DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 6/22/2026 has been entered.
Information Disclosure Statement
The information disclosure statement filed 6/22/2026 fails to comply with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. It has been placed in the application file, but the information referred to therein has not been fully considered. References that were not considered have been stuck-through in the signed 1449 form. The following references have not been considered because no English language translation was provided: CN107557426 and CN101945673.
Response to Amendment
Applicant’s remarks and amendments filed 6/22/2026, in response to the final rejection mailed 12/22/2025, are acknowledged and have been fully considered.
Any previous rejection or objection not mentioned herein is withdrawn in view of Applicant’s amendments to the claims.
Applicant’s amendment to the claims is acknowledged. This listing of the claims replaces all prior versions and listings of the claims. Claims 1 and 3-20 are pending, of which claims 11-20 remain withdrawn as being drawn to a non-election invention.
Claims 1 and 3-10 have been examined on the merits herein.
Response to Arguments
Applicant’s arguments, on pages 7-11 of the remarks filed 6/22/2026, with respect to the rejections of claims 1-10 under 35 U.S.C. § 103 have been fully considered and are also persuasive in light of the amendments to claim 1 to recite that the tissue sample is sonicated and that the dissociated cells are transferring into a “profiling unit for microtissue generation”. Therefore, the rejection has been withdrawn.
However, upon further consideration, new and/or modified grounds of rejection are presented below, in view of applicant’s amendments to the claims, prompting additional searching of the art and further consideration of the amended limitations.
Claim Interpretation
As previously set forth, the term “patient-derived microtumor (PMT)”, as recited in the amended claims, is being interpreted according to the broadest reasonable interpretation (B.R.I.) of the language in view of the specification. In this case the term is being interpreted as encompassing any artificially grown (in vitro) three-dimensional tissue models that comprises structures of patient-tumor derived cancer cells. Such structures are also known as microtumors, spheroids, and microtissues in the art. The specification, at [11], states that “Consequently, a microtumor shall mean a 3D microtissue generated from, at least in part, selected cancer cells derived from a cell line or a neoplastic sample, such as a tumor”.
The claim term “profiling unit” is being interpreted under the B.R.I. as described in the specification at [0094], as a fully contained (housed) and sterile environment which includes a loading port to load a cartridge or plate containing microtumors as well as cancer-type specific maintenance medium. See also [0115] of the specification which states “the thus obtained plate is transferred directly into a so-called profiling device (unit) for tissue maturation (microtissue generation).”
Specification
The disclosure is objected to because of the following informalities:
Used in various places in the specification, the terms “sonification” ([84], [91],[92], [93], [94],and [111]) and “sonificator” (see e.g. [111]) appear to be referring to “sonication” and “sonicator”, which are the correct terms used in the art for disrupting cells with ultrasonic frequencies and the instrument used to do so (see “sonicated” as recited in [17] and item 4 on page 19). Appropriate correction is required.
Claim Objections
Claim 1 is objected to because of the following informalities:
The term “sonificator” appears in line 5 of amended claim 1. This appears to be a misspelling of the term “sonicator”, the lab instrument for sonicating samples.
Appropriate correction is required.
Claim Rejections - 35 USC § 103
(Modified as necessitated by Applicant’s amendments)
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 and 3-8 are rejected under 35 U.S.C. 103 as being unpatentable over Pongracz et al. (US PGPub No. 20190128870) in view of Benton et al. (“In Vitro Microtumors Provide a Physiologically Predictive Tool for Breast Cancer Therapeutic Screening”, Plos One, April 9, 2015, of record), Jovanovich et al. (US PGPub No. 20210214673, with an effective filing date of Jun. 1, 2019), and Macleod et al. (2004. “Essential Techniques of Cancer Cell Culture” Methods Mol Med.; 88:17-29, of record).
Pongracz is drawn to a 3-Dimensional (3D) tissue culture aggregate of cells derived from a neoplastic tissue sample and a method for assessing the effectiveness of an anti-neoplasm treatment by measuring the effect of said treatment on the viability of a three dimensional (3D) neoplasm tissue culture aggregate (Abstract). Pongracz teaches that “The method of the present invention uses patient-derived cells so the aggregate formed can be used to select the most effective treatment. Anti-neoplasm compounds or treatments, such as chemotherapeutic agents, or combinations thereof can be tested, and those which reduce the tumour cell viability can be used to treat the patient.” ([0026]). Thus, Pongracz pertains to methods for generating and testing patient-derived microtumors, as it teaches using cells from neoplastic tissue, e.g. a tumor.
Pongracz teaches dissociating the cells of a patient-derived tissue sample in order to obtain dissociated cells ([0050]: “Solid tumour samples can be reduced in size and undergo mechanical dissociation by cutting or mincing, for example using sterile scalpels. The cells in the tissue sample are dislocated according to known tumour dissociation methods”)
Pongracz teaches next generating a 3D aggregate, i.e., a 3D microtissue, using dissociated tumor cells ([0047]; [0059]-[0060]), and generating an array of the 3D aggregates or microtissues which comprises using a multi-well plate containing a number of 3D aggregates ([0109]: “Pipette 200 μl/well mixed suspension into a sterile 96-well, U-bottom cell culture plate with Ultra-low attachment surface” and [0167]).
