RT Journal Article
SR Electronic
T1 LEVERAGING THE POWER OF 3D BRAIN-WIDE IMAGING AND MAPPING TOOLS FOR BRAIN INJURY RESEARCH IN MURINE MODELS
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2023.04.27.537761
DO 10.1101/2023.04.27.537761
A1 Mehwish Anwer
A1 Jeffrey LeDue
A1 Zefang Wang
A1 Sarah Wang
A1 Wai Hang Cheng
A1 Mariia Burdyniuk
A1 Honor Cheung
A1 Jianjia Fan
A1 Carlos Barron
A1 Peter A Cripton
A1 Mark S Cembrowski
A1 Fabio Rossi
A1 Timothy H Murphy
A1 Cheryl L Wellington
YR 2023
UL http://biorxiv.org/content/early/2023/04/28/2023.04.27.537761.abstract
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.