Effect of Fluorinert on the Histological Properties of Formalin-Fixed Human Brain Tissue

Ultrahigh field diffusion magnetic resonance imaging uncovers intriguing microstructural changes in the adult zebrafish brain caused by Toll-like receptor 2 genomic deletion

Toll-like receptor 2 (TLR2) belongs to the TLR protein family that plays an important role in the immune and inflammation response system. While TLR2 is predominantly expressed in immune cells, its expression has also been detected in the brain, specifically in microglia and astrocytes. Recent studies indicate that genomic deletion of TLR2 can result in impaired neurobehavioural function. It is currently not clear if the genomic deletion of TLR2 leads to any alterations in the microstructural features of the brain. In the current study, we noninvasively assess microstructural changes in the brain of TLR2-deficient (tlr2-/-) zebrafish using state-of-the art magnetic resonance imaging (MRI) methods at ultrahigh magnetic field strength (17.6 T). A significant increase in cortical thickness and an overall trend towards increased brain volumes were observed in young tlr2-/- zebrafish. An elevated T2 relaxation time and significantly reduced apparent diffusion coefficient (ADC) unveil brain-wide microstructural alterations, potentially indicative of cytotoxic oedema and astrogliosis in the tlr2-/- zebrafish. Multicomponent analysis of the ADC diffusivity signal by the phasor approach shows an increase in the slow ADC component associated with restricted diffusion. Diffusion tensor imaging and diffusion kurtosis imaging analysis revealed diminished diffusivity and enhanced kurtosis in various white matter tracks in tlr2-/- compared with control zebrafish, identifying the microstructural underpinnings associated with compromised white matter integrity and axonal degeneration. Taken together, our findings demonstrate that the genomic deletion of TLR2 results in severe alterations to the microstructural features of the zebrafish brain. This study also highlights the potential of ultrahigh field diffusion MRI techniques in discerning exceptionally fine microstructural details within the small zebrafish brain, offering potential for investigating microstructural changes in zebrafish models of various brain diseases.

Micro-magnetic resonance imaging of ex vivo mouse embryos with potato starch suspension

Potato starch suspension (PSS) holds promise as a solution to issues, such as air bubbles and specimen motion, associated with micro-magnetic resonance imaging (micro-MRI) of ex vivo embryos. Here, we present a protocol for using PSS when scanning specimens with micro-MRI. We describe steps for preparing samples and potato starch with phosphate-buffered saline. We then detail steps for specimen immersion and micro-MRI scanning. This protocol will enable micro-MRI of not only embryos but also other specimens, such as insects. For complete details on the use and execution of this protocol, please refer to Tsurugizawa et al.1.

High-field ex vivo and in vivo two-dimensional nuclear magnetic resonance spectroscopy in murine brain: Resolving and exploring the molecular environment

The structural and chemical complexities within the brain pose a challenge that few noninvasive techniques can tackle with the dexterity of nuclear magnetic resonance (NMR) spectroscopy. Still, even with the advent of ultrahigh fields and of cryogenically cooled coils for in vivo research, the superposition of metabolic resonances arising from the brain remains a challenge. The present study explores the potential to tackle this milieu using a combination of two-dimensional (2D) NMR techniques, implemented on murine brains in vivo at 15.2 T and ex vivo at 14.1 T. While both experiments were affected by substantial inhomogeneous broadenings conveying distinct elongated lineshapes to the cross-peaks, the ability of increased fields to resolve off-diagonal resonances was clear. A comparison between the corresponding conventional and double quantum-filtered correlated spectroscopy traces enabled an improved assignment of in vivo resonances on the basis of more sensitive ex vivo 2D acquisitions, foremost on the basis of homonuclear cross-relaxation-driven correlations for peaks resonating downfield from water, and of heteronuclear correlations at natural abundance for the upfield protons. With the aid of such 2D correlations approximately 29 metabolites could be resolved and identified. This enhanced resolution was used to explore features related to the metabolites' diffusivities, their exposure to water, and their facility to undergo magnetization transfers to amide/amine/hydroxyl resonances. Cross-peaks from main murine brain biomolecules, including choline, creatine, γ-aminobutyric acid, N-acetyl aspartate, glutamine, and glutamate, showed enhancements in several of these various features, opening interesting vistas about metabolite compartmentalization as viewed by these 2D NMR experiments.

