Human Brain Tissue Research Articles

Expression profiles of the autism-related SHANK proteins in the human brain

BackgroundSHANKs are major scaffolding proteins at postsynaptic densities (PSDs) in the central nervous system. Mutations in all three family members have been associated with neurodevelopmental disorders such as autism spectrum disorders (ASDs). Despite the pathophysiological importance of SHANK2 and SHANK3 mutations in humans, research on the expression of these proteins is mostly based on rodent model organisms.ResultsIn the present study, cellular and neuropil SHANK2 expression was analyzed by immunofluorescence (IF) staining of post mortem human brain tissue from four male individuals (19 brain regions). Mouse brains were analyzed in comparison to evaluate the degree of phylogenetic conservation. Furthermore, SHANK2 and SHANK3 isoform patterns were compared in human and mouse brain lysates. While isoform expression and subcellular distribution were largely conserved, differences in neuropil levels of SHANK2 were found by IF staining: Maximum expression was concordantly measured in the cerebellum; however, higher SHANK2 expression was detected in the human brainstem and thalamus when compared to mice. One of the lowest SHANK2 levels was found in the human amygdala, a moderately expressing region in mouse. Quantification of SHANK3 IF in mouse brains unveiled a distribution comparable to humans.ConclusionsIn summary, these data show that the overall expression pattern of SHANK is largely conserved in defined brain regions; however, differences do exist, which need to be considered in the translation of rodent studies. The summarized expression patterns of SHANK2 and SHANK3 should serve as a reference for future studies.

Lipofuscin-like autofluorescence within microglia and its impact on studying microglial engulfment

Engulfment of cellular material and proteins is a key function for microglia, a resident macrophage of the central nervous system (CNS). Among the techniques used to measure microglial engulfment, confocal light microscopy has been used the most extensively. Here, we show that autofluorescence (AF) likely due to lipofuscin (lipo-AF) and typically associated with aging, can also be detected within microglial lysosomes in the young mouse brain by light microscopy. This lipo-AF signal accumulates first within microglia and it occurs earliest in white versus gray matter. Importantly, in gray matter, lipo-AF signal can confound the interpretation of antibody-labeled synaptic material within microglia in young adult mice. We further show that there is an age-dependent accumulation of lipo-AF inside and outside of microglia, which is not affected by amyloid plaques. We finally implement a robust and cost-effective strategy to quench AF in mouse, marmoset, and human brain tissue.

Integrative multi-omic profiling of adult mouse brain endothelial cells and potential implications in Alzheimer’s disease

The blood-brain barrier (BBB) is primarily manifested by a variety of physiological properties of brain endothelial cells (ECs), but the molecular foundation for these properties remains incompletely clear. Here, we generate a comprehensive molecular atlas of adult brain ECs using acutely purified mouse ECs and integrated multi-omics. Using RNA sequencing (RNA-seq) and proteomics, we identify the transcripts and proteins selectively enriched in brain ECs and demonstrate that they are partially correlated. Using single-cell RNA-seq, we dissect the molecular basis of functional heterogeneity of brain ECs. Using integrative epigenomics and transcriptomics, we determine that TCF/LEF, SOX, and ETS families are top-ranked transcription factors regulating the BBB. We then validate the identified brain-EC-enriched proteins and transcription factors in normal mouse and human brain tissue and assess their expression changes in mice with Alzheimer's disease. Overall, we present a valuable resource with broad implications for regulation of the BBB and treatment of neurological disorders.

Ultrastructural Changes in Brain Tissue in Drug-Resistant Mesial Temporal Lobe Epilepsy in Humans: A Mini-Review

Epilepsy is a group of chronic neurological diseases of the brain characterized by a persistent predisposition to epileptic seizures, affecting more than 70 million people worldwide. Drug-resistance is a key problem in the theory and practice of epileptology. The literature contains many publications devoted to ultrastructural changes in brain tissue in experimental animal models, but the features of ultrastructural changes in human brain tissue in drug-resistant mesial Temporal Lobe Epilepsy (TLE) remain unknown. This brief review presents the current state of the art of problems devoted to the study of the ultrastructure of neurons, glia, and blood vessels in patients with drug-resistant mesial TLE.

