DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This application has been transferred from Examiner B. Sisson to Examiner D. Johannsen. The application remains assigned to Art Unit 1682.
It is noted that prosecution has been re-opened pursuant to the Pre-Appeal conference referenced in the Notice mailed 30 July 2026. All prior rejections of the claims have been withdrawn, and the claims are now rejected on the grounds set forth below (and it is noted that as all prior rejections have been withdrawn, Applicant’s arguments regarding those rejections are now moot). Claim 103 remains withdrawn, and claims 65-67, 69-70, 73, 76-77, 79-83, 85-90, 93, 96, 99, 101, 104-106, and 108 remain under consideration herein. This action is non-final.
Priority
This application is a continuation of PCT/US22/78462, filed 20 October 2022, claiming priority to US provisional applications 63/350,854 (filed 09 June 2022), 63/350,858 (filed 09 June 2022), 63/297,077 (filed 06 January 2022), and 63/271,456 (filed 25 October 2021).
Election/Restrictions
Claim 103 remain withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 25 January 2024.
Claim Interpretation
Regarding the recitations in dependent claims 66-67 and 69 of the limitation “step E)”, it is noted that this has been interpreted as referring to “E)” of independent claim 65 (as this is the only reasonable interpretation of the claim language; the failure of the claims to previously employ the term “step” thus does not render these dependent claims indefinite). This also applies to the limitations “step C)” in dependent claim 90 and “step D)” in dependent claim 99.
Regarding claim 108, and particularly the recitation therein of the term “specific antibody”, it is noted that the specification (at paragraph 84 of the published application) states that the term “specific” used in reference to a compound “refers to the substance’s ability to cause a particular action, such as binding, to a particular molecular target with minimal or no action to other substances (e.g., an antibody and antigen”. The application as filed discloses the use of “antigen-specific antibodies” (see, e.g., paragraph 109 of the application as filed, where such antibodies are taught as a preferred type of “protein-specific binding agent”), as well as “carbohydrate-specific antibodies” (see paragraph 199), and teaches detection of proteins in a cell via use of a “specific binding reagent” that may be an antibody, which reagent is bound to protein (see, e.g., paragraph 186 of the published application). Accordingly, the term “specific antibody” as employed in the claim, particularly given the requirement in the body of the claim for “binding the specific antibody to a specific antigen present in the tissue section”, has been interpreted as simply referring to the specificity of the antibody used for a particular partner antigen target in the tissue sample (i.e., the term “specific” does not render the claim indefinite in this context, as the claim language requires binding of that “specific antibody” to a corresponding “specific antigen” in the target sample).
Claim Rejections - 35 USC § 112(b)/second paragraph
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 65-67, 69-70, 73, 76-77, 79-83, 85-90, 93, 96, 99, 101, 104-106, and 108 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.
Claims 65-67, 69-70, 73, 76-77, 79-83, 85-90, 93, 96, 99, 101, 104-106, and 108 are indefinite over the recitation in independent claim 65 (at line 3) of the limitation “mounting the tissue section embedded in an embedding material onto a surface of a hydrogel carrier substrate”. It is noted that the preamble of claim 65 recites a method “of obtaining an image of a portion of a tissue section”, however there is no prior recitation of a “tissue section embedded in an embedding material”. Accordingly, clear antecedent basis is lacking for the limitation “the tissue section embedded in an embedding material”, and it is further unclear how this language further limits the claimed method, particularly with regard to whether the claim may require some type of further activity to produce a tissue section meeting the requirement of being “embedded in an embedding material” and how/whether this relates in some way to the action of “mounting the tissue section”, and/or whether the claim may embrace (or even require) a tissue section that is already “embedded in an embedding material”, etc. Thus, there are multiple reasonable interpretations of this claim language that potentially impart very different boundaries on what is being claimed, and further clarification is therefore needed.
