DETAILED ACTION
Applicant’s response, filed Oct 8 2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 .
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 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.
Claim Status
Claims 1, 3-10, 13, and 17-22 are pending.
Claim 17 is withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, as set forth in the Non-Final Office Action dated Aug 5 2025.
Claims 2, 11-12, and 14-16 are canceled.
Claims 18-22 are newly added.
Claims 1, 3-10, 13, and 18-22 are rejected.
Priority
This application is a DIV of 15/246,409 filed Aug 24 2016 (now USP 11,079,382), which claims priority to PCT/EP2015/053643, filed Feb 20 2015, and US provisional application 61943939, filed Feb 24 2014.
Accordingly, each of claims 1-15 are afforded the effective filing date of Feb 24 2014.
Information Disclosure Statement
The information disclosure statement (IDS) filed on Sep 2 2025 is in compliance with the provisions of 37 CFR 1.97 and has therefore been considered. A signed copy of the IDS document is included with this Office Action.
Claim Objections
The outstanding objections to the claims are withdrawn in view of the amendments submitted herein.
Claim Rejections- 35 USC § 112
The outstanding rejections to the claims are withdrawn in view of the amendments submitted herein.
Claim Rejections - 35 USC § 103
The outstanding rejections from the previous Office Action are withdrawn in view of the amendments submitted herein. Specifically, neither van der Loos (Journal of Histochemistry & Cytochemistry, 2008, 56(4):313-328) nor Cimino-Mathews et al. (Human Pathology, 2013, 44:2055-2063) disclose staining a sample with 5 specific binding moieties as recited in amended claim 1.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1, 3-10, 13, 18-22 are rejected under 35 U.S.C. 103 as being unpatentable over the features of van der Loos (Journal of Histochemistry & Cytochemistry, 2008, 56(4):313-328; cited on the Jun 17 2021 IDS) in view of Cimino-Mathews et al. (Human Pathology, 2013, 44:2055-2063; cited on the Jun 17 2021 IDS) and Jennings et al. (ACS Nano, 2011, 5(7):5579-5593; previously cited). The rejection is newly stated and is necessitated by claim amendment.
The prior art to van der Loos discloses practical suggestions for immunoenzyme double, triple, and quadruple staining procedures (abstract). van der Loos, indicated by the open circles, teaches the instant features, indicated by the closed circles, as follows. Instantly claimed elements which are considered to be equivalent to the prior art teachings are described in bold for all claims.
Claims 1 and 22 disclose a method of scoring the immune response in cancer using tissue infiltrating lymphocytes comprising:
contacting a sample with a plurality of different binding moieties specific for different lymphocyte markers, wherein the plurality of different binding moieties specific for the different lymphocyte markers include a binding moiety specific for CD3 marker, a binding moiety specific for CD8 marker, a binding moiety specific for CD20 marker, and a binding moiety specific for FoxP3 marker,
van der Loos teaches using, among others, the primary antibodies CD3, CD8, CD20, and Foxp3 (Table 1). van der Loos teaches contacting tissue section samples with two, three, or four of the primary antibodies listed in Table 1 (p. 318, col. 2, par. 2 through p. 324, col. 2, par. 1). van der Loos does not teach contacting a sample with binding moieties specific for CD3, CD8, CD20, and FoxP3 which serve as lymphocyte markers.
contacting the sample with a binding entity specific for a tumor marker;
van der Loos does not teach staining a sample with 5 specific binding moieties.
removing excess specific binding moieties from the sample,
van der Loos teaches washing the tissue samples after contact with the primary antibodies (p. 319, col. 1, par. 2-3).
contacting the sample with a first chromogenic detection reagent for the CD3 marker, a second chromogenic detection reagent for the CD8 marker, a third chromogenic detection reagent for the CD20 marker, a fourth chromogenic detection reagent for the FoxP3 marker, and a fifth chromogenic detection reagent for the tumor marker, wherein each of the first, second, third, fourth, and fifth chromogenic detection reagents are different;
van der Loos teaches double, triple and quadruple staining with different colored stains (p. 324, col. 1, par. 3 through col. 2, par. 1; Figure 14), but does not teach a fifth chromogenic detection reagent as claimed.
detecting the first, second, third, fourth, and fifth chromogenic detection reagents in the sample,
van der Loos teaches enzymatic visualization of the tissue samples stained with four antibodies (p. 319, col. 1, par. 3 through col. 2, par. 2; Fig. 1-8), but not five.