Single-cell transcriptomics of human traumatic brain injury reveals activation of endogenous retroviruses in oligodendroglia

Traumatic brain injury (TBI) is a leading cause of chronic brain impairment and results in a robust, but poorly understood, neuroinflammatory response that contributes to the long-term pathology. We used single-nuclei RNA sequencing (snRNA-seq) to study transcriptomic changes in different cell populations in human brain tissue obtained acutely after severe, life-threatening TBI. This revealed a unique transcriptional response in oligodendrocyte precursors and mature oligodendrocytes, including the activation of a robust innate immune response, indicating an important role for oligodendroglia in the initiation of neuroinflammation. The activation of an innate immune response correlated with transcriptional upregulation of endogenous retroviruses in oligodendroglia. This observation was causally linked invitro using human glial progenitors, implicating these ancient viral sequences in human neuroinflammation. In summary, this work provides insight into the initiating events of the neuroinflammatory response in TBI, which has therapeutic implications.

Acoustoelectric brain imaging with different conductivities and acoustic distributions.

Objective: Acoustoelectric brain imaging (AEBI) is a promising imaging method for mapping brain biological current densities with high spatiotemporal resolution. Currently, it is still challenging to achieve human AEBI with an unclear acoustoelectric (AE) signal response of medium characteristics, particularly in conductivity and acoustic distribution. This study introduces different conductivities and acoustic distributions into the AEBI experiment, and clarifies the response interaction between medium characteristics and AEBI performance to address these key challenges. Approach: AEBI with different conductivities is explored by the imaging experiment, potential measurement, and simulation on a pig's fat, muscle, and brain tissue. AEBI with different acoustic distributions is evaluated on the imaging experiment and acoustic field measurement through a deep and surface transmitting model built on a human skullcap and pig brain tissue. Main results: The results show that conductivity is not only inversely proportional to the AE signal amplitude but also leads to a higher AEBI spatial resolution as it increases. In addition, the current source and sulcus can be located simultaneously with a strong AE signal intensity. The transcranial focal zone enlargement, pressure attenuation in the deep-transmitting model, and ultrasound echo enhancement in the surface-transmitting model cause a reduced spatial resolution, FFT-SNR, and timing correlation of AEBI. Under the comprehensive effect of conductivity and acoustics, AEBI with skull finally shows reduced imaging performance for both models compared with no-skull AEBI. On the contrary, the AE signal amplitude decreases in the deep-transmitting model and increases in the surface-transmitting model. Significance: This study reveals the response interaction between medium characteristics and AEBI performance, and makes an essential step toward developing AEBI as a practical neuroimaging technique.

Radium deposition in human brain tissue: A Geant4-DNA Monte Carlo toolkit study

NASA has encouraged studies on 226Ra deposition in the human brain to investigate the effects of exposure to alpha particles with high linear energy transfer, which could mimic some of the exposure astronauts face during space travel. However, this approach was criticized, noting that radium is a bone-seeker and accumulates in the skull, which means that the radiation dose from alpha particles emitted by 226Ra would be heavily concentrated in areas close to cranial bones rather than uniformly distributed throughout the brain. In the high background radiation areas of Ramsar, Iran, extremely high levels of 226Ra in soil contribute to a large proportion of the inhabitants' radiation exposure. A prospective study on Ramsar residents with a calcium-rich diet was conducted to improve the dose uniformity due to 226Ra throughout the cerebral and cerebellar parenchyma. The study found that exposure of the human brain to alpha particles did not significantly affect working memory but was significantly associated with increased reaction times. This finding is crucial because astronauts on deep space missions may face similar cognitive impairments due to exposure to high charge and energy particles. The current study was aimed to evaluate the validity of the terrestrial model using the Geant4 Monte Carlo toolkit to simulate the interactions of alpha particles and representative cosmic ray particles, acknowledging that these radiation types are only a subset of the complete space radiation environment.