Claim 86 is indefinite over the recitation of the limitation “wherein the sample-carrier construct comprises interfacial water, wherein the interfacial water is between the hydrogel carrier substrate and the tissue section, wherein the interfacial water is useful at facilitating removal of the hydrogel carrier substrate from the immobilized tissue section and does not significantly affect the structural integrity of the tissue section upon subsequent removal”. First, it is noted that the “sample-carrier construct” is initially referenced in A) of claim 65, and is subsequently referenced at B), with a “portion” being produced in B) (and subsequently referenced in C)). It is not clear at what point during the recited method the limitations of claim 86 regarding “interfacial water” apply, such that further clarification is needed, i.e., is this claim requiring the presence of interfacial water in A) (which itself is indefinite), or does this relate to later method steps/activities (given the reference to facilitating “removal”, immobilization, etc.). Additionally, while it is noted that the language “wherein the interfacial water is useful…” is considered non-limiting (as there is no actual reference in the claim to any use of such water, i.e., this just recites a characteristic of the “interfacial water”), further clarification is needed regarding the language “does not significantly affect…upon subsequent removal”, as it is not clear whether this refers to removal of the water, removal of carrier substrate, etc. (i.e., there are multiple reasonable interpretations of the present claim language that impart different boundaries on what is claimed).
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 65, 67, 69-70, 73, 76-77, 79-81, 85, 90, 93, 96, 99, 101, and 104-106 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Columbia (WO 2008/054421 A2 [08 May 2008]; cited herein), and with further regard to claim 85, as evidenced by Kazi et al (Journal of Biomedical Materials Research Part A 107A:6-11 [2019; online 13 Nov 2018]; cited herein).
Independent claim 65 is directed to a method “of obtaining an image of a portion of a tissue section, said method comprising” steps/activities of A)-E) as follows:
A) mounting the tissue section embedded in an embedding material onto a surface of a hydrogel carrier substrate that is a solid or semi-solid to generate a sample-carrier construct comprising the hydrogel carrier substrate and the tissue section;
B) cutting the sample-carrier construct to form a portion of the sample-carrier construct, comprising a portion of the hydrogel carrier substrate and a portion of the tissue section;
C) contacting the tissue section of the portion of the sample-carrier construct with a receiving substrate to generate an immobilized tissue section;
D) removing the hydrogel carrier substrate from the immobilized tissue section; and
E) imaging the immobilized tissue section using microscopy, thereby obtaining an image of a portion of the tissue section.
Initially, it is reiterated that the limitation “the tissue section embedded in an embedding material…” lacks antecedent basis and is indefinite for the reasons discussed above. It is also noted that while A)-C) as recited must be performed in order (given that B) refers to “the sample-carrier construct” and C) to “the tissue section of the portion” (referring back to the “portion of the tissue section” recited in B)), activities/steps D) and E) each refer to “the immobilized tissue section” (a term recited in C), and these may be performed in either the recited order (with E) following D)) or with E) occurring prior to D) (given the open transitional language “comprising” and the wording of D) and E)).
Columbia teaches methods “for making a frozen section microarray of fresh non-fixed frozen cell or tissue samples” for use in biological assays (see entire reference).
Columbia teaches that their methods preferably employ “Agarose-OCT” in preparation of their microarrays (which include tissue microarrays, “TMAs”); “Agarose-OCT” is described as a composition including 0.5% to 15% agarose in OCT (see, e.g., the Summary at pages 7-8 and the description of “Agarose-OCT” on pages 9-11, as well as the definitions on page 4), and it is noted that agarose is a preferred hydrogel of the claimed invention (see, e.g., dependent claims 79-80), and that OCT compositions are a preferred “embedding material” of the claimed invention (see, e.g., dependent claim 76).
With regard to TMA embodiments, Columbia teaches multiple methods of preparing samples for analysis, including methods in which tissue samples are loaded into holes in a prepared block of agarose-OTC (preferably 3%-7% OCT), with the block then being rapid frozen prior to “cryosectioning right away” or placement in “long-term storage”, with Columbia further teaching that sections may subsequently be subjected to further types of analysis that may include mounting on glass slides for immunohistochemical analysis, in situ PCR analysis, staining and imaging, etc. (see page 9 bridging to page 10). Columbia also discloses preferred embodiments in which holes in the Agarose-OCT block are filled with liquid OCT “before the tissue sample is inserted”, creating a type of tissue section that has been mounted “in an embedding material onto a surface of a hydrogel carrier substrate…..to generate a sample-carrier construct comprising the hydrogel carrier substrate and the tissue section” (see, e.g., page 12 and pages 18-19). Furthermore, Columbia also teaches an embodiment in which – in order to avoid potentially damaging pieces of tissue too large to be “forced into a hole” – an Agarose-OCT housing block is cut in half along the length of holes in the block to create grooves in which tissue sections may be placed, and then covered with liquid OCT (see pages 19 and 27). Thus, while the meaning of “mounting the tissue section embedded in an embedding material….” is unclear, Columbia teach multiple embodiments of their method in which the mounting of tissues/portions of tissues involves mounting comprising embedding onto a surface of a hydrogel, meeting the requirements of A) of the claims. Further, Columbia teach that their TMAs are subsequently frozen and cryosectioned (which may occur immediately or following storage), thus meeting the requirements of the “cutting” of B) of the claims (see again, e.g., pages 12 and 18). It is also noted that Columbia exemplify the preparation of TMAs via methods in which tissue samples are first loaded into an Agarose-OCT block, covered with OCT, frozen, and cryosectioned; see Example 2 particularly at pages 25-26, as well as “Method 2” on page 27).
