SM3DD with Segmented PCA: A Comprehensive Method for Interpreting 3D Spatial Transcriptomics Article Swipe
Tony Blick
,
A. Kilgallon
,
James Monkman
,
Caroline Cooper
,
Chin Wee Tan
,
Emily Killingbeck
,
Liuliu Pan
,
Youngmi Kim
,
Yan Liang
,
Andy Nam
,
Michael Leon
,
Paulo Souza‐Fonseca‐Guimaraes
,
Seigo Nagashima
,
Ana Paula Camargo Martins
,
Cleber Machado‐Souza
,
Lúcia de Noronha
,
John F. Fraser
,
Gabrielle T. Belz
,
Fernando Souza-Fonseca-Guimarães
,
Arutha Kulasinghe
·
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.04.17.649456
YOU?
·
· 2025
· Open Access
·
· DOI: https://doi.org/10.1101/2025.04.17.649456
We developed Standardised Minimum 3D Distance (SM3DD), an entirely cell segmentation/annotation-free approach to the analysis of spatial RNA datasets, using it to compare lung tissue from 16 clinically normal individuals to those of 18 SARS-CoV-2 patients who died from acute respiratory distress syndrome. RNA spatial coordinates were determined using the CosMx™ Spatial Molecular Imager (Bruker Spatial Biology, US). For each individual transcript location, we calculated the three-dimensional distances to the nearest transcript of each transcript type, standardising the distances to each transcript type. Mean SM3DDs were compared between normal and SARS-CoV-2 patients. Notably, hierarchical clustering of the directional log10(P) values organized genes by functionality, making it easier to interpret biological contexts and for FKBP11, where a decrease in distance to MZT2A was the most significant difference, suggesting a role in interferon signaling. Using a segmented principal components analysis of the entire SM3DD dataset, we identified multiple pathways, including ‘SARS-CoV-2 infection’, even though the assay did not include any SARS-CoV-2 transcripts.
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- Type
- preprint
- Language
- en
- Landing Page
- https://doi.org/10.1101/2025.04.17.649456
- https://www.biorxiv.org/content/biorxiv/early/2025/04/18/2025.04.17.649456.full.pdf
- OA Status
- green
- References
- 35
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4409640573
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- OpenAlex ID
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https://openalex.org/W4409640573Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1101/2025.04.17.649456Digital Object Identifier
- Title
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SM3DD with Segmented PCA: A Comprehensive Method for Interpreting 3D Spatial TranscriptomicsWork title
- Type
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preprintOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2025Year of publication
- Publication date
-
2025-04-18Full publication date if available
- Authors
-
Tony Blick, A. Kilgallon, James Monkman, Caroline Cooper, Chin Wee Tan, Emily Killingbeck, Liuliu Pan, Youngmi Kim, Yan Liang, Andy Nam, Michael Leon, Paulo Souza‐Fonseca‐Guimaraes, Seigo Nagashima, Ana Paula Camargo Martins, Cleber Machado‐Souza, Lúcia de Noronha, John F. Fraser, Gabrielle T. Belz, Fernando Souza-Fonseca-Guimarães, Arutha KulasingheList of authors in order
- Landing page
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https://doi.org/10.1101/2025.04.17.649456Publisher landing page
- PDF URL
-
https://www.biorxiv.org/content/biorxiv/early/2025/04/18/2025.04.17.649456.full.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
-
greenOpen access status per OpenAlex
- OA URL
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https://www.biorxiv.org/content/biorxiv/early/2025/04/18/2025.04.17.649456.full.pdfDirect OA link when available
- Concepts
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Computer science, Transcriptome, Pattern recognition (psychology), Artificial intelligence, Computational biology, Data mining, Biology, Genetics, Gene expression, GeneTop concepts (fields/topics) attached by OpenAlex
- Cited by
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0Total citation count in OpenAlex
- References (count)
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35Number of works referenced by this work
- Related works (count)
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10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W3081487801, https://openalex.org/W3129895712, https://openalex.org/W4405127265, https://openalex.org/W3119379269, https://openalex.org/W3171488579, https://openalex.org/W4388399388, https://openalex.org/W1981276685, https://openalex.org/W4407107633, https://openalex.org/W4302362633, https://openalex.org/W1980361506, https://openalex.org/W2170637386, https://openalex.org/W2079474709, https://openalex.org/W3131820551, https://openalex.org/W4388656499, https://openalex.org/W4403136210, https://openalex.org/W4388827256, https://openalex.org/W3154372950, https://openalex.org/W3176910263, https://openalex.org/W4327950606, https://openalex.org/W3039136126, https://openalex.org/W3093867667, https://openalex.org/W2046034465, https://openalex.org/W1974381392, https://openalex.org/W4379768951, https://openalex.org/W3203904369, https://openalex.org/W4313246279, https://openalex.org/W2071009656, https://openalex.org/W4230151956, https://openalex.org/W2116622733, https://openalex.org/W2136555350, https://openalex.org/W4318708235, https://openalex.org/W2883371150, https://openalex.org/W4379768381, https://openalex.org/W2106379906, https://openalex.org/W4288447807 |
| referenced_works_count | 35 |
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