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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 February 12, 2026 has been entered.
Status of the Claims
The office action is in response to the remarks filed on December 15, 2025 and claims filed June 26, 2025 for the application filed March 19, 2024 which claims priority to a provisional application filed on September 27, 2017. Claims 25-43 are currently pending and have been examined.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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 25-36 and 39-43 are rejected under 35 U.S.C. 103 as being unpatentable over Pauli et al. (Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine) in view of Chen et al. (A recellularized human colon model identifies cancer driver genes).
Regarding claims 25 and 30, Pauli discloses a method of treatment for a patient and a clinical trial system (Abstract, platform thereby promotes the discovery of novel therapeutic approaches that can be assessed in clinical trials and provides personalized therapeutic options for individual patients.) comprising:
generating a patient specific tumor model comprising an organoid (Abstract, patient-derived tumor organoids. Page 4646, second column, last paragraph, Patient-Derived Tumor Organoids, tumor tissue biopsies, 145 specimens have been collected, representing 18 different tumor types derived from patients.);
wherein the organoid is prepared by obtaining a biopsy of tissue from a patient’s tumor (Abstract, patient-derived tumor organoids. Page 4646, second column, last paragraph, Patient-Derived Tumor Organoids, tumor tissue biopsies, 145 specimens have been collected, representing 18 different tumor types derived from patients.);
digesting cells from the biopsied tissue (Page 474, Enzymatic digestion was done.); and
seeding the cells in a Matrigel culture medium to generate the organoid (Page 474, column 2, 2nd paragraph, Up to ten 50- to 80-μL drops of Matrigel/cell suspension were distributed into a 6-well cell suspension culture plate. Page 464, second column, last paragraph, derived from patients with metastatic solid tumors of epithelial and mesenchymal origin. Also see page 475, right column, 2nd paragraph, we simultaneously seeded patient B in the presence and absence of Matrigel.),
wherein the organoid comprises Page 4646, second column, last paragraph, derived from patients with metastatic solid tumors of epithelial and mesenchymal origin.);
testing one or more drugs on the patient specific tumor model wherein the model is generated and the one or more drugs are tested within 3 days of acquiring the patient biopsy (Abstract, high throughput drug screens on patient-derived tumor organoids. Pages 473-474, spanning paragraph, Time is also a critical component for the utility of our functional pipeline to inform and succeed in precision oncology. If sufficient tumor material is available from surgical excisions, blood, ascites, or pleural effusions, these data demonstrate that single-agent and combination drug testing can be completed within one to two weeks of biopsy. Page 475 column 2, 2nd paragraph, Cell viability was measured at 4 to 6 days following the drug treatment depending on the drugs of interest. Page 476 column 1, 1st paragraph, Assay times were in general 96 hours with an extension to 144 hours. If drug testing can be completed in one week/seven days and assay times for drug testing take a minimum of 96 hours/4 days, drugs can be tested on organoids within 3 days of patient biopsy. Furthermore, since reducing the time from biopsy to drug testing completion is a critical issue, one of ordinary skill in art would have the reasonable expectation of successfully testing drugs on a generated organoid within 3 days of obtaining the biopsy using routine optimization to minimize the time from biopsy to drug testing . Therefore, it would have been obvious to one of ordinary skill in the art of organoids at the time of the filing to arrive at the invention of generating an organoid and testing a drug within 3 days of acquiring the patient biopsy through routine optimization.); and
treating a patient based on the results of the patient specific tumor model tests (Abstract, This platform thereby promotes the discovery of novel therapeutic approaches that can be assessed in clinical trials and provides personalized therapeutic options for individual patients.).
Pauli does not explicitly disclose that the organoid comprises tumor immune and endothelial cells.
Chen teaches that it was old and well known in the art of cancer research at the time of the filing that organoids comprise tumor immune, endothelial and mesenchymal cells (Chen, abstract, organoid model for studying cancer biology. Pages 2-3, spanning paragraph, epithelial cells, endothelial cells and myofibroblasts. Page 9, last paragraph, incorporating engineering of vascular networks, the immune system and organ-specific microbes.) to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases (Chen, pages 2-3 spanning paragraph and page 9 last paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art of cancer research at the time of the filing to modify the organoid of Pauli to include tumor immune, endothelial and mesenchymal cells, as taught by Chen, in order to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases.
