50DETAILED 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 .
Election/Restrictions
Applicant’s election without traverse of group II, clearing reagent, epi-fluorescence and proteinase in the reply filed on 9/2/2026 is acknowledged.
Claims 119-124, 126, 129-130, 132-134, 136-137, 146, 170 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 9/2/2026.
Priority
The instant application was filed 12/21/2023 and is a Continuation of 18310477 , filed 05/01/2023 which is a continuation of 16347874 , filed 05/07/2019, which is a national stage entry of PCT/US2017/060570 with an international filing date: 11/08/2017
and claims priority from provisional application 62419033 , filed 11/08/2016.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 9/2/2026 is being considered by the examiner.
Several of the cited references are Office actions or other correspondence from foreign offices, some translated and some providing a summary. It is noted that for review of these, the pending claims that were reviewed in these actions were not provided, but for completeness and clarity of the record the cited references when provided in this prosecution were not considered in light of the instant claims. The foreign statutes and comments of the reviewers were not clearly in context of the pending claims and were not considered for their logic nor factual accuracy of comments in actions from other foreign offices.
Nucleotide and/or Amino Acid Sequence Disclosures
Summary of Requirements for Patent Applications Filed On Or After July 1, 2022, That Have Sequence Disclosures
37 CFR 1.831(a) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.831(b) must contain a “Sequence Listing XML”, as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.831-1.835. This “Sequence Listing XML” part of the disclosure may be submitted:
1. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter “Legal Framework”) in XML format, together with an incorporation by reference statement of the material in the XML file in a separate paragraph of the specification (an incorporation by reference paragraph) as required by 37 CFR 1.835(a)(2) or 1.835(b)(2) identifying:
a. the name of the XML file
b. the date of creation; and
c. the size of the XML file in bytes; or
2. In accordance with 37 CFR 1.831(a) using the symbols and format requirements of 37 CFR 1.832 through 1.834 on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation by reference statement of the material in the XML format according to 37 CFR 1.52(e)(8) and 37 CFR 1.835(a)(2) or 1.835(b)(2) in a separate paragraph of the specification identifying:
a. the name of the XML file;
b. the date of creation; and
c. the size of the XML file in bytes.
SPECIFIC DEFICIENCIES AND THE REQUIRED RESPONSE TO THIS NOTICE ARE AS FOLLOWS:
Specific deficiency - Sequences appearing in the specification are not identified by sequence identifiers (i.e., “SEQ ID NO:X” or the like) in accordance with 37 CFR 1.831(c). Table 1 page 35
Required response – Applicant must provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3), and 1.125 inserting the required sequence identifiers, consisting of:
• A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
• A copy of the amended specification without markings (clean version); and
• A statement that the substitute specification contains no new matter.
Drawings
The specification teaches, “FIGS. 3A-3E illustrate a reduction of background in multiple color imaging, in yet another embodiment of the invention;.” Thus the drawings appear to be in color. “Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
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.
Claim(s) 171-173 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chen (WO2015127183), Trafton (MIT news 1/15/2015), Alon (2015 SCSB FALL POSTER SESSION ABSTRACTS)
Chen teaches, “The present invention relates to an enlarged sample of interest for microscopy and methods for enlarging a sample of interest and the optical imaging of a sample of interest with resolution better than the classical microscopy diffraction limit, by synthesizing a swellable polymer network within a sample, it can be physically expanded, resulting in physical magnification.”
Chen teaches, “[0008] In an embodiment of this concept, the composition comprises a polyelectrolyte hydrogel ( or the components thereof), which can swell macroscopically, for example, in low-salt water. The composition can comprise a tag or other feature of interest (for example, fluorescent dye molecules that have been delivered to the biological sample via antibody staining) which can be anchored (e.g., chemically) into the hydrogel before expansion. Following anchoring, the specimen is subjected to an enzymatic digestion ( or other digestion) to disrupt the underlying network of biological molecules, leaving the tags of interest (e.g., the fluorescent dye molecules) intact and anchored to the gel. In this way, the mechanical properties of the gel-biomolecule hybrid material are rendered more spatially uniform, allowing isotropic expansion with minimal artifacts.”
Chen teaches, “ [0026] In a preferred embodiment, the sample of interest can be labeled or tagged. Typically, the label or tag will bind chemically ( e.g., covalently, hydrogen bonding or ionic bonding) to the sample, or a component thereof. The tag can be selective for a specific target (e.g., a biomarker or class of molecule), as can be accomplished with a 20 antibody or other target specific binder. The tag preferably comprises a visible component, as is typical of a dye or fluorescent molecule. Contacting the sample of interest with a label or tag results in a "labeled sample of interest." A fluorescently labeled sample of interest, fix example, is a sample of interest labeled through techniques such as, but not limited to, immunofluorescence, immunohistochemical or immunocytochemical staining to assist in microscopic analysis. Thus, the label or tag is preferably chemically attached to the sample of interest, or a targeted component thereof. In a preferred embodiment, the label or tag, e.g. the antibody and/or fluorescent dye, further comprises a physical, biological, or chemical anchor or moiety that attaches or crosslinks the sample to the composition, hydrogel or other swellable material. The labeled sample may furthermore include more than one label. For example, each label can have a particular or distinguishable fluorescent property, e.g., distinguishable excitation and emission wavelengths. Further, each label can have a different target specific binder that is selective for a specific and distinguishable target in, or component of the sample.” Chen teaches an anchor moiety.
