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| Status |
Public on Nov 19, 2022 |
| Title |
Discovering Haematoma-Stimulated Circuits for Secondary Brain Injury after Intraventricular Haemorrhage by Spatial Transcriptome Analysis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Intraventricular haemorrhage (IVH) is one of the common complications after various acute brain injuries, leading to severe mortality and mobility, with great burdens on economics and society. Recently, a CLEAR III trial (NCT00784134) employing alteplase effectively cleared intraventricular haematoma but did not demonstrate adequate neuro behavioural benefits for patients. Therefore, the present study sought to investigate the pathophysiology of how these haematoma stimulations in ventricles cause neurological dysfunction. An autologous blood stereotactic injection model was employed to establish and mimic secondary IVH in mice, followed by our innovated spatial transcriptome sequencing-based bioinformatic algorithm to investigate the 3D spatial brain regions affected by the primary stimulation of haematoma in the ipsilateral ventricle after IVH, as well as related cell-cell communication strength and pathway analysis. These data illustrate that the three main 3D global pseudospace-time trajectory bundles represent the main neural circuits from the lateral ventricle to the hippocampus and primary cortex induced by experimental intraventricular haematoma stimulation. Further analysis indicated a rapid response in the primary cortex, as well as a direct and integrated effect on the hippocampus after IVH. To the best of our knowledge, this is the first study to interrogate secondary brain injury after IVH by using spatial transcriptome sequencing and bioinformatics analysis. These data could provide more helpful information on the pathophysiological mechanism of IVH in patients after acute brain injury, as well as for the bioinformatics analysis strategies for similar studies in the future.
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| Overall design |
We collected wild-type C57/BL6 mouse brains, which were classified into the no-surgery group (control), the needle-puncture group without blood injection (sham), and the needle-puncture group with blood injection at 1st, 3rd and 7th day. Then, these brains were frozen on dry ice in OCT.Frozen brains were then sectioned coronally at 10 μm on a cryostat and mounted on 10x Genomics Visium spatial transcriptome slides. The tissue locations of the library patches started from the emergence of the lateral ventricle with 20 μm intervals and a 10 μm margin of error.
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| Contributor(s) |
Zhang L, Badai J, Wang G, Ru X, Song W, You Y, He J, Huang S, Feng H, Chen R, Zhao Y, Chen Y |
| Citation(s) |
36825001 |
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| Submission date |
Sep 28, 2022 |
| Last update date |
Mar 15, 2023 |
| Contact name |
Jiayidaer Badai |
| E-mail(s) |
2019323040006@stu.scu.edu.cn
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| Organization name |
Sichuan University
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| Street address |
No. 24, South Section 1, First Ring Road, Wuhou District
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| City |
Chengdu |
| ZIP/Postal code |
610065 |
| Country |
China |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (19)
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| Relations |
| BioProject |
PRJNA885047 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE214349_RAW.tar |
7.8 Gb |
(http)(custom) |
TAR (of TAR) |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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