Regarding claims 26 and 31, Pauli further discloses wherein the patient's tumor is a colorectal cancer tumor (Page 466 and 468, spanning paragraph, Tumor organoids, derived from biopsies and surgical specimens of four patients with cancer, patient’s B and D had colorectal cancer.).
Regarding claims 27 and 32, Pauli further discloses entering patient specific information into a computational model (Page 475, column 1, 4th paragraph, Computational Analysis, We applied CLONET (32) to study WES tumor and matched germline data to first assess tumor ploidy and purity.); and treating a patient based on the results of the patient specific tumor model tests and the computational model (Page 464, column 1, 1st full paragraph, we describe a precision oncology approach that combines WES, patient-derived tumor organoids (PDTO), high-throughput drug screening, and patient-derived xenografts (PDX).).
Regarding claims 28 and 33, Pauli further discloses wherein the patient specific information comprises at least one of biopsy immunohistochemistry (IHC), biopsy sequencing data, biomarkers, diagnostic information, genetic mutations present in the tumor, medical images, histology images, immunohistochemistry images, patient disease progression throughout treatment, and results of patient specific tumor model tests (Page 474, column 2, last paragraph, Imaging was performed. Page 474, column 1, 1st paragraph, As previously described, 3-D cultures are characterized using our developed cytology and histology platforms. Page 473, column 1, last paragraph, drug-response profiles. Page 464, column 2, last paragraph, Fresh tumor tissue biopsies or formalin-fixed, paraffin-embedded (FFPE) material was used for sequencing. Page 466 and 468, spanning paragraph, Patients A-D diagnostic data and biomarkers. Page 464, column 2, 2nd paragraph, mutations were found only in genes with unknown clinical or biological significance.)
Regarding claims 29 and 34, Pauli further discloses wherein the tested drug comprises oxaliplatin (Page 470, Figure 5, Drug sensitivity was validated in our 3-D Matrigel system using oxaliplatin and 5-FU in comparison with what the patient was initially treated with.).
Regarding claim 35, Pauli further discloses wherein the model is generated and the one or more drugs are tested within 2-3 days of acquiring the patient biopsy (Abstract, high throughput drug screens on patient-derived tumor organoids. Pages 473-474, spanning paragraph, Time is also a critical component for the utility of our functional pipeline to inform and succeed in precision oncology. If sufficient tumor material is available from surgical excisions, blood, ascites, or pleural effusions, these data demonstrate that single-agent and combination drug testing can be completed within one to two weeks of biopsy. Page 475 column 2, 2nd paragraph, Cell viability was measured at 4 to 6 days following the drug treatment depending on the drugs of interest. Page 476 column 1, 1st paragraph, Assay times were in general 96 hours with an extension to 144 hours. If drug testing can be completed in one week/seven days from biopsy and assay times for drug testing take up to 144 hours/6 days, drugs can be tested on organoids within 1 day of patient biopsy. Furthermore, since reducing the time from biopsy to drug testing completion is a critical issue, one of ordinary skill in art would have the reasonable expectation of successfully testing drugs on a generated organoid within 2-3 days of obtaining the biopsy using routine optimization to minimize the time from biopsy to drug testing. Therefore, it would have been obvious to one of ordinary skill in the art of organoids at the time of the filing to arrive at the invention of generating an organoid and testing a drug within 2-3 days of acquiring the patient biopsy through routine optimization.).
Regarding claim 36, Pauli further discloses wherein the organoids are implemented in a 2-D monolayer culture (Page 469, column 1, 1st paragraph, culture of organoids in 2-D.).