Regarding C)-E) of claim 65, Columbia teach subsequent analysis of their sections via methods including, e.g., mounting of frozen sections on glass slides, followed by drying, fixing, and imaging via use of an FITC-conjugated antibody; see page 18 bridging to page 19, and Figure 9; see also page 20 (disclosing detection/measurement of intact antigens, DNA/RNA levels, and enzyme activity in samples, including “directly on microarray slides”). Columbia also teaches that their cryosections “can be fixed in any way that the desired protocol for the assay suggests to optimize/preserve biological activity of the molecule being assayed”, further facilitating the analysis of different targets of interest (such as polynucleotides and polypeptides) “on the same slide or on different slides” (page 20). Turning to specific assay protocols taught by Columbia that employ tissue sections as prepared by their methods (following cryosectioning and possible storage), Columbia exemplifies performing immunohistochemistry on cryosections via a staining method performed on a glass slide that employs the noted FITC-conjugated antibody to label alpha-smooth muscle actin in mouse tissues including “brain, heart, lung, spleen, liver, kidney, and testis” (see pages 28-29). Following fixing of cryosections on slides and prior to microscopic analysis/imaging, Columbia discloses a procedure in which multiple steps of washing in PBS (i.e., an aqueous solution) occur (see page 29). It is noted that Columbia teaches with regard to their agarose-OCT composition that “Agarose-OCT washes off of a support such as a glass slide in an aqueous solution, or in solvents such as xylene” (see pages 10-11, particularly lines 1-2 on page 11). Thus, the procedures described by Columbia that comprising all of a contacting of tissue sections of the cryosections with a receiving substrate and generation of an “immobilized tissue section” (including via fixation), removing Agarose-OTC “hydrogel carrier substrate” by washing (achieved by the PBS washes disclosed by Columbia), and imaging using microscopy to obtain an image (see again, e.g., Figure 9).
Columbia thus anticipates independent claim 65.
With further regard to dependent claim 67, the procedures described above are not disclosed by Columbia as including permeabilization, such that Columbia also meets the requirements of this claim.
Regarding claims 69-70, it is reiterated that the preferred procedure described above includes use of multiple imaging reagents (the labeled anti-alphaSMA antibody, as well as the propidium iodide counterstain)(see again page 29); Columbia also disclose embodiments in which eosin as employed as a stain (see, e.g., the staining of TMA sections with hematoxylin and eosin depicted in Figure 7), such that Columbia disclose embodiments of their methods meeting the requirements of these claims.
With further regard to claims 73 and 104-106, Columbia teach multiple tissue types meeting the requirements of claims 104-105 (as recited above), and teach cryosections having a “usual” thickness of 5 um (while noting that such sections may be as thin as 3 um; see, e.g., page 26).
Regarding claims 76-77, Columbia’s teachings regarding the use of OCT compositions, as well as removal of their “embedding materials” by washing, are described above; it is noted that Columbia also teach that agar may be used in lieu of agarose (although agarose is preferred); see page 12 bridging to page 13).
Regarding claims 79-80, the preferred hydrogel carrier of agarose is discussed above (as this is the preferred embodiment taught by Columbia); it is also noted that Columbia teach that OCT comprises polyvinyl alcohol and polyethylene glycol (see page 4).
