DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 3/12/2025 has been entered.
Claim Status and Formal matters
This action is in response to papers filed 3/12/2025.
Claims 56, 67-70, 72-73, 77-79 have been amended.
Claims 56 and 66-75, 77-79 are being examined.
The previous objection to the claims have been withdrawn in view of the amendment to the claims.
The prior 1112(a) rejection has been withdrawn in view of the amendment.
Priority
The instant application was filed 2/28/2007 and claims priority to provisional application 60/777,631 filed 2/28/2006.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 56 and 66-75, 77-79 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 56 has been amended to recite, “amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13 prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” The claim is confusing and unclear. The issues begin with the claim requires a region of the bisulfite treated DNA comprising a portion of SEQ ID NO 13. Thus the claim requires only a region which is a portion of SEQ ID NO 13, which encompasses any portion from 1 nucleotide to the full length of SEQ ID NO 13. However, the claim concludes with “produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” Thus it is unclear how an amplicon comprises a portion of SEQ ID NO 13 which encompasses 1 nucleotide and has more than 70% of the CpG of SEQ ID NO 13.
Further the claim recites, “amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13] prior to bisulfite treatment.” The recitation is confusing and unclear as to what is required as the claim requires bisulfite treatment and also requires prior to bisulfite treatment. Thus it is confusing and unclear.
Further claim 56 recites, “primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13.” This is confusing and unclear as it appears to provide the functional limitation with respect to “primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13” but continues with corresponds to a region. Corresponds is a relative term. The specification and claims do not provide a standard to differentiate something that is corresponding from something that is not corresponding. It is unclear if corresponding is sequence identity, position, homology, etc. Then the claim recites, “primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4.” Thus it is unclear of the SEQ ID NO are required or only sequences that can hybridize to the SEQ ID NO or sequences to which the SEQ ID NO hybridize. The claim becomes more confusing as it recites, “mouse ortholog of SEQ ID NO: 13.” This is confusing as the sequence listing teaches SEQ ID NO 13 is a human sequence and the claim require human T cells. Thus it is unclear how mouse ortholog relates to SEQ ID NO 13 or what is encompassed or required of mouse ortholog of SEQ ID NO 13.
Finally the recitation of “to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13” is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 67 recites, “wherein the primer pair comprises a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which the primer pair of SEQ ID NOs: 3 and 4 hybridizes on a bisulfite treated mouse ortholog of SEQ ID NO: 13.” This is confusing and unclear as it appears to provide the functional limitation with respect to “primer pair that hybridizes t a bisulfite treated mouse ortholog of SEQ ID NO: 13” but continues with corresponds to a region. Corresponds is a relative term. The specification and claims do not provide a standard to differentiate something that is corresponding from something that is not corresponding. It is unclear if corresponding is sequence identity, position, homology, etc. Then the claim recites, “primer pair of SEQ ID NOs: 3 and 4.” Thus it is unclear of the SEQ ID NO are required or only sequences that can hybridize to the SEQ ID NO or sequences to which the SEQ ID NO hybridize. The claim becomes more confusing as it recites, “mouse ortholog of SEQ ID NO: 13.” This is confusing as the sequence listing teaches SEQ ID NO 13 is a human sequence and the claim require human T cells. Thus it is unclear how mouse ortholog relates to SEQ ID NO 13 or what is encompassed or required of mouse ortholog of SEQ ID NO 13.
Claim 68 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 80% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 69 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 90% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 70 has been amended to recite, “amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13 prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” The claim is confusing and unclear. The issues begin with the claim requires a region of the bisulfite treated DNA comprising a portion of SEQ ID NO 13. Thus the claim requires only a region which is a portion of SEQ ID NO 13, which encompasses any portion from 1 nucleotide to the full length of SEQ ID NO 13. However, the claim concludes with “produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” Thus it is unclear how an amplicon comprises a portion of SEQ ID NO 13 which encompasses 1 nucleotide and has more than 70% of the CpG of SEQ ID NO 13.