Tensor image registration library: Deformable registration of stand-alone histology images to whole-brain post-mortem MRI data

BACKGROUND

Accurate registration between microscopy and MRI data is necessary for validating imaging biomarkers against neuropathology, and to disentangle complex signal dependencies in microstructural MRI. Existing registration methods often rely on serial histological sampling or significant manual input, providing limited scope to work with a large number of stand-alone histology sections. Here we present a customisable pipeline to assist the registration of stand-alone histology sections to whole-brain MRI data.

METHODS

Our pipeline registers stained histology sections to whole-brain post-mortem MRI in 4 stages, with the help of two photographic intermediaries: a block face image (to undistort histology sections) and coronal brain slab photographs (to insert them into MRI space). Each registration stage is implemented as a configurable stand-alone Python script using our novel platform, Tensor Image Registration Library (TIRL), which provides flexibility for wider adaptation. We report our experience of registering 87 PLP-stained histology sections from 14 subjects and perform various experiments to assess the accuracy and robustness of each stage of the pipeline.

RESULTS

All 87 histology sections were successfully registered to MRI. Histology-to-block registration (Stage 1) achieved 0.2-0.4 mm accuracy, better than commonly used existing methods. Block-to-slice matching (Stage 2) showed great robustness in automatically identifying and inserting small tissue blocks into whole brain slices with 0.2 mm accuracy. Simulations demonstrated sub-voxel level accuracy (0.13 mm) of the slice-to-volume registration (Stage 3) algorithm, which was observed in over 200 actual brain slice registrations, compensating 3D slice deformations up to 6.5 mm. Stage 4 combined the previous stages and generated refined pixelwise aligned multi-modal histology-MRI stacks.

CONCLUSIONS

Our open-source pipeline provides robust automation tools for registering stand-alone histology sections to MRI data with sub-voxel level precision, and the underlying framework makes it readily adaptable to a diverse range of microscopy-MRI studies.

Utilization of potato starch suspension for MR-microimaging in ex vivo mouse embryos

Magnetic resonance (MR) microimaging of the mouse embryo is a promising tool to noninvasively investigate the microstructure of the brain of a developing mouse. The proton-free fluid is used for the liquid surrounding the specimen in MR microimaging, but the potential issue of image quality remains due to the air bubbles on the specimen and the retained water proton in the curvature of the embryo. Furthermore, the specimen may move during the scanning, resulting in motion artifact. Here, we developed the new concept of the ex vivo microimaging protocol with the robust method using the potato starch-containing biological polymers. Potato starch suspension with PBS significantly reduced T1 and T2 signal intensity of the suspension and strongly suppressed the motion of the embryo. Furthermore, potato starch-PBS suspension is stable for long-time scanning at room temperature. These results indicate the utility of potato starch suspension for MR microimaging in mouse embryos.

Post-mortem correlates of Virchow-Robin spaces detected on in vivo MRI

The purpose of our study is to quantify the extent to which Virchow-Robin spaces (VRS) detected on in vivo MRI are reproducible by post-mortem MRI.Double Echo Steady State 3T MRIs were acquired post-mortem in 49 double- and 32 single-hemispheric formalin-fixed brain sections from 12 patients, who underwent conventional diagnostic 1.5 or 3T MRI in median 22 days prior to death (25% to 75%: 12 to 134 days). The overlap of in vivo and post-mortem VRS segmentations was determined accounting for potential confounding factors.The reproducibility of VRS found on in vivo MRI by post-mortem MRI, in the supratentorial white matter was in median 80% (25% to 75%: 60 to 100). A lower reproducibility was present in the basal ganglia, with a median of 47% (25% to 75%: 30 to 50).VRS segmentations were histologically confirmed in one double hemispheric section.Overall, the majority of VRS found on in vivo MRI was stable throughout death and formalin fixation, emphasizing the translational potential of post-mortem VRS studies.

Neuropathology of Pediatric SARS-CoV-2 Infection in the Forensic Setting: Novel Application of Ex Vivo Imaging in Analysis of Brain Microvasculature