Regarding claim 81, it is again noted that Columbia teach that 3% to 7% is preferably employed in their Agarose-OCT blocks (see again page 9), and Columbia exemplifies the use of 5% agarose in OCT (see, e.g., page 22, item 1); thus, Columbia anticipate the claim.
With further regard to claim 85, while Columbia does not disclose Young’s modulus values for their hydrogel compositions, Kazi et al teach corresponding Young’s modulus values for a range of agarose concentrations encompassing 0.5%-6%, establishing that the 3%-7% range of agarose taught by Columbia embraces Young’s modulus values as set forth in claim 85 (see in particular Kazi et al Figure 2B). Thus, as evidenced by the teachings of Kazi et al, Columbia inherently anticipates hydrogel carrier substrates meeting the requirements of claim 85.
Regarding claims 90 and 93, Columbia teach that their sample-carrier constructs may be cryosectioned “right away” or stored indefinitely (by freezing), which encompasses at least some embodiments embraced by the claims (see, e.g., page 18).
Regarding claim 96, the washing in PBS described above meets the requirement of “physically removing”.
Regarding claim 99, in disclosing, e.g., their “groove” embodiment of tissue storage, Columbia states that tissues are placed into grooves and covered with OCT compound (see again pages 19 and 27), and Columbia further teaches loading tissues into holes filled with liquid OCT compound (see, e.g., page 18); Columbia thus discloses a type of “uniform adhesion” between tissue and carrier.
Regarding claim 101, as Columbia disclose embodiments in which an entire cryosection is transferred to a slide, they disclose methods in which “all of the tissue section of the portion” is immobilized on the receiving substrate (i.e., a slide).
Claim Rejections - 35 USC § 103
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.
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.
Claim(s) 66 and 88-89 are rejected under 35 U.S.C. 103 as being unpatentable over Columbia (WO 2008/054421 A2 [08 May 2008]; cited herein) in view of Gao et al (The Journal of Histochemistry and Cytochemistry 39(4):537-540 [1991]; cited herein), and with regard to claim 66, as evidenced by the specification, and with regard to claims 88-89, as evidenced by Samoszuk (Am. J. Pathol. 96:448-453 [1991]; cited herein).
Independent claim 65 (from which the rejected claims depend) is directed to a method “of obtaining an image of a portion of a tissue section, said method comprising” steps/activities of A)-E) as follows:
A) mounting the tissue section embedded in an embedding material onto a surface of a hydrogel carrier substrate that is a solid or semi-solid to generate a sample-carrier construct comprising the hydrogel carrier substrate and the tissue section;
B) cutting the sample-carrier construct to form a portion of the sample-carrier construct, comprising a portion of the hydrogel carrier substrate and a portion of the tissue section;
C) contacting the tissue section of the portion of the sample-carrier construct with a receiving substrate to generate an immobilized tissue section;
D) removing the hydrogel carrier substrate from the immobilized tissue section; and
E) imaging the immobilized tissue section using microscopy, thereby obtaining an image of a portion of the tissue section.
It is also again noted that the limitation “the tissue section embedded in an embedding material…” lacks antecedent basis and is indefinite for the reasons discussed above. It is also noted that while A)-C) as recited must be performed in order (given that B) refers to “the sample-carrier construct” and C) to “the tissue section of the portion” (referring back to the “portion of the tissue section” recited in B)), activities/steps D) and E) each refer to “the immobilized tissue section” (a term recited in C), and these may be performed in either the recited order (with E) following D)) or with E) occurring prior to D) (given the open transitional language “comprising” and the wording of D) and E)).
Columbia teaches methods “for making a frozen section microarray of fresh non-fixed frozen cell or tissue samples” for use in biological assays (see entire reference).
Columbia teaches that their methods preferably employ “Agarose-OCT” in preparation of their microarrays (which include tissue microarrays, “TMAs”); “Agarose-OCT” is described as a composition including 0.5% to 15% agarose in OCT (see, e.g., the Summary at pages 7-8 and the description of “Agarose-OCT” on pages 9-11, as well as the definitions on page 4), and it is noted that agarose is a preferred hydrogel of the claimed invention (see, e.g., dependent claims 79-80), and that OCT compositions are a preferred “embedding material” of the claimed invention (see, e.g., dependent claim 76).