Further the claim recites, “amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13 prior to bisulfite treatment.” The recitation is confusing and unclear as to what is required as the claim requires bisulfite treatment and also requires prior to bisulfite treatment. Thus it is confusing and unclear.
Further claim 70 recites, “primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13.” This is confusing and unclear as it appears to provide the functional limitation with respect to “primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13” but continues with corresponds to a region. Corresponds is a relative term. The specification and claims do not provide a standard to differentiate something that is corresponding from something that is not corresponding. It is unclear if corresponding is sequence identity, position, homology, etc. Then the claim recites, “primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4.” Thus it is unclear of the SEQ ID NO are required or only sequences that can hybridize to the SEQ ID NO or sequences to which the SEQ ID NO hybridize. The claim becomes more confusing as it recites, “mouse ortholog of SEQ ID NO: 13.” This is confusing as the sequence listing teaches SEQ ID NO 13 is a human sequence and the claim require human T cells. Thus it is unclear how mouse ortholog relates to SEQ ID NO 13 or what is encompassed or required of mouse ortholog of SEQ ID NO 13.
Finally the recitation of “to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13” is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 72 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 80% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 73 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 90% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 77 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 95% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 78 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 80% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Claim 79 recites, “wherein the amplifying is performed by polymerase chain reaction (PCR) and at least 90% of the one or more CpG positions in SEQ ID NO: 13 comprise thymidine instead of cytosine in the amplicon.” This is confusing and unclear as previous claims require mouse ortholog of SEQ ID NO 13, but this claim requires SEQ ID NO: 13. Further it is unclear as the claim provides no active step in which thymidine instead of cytosine is detected. Thus it is unclear how this limits the active steps of the claims.
Response to Arguments
The response traverses the rejection stating, “As discussed above and as shown in the above alignment, those of skill in the art would know that a single primer would be generated from each one of SEQ ID NO: 1, 2, 3, or 4 (and not a genus of primers) and those primers would be complementary to the bisulfite treated human FOXP3 gene region (as SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 are complementary to the bisulfite treated mouse foxp3 gene region). And, as noted above, these orthologous regions are clearly described in the application with respective nucleic acid sequences. Accordingly, the claims would be clear to those of skill in the art when the claims are read in light of the application” This argument has been thoroughly reviewed but is not considered persuasive as the claim has introduced new issues. Further the claims merely appear are not limited to orthologs of the moue primers, but primers which hybridize under any conditions to anything which can be considered to correspond to the recited SEQ ID NO in anything that can be considered a mouse ortholog of SEQ ID NO 13. This is broader than the assertion Further, this is considered arguments of counsel. As stated in the MPEP, 2145 “Arguments of Counsel”
“If a prima facie case of obviousness is established, the burden shifts to the applicant to come forward with arguments and/or evidence to rebut the prima facie case. See, e.g., In re Dillon, 919 F.2d 688, 692, 16 USPQ2d 1897, 1901 (Fed. Cir. 1990) (en banc). Rebuttal evidence and arguments can be presented in the specification, In re Soni, 54 F.3d 746, 750, 34 USPQ2d 1684, 1687 (Fed. Cir. 1995), by counsel, In re Chu, 66 F.3d 292, 299, 36 USPQ2d 1089, 1094-95 (Fed. Cir. 1995), or by way of an affidavit or declaration under 37 CFR 1.132, e.g., Soni, 54 F.3d at 750, 34 USPQ2d at 1687; In re Piasecki, 745 F.2d 1468, 1474, 223 USPQ 785, 789-90 (Fed. Cir. 1984). However, arguments of counsel cannot take the place of factually supported objective evidence. See, e.g., In re Huang, 100 F.3d 135, 139-40, 40 USPQ2d 1685, 1689 (Fed. Cir. 1996); In re De Blauwe, 736 F.2d 699, 705, 222 USPQ 191, 196 (Fed. Cir. 1984)..”
This should not be construed as an invitation for providing evidence.