assessing a presence and a distribution for the plurality of different binding moieties specific for the different lymphocyte markers and the binding moiety specific for the tumor marker within the sample based on the detected first, second, third, fourth, and fifth chromogenic reagents, wherein the distribution for all of the plurality of binding moieties specific for the lymphocyte markers and the binding moiety specific for the tumor marker reflects a type, number, and location of tissue infiltrating lymphocytes within the sample (claim 1);
assessing a presence and a distribution for the plurality of different binding moieties specific for the different lymphocyte markers and the binding moiety specific for the tumor marker within the sample based on the detected first, second, third,fourth, and fifth chromogenic reagents (claim 22); and
van der Loos teaches analyzing the immunoenzyme staining patterns in tissue samples stained with two, three, or four primary antibodies (Fig. 11-14), but does not teach a fifth primary antibody.
scoring the sample by analyzing the presence and the distribution of the specific binding moieties.
van der Loos does not teach this limitation.
See below for teachings by Cimino-Mathews regarding this limitation.
van der Loos does not teach contacting a sample with CD3, CD8, CD20, FoxP3, and tumor marker specific binding moieties or scoring cancer using tissue infiltrating lymphocytes by analyzing the presence and the distribution of the specific binding moieties.
However, Cimino-Mathews discloses a characterization of CD3, CD4, CD8, FoxP3, and CD20 in tumor-infiltrating lymphocytes (TILs) in primary breast cancer and metastatic breast cancer samples, as well as other types of cancer (abstract). Cimino-Mathews teaches scoring the immunohistochemistry of the samples (p. 2056, col. 2, par. 2 through p. 2057, col. 1, par. 2). Cimino-Mathews teaches that, overall, metastatic breast cancer samples had fewer numbers of CD3+, CD8+ CD4+, and FoxP3+ T lymphocytes and tumor-infiltrating CD20+ B cells than their matched primary tumors, suggesting that the immunological milieu in patients with metastases is more suppressed (i.e., scoring cancer) (p. 2057, col. 2, par. 3 through p. 2059, col. 2, par. 1; Fig. 1-2). Cimino-Mathews teaches that triple-negative breast cancer cells have greater numbers of tumor-infiltrating lymphocytes than luminal breast cancers (i.e., scoring cancer) (p. 2059, col. 2, par. 2 through p. 2060, col. 1, par. 1; Fig. 3). Cimino-Mathews teaches finding similar findings of fewer lymphocytes in breast cancer metastases of the brain (p. 2060, col. 1, par. 2; Table 2).
Regarding claims 1 and 22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos and Cimino-Mathews because both references disclose methods for staining cancer tissue sections using CD3, CD8, CD20, and FoxP3 primary antibodies. The motivation would have been to characterize the expression of different known markers in the tumor-infiltrating lymphocytes of different types of breast cancer samples, as taught by Cimino-Mathews (p. 2056, col. 1, par. 1). Further, 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 modify, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos to contact a sample with CD3, CD8, CD20, and FoxP3 primary antibodies because van der Loos teaches using each of the primary antibodies for at least double staining, and teaches a method for quadruple staining which involves CD3 and CD20 already (p. 324, col. 1, par. 3 through col. 2, par. 1; Fig. 14). It would have been obvious to choose the primary antibodies against CD3, CD8, CD20, and FoxP3 from the list of Table 1 in the quadruple staining protocol taught by van der Loos because there are only a finite number of primary antibodies (9) examined by van der Loos. One of ordinary skill in the art would have further been motivated to choose the primary antibodies of CD3, CD8, CD20, and FoxP3 in the quadruple staining protocol of van der Loos because Cimino-Mathews teaches that these antibodies are useful in characterizing tumor infiltrating lymphocytes, as described above.
Neither van der Loos nor Cimino-Mathews teach staining a sample with 5 specific binding moieties.
However, the prior art to Jennings discloses nanocrystal bioconjugation chemistries for multi target immunolabelling (abstract). Jennings teaches multicolor immunocytochemical labelling using the simultaneous detection of five different nanocrystal materials using fluorescence (Fig. 1 and 5), where five separate nanocrystal-antibody conjugates were analyzed simultaneously (Fig. 5B). Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin (i.e., claim 3), where cytokeratins are often expressed in tumors (i.e., a tumor marker as in claim 2) in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A).