With regard to TMA embodiments, Columbia teaches multiple methods of preparing samples for analysis, including methods in which tissue samples are loaded into holes in a prepared block of agarose-OTC (preferably 3%-7% OCT), with the block then being rapid frozen prior to “cryosectioning right away” or placement in “long-term storage”, with Columbia further teaching that sections may subsequently be subjected to further types of analysis that may include mounting on glass slides for immunohistochemical analysis, in situ PCR analysis, staining and imaging, etc. (see page 9 bridging to page 10). Columbia also discloses preferred embodiments in which holes in the Agarose-OCT block are filled with liquid OCT “before the tissue sample is inserted”, creating a type of tissue section that has been mounted “in an embedding material onto a surface of a hydrogel carrier substrate…..to generate a sample-carrier construct comprising the hydrogel carrier substrate and the tissue section” (see, e.g., page 12 and pages 18-19). Furthermore, Columbia also teaches an embodiment in which – in order to avoid potentially damaging pieces of tissue too large to be “forced into a hole” – an Agarose-OCT housing block is cut in half along the length of holes in the block to create grooves in which tissue sections may be placed, and then covered with liquid OCT (see pages 19 and 27). Thus, while the meaning of “mounting the tissue section embedded in an embedding material….” is unclear, Columbia teach multiple embodiments of their method in which the mounting of tissues/portions of tissues involves mounting comprising embedding onto a surface of a hydrogel, meeting the requirements of A) of the claims. Further, Columbia teach that their TMAs are subsequently frozen and cryosectioned (which may occur immediately or following storage), thus meeting the requirements of the “cutting” of B) of the claims (see again, e.g., pages 12 and 18). It is also noted that Columbia exemplify the preparation of TMAs via methods in which tissue samples are first loaded into an Agarose-OCT block, covered with OCT, frozen, and cryosectioned; see Example 2 particularly at pages 25-26, as well as “Method 2” on page 27).
Regarding C)-E) of claim 65, Columbia teach subsequent analysis of their sections via methods including, e.g., mounting of frozen sections on glass slides, followed by drying, fixing, and imaging via use of an FITC-conjugated antibody; see page 18 bridging to page 19, and Figure 9; see also page 20 (disclosing detection/measurement of intact antigens, DNA/RNA levels, and enzyme activity in samples, including “directly on microarray slides”). Columbia also teaches that their cryosections “can be fixed in any way that the desired protocol for the assay suggests to optimize/preserve biological activity of the molecule being assayed”, further facilitating the analysis of different targets of interest (such as polynucleotides and polypeptides) “on the same slide or on different slides” (page 20). Turning to specific assay protocols taught by Columbia that employ tissue sections as prepared by their methods (following cryosectioning and possible storage), Columbia exemplifies performing immunohistochemistry on cryosections via a staining method performed on a glass slide that employs the noted FITC-conjugated antibody to label alpha-smooth muscle actin in mouse tissues including “brain, heart, lung, spleen, liver, kidney, and testis” (see pages 28-29). Following fixing of cryosections on slides and prior to microscopic analysis/imaging, Columbia discloses a procedure in which multiple steps of washing in PBS (i.e., an aqueous solution) occur (see page 29). It is noted that Columbia teaches with regard to their agarose-OCT composition that “Agarose-OCT washes off of a support such as a glass slide in an aqueous solution, or in solvents such as xylene” (see pages 10-11, particularly lines 1-2 on page 11). Thus, the procedures described by Columbia that comprising all of a contacting of tissue sections of the cryosections with a receiving substrate and generation of an “immobilized tissue section” (including via fixation), removing Agarose-OTC “hydrogel carrier substrate” by washing (achieved by the PBS washes disclosed by Columbia), and imaging using microscopy to obtain an image (see again, e.g., Figure 9).
Columbia thus discloses methods meeting all requirements of independent claim 65. However, while Columbia teach that samples prepared by their methods may be further analyzed with regard to any target type of interest (including polypeptides targeted for detection by corresponding antibodies), and exemplify the use of glass slides in their methods (again as discussed above; e.g. Columbia exemplifies performing immunohistochemistry on cryosections via a staining method performed on a glass slide that employs an FITC-conjugated antibody to label alpha-smooth muscle actin in mouse tissues including “brain, heart, lung, spleen, liver, kidney, and testis” [pages 28-29]), Columbia do not explicitly teach an activity corresponding to “permeabilizing” tissues (as recited in claim 66), and do not teach the use of slides (such as silanated/silanized slides) meeting the requirements of claims 88-89.