Regarding claim 39, Pauli discloses a method of creating a patient-derived tumor organoid (Abstract and page 474), the method comprising:
obtaining a biopsy of tissue from a patient's tumor (Page 474, column 2, 1st paragraph, Fresh tissue biopsies were transported to the laboratory to establish primary tumor organoid culture.);
digesting cells from the biopsied tissue (Page 474, Enzymatic digestion was done.); and
seeding the cells in Matrigel culture medium wherein Page 474, column 2, 2nd paragraph, Up to ten 50- to 80-μL drops of Matrigel/cell suspension were distributed into a 6-well cell suspension culture plate. Page 4646, second column, last paragraph, derived from patients with metastatic solid tumors of epithelial and mesenchymal origin. Also see page 475, right column, 2nd paragraph, we simultaneously seeded patient B in the presence and absence of Matrigel.) and wherein the organoid is ready for drug sensitivity testing on the organoid within 3 days after obtaining the biopsy (Abstract, high throughput drug screens on patient-derived tumor organoids. Pages 473-474, spanning paragraph, Time is also a critical component for the utility of our functional pipeline to inform and succeed in precision oncology. If sufficient tumor material is available from surgical excisions, blood, ascites, or pleural effusions, these data demonstrate that single-agent and combination drug testing can be completed within one to two weeks of biopsy. Page 475 column 2, 2nd paragraph, Cell viability was measured at 4 to 6 days following the drug treatment depending on the drugs of interest. Page 476 column 1, 1st paragraph, Assay times were in general 96 hours with an extension to 144 hours. If drug testing can be completed in one week/seven days and assay times for drug testing take a minimum of 96 hours/4 days, drugs can be tested on organoids within 3 days of patient biopsy. Furthermore, since reducing the time from biopsy to drug testing completion is a critical issue, one of ordinary skill in art would have the reasonable expectation of successfully testing drugs on a generated organoid within 3 days of obtaining the biopsy using routine optimization to minimize the time from biopsy to drug testing . Therefore, it would have been obvious to one of ordinary skill in the art of organoids at the time of the filing to arrive at the invention of generating an organoid and testing a drug within 3 days after obtaining the biopsy through routine optimization.).
Pauli does not explicitly disclose that tumor immune and endothelial cells are included in the organoid.
Chen teaches that it was old and well known in the art of cancer research at the time of the filing to include tumor immune, endothelial and mesenchymal cells in the organoid (Chen, abstract, organoid model for studying cancer biology. Pages 2-3, spanning paragraph, epithelial cells, endothelial cells and myofibroblasts. Page 9, last paragraph, incorporating engineering of vascular networks, the immune system and organ-specific microbes.) to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases (Chen, pages 2-3 spanning paragraph and page 9 last paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art of cancer research at the time of the filing to modify the organoid of Pauli to include tumor immune, endothelial and mesenchymal cells, as taught by Chen, in order to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases.
Regarding claim 40, Pauli further discloses wherein the patient’s tumor is a colorectal cancer tumor (Page 466 and 468, spanning paragraph, Tumor organoids, derived from biopsies and surgical specimens of four patients with cancer, patient’s B and D had colorectal cancer.).
Regarding claim 41, Pauli discloses an organoid comprising Abstract, patient-derived tumor organoids. Page 474, column 2, 2nd paragraph, Up to ten 50- to 80-μL drops of Matrigel/cell suspension were distributed into a 6-well cell suspension culture plate. Page 4646, second column, last paragraph, Patient-Derived Tumor Organoids, tumor tissue biopsies, 145 specimens have been collected, representing 18 different tumor types derived from patients with metastatic solid tumors of epithelial and mesenchymal origin.) and wherein the organoid is ready for drug sensitivity testing on the organoid within 3 days after obtaining the biopsy (Abstract, high throughput drug screens on patient-derived tumor organoids. Pages 473-474, spanning paragraph, Time is also a critical component for the utility of our functional pipeline to inform and succeed in precision oncology. If sufficient tumor material is available from surgical excisions, blood, ascites, or pleural effusions, these data demonstrate that single-agent and combination drug testing can be completed within one to two weeks of biopsy. Page 475 column 2, 2nd paragraph, Cell viability was measured at 4 to 6 days following the drug treatment depending on the drugs of interest. Page 476 column 1, 1st paragraph, Assay times were in general 96 hours with an extension to 144 hours. If drug testing can be completed in one week/seven days and assay times for drug testing take a minimum of 96 hours/4 days, drugs can be tested on organoids within 3 days of patient biopsy. Furthermore, since reducing the time from biopsy to drug testing completion is a critical issue, one of ordinary skill in art would have the reasonable expectation of successfully testing drugs on a generated organoid within 3 days of obtaining the biopsy using routine optimization to minimize the time from biopsy to drug testing . Therefore, it would have been obvious to one of ordinary skill in the art of organoids at the time of the filing to arrive at the invention of generating an organoid and testing a drug within 3 days after obtaining the biopsy through routine optimization.).