Pongracz thus teaches dissociating the cells of a patient-derived tissue sample in order to obtain dissociated cells ([0050]), generating a 3D aggregate (i.e. a 3D microtissue), using dissociated tumor cells ([0047]; [0059]-[0060]), and generating an array of the 3D aggregates or microtissues which comprises using a multi-well plate containing a number of 3D aggregates ([0109]; [0167]).
Pongracz teaches contacting the array of said 3D microtissues with at least two drugs and/or combinations thereof and determining an effect of said drugs and/or combinations on the 3D microtissues ([0063]-[0067]; and see specific embodiments of FIGs. 3-4 and FIGs. 7-8).
Pongracz teaches next identifying a patient-specific drug or drug combination based on the effect as determined ([0064]: “Anti-neoplasm treatments identified as reducing cell viability can then be used to treat the patient.”).
Regarding claim 3, Pongracz teaches: that lymphoid CD45+ cells are removed from the aggregates, i.e. thus removing immune cells ([0054-0056]; [0112]); fibroblasts may be added to the cells in order to form an aggregate ([0057]; [0118]); that the number of cells in the cell population are counted and controlled and a set amount is determined for the aggregates ([0058]; [0116]-[0117]); and that the 3D microtissues are generated with a hanging drop system ([0059]), and using multi-well plates (e.g. in [0121]: “96-well, U-bottom cell culture plate with Ultra-low attachment surface”). Thus Pongracz discloses, in specific embodiments, one or more of the claimed alternatives encompassed in claim 3.
In regards to claim 4, Pongracz teaches that the method therein does not use a scaffold or artificial extracellular matrix ([0024]-[0027]; [0061]: “it is preferred that the aggregates are formed and cultured in the absence of an artificial scaffold or matrix”. One skilled in the art would recognize that this would exclude the use of a solubilized basement membrane preparation (evidenced from [0011] of Pongracz).
In regards to claim 5, Pongracz discloses a continuous exposure to at least two drugs, and to combinations thereof ([0063]-[0067] and [0167], as an example: “aggregates were cultured for 24, 48 or 72 h respectively, at 37° C. using the drugs”, i.e. a continuous exposure). Pongracz also discloses that “following treatment with a antineoplastic treatment, any residual cells can be tested for sensitivity to a second antineoplastic treatment”, which one of skill in the art would understand to encompass removing the drug and then applied a different drug ([0068]-[0072]).
Claim 6 recites that the determining of the effect on the microtissues is selected from one of: size determination, quantification of internal reporter gene expression in the patient-derived microtumor, determination of the intracellular ATP content in the microtumor, and determination of pre-selected biomarkers in the microtumor. Pongracz teaches assessing cell viability following the drug treatment, including the determination of intracellular ATP content ([0064]; [0067]: “Methods of assessing cell viability are well known to the person skilled in the art. For example, ATP production can be measured, or the incorporation of propidium iodide”; and [0131]-[0133]). Pongracz also teaches that following treatment, cell surface markers are assayed to determine the presence of neoplastic stem cells ([0073]; [0135]-[0138]), thus teaching determination of pre-selected biomarkers in the 3D cultured patient-derived tissue.
In regards to claim 7, Pongracz discloses that the methods may include steps of cryopreserving the suspension culture and thawing the cryopreserved culture ([0045]-[0046]; [0062]). Pongracz also discloses that the cells are obtained from a patient-derived tissue sample and may be derived from a primary tissue sample, a solid tumor sample, or a metastatic tissue sample (i.e. from lymph nodes or other organs) ([0033]-[0034]). Pongracz discloses that the cells may split into additional samples (i.e. thus a sub-sample of a tissue sample, see [0159]-[0161]).
In regards to claim 8, Pongracz teaches, in one embodiment, processing and culturing of cells from a patient-derived glioblastoma sample (thus a primary tissue sample), including steps of collecting of additional samples for DNA and RNA isolation (which were collected and stored at −80° C), and used for additional sequencing or comparative gene expression studies ([0159]-[0161]), thus disclosing molecular profiling of a subsample.
Pongracz also teaches that a cellular composition of the tissue culture aggregate may be identified using surface cell marker analysis, and that surface cell markers can be identified using antibodies such as CD31-APC Cy7, CD44-FITC, CD45-PerCp, CD90-BV421, EpCam-APC. Thus Pongracz teaches and suggests means for histochemical analysis. Pongracz teaches that when the glioblastoma sample was acquired, samples of it were analyzed by a pathologist, thus intrinsically disclosing a step for histological analysis in that embodiment ([0161]).
However, the combination of Pongracz and Benton does not teach a tissue sample treated with an enzyme capable of dissociating cells, producing a supernatant comprising dissociated cells, and removing the supernatant comprising the dissociated cells, wherein the steps of enzymatic treatment and cell collection are repeated at least once, as recited in claim 2.
However, Pongracz does not explicitly teach: a microtumor culture having a maturation time of 2-5 days, that the cells are treated with drugs for a period of 7 to 14 days, nor that the tissue sample is sonicated using a sonicator (e.g. the “sonificator”) or that the dissociated cells are transferring into a “profiling unit for microtissue generation”. Nor does Pongracz expressly teach treating the sample with an enzyme capable of dissociating cells, producing a supernatant comprising dissociated cells, and removing the supernatant comprising the dissociated cells, wherein the steps of enzymatic treatment and cell collection are repeated at least once.
Benton teaches in vitro microtumor models using a tumor-aligned ECM, a tumor-aligned medium, MCF-7 and MDA-MB-231 breast cancer spheroids, human umbilical vein endothelial cells, and human stromal cells that recapitulates the tissue architecture, chemical environment, and cellular organization of a growing and invading tumor (Abstract), in order to provide a model system that has more authentic responses to anti-cancer treatments (pg. 2, last ¶).