Regarding claims 1 and 22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos in view of Cimino-Mathews with Jennings because each reference discloses methods for staining cancer tissue sections with multiple primary antibodies. The motivation to use the method of Jennings for attaching nanocrystals to primary antibodies would have been to use the narrow emission of nanocrystals for cellular labelling, as taught by Jennings (p. 5579, col. 1, par. 1; p. 5580, col. 2, par. 4; Fig. 1). Further, 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 modify, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos in view of Cimino-Mathews and Jennings to additionally select the primary antibody against cytokeratin for imaging with CD3, CD8, CD20, and FoxP3 primary antibodies because van der Loos and Jennings, in combination, teach using each of these primary antibodies, as described above, and Jennings teaches a general method for staining with five different nanocrystal labeled primary antibodies, as described above. It would have been obvious to choose the primary antibody against cytokeratin in the five primary antibody staining protocol taught by Jennings because there are only a finite number of primary antibodies examined by Jennings. One of ordinary skill in the art would have further been motivated to choose the primary antibodies of cytokeratin, CD3, CD8, CD20, and FoxP3 in the five primary antibody staining protocol taught by Jennings because Jennings teaches that cytokeratin is useful in characterizing tumors (p. 5586, col. 1, par. 2; Fig. 5A).
Regarding claim 3, the features of van der Loos in view of Cimino-Mathews and Jennings teach the method of claim 1 as described above. Claim 3 further adds that the tumor marker is selected from cytokeratin and S100. Neither van der Loos nor Cimino-Mathews teach staining a sample with 5 specific binding moieties.
However, Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin, where cytokeratins are often expressed in tumors (i.e., a tumor marker) in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A).
Regarding claims 4-9, the features of van der Loos in view of Cimino-Mathews and Jennings teaches the method of claim 1 as described above. Claims 4-9 further add that:
the specific binding moieties for CD3 (claim 4), CD8 (claim 5), CD20 (claim 6), and FoxP3 (claim 7) are rabbit or mouse monoclonal antibodies (claim 8);
van der Loos teaches that CD8, CD20, and Foxp3 are primary antibodies from mouse and CD3 is a primary antibody from a rabbit (Table 1).
detecting comprises contacting the sample with an anti-species antibody specific to the rabbit or mouse monoclonal antibodies (claim 9).
van der Loos teaches using anti-mouse and anti-rabbit secondary antibodies (Table 2) which are monoclonal (p. 320, col. 1, par. 2; p. 321, col. 1, par. 3 through col. 2, par. 1; p. 322, col. 1, par. 3; Figures 11 and 13-14).
Regarding claims 10 and 13, the features of van der Loos in view of Cimino-Mathews and Jennings teaches the method of claims 1 and 8-9 as described above. Claims 10 and 13 further add that:
the anti-species antibody is haptenated, that detecting the haptenated antibody further comprises contacting the sample with an anti-hapten antibody conjugated to an enzyme (claim 10);
the specific binding moieties are haptenated, and wherein detecting the specific binding moieties further comprises contacting the sample with an anti-hapten antibody conjugated to an enzyme (claim 13).
van der Loos teaches an indirect/direct multistep protocol where an unlabeled mouse primary antibody is combined with a second mouse primary antibody directly conjugated with hapten or enzyme and performing detection with an enzyme labeled anti-fluorochrome or hapten or enzyme-labeled streptavidin (i.e., detection compound) (p. 322, col. 2, par. 3; Figure 7).
Regarding claims 18-21, the features of van der Loos in view of Cimino-Mathews and Jennings teaches the method of claim 1 as described above. Claims 18-21 further add that the first, second, third, fourth, and fifth chromogenic reagents include a chromogenic moiety having a spectral absorbance having a full- width half-maximum of between 30nm and 250nm (claim 18), 30nm and 150nm (claim 19), 30nm and 100nm (claim 20), and 30nm and 60nm (claim 21), which neither van der Loos nor Cimino-Mathews teach.
However, Jennings teaches that the nanocrystals used have a full width half maximum (fwhm) of 27-35 nm (p. 5580, col. 1, par. 2 and col. 2, par. 4 through p. 5581, col. 1, par. 1; Table 1). Jennings therefore teaches an overlapping range which anticipates or alternatively makes obvious the instantly claimed range of between 30nm and 60nm as the narrowest claimed range in claim 21, which also anticipates or alternatively makes obvious the broader ranges in claims 18-20. It would have been prima facie obvious to one of ordinary skill in the art to select any portions of the disclosed ranges including the instantly claimed ranges from the ranges disclosed in the prior art references, particularly in view of the fact that: "The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set percentage ranges is the optimum combination of percentages" In re Peterson 65 USPQ2d 1379 (CAFC 2003). Also In re Malagari, 182 USPQ 549,533 (CCPA 1974) and MPEP 2144.05. One of ordinary skill in the art would have been motivated to use the nanocrystals as taught by Jennings because their narrow fwhm values minimize spectral cross-talk and simplify the Gaussian fitting and deconvolution during subsequent analysis, as taught by Jennings (p. 5584, col. 2, par. 1).
