3D Modeling of the Lateral Ventricles and Histological Characterization of Periventricular Tissue in Humans and Mouse

Abstract

The ventricular system carries and circulates cerebral spinal fluid (CSF) and facilitates clearance of solutes and toxins from the brain. The functional units of the ventricles are ciliated epithelial cells termed ependymal cells, which line the ventricles and through ciliary action are capable of generating laminar flow of CSF at the ventricle surface. This monolayer of ependymal cells also provides barrier and filtration functions that promote exchange between brain interstitial fluids (ISF) and circulating CSF. Biochemical changes in the brain are thereby reflected in the composition of the CSF and destruction of the ependyma can disrupt the delicate balance of CSF and ISF exchange. In humans there is a strong correlation between lateral ventricle expansion and aging. Age-associated ventriculomegaly can occur even in the absence of dementia or obstruction of CSF flow. The exact cause and progression of ventriculomegaly is often unknown; however, enlarged ventricles can show regional and, often, extensive loss of ependymal cell coverage with ventricle surface astrogliosis and associated periventricular edema replacing the functional ependymal cell monolayer. Using MRI scans together with postmortem human brain tissue, we describe how to prepare, image and compile 3D renderings of lateral ventricle volumes, calculate lateral ventricle volumes, and characterize periventricular tissue through immunohistochemical analysis of en face lateral ventricle wall tissue preparations. Corresponding analyses of mouse brain tissue are also presented supporting the use of mouse models as a means to evaluate changes to the lateral ventricles and periventricular tissue found in human aging and disease. Together, these protocols allow investigations into the cause and effect of ventriculomegaly and highlight techniques to study ventricular system health and its important barrier and filtration functions within the brain. Video LinkThe video component of this article can be found at

Characterization of the ventricular-subventricular stem cell niche during human brain development

“…3A,B). Semi-automated segmentation using ITK-SNAP (Shook et al, 2014;Snippert et al, 2010;Todd et al, 2017;Yushkevich et al, 2006) followed by 3D reconstruction of the lateral ventricles and whole brain using 3D Slicer (Acabchuk et al, 2015;Shook et al, 2014) revealed that the average total brain volume increases rapidly from 15 gw to 1 year. Regression analysis predicts that from 19 gw to birth, the brain grows at a nearly linear rate of 1.2×10 6 mm 3 /year (23 cm 3 /week) and from birth to 1 year at 5.5×10 5 mm 3 /year (11 cm 3 /week) (see also Kinoshita et al, 2001).…”

“…Mouse brain tissue sections were stained with β-catenin overnight (rabbit polyclonal anti-β-catenin, 1:100; Cell Signaling Technology, #9562), secondary antibody for 1 h (donkey anti-rabbit 546, 1:500; Invitrogen, #A10040), nuclear stain DAPI (300 mM; Molecular Probes, #D-1306) for 10 min and imaged on a Zeiss Axio Imager M2 microscope with ApoTome (Carl Zeiss MicroImaging) with a Hamamatsu Photonics ORCA-R 2 digital camera (C10600). Alternating coronal sections were imaged, and the contours of the lateral ventricle walls and surface of the brain were traced to generate 3D reconstructions, as described (Acabchuk et al, 2015). Volume and surface area analysis were performed using StereoInvestigator and Neurolucida Explorer software (MBF Bioscience).…”

Dynamic 11C-PiB PET shows cerebrospinal fluid flow alterations in Alzheimer’s disease and multiple sclerosis

“…Both datasets: Manual lateral ventricle ROIs were generated for all subjects using the subject T1-weighted structural MRI data and the ITK-SNAP (39) (itksnap.org) snake tool, following previously described guidelines for lateral ventricle extraction (40). The lateral ventricle ROIs were then eroded by two voxels (5.2 mm) using the erode function given by FSL's 'fslmaths' utility package (version 5.0.9) (36) in order to reduce partial volume effects of the surrounding tissues.…”

Repeated mild traumatic brain injury causes focal response in lateral septum and hippocampus

“…Lateral ventricle volumes were calculated based on the tracing protocol we developed and described previously [18]. Briefly, volumes were generated from serial coronal sections of the lateral ventricles, marked by S100β + ependymal cells that line the ventricles, traced in StereoInvestigator ® (MBF Bioscience, VT, USA) and then compiled in Neurolucida Explorer ® (MBF Bioscience), generating 3D volumetric renderings.…”