Benton teaches that cancer cells can be directed to adopt an appropriate tumor morphology as multicellular tumor spheroids (MCTS) (pg. 2, 2nd ¶). Benton teaches a method of producing tumor microtumors (see pg. 7, under “In Vitro Microtumors”), comprising providing human breast cancer cells (from cell lines originally derived from human tumor samples) and human mesenchymal stem/stroma cells (hMSCs) which are incubated for 72 hour at 37°C (see also S2 Fig. “The stepwise process for the in vitro microtumor model for evaluating breast cancer progression.”). Benton teaches that using “preformed spheroids containing both breast cancer cells and hMSCs to endothelial tubules composed of both HUVECS and hMSCs provided an improved cell environment, promoting physiological architecture and activity for each microtumor model” (pg 10, 4th ¶).
Benton teaches applying varying doses of the anti-tumor drugs fluorouracil or paclitaxel and measuring the effect on proliferation in MCF-7 and MDA-MB-231 microtumors, for at least 7 days and up to 10 days (see Figure 6), and teaches that the microtumors exhibit near physiological responses regarding cell proliferation to paclitaxel or fluorouracil treatment.
Jovanovich discloses a system, methods, and an apparatus to collect and prepare cells, nuclei, subcellular components, and biomolecules from specimens including tissues and use the single cells to form organoids or microtissues (Abstract, Fig. 1). Jovanovich teaches that the specimens can include tumor samples ([0098]; [0121]).
Jovanovich teaches that this system can perform the dissociation of tissue into single cells which are then used to form microtissues 6001 or organoids 6002 on a cartridge 200, which can be used to create microtissues 6001 or organoids 6002 ([0119]; FIGs. 5 and 6). Jovanovich teaches that the system processes tissue specimens 120 and other samples into single cell 1000 suspensions and then form microtissues 6001 or organoids 6002 with little or no intervention by the operator once the process is started ([0121]). Jovanovich specifically teaches that the “Tissue Processing System” can be used to create microtissues or organoids directly in a cartridge using the hanging droplet method or other methods, or the output of the system can be used as the starting point for creating microtissues or organoids off of the cartridge ([0032], claims 82 and 83, see also [0199]).
Jovanovich also teaches that the system has physical dissociation subsystems and enzymatic and chemical dissociation subsystem ([0033]; [0106]-[0107]) for disrupting and dissociating cells. Jovanovich teaches that the system can perform steps of sonication for processing the tissue, a technique known to the art for such tissue processing ([0017]; [0039]: “physical dissociation modalities include passing the specimen through screens, filters, orifices, grinding, blending, sonication, smearing, bead beating, and other methods known to one skilled in the art to physically disrupt tissue to help produce single cell”).
Thus the automated system in Jovanovich appears to having similar structural components and will fulfill the same role as the recited profiling unit, because this system is taught to be used to dissociate specimens and tissues into single cells- including tumor specimens- and to be used for maturing the cells into microtissues/organoids.
Macleod teaches methods for obtaining cancerous cells from primary tissue samples, including solid primary tumors (3.1. Primary Culture, section: 3.1.1. Initial Establishment from Solid Primary Tumor or Solid Metastasis). Regarding dissociating the tumor sample, Macleod states that “Two options are then available for tumor disaggregation—mechanical or enzymatic dispersion” (pg. 22, step 3). In the enzymatic method, Macleod teaches that cells in the sample may be disaggregated (broadly, broken up or dissociated) by the use of proteolytic enzymes, which include trypsin, collagenase, hyaluronidase, elastase, dispase, and papain (pg. 22, step 5). Macleod then states that “the supernatant is collected and centrifuged at 600g for 5 min to collect a cell pellet. This cell pellet is resuspended in full culture medium (containing serum which will inactivate the trypsin).” Macleod teaches that the fragments will not necessarily disaggregate fully after a single 30-min step and thus the process may be repeated until most cells have become suspended in the supernatant (pg. 22, step 6).
Therefore, before the effective filing date of the instant invention, to one of ordinary skill in the art, it would have been prima facie obvious to modify the method taught in Pongracz for assaying the effectiveness of an anti-neoplasm treatment, such that the patient-derived 3D spheroids (e.g. patient-derived microtumors) are produced according to the teachings of Benton, wherein the culturing of the spheroids is performed for 72 hours, it would have been obvious over the combined teachings of Pongracz and Benton to apply the combination of drugs for at least 7 days, in order to better assay the effects of cancer drugs on cell proliferation, and it would have been obvious to one of ordinary skill to incorporate an automated tissue culturing system for generating the patient-derived microtissues according to the teachings of Jovanovich, a system which includes means for physically disrupting samples, including sonicating, and further to incorporate the teachings of Macleod such that the dissociating of the primary tissue or tumor sample comprises steps of applying a solution containing a proteolytic enzyme- also taught in Jovanovich- then collecting a supernatant that contains dissociated cells, and repeating the process at least once in order to fully disaggregate the collected sample cells.