Claim Rejections - 35 USC § 103
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, 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.
Claim 56 and 66-75, 77-79 are is/are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Katoh (International Journal of Oncology (2004) volume 25, pages 1495-1500), Fantini ( Journal of Immunology (2004) volume 172, pages 5149-5153), Khattri (WO2002/090600A2), Gen Bank Accession Number NC_0023.8 GI:51511752 (Oct 25, 2004), Wildin (Nature Genetics (2001) volume 27, pages 18-20), OLEK et al (US20030082609A1), Rose ( Nucleic Acids Research, 2003, Vol. 31, No. 13 3763–3766).
The active steps of the claims require bisulfite treating of isolated human genomic DNA and amplifying a sequence comprising a region of a portion of SEQ ID NO 13. The claims provide language about the primers, which are confusing and unclear as detailed previously.
Claims 56 and 70 recite, “a amplifying athe region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13[[14]] prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which selected from human orthologs of primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” The broadest reasonable interpretation is the claim encompasses any primers capable of amplifying a region of a portion of SEQ ID NO 13. “A region” of “a portion” broadly encompasses a single nucleotide to a sequence comprising SEQ ID NO 13.
Further the claims provide, “a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which of primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13.” The broadest reasonable interpretation is any primer that can broadly be interpreted to corresponding to the recited SEQ ID NO and hybridize under any condition to the mouse homolog of SEQ ID NO 13, which encompasses a single nucleotide to completely complementary to SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4
Katoh presents a review on the human FOX gene family, including FOXP3. Katoh concludes, “Because deregulation of FOX family genes leads to congenital disorders or carcinogenesis, it is necessary to establish a public database on the human FOX gene family, in which expression profiles, genetic alterations, epigenetic changes of FOX family genes as well as binding proteins and target genes of FOX family transcription factors are freely available to develop novel therapeutics and preventives for human diseases, such as diabetes mellitus and cancer.” Katoh teaches the sequence of FOXP3 was known Xp11.23 (figure 2)
While Katoh suggests examination of epigenetic changes (methylation ) in human FOX gene family members, Katoh does not specifically teach CD4+CD25+ regulatory T cells, bisulfite treating, amplification of a sequence comprising SEQ ID NO 14 using primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which of primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13..
However, Fantini teaches, “Recent evidence suggests that naturally occurring CD4+CD25+ regulatory T cells are characterized by the exclusive expression of the winged-helix/ forkhead transcription factor Foxp3 (4–6). Although the thymic origin of CD4+CD25+ T cells has been demonstrated, several findings suggest that such cells may also be generated in the periphery by an unknown mechanism. In the present report, we provide evidence that TGF-β is able to induce Foxp3 expression in CD4+CD25+ T cells and promotes the acquisition of regulatory properties in these cells.” Fantini further teaches, “Taken together, these data suggest a dispensable role of TGF- β in mediating CD4+CD25+ regulatory function, but underline a new role for TGF- β in the maintenance of the regulatory compartment in the periphery via its effects on CD4+CD25+ T cells.” Fantini teaches TGF-beta stimulates FOXP3 expression in CD25-CD4+ T cells. Fantini teaches PCR amplification of FOXP3 to determine expression (figure 1). Thus Fantini demonstrates the sequence of FOXP3 was known.
Khatttri teaches, “The relatively exclusive expression of Foxp3 within the T-reg subset might indicate that this transcription factor is either required for the generation of this subset or is directly involved in its function. To determine if Foxp3 plays a role in CD4+CD25+ T-reg cell function, the functional activity of CD4+CD25+ and CD4+CD25" T cell subset from Foxp3 transgenic mice was examined. These animals have 16 fold more Foxp3 message than found in wildtype animals, with very high amounts in the CD4+CD25+ subset.”(example 22) Khattri teaches, “Further, while the CD4+CD25+ subset from transgenic animals does not appear inhibitory on a per cell basis, the expression of Foxp3 is still elevated in this subset relative to their CD25- counterparts” (page 12).Khattri teaches, “The role of the Foxp3 gene in thymic selection remains unclear. Deletion of superantigen-specific Vβ-bearing thymocytes appears normal in both sf/Y as well as 2826 transgenic mice. Consistent with this, overexpression of the Foxp3 gene using its own endogenous promoter (2826 line) also does not appear to result in any gross changes in thymic development or selection.“ Khatttri teaches US Patent application 09/372668 and AF235097 disclose FOXP3 genomic sequence.
