DETAILED ACTION
Response to Amendment
Applicant’s responses to the office action filed on October 8, 2025 have been entered. The claims pending in this application are claims 15, 17, 19-28, 37, 38, and 43-48 wherein claims 21, 22, and 37 have been withdrawn due to the restriction requirement mailed on July 23, 2014. The objection and rejection not reiterated from the previous office action are hereby withdrawn in view of applicant’s amendment filed on October 8, 2025. Claims 15, 17, 19, 20, 23-28, 38, and 43-48 will be examined.
Claim Rejections - 35 USC § 112
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.
New Matter
Claims 15, 17, 19, 20, 23-28, 38, and 43-48 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
A limitation “wherein the reference RIN value is the RIN value of RNA that is isolated from the biological sample before any of steps (1) to (6) is performed” is added to independent claim 15 and is read as “wherein the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) or (2) or (3) or (4) or (5) or (6) of claim 15 is performed”. Although the specification describes that “[F]IG. 2: RNA Integrity of RNA isolated from decreasing areas of 6 µm sections mounted on a slide and the reference according to Example 1. Integrity measured as RIN--RNA Integrity Number”, “[F]IG. 5: RNA Integrity of the RNA isolated according to Example 2, measured as RIN value using the Agilent Bioanalyzer. RNA was isolated from one 4 µm section of paraffin embedded tissue. Reference: section transferred into microcentrifuge tube for RNA isolation; staining 1 and 2: RNA extraction from the slides after quick-staining; all extractions done in triplicate”, and “[The RNA is comparable in quality and yield to a reference, where the sections was directly transferred into a microcentrifuge 10 tube and processed according to the PAXgene® Tissue RNA protocol” (see paragraphs [0092]. [0096], and [0131] and Figures 2 and 5 of US 2013/0095473A1, which is US application of this instant application), Figure 5, page 17, line 31 to page 18, line 2 and Example 2 in pages 22 to 24 of the specification suggested by applicant do not describe such limitation recited in claim 15 since the specification does not describe that the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) or (2) or (3) or (4) or (5) or (6) of claim 15 is performed.
MPEP 2163.06 notes “If new matter is added to the claims, the examiner should reject the claims under 35 U.S.C. 112, first paragraph - written description requirement. In re Rasmussen, 650 F.2d 1212, 211 USPQ 323 (CCPA 1981).” MPEP 2163.02 teaches that “Whenever the issue arises, the fundamental factual inquiry is whether a claim defines an invention that is clearly conveyed to those skilled in the art at the time the application was filed...If a claim is amended to include subject matter, limitations, or terminology not present in the application as filed, involving a departure from, addition to, or deletion from the disclosure of the application as filed, the examiner should conclude that the claimed subject matter is not described in that application.” MPEP 2163.06 further notes “When an amendment is filed in reply to an objection or rejection based on 35 U.S.C. 112, first paragraph, a study of the entire application is often necessary to determine whether or not “new matter” is involved. Applicant should therefore specifically point out the support for any amendments made to the disclosure” (emphasis added).
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
Claims 15, 17, 19, 20, 23-28, 38, and 43-46 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Xiang et al., (US 2006/0040283 A1, published on February 23, 2006) in view of Lenz et al., (US 2010/0173295 A1), Cory et al., (US 2006/ 0090214A1, published on April 27, 2006), Chu (US Patent No. 6,291,180 B1, published on September 18, 2001), Espina et al., (US 2013/0137094 A1, priority date: January 25, 2010) and Kennedy et al., (US 2010/0131432 A1, priority date: November 17, 2008).
This rejection was made by modifying the rejection under pre-AIA 35 U.S.C. 103(a) mailed on April 11, 2025. Since the phrase “wherein the reference RIN value is the RIN value of RNA that is isolated from the biological sample before any of steps (1) to (6) is performed” in claim 15 is read as “wherein the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) is performed”, the method for isolating a reference RNA with a reference RIN value is different from the method of claim 15.
