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Size matters :
Size matters : the impact of nucleus size on results from spatial transcriptomics
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- Mohammadi, Elyas (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Chojnowska, Katarzyna (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Bienkowski, Michal (author)
- Med Univ Gdansk, Dept Pathomorphol, PL-80210 Gdansk, Poland.
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- Kostecka, Anna (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Koczkowska, Magdalena (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Zmijewski, Michal A. (author)
- Med Univ Gdansk, Dept Histol, PL-80210 Gdansk, Poland.
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- Jakalski, Marcin (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Ingelsson, Martin (author)
- Uppsala universitet,Geriatrik,Univ Hlth Network, Krembil Brain Inst, Toronto, ON M5G 2C4, Canada.;Univ Toronto, Dept Med, Toronto, ON M5S 1A8, Canada.;Univ Toronto, Tanz Ctr Res Neurodegenerat Dis, Toronto, ON M5S 1A8, Canada.
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- Filipowicz, Natalia (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Olszewski, Pawel (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Davies, Hanna (author)
- Uppsala universitet,Medicinsk genetik,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik,Cancerprecisionsmedicin
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- Wierzbicka, Justyna M. M. (author)
- Med Univ Gdansk, Dept Histol, PL-80210 Gdansk, Poland.
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- Hyman, Bradley T. T. (author)
- Massachusetts Gen Hosp, Dept Neurol, Boston, MA 02114 USA.;Massachusetts Alzheimers Dis Res Ctr, Charlestown, MA 02129 USA.;Harvard Med Sch, Boston, MA 02115 USA.
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- Dumanski, Jan P. (author)
- Uppsala universitet,Medicinsk genetik,Science for Life Laboratory, SciLifeLab,Medicinsk genetik och genomik,Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Piotrowski, Arkadiusz (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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- Mieczkowski, Jakub (author)
- Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland.
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Med Univ Gdansk, 3P Med Lab, PL-80210 Gdansk, Poland Med Univ Gdansk, Dept Pathomorphol, PL-80210 Gdansk, Poland. (creator_code:org_t)
- Springer Nature, 2023
- 2023
- English.
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In: Journal of Translational Medicine. - : Springer Nature. - 1479-5876. ; 21:1
- Related links:
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https://uu.diva-port... (primary) (Raw object)
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https://urn.kb.se/re...
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https://doi.org/10.1...
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Abstract
Subject headings
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- Background: Visium Spatial Gene Expression (ST) is a method combining histological spatial information with transcriptomics profiles directly from tissue sections. The use of spatial information has made it possible to discover new modes of gene expression regulations. However, in the ST experiment, the nucleus size of cells may exceed the thickness of a tissue slice. This may, in turn, negatively affect comprehensive capturing the transcriptomics profile in a single slice, especially for tissues having large differences in the size of nuclei.Methods: Here, we defined the effect of Consecutive Slices Data Integration (CSDI) on unveiling accurate spot clustering and deconvolution of spatial transcriptomic spots in human postmortem brains. By considering the histological information as reference, we assessed the improvement of unsupervised clustering and single nuclei RNA-seq and ST data integration before and after CSDI.Results: Apart from the escalated number of defined clusters representing neuronal layers, the pattern of clusters in consecutive sections was concordant only after CSDI. Besides, the assigned cell labels to spots matches the histological pattern of tissue sections after CSDI.Conclusion: CSDI can be applied to investigate consecutive sections studied with ST in the human cerebral cortex, avoiding misinterpretation of spot clustering and annotation, increasing accuracy of cell recognition as well as improvement in uncovering the layers of grey matter in the human brain.
Subject headings
- MEDICIN OCH HÄLSOVETENSKAP -- Medicinska och farmaceutiska grundvetenskaper -- Medicinsk genetik (hsv//swe)
- MEDICAL AND HEALTH SCIENCES -- Basic Medicine -- Medical Genetics (hsv//eng)
Keyword
- Spatial transcriptomics
- Cerebral cortex
- Neuronal nuclei
- Consecutive tissue sections
- Data integration
Publication and Content Type
- ref (subject category)
- art (subject category)
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- By the author/editor
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Mohammadi, Elyas
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Chojnowska, Kata ...
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Bienkowski, Mich ...
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Kostecka, Anna
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Koczkowska, Magd ...
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Zmijewski, Micha ...
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show more...
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Jakalski, Marcin
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Ingelsson, Marti ...
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Filipowicz, Nata ...
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Olszewski, Pawel
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Davies, Hanna
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Wierzbicka, Just ...
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Hyman, Bradley T ...
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Dumanski, Jan P.
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Piotrowski, Arka ...
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Mieczkowski, Jak ...
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- About the subject
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- MEDICAL AND HEALTH SCIENCES
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MEDICAL AND HEAL ...
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and Basic Medicine
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and Medical Genetics
- Articles in the publication
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Journal of Trans ...
- By the university
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Uppsala University