One would have been motivated to improve upon the 3D aggregate cultures used in Pongracz for predicting the effect of a particular patient’s response to at least two drugs or combinations thereof and determining an effect of said drugs and/or combinations on the 3D microtissue by incorporating knowledge known in the art, including the microtumor structures disclosed in Benton. Benton teaches that such microtumors (comprised of cancer cells originally derived from human patient tumor samples) can be used to better model the tumor micro-environment, and that treatment of such microtumor structures with anti-cancer drugs leads to predictably improved assay behavior, better mimicking the effects of the drugs on cell proliferation of an in-vivo tumor.
One would have been motivated to apply the methods for optimizing a 3D microtumor culture taught in Benton to the individualized medicine assays, using patient-derived tumor cells, as taught in Pongracz to select the most effective treatment. In doing so, one would have arrived at the instantly claimed methods, wherein microtumors are produced by “self-assembling” cancer cells, the microtumors mature for 72 hours (as taught in Benton), and the drugs used for testing are applied to the microtumor culture for 7-10 days, because Benton teaches such application, and the microtumors are viable for at least that long.
Means for physical disruption of tissue and cell samples are known in the art, including the use of sonicating (i.e. using a sonicator on tissues), as taught in Jovanovich. The selection of sonication as means for physically disrupting a tissue sample containing cells would have been a matter of judicious selection to one having ordinary skill and knowledge in the art. Jovanovich further teaches a system for the automated preparation of single cells from specimens, including from tumor samples, to then be used for the preparation of organoids or microtissues. The system taught in Jovanovich (see e.g. Figures 5 and 6) appear to fulfill the requirements of the recited element “transferring the dissociated cells into a profiling unit for microtissue generation”, according to the B.R.I. of the claim words, given their normal meaning and knowledge in the art. It is noted that although the specification is used to interpret claim terms, it does not serve to limit the claims unduly, and claim limitations are not imported from the specification. Jovanovich teaches that such a system provides the obvious advantage of automated cell handling, meaning less physical labor and more repeatable results with higher throughput.
One would have been motivated to use the proteolytic enzyme dissociating method of Macleod because Pongracz teaches that “the cells in the tissue sample are dislocated according to known tumour dissociation methods, known in the art (see Langdon and Macleod (2004)” Essential Techniques of Cancer Cell Culture” Methods Mol Med.; 88:17-29.)”, citing to Macleod. One of ordinary skill in the art would have been motivated to select the dissociation method using an enzyme, such as trypsin, as this was one of two finite method choices presented in Macleod, and known in the art. Further, Macleod explicitly teaches that repeating the enzymatic digestion steps is advantageous because the repetition will increase the amount of dissociated cells in the supernatant. Macleod teaches that the use of proteolytic enzymes is commonly and successfully used to disaggregate or dissociate tumor samples.
One having ordinary skill in the art would have been able to select from known methods of dissociating cells, as required in the method of Pongracz, and as evidenced from the teachings of Macleod and Jovanovich. The particular selection of sonicating and enzymatic digestion would have both been a matter of judicious selection from among well-known methods in the art. Repeating steps of dissociating cells would have likewise been obvious over the cited art.
Regarding claims 3-8, these additional limitations are all taught in either Pongracz or Benton, as described above, and represent obvious variations and matter of judicious selection to one having ordinary skill in the art.
From the teachings of the cited references, it is apparent that there would have been a reasonable expectation of success in combining the teachings therein to arrive at the claimed invention because both Pongracz and Benton pertain to 3D tumor culture models with cancer cells, Pongracz teaches culturing primary dissociated tumor cells, and Benton teaches means for improving a 3D microtumor culture, such that drugs can be applied for over 7 days. Further, Macleod and Jovanovich both teach methods known in the art for disassociating cells, including using enzymatic digestion and physical disruption, such as sonicating whereas Jovanovich demonstrates successfully automating these cell handling and maturating methods (e.g. growing organoids in an automated system). One would have reasonably expected to successfully produce a culture system for patient-derived microtumors, wherein drugs can be applied for an extended period of time.
Therefore, the invention of claims 1 and 3-8 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date, as evidenced by the cited references, especially in the absence of evidence to the contrary.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Pongracz et al. (US PGPub No. 20190128870), Benton et al. (“In Vitro Microtumors Provide a Physiologically Predictive Tool for Breast Cancer Therapeutic Screening”, Plos One, April 9, 2015, of record), Jovanovich et al. (US PGPub No. 20210214673), and Macleod et al. (2004. “Essential Techniques of Cancer Cell Culture” Methods Mol Med.; 88:17-29, of record) as applied to claim 1 above, and further in view of Shuford et al. ("Prospective Validation of an Ex Vivo, Patient-Derived 3D Spheroid Model for Response Predictions in Newly Diagnosed Ovarian Cancer”, Scientific Reports, of record).
The combined teachings of Pongracz, Benton, Jovanovich and Macleod make obvious a method for assessing the effectiveness of an anti-cancer treatment by measuring the effect of said treatment on the viability of three dimensional (3D) microtumor cultures, including the particular limitations of the amended claim 1, as discussed above (Abstract; [0026]). The relevant teachings of Pongracz, Benton, Jovanovich and Macleod include all those discussed above.
However, the combination of Pongracz, Benton, Jovanovich and Macleod does not explicitly teach performing a stratification of patients based on a patient-specific drug or drug combination, as recited in claim 9.
Shuford et al. teaches a method that utilizes primary patient tissue in 3D cell culture to make patient-specific response predictions prior to initiation of treatment in the clinic (Abstract).