Regarding claims 15, 17, 20, 23-28, and 43, Xiang et al., teach (1) mounting at least one part of the biological sample (ie., supraoptic nucleus (SON) from brain) on at least one support (ie., the glass slide), (2) optionally treating the at least one part of the biological sample with a sample treatment agent (eg., ethanol or xylene), wherein said treatment can be carried out at any stage of the procedure before step (6), (3) staining the at least one part of the fixed biological sample mounted on the at least one support with a first cell or tissue staining agent (ie., stained with anti-oxytocin-neurophysin antibody), (4) determining target cells or tissue comprising biomolecules of interest by observing the at least one part stained in step (3) (ie., red color stained by anti-oxytocin-neurophysin antibody), (5) separating the target cells or tissue (ie., the tissue stained by anti-oxytocin-neurophysin antibody) comprising biomolecules of interest (ie., RNA) from the remainder of the biological sample mounted on the at least one support, and (6) isolating the biomolecules from the target cells or tissue separated in step (5) wherein the biomolecules comprise RNA as recited in claim 15, the method comprises step (2) and the sample treatment agent is a de-waxing agent (ie., xylene) as recited in claim 17 wherein the de-waxing agent is a de-paraffinizing agent such as xylene as recited in claims 20 and 23 (see page 33, paragraph [0375]), the at least one support (ie., the glass slide) is transparent as recited in claim 24, the at least one support is made of glass (ie., the glass slide) or a transparent polymer as recited in claim 25, the target cells or tissue comprising biomolecules of interest from the biological sample in step (4) is observed under light or backlight (eg., by using Leica DM RX microscope) as recited in claim 26, the target cells or tissue comprising biomolecules of interest from the biological sample in step (4) is observed under a microscope (eg., Leica DM RX microscope) as recited in claim 27, the target cells or tissue is/are separated in step (5) by microdissection, laser capture microdissection, scraping, or cutting out as recited in claim 28, and the biological sample comprises at least one section of 0.5 to 12 µm (ie., 8 µm) thickness of a non-formalin-fixed paraffin-embedded sample as recited in claim 43 (see pages 32-36, Example 14, paragraphs [0368] to [390]).
Regarding claim 38, Xiang et al., teach that the fixed biological sample is divided in sections of 0.5 to 12 µm thickness (ie., 8µm), and in step (1), the at least one of the support is a transparent support, in step (2) the at least one part of the biological sample is treated with the sample treatment agent and the sample treatment agent is a de-waxing agent (ie., xylene), and in step (4), the target cells or tissue is/are determined in the stained sample section (see pages 32-36, Example 14, paragraphs [0368] to [390]). Although Xiang et al., do not teach that, in step (5) of claim 15, the remainder of the fixed sample (ie., fixed sections stained by anti-oxytocin-neurophysin antibody) is discarded, in view of the teachings of Xiang et al., it is obvious to one having ordinary skill in the art at the time the invention was made to discard the slides after scraping fixed sections stained by anti-oxytocin-neurophysin antibody from the slides into Eppendorf tubes (see paragraph [0371]).
Xiang et al., do not disclose that the biological sample is fixed with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition, and a wax embedded and staining the at least one part of the biological sample mounted on the at least one support for a time period that is not more than 60 seconds with a first cell or tissue staining agent and rinsing the at least one part of the biological sample with water wherein the non-crosslinking composition does not comprise formaldehyde and the isolated RNA has an RNA Integrity Number (RIN) value comparable to a reference RIN value, and the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) is performed as recited in claim 15, the fixed biological sample is non-formalin-fixed paraffin-embedded sample (non-FFPE- sample) as recited in claim 19, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 45 seconds with the first cell or tissue staining agent as recited in claim 44, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 30 seconds with the first cell or tissue staining agent as recited in claim 45, and step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 15 seconds with the first cell or tissue staining agent as recited in claim 46.
Lenz et al., teach that a biological sample is fixed with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition, and wax embedded (see abstract, Examples 8 and 9, and claims 1-21).
Regarding claims 15 and 19, since Cory et al., teach that brain tissue fixed in Bouin’s solution for 5 hr are embedded in paraffin, and 8 µm sections are transferred to silane-coated microscope slides and stained with hematoxylin and eosin (see pages 6 and 7, paragraph [0098]), Cory et al., disclose that the fixed biological sample is a wax embedded sample as recited in claim 15 and the fixed biological sample is non-formalin-fixed paraffin-embedded sample (non-FFPE- sample) as recited in claim 19.
Regarding claims 15, 38, and 44-46, since Chu teaches that “[D]eparaffinized tissue section slides which are in slide holders are placed vertically into a staining dish with 500 mL of hematoxylin solution for 10 seconds with ultrasound followed by washing with running tap water in a staining dish for 5 seconds with ultrasound. The slides are placed in 95% ethyl alcohol for 5 seconds with ultrasound and counterstained in eosin-phloxine solution for 10
seconds with ultrasound” (see column 18), Chu discloses staining the at least one part of the biological sample mounted on the at least one support for a time period that is not more than 60 seconds with a first cell or tissue staining agent and rinsing the at least one part of the biological sample with water as recited in claim 15 wherein said section is stained for not more than 60 seconds with a first tissue staining agent and rinsed said section with water as recited in claim 38, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 45 seconds with the first cell or tissue staining agent as recited in claim 44, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 30 seconds with the at least one cell or tissue staining agent as recited in claim 45, and step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 15 seconds with the at least one cell or tissue staining agent as recited in claim 46.
Espina et al., teach that preservation of RNA in a tissue is evaluated by calculating the RNA integrity number (RIN) of a RNA and the RIN of the RNA fixed by their method is compared with the RIN of the RNA preserved by a commercially available, room temperature RNA preservation method, “RNALater®”, and the RIN of an untreated RNA (see paragraphs [0014], [0044] and [0045] and Figure 10).