Pauli does not explicitly disclose that the organoid comprises tumor immune and tumor endothelial cells.
Chen teaches that it was old and well known in the art of cancer research at the time of the filing that organoids comprise tumor immune, tumor endothelial and tumor mesenchymal cells (Chen, abstract, organoid model for studying cancer biology. Pages 2-3, spanning paragraph, epithelial cells, endothelial cells and myofibroblasts. Page 9, last paragraph, incorporating engineering of vascular networks, the immune system and organ-specific microbes.) to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases (Chen, pages 2-3 spanning paragraph and page 9 last paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art of cancer research at the time of the filing to modify the organoid of Pauli to include tumor immune, tumor endothelial and tumor mesenchymal cells, as taught by Chen, in order to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases.
Regarding claim 42, Pauli further discloses wherein the patient's tumor is a colorectal cancer tumor (Page 466 and 468, spanning paragraph, Tumor organoids, derived from biopsies and surgical specimens of four patients with cancer, patient’s B and D had colorectal cancer.).
Regarding claim 43, Pauli further discloses wherein less than 2 mm3 of tissue is digested (Page 474, column 2, 2nd paragraph, Tissue samples were washed a minimum of three times with transport media and placed in a sterile 3-cm petri dish (Falcon) for either total mechanical dissociation.).
Claims 37-38 are rejected under 35 U.S.C. 103 as being unpatentable over Pauli et al. (Personalized In Vitro and In Vivo Cancer Models to Guide Precision Medicine) in view of Chen et al. (A recellularized human colon model identifies cancer driver genes) and Drost et al. (Translational applications of adult stem cell-derived organoids).
Regarding claim 37, Pauli as modified by Chen does not appear to explicitly disclose wherein isolated patient blood or T cells are added to the organoid.
Drost teaches that it was old and well known in the art of organoids at the time of the filing to add isolated patient blood or T cells to the organoid (Drost, page 970, column 2, 2nd paragraph, Co-culturing donor-derived T cells with tumor-derived organoids might therefore be used to predict the cytotoxicity of these T cells towards patient-derived tumor organoids, potentially predicting the in vivo patient response.).
Therefore, it would have been obvious to one of ordinary skill in the art of organoids at the time of the filing to modify the organoid of Pauli as modified by Chen to add T cells, as taught by Drost, in order to predict the cytotoxicity of these T cells towards patient-derived tumor organoids, potentially predicting the in vivo patient response.
Regarding claim 38, Pauli as modified by Chen does not appear to explicitly disclose wherein a CRISPR screen with pooled guide RNAs is conducted.
Drost teaches that it was old and well known in the art of organoids at the time of the filing to conduct a CRISPR screen with pooled guide RNAs (Drost, page 971, column 2, 3rd paragraph, combinatorial CRISPR-modified human organoids will serve as a valuable, high-throughput tool to evaluate potentially oncogenic mutations observed in genome-wide sequencing efforts on large tumor panels. Page 973, column 1, 2nd paragraph, CRISPR/Cas9 gene editing was utilized to correct a CFTR mutation in small intestinal and rectal organoids from two CF patients. Crisper-Cas9 uses pooled guide RNAs. Also see Fig. 3.).
Therefore, it would have been obvious to one of ordinary skill in the art of organoids at the time of the filing to modify the system of Pauli as modified by Chen such that a CRISPR screen with pooled guide RNAs is conducted, as taught by Drost, in order to evaluate potentially oncogenic mutations observed in genome-wide sequencing efforts on large tumor panels.
Response to Arguments
Applicant's arguments filed December 15, 2025 regarding claims 25-43 being rejected under 35 U.S.C. §103 have been fully considered but they are not persuasive.
Applicant argues that the claims are directed to testing drugs on 3-D structures, organoids, not biopsied drug tissue per se, patient tumor cells per se, or 2-D cell cultures and that Pauli only discloses that high-throughput drug screening on 2-D tumor cell cultures can be completed within one to two weeks of biopsy.