Two years into the COVID-19 pandemic, there are few published accounts of postmortem SARS-CoV-2 pathology in children. We report 8 such cases (4 infants aged 7–36 weeks, 4 children aged 5–15 years). Four underwent ex vivo magnetic resonance neuroimaging, to assist in identification of subtle lesions related to vascular compromise. All infants were found unresponsive (3 in unsafe sleeping conditions); all but 1 had recent rhinitis and/or influenza-like illness (ILI) in the family; 1 had history of sickle cell disease. Ex vivo neuroimaging in 1 case revealed white matter (WM) signal hyperintensity and diffuse exaggeration of perivascular spaces, corresponding microscopically to WM mineralization. Neurohistology in the remaining 3 infants variably encompassed WM gliosis and mineralization; brainstem gliosis; perivascular vacuolization; perivascular lymphocytes and brainstem microglia. One had ectopic hippocampal neurons (with pathogenic variant in DEPDC5). Among the children, 3 had underlying conditions (e.g., obesity, metabolic disease, autism) and all presented with ILI. Three had laboratory testing suggesting multisystem inflammatory syndrome (MIS-C). Two were hospitalized for critical care including mechanical ventilation and extracorporeal membrane oxygenation (ECMO); one (co-infected with adenovirus) developed right carotid stroke ipsilateral to the ECMO cannula and the other required surgery for an ingested foreign body. Autopsy findings included: acute lung injury in 3 (1 with microthrombi); and one each with diabetic ketoacidosis and cardiac hypertrophy; coronary and cerebral arteritis and aortitis, resembling Kawasaki disease; and neuronal storage and enlarged fatty liver. All 4 children had subtle meningoencephalitis, focally involving the brainstem. On ex vivo neuroimaging, 1 had focal pontine susceptibility with corresponding perivascular inflammation/expanded perivascular spaces on histopathology. Results suggest SARS-CoV-2 in infants may present as sudden unexpected infant death, while in older children, signs and symptoms point to severe disease. Underlying conditions may predispose to fatal outcomes. As in adults, the neuropathologic changes may be subtle, with vascular changes such as perivascular vacuolization and gliosis alongside sparse perivascular lymphocytes. Detection of subtle vascular pathology is enhanced by ex vivo neuroimaging. Additional analysis of the peripheral/autonomic nervous system and investigation of co-infection in children with COVID-19 is necessary to understand risk for cardiovascular collapse/sudden death.

Mapping the human lateral geniculate nucleus and its cytoarchitectonic subdivisions using quantitative MRI

The human lateral geniculate nucleus (LGN) of the visual thalamus is a key subcortical processing site for visual information analysis. Due to its small size and deep location within the brain, a non-invasive characterization of the LGN and its microstructurally distinct magnocellular (M) and parvocellular (P) subdivisions in humans is challenging. Here, we investigated whether structural quantitative MRI (qMRI) methods that are sensitive to underlying microstructural tissue features enable MR-based mapping of human LGN M and P subdivisions. We employed high-resolution 7 Tesla in-vivo qMRI in N = 27 participants and ultra-high resolution 7 Tesla qMRI of a post-mortem human LGN specimen. We found that a quantitative assessment of the LGN and its subdivisions is possible based on microstructure-informed qMRI contrast alone. In both the in-vivo and post-mortem qMRI data, we identified two components of shorter and longer longitudinal relaxation time (T₁) within the LGN that coincided with the known anatomical locations of a dorsal P and a ventral M subdivision, respectively. Through ground-truth histological validation, we further showed that the microstructural MRI contrast within the LGN pertains to cyto- and myeloarchitectonic tissue differences between its subdivisions. These differences were based on cell and myelin density, but not on iron content. Our qMRI-based mapping strategy paves the way for an in-depth understanding of LGN function and microstructure in humans. It further enables investigations into the selective contributions of LGN subdivisions to human behavior in health and disease.

Dedicated container for postmortem human brain ultra-high field magnetic resonance imaging

BACKGROUND

The emerging field of ultra-high field MRI (UHF-MRI, 7 Tesla and higher) provides the opportunity to image human brains at a higher resolution and with higher signal-to-noise ratios compared to the more widely available 1.5 and 3T scanners. Scanning postmortem tissue additionally allows for greatly increased scan times and fewer movement issues leading to improvements in image quality. However, typical postmortem neuroimaging routines involve placing the tissue within plastic bags that leave room for susceptibility artifacts from tissue-air interfaces, inadequate submersion, and leakage issues. To address these challenges in postmortem imaging, a custom-built nonferromagnetic container was developed that allows whole brain hemispheres to be scanned at sub-millimeter resolution within typical head-coils.

METHOD

The custom-built polymethylmethacrylaat container consists of a cylinder with a hemispheric side and a lid with valves on the adjacent side. This shape fits within common MR head-coils and allows whole hemispheres to be submerged and vacuum sealed within it reducing imaging artifacts that would otherwise arise at air-tissue boundaries. Two hemisphere samples were scanned on a Siemens 9.4T Magnetom MRI scanner. High resolution T2* weighted data was obtained with a custom 3D gradient echo (GRE) sequence and diffusion-weighted imaging (DWI) scans were obtained with a 3D kT-dSTEAM sequence along 48 directions.