Kennedy et al., teach that RNA quality can be measured by a calculated RIN and “[A]dvantages of RIN include obtain a numerical assessment of the integrity of RNA; directly comparing RNA samples, e.g. before and after archival, compare integrity of same tissue across different labs; and ensuring repeatability of experiments, e.g. if RIN shows a given value and is suitable for microarray experiments, then the RIN of the same value can always be used for similar experiments given that the same organism/tissue/extraction method is used” (see paragraph [0111]).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the methods as recited in claims 15, 19, 38, and 44-46 by staining the at least one part of the biological sample mounted on the at least one support for a time period that is less than 15 seconds with a first cell or tissue staining agent and rinsing the at least one support with water wherein the biological sample is fixed with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition and a wax embedded, the non-crosslinking composition does not comprise formaldehyde, and is not Methacarn solution, the fixed biological sample is non-formalin-fixed paraffin-embedded sample (non-FFPE-sample such as DSP-fixed paraffin-embedded biological sample), the isolated RNA has an RNA Integrity Number (RIN) value comparable to a reference RIN value, and the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) is performed in view of the prior arts of Xiang et al., Lenz et al., Cory et al., Chu, Espina et al., and Kennedy et al.. One having ordinary skill in the art would have been motivated to do so because Lenz et al., have successfully fixed a biological sample with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition, and wax embedded (see abstract, Examples 8 and 9, and claims 1-21), and provided advantages of their composition and the method “[T]he present compositions and method provide samples which are treated in a way that isolation of most of the biological components originally contained in the sample is still possible. The biomolecules have a very low degree of degradation, thus still RNA isolation (RNA is the molecule which usually has the highest degree of degradation for reason of ubiquitous RNAses) is possible with a very high yield. Comparison with prior compositions, developed for RNA maintenance only, e.g. RNAlater (Ambion), shows that the samples give nearly the same RNA yield, however, different to RNAlater the morphology of the sample is perfectly maintained when the present compositions and method is used. Thus, the same samples can be used for molecular biological as well as for histological analysis. In addition present compositions and methods enable extraction of biomolecules from tiny samples or single cells even after histological analysis e.g. with the use of a laser microdissection device” (see paragraph [0082]), Cory et al., have successfully shown that brain tissue fixed in Bouin’s solution for 5 hr are embedded in paraffin, and 8 µm sections are transferred to silane-coated microscope slides and stained with hematoxylin and eosin (see pages 6 and 7, paragraph [0098]), Chu has successfully shown that “[D]eparaffinized tissue section slides which are in slide holders are placed vertically into a staining dish with 500 mL of hematoxylin solution for 10 seconds with ultrasound followed by washing with running tap water in a staining dish for 5 seconds with ultrasound. The slides are placed in 95% ethyl alcohol for 5 seconds with ultrasound and counterstained in eosin-phloxine solution for 10 seconds with ultrasound” (see column 18), Espina et al., teach that preservation of RNA in a tissue is evaluated by calculating the RNA integrity number (RIN) of a RNA and the RIN of the RNA fixed by their method is compared with the RIN of the RNA preserved by a commercially available, room temperature RNA preservation method, “RNALater®”, and the RIN of an untreated RNA (see paragraphs [0014], [0044] and [0045] and Figure 10), Kennedy et al., teach that RNA quality can be measured by a calculated RIN and “[A]dvantages of RIN include obtain a numerical assessment of the integrity of RNA; directly comparing RNA samples, e.g. before and after archival, compare integrity of same tissue across different labs; and ensuring repeatability of experiments, e.g. if RIN shows a given value and is suitable for microarray experiments, then the RIN of the same value can always be used for similar experiments given that the same organism/tissue/extraction method is used” (see paragraph [0111]), and the simple substitution of one kind of fixing method (ie., the fixing method using DSP taught by Xiang et al.,) from another kind of fixing method (ie., the fixing method using the non-crosslinking composition comprising methanol and then contacted the biological sample with an ethanol-containing composition taught by Lenz et al.,) during the process of isolating biomolecules from target cells or tissue of a biological sample recited in claim 15, in the absence of convincing evidence to the contrary, would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made since the fixing method using DSP taught by Xiang et al., and the fixing method using the non-crosslinking composition comprising methanol and then contacted the biological sample with an ethanol-containing composition taught by Lenz et al., are used for the same purpose (ie., fixing a biological sample) and are exchangeable. One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to fix the biological sample taught by Xiang et al., using a non-crosslinking composition comprising methanol, then contacted the biological sample with an ethanol-containing composition, and embed the biological sample in paraffin mentioned in the methods taught by Lenz et al., mount the paraffin embedded sample on a support, stain said section recited in claim 15 for a time period that is less than 15 seconds with a first tissue staining agent (ie., hematoxylin) and rinse said section with water, and stain said section recited in claim 15 for a time period that is less than 1 seconds with a second tissue staining agent (ie., Eosin) based on his or her experimental requirement, and comparing an RIN value of the RNA isolated from target cells or tissues in a biological sample using the method recited in claim 15 with an RIN value of the RNA isolated from target cells or tissues in a biological sample using a method different from the method recited in claim 15 in view of the prior arts of Xiang et al., Lenz et al., Cory et al., Chu, Espina et al., and Kennedy et al., so that the methods recited in claims 15, 19, 38, and 44-46 would be performed in order to perfectly maintain the morphology of the biological sample, reduce the degradation of isolated biomolecules comprising RNA, increase yield of the isolated biomolecules comprising RNA and check quality of the isolated RNA such that the target cells or tissue comprising biomolecules of interest would be easily determined by observing a better image of the at least one part of the biological sample mounted on the at least one support stained and rinsed in step (3) of claim 15.