In response, Pauli makes clear that the contemplated completion of single-agent and combination drug testing within one to two weeks of patient biopsy is in reference to organoid cultures. Pauli, page 473, last full paragraph “The major limitation to the successful establishment of organoid cultures was insufficient amounts of fresh tissue with viable tumor cells. Increasing the tumor tissue available for organoid production would allow for culture media optimization and lead to a greater success rate. More viable tumor tissue could be made available through the acquisition of larger samples through surgical biopsies or resections as well as the use of noninvasive approaches, including ascites fluid and pleural effusions.” and Pauli, pages 473-474, spanning paragraph, “If sufficient tumor material is available from surgical excisions, blood, ascites, or pleural effusions, these data demonstrate that single-agent and combination drug testing can be completed within one to two weeks of biopsy.”. Furthermore, Applicant’s specification, paragraph [0065] makes clear that an organoid is a cell model designed to more closely resemble the original cellular environment when compared to normal 2D cell culture and may grown from tumor stem cells that closely mimics the original tumors cellular environment may be an organoid. This includes 2D monolayer cultures as per Applicant’s claim 36.
Applicant again argues that Pauli discloses a method of generating an organoid and testing a drug on the organoid which takes weeks to months as evidenced by the supplement-1 of Pauli and therefore does not disclose generating the model and testing a drug on the model within 3 days.
In response, while the experimentation of Pauli may have taken weeks to generate the model and test a drug on the model, Applicant ignores that Pauli contemplates minimizing time between biopsy and drug test completion and discloses that the process could take as little as one week as discussed above.
Applicant’s arguments with regards to the passage of organoids of Pauli is moot as the claims do not discuss passage of organoids.
Applicant argues that Chen does not emphasis the use of immune cells and mesenchymal cells and teaches away from using Matrigel, such that the combination of Pauli and Chen is based on hindsight reasoning.
In response, Pauli is used to disclose the organoid including Matrigel and mesenchymal cells and Chen is merely used to teach that it was old and well known in the art of cancer research at the time of the filing that organoids can comprise tumor immune and endothelial cells (Chen, abstract, organoid model for studying cancer biology. Pages 2-3, spanning paragraph, epithelial cells, endothelial cells and myofibroblasts. Page 9, last paragraph, incorporating engineering of vascular networks, the immune system and organ-specific microbes.) to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases (Chen, pages 2-3 spanning paragraph and page 9 last paragraph). Therefore, it would have been obvious to one of ordinary skill in the art of cancer research at the time of the filing to modify the organoid of Pauli to include tumor immune, endothelial and mesenchymal cells, as taught by Chen, in order to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases. Put simply, the claimed combination of cells in a organoid is well-understood routine and conventional and one of ordinary skill in the art would be motivated to use these cells to create an organoid for drug testing in the method of Pauli when testing drugs for colorectal cancer in order to create an physiologically active ex vivo model of the human colon that mimics physiological conditions and to create specialized physiological microenvironments for mimicking clinical diseases.
Applicant argues that the claims system and method differ from Pauli and Chen in that they are substantially faster and better. However, Applicant’s specification provides no disclosure as to the importance of generating an organoid within 3 days or any details as to how it is accomplished other than a mere assertion that it may be done in paragraph [0090]. In paragraph [0073] of the specification, generating a organoid takes at least 3-4 days.
Applicant argues that the addition of T-cells in Drost is for a different reason than the Applicant’s invention.
In response, while predicting the cytotoxicity of these T cells may not by the purpose of the Applicant’s invention, it is still a motivation to incorporate T cells when generating an organoid and it is maintained that the combination is not based on hindsight reasoning.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure.
Walsh et al. (Drug response in organoids generated from frozen primary tumor tissues) discusses comparing drug response in organoids generated from frozen primary tumor tissues and fresh primary tumor tissues and discloses immediately processing fresh tissue into organoids, that the organoids were grown for 3 days, and immediately treating the organoids with drugs to evaluate drug response.
All claims are identical to or patentably indistinct from, or have unity of invention with claims in the application prior to the entry of the submission under 37 CFR 1.114 (that is, restriction (including a lack of unity of invention) would not be proper) and all claims could have been finally rejected on the grounds and art of record in the next Office action if they had been entered in the application prior to entry under 37 CFR 1.114. Accordingly, THIS ACTION IS MADE FINAL even though it is a first action after the filing of a request for continued examination and the submission under 37 CFR 1.114. See MPEP § 706.07(b). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Devin C. Hein whose telephone number is (303)297-4305. The examiner can normally be reached 9:00 AM - 5:00 PM M-F MDT.
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/DEVIN C HEIN/Examiner, Art Unit 3686