A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens
Abstract Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. We propose a quantitative framework that catalogs significant, normalized, colocalizations between pairs of cell subp...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-02-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-024-55129-6 |
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| author | Gina Bouchard Weiruo Zhang Ilayda Ilerten Irene Li Asmita Bhattacharya Yuanyuan Li Winston Trope Joseph B. Shrager Calvin Kuo Michael G. Ozawa Amato J. Giaccia Lu Tian Sylvia K. Plevritis |
| author_facet | Gina Bouchard Weiruo Zhang Ilayda Ilerten Irene Li Asmita Bhattacharya Yuanyuan Li Winston Trope Joseph B. Shrager Calvin Kuo Michael G. Ozawa Amato J. Giaccia Lu Tian Sylvia K. Plevritis |
| author_sort | Gina Bouchard |
| collection | DOAJ |
| description | Abstract Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. We propose a quantitative framework that catalogs significant, normalized, colocalizations between pairs of cell subpopulations, enabling comparisons among a variety of biological samples. We perform cell-pair colocalization analysis on multiplexed immunofluorescence images of assembloids constructed with lung adenocarcinoma (LUAD) organoids and cancer-associated fibroblasts derived from human tumors. Our data show that assembloids recapitulate human LUAD tumor-stroma spatial organization, justifying their use as a tool for investigating the spatial biology of human disease. Intriguingly, drug-perturbation studies identify drug-induced spatial rearrangements that also appear in treatment-naïve human tumor samples, suggesting potential directions for characterizing spatial (re)-organization related to drug resistance. Moreover, our work provides an opportunity to quantify spatial data across different samples, with the common goal of building catalogs of spatial features associated with disease processes and drug response. |
| format | Article |
| id | doaj-art-cfff26dbebd14cb4aa44862b9ef5a337 |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-cfff26dbebd14cb4aa44862b9ef5a3372025-02-09T12:46:06ZengNature PortfolioNature Communications2041-17232025-02-0116111710.1038/s41467-024-55129-6A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimensGina Bouchard0Weiruo Zhang1Ilayda Ilerten2Irene Li3Asmita Bhattacharya4Yuanyuan Li5Winston Trope6Joseph B. Shrager7Calvin Kuo8Michael G. Ozawa9Amato J. Giaccia10Lu Tian11Sylvia K. Plevritis12Department of Biomedical Data Science, Stanford UniversityDepartment of Biomedical Data Science, Stanford UniversityDepartment of Biomedical Data Science, Stanford UniversityDepartment of Biomedical Data Science, Stanford UniversityDivision of Hematology, Department of Medicine, Stanford UniversityDepartment of Biomedical Data Science, Stanford UniversityDepartment of Cardiothoracic Surgery, Stanford UniversityDepartment of Cardiothoracic Surgery, Stanford UniversityDivision of Hematology, Department of Medicine, Stanford UniversityDepartment of Pathology, Stanford UniversityDepartment of Radiation Oncology, Stanford UniversityDepartment of Biomedical Data Science, Stanford UniversityDepartment of Biomedical Data Science, Stanford UniversityAbstract Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. We propose a quantitative framework that catalogs significant, normalized, colocalizations between pairs of cell subpopulations, enabling comparisons among a variety of biological samples. We perform cell-pair colocalization analysis on multiplexed immunofluorescence images of assembloids constructed with lung adenocarcinoma (LUAD) organoids and cancer-associated fibroblasts derived from human tumors. Our data show that assembloids recapitulate human LUAD tumor-stroma spatial organization, justifying their use as a tool for investigating the spatial biology of human disease. Intriguingly, drug-perturbation studies identify drug-induced spatial rearrangements that also appear in treatment-naïve human tumor samples, suggesting potential directions for characterizing spatial (re)-organization related to drug resistance. Moreover, our work provides an opportunity to quantify spatial data across different samples, with the common goal of building catalogs of spatial features associated with disease processes and drug response.https://doi.org/10.1038/s41467-024-55129-6 |
| spellingShingle | Gina Bouchard Weiruo Zhang Ilayda Ilerten Irene Li Asmita Bhattacharya Yuanyuan Li Winston Trope Joseph B. Shrager Calvin Kuo Michael G. Ozawa Amato J. Giaccia Lu Tian Sylvia K. Plevritis A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens Nature Communications |
| title | A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens |
| title_full | A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens |
| title_fullStr | A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens |
| title_full_unstemmed | A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens |
| title_short | A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens |
| title_sort | quantitative spatial cell cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens |
| url | https://doi.org/10.1038/s41467-024-55129-6 |
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