Furthermore, the motivation to make the substitution cited above arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making the obviousness rejection comes from the M.P.E.P. at 2144.06, 2144.07 and 2144.09.
Also note that there is no invention involved in combining old elements is such a manner that these elements perform in combination the same function as set forth in the prior art without giving unobvious or unexpected results. In re Rose 220 F.2d. 459, 105 USPQ 237 (CCPA 1955).
More particularly, where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.
Where the general conditions of a claim are disclosed in the prior art, it is not inventive, in the absence of an unexpected result, to discover the optimum or workable ranges by routine experimentation. In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Claims 15, 17, 19, 20, 23-28, 38, 43-45, 47, and 48 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Xiang et al., in view of Lenz et al., Cory et al., Abate-Shen et al., (US 2008/0216180 A1, published on September 4, 2006), Espina et al., and Kennedy et al..
This rejection was made by modifying the rejection under pre-AIA 35 U.S.C. 103(a) mailed on April 11, 2025. Since the phrase “wherein the reference RIN value is the RIN value of RNA that is isolated from the biological sample before any of steps (1) to (6) is performed” in claim 15 is read as “wherein the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) is performed”, the method for isolating a reference RNA with a reference RIN value is different from the method of claim 15.
Regarding claims 15, 17, 20, 23-28, and 43, Xiang et al., teach (1) mounting at least one part of the biological sample (ie., supraoptic nucleus (SON) from brain) on at least one support (ie., the glass slide), (2) optionally treating the at least one part of the biological sample with a sample treatment agent (eg., ethanol or xylene), wherein said treatment can be carried out at any stage of the procedure before step (6), (3) staining the at least one part of the fixed biological sample mounted on the at least one support (ie., stained with anti-oxytocin-neurophysin antibody), (4) determining target cells or tissue comprising biomolecules of interest by observing the at least one part stained in step (3) (ie., red color stained by anti-oxytocin-neurophysin antibody), (5) separating the target cells or tissue (ie., the tissue stained by anti-oxytocin-neurophysin antibody) comprising biomolecules of interest (ie., RNA) from the remainder of the biological sample mounted on the at least one support, and (6) isolating the biomolecules from the target cells or tissue separated in step (5) wherein the biomolecules comprise RNA as recited in claim 15, the method comprises step (2) and the sample treatment agent is a de-waxing agent (ie., xylene) as recited in claim 17 wherein the de-waxing agent is a de-paraffinizing agent such as xylene as recited in claims 20 and 23 (see page 33, paragraph [0375]), the at least one support (ie., the glass slide) is transparent as recited in claim 24, the at least one support is made of glass (ie., the glass slide) or a transparent polymer as recited in claim 25, the target cells or tissue comprising biomolecules of interest from the biological sample in step (4) is observed under light or backlight (eg., by using Leica DM RX microscope) as recited in claim 26, the target cells or tissue comprising biomolecules of interest from the biological sample in step (4) is observed under a microscope (eg., Leica DM RX microscope) as recited in claim 27, the target cells or tissue is/are separated in step (5) by microdissection, laser capture microdissection, scraping, or cutting out as recited in claim 28, and the biological sample comprises at least one section of 0.5 to 12 µm (ie., 8 µm) thickness of a non-formalin-fixed paraffin-embedded sample as recited in claim 43 (see pages 32-36, Example 14, paragraphs [0368] to [390]).
