Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer
Pancreatic and ampullary cancers remain highly morbid diseases for which accurate clinical predictions are needed for precise therapeutic predictions. Patient-derived cancer organoids have been widely adopted; however, prior work has focused on well-level therapeutic sensitivity. To characterize ind...
| Main Authors: | , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Bioengineering |
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| Online Access: | https://www.mdpi.com/2306-5354/10/1/91 |
| _version_ | 1797445971084312576 |
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| author | Md Shahadat Hossan Ethan Samuel Lin Eleanor Riedl Austin Stram Eric Mehlhaff Luke Koeppel Jamie Warner Inem Uko Lori Mankowski Gettle Sam Lubner Stephanie M. McGregor Wei Zhang William Murphy Jeremy D. Kratz |
| author_facet | Md Shahadat Hossan Ethan Samuel Lin Eleanor Riedl Austin Stram Eric Mehlhaff Luke Koeppel Jamie Warner Inem Uko Lori Mankowski Gettle Sam Lubner Stephanie M. McGregor Wei Zhang William Murphy Jeremy D. Kratz |
| author_sort | Md Shahadat Hossan |
| collection | DOAJ |
| description | Pancreatic and ampullary cancers remain highly morbid diseases for which accurate clinical predictions are needed for precise therapeutic predictions. Patient-derived cancer organoids have been widely adopted; however, prior work has focused on well-level therapeutic sensitivity. To characterize individual oligoclonal units of therapeutic response, we introduce a low-volume screening assay, including an automated alignment algorithm. The oligoclonal growth response was compared against validated markers of response, including well-level viability and markers of single-cell viability. Line-specific sensitivities were compared with clinical outcomes. Automated alignment algorithms were generated to match organoids across time using coordinates across a single projection of Z-stacked images. After screening for baseline size (50 μm) and circularity (>0.4), the match efficiency was found to be optimized by accepting the diffusion thresholded with the root mean standard deviation of 75 μm. Validated well-level viability showed a limited correlation with the mean organoid size (R = 0.408), and a normalized growth assayed by normalized changes in area (R = 0.474) and area (R = 0.486). Subclonal populations were defined by both residual growth and the failure to induce apoptosis and necrosis. For a culture with clinical resistance to gemcitabine and nab-paclitaxel, while a therapeutic challenge induced a robust effect in inhibiting cell growth (GΔ = 1.53), residual oligoclonal populations were able to limit the effect on the ability to induce apoptosis (GΔ = 0.52) and cell necrosis (GΔ = 1.07). Bioengineered approaches are feasible to capture oligoclonal heterogeneity in organotypic cultures, integrating ongoing efforts for utilizing organoids across cancer types as integral biomarkers and in novel therapeutic development. |
| first_indexed | 2024-03-09T13:33:29Z |
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| institution | Directory Open Access Journal |
| issn | 2306-5354 |
| language | English |
| last_indexed | 2024-03-09T13:33:29Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Bioengineering |
| spelling | doaj.art-b5633220274c4edbb458f908775e1f792023-11-30T21:15:30ZengMDPI AGBioengineering2306-53542023-01-011019110.3390/bioengineering10010091Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary CancerMd Shahadat Hossan0Ethan Samuel Lin1Eleanor Riedl2Austin Stram3Eric Mehlhaff4Luke Koeppel5Jamie Warner6Inem Uko7Lori Mankowski Gettle8Sam Lubner9Stephanie M. McGregor10Wei Zhang11William Murphy12Jeremy D. Kratz13Division of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USADepartment of Radiology, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53792, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USAUniversity of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, 600 Highland Ave., Madison, WI 53705, USAUniversity of Wisconsin Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, 600 Highland Ave., Madison, WI 53705, USADepartment of Biomedical Engineering, University of Wisconsin, Madison, WI 53706, USADivision of Hematology, Medical Oncology and Palliative Care, Department of Medicine, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53705, USAPancreatic and ampullary cancers remain highly morbid diseases for which accurate clinical predictions are needed for precise therapeutic predictions. Patient-derived cancer organoids have been widely adopted; however, prior work has focused on well-level therapeutic sensitivity. To characterize individual oligoclonal units of therapeutic response, we introduce a low-volume screening assay, including an automated alignment algorithm. The oligoclonal growth response was compared against validated markers of response, including well-level viability and markers of single-cell viability. Line-specific sensitivities were compared with clinical outcomes. Automated alignment algorithms were generated to match organoids across time using coordinates across a single projection of Z-stacked images. After screening for baseline size (50 μm) and circularity (>0.4), the match efficiency was found to be optimized by accepting the diffusion thresholded with the root mean standard deviation of 75 μm. Validated well-level viability showed a limited correlation with the mean organoid size (R = 0.408), and a normalized growth assayed by normalized changes in area (R = 0.474) and area (R = 0.486). Subclonal populations were defined by both residual growth and the failure to induce apoptosis and necrosis. For a culture with clinical resistance to gemcitabine and nab-paclitaxel, while a therapeutic challenge induced a robust effect in inhibiting cell growth (GΔ = 1.53), residual oligoclonal populations were able to limit the effect on the ability to induce apoptosis (GΔ = 0.52) and cell necrosis (GΔ = 1.07). Bioengineered approaches are feasible to capture oligoclonal heterogeneity in organotypic cultures, integrating ongoing efforts for utilizing organoids across cancer types as integral biomarkers and in novel therapeutic development.https://www.mdpi.com/2306-5354/10/1/91organoidstherapeutic responsecancer heterogeneitypancreatic cancerampullary cancerapoptosis |
| spellingShingle | Md Shahadat Hossan Ethan Samuel Lin Eleanor Riedl Austin Stram Eric Mehlhaff Luke Koeppel Jamie Warner Inem Uko Lori Mankowski Gettle Sam Lubner Stephanie M. McGregor Wei Zhang William Murphy Jeremy D. Kratz Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer Bioengineering organoids therapeutic response cancer heterogeneity pancreatic cancer ampullary cancer apoptosis |
| title | Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer |
| title_full | Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer |
| title_fullStr | Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer |
| title_full_unstemmed | Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer |
| title_short | Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer |
| title_sort | spatial alignment of organoids tracking subclonal chemotherapy resistance in pancreatic and ampullary cancer |
| topic | organoids therapeutic response cancer heterogeneity pancreatic cancer ampullary cancer apoptosis |
| url | https://www.mdpi.com/2306-5354/10/1/91 |
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