Shuford discusses that biopsy samples of primary tumor sites were obtained from patients, the tumor tissue was enzymatically dissociated into single cells, and the cells were formed as 3D spheroids in 384-well spheroid microplates, i.e. an array of 3D microtissues (pg. 11, ¶ “Assay performance”, entire paragraph). Shuford discloses that the array of cells were exposed to standard of care chemotherapies as single agents, and at least two drugs were tested on different wells of the array so that cell viability could be calculated for each treatment, thus disclosing determining an effect of the drugs (pg. 11, ¶ “Assay performance”, lines 4-7).
Shuford teaches patients were categorized using the ex vivo assay results as either test Responders or Non-Responders to individual chemotherapeutics (see Figure 3 and pg. 11, ¶ “Test response determination”), thus teaching identifying patient-specific drug or drug combination based on the determined effect, i.e. prediction of patient-specific response before treatment (see Abstract), and performing a stratification of the patient based on the assay results (e.g. the patients are stratified as responder or non-responder).
Thus, before the effective filing date of the claimed invention, to one of ordinary skill in the art it would have been obvious when performing the method taught in the combination of Pongracz, Benton, Jovanovich and Macleod for predicting a patient’s response to a drug treatment using 3D microtumor cultures, as recited in claim 1, to then further analyze the data as taught in Shuford by performing a stratification of the patient based on the assay results such that the patients are stratified as responder or non-responder.
One would have been motived by the teachings of Shuford to do so, as an analogous ex vivo assay is taught therein, and the stratification or classification of patients is taught to be useful for making patient-specific response predictions prior to initiation of treatment. The analysis of data and stratification of patients amounts to nothing more than gathering and processing of data which may be performed by the mind of an observer. These steps do not result in any patentable distinct over those methods and knowledge of the cited prior art.
To one having ordinary skill in the art, with knowledge of the cited references wherein cell culture chemotherapy data is useful for predicting patient responses, the categorizing of patients as responders or non-responders would have been a normal and routine analysis method.
From the teachings of the cited references, particularly the stratification taught in Shuford, it is apparent that there would have been a reasonable expectation of success in combining the teachings therein to arrive at the claimed invention because all of the reference pertain to methods for personalized chemotherapy medicine, using 3D tissue cultures.
Therefore, the invention as a whole would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date, as evidenced by the cited references, especially in the absence of evidence to the contrary.
Claim 10 is rejected under 35 U.S.C. 103 as being unpatentable over Pongracz et al. (US PGPub No. 20190128870), Benton et al. (“In Vitro Microtumors Provide a Physiologically Predictive Tool for Breast Cancer Therapeutic Screening”, PLOS One, April 9, 2015, of record), Jovanovich et al. (US PGPub No. 20210214673), and Macleod et al. (2004. “Essential Techniques of Cancer Cell Culture” Methods Mol Med.; 88:17-29, of record) as applied to claim 1 above, and further in view of Pongracz et al. (US Patent No. 9151744 B2, referred to hereafter as “Pongracz ‘744”) and Moen et al. (2012. “Pharmacogenomics of chemotherapeutic susceptibility and toxicity.” Genome medicine vol. 4,11 90, of record).
The combination of Pongracz et al. (hereafter “Pongracz ‘870”), Benton, Jovanovich and Macleod teaches a method for assessing the effectiveness of an anti-neoplasm treatment by measuring the effect of said treatment on the viability of three dimensional (3D) microtumor cultures, including the particular limitations of the amended claim 1, as discussed above (Abstract; [0026]). The relevant teachings of Pongracz ‘870, Benton, Jovanovich and Macleod include all those discussed above.
Claim 10 recites identifying adverse effects associated with a treatment with a patient-specific drug or drug combination in a patient, comprising performing the method according to claim 1, and further comprising the step of testing and analyzing said patient-specific drug or drug combination for adverse effects in said patient.
However, the combination of Pongracz ‘870, Benton, Jovanovich and Macleod does not teach a step of testing and analyzing said patient-specific drug or drug combination for adverse effects in said patient, as required in claim 10.
Pongracz ‘744 teaches an engineered three dimensional (3D) pulmonary model tissue culture, free of any artificial scaffold (Abstract), and wherein the model tissue is a pulmonary disease model tissue culture (Col. 9, lines 13-36). Particularly, Pongracz ‘744 teaches that the disease model is a tumor model, such as a non-small cell lung carcinoma (Col 9, lines 32-45), and that the models may comprise cells obtained from a patient and may be used for establishing personalized therapy (Col 10, lines 6-9). Pongracz ‘744 teaches using a model to test an adverse effect of a drug, wherein alteration or modification which is detrimental to the cells of test sample is considered as a toxic or adverse effect of said drug (Col 11, lines 46-50).
Moen et al. is a review article that teaches that a goal of personalized medicine is to tailor a patient’s treatment strategy on the basis of his or her unique genetic make-up (Abstract). Moen states that the goal of pharmacogenomics is to use a patient’s genotype to inform clinical decision making regarding treatment strategies, with the ultimate goal of avoiding adverse drug reactions while achieving the best drug response (pg. 7, left col). Moen teaches that Genome-wide association studies (GWAS) can be utilized to identify genetic markers that will facilitate physician decision-making regarding optimal drug selection, dose and treatment duration on a patient-by-patient basis, with consequent improvement in drug efficacy and decreased toxicity (pg. 1, right hand col). Moen teaches the art recognizes genetic markers associated with response to chemotherapy (see pg. 2, left hand col). Moen discusses the use of genomics to associate toxicity with particular drug responses (Table 1: “The top half of the table shows tumor genome mutations associated with drug response and the bottom half shows germline mutations associated with drug toxicity”).