Regarding claim 38, Xiang et al., teach that the fixed biological sample is divided in sections of 0.5 to 12 µm thickness (ie., 8µm), and in step (1), the at least one of the support is a transparent support, in step (2), the section is treated with the sample treatment agent and the sample treatment agent is a de-waxing agent (ie., xylene), and in step (4), the target cells or tissue is/are determined in the stained sample section (see pages 32-36, Example 14, paragraphs [0368] to [390]). Although Xiang et al., do not teach that, in step (5) of claim 15, the remainder of the fixed sample (ie., fixed sections stained by anti-oxytocin-neurophysin antibody) is discarded, in view of the teachings of Xiang et al., it is obvious to one having ordinary skill in the art at the time the invention was made to discard the slides after scraping fixed sections stained by anti-oxytocin-neurophysin antibody from the slides into Eppendorf tubes (see paragraph [0371]).
Xiang et al., do not disclose that the biological sample is fixed with a non-crosslinking composition with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition, and a wax embedded and staining the at least one part of the biological sample mounted on the at least one support for not more than 60 seconds with at least one cell or tissue staining agent and rinsing the at least one part of the biological sample with water wherein the non-crosslinking composition does not comprise formaldehyde, the isolated RNA has an RNA Integrity Number (RIN) value comparable to a reference RIN value, and the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) is performed as recited in claim 15, the fixed biological sample is non-formalin-fixed paraffin-embedded sample (non-FFPE- sample) as recited in claim 19, step (3), said section is stained for not more than 60 seconds with a first tissue staining agent and rinsed said section with water as recited in claim 38, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for less than 45 seconds with the at least one cell or tissue staining agent as recited in claim 44, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for less than 30 seconds with the at least one cell or tissue staining agent as recited in claim 45, step (3) comprises: (a) staining the at least one part of the biological sample mounted on the at least one support for up to 30 seconds with Hematoxylin, (b) rinsing the at least one part of the biological sample stained in step (a) with water, and (c) staining the at least one part of the biological sample rinsed in step (b) for less than 3 seconds with Eosin as recited in claim 47, and step (c) comprises staining the at least one part of the biological sample rinsed in step (b) for less than 1 second with Eosin as recited in claim 48.
Lenz et al., teach that a biological sample is fixed with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition, and wax embedded (see abstract, Examples 8 and 9, and claims 1-21).
Regarding claims 15 and 19, since Cory et al., teach that brain tissue fixed in Bouin’s solution for 5 hr are embedded in paraffin, and 8 µm sections are transferred to silane-coated microscope slides and stained with hematoxylin and eosin (see pages 6 and 7, paragraph [0098]), Cory et al., disclose that the fixed biological sample is a wax embedded sample as recited in claim 15 and the fixed biological sample is non-formalin-fixed paraffin-embedded sample (non-FFPE- sample) as recited in claim 19.
Regarding claims 15, 38, 44, 45, and 47, since Abate-Shen et al., teach that “[F]rozen sections were allowed to thaw briefly for 1 hour. Slides were then rehydrated (100% ethanol 2×for 2 minutes, 95% EtOH for 2 minutes, 70% ethanol for 2 minutes, 50% ethanol for 2 minutes, Milli-Q diH2O 2 ×for 5 minutes). Staining was as follows: slides immersed in filtered Harris Modified Hematoxylin (Fisher SH26D-500) for ̴ 15 seconds, rinsed with Milli-Q diH2O until water, immersed in Eosin for 5 seconds, dehydrated in ascending alcohol solutions
(95%, 2×100% for 2 mins each), cleared with xylene 3×for 5 minutes each, and coverslipped with Clear Mount” (see paragraph [0181]), Abate-Shen et al., disclose staining the at least one part of the biological sample mounted on the at least one support for not more than 60 seconds with at least one cell or tissue staining agent and rinsing the at least one part of the biological sample with water as recited in claim 15, staining the at least one part of the biological sample mounted on the at least one support for not more than 60 seconds with at least one cell or tissue staining agent and rinsing the at least one part of the biological sample with water as recited in claim 15 wherein said section is stained for not more than 60 seconds with a first tissue staining agent and rinsed said section with water as recited in claim 38, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for less than 45 seconds with the at least one cell or tissue staining agent as recited in claim 44, step (3) comprises staining the at least one part of the biological sample mounted on the at least one support for less than 30 seconds with the at least one cell or tissue staining agent as recited in claim 45, step (3) comprises: (a) staining the at least one part of the biological sample mounted on the at least one support for up to 30 seconds with Hematoxylin, and (b) rinsing the at least one part of the biological sample stained in step (a) with water as recited in claim 47.
Espina et al., teach that preservation of RNA in a tissue is evaluated by calculating the RNA integrity number (RIN) of a RNA and the RIN of the RNA fixed by their method is compared with the RIN of the RNA preserved by a commercially available, room temperature RNA preservation method, “RNALater®”, and the RIN of an untreated RNA (see paragraphs [0014], [0044] and [0045] and Figure 10).