Comprehensive analyses identify potential biomarkers for encephalitis in HIV infection

Human immunodeficiency virus encephalitis (HIVE) is a severe neurological complication after HIV infection. Evidence shows that genetic factors play an important role in HIVE. The aim of the present study was to identify new potential therapeutic targets for HIVE. Differentially expressed gene (DEG), functional annotation and pathway, and protein–protein interaction analyses were performed to identify the hub genes associated with HIVE. Gene co-expression analysis was carried out to confirm the association between the hub genes and HIVE. Finally, the role of the hub genes in HIVE therapy was evaluated by conducting drug–gene interaction analysis. A total of 20 overlapping DEGs closely related to HIVE were identified. Functional annotation and pathway enrichment analysis indicated that the markedly enriched DEG terms included ion transport, type II interferon signaling, and synaptic signaling. Moreover, protein–protein interaction analysis revealed that 10 key HIVE-related genes were hub genes, including SCN8A, CDK5R2, GRM5, SCN2B, IFI44L, STAT1, SLC17A7, ISG15, FGF12, and FGF13. Furthermore, six hub genes were co-expressed with HIVE-associated host genes in human brain tissue. Finally, three hub genes (STAT1, ISG15, and SCN2B) interacted with several inflammation-associated drugs. These findings suggested that SCN8A, CDK5R2, GRM5, SCN2B, IFI44L, STAT1, SLC17A7, ISG15, FGF12, and FGF13 may be new targets for diagnosis and therapy of HIVE.

Multi-Scale Label-Free Human Brain Imaging with Integrated Serial Sectioning Polarization Sensitive Optical Coherence Tomography and Two-Photon Microscopy.

The study of aging and neurodegenerative processes in the human brain requires a comprehensive understanding of cytoarchitectonic, myeloarchitectonic, and vascular structures. Recent computational advances have enabled volumetric reconstruction of the human brain using thousands of stained slices, however, tissue distortions and loss resulting from standard histological processing have hindered deformation-free reconstruction. Here, the authorsdescribe an integrated serial sectioning polarization-sensitive optical coherence tomography (PSOCT) and two photon microscopy (2PM) system to provide label-free multi-contrast imaging of intact brain structures, including scattering, birefringence, and autofluorescence of human brain tissue. The authors demonstrate high-throughput reconstruction of 4 × 4 × 2cm3 sample blocks and simple registration between PSOCT and 2PM images that enablecomprehensive analysis of myelin content, vascular structure, and cellular information. The high-resolution 2PM images provide microscopic validation and enrichment of the cellular information provided by the PSOCT optical properties on the same sample, revealing the densely packed fibers, capillaries, and lipofuscin-filled cell bodies in the cortex and white matter. It is shown that theimaging system enables quantitative characterization of various pathological features in aging process, including myelin degradation, lipofuscin accumulation, and microvascular changes, which opens up numerous opportunities in the study of neurodegenerative diseases in the future.

Multiscale label-free imaging of myelin in human brain tissue with polarization-sensitive optical coherence tomography and birefringence microscopy.

The combination of polarization-sensitive optical coherence tomography (PS-OCT) and birefringence microscopy (BRM) enables multiscale assessment of myelinated axons in postmortem brain tissue, and these tools are promising for the study of brain connectivity and organization. We demonstrate label-free imaging of myelin structure across the mesoscopic and microscopic spatial scales by performing serial-sectioning PS-OCT of a block of human brain tissue and periodically sampling thin sections for high-resolution imaging with BRM. In co-registered birefringence parameter maps, we observe good correspondence and demonstrate that BRM enables detailed validation of myelin (hence, axonal) organization, thus complementing the volumetric information content of PS-OCT.

Exploring the reactivity of bicyclic α-iminophosphonates to access new imidazoline I2 receptor ligands

Recent studies pointed out the modulation of imidazoline I2 receptors (I2-IR) by selective ligands as a putative strategy to face neurodegenerative diseases. Foregoing the classical 2-imidazoline/imidazole-containing I2-IR ligands, we report a family of bicyclic α-iminophosphonates endowed with high affinity and selectivity upon I2-IR and we advanced a representative compound B06 in preclinical phases. In this paper, we describe the synthetic possibilities of bicyclic α-iminophosphonates by exploring its ambivalent reactivity, leading to unprecedented molecules that showed promising activities as I2-IR ligands in human brain tissues and good BBB permeation capabilities. After in silico ADME prediction studies, we assessed the neuroprotective properties of selected compounds and beneficial effect in an in vitro model of Alzheimeŕs and Parkinson’s disease. Along with their neuroprotective effect, compounds showed a potent anti-inflammatory response when evaluated in a neuroinflammation cellular model. Moreover, this is the first time that the neuroprotective effects of imidazoline I2-IR ligands in a transgenic Alzheimer’s disease Caenorhabditis elegans strain are investigated. Using a thrashing assay, we found a significant cognition improvement in this in vivo model after treatment with the new bicyclic α-phosphoprolines. Therefore, our results confirmed the need of exploring structurally new I2-IR ligands and their potential for therapeutic strategies in neurodegeneration.