Gao et al teach methods in which embedded tissue sections (in this case, embedded in polyethylene glycol) – which tissue sections are cut, transferred via agarose blocks, and inverted on silanated slides – are analyzed via immunohistochemical techniques employing labeled antibodies (i.e., methods involving both similar sample types and sample analysis on slides) (see entire reference, particularly page 537, right column-page 539, left column).
The methods of Gao et al employ detergent treatment of samples prior to antibody incubation/staining (specifically with Surfact-Amp X-100) tissue samples (see Gao at page 539, left column); as washing/treating with detergent is disclosed in applicant’s specification as a preferred method of permeabilization (see, e.g., paragraph 162 of the published application), this step of Gao et al meets the requirements of claim 66 (as evidenced by the specification). Gao et al also teach that their methods facilitated multiple types of analysis of the same tissue samples (see, e.g., the Abstract).
Further, Gao et employ the use in their methods of Digene silanated slides (see page 539, left column) (and it is also noted that Gao et al teach that tissue sections transferred via agarose blocks were successfully transferred to such slides, with the agarose blocks releasing and the tissue sections adhering firmly [see page 539, left column, first full paragraph]). As evidenced by Samoszuk, the slides taught by Gao as “Digene silanated slides” meet the requirement of comprising 3-aminopropyltriethoxysilane (see Samoszuk, page 449, left column, first paragraph)). Accordingly, it is a property of the slides employed by Gao et al that they meet the requirements of claims 88-89.
In view of the teachings of Gao et al, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Columbia so as to have analyzed tissue samples via methods employing permeabilization with detergent and silanated slides, and thereby to have performed methods meeting the requirements of the claims. An ordinary artisan would have recognized such a modification as the simple substitution of one immunohistochemistry protocol for another to achieve the predictable result of analyzing/detecting targets of interest in a tissue sample. Additionally or alternatively, given Gao et al’s statements regarding successful tissue adherence to silanated slides and successful analysis of samples in multiple different ways, an ordinary artisan would have been motivated to have made such a modification for either or both of these benefits. Given the detailed guidance provided by both Columbia and Gao et al, an ordinary artisan also would have had a reasonable expectation of success in performing such methods.
Claim(s) 82-83 and 86 are rejected under 35 U.S.C. 103 as being unpatentable over Columbia (WO 2008/054421 A2 [08 May 2008]; cited herein) in view of Williamson et al (WO 00/19897 [13 April 2000]; cited herein).
The relevant teachings of Columbia are set forth above. While Columbia teaches hydrogel carrier substrates meeting the requirements of the claims, Columbia does not teach use of a support scaffold as required by claims 82-83, and does not teach a method in which “the sample-carrier construct comprises interfacial water” as recited in claim 86.
Williamson et al teach methods employing a “tissue trap” cassette/support to aid in handling tissue samples, which samples are immobilized within the cassette and subsequently cut for mounting on slides (see entire reference). While it is noted that Williamson et al teach preferred embodiments in which tissue samples are supported by a filter, they also teach embodiments in which hydrogels (among other alternatives) are employed to modify “surface tension or wetting characteristics”, as well as to aide in retaining tissues (see page 26; see also page 15, which refers to use of “gels” in immobilization). Williamson et al teach that their cassettes provide benefits in provide for clean sectioning of a sample (page 11), avoidance of contamination (page 12, page 15), and tracking samples (page 19). With particular regard to claim 83, Williamson et al teach that embodiments of their cassette/support may comprise thermoplastic elastomers (see, e.g., claim 4 and page 25). With regard to claim 86, Williamson et al also teach that a known method for transfer of tissue sections is floating such samples onto glass slides for further processing (see page 6).
In view of the teachings of Williamson et al, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the method of Columbia so as to have employed a cassette support “scaffold” as taught by Williamson et al, including by containing or incorporating the carrier substrate of Columbia on or into a support scaffold as taught by Williamson et al. An ordinary artisan would have been motivated to have made such a modification for any of the noted benefits taught by Wiliamson et al. Further, given the detailed guidance provided by both Columbia and Williamson et al, an ordinary artisan also would have had a reasonable expectation of success in performing such methods.
