an applicant’s reply establishes that each of the applied references fails to teach a limitation and addresses the combined teachings and/or suggestions of the applied prior art, the reply as a whole does not attack the references individually as the phrase is used in Keller and reliance on Keller would not be appropriate. This is because "[T]he test for obviousness is what the combined teachings of the references would have suggested to [a PHOSITA]." In re Mouttet, 686 F.3d 1322, 1333, 103 USPQ2d 1219, 1226 (Fed. Cir. 2012).
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a construction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
In the instant case, 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 (see paragraphs [0050], [0104], Figure 27, Examples 22-24 and claim 66). 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 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. However, the claims encompass using a reagent which comprises a first and second polypeptide each comprising an amino acid sequence having at least 95% or 98% identity to residues 29-115 of SEQ ID NO:2 fused to Fc. 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% or 98% 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).
Note that the rejection of claim 23 is withdrawn is view of applicant’s argument of unexpected results.
Double Patenting
12. 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.
13. Claims 1-11, 16, 18, 20-23 and new claim 24 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.
14. Claims 1-11, 16, 18, 20-23 and new claim 24 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.
15. Claims 1-11, 16, 18, 20-23 and new claim 24 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.
16. Claims 1-11, 16, 18, 20-23 and new claim 24 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
Claim Objections
17. Claims 1 and 18 are objected to because the phrase “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” is recited twice.
Claim 18 is objected to as being a substantial duplicate of claim 1.
Conclusion
18. No claims are allowed.
THIS ACTION IS MADE FINAL. 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.
19. Any inquiry concerning this communication or earlier communications from the examiner should be directed to HONG SANG whose telephone number is (571)272-8145. The examiner can normally be reached on Monday-Friday 8am-5pm.
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/HONG SANG/Primary Examiner, Art Unit 1643
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