Kennedy et al., teach that RNA quality can be measured by a calculated RIN and “[A]dvantages of RIN include obtain a numerical assessment of the integrity of RNA; directly comparing RNA samples, e.g. before and after archival, compare integrity of same tissue across different labs; and ensuring repeatability of experiments, e.g. if RIN shows a given value and is suitable for microarray experiments, then the RIN of the same value can always be used for similar experiments given that the same organism/tissue/extraction method is used” (see paragraph [0111]).
Therefore, it would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made to have performed the methods as recited in claims 15, 19, 38, 44, 45, 47, and 48 by staining the at least one part of the biological sample mounted on the at least one support for less than 30 seconds with at least one cell or tissue staining agent or hematoxylin, rinsing the at least one support with water, and staining the at least one part of the biological sample rinsed for less than 1 second with Eosin wherein the biological sample is fixed with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition and a wax embedded, the non-crosslinking composition does not comprise formaldehyde, and is not Methacarn solution, and the fixed biological sample is non-formalin-fixed paraffin-embedded sample (non-FFPE-sample such as DSP-fixed paraffin-embedded biological sample), the isolated RNA has an RNA Integrity Number (RIN) value comparable to a reference RIN value, and the reference RIN value is the RIN value of RNA that is isolated from the biological sample before step (1) is performed in view of the prior arts of Xiang et al., Lenz et al., Cory et al., Abate-Shen et al., Espina et al., and Kennedy et al.. One having ordinary skill in the art would have been motivated to do so because Lenz et al., have successfully fixed a biological sample with a non-crosslinking composition comprising methanol, then contacted with an ethanol-containing composition, and wax embedded (see abstract, Examples 8 and 9, and claims 1-21), and provided advantages of their composition and the method “[T]he present compositions and method provide samples which are treated in a way that isolation of most of the biological components originally contained in the sample is still possible. The biomolecules have a very low degree of degradation, thus still RNA isolation (RNA is the molecule which usually has the highest degree of degradation for reason of ubiquitous RNAses) is possible with a very high yield. Comparison with prior compositions, developed for RNA maintenance only, e.g. RNAlater (Ambion), shows that the samples give nearly the same RNA yield, however, different to RNAlater the morphology of the sample is perfectly maintained when the present compositions and method is used. Thus, the same samples can be used for molecular biological as well as for histological analysis. In addition present compositions and methods enable extraction of biomolecules from tiny samples or single cells even after histological analysis e.g. with the use of a laser microdissection device” (see paragraph [0082]), Cory et al., have successfully shown that brain tissue fixed in Bouin’s solution for 5 hr are embedded in paraffin, and 8 µm sections are transferred to silane-coated microscope slides and stained with hematoxylin and eosin (see pages 6 and 7, paragraph [0098]), Abate-Shen et al., successfully shown that “[F]rozen sections were allowed to thaw briefly for 1 hour. Slides were then rehydrated (100% ethanol 2×for 2 minutes, 95% EtOH for 2 minutes, 70% ethanol for 2 minutes, 50% ethanol for 2 minutes, Milli-Q diH2O 2 ×for 5 minutes). Staining was as follows: slides immersed in filtered Harris Modified Hematoxylin (Fisher SH26D-500) for ̴ 15 seconds, rinsed with Milli-Q diH2O until water, immersed in Eosin for 5 seconds, dehydrated in ascending alcohol solutions (95%, 2×100% for 2 mins each), cleared with xylene 3×for 5 minutes each, and coverslipped with Clear Mount” (see paragraph [0181]), Espina et al., teach that preservation of RNA in a tissue is evaluated by calculating the RNA integrity number (RIN) of a RNA and the RIN of the RNA fixed by their method is compared with the RIN of the RNA preserved by a commercially available, room temperature RNA preservation method, “RNALater®”, and the RIN of an untreated RNA (see paragraphs [0014], [0044] and [0045] and Figure 10), Kennedy et al., teach that RNA quality can be measured by a calculated RIN and “[A]dvantages of RIN include obtain a numerical assessment of the integrity of RNA; directly comparing RNA samples, e.g. before and after archival, compare integrity of same tissue across different labs; and ensuring repeatability of experiments, e.g. if RIN shows a given value and is suitable for microarray experiments, then the RIN of the same value can always be used for similar experiments given that the same organism/tissue/extraction method is used” (see paragraph [0111]), and the simple substitution of one kind of fixing method (ie., the fixing method using DSP taught by Xiang et al.,) from another kind of fixing method (ie., the fixing method using the non-crosslinking composition comprising methanol and then contacted the biological sample with an ethanol-containing composition taught by Lenz et al.,) during the process of isolating biomolecules from target cells or tissue of a biological sample recited in claim 15, in the absence of convincing evidence to the contrary, would have been prima facie obvious to one having ordinary skill in the art at the time the invention was made since the fixing method using DSP taught by Xiang et al., and the fixing method using the non-crosslinking composition comprising methanol and then contacted the biological sample with an ethanol-containing composition taught by Lenz et al., are used for the same purpose (ie., fixing a biological sample) and are exchangeable. One having ordinary skill in the art at the time the invention was made would have a reasonable expectation of success to fix the biological sample taught by Xiang et al., using the non-crosslinking composition comprising methanol, then contacted the biological sample with an ethanol-containing composition, and embed the biological sample in paraffin and embed the biological sample fixed by the non-crosslinking fixative composition in paraffin mentioned in the methods taught by Lenz et al., mount the paraffin embedded sample on a support, stain the at least one part of the biological sample mounted on the at least one support for a time period that is less than 15 seconds with a first cell