Additionally, and particularly given the indefiniteness of claim 86, Williamson et al’s teaching of the floating of sample sections onto slides is sufficient to suggest the presence of “interfacial water” when this technique is employed, and – given Williamson et al’s teaching of this transfer method, and the lack of a disclosure by Columbia of a preferred method of sample transfer to slides – it would have been prima facie obvious to an ordinary artisan to have employed this technique (or any such known technique) for the predictable result of transferring samples for further analysis. Further, given the simplicity of this method, an ordinary artisan would have had a reasonable expectation of success in performing it.
Claim(s) 87 is rejected under 35 U.S.C. 103 as being unpatentable over Columbia (WO 2008/054421 A2 [08 May 2008]; cited herein) in view of de Graaf et al (Nature Protocols 5(9):1540 [2010]; cited herein).
The relevant teachings of Columbia are set forth above. While Columbia teaches hydrogel carrier substrates meeting the requirements independent claim 65, Columbia does not teach such a substrate that is 80% to 99% water (given Columbia’s disclosure of the use of agarose-OTC).
De Graaf et al, like Columbia, teach methods for preparing tissue samples for analysis, particularly teaching analysis of liver and intestinal slices (see entire reference). De Graaf et al disclose the use in their methods of 3% agarose prepared using distilled water (see, e.g., page 1543, right column, second to last paragraph), and de Graaf et al exemplify the successful sectioning and analysis of samples prepared in this manner (again see entire reference).
In view of the teachings of de Graaf et al, it would have been prima facie obvious to one of ordinary skill in the art to have modified the methods of Columbia et al so as to have employed therein agarose (such as 3% agarose) dissolved in water (meeting the requirements of claim 87), particularly when preparing liver and intestinal tissue samples as taught by de Graaf et al. An ordinary artisan would have been motivated to have made such a modification for the benefit of successfully preparing tissue samples of these types, while employing a lower cost hydrogen carrier substrate (given the cost of water relative to OTC as used by Columbia). Given de Graaf et al’s disclosure, an ordinary artisan also would have recognized such a modification of the simple substitution of one carrier type for another to achieve a predictable result. Further, given the detailed guidance provided by both Columbia and de Graaf et al, an ordinary artisan also would have had a reasonable expectation of success in performing such methods.
Claim(s) 108 is rejected under 35 U.S.C. 103 as being unpatentable over Columbia (WO 2008/054421 A2 [08 May 2008]; cited herein) in view of Soderberg et al (Methods 45:227-232 [2008]; cited herein).
The relevant teachings of Columbia are set forth above. While Columbia teach that samples prepared by their methods may be further analyzed with regard to any target type of interest - including polypeptides targeted for detection by corresponding antibodies (as discussed above), as well as nucleic acids, which may be detected using, e.g., hybridization based assays, in situ PCR, etc. (see, e.g., pages 8 and 10), Columbia do not teach assays in which immobilized tissue sections are contacted with an antibody comprising a nucleic acid that is bound to the target antigen of the antibody, with amplification of a bound polynucleotide being employed to generate amplification products (as required by claim 108).
Soderberg et al teach a technique for characterizing protein interactions using “in situ proximity ligation assay”, in which antibodies with attached DNA strands are bound to their corresponding antigens, with the attached DNA strands being ligated and amplified (see entire reference, particularly Figures 1-2); i.e., Soderberg et al teach a method including further steps meeting the requirements of claim 108. Soderberg et al teach that this method aids in visualization of protein interactions (see entire reference, particularly the Abstract). Accordingly, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have modified the methods of Columbia so as to have performed an analysis of the type taught by Soderberg et al, for the benefit of analyzing protein proximity/interactions in samples. Further, given the detailed guidance provided by both Columbia and Soderberg et al, an ordinary artisan also would have had a reasonable expectation of success in performing such methods.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Meekel et al (Scientific Reports 8:8094 [2018]; cited herein) teach preparation of aortic tissue sections via a process that involves attaching samples to an anvil, embedding tissue cubes in agarose, and sectioning the samples (see entire reference, particularly pages 2-3, including Figure 1).
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/DIANA B JOHANNSEN/Primary Examiner, Art Unit 1682