Response to Applicant Arguments
At p. 1, par. 4 through p. 3, par. 1, Applicant submits that the combination of van der Loos, Cimino-Mathews, and Jennings does not teach all the recitations of the claimed invention because van der Loos describes color combinations for double immunoenzyme staining only, describing drawbacks of certain color combinations, which indicates that there is no rationale for the skilled artisan to add further chromogenic detection reagents to the assays and there would be no reasonable expectation of success. Applicant submits that neither Cimino-Mathews or Jennings cure this deficiency, particularly because Jennings describes the use of quantum dots.
It is respectfully submitted that this is not persuasive. Even though van der Loos does not explicitly teach combining five different color combinations of chromogenic detection reagents, Jennings provides such a teaching. If one of ordinary skill in the art wanted to perform immunohistochemistry on five different targets at once, one of ordinary skill would be motivated to look for such methods in the prior art. One of ordinary skill in the art would have recognized that the methods described by Jennings would provide such a method and applied their quantum dots to the desired lymphocyte infiltration markers as are known in the art, for the predictable result of imaging those markers all at once. That one of ordinary skill in the art would read that there are difficulties in applying and detecting multiple binding moieties in one sample in van der Loos and not look elsewhere in the art for a solution is not convincing because van der Loos does not explicitly teach that one cannot do this task, simply that it is difficult. Additionally, the prior art to Jennings was published several years after van der Loos but prior to the effective filing date of the instant application. It is considered that one of ordinary skill in the art would have understood to look for more recent advances in the field of microscopy and not been restricted to those earlier teachings. It is noted that it is not necessary that the prior art suggest the combination to achieve the same advantage or result discovered by applicant (see MPEP 2144(IV)).
Double Patenting
The terminal disclaimer filed on Oct 8 2025 disclaiming the terminal portion of any patent granted on this application which would extend beyond the expiration date of U.S. Patent No. 11,079,382 has been reviewed and is accepted. The terminal disclaimer has been recorded.
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.
A. Claims 1, 3-10, 13, and 18-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 10 of U.S. Patent No. 11,250,566 in view of van der Loos (Journal of Histochemistry & Cytochemistry, 2008, 56(4):313-328; cited on the Jun 17 2021 IDS) and Jennings et al. (ACS Nano, 2011, 5(7):5579-5593; previously cited). The instant rejection is newly stated and is necessitated by claim amendment.
Regarding instant claims 1 and 22, reference patent claim 10 (“(A) obtaining a digital image of at least one tissue section of a tissue sample… (C1) calculating a feature vector for the ROI, the feature vector comprising: (C1a) one or more feature metrics comprising a quantitative measure of cells expressing a human immune cell marker or cells having morphological characteristics of lymphocytes… (C2) applying a continuous scoring function to the feature vector to obtain an immune context score for the tissue section, wherein… the feature vector includes: a CD3+ cell density of the ROI, and a CD8+ cell density of the ROI”) discloses the limitations of instant claim 1 except for the limitations “contacting a sample with CD3, CD8, CD20, and FoxP3 specific binding moieties, contacting the sample with a binding entity specific for a tumor marker, removing excess specific binding moieties from the sample, detecting the specific binding moieties, assessing a presence and a distribution for the specific binding moieties within the sample”.
However, the prior art to van der Loos discloses practical suggestions for immunoenzyme double, triple, and quadruple staining procedures (abstract). van der Loos teaches using, among others, the primary antibodies CD3, CD8, CD20, and Foxp3 (Table 1). van der Loos teaches contacting tissue section samples with two, three, or four of the primary antibodies listed in Table 1 (p. 318, col. 2, par. 2 through p. 324, col. 2, par. 1). van der Loos teaches washing the tissue samples after contact with the primary antibodies (p. 319, col. 1, par. 2-3). van der Loos teaches enzymatic visualization of the stained tissue samples (p. 319, col. 1, par. 3 through col. 2, par. 2; Fig. 1-8). van der Loos teaches analyzing the immunoenzyme staining patterns in tissue samples stained with two, three, or four primary antibodies (Fig. 11-14).
van der Loos does not teach contacting a sample with CD3, CD8, CD20, FoxP3 specific binding moieties and a binding entity specific for a tumor marker.
However, 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 modify, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos to contact a sample with CD3, CD8, CD20, and FoxP3 primary antibodies because van der Loos teaches using each of the primary antibodies for at least double staining, and teaches a method for quadruple staining which involves CD3 and CD20 already (p. 324, col. 1, par. 3 through col. 2, par. 1; Fig. 14). It would have been obvious to choose the primary antibodies against CD3, CD8, CD20, and FoxP3 from the list of Table 1 in the quadruple staining protocol taught by van der Loos because there are only a finite number of primary antibodies (9) examined by van der Loos.