Thus, to one of ordinary skill in the art before the effective filing date of the claimed invention, it would have been prima facie obvious after performing the method made obvious by the combination of Pongracz ‘870, Benton, Jovanovich and Macleod for predicting a patient’s response to a drug treatment using 3D microtumor cultures and evaluating tumor cell viability with exposure to chemotherapeutics, to further assay the patient-derived cells as taught in Pongracz ‘744 and to monitor the patient’s response to the drug as taught in Moen for the expected purpose of identifying any possible adverse effects in said patient, as suggested by the teachings of Moen and Pongracz ‘744.
Moen teaches that many chemotherapy drugs are known for their cytotoxicity and possibility of inducing adverse events, and thus one would have been adequately motivated to monitor patients for any adverse effects. The administering of the identified drug, identified by the method made obvious by the combined teachings of Benton and Pongracz ‘870, to a patient would have been a clearly obvious step to perform in view of the combined teachings of the cited art. Further, the monitoring and assaying of the patients encompasses steps that amount to nothing more than gathering and processing of data, steps which may be performed by the mind of an observer. These steps do not result in any patentable distinct over those methods and knowledge of the cited prior art.
Although the steps do not absolutely require monitoring the 3D microtissue model for adverse effects, such a step is not outside the breadth of the disclosure, and Pongracz ‘744 establishes that in vitro cellular models may be used to obtain useful information regarding potential normal tissue toxicity and thus adverse effects of drugs using microtissue models.
Moen and Pongracz ‘744 are relied upon for the reasons discussed above. If not expressly taught by the cited art, based upon the overall beneficial teaching provided by the references with respect to the knowledge in the art of adverse effects and cytotoxicity of chemotherapeutics, it is deemed obvious that further clinical or in-vivo testing of a drug or drug combination identified by the method according to Pongracz ‘870 in view of Benton would have lead one to determine if there are any adverse effects.
Therefore, from the teachings of the cited references, it is apparent that one of ordinary skill in the art would have had a reasonable expectation of success and adequate motivation in performing the method as claimed before the effective filing date of the claimed invention.
Response to Arguments
The Applicant’s arguments regarding the obviousness of the claimed methods have been fully considered, however as indicated above, the additional reference Jovanovich has been applied in view of the amendments to the claims, which teaches the newly added features of sonicating cells for physical disruption and of using an automated tissue handler and culture machine (i.e. a profiling unit) for the maturation of organoids and/or microtissues (e.g. microtissue generation). Arguments regarding relevant portions of the previous rejections are expressly responded to below.
Applicant’s argument that neither Pongracz nor Benton teach or suggest the recited patient-derived microtumors (PMTs) has been fully considered but is not persuasive.
Applicant argues that Pongracz generates cellular aggregates from dissociated tumor cells, and remove CD45+ immune cells before aggregate formation. Pongracz does teach removing CD45+ immune cells, but it is noted that such steps are not excluded by the instant claims (comprising type claims). Further, claim 3 of the instant invention recites “adding or removing stroma cells, stromal fibroblasts, endothelia cells, and immune cells to said dissociated cells”. Thus, the removing of CD45+ and other cells in Pongracz is the same as the steps instantly claimed. Therefore, Applicant’s argument that these aggregates are different from the instantly recited PMTs, interpreted under the B.R.I., is not persuasive.
In response to applicant's argument on page 8 that the references fail to show certain features of the invention, specifically that the recited PMTs undergo growth and self-organization to form microtumors that mimic the original tumor, it is noted that the features upon which applicant relies (i.e., the similarity to the original tumor) are not recited in the rejected claims. Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
The applicant has previously argued that the PMTs of the instant invention are ready for drug testing within 4 days after taking tumor samples, yet Benton addresses this shortcoming, as the microtumors comprised of cancer cells therein are generated in 72 hours. Applicant further argues that this is not relevant as the spheroids of Benton are different from the instantly claimed patient-derived structures. As discussed above, this argument depends on features of the “PMTs” that are not expressly recited in the claims, only described in the specification. If Applicant wishes to further limit the meaning of the claimed “patient-derived microtumors”, then additional limitations describing these structures may be amended into the claims.
Further, the portion of Benton that Applicant discusses on page 8 of the remarks, that “Benton et al. teach that the spheroids need to be further embedded in ECM or in Invasion matrix... for at least additional 96 hours” is in regard to a specific test of the spheroids of Benton for Invasion ability testing. This is not required of the instant claims. The particular passage of Benton states that “Breast cancer cells were harvested, diluted as indicated in RPMI, 10% FBS, 1X Spheroid Formation ECM, seeded at 50 μl/well in 96 well ultra-low adhesion plates, and incubated for 72 hour at 37°C, 5% CO2 to promote spheroid formation. The resulting spheroids could be photographed and measured (Fig 1A–1C). Alternatively, they could be embedded in ECM to assess environmental conditions.” Further on page 7, in the paragraph titled “In Vitro Microtumors”, Benton describes that “Breast cancer cells and hMSCs were harvested, diluted to 40,000 cells/ml and to 10,000 cells/ml, respectively in TARPMI, 10% FBS, 1X Spheroid Formation ECM, seeded at 50 μl/well in 96 well ultra-low adhesion plates, and incubated for 72 hour at 37°C, 5% CO2 to promote spheroid formation”, then describes that testing was started following this (after one additional hour on a new plate) with or without a drug treatment. Thus it is evident that, contrary to the Applicant’s argument, Benton does teach microtumors which are viable for testing within 72 hours.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
It is noted that Benton’s teachings are to be viewed in addition to those of Pongracz. The test for obviousness is not whether the features of a secondary reference may be bodily incorporated into the structure of the primary reference; nor is it that the claimed invention must be expressly suggested in any one or all of the references. Rather, the test is what the combined teachings of the references would have suggested to those of ordinary skill in the art. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981). In the instant case, when taking into account all of the teachings of Pongracz and Benton et al. regarding the production of ex vivo patient-derived 3D cultures or microtumors, the instantly claimed invention would have been a matter of routine optimization and judicious selection to one of ordinary skill.
