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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...

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Autores principales: Hossan, Md Shahadat, Lin, Ethan Samuel, Riedl, Eleanor, Stram, Austin, Mehlhaff, Eric, Koeppel, Luke, Warner, Jamie, Uko, Inem, Mankowski Gettle, Lori, Lubner, Sam, McGregor, Stephanie M., Zhang, Wei, Murphy, William, Kratz, Jeremy D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9854538/
https://www.ncbi.nlm.nih.gov/pubmed/36671664
http://dx.doi.org/10.3390/bioengineering10010091
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author Hossan, Md Shahadat
Lin, Ethan Samuel
Riedl, Eleanor
Stram, Austin
Mehlhaff, Eric
Koeppel, Luke
Warner, Jamie
Uko, Inem
Mankowski Gettle, Lori
Lubner, Sam
McGregor, Stephanie M.
Zhang, Wei
Murphy, William
Kratz, Jeremy D.
author_facet Hossan, Md Shahadat
Lin, Ethan Samuel
Riedl, Eleanor
Stram, Austin
Mehlhaff, Eric
Koeppel, Luke
Warner, Jamie
Uko, Inem
Mankowski Gettle, Lori
Lubner, Sam
McGregor, Stephanie M.
Zhang, Wei
Murphy, William
Kratz, Jeremy D.
author_sort Hossan, Md Shahadat
collection PubMed
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.
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spelling pubmed-98545382023-01-21 Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer Hossan, Md Shahadat Lin, Ethan Samuel Riedl, Eleanor Stram, Austin Mehlhaff, Eric Koeppel, Luke Warner, Jamie Uko, Inem Mankowski Gettle, Lori Lubner, Sam McGregor, Stephanie M. Zhang, Wei Murphy, William Kratz, Jeremy D. Bioengineering (Basel) Article 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. MDPI 2023-01-10 /pmc/articles/PMC9854538/ /pubmed/36671664 http://dx.doi.org/10.3390/bioengineering10010091 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Hossan, Md Shahadat
Lin, Ethan Samuel
Riedl, Eleanor
Stram, Austin
Mehlhaff, Eric
Koeppel, Luke
Warner, Jamie
Uko, Inem
Mankowski Gettle, Lori
Lubner, Sam
McGregor, Stephanie M.
Zhang, Wei
Murphy, William
Kratz, Jeremy D.
Spatial Alignment of Organoids Tracking Subclonal Chemotherapy Resistance in Pancreatic and Ampullary Cancer
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 Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9854538/
https://www.ncbi.nlm.nih.gov/pubmed/36671664
http://dx.doi.org/10.3390/bioengineering10010091
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