PT  - JOURNAL ARTICLE
AU  - Mehwish Anwer
AU  - Jeffrey LeDue
AU  - Zefang Wang
AU  - Sarah Wang
AU  - Wai Hang Cheng
AU  - Mariia Burdyniuk
AU  - Honor Cheung
AU  - Jianjia Fan
AU  - Carlos Barron
AU  - Peter A Cripton
AU  - Mark S Cembrowski
AU  - Fabio Rossi
AU  - Timothy H Murphy
AU  - Cheryl L Wellington
TI  - LEVERAGING THE POWER OF 3D BRAIN-WIDE IMAGING AND MAPPING TOOLS FOR BRAIN INJURY RESEARCH IN MURINE MODELS
AID  - 10.1101/2023.04.27.537761
DP  - 2023 Jan 01
TA  - bioRxiv
PG  - 2023.04.27.537761
4099  - http://biorxiv.org/content/early/2023/04/28/2023.04.27.537761.short
4100  - http://biorxiv.org/content/early/2023/04/28/2023.04.27.537761.full
AB  - Despite the fundamental importance of understanding impaired brain activity exhibited in post-traumatic epilepsy and other neurological impairments associated with traumatic brain injury (TBI), knowledge of how brain injury affects neuronal activity remains remarkably incomplete. We describe a whole-brain imaging and analysis approach to identify alterations in neuronal activity after TBI as a complementary method to conventional two-dimensional (2D) histological approaches. Here we report an easy-to-follow experimental pipeline to quantify changes in the whole mouse brain using tissue clearing, light sheet microscopy (LSM) and an optimised open-access atlas registration workflow. We validated the outcome of the pipeline using high throughput image analysis software and a secondary atlas registration method. Using the CHIMERA (Closed-Head Impact Model of Engineered Rotational Acceleration) TBI model, TRAP2 mice were subjected to repeated mild TBI or sham treatment followed by tamoxifen injection to lock c-Fos activity after TBI. Brains were SHIELD fixed and passively cleared for imaging of c-Fos+ cells throughout the rostro-caudal axis of the brain using a light sheet microscope equipped with a specialized whole-brain imaging chamber. Volumetric images were stitched and 3D rendered using Arivis Vision4D image analysis software. For quantitative analysis, 2D image stacks were exported to segment c-Fos+ cells and register them to the Allen Mouse Brain Atlas using the BrainQuant3D python package. As a result, c-Fos+ cell counts were estimated throughout the brain and heatmaps were generated. We identified a brain-wide reduction in c-Fos cell density in the TBI group compared to sham controls, indicative of TBI-induced changes in whole brain neuronal activity. Further studies using multi-dimensional imaging coupled with analysis tools will deepen our understanding of post-TBI brain-wide dynamics.Competing Interest StatementThe authors have declared no competing interest.