It is also noted that "A person of ordinary skill in the art is also a person of ordinary creativity, not an automaton."KSR, 550 U.S. at 421, 82 USPQ2d at 1397. "[I]n many cases a person of ordinary skill will be able to fit the teachings of multiple patents together like pieces of a puzzle."Id. at 420, 82 USPQ2d at 1397. Office personnel may also take into account "the inferences and creative steps that a person of ordinary skill in the art would employ."Id. at 418, 82 USPQ2d at 1396 (see MPEP 2141.II.C).
Benton is herein relied upon to teach generally the generation methods and the level of skill in the art regarding 3D tumor models. It is evident that one having ordinary skill would have been motivated to optimize the 3D microtissues of Pongracz, according to teachings in the art such as those of Benton, Jovanovich, and Macleod. One having skill and knowledge in the art would apply and/or optimize the teachings in Benton for generating useful 3D microtissues structures for drug testing. It would have been obviously beneficial to use the patient-derived microtissues (e.g. PMTs) of Pongracz because then the data could be used for optimizing drug treatments (e.g. personalized medicine). Such means for generating PMTs and performing drug testing was thus known in the art prior to the effective filing date of the instant invention.
Finally, the newly recited limitations involving the specifics of the tissue disruption, using sonication, and the maturating of the tissues in a dedicated automated culture device, have also been addressed in the newly recited teachings of Jovanovich.
Thus, claims 1 and 3-10 are obvious over the cited art for the reasons set forth above.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 1 and 3-10 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 6-8, 10-19, and 22 of copending Application No. 18726740 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because the claimed subject matter of the conflicting application anticipate or make obvious each and every of the features of the instant claims.
The claims of the reference application are drawn to a method for determining the effectivity of at least one drug or drug combination for the treatment of a patient, the method comprising at least the following steps, as recited in claim 1:
providing at least one culture of a 3D microtissue comprising a microtumor based on dissociated cells of a tissue sample derived from a patient;
providing at least one drug or a combination of drugs or a panel of drugs to be tested;
contacting the at least one 3D microtissue culture with the drug or combination of drugs or panel of drugs identified to have a longest t½ time period(s);
incubating said at least one 3D microtissue culture with the drug or combination of drugs or panel of drugs with the longest t½ time period;
determining an effect of said drug or combination of drugs or panel of drugs thereof on at least one physiological parameter of the at least one 3D microtissue culture; and
selecting at least one of the drug or combination of drugs or panel of drugs… based on the determined effect as specific to the patient.
Claim 7 of the reference application recites that the incubation time is between 7 to 28 days, thus fully encompassing the claimed range of 7-14 days.
Claim 13 of the reference application recites that the tissue sample is sonicated with ultrasound.
Claim 22 recites that the method is performed via a testing system, wherein the testing system comprises a unit for culturing an array of the 3D microtissues based on dissociated cells of a tissue sample derived from the patient. See also ¶ [0084] of the reference specification which defines an array of separated 3D microtissue cultures. This testing system amounts to a profiling unit, which can culture the array of microtissues and perform drug testing.
Further, the specification of the ‘740 application, referenced herein to determine the full breadth and scope of the claimed element “3D microtissues”, describes that the generation of the 3D microtissues comprises a maturation time of about 6 hours to 7 days, thus fully encompassing the claimed time of 2-5 days. MPEP §804.II.B.1. establishes that "The Patent and Trademark Office (‘PTO’) determines the scope of the claims in patent applications not solely on the basis of the claim language, but upon giving claims their broadest reasonable construction ‘in light of the specification as it would be interpreted by one of ordinary skill in the art.’ " Phillips v. AWH Corp., 415 F.3d 1303, 1316, 75 USPQ2d 1321, 1329 (Fed. Cir. 2005) (en banc) (quoting In re Am. Acad. of Sci. Tech. Ctr., 367 F.3d 1359, 1364, 70 USPQ2d 1827, 1830 (Fed. Cir. 2004);” and also describes that “the portion of the specification of the reference that describes subject matter that falls within the scope of a reference claim may be relied upon to properly construe the scope of that claim. In particular, when ascertaining the scope of the reference’s claim(s) to a compound, the examiner should consider the reference’s specification, including all of the compound’s uses that are disclosed. See Sun Pharm. Indus., 611 F.3d at 1386-88, 95 USPQ2d at 1801-02.” Further, MPEP §804.II.B.1. also states that “If the reference patent discloses several species within the scope of the reference genus claim, that portion of the disclosure should be analyzed to properly construe the reference patent claim and determine whether it anticipates or renders obvious the claim in the application being examined”.
