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Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments
Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SP...
| Autores principales: | , , , , , , , , , , , , , , , , , , , |
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| Formato: | Online Artículo Texto |
| Lenguaje: | English |
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Nature Publishing Group UK
2023
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| Materias: | |
| Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10185501/ https://www.ncbi.nlm.nih.gov/pubmed/37188662 http://dx.doi.org/10.1038/s41467-023-37822-0 |
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| author | Feng, Yuzhou Yang, Tianpei Zhu, John Li, Mabel Doyle, Maria Ozcoban, Volkan Bass, Greg T. Pizzolla, Angela Cain, Lachlan Weng, Sirui Pasam, Anupama Kocovski, Nikolce Huang, Yu-Kuan Keam, Simon P. Speed, Terence P. Neeson, Paul J. Pearson, Richard B. Sandhu, Shahneen Goode, David L. Trigos, Anna S. |
| author_facet | Feng, Yuzhou Yang, Tianpei Zhu, John Li, Mabel Doyle, Maria Ozcoban, Volkan Bass, Greg T. Pizzolla, Angela Cain, Lachlan Weng, Sirui Pasam, Anupama Kocovski, Nikolce Huang, Yu-Kuan Keam, Simon P. Speed, Terence P. Neeson, Paul J. Pearson, Richard B. Sandhu, Shahneen Goode, David L. Trigos, Anna S. |
| author_sort | Feng, Yuzhou |
| collection | PubMed |
| description | Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated with spaSim. We show how SPIAT can uncover cancer immune subtypes correlated with prognosis in cancer and characterize cell dysfunction in diabetes. Our results suggest SPIAT and spaSim as useful tools for quantifying spatial patterns, identifying and validating correlates of clinical outcomes and supporting method development. |
| format | Online Article Text |
| id | pubmed-10185501 |
| institution | National Center for Biotechnology Information |
| language | English |
| publishDate | 2023 |
| publisher | Nature Publishing Group UK |
| record_format | MEDLINE/PubMed |
| spelling | pubmed-101855012023-05-17 Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments Feng, Yuzhou Yang, Tianpei Zhu, John Li, Mabel Doyle, Maria Ozcoban, Volkan Bass, Greg T. Pizzolla, Angela Cain, Lachlan Weng, Sirui Pasam, Anupama Kocovski, Nikolce Huang, Yu-Kuan Keam, Simon P. Speed, Terence P. Neeson, Paul J. Pearson, Richard B. Sandhu, Shahneen Goode, David L. Trigos, Anna S. Nat Commun Article Spatial proteomics technologies have revealed an underappreciated link between the location of cells in tissue microenvironments and the underlying biology and clinical features, but there is significant lag in the development of downstream analysis methods and benchmarking tools. Here we present SPIAT (spatial image analysis of tissues), a spatial-platform agnostic toolkit with a suite of spatial analysis algorithms, and spaSim (spatial simulator), a simulator of tissue spatial data. SPIAT includes multiple colocalization, neighborhood and spatial heterogeneity metrics to characterize the spatial patterns of cells. Ten spatial metrics of SPIAT are benchmarked using simulated data generated with spaSim. We show how SPIAT can uncover cancer immune subtypes correlated with prognosis in cancer and characterize cell dysfunction in diabetes. Our results suggest SPIAT and spaSim as useful tools for quantifying spatial patterns, identifying and validating correlates of clinical outcomes and supporting method development. Nature Publishing Group UK 2023-05-15 /pmc/articles/PMC10185501/ /pubmed/37188662 http://dx.doi.org/10.1038/s41467-023-37822-0 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
| spellingShingle | Article Feng, Yuzhou Yang, Tianpei Zhu, John Li, Mabel Doyle, Maria Ozcoban, Volkan Bass, Greg T. Pizzolla, Angela Cain, Lachlan Weng, Sirui Pasam, Anupama Kocovski, Nikolce Huang, Yu-Kuan Keam, Simon P. Speed, Terence P. Neeson, Paul J. Pearson, Richard B. Sandhu, Shahneen Goode, David L. Trigos, Anna S. Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments |
| title | Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments |
| title_full | Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments |
| title_fullStr | Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments |
| title_full_unstemmed | Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments |
| title_short | Spatial analysis with SPIAT and spaSim to characterize and simulate tissue microenvironments |
| title_sort | spatial analysis with spiat and spasim to characterize and simulate tissue microenvironments |
| topic | Article |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10185501/ https://www.ncbi.nlm.nih.gov/pubmed/37188662 http://dx.doi.org/10.1038/s41467-023-37822-0 |
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