However, the prior art to Jennings discloses nanocrystal bioconjugation chemistries for multi target immunolabelling (abstract). Jennings teaches multicolor immunocytochemical labelling using the simultaneous detection of five different nanocrystal materials using fluorescence (Fig. 1 and 5), where five separate nanocrystal-antibody conjugates were analyzed simultaneously (Fig. 5B). Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin, where cytokeratins are often expressed in tumors (i.e., a tumor marker) in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A).
The reference patent does not disclose the limitations of instant claims 3-10, 13, and 18-21.
However, Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin, where cytokeratins (instant claim 3) are often expressed in tumors (i.e., a tumor marker) in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A). Jennings teaches that the nanocrystals used have a full width half maximum (fwhm) of 27-35 nm (p. 5580, col. 1, par. 2 and col. 2, par. 4 through p. 5581, col. 1, par. 1; Table 1). Jennings therefore teaches an overlapping range which anticipates or alternatively makes obvious the instantly claimed range of between 30nm and 60nm as the narrowest claimed range in claim 21, which also anticipates or alternatively makes obvious the broader ranges in claims 18-20. It would have been prima facie obvious to one of ordinary skill in the art to select any portions of the disclosed ranges including the instantly claimed ranges from the ranges disclosed in the prior art references, particularly in view of the fact that: "The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set percentage ranges is the optimum combination of percentages" In re Peterson 65 USPQ2d 1379 (CAFC 2003). Also In re Malagari, 182 USPQ 549,533 (CCPA 1974) and MPEP 2144.05. One of ordinary skill in the art would have been motivated to use the nanocrystals as taught by Jennings because their narrow fwhm values minimize spectral cross-talk and simplify the Gaussian fitting and deconvolution during subsequent analysis, as taught by Jennings (p. 5584, col. 2, par. 1).
However, van der Loos teaches that CD8, CD20, and Foxp3 are primary antibodies from mouse and CD3 is a primary antibody from a rabbit (Table 1) (instant claims 4-8). van der Loos teaches using anti-mouse and anti-rabbit secondary antibodies (Table 2) which are monoclonal (p. 320, col. 1, par. 2; p. 321, col. 1, par. 3 through col. 2, par. 1; p. 322, col. 1, par. 3; Figures 11 and 13-14) (instant claim 9). van der Loos teaches an indirect/direct multistep protocol where an unlabeled mouse primary antibody is combined with a second mouse primary antibody directly conjugated with hapten or enzyme and performing detection with an enzyme labeled anti-fluorochrome or hapten or enzyme-labeled streptavidin (i.e., detection compound) (p. 322, col. 2, par. 3; Figure 7) (instant claims 10 and 13).
Regarding claims 1, 3-10, 13, and 18-22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the method of the reference patent, van der Loos, and Jennings because each reference discloses methods for staining cancer tissue sections with multiple primary antibodies. The motivation to use the multiple staining techniques of van der Loos would have been to use protocols which can easily be adapted to many different applications and antibody combinations, as taught by van der Loos (p. 313, col. 1-2). The motivation to use the method of Jennings for attaching nanocrystals to primary antibodies would have been to use the narrow emission of nanocrystals for cellular labelling, as taught by Jennings (p. 5579, col. 1, par. 1; p. 5580, col. 2, par. 4; Fig. 1). It would have been obvious to choose the primary antibody against cytokeratin in the five primary antibody staining protocol taught by Jennings because there are only a finite number of primary antibodies examined by Jennings. One of ordinary skill in the art would have further been motivated to choose the primary antibodies of cytokeratin, CD3, CD8, CD20, and FoxP3 in the five primary antibody staining protocol taught by Jennings because Jennings teaches that cytokeratin is useful in characterizing tumors (p. 5586, col. 1, par. 2; Fig. 5A).
B. Claims 1, 3-10, 13, and 18-22 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 12,154,275 in view of van der Loos (Journal of Histochemistry & Cytochemistry, 2008, 56(4):313-328; cited on the Jun 17 2021 IDS) and Jennings et al. (ACS Nano, 2011, 5(7):5579-5593; previously cited). The instant rejection is newly stated and is necessitated by claim amendment.