Therefore, the instantly claimed method, as recited in claim 1, is found prima facie obvious over, if not anticipated by, the subject matter of the claims of the ‘740 application. The conflicting claims of the reference application share overlapping subject matter with that of the instant application. The instant claims are comprising type claims and thus do not exclude the additional subject matter recited in the reference application claims such as “identifying a t½ period for each of said drug or combination of drugs or panel of drugs of drugs”.
Further, claim 7 recites that the treatment is for at least 7 days and up to 28 days, therefore 7-14 days would be clearly anticipated by these claims. Regarding the generation of the microtumor, the maturation time of 2-5 days, as recited in the amended claim 1, is well within the times given of the preferred embodiments in the reference application. In order to produce and use the microtissue cultures of the reference application claims, one would turn to the specification for determining the metes and bounds of the incubating step, such that an optimal time of culturing can be found. This amounts to optimization of routine steps in the art.
Claim 12 of the ‘740 application recites that “the tissue sample is derived by physically dissecting said tissue sample into smaller pieces comprising cells, by treating said tissue sample with a solution comprising at least one enzyme capable of dissociating cells in said tissue sample, wherein the enzyme is selected from a protease, a collagenase, trypsin, elastase, hyaluronidase, papain, chymotrypsin, deoxyribonuclease I, and neutral protease. Repeating any one or more of the dissociating steps to obtain fully separated cells would have been obvious to one of ordinary skill in the art. Mere repetition of the enzyme treatment and cell collection steps does not result in a patentable distinction from the method of the reference claims.
In regards to the instant claim 3, claim 14 of the reference application recites adding or removing stroma cells, stromal fibroblasts, endothelial cells and immune cells to the dissociated cells, wherein for each 3D microtissue a predetermined number of cells is provided.
Regarding claim 4, the claims 1 and 22 of the reference application recite providing at least one culture of a 3D microtissue comprising a microtumor based on dissociated cells of a tissue sample derived from a patient, however specific methods for generating the 3D microtissues are not explicitly recited in the reference claims. However, the specification of the ‘740 application, referenced herein to determine the full breadth and scope of the claimed element “3D microtissues”, describes that the production of the 3D microtissues of the claimed invention does not require the use of a solubilized basement membrane preparation; that the generation of said 3D microtissues comprises self-assembly of said cells comprised in said dissociated cell, that the generation of the 3D microtissues comprises a maturation time of about 6 hours to 7 days, and that the 3D microtissues as generated have a size of about 350 μm +/−100 μm ([0086]-[0087]). Thus, it is determined from the full disclosure of the application that the claimed 3D microtissues of the reference application claims encompasses those having one or more of the properties recited in the instant claim 4.
Regarding the instant claim 5, claim 1 of the reference application recites that the drugs or the drug combination or the panel of drugs are removed from the sample after exposure (“wherein an end of the longest t½ time period defines the time point for a removal R of the drug, the combination of drugs, or the panel of drugs from the culture”).
Claim 15 of the reference application recites that the measured physiological parameter, i.e. the determined effect of the drug, is selected from size determination of said 3D microtissue, quantification of internal reporter gene expression in said 3D microtissue, determination of intracellular ATP content in said 3D microtissue, and determination of pre-selected biomarkers in said 3D microtissue, as recited as alternatives in claim 6 of the instant application.
Regarding the instant claim 7, claim 11 of the reference application states: “wherein said tissue sample is selected from a sub-sample derived from at least one of a primary tissue sample, a primary tumor sample, and a metastasis sample, and wherein said tissue sample has been obtained by a method comprising one or more of core biopsy, tumor resection, liquid biopsy and/or needle aspiration, and/or wherein said tissue sample is frozen and re-thawed prior to generation of said 3D microtissues”. Thus the reference claims encompasses the same subject matter as the instant claim 7.
Claim 16 of the reference application is drawn to the same subject matter as the instant claim 8, as claim 16 recites that “a fraction of the cells is analyzed, and further comprising: providing a primary tissue, sample as the tissue sample; obtaining a subsample in addition to the tissue sample; and subjecting said subsample to at least one of molecular profiling, histological analysis, and histochemical analysis”.
Claim 18 of the reference application recites stratifying of said patient based on the patient-specific drug or combination of drugs or panel of drugs or the other drug or combination of drugs or panel of drugs, as recited in the instant claim 9.
Claim 17 of the reference application recites testing and analyzing said drug or combination of drugs or panel of drugs for adverse effects in said patient, as recited in the instant claim 10.
Therefore, the claims of the instant application are not patentably distinct from the subject matter encompassed by the claims of the reference ‘740 application. Claims 1 and 3-10 are rejected under the grounds of nonstatutory double patenting.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
Applicant’s argument filed 6/22/2026 to the Provisional Double Patenting rejection amounts to nothing more than a request that the rejections be held in abeyance. See MPEP § 804 Subsection I.B.1. which states “A complete response to a nonstatutory double patenting (NSDP) rejection is either a reply by applicant showing that the claims subject to the rejection are patentably distinct from the reference claims, or the filing of a terminal disclaimer in accordance with 37 CFR 1.321 in the pending application(s) with a reply to the Office action. Such a response is required even when the nonstatutory double patenting rejection is provisional”
The rejections of record are maintained as stated in the section above, and updated to reflect any amendments to the claims.
Conclusion
No claims are allowable.
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/A.T.M./Examiner, Art Unit 1655
/ANAND U DESAI/Supervisory Patent Examiner, Art Unit 1655