Wildin (Nature Genetics) teaches the human Foxp3 cDNA sequence and genomic sequence (“Human FOXP3 genomic sequence, AF235097; human FOXP3 cDNA, AF277993.” (page 19, 3rd column, bottom) AF235097 comprises SEQ ID NO 14 (nt 67919-67548).Wildin teaches amplification of FOXP3 exons -1 to 11 and 5’ and 3’ UTR (page 19, 1st column top).
The specification on page 14 teaches NC_0000023 comprises the sequence of FOXP3.
Olek teaches, “A relatively new and currently the most frequently used method for analyzing DNA for 5-methylcytosine is based upon the specific reaction of bisulfite with cytosine which, upon subsequent alkaline hydrolysis, is converted to uracil which corresponds to thymidine in its base pairing behavior. However, 5-methylcytosine remains unmodified under these conditions. Consequently, the original DNA is converted in such a manner that methylcytosine, which originally could not be distinguished from cytosine by its hybridization behavior, can now be detected as the only remaining cytosine using "normal" molecular biological techniques, for example, by amplification and hybridization or sequencing. All of these techniques are based on base pairing which can now be fully exploited. In terms of sensitivity, the prior art is defined by a method which encloses the DNA to be analyzed in an agarose matrix, thus preventing the diffusion and renaturation of the DNA (bisulfite only reacts with single-stranded DNA), and which replaces all precipitation and purification steps with fast dialysis (Olek A, Oswald J, Walter J. A modified and improved method for bisulphite based cytosine methylation analysis. Nucleic Acids Res. Dec. 15, 1996;24(24):5064-6). Using this method, it is possible to analyze individual cells, which illustrates the potential of the method.” Olek further teaches, “Further publications dealing with the use of the bisulfite technique for methylation detection in individual genes are: Grigg G, Clark S. Sequencing 5-methylcytosine residues in genomic DNA. Bioessays. June 1994;16(6):431-6, 431; Zeschnigk M, Schmitz B, Dittrich B, Buiting K, Horsthemke B, Doerfler W. Imprinted segments in the human genome: different DNA methylation patterns in the Prader-Willi/Angelman syndrome region as determined by the genomic sequencing method. Hum Mol Genet. March 1997;6(3):387-95; Feil R, Charlton J, Bird AP, Walter J, Reik W. Methylation analysis on individual chromosomes: improved protocol for bisulphite genomic sequencing. Nucleic Acids Res. Feb. 25, 1994;22(4):695-6; Martin V, Ribieras S, Song-Wang X, Rio MC, Dante R. Genomic sequencing indicates a correlation between DNA hypomethylation in the 5' region of the pS2 gene and its expression in human breast cancer cell lines. Gene. May 19, 1995;157(1-2):261-4; WO 97/46705, WO 95/15373 and WO 97/45560.”
The specification teaches, “In a preferred embodiment of the method according to the present invention, the analysis of the methylation status comprises a method selected from methylation specific enzymatic digests, bisulphite sequencing, analysis selected from promoter methylation, CpG island methylation, MSP, HeavyMethyl, MethyLight, Ms-SNuPE or other methods relying on a detection of amplified DNA. These methods are well known to the person of skill, and can be found in the respective literature..”