Regarding instant claims 1 and 22, reference patent claim 1 (“A method of evaluating a tumor, the method comprising: (a) quantitating on an image analysis system: (a1) a density of total lymphocytes within a region of interest (ROI) of a digital image of a tissue section of the tumor, wherein the ROI is selected from at least one of a tumor core (TC) region, an invasive margin (IM) region, and/or a peritumoral (PT) region of the tissue section; and (a2) a density of cells stained for at least one immune cell marker within a ROI of a digital image of a tissue section of the tumor, wherein: (a2a) the at least one immune cell marker is selected from the group consisting of CD8… and FoxP3… (b) applying a non-linear continuous scoring function to a feature vector comprising the cell density of the lymphocytes and the density of cells staining for the at least one additional marker to obtain an immune context score (ICS) for the tumor, wherein the ICS is indicative of an outcome of a patient having the tumor”) except for the limitations “contacting a sample with CD3, CD8, CD20, and FoxP3 specific binding moieties, contacting the sample with a binding entity specific for a tumor marker, removing excess specific binding moieties from the sample, detecting the specific binding moieties, assessing a presence and a distribution for the specific binding moieties within the sample”.
However, the prior art to van der Loos discloses practical suggestions for immunoenzyme double, triple, and quadruple staining procedures (abstract). van der Loos teaches using, among others, the primary antibodies CD3, CD8, CD20, and Foxp3 (Table 1). van der Loos teaches contacting tissue section samples with two, three, or four of the primary antibodies listed in Table 1 (p. 318, col. 2, par. 2 through p. 324, col. 2, par. 1). van der Loos teaches washing the tissue samples after contact with the primary antibodies (p. 319, col. 1, par. 2-3). van der Loos teaches enzymatic visualization of the stained tissue samples (p. 319, col. 1, par. 3 through col. 2, par. 2; Fig. 1-8). van der Loos teaches analyzing the immunoenzyme staining patterns in tissue samples stained with two, three, or four primary antibodies (Fig. 11-14).
van der Loos does not teach contacting a sample with CD3, CD8, CD20, and FoxP3 specific binding moieties and a binding entity specific for a tumor marker.
However, 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 modify, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos to contact a sample with CD3, CD8, CD20, and FoxP3 primary antibodies because van der Loos teaches using each of the primary antibodies for at least double staining, and teaches a method for quadruple staining which involves CD3 and CD20 already (p. 324, col. 1, par. 3 through col. 2, par. 1; Fig. 14). It would have been obvious to choose the primary antibodies against CD3, CD8, CD20, and FoxP3 from the list of Table 1 in the quadruple staining protocol taught by van der Loos because there are only a finite number of primary antibodies (9) examined by van der Loos.
However, the prior art to Jennings discloses nanocrystal bioconjugation chemistries for multi target immunolabelling (abstract). Jennings teaches multicolor immunocytochemical labelling using the simultaneous detection of five different nanocrystal materials using fluorescence (Fig. 1 and 5), where five separate nanocrystal-antibody conjugates were analyzed simultaneously (Fig. 5B). Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin, where cytokeratins are often expressed in tumors (i.e., a tumor marker) in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A).
The reference patent does not disclose the limitations of instant claims 3-10, 13, and 18-21.
However, Jennings teaches multicolor immunocytochemical labelling using the simultaneous detection of five different nanocrystal materials using fluorescence (Fig. 1 and 5), where five separate nanocrystal-antibody conjugates were analyzed simultaneously (Fig. 5B). Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin (instant claim 3), where cytokeratins are often expressed in tumors in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A). Jennings therefore teaches an overlapping range which anticipates or alternatively makes obvious the instantly claimed range of between 30nm and 60nm as the narrowest claimed range in claim 21, which also anticipates or alternatively makes obvious the broader ranges in claims 18-20. It would have been prima facie obvious to one of ordinary skill in the art to select any portions of the disclosed ranges including the instantly claimed ranges from the ranges disclosed in the prior art references, particularly in view of the fact that: "The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set percentage ranges is the optimum combination of percentages" In re Peterson 65 USPQ2d 1379 (CAFC 2003). Also In re Malagari, 182 USPQ 549,533 (CCPA 1974) and MPEP 2144.05. One of ordinary skill in the art would have been motivated to use the nanocrystals as taught by Jennings because their narrow fwhm values minimize spectral cross-talk and simplify the Gaussian fitting and deconvolution during subsequent analysis, as taught by Jennings (p. 5584, col. 2, par. 1).
However, van der Loos teaches that CD8, CD20, and Foxp3 are primary antibodies from mouse and CD3 is a primary antibody from a rabbit (Table 1) (instant claims 4-8). van der Loos teaches using anti-mouse and anti-rabbit secondary antibodies (Table 2) which are monoclonal (p. 320, col. 1, par. 2; p. 321, col. 1, par. 3 through col. 2, par. 1; p. 322, col. 1, par. 3; Figures 11 and 13-14) (instant claim 9). van der Loos teaches an indirect/direct multistep protocol where an unlabeled mouse primary antibody is combined with a second mouse primary antibody directly conjugated with hapten or enzyme and performing detection with an enzyme labeled anti-fluorochrome or hapten or enzyme-labeled streptavidin (i.e., detection compound) (p. 322, col. 2, par. 3; Figure 7) (instant claims 10 and 13).