Modeling the finite viscoelasticity of human brain tissue based on microstructural information

AbstractContinuum‐mechanics‐based computational models are a valuable tool to advance our understanding of mechanics‐related physiological and pathological processes in the brain. Current numerical predictions of brain tissue behavior are mainly based on phenomenological material models. Such models rely on parameters that often lack physical interpretation and only provide adequate estimates for brain regions with a similar microstructure as those used for calibration. These issues can be overcome by establishing advanced constitutive models that are microstructurally motivated and account for regional and temporal changes through microstructural parameters. In a previous study, we have proposed a microstructure‐informed finite viscoelastic constitutive model for porcine brain tissue based on experimental insights into the link between macroscopic deformations and cell displacements during compression tests. Here, we test whether the model can be applied to the material response of human brain tissue from different brain regions during compression and tension tests. We calibrate the model using a combination of cyclic loadings in compression and tension as well as stress relaxation experiments in compression. Furthermore, we include cell densities and the percentage area covered by cell nuclei from microstructural analyses of the tested samples into the model. While it was not possible to identify one set of material parameters for all four considered brain regions, we successfully applied the model to tissue from the cerebellar white matter. Our results show that the microstructure‐based time constant that we had determined based on experiments on porcine brain tissue is also valid for human tissue. Furthermore, the microstructure‐informed material model is capable of capturing the pronounced compression‐tension asymmetry of brain tissue.

SUZ12 inhibition attenuates cell proliferation of glioblastoma via post-translational regulation of CDKN1B.

Human gliomas are aggressive brain tumors characterized by uncontrolled cell proliferation. Differential expression of Polycomb repressive complex 2 (PRC2) has been reported in various subtypes of glioma. However, the role of PRC2 in uncontrolled growth in glioma and its underlying molecular mechanisms remain to be elucidated. We aimed to investigate the functional role of PRC2 in human glioblastoma cell growth by silencing SUZ12, the non-catalytic core component of PRC2. Knockdown of SUZ12 was achieved by infecting T98G cells with lentivirus carrying sequences specifically targeting SUZ12 (shSUZ12). Gene expression was examined by quantitative PCR and western analysis. The impact of shSUZ12 on cell growth was assessed using a cell proliferation assay. Cell cycle distribution was analyzed by flow cytometry, and protein stability was evaluated in cycloheximide-treated cells. Subcellular localization was examined through immunofluorescence staining and biochemical cytoplasmic-nuclear fractionation. Gene expression analysis was also performed on human specimens from normal brain and glioblastoma patients. SUZ12 knockdown (SUZ12 KD) led to widespread decrease in the PRC2-specific histone mark, accompanied by a slowdown of cell proliferation through G1 arrest. In SUZ12 KD cells, the degradation of CDKN1B protein was reduced, resulting from alterations in the MYC-SKP2-CDKN1B axis. Furthermore, nuclear localization of CDKN1B was enhanced in SUZ12 KD cells. Analysis of human glioblastoma samples yielded increased expression of EZH2 and MYC along with reduced CDKN1B compared to normal human brain tissue. Our findings suggest a novel role for SUZ12 in cell proliferation through post-translational regulation of CDKN1B in glioblastoma.