Rose teaches, “Since publication of the original CODEHOP manuscript (1) and implementation of the CODEHOP designer program on the WWW in 1998 more than 70 studies have been published in which CODEHOP PCR primers have been designed and successfully utilized to amplify distantly related sequences from organisms as diverse as fish, frog, protozoa, plants, viruses and bacteria (http://courses.washington.edu/bioinfo/ CODEHOP/Codehop%20Genes.html). The methodology has been further expanded in the exploration of conservation and diversity of gene families in higher plants (6) and the characterization of viral genomes (7,8). Useful features of the CODEHOP designer include reweighting sequences in order to bias the design of CODEHOPs towards targeted protein families and the ProWeb TreeView selection of input sequences based on their phylogenetic relationship.” (page 3765, 2nd column).
The specification teaches, “Based on the above information and the data as obtained from the murine and/or human system, orthologous or paralogous primer pairs can be designed by the person of skill having a sequence identity with the above primers of preferably about 75%, more preferably about 80%, and most preferred about 90%.”
Therefore it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made to examine methylation of FOXP3 ia region or portion of SEQ ID NO 13 in T cells by isolating genomic DNA from human CD4+CD25+ T regulatory cells, treating the isolated DNA with bisulfite, amplifying a sequence comprising SEQ ID NO 13 using primers and sequencing FOXP3 (a sequence comprising a portion or region of SEQ ID NO 13) . The artisan would be motivated as FOXP3 is implicated in the regulation of CD4+CD25+ Treg cells and Khatoh specifically suggest the examination of epigenetic (methylation) regulation of all human FOX members. The artisan would be motivated to treat with bisulfite as it converts cytosines which are not methylated to uracil and when amplified to thymine, to determine methylation. The artisan would have a reasonable expectation of success as the artisan is merely using known methods to examine a known gene as the specification demonstrates the gene was known in the prior art and indicates methods including bisulfite sequencing were known.
It would have been further prima facie obvious to one of ordinary skill in the art at the time of the invention to examine methylation following treatment with TGF- β. The artisan would be motivated to determine if TGF- β alters or regulates FOXP3 methylation as the art teaches TGF- β regulates expression of FOXP3. The artisan would have a reasonable expectation of success as the artisan is merely using known methods to examine known genes and regulation by known cytokine. The artisan would have a reasonable expectation of success as the artisan is merely using known methods to design primers to amplify known sequences.
Claims 67-69, 70-73, 76-79 the claims indicate the percentage of uracils or thymines in an amplicon comprising SEQ ID NO 13. The claim and specification provide for the active steps are bisulfite treating isolated DNA from a human T cells cell and amplifying. Review of the teachings of the specification and prosecution history reveals the recitations with respect to percentage of uracils or thymines does not inherently or explicitly change the active steps of bisulfite treatment and amplifying. Further based on the teachings of the specification the percentage of thymine or uracils appear to be a property of using CD25+CD4+ regulatory T cell DNA amplicon comprising SEQ ID NO 13 and thus are obvious over the prior art of record.
With regards to claims 74-75, the art teaches sequencing and thus the quantifying methylation signal.
Response to Arguments
The response begins traversing the rejection by asserting the claims require a specific amplicon. This argument has been thoroughly reviewed but is not considered persuasive as the claim recites, “amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13 prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” The recitation of “a region” and “a portion” demonstrate the claims do not require a specific amplicon, but a encompass anything that can be considered a region and/or a portion. Thus the claims encompass anything that can be considered a region or portion of SEQ ID NO 13, which encompasses a single nucleotide to the full sequence. Further the claim is confusing as to what is required as detailed in 112 (b) rejections.
The response continues by providing what the representative views as the teachings of the specification which the representative views as informative to the invention. These argument have been thoroughly reviewed but is not considered persuasive as the claims are not limited to what the representative is arguing as detailed in the 112(b) and the claim interpretation at the beginning of the art rejection.