Regarding claims 1, 3-10, 13, and 18-22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the method of the reference patent, van der Loos, and Jennings because each reference discloses methods for staining cancer tissue sections with multiple primary antibodies. The motivation to use the multiple staining techniques of van der Loos would have been to use protocols which can easily be adapted to many different applications and antibody combinations, as taught by van der Loos (p. 313, col. 1-2). The motivation to use the method of Jennings for attaching nanocrystals to primary antibodies would have been to use the narrow emission of nanocrystals for cellular labelling, as taught by Jennings (p. 5579, col. 1, par. 1; p. 5580, col. 2, par. 4; Fig. 1). It would have been obvious to choose the primary antibody against cytokeratin in the five primary antibody staining protocol taught by Jennings because there are only a finite number of primary antibodies examined by Jennings. One of ordinary skill in the art would have further been motivated to choose the primary antibodies of cytokeratin, CD3, CD8, CD20, and FoxP3 in the five primary antibody staining protocol taught by Jennings because Jennings teaches that cytokeratin is useful in characterizing tumors (p. 5586, col. 1, par. 2; Fig. 5A).
C. Claims 1, 3-10, 13, and 18-22 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 12-16 of copending Application No. 18/920,871 in view of van der Loos (Journal of Histochemistry & Cytochemistry, 2008, 56(4):313-328; cited on the Jun 17 2021 IDS) and Jennings et al. (ACS Nano, 2011, 5(7):5579-5593; previously cited). The instant rejection is newly stated and is necessitated by claim amendment.
This is a provisional nonstatutory double patenting rejection.
Regarding instant claims 1 and 22, reference application claim 12 (“A method of prognosing a chemo-naive stage II colorectal cancer patient having a tumor that is determined to be mismatch repair proficient (pMMR), the method comprising: (a) calculating a feature vector for a sample of the tumor, wherein the feature vector comprises a density of CD3+ lymphocytes… (b) applying a continuous scoring function to the feature vector to obtain an immune context score (ICS)”) and claims 13-16 (features vectors comprise CD3+ and CD8+ lymphocyte features) disclose the limitations of instant claim 1 except for the limitations “contacting a sample with CD3, CD8, CD20, and FoxP3 specific binding moieties, contacting the sample with a binding entity specific for a tumor marker, removing excess specific binding moieties from the sample, detecting the specific binding moieties, assessing a presence and a distribution for the specific binding moieties within the sample”.
However, the prior art to van der Loos discloses practical suggestions for immunoenzyme double, triple, and quadruple staining procedures (abstract). van der Loos teaches using, among others, the primary antibodies CD3, CD8, CD20, and Foxp3 (Table 1). van der Loos teaches contacting tissue section samples with two, three, or four of the primary antibodies listed in Table 1 (p. 318, col. 2, par. 2 through p. 324, col. 2, par. 1). van der Loos teaches washing the tissue samples after contact with the primary antibodies (p. 319, col. 1, par. 2-3). van der Loos teaches enzymatic visualization of the stained tissue samples (p. 319, col. 1, par. 3 through col. 2, par. 2; Fig. 1-8). van der Loos teaches analyzing the immunoenzyme staining patterns in tissue samples stained with two, three, or four primary antibodies (Fig. 11-14).
van der Loos does not teach contacting a sample with CD3, CD8, CD20, and FoxP3 specific binding moieties.
However, 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 modify, in the course of routine experimentation and with a reasonable expectation of success, the method of van der Loos to contact a sample with CD3, CD8, CD20, and FoxP3 primary antibodies because van der Loos teaches using each of the primary antibodies for at least double staining, and teaches a method for quadruple staining which involves CD3 and CD20 already (p. 324, col. 1, par. 3 through col. 2, par. 1; Fig. 14). It would have been obvious to choose the primary antibodies against CD3, CD8, CD20, and FoxP3 from the list of Table 1 in the quadruple staining protocol taught by van der Loos because there are only a finite number of primary antibodies (9) examined by van der Loos.
However, the prior art to Jennings discloses nanocrystal bioconjugation chemistries for multi target immunolabelling (abstract). Jennings teaches multicolor immunocytochemical labelling using the simultaneous detection of five different nanocrystal materials using fluorescence (Fig. 1 and 5), where five separate nanocrystal-antibody conjugates were analyzed simultaneously (Fig. 5B). Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin, where cytokeratins are often expressed in tumors (i.e., a tumor marker) in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A).