Determinants of astrocytic pathology in stem cell models of primary tauopathies

Astrocytic tau aggregates are seen in several primary and secondary tauopathies, including progressive supranuclear palsy (PSP), corticobasal degeneration (CBD), and chronic traumatic encephalopathy (CTE). In all of these diseases, astrocytic tau consists mostly of the longer (4R) tau isoform, even when adjacent neuronal aggregates consist of a mixture of 3- and 4R tau, as in CTE. Even the rare astrocytic tau aggregates seen in Pick’s disease appear to contain both 3R and 4R tau. The reasons for this, and the mechanisms by which astrocytic tau aggregates form, remain unclear. We used a combination of RNA in situ hybridization and immunofluorescence in post-mortem human brain tissue, as well as tau uptake studies in human stem cell-derived astrocytes, to determine the origins of astrocytic tau in 4R tauopathies. We found no differences in tau mRNA expression between diseases or between tau positive and negative astrocytes within PSP. We then found that stem cell-derived astrocytes preferentially take up long isoform (4R) recombinant tau and that this uptake is impaired by induction of reactivity with inflammatory stimuli or nutritional stress. Astrocytes exposed to either 3R or 4R tau also showed downregulation of genes related to astrocyte differentiation. Our findings suggest that astrocytes preferentially take up neuronal 4R tau from the extracellular space, potentially explaining why 4R tau is the predominant isoform in astrocytic tau aggregates.

C9orf72 proline-arginine dipeptide repeats disrupt the proteasome and perturb proteolytic activities.

The hexanucleotide G4C2 repeat expansion in C9orf72 is the most frequent genetic cause of familial amyotrophic lateral sclerosis (ALS). Aberrant translation of this hexanucleotide sequence leads to production of 5 dipeptide repeats (DPRs). One of these DPRs is proline-arginine (polyPR), which is found in C9orf72-expanded ALS (C9ALS) patient brain tissue and is neurotoxic across multiple model systems. PolyPR was previously reported to bind and impair proteasomes in vitro. Nevertheless, the clinical relevance of the polyPR-proteasome interaction and its functional consequences in vivo are yet to be established. Here, we aim to confirm and functionally characterize polyPR-induced impairment of proteolysis in C9ALS patient tissue and an in vivo model system. Confocal microscopy and immunofluorescence studies on both human and Drosophila melanogaster brain tissues revealed sequestration of proteasomes by polyPR into inclusion-like bodies. Co-immunoprecipitation in D. melanogaster showed that polyPR strongly binds to the proteasome. In vivo, functional evidence for proteasome impairment is further shown by the accumulation of ubiquitinated proteins along with lysosomal accumulation and hyper-acidification, which can be rescued by a small-molecule proteasomal enhancer. Together, we provide the first clinical report of polyPR-proteasome interactions and offer in vivo evidence proposing polyPR-induced proteolytic dysfunction as a pathogenic mechanism in C9ALS.

Segmentation of brain tissue using improved kernelized rough-fuzzy c-means technique

<p><span>Brain magnetic resonance imaging (MRI) data is a hot topic in the domains of biomedical engineering and machine learning. Without locating anomalies, such as tumors and edema, radiologists and other medical experts cannot effectively recommend or administer therapy for patients. Having three different magnetic resonance techniques (T1 weighted, T2 weighted, and T3 weighted), MRI can produce detailed multimodal scans of different human brain tissues with varying contrast, which can help pinpoint the source of any abnormalities. The cerebrospinal fluid (CSF), white matter (WM), and grey matter (GM) are all components of the brain, and their boundaries are sometimes hazy and difficult to nail down. In light of the problems above, this paper makes an effort to tackle issues like: i) the noise that exists in the brain datasets for MRI, ii) the fuzziness, uncertainty, overlap, indiscernibility of complex brain tissue regions, iii) the inability of traditional unsupervised methods to reliably distinguish between various brain tissue locations, and iv) ineffective performance. We propose some robust techniques by utilise spatial contextual data, a rough set, a fuzzy set, and ultimately a fuzzy set to steer the clustering process in a better direction, allowing it to deal with likely noise, outliers, and other artifacts.</span></p>

Influence of Alzheimer's disease related neuropathology on local microenvironment gene expression in the human inferior temporal cortex.

Neuropathological lesions in the brains of individuals affected with neurodegenerative disorders are hypothesized to trigger molecular and cellular processes that disturb homeostasis of local microenvironments. Here, we applied the 10x Genomics Visium Spatial Proteogenomics (Visium-SPG) platform, which couples spatial gene expression with immunofluorescence protein co-detection, to evaluate its ability to quantify changes in spatial gene expression with respect to amyloid-β (Aβ) and hyperphosphorylated tau (pTau) pathology in post-mortem human brain tissue from individuals with Alzheimer's disease (AD). We identified transcriptomic signatures associated with proximity to