or tissue staining agent and rinse the at least one support with water, and stain said section recited in claim 15 for a time period that is less than 1 seconds with a second tissue staining agent (ie., Eosin) based on his or her experimental requirement and comparing an RIN value of the RNA isolated from target cells or tissues in a biological sample using the method recited in claim 15 with an RIN value of the RNA isolated from target cells or tissues in a biological sample using a method different from the method recited in claim 15 in view of the prior arts of Xiang et al., Lenz et al., Cory et al., Abate-Shen et al., Espina et al., and Kennedy et al., so that the methods recited in claims 15, 18, 38, 44, 45, 47, and 48 would be performed in order to perfectly maintain the morphology of the biological sample, reduce the degradation of isolated biomolecules comprising RNA, increase yield of the isolated biomolecules comprising RNA, and check quality of the isolated RNA such that the target cells or tissue comprising biomolecules of interest would be easily determined by observing a better image of the at least one part of the biological sample mounted on the at least one support stained and rinsed in step (3) of claim 15.
Furthermore, the motivation to make the substitution cited above arises from the expectation that the prior art elements will perform their expected functions to achieve their expected results when combined for their common known purpose. Support for making the obviousness rejection comes from the M.P.E.P. at 2144.06, 2144.07 and 2144.09.
Also note that there is no invention involved in combining old elements is such a manner that these elements perform in combination the same function as set forth in the prior art without giving unobvious or unexpected results. In re Rose 220 F.2d. 459, 105 USPQ 237 (CCPA 1955).
More particularly, where the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.
Where the general conditions of a claim are disclosed in the prior art, it is not inventive, in the absence of an unexpected result, to discover the optimum or workable ranges by routine experimentation. In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955)
Response to Arguments
I. In page 9, fourth paragraph bridging to page 11, first paragraph of applicant’s remarks, applicant argues that “one of ordinary skill in the art would not have been motivated to substitute the fixative DSP of Xiang with that of Lenz because doing so would change the primary teaching of Xiang and thus eliminate the associated advantages. In this regard, Applicant incorporates by reference relevant arguments in its previous submissions (e.g., pages 7 to 10 of the response filed November 10, 2022). Briefly, Xiang relates to labeling nucleic acid molecules for use in hybridization reactions and is not closely related to the present application. Example 14 of Xiang on pages 32- 36 relates to using Dithio-bis(Succinimidyl Propionate) (DSP, a crosslinking fixative) to fix tissue section for immunostaining, microdissection and expression profiling. This Example was concerned with fixing tissue sections for immunostaining, such as sections intended for laser capture microdissection (LCM), to extract intact, unmodified RNA (see paragraph [0368]). Immunostaining involves recognizing cell populations of interest within the tissue sections using dye conjugated antibodies (see paragraphs [0370], [0375], [0381], and [0382]). Example 14 shows that (1) ethanol fixation was not satisfactory in immunostaining the tissue, and also resulted in degradation of RNA isolated from the fixed sample (see paragraphs [0381], [0382] and [0384]), (2) it was difficult, if not impossible, to extract RNA from formalin (i.e., formaldehyde) fixed tissues (see paragraphs [0384] and [0369]), but (3) DSP fixed soluble antigens and protected RNA in tissue sections, even ones that have been immunostained (see
paragraph [0390]). Xiang describes their DSP fixing method as ‘a novel, fast, and simple method to fix and immunostain tissue sections, such as sections intended for laser capture microdissection, in order to extract intact, unmodified RNA’ (see paragraph [0368], emphasis added). Thus, Xiang shows that ethanol as a non-crosslinking fixing reagent is not suitable, one crosslinking fixing reagent (formalin) is not suitable either, but another crosslinking fixing reagent (DSP) is suitable, for isolating RNA from a biological material fixed with the indicated fixing reagent and then immunostained. Therefore, Xiang teaches that neither crosslinking nor non-crosslinking fixatives can be easily exchanged when intending to isolate RNA from a correspondingly fixed and immunostained sample. In view of the above-noted lack of interchangeability among fixatives disclosed in Xiang, one skilled in the art would not have been motivated to use another fixative (e.g., the non-crosslinking fixative and treatment as disclosed in Lenz) in the method of Xiang without experimental evidence showing that the other fixative is suitable for fixing biological samples for immunostaining followed by isolating RNA from immunostained tissue. Doing so would change the primary teaching of using DSP in Xiang and thus eliminate the associated advantages. In addition, one skilled in the art would not have been motivated to use the fixative and related treatment of Lenz in the method of Xiang because Xiang teaches away using methanol- or ethanol-based fixatives. Xiang discloses that ‘fixing cells or tissue sections with precipitating fixatives (for example, alcohol, acetone, etc.) results in the diffusion of small, soluble molecules including antigens, such as peptides’ (see paragraph [0363]) (emphasis added). Xiang reiterates its purpose ‘to generate a protocol, whereby the cell can be fixed in such a way that RNA can be preserved (for subsequent harvest and analysis) without the loss of cell morphology or other cell contents’ (Id., emphasis added). Because methanol is a precipitating agent,1 Xiang teaches away from using methanol as a fixative. In addition, Example 13 of Xiang shows that ethanol was unsatisfactory in fixing tissue for immunostaining (see e.g., paragraph [0366], indicating soluble antigens could not be stained in ethanol-fixed cells). In view of the failure in immunostaining and identifying target cells using an alcohol- containing fixative as disclosed in Xiang, one of ordinary skill in the art would not have expected to isolate RNA from such target cells. As such, such a person would not have been motivated to replace the fixative DSP of Xiang with an alcohol-containing fixative of Lenz”.