The reference application does not disclose the limitations of instant claims 3-10, 13, and 18-21.
However, the prior art to Jennings discloses nanocrystal bioconjugation chemistries for multi target immunolabelling (abstract). Jennings teaches multicolor immunocytochemical labelling using the simultaneous detection of five different nanocrystal materials using fluorescence (Fig. 1 and 5), where five separate nanocrystal-antibody conjugates were analyzed simultaneously (Fig. 5B). Jennings also teaches nanocrystal labeling of antibodies targeting cytokeratin (instant claim 3), where cytokeratins are often expressed in tumors in two color immunolabelling (p. 5586, col. 1, par. 2; Fig. 5A). Jennings therefore teaches an overlapping range which anticipates or alternatively makes obvious the instantly claimed range of between 30nm and 60nm as the narrowest claimed range in claim 21, which also anticipates or alternatively makes obvious the broader ranges in claims 18-20. It would have been prima facie obvious to one of ordinary skill in the art to select any portions of the disclosed ranges including the instantly claimed ranges from the ranges disclosed in the prior art references, particularly in view of the fact that: "The normal desire of scientists or artisans to improve upon what is already generally known provides the motivation to determine where in a disclosed set percentage ranges is the optimum combination of percentages" In re Peterson 65 USPQ2d 1379 (CAFC 2003). Also In re Malagari, 182 USPQ 549,533 (CCPA 1974) and MPEP 2144.05. One of ordinary skill in the art would have been motivated to use the nanocrystals as taught by Jennings because their narrow fwhm values minimize spectral cross-talk and simplify the Gaussian fitting and deconvolution during subsequent analysis, as taught by Jennings (p. 5584, col. 2, par. 1).
However, van der Loos teaches that CD8, CD20, and Foxp3 are primary antibodies from mouse and CD3 is a primary antibody from a rabbit (Table 1) (instant claims 4-8). van der Loos teaches using anti-mouse and anti-rabbit secondary antibodies (Table 2) which are monoclonal (p. 320, col. 1, par. 2; p. 321, col. 1, par. 3 through col. 2, par. 1; p. 322, col. 1, par. 3; Figures 11 and 13-14) (instant claim 9). van der Loos teaches an indirect/direct multistep protocol where an unlabeled mouse primary antibody is combined with a second mouse primary antibody directly conjugated with hapten or enzyme and performing detection with an enzyme labeled anti-fluorochrome or hapten or enzyme-labeled streptavidin (i.e., detection compound) (p. 322, col. 2, par. 3; Figure 7) (instant claims 10 and 13).
Regarding claims 1, 3-10, 13, and 18-22, 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 combine, in the course of routine experimentation and with a reasonable expectation of success, the method of the reference application, van der Loos, and Jennings because each reference discloses methods for staining cancer tissue sections with multiple primary antibodies. The motivation to use the multiple staining techniques of van der Loos would have been to use protocols which can easily be adapted to many different applications and antibody combinations, as taught by van der Loos (p. 313, col. 1-2). The motivation to use the method of Jennings for attaching nanocrystals to primary antibodies would have been to use the narrow emission of nanocrystals for cellular labelling, as taught by Jennings (p. 5579, col. 1, par. 1; p. 5580, col. 2, par. 4; Fig. 1). It would have been obvious to choose the primary antibody against cytokeratin in the five primary antibody staining protocol taught by Jennings because there are only a finite number of primary antibodies examined by Jennings. One of ordinary skill in the art would have further been motivated to choose the primary antibodies of cytokeratin, CD3, CD8, CD20, and FoxP3 in the five primary antibody staining protocol taught by Jennings because Jennings teaches that cytokeratin is useful in characterizing tumors (p. 5586, col. 1, par. 2; Fig. 5A).
Response to Applicant Arguments
At p. 3-4, Applicant submits that the reference patents 11,250,566 and 12,154,275 and reference application 18/920,871 do not disclose a multiplex assay for a CD3 marker, a CD8 marker, a CD20 marker, a FoxP3 marker, and a tumor marker, where each of the individual markers are detected using different chromogenic detection reagents, and should be withdrawn.
It is respectfully submitted that this is not persuasive. As set forth in the above rejections, even though the reference patents and applications do not disclose these features, they are not patentable in view of van der Loos and Jennings.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/J.N.S./Examiner, Art Unit 1685
/OLIVIA M. WISE/Supervisory Patent Examiner, Art Unit 1685
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