DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Response to Amendment/Status of Claims
Receipt of the amendment filed on 08/27/2026 is acknowledged. Claims 1-17 were cancelled. Claim 18 was amended. Claims 19-31 are new.
Election/Restrictions
Applicant’s election without traverse of Group III (Claim 18) in the reply filed on 08/27/2026 is acknowledged. As the non-elected claims (claims 1-17) have been canceled, and new claims 19-31 have been added which correspond to elected claim 18, no claims are withdrawn.
Claims 18-31 are under examination.
Priority
This application is a 371 of PCT/JP2022/026323, filed 06/30/2022 and claims foreign priority to JAPAN 2021-128492, filed 08/04/2021 as reflected by the most recent filing receipt.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. See page 47, paragraph 0145.
Drawings
The drawings are objected to because figure(s) 1,2 and 9 have multiple views but are not labeled correctly. See 37 CFR 1.84(u). For example, the correct label for Fig. 1 is FIG. 1A, FIG. 1B, FIG. 1C.
(u) Numbering of views.
(1) The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG."
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 18 is objected to because of the following informalities: line 1 recites “selected from a group consisting of”. The examiner suggests replacing “a” with “the” to recite “selected from the group consisting of” which is more consistent with appropriate Markush language. See MPEP 2117. Appropriate correction is required.
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 24,26 and 28 are 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 24 recites the limitation "the target RNA-binding cassette" in lines 1-2, as well as “the elongating hairpin DNA-binding cassette” in line 3, and “the protruding region cassette of the elongating hairpin DNA” in lines 3-4, and “the non-protruding region cassette” in lines 5-6. There is insufficient antecedent basis for these limitations in the claim, because claim 24 depends on claim 18, which does not recite any of the above cassettes. While claim 18 recites a starting hairpin DNA and an elongating hairpin DNA, no cassettes are recited and cassettes are not inherently present in the starting hairpin DNA and elongating hairpin DNA, and therefore there is no antecedent basis for the above limitations.
Claim 26 recites the limitation “the target RNA-binding cassette” in line 1. There is insufficient antecedent basis for these limitations in the claim, because claim 26 depends on claim 18, which does not recite any cassette.
Claim 28 recites the limitation, “wherein the nucleotides comprise a modified nucleotide”. Claim 28 depends on claim 18. While the term “nucleotide” is not recited in claim 18, it would be inherently implied that the starting hairpin DNA and elongating hairpin DNA contains nucleotides. However, it is not clear which of these components or how many nucleotides claim 28 is referring to (nucleotides in the starting hairpin DNA or nucleotides in the elongating hairpin DNA or both and how many of the nucleotides this refers to). Therefore, the metes and bounds of claim 28 regarding the nucleotides comprise a modified nucleotide are not clear.
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.
Written Description Rejection
Claims 18-31 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Instant claims 18,20-22 and 24-28 encompass a method of treating a disease selected from a group consisting of a genus of cancers, genus of immune system diseases, and genus of neurodegenerative diseases in any subject in need thereof, comprising administering to the subject an effective amount of a composition comprising a genus of a starting hairpin DNA and genus of elongating hairpin DNA, wherein the starting hairpin DNA hybridizes with a genus of target RNA expressed in any cell of interest, wherein the starting hairpin DNA and elongating hairpin DNA undergo a hybridization chain reaction in any cell of interest, thereby forming a double-stranded DNA product.
Claim 19 limits the disease to cancer and the cell of interest to a cancer cell, but still encompasses a genus of cancers and cancer cells and the target RNA can be any target RNA expressed in the cancer cell.
Instant claim 23 further defines the starting hairpin DNA as comprising a target RNA-binding cassette that hybridizes with a target RNA and an elongating hairpin DNA-binding cassette that hybridizes with the elongating hairpin DNA, and the elongating hairpin DNA comprises a protruding region cassette that hybridizes with the starting hairpin DNA or another elongating hairpin DNA and a non-protruding region cassette that hybridizes with further another elongating hairpin DNA, but still encompasses a large genus of starting hairpin DNA and elongating hairpin DNA.
Claim 29 further limits the target RNA to mRNA or miRNA, however, this still encompasses a large genus of target mRNA or targeting miRNAs. Claim 30 recites the target RNA is RNA that is expressed or highly expressed in a cell-specific manner, and still recites a large genus of target RNAs.
Claim 31 recites the target RNA is miR-21, and therefore specifically defines the target, however the method still encompasses treating the recited genus of diseases by administering to the subject an effective amount of a composition comprising a genus of a starting hairpin DNA and genus of elongating hairpin DNA.
The instant specification discloses sets of three kinds of hairpin nucleic acids in which miR-21 (SEQ ID NO: 1) was a target RNA (Example 1, page 47), and Table 1 on page 48 lists the nucleotide sequences of the hairpin nucleic acids.
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Additionally, Table 2 lists 2 sequences of hairpin nucleic acids, which are modified sequences, used in Examples 3 and 4 (page 51).
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Example 4 (pages 51-52) evaluates HCR efficiency in HEK293T cells and HeLa cells using FAM-HP1(16) and HP2(16) with fluorescent modification by TAMRA (TAMRA-HP2(16)). Results are shown in Fig. 6. HP(16) was found to induce HCR in a manner specific to cells expressing miR-21, and HEK293T cells express little miR-21, while human cervical cancer HeLa cells express miR-21.
Example 5 (pages 52-53) pertains to evaluating efficiency of cell death by HCR in human cells (HEK293T and HeLa) and HP1(16) and HP2(16) was used. Results in FIG. 7 show that in HEK293 T cells which express little miR-21 a significant decrease in cell survival rate was not observed, but in HeLa cells which express miR-21, a cell survival rate was prominently decreased by introducing the hairpin NA and cell death was dependent on the amount of the hairpin NA. It was suggested that the aggregate was formed by capturing NF-kB whereby the cell death was promoted.
Example 6 (pages 53-54 and FIG. 8) pertains to induction of immune response by HCR in cells using HP(16) in human breast cancer MCF7 cells which express miR-21 and HCR product was found to induce nucleic acid immunity.
Example 7 (pages 54-57) evaluates HCR efficiency according to cell type, using human breast cancer MDA-MB-231 cells and human alveolar basement epithelial glandular cancer A549 cells, HEK293T and HeLa cells, and introduced HP(16) (0.5ug per well). Table 3 page 56 shows the hairpin NA sequences used (SEQ ID NO 10,11). Fig. 10 shows results in which increase in FRET signal intensity in HeLa, breast cancer and the A549 cells which express miR-21 and therefore the hairpins induced HCR in a manner specific to cell expressing miR-21. Cells expressing miR-21 were found to induce HCR regardless of the kind of cancer.
Example 8 (pages 57-58) evaluates efficiency of promotion of cell death according to cell types. MDA-MB-231 cells and mouse malignant melanoma B16 cells showed decrease in cell survival rate after introduction of HP(16), but was not observed in A549 cells, even though they all express miR-21. However, this shows that even in cells that express miR-21 the hairpin may not induce cell death, as was the case for the A549 cells.
Example 11 (pages 60-62) is the only in vivo test, and evaluates efficiency of inducing cell death against in vivo cancer cells. Mice with B16 cells (Melanoma) were administered 8.4 ug of HP(16). Results are shown in FIG. 14 and show prominent suppression of an increase in tumor volume in comparison with control group and induction of cell death of tumor cells by an HCR product was found effective in vivo.
Therefore, the genus of cancers, immune system diseases, and neurodegenerative diseases, the genus of starting hairpin DNA and elongating hairpin DNA and the genus of target RNA expressed in a cell of interest of claims 18-31 do not meet the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, due to lacking chemical structural information for what they are and chemical structures are highly variant and encompass a myriad of possibilities. The specification provides insufficient written description to support the genus encompassed by the claim.
Note: MPEP 2163. For each claim drawn to a genus, the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. A "representative number of species" means that the species which are adequately described are representative of the entire 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. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014).
Vas-Cath Inc. v. Mahurkar, 19 USPQ2d 1111, (Fed. Cir. 1991), makes clear that "applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the 'written description' inquiry, whatever is now claimed." (See page 1117.) The specification does not "clearly allow persons of ordinary skill in the art to recognize that [he or she] invented what is claimed." (See Vas-Cath at page 1116.)
Univ. of Rochester v. G.D. Searle, 69 USPQ2d 1886, 1892 (CAFC 2004), further supports this by stating that:
The appearance of mere indistinct words in a specification or a claim, even an original claim, does not necessarily satisfy that requirement. A description of an anti-inflammatory steroid, i.e., a steroid (a generic structural term) described even in terms of its functioning of lessening inflammation of tissues fails to distinguish any steroid from others having the same activity or function. A description of what a material does, rather than of what it is, usually does not suffice…. The disclosure must allow one skilled in the art to visualize or recognize the identity of the subject matter purportedly described. (Emphasis added).
Therefore, the specification only provides written description for a method of treating melanoma or triple-negative breast cancer in a subject comprising administering to the subject an effective amount of a composition comprising HP(16) of SEQ ID NO: 2 and SEQ ID NO: 3, and only provides support for the target RNA as being miR-21. The specification has not shown other structures or sequences of the starting hairpin DNA and elongating hairpin DNA, or other target RNAs expressed in a cell of interest, as resulting in treatment of any other diseases. No core structure, or structure-function correlation has been provided by the specification for the genus of starting hairpin DNA and elongating hairpin DNA that results in the functional limitations that are recited. The skilled artisan cannot envision the detailed chemical structure of the encompassed starting hairpin DNA and elongating hairpin DNA, wherein the starting hairpin DNA hybridizes with a target RNA expressed in a cell of interest; wherein the starting hairpin DNA and the elongating hairpin DNA undergo a hybridization chain reaction in a cell of interest, thereby forming a double-stranded DNA product, and which results in treating a genus of cancers, genus of immune system diseases and genus of neurodegenerative diseases.
Adequate written description requires more than a mere statement that it is part of the invention and reference to a potential method for isolating it. The chemical structure itself is required. See Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Circ. 1993) and Amgen Inc. V. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016, (Fed. Cir. 1991). In Fiddes v. Baird, 30 USPQ2d 1481, 1483, (Bd. Pat. App. & Int. 1993), claims directed to mammalian FGF's were found unpatentable due to lack of written description for the broad class. The specification provided only the bovine sequence. Finally, University of California v. Eli Lilly and Co., 43 USPQ2d 1398, 1404, 1405 (Fed. Cir. 1997) held that:
...To fulfill the written description requirement, a patent specification must describe an invention and do so in sufficient detail that one skilled in the art can clearly conclude that "the inventor invented the claimed invention." Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997); In re Gosteli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) (" [T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using "such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2d at 1966.
Furthermore, to the extent that a functional description can meet the requirement for an adequate written description, it can do so only in accordance with PTO guidelines stating that the requirement can be met by disclosing “sufficiently detailed, relevant identifying characteristics,” including “functional characteristics when coupled with a known or disclosed correlation between function and structure.” Univ. of Rochester v. G.D. Searle, 68 USPQ2d 1424, 1432 (DC WNY 2003).
Therefore, the full breadth of the claim(s) do not meet the written description provision of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph. The species specifically disclosed are not representative of the genus because the genus is highly variant. Applicant is reminded that Vas-Cath makes clear that the written description provision of 35 USC § 112 is severable from its enablement provision. (See page 1115.)
Claim Rejections-Scope of Enablement
Claims 18-31 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a method of treating cancer in a subject in need thereof, comprising administering to the subject an effective amount of a composition comprising hairpins HP1(16) and HP2(16) of instant SEQ ID NOs: 2 and 3, respectively, and in which the target RNA is miR-21, or administering the hairpin monomers, H1 (SEQ ID NO: 2) and H2 (SEQ ID NO: 3) in which the target RNA is SEQ ID NO: 4 by way of the prior art (Dirks et al.), does not reasonably provide enablement for a method of treating a genus of cancers, a genus of immune system diseases and a genus of neurodegenerative diseases in a subject in need thereof comprising administering to the subject an effective amount of a composition comprising a genus of starting hairpin DNA and elongating hairpin DNA wherein the starting hairpin DNA hybridizes to a genus of target RNA expressed in a cell of interest. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
As stated in MPEP §2164.01(a), “there are many factors to consider when determining whether there is sufficient evidence to support a determination that a disclosure does not satisfy the enablement requirement and whether any experimentation is ‘undue’.” These factors include, but are not limited to:
1. The breadth of the claims;
2. The nature of the invention;
3. The state of the prior art;
4. The level of skill in the art;
5. The level of predictability in the art;
6. The amount of direction provided by the inventor;
7. The presence or absence of working examples;
8. The quantity of experimentation necessary needed to make or use the invention based on the disclosure.
See In re Wands USPQ 2d 1400 (CAFC 1988).
The Breadth of the Claims and The Nature of the Invention
Instant claims 18,20-22 and 24-28 encompass a method of treating a disease selected from a group consisting of a genus of cancers, genus of immune system diseases, and genus of neurodegenerative diseases in any subject in need thereof, comprising administering to the subject an effective amount of a composition comprising a genus of a starting hairpin DNA and genus of elongating hairpin DNA, wherein the starting hairpin DNA hybridizes with a genus of target RNA expressed in any cell of interest, wherein the starting hairpin DNA and elongating hairpin DNA undergo a hybridization chain reaction in any cell of interest, thereby forming a double-stranded DNA product.
Claim 19 limits the disease to cancer and the cell of interest to a cancer cell, but still encompasses a genus of cancers and cancer cells and the target RNA can be any target RNA expressed in the cancer cell.
Instant claim 23 further defines the starting hairpin DNA as comprising a target RNA-binding cassette that hybridizes with a target RNA and an elongating hairpin DNA-binding cassette that hybridizes with the elongating hairpin DNA, and the elongating hairpin DNA comprises a protruding region cassette that hybridizes with the starting hairpin DNA or another elongating hairpin DNA and a non-protruding region cassette that hybridizes with further another elongating hairpin DNA, but still encompasses a large genus of starting hairpin DNA and elongating hairpin DNA.
Claim 29 further limits the target RNA to mRNA or miRNA, however, this still encompasses a large genus of target mRNA or targeting miRNAs. Claim 30 recites the target RNA is RNA that is expressed or highly expressed in a cell-specific manner, and still recites a large genus of target RNAs.
Claim 31 recites the target RNA is miR-21, and therefore specifically defines the target, however the method still encompasses treating the recited genus of diseases by administering to the subject an effective amount of a composition comprising a genus of a starting hairpin DNA and genus of elongating hairpin DNA.
The State of the Prior Art
Regarding the state of the art, Choi et al. (ACS Nano, Vol. 8, No. 5, pgs 4284-4294, 2014) taught in situ hybridization, in which nucleic acid probes are used to detect complementary nucleic acid targets within fixed samples (page 4284). Choi et al. taught an HCR amplifier consists of two kinetically trapped nucleic acid hairpin molecules (H1 and H2) that coexist metastably in the absence of a cognate initiator strand. Arrival of the initiator triggers a chain reaction in which H1 and H2 hairpins sequentially nucleate and open to assemble into a long nicked double-stranded amplification polymer. HCR signal amplification has been exploited for diverse technological purposes in vitro and in situ (page 4285, left column). Figure 1 of Choi et al. shows the structure of DNA hairpins and the HCR reaction.
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Choi et al. taught to decrease reagent cost and improve reagent durability, we set the hard constraint that RNA probes and amplifiers be replaced by new DNA probes and amplifiers engineered to be suitable for use in situ. To increase the signal gain per amplifier, we set out to increase the energetic driving force for HCR polymerization via two complementary approaches: first, by establishing permissive in situ amplification conditions that avoid the expected increase in nonspecific reagent binding; second, by engineering DNA HCR hairpins that maximize the free energy benefit per polymerization step while preserving the kinetic trapping property that underlies conditional polymerization. These engineering efforts yielded a next-generation DNA HCR in situ amplification technology that dramatically improves on the performance, cost, and durability of the first-generation RNA technology (page 4286). However, Choi et al. does not disclose using the DNA HCR hairpins for any sort of therapeutic purpose.
Dirks et al. (US 20070087334), cited on an IDS, recite a method of treating cancer comprising providing a first hairpin monomer to a cell comprising a target nucleic acid associated with the disease or disorder; and providing a second RNA hairpin monomer to the cell, wherein the second monomer comprises a propagation region that is substantially complementary to a portion of the first monomer, and wherein the first and second monomers polymerize in the presence of the target nucleic acid to form an RNA polymer that activates RNA-dependent kinase PKR (claim 18), and the method is carried out in vivo (claim 20). Dirks et al. recite the first RNA polymer comprises an initiator complement region that is complementary to a nucleic acid initiator, which is a portion of the target nucleic acid sequence (Claim 23). Dirks et al. teaches HCR polymerization in the presence of target mRNA from Ewing’s sarcoma and glioma in which the target mRNA is a fusion comprising SEQ ID NO: 4, using hairpin 1 and hairpin 2 and discloses sequences of the RNA hairpin monomers, H1 as SEQ ID NO: 2 and H2 as SEQ ID NO: 3 (Example 1, page 10). Dirks et al. disclose that in the presence of an intracellular mRNA target, HCR polymerization is initiated and the product of the polymerization chain rection serves as PKR binding domains to activate PKR which leads to inhibition of translation and cell apoptosis in diseased cells that contain the intracellular target (Example 3, page 11). Dirks et al. teach hairpin monomers are introduced in vivo into tumor cells by gene delivery methods and recognition of the target by the HCR-RNA monomers initiates hybridization chain reaction which produces long nicked RNA duplexes in the tumor cells, activates PKR in the tumor cells which also induces apoptosis and can reverse the growth of the tumor (Example 4, paragraph 0112). Therefore, while Dirks et al. pertains to RNA based hairpins, Dirks et al. does teach the structure of the RNA hairpins and the HCR polymerization process and which results in cell death and treatment of a specific cancer (Ewing’s sarcoma and glioma).
Morihiro (Kurata Encouragement Fund Research Report, 2018, (50th) Grant, No. 1384, pp. 1-6, English translation, 3 pages), cited on an IDS, taught decoy nucleic acids which function as “decoys” that capture transcription factors and exert therapeutic effects by regulating the expression of genes that are abnormally acting in diseased cells, and taught a study aimed at developing decoy nucleic acids that respond to microRNA (miRNA) specifically expressed in diseased cells and exert their medicinal effects by making full use of DNA nanotechnology (Section 1, left column). Morihiro taught that three types of hairpin-type DNA probe sets (HP1 and HP2) were designed and synthesized for use in HCR triggered by miR-21 overexpressed in many cancer cells (Section 2.1, right column). Morihiro taught the sequences alter the length of the single-stranded regions called toeholds that most greatly affect HCR progression, and the toehold portion is phosphorothioated to increase the resistance to nucleases (Section 2.1, right column). Morihiro taught that HP1 and HP2 were lipofected into human cervical cancer cells (HeLa) known to overexpress miR-21, and results were that HCR triggered by miR-21 can proceed in living cells, while transfecting HEK293T cells which express little miR-21 resulted in a decrease in FRET efficacy compared to HeLa cells which suggests HCR dependent progression. Morihiro taught that HCR progressed depending on intracellular miR-21 concentrations and the possibility of the cell-selective disease treatment (Section 2.3 right column).
The state of the art is silent as to treating immune system diseases and neurodegenerative diseases using the recited hairpin DNAs.
The Level of Predictability in the Art
The instant claimed invention is highly unpredictable due to the claims encompassing that the recited method is capable of treating any cancer, immune system disease and any neurodegenerative disease in any subject in need thereof comprising administering to the subject an effective amount of a composition comprising a genus of starting hairpin DNA and elongating hairpin DNA, wherein the starting hairpin DNA hybridizes to any target RNA expressed in any cell of interest.
No specific routes of administration are recited regarding the ability for the hairpin DNA to reach cells of the nervous system and result in treatment of any neurodegenerative disease as well as the lack of teaching in the state of the art regarding treating immune system diseases and neurodegenerative diseases using the recited methods and hairpin DNAs, adds to the unpredictability to the full scope of the claims.
The Amount of Direction Provided by the Inventor and
The Presence or Absence of Working Examples
Regarding claims 18-31, the specification does not enable any person skilled in the art to which it pertains to make and/or use the invention commensurate in scope with the claims. The instant specification discloses sets of three kinds of hairpin nucleic acids in which miR-21 (SEQ ID NO: 1) was a target RNA (Example 1, page 47), and Table 1 on page 48 lists the nucleotide sequences of the hairpin nucleic acids.
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Additionally, Table 2 lists 2 sequences of hairpin nucleic acids, which are modified sequences, used in Examples 3 and 4 (page 51).
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Example 4 (pages 51-52) evaluates HCR efficiency in HEK293T cells and HeLa cells using FAM-HP1(16) and HP2(16) with fluorescent modification by TAMRA (TAMRA-HP2(16)). Results are shown in Fig. 6. HP(16) was found to induce HCR in a manner specific to cells expressing miR-21, and HEK293T cells express little miR-21, while human cervical cancer HeLa cells express miR-21.
Example 5 (pages 52-53) pertains to evaluating efficiency of cell death by HCR in human cells (HEK293T and HeLa) and HP1(16) and HP2(16) was used. Results in FIG. 7 show that in HEK293 T cells which express little miR-21 a significant decrease in cell survival rate was not observed, but in HeLa cells which express miR-21, a cell survival rate was prominently decreased by introducing the hairpin NA and cell death was dependent on the amount of the hairpin NA. It was suggested that the aggregate was formed by capturing NF-kB whereby the cell death was promoted.
Example 6 (pages 53-54 and FIG. 8) pertains to induction of immune response by HCR in cells using HP(16) in human breast cancer MCF7 cells which express miR-21 and HCR product was found to induce nucleic acid immunity.
Example 7 (pages 54-57) evaluates HCR efficiency according to cell type, using human breast cancer MDA-MB-231 cells and human alveolar basement epithelial glandular cancer A549 cells, HEK293T and HeLa cells, and introduced HP(16) (0.5ug per well). Table 3 page 56 shows the hairpin NA sequences used (SEQ ID NO 10,11). Fig. 10 shows results in which increase in FRET signal intensity in HeLa, breast cancer and the A549 cells which express miR-21 and therefore the hairpins induced HCR in a manner specific to cell expressing miR-21. Cells expressing miR-21 were found to induce HCR regardless of the kind of cancer.
Example 8 (pages 57-58) evaluates efficiency of promotion of cell death according to cell types. MDA-MB-231 cells and mouse malignant melanoma B16 cells showed decrease in cell survival rate after introduction of HP(16), but was not observed in A549 cells, even though they all express miR-21.
Example 11 (pages 60-62) is the only in vivo test, and evaluates efficiency of inducing cell death against in vivo cancer cells. Mice with B16 cells (Melanoma) were administered 8.4 ug of HP(16). Results are shown in FIG. 14 and show prominent suppression of an increase in tumor volume in comparison with control group and induction of cell death of tumor cells by an HCR product was found effective in vivo.
Therefore, the instant specification shows cell death by HCR in human cervical cancer cells, breast cancer cells and mouse melanoma cells using the HP(16) DNA sequences. The specification has not shown that the recited method is capable of treating any immune system diseases or neurodegenerative diseases, and what the target RNA and hairpin structure would be to result in cell death and therefore treatment.
The Quantity of Experimentation Necessary
Regarding claims 18-31, in light of the unpredictability surrounding the breadth of the claimed method, one wishing to practice the presently claimed invention would be unable to do so without engaging in undue experimentation. Further experimentation would be required to determine if the recited method is capable of treating any cancer, any immune system diseases and any neurodegenerative diseases with a genus of starting hairpin DNA and genus of elongating hairpin DNA. Additional tests in cells of interest pertaining to immune system diseases and neurodegenerative diseases and different target RNAs expressed in the cells of interest would be needed to determine if the recited method is capable of carryout out the invention, and what other structures of the recited starting hairpin DNA and elongating hairpin DNA are that would result in treatment. Due to the number of diseases encompassed by the claims as well as the difficulty known in the art regarding treating neurodegenerative diseases and routes of administration that effectively delivery oligonucleotide therapeutics to the central nervous system, the quantity of experimentation would be considered undue.
Conclusion of 35 U.S.C. 112(a) (Enablement) Analysis
After applying the Wands factors and analysis to claims 18-31, in view of the applicant’s entire disclosure, it is concluded that the specification is not enabled for the full scope as discussed above. Therefore, claims 18-31 are rejected under 35 U.S.C. §112(a) for failing to disclose sufficient information to enable a person of skill in the art to use the invention commensurate in scope with these claims.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 18-31 are rejected under 35 U.S.C. 103 as being unpatentable over Dirks et al. (US 20070087334) in view of Morihiro (Kurata Encouragement Fund Research Report, 2018, (50th) Grant, No. 1384, pp. 1-6, English translation, 3 pages), both cited on an IDS.
Claim Interpretation: Regarding the “wherein clauses” in claims 18-22,24,26 and 27, these claims do not further limit the active method step(s) defined by the claim, namely administering to the subject an effective amount of a composition comprising a starting hairpin DNA and an elongating hairpin DNA. "A wherein '' clause that merely states the result of the limitations in the claim adds nothing to the patentability or substance of the claim." Texas Instruments, Inc. v. International Trade Comm., 988 F.2d 1165, 1172 (Fed. Cir. 1993). See also Minton v. National Assoc. of Securities Dealers, Inc., 336 F.3d 1373, 1381 (Fed. Cir. 2003) ("A clause in a method claim is not given weight when it simply expresses the intended result of a process step positively recited."). Note MPEP 2111.04.
In this case, claims 18-22,24,26 and 27 use the term "wherein", rather than "whereby", but it is concluded that the terms should be treated the same…the wherein clause does not inform the artisan of how the administering steps are performed; rather, the wherein clause merely characterizes the results of those steps.
Regarding claims 18-22,24,26,27 and 29, Dirks et al. recite a method of treating a disease or disorder, which is cancer comprising providing a first hairpin monomer to a cell comprising a target nucleic acid associated with the disease or disorder; and providing a second RNA hairpin monomer to the cell, wherein the second monomer comprises a propagation region that is substantially complementary to a portion of the first monomer, and wherein the first and second monomers polymerize in the presence of the target nucleic acid to form an RNA polymer that activates RNA-dependent kinase PKR (claim 18), and the method is carried out in vivo (claim 20). Dirks et al. teach treating a patient suffering from cancer comprising administering to target cells in the patient, such as tumor cells, an effective amount of HCR monomers (paragraph 0034). Dirks et al. recite the first RNA polymer comprises an initiator complement region that is complementary to a nucleic acid initiator, which is a portion of the target nucleic acid sequence (Claim 23).
Dirks et al. teaches HCR polymerization in the presence of target mRNA from Ewing’s sarcoma and glioma in which the target mRNA is a fusion comprising SEQ ID NO: 4, using hairpin 1 and hairpin 2 and discloses sequences of the RNA hairpin monomers, H1 as SEQ ID NO: 2 and H2 as SEQ ID NO: 3 (Example 1, page 10). Dirks et al. disclose that in the presence of an intracellular mRNA target, HCR polymerization is initiated and the product of the polymerization chain rection serves as PKR binding domains to activate PKR which leads to inhibition of translation and cell apoptosis in diseased cells that contain the intracellular target (Example 3, page 11). Dirks et al. teach hairpin monomers are introduced in vivo into tumor cells by gene delivery methods and recognition of the target by the HCR-RNA monomers initiates hybridization chain reaction which produces long nicked RNA duplexes in the tumor cells, activates PKR in the tumor cells which also induces apoptosis and can reverse the growth of the tumor (Example 4, paragraph 0112).
Dirks et al. do not teach the hairpins are DNA as recited in instant claim 18, or that the target RNA is miR-21 as in instant claim 31.
Before the effective filing date, Morihiro taught decoy nucleic acids which function as “decoys” that capture transcription factors and exert therapeutic effects by regulating the expression of genes that are abnormally acting in diseased cells, and taught a study aimed at developing decoy nucleic acids that respond to microRNA (miRNA) specifically expressed in diseased cells and exert their medicinal effects by making full use of DNA nanotechnology (Section 1, left column). Morihiro taught that three types of hairpin-type DNA probe sets (HP1 and HP2) were designed and synthesized for use in HCR triggered by miR-21 overexpressed in many cancer cells (Section 2.1, right column). Morihiro taught the sequences alter the length of the single-stranded regions called toeholds that most greatly affect HCR progression, and the toehold portion is phosphorothioated to increase the resistance to nucleases (Section 2.1, right column). Morihiro taught that HP1 and HP2 were lipofected into human cervical cancer cells (HeLa) known to overexpress miR-21, and results were that HCR triggered by miR-21 can proceed in living cells, while transfecting HEK293T cells which express little miR-21 resulted in a decrease in FRET efficacy compared to HeLa cells which suggests HCR dependent progression. Morihiro taught that HCR progressed depending on intracellular miR-21 concentrations and the possibility of the cell-selective disease treatment (Section 2.3 right column).
Regarding claims 23 and 25, Dirks et al. taught the first monomer in the monomer pair typically comprises an initiator complement region that is complementary to a portion of an initiator molecule, and the initiator complement region is preferably a sticky end, and the first monomer comprises a recognition molecule that binds or interacts with an initiator molecule (instant target RNA-binding cassette in claim 23), and interaction of the initiator to the initiator complement region or to the recognition molecule begins an HCR reaction (paragraph 0039). The second monomer in the pair preferably comprises a propagation region that is able to hybridize to a complementary region of another monomer, preferably another copy of the first monomer to continue the HCR region begun by the initiator and the propagation region can be the loop region of a hairpin monomer (paragraph 0040). The propagation region of the second monomer is only available to interact with the initiator complement region of the first monomer when an HCR reaction has been started by interaction between the initiator and first monomer (the propagation becomes available to hybridize to complementary region of another monomer) (paragraph 0041). Dirks et al. teach the hairpins H1 and H2, which comprise sticky ends ‘a’ and ‘c*’ (equivalent to the instant protruding regions) and potential energy is stored in the hairpin loops (Fig. 1A and paragraph 0016), and a single initiator strand ‘I’ can nucleate or bind to the sticky end of H1 and displace one arm to open up the hairpin, which frees up the bases that were trapped in the hairpin allowing them to perform a similar displacement reaction on H2 (Fig. 1B and paragraph 0017). Fig. 1C shows the newly exposed c region of H1 nucleates at the sticky end of H2 and opens the hairpin to expose a region of H2 (a*) that is identical in sequence to the initiator I, and as a result each copy of I can propagate a chain reaction of hybridization between alternating H1 and H2 hairpins to form a nicked double helix (paragraph 0018). Therefore, while Dirks et al. goes by different names for the parts of the first and second hairpin monomers than the instant claims, Dirks et al. teach the structures of the instant starting hairpin and elongating hairpin, other than it being RNA rather than DNA.
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It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention, to have modified the method of treating cancer of Dirks et al. by modifying the first and second RNA hairpin monomers of Dirks et al. to be DNA hairpins, and for the target RNA to be miR-21, based on the teachings regarding hairpin DNAs and target miR-21 of Morihiro. There would be a reasonable expectation of success because both Dirks et al. and Morihiro pertain to using a set of hairpin nucleic acids in cancer cells containing a target RNA and that the hairpins undergo HCR. Morihiro also suggests their study showed the possibility of cell-selective disease treatment and therefore there would be a reasonable expectation of success of treating cancer. One of ordinary skill in the art would have been motivated to administer DNA hairpins rather than RNA hairpins in the treatment method of Dirks et al. and for the target RNA to be miR-21, because Morihiro taught the decoy nucleic acids that respond to miRNA specifically expressed in diseased cells and exert their medicinal effects by making full use of DNA nanotechnology and taught that the DNA hairpins (HP1 and HP2) when lipofected into human cervical cancer cells (HeLa) known to overexpress miR-21 underwent HCR and also found that HCR progressed depending on intracellular miR-21 concentrations and suggested the possibility of cell-selective disease treatment. Therefore, Morihiro suggests using two DNA hairpins in cervical cancer cells that overexpress miR-21 and that HCR was triggered by the miR-21 in the cells, and Dirks et al. teach HCR polymerization is initiated and results in cell apoptosis in diseased cells that contain the intracellular target and that hairpin monomers are introduced in vivo into tumor cells by gene delivery methods and recognition of the target by the HCR-RNA monomers initiates hybridization chain reaction which produces long nicked RNA duplexes in the tumor cells, activates PKR in the tumor cells which also induces apoptosis and can reverse the growth of the tumor.
Accordingly, the limitations of claims 18-31 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date.
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 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); 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 nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined 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 § 2146 et seq. 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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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 www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 18-31 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 19/154,529 (‘529) (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because claims 1-14 of ‘529 recite a cell death-inducing composition comprising a set of hairpin nucleic acids consisting of a starting hairpin nucleic acid comprising a structure of formula I and an elongating hairpin nucleic acid comprising a structure represented by formula II, wherein the cell death is induced specifically in a cell expressing miR-21. Formulas I and II recite components of each hairpin nucleic acid, including protruding region, stem region, loop region, and claim 3 recites specific sequences of the miR-21 binding domain. Claim 7 of ‘529 recites the hairpin nucleic acid is composed of DNA nucleotides. Claims 12-13 of ‘529 recite a pharmaceutical composition for treating cancer comprising the cell death-inducing composition of claim 1, and claim 14 of ‘529 recites an anticancer agent for preventing or treating cancer comprising cells expressing miR-21 comprising a set of hairpin nucleic acids comprising a starting hairpin nucleic acid comprising formula I and an elongating hairpin nucleic acid comprising formula II.
Instant claims 18-31 recite a method of treating a disease selected from a group consisting of cancers, immune system diseases, and neurodegenerative diseases in a subject in need thereof, comprising administering to the subject an effective amount of a composition comprising a starting hairpin DNA and an elongating hairpin DNA, wherein the starting hairpin DNA hybridizes with a target RNA expressed in a cell of interest, wherein the starting hairpin DNA and the elongating hairpin DNA undergo a hybridization chain reaction in the cell of interest, thereby forming a double-stranded DNA product, and wherein the administration of the composition treats the disease in the subject. Instant claim 19 limits the disease to cancer and the cell of interest to a cancer cell, and claim 31 recites the target RNA is miR-21 which is the same target recited in claims 1-14 of ‘529.
Therefore, claims 1-14 of ‘529 recite a product (composition) comprising a species of a starting hairpin nucleic acid and an elongating hairpin nucleic acid encompassed by the genus of starting hairpin DNA and elongating hairpin DNA used in the treatment method of instant claims 18-31, which recites a method of treating cancer, immune system diseases and neurodegenerative diseases. The composition of claims 1-14 of ‘529 is an obvious product that would be used in a treatment method of the instant claims. The species of the starting hairpin and elongating hairpin recited in ‘529 anticipates the claimed genus in the instant application being examples, and a patent to the genus would improperly extend the right to exclude granted by a patent to the species of sub-genus should the genus issue as a patent after the species or sub-genus.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
Claims 18-31 are rejected.
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/STEPHANIE L SULLIVAN/Examiner, Art Unit 1635
/ABIGAIL VANHORN/Primary Examiner, Art Unit 1636