The response continues by asserting the rejection does not indicate how the artisan would put together to come to the invention . This argument has been thoroughly reviewed, but is not considered persuasive as the claims recites, “amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13 prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” Thus the claims are to portion or region comprising SEQ ID NO 13, not consisting of SEQ ID NO 13. Further the specification concedes, “Mutation or deletion of the gene encoding Foxp3 causes severe autoimmune disease in mice and humans, due to a failure to generate CD25+CD4+ Tregs (Bennett, C.L. et al. The immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome (IPEX) is caused by mutations of FOXP3. Nat Genet 27, 20-120-1 (2001). Fontenot, J.D., Gavin, M.A. and Rudensky, A.Y. Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat Immunol 4, 330-6 (2003)), whereas ectopic expression of Foxp3 in conventional T cells confers suppressive activity (Fontenot, J.D., Gavin, M.A. and Rudensky, A.Y. Foxp3 programs the development and function of CD4+CD25+ regulatory T cells. Nat Immunol 4, 330-6 (2003). Hori, S., Nomura, T. and Sakaguchi, S. Control of regulatory T cell development by the transcription factor Foxp3. Science 299, 1057-61 (2003)).” Thus the specification acknowledges FOXP3 sequence was known and thus the artisan knows where to look.
The response continues to provide the representatives interpretation of the rejection. This is noted.
The response alleges the rejection has not articulated reasoning with rationale underpinning. This argument has been thoroughly reviewed but is not considered persuasive as the rejection states, “The artisan would be motivated as FOXP3 is implicated in the regulation of CD4+CD25+ Treg cells and Khatoh specifically suggest the examination of epigenetic (methylation) regulation of all human FOX members. The artisan would be motivated to treat with bisulfite as it converts cytosines which are not methylated to uracil and when amplified to thymine, to determine methylation.” Thus the art recognizes the role of FOXP3 in Tregs and suggests methylation regulates expression of FOXP3 family members. Thus the rejection does provide rationale and reasoning why the skilled artisan would be motivated.
The response continues by asserting there is nothing articulated which renders the claims obvious. This argument is not persuasive as the art (Katoh) suggests examining methylation of all human FOX genes. The art suggests FOXP3 is important in CD4+ CD25+ Treg cells. The art also demonstrates the sequence of the FOXP3 gene was known as were methods of bisulfite treatment of genomic DNA and amplification. Thus this argument is inconsistent with the rejection of record.
Double Patenting
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 obviousness-type double patenting rejection is appropriate where the conflicting claims 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 conflicting 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.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b).
Claims 56 and 66-75, 77-79 provisionally rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-12 of US Patent 10,876,163. Although the conflicting claims are not identical, they are not patentably distinct from each other because they are co-extensive in scope.
This is a provisional obviousness-type double patenting rejection because the conflicting claims have not in fact been patented.
The active steps of the claims require bisulfite treating of isolated human genomic DNA and amplifying a sequence comprising a region of a portion of SEQ ID NO 13. The claims provide language about the primers, which are confusing and unclear as detailed previously.
Claims 56 and 70 recite, “a amplifying a region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13[[14]] prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which selected from human orthologs of primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13.” The broadest reasonable interpretation is the claim encompasses any primers capable of amplifying a region of a portion of SEQ ID NO 13. “A region” of “a portion” broadly encompasses a single nucleotide to a sequence comprising SEQ ID NO 13.
Further the claims provide, “a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which of primer pairs SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13.” The broadest reasonable interpretation is any primer that can broadly be interpreted to corresponding to the recited SEQ ID NO and hybridize under any condition to the mouse homolog of SEQ ID NO 13, which encompasses a single nucleotide to completely complementary to SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4
Instant claims are drawn to towards a method for producing an amplicon from a bisulfite treated human forkhead box P3 (Foxp3) gene region from human positive stable CD25+CD4+ regulatory T cells, the method comprising:a) bisulfite treating isolated DNA from a human T cell sample to thereby generate bisulfite treated DNA whereby unmethylated cytosines are converted to uracils, and(b) amplifying athe region of the bisulfite treated DNA comprising a portion of SEQ ID NO: 13 prior to bisulfite treatment with a primer pair that hybridizes to a region of the bisulfite treated SEQ ID NO: 13 that corresponds to a region to which s SEQ ID NOs: 1 and 2 or SEQ ID NOs: 3 and 4 hybridize on a bisulfite treated mouse ortholog of SEQ ID NO: 13 to produce the amplicon comprising thymidine instead of cytosine at more than 70% of cytosine-phosphate-guanine (CpG) positions relative to SEQ ID NO: 13..