These arguments have been fully considered but they are not persuasive toward the
withdrawal of the rejection.
First, although applicant argues that “ethanol fixation was not satisfactory in immunostaining the tissue, and also resulted in degradation of RNA isolated from the fixed sample (see paragraphs [0381], [0382] and [0384])” and “[E]xample 13 of Xiang shows that ethanol was unsatisfactory in fixing tissue for immunostaining (see e.g., paragraph [0366], indicating soluble antigens could not be stained in ethanol-fixed cells)”, since Xiang et al., teach that “[T]he morphology of DSP-, ethanol-, and formalin-fixed cells was well preserved. Immunostaining with an anti-beta-actin antibody indicated that soluble antigens could be stained in DSP-fixed but no in ethanol-fixed cells’ and “[E]thanol fixation was even less satisfactory when an antibody directed against the oxytocin-neurophysin was used to stain hypothalamic magnocellular neurons in sections prepared from frozen rat brains” (see paragraphs [0366] and [0382]), Xiang et al., clearly indicate that ethanol fixation is not satisfactory in immunostaining the tissue only when anti-beta-actin antibody or an antibody directed against the oxytocin-neurophysin is used. In fact, claim 15 does not require that the staining step is performed using an antibody while claim 47 requires that the first cell or tissue staining agent is Hematoxylin and the second cell or tissue staining agent is Eosin and Lenz et al., have clearly shown that ethanol fixation is satisfactory in immunostaining the tissue when this tissue has been stained with Hematoxylin and Eosin (see paragraph [0155] and Figure 11).
Second, although applicant argues that “[X]iang discloses that ‘fixing cells or tissue sections with precipitating fixatives (for example, alcohol, acetone, etc.) results in the diffusion of small, soluble molecules including antigens, such as peptides’ (see paragraph [0363]) (emphasis added). Xiang reiterates its purpose ‘to generate a protocol, whereby the cell can be fixed in such a way that RNA can be preserved (for subsequent harvest and analysis) without the loss of cell morphology or other cell contents’ (Id., emphasis added). Because methanol is a precipitating agent,1 Xiang teaches away from using methanol as a fixative”, paragraph [0363] of Xiang et al., does not indicate that precipitating fixatives (e.g., alcohol) results in the loss of cell morphology or other cell contents such that RNA cannot be preserved and results in the diffusion. In fact, RNA has been successfully isolated from the biological sample fixed using the method taught by Lenz et al., (using the non-crosslinking composition comprising methanol and then contacted the biological sample with an ethanol-containing composition) (see page 12).
II. In page 11, second paragraph bridging to page 12, last paragraph of applicant’s remarks, applicant argues that “one of ordinary skill in the art would not have had a reasonable expectation of success to modify Xiang in view of Lenz to arrive at the presently claimed methods. As indicated above, to expedite prosecution, Applicant has amended claim 15 to recite: ‘wherein the isolated RNA has an RIN value comparable to a reference RIN value, and wherein the reference RIN value is the RIN value of RNA isolated from the biological sample before any of steps (1) to (6) is performed.’ Applicant submits that one of ordinary skill in the art would not have a reasonable expectation to modify Xiang in view of Lenz to arrive at a method that allows RNA isolated from a biological sample after being stained to have RNA integrity comparable to that of RNA isolated from the biological sample without being stained. Specifically, RNA degradation is the one of the major issues when fixing and staining a biological sample to prepare for laser capture microdissection (LCM). See Kihara et al., Journal