RESULTS

The custom-built container proved to submerge and contain tissue samples effectively and showed no interferences with MR scanning acquisition. The 3D GRE sequence provided high resolution isotropic T2* weighted data at 250 μm which showed a clear visualization of gray and white matter structures. DWI scans allowed for dense reconstruction of structural white matter connections via tractography.

CONCLUSION

Using this custom-built container worked towards achieving high quality MR images of postmortem brain material. This procedure can have advantages over traditional schemes including utilization of a standardized protocol and the reduced likelihood of leakage. This methodology could be adjusted and used to improve typical postmortem imaging routines.

A multimodal computational pipeline for 3D histology of the human brain

Ex vivo imaging enables analysis of the human brain at a level of detail that is not possible in vivo with MRI. In particular, histology can be used to study brain tissue at the microscopic level, using a wide array of different stains that highlight different microanatomical features. Complementing MRI with histology has important applications in ex vivo atlas building and in modeling the link between microstructure and macroscopic MR signal. However, histology requires sectioning tissue, hence distorting its 3D structure, particularly in larger human samples. Here, we present an open-source computational pipeline to produce 3D consistent histology reconstructions of the human brain. The pipeline relies on a volumetric MRI scan that serves as undistorted reference, and on an intermediate imaging modality (blockface photography) that bridges the gap between MRI and histology. We present results on 3D histology reconstruction of whole human hemispheres from two donors.

Graft assessment of the ex vivo perfused porcine kidney using hyperpolarized [1-13 C]pyruvate

PURPOSE

Normothermic perfusion is an emerging strategy for donor organ preservation and therapy, incited by the high worldwide demand for organs for transplantation. Hyperpolarized MRI and MRS using [1-¹³ C]pyruvate and other ¹³ C-labeled molecules pose a novel way to acquire highly detailed information about metabolism and function in a noninvasive manner. This study investigates the use of this methodology as a means to study and monitor the state of ex vivo perfused porcine kidneys, in the context of kidney graft preservation research.

METHODS

Kidneys from four 40-kg Danish domestic pigs were perfused ex vivo with whole blood under normothermic conditions, using an MR-compatible perfusion system. Kidneys were investigated using ¹ H MRI as well as hyperpolarized [1-¹³ C]pyruvate MRI and MRS. Using the acquired anatomical, functional and metabolic data, the state of the ex vivo perfused porcine kidney could be quantified.

RESULTS

Four kidneys were successfully perfused for 120 minutes and verified using a DCE perfusion experiment. Renal metabolism was examined using hyperpolarized [1-¹³ C]pyruvate MRI and MRS, and displayed an apparent reduction in pyruvate turnover compared with the usual case in vivo. Perfusion and blood gas parameters were in the normal ex vivo range.

CONCLUSION

This study demonstrates the ability to monitor ex vivo graft metabolism and function in a large animal model, resembling human renal physiology. The ability of hyperpolarized MRI and MRS to directly compare the metabolic state of an organ in vivo and ex vivo, in combination with the simple MR implementation of normothermic perfusion, renders this methodology a powerful future tool for graft preservation research.

Constant gradient FEXSY: A time-efficient method for measuring exchange

Filter-Exchange NMR Spectroscopy (FEXSY) is a method for measurement of apparent transmembranal water exchange rates. The experiment is comprised of two co-linear sequential pulsed-field gradient (PFG) blocks, separated by a mixing period in which exchange takes place. The first block remains constant and serves as a diffusion-based filter that removes signal coming from fast-diffusing water. The mixing time and the gradient area (q-value) of the second block are varied on repeated iterations to produce a 2D data set that is analyzed using a bi-compartmental model which assumes that intra- and extra-cellular water are slow and fast diffusing, respectively. Here we suggest a variant of the FEXSY method in which measurements for different mixing times are taken at a constant gradient. This Constant Gradient FEXSY (CG-FEXSY) allows for the determination of the exchange rate by using a smaller 1D data set, so that the same information can be gathered during a considerably shorter scan time. Furthermore, in the limit of high diffusion weighting, such that the extra-cellular water signal is removed while the intra-cellular signal is retained, CG-FEXSY also allows for determination of the intra-cellular mean residence time (MRT). The theoretical results are validated on a living yeast cells sample and on a fixed porcine optic nerve, where the values obtained from the two methods are shown to be in agreement.