Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity
Abstract Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. Yet, this potential is presently limited by technical and financial challenges of spatial omics methods and 3D cultures. To address this, we combine d...
Saved in:
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
|
| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-024-83989-x |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1832571721658400768 |
|---|---|
| author | Antony Cougnoux Loay Mahmoud Per A. Johnsson Alper Eroglu Louise Gsell Jakob Rosenbauer Rickard Sandberg Jean Hausser |
| author_facet | Antony Cougnoux Loay Mahmoud Per A. Johnsson Alper Eroglu Louise Gsell Jakob Rosenbauer Rickard Sandberg Jean Hausser |
| author_sort | Antony Cougnoux |
| collection | DOAJ |
| description | Abstract Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. Yet, this potential is presently limited by technical and financial challenges of spatial omics methods and 3D cultures. To address this, we combine dye diffusion, the Smart-seq3xpress protocol for deep single-cell gene expression profiling, and dedicated probabilistic inference methods into diffusion Smart-seq3 (Smart-seq3D), to reveal the transcriptome of single cells along with their position along the core-periphery axis of spheroids. Applying Smart-seq3D to triple-negative breast tumor spheroids identifies thousands of spatial genes and reveals continuous, ungated spatial gene expression. Spatial gene and pathway expression patterns suggest biologies specific to spheroid regions, which we validate by immunostainings and pharmacological interventions. We use the Smart-seq3D data to test evolutionary principles of spatial tumor heterogeneity. Finally, we characterize aspects of tumor heterogeneity captured by 3D spheroids that are missing from 2D cultures but found in tumors in vivo. Smart-seq3D can offer a cost-efficient approach to explore how cells adapt their transcriptome to different micro-environments, reveal spatial determinants of drug resistance and could serve to characterize spatial interactions between cancer and stromal/immune cells in 3D co-cultures. |
| format | Article |
| id | doaj-art-5457c3f183824c55bb400086997a1a9a |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-5457c3f183824c55bb400086997a1a9a2025-02-02T12:20:29ZengNature PortfolioScientific Reports2045-23222025-01-0115111610.1038/s41598-024-83989-xDiffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneityAntony Cougnoux0Loay Mahmoud1Per A. Johnsson2Alper Eroglu3Louise Gsell4Jakob Rosenbauer5Rickard Sandberg6Jean Hausser7Department of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetDepartment of Cell and Molecular Biology, Karolinska InstitutetAbstract Combining 3D cultures such as tumor spheroids and organoids with spatial omics holds great potential for tissue biology and cancer research. Yet, this potential is presently limited by technical and financial challenges of spatial omics methods and 3D cultures. To address this, we combine dye diffusion, the Smart-seq3xpress protocol for deep single-cell gene expression profiling, and dedicated probabilistic inference methods into diffusion Smart-seq3 (Smart-seq3D), to reveal the transcriptome of single cells along with their position along the core-periphery axis of spheroids. Applying Smart-seq3D to triple-negative breast tumor spheroids identifies thousands of spatial genes and reveals continuous, ungated spatial gene expression. Spatial gene and pathway expression patterns suggest biologies specific to spheroid regions, which we validate by immunostainings and pharmacological interventions. We use the Smart-seq3D data to test evolutionary principles of spatial tumor heterogeneity. Finally, we characterize aspects of tumor heterogeneity captured by 3D spheroids that are missing from 2D cultures but found in tumors in vivo. Smart-seq3D can offer a cost-efficient approach to explore how cells adapt their transcriptome to different micro-environments, reveal spatial determinants of drug resistance and could serve to characterize spatial interactions between cancer and stromal/immune cells in 3D co-cultures.https://doi.org/10.1038/s41598-024-83989-x |
| spellingShingle | Antony Cougnoux Loay Mahmoud Per A. Johnsson Alper Eroglu Louise Gsell Jakob Rosenbauer Rickard Sandberg Jean Hausser Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity Scientific Reports |
| title | Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity |
| title_full | Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity |
| title_fullStr | Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity |
| title_full_unstemmed | Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity |
| title_short | Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity |
| title_sort | diffusion smart seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity |
| url | https://doi.org/10.1038/s41598-024-83989-x |
| work_keys_str_mv | AT antonycougnoux diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT loaymahmoud diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT perajohnsson diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT alpereroglu diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT louisegsell diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT jakobrosenbauer diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT rickardsandberg diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity AT jeanhausser diffusionsmartseq3ofbreastcancerspheroidstoexplorespatialtumorbiologyandtestevolutionaryprinciplesoftumorheterogeneity |