The active steps of the claims require bisulfite treating of isolated human genomic DNA and amplifying a sequence comprising SEQ ID NO 13.
Claim 1 of ‘163 is drawn to A method of identifying stable FoxP3 positive regulatory T cells and treating a disease in a human subject, the method comprising: a) obtaining a sample containing human regulatory T cells from a donor or a cell culture; b) identifying stable FoxP3 positive human regulatory T cells from a portion of the sample comprising: i) isolating genomic DNA from the portion of the sample; ii) treating the isolated genomic DNA with bisulfite to convert unmethylated cytosines to uracils; iii) amplifying the treated isolated genomic DNA by polymerase chain reaction (PCR) using a pair of oligonucleotide primers comprising SEQ ID NO: 13 and SEQ ID NO: 14, or SEQ ID NO: 15 and SEQ ID NO: 16, or SEQ ID NO: 17 and SEQ ID NO: 18, or SEQ ID NO: 29 and SEQ ID NO: 30 to produce an amplicon; iv) sequencing the amplicon; and v) analyzing the amplicon for a lack of methylation at cytosine phosphate guanine (CpG) positions in the human FoxP3 gene in the amplicon, wherein a lack of methylation at the CpG positions is indicative of stable FoxP3 positive human regulatory T cells in the sample; and c) administering a portion of the sample from step a), wherein the sample contains stable FoxP3 positive human regulatory T cells as identified in step b) to thereby treat an autoimmune disease, adverse effects in allotransplant recipients, tumorous diseases, allergic asthma, ovarian cancer, chronic graft-versus host disease, multiple sclerosis, or immunodysregulation polyendocrinopathy enteropathy X-linked (IPEX) syndrome in the human subject..
Therefore it would have been prima facie obvious to one of ordinary skill in the art at the time the invention was made the instant claims are obvious variant of the claims of 163 as the instant claims are encompassed by the claims of ‘163 as an amplicon comprising a region or portion of SEQ ID NO 13. encompasses FOXP3. SEQ ID NO 14 is a species encompassed by the genus of the claims of ‘163.
Claims 67-69, 70-73, 76-79 the claims indicate the percentage of uracils or thymines in an amplicon comprising SEQ ID NO 13. The claim and specification provide for the active steps are bisulfite treating isolated DNA from a human T cells cell and amplifying. Review of the teachings of the specification and prosecution history reveals the recitations with respect to percentage of uracils or thymines does not inherently or explicitly change the active steps of bisulfite treatment and amplifying. Further based on the teachings of the specification the percentage of thymine or uracils appear to be a property of using CD25+CD4+ regulatory T cell DNA amplicon comprising SEQ ID NO 14 and thus are obvious over the prior art of record.
It would have been prima facie obvious to one of ordinary skill in the art that amplifying a sequence comprising or corresponding to SEQ ID NO 13, after it was treated with bisulfite would result in amplification of at least one amplicon with at least, 70%, 80% or 90% of the amplicons having a cytosine converted to a thymine as bisulfite converts cytosine to uracils ( and by amplification thymines) and PCR amplification results in exact duplicates of a sequences, thus if one sequence has a cytosine converted to thymine all of the copies of that (100%) will be identical. The artisan would have a reasonable expectation of success as the artisan is merely using known methods to treat known sequences with bisulfite and amplify them.
Response to Arguments
The response traverses the rejection asserting that one of skill in the art would not be held as obvious. This argument is not considered persuasive as the rejection indicates they would be obvious.
Summary
No claims are allowed.
Conclusion
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/Steven Pohnert/Primary Examiner, Art Unit 1683