With regards to claim 171, Chen teaches tissue preparation (0040) including slices were incubated with DNA-labeled secondary antibodies in hybridization buffer at a concentration of approximately 10 ug/mL for 6-12 hours, then washed in slice blocking buffer as for primary. Specimens were incubated with dye-labeled DNA tertiaries in hybridization buffer at a concentration of 1 ng/uL for 6-1 hours, then washed in slice blocking buffer as for primary.” Chen further teaches hydrogel embedding (polymerization) to anchor the probes via the acrylate modified 5’ end of the probes (0041). Chen teaches digestion of DNA by digestion with proteinase K and expansion (0042). Chen teachings imaging (0043).
Thus Chen anticipates the active steps of the claims by exposing ta fixed sample to the oligonucleotide modified with 5’ acryalate moieties, anchoring (embedding) the target and modified oligonucleotide in the gel by polymerization, expanding, clearing the gel by use of a proteinase K and imaging by using secondary nucleic acid probes.
Chen teaches polymerization is a separate step followed by swelling or expansion (0027-0032) and (0041-0042). Chen (wo) states, “[0035] In one embodiment, the addition of water allows for the embedded sample to expand 4x to 5x (e.g., 4.5x) or more its original size in 3-dimensions. Thus, the sample can be increased 100-fold or more in volume. This is because the polymer is embedded throughout the sample, therefore, as the polymer swells (grows) it expands the tissue as well. Thus, the tissue sample itself becomes bigger. Surprisingly, as the material swells isotopically, the anchored tags maintain their relative spatial relationship. [0036] The swollen material with the embedded sample of interest can be imaged on any optical microscope, allowing effective imaging of features below the classical diffraction limit. Since the resultant specimen is preferably transparent, custom microscopes capable of large volume, wide field of view, 3-D scanning may also be used in conjunction with the expanded sample.”
Chen does not specifically teach detection of mRNA.
However, Trafton teaches, “Before enlarging the tissue, the researchers first label the cell components or proteins that they want to examine “
Alon suggest expansion microscopy for RNA expression.
Trafton and Alon teaches detection of RNA (example 4)
Therefore it would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claims to replace the antibody with a nucleic acid probe as a replacement for the antibody and in anchor probe in a gel. The artisan would be motivated to take advantage of the unprecedented affinity and/or sensitivity in the method and determine if gel expansion alters specificity or distortion. The artisan would be motivated to detect mRNA location at the cellular levels. The artisan would have a reasonable expectation of success as the artisan is merely substituting one detection reagent for another.
With regards to claim 172, Chen teaches epifluorescence (0052).
With regards to claim 173, Chen teaches proteinase K digestion with degrades proteins which encompasses the extracellular matrix. (0042)
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.
Claim 171-173 provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 170-189 of copending Application No. 18/310477. Although the claims at issue are not identical, they are not patentably distinct from each other because coextensive of scope.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
The instant claims are drawn to a method for anchoring target mRNA transcripts within a matrix, clearing non-target cellular components and imaging the target mRNA, comprising: exposing a sample comprising a cell or a tissue to a plurality of anchor probes and a plurality of primary probes, wherein the anchor probes comprise a moiety that is complementary and hybridizes to the target mRNA transcript and a moiety that covalently binds to the matrix, and wherein the primary probes do not comprise a fluorescent label; polymerizing a polymer matrix within the sample; anchoring the target mRNA transcript to the polymer matrix wherein the anchor probe covalently binds the polymer matrix; clearing the non-target cellular components from the polymer matrix wherein the target mRNA transcripts remain anchored in the polymer matrix; and, contacting the primary nucleic acid probes with a plurality of secondary nucleic acid probes comprising a fluorescent dye and a recognition sequence that hybridizes to a read sequence of the primary nucleic acid probe and imaging.
The claims of 477 are drawn to method for gel embedding a sample. comprising: exposing a sample comprising nucleic acid targets to a plurality of primary nucleic acid probes comprising a target binding sequence and one or more read sequences; exposing a sample to a plurality of anchor nucleic acid probes, wherein the anchor probes comprise poly-dT portion that is complementary to and hybridizes to the nucleic acid mRNA transcript targets ;embedding at least a portion of the sample within a polyacrylamide gel: immobilizing at least some of the anchor nucleic acid probes to the polyacrylamide gel: clearing proteins and/or lipids and/or DNA and or extracellular matrix and/or RNA molecules from the sample; and determining binding of the primary acid probes to the nucleic acid targets by imaging the polyacrylamide gel wherein the primary probes are contacted with a plurality of secondary nucleic acid probes comprising a fluorescent dye and a recognition sequence that hybridizes to the one or more read sequence of the primary probe.
Therefore it would have been prima facie obvious to one of ordinary skill int the art prior to the effective filing date of the claims the claims of 477 are a species encompassed by the instant claims. Thus the instant claim are obvious over the claims of 477.
Dependent claims are rejected as they are coextensive in scope.
Summary
No claims are allowed.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to STEVEN C POHNERT PhD whose telephone number is (571)272-3803. The examiner can normally be reached Monday- Friday about 6:00 AM-5:00 PM, every second Friday off.
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/Steven Pohnert/ Primary Examiner, Art Unit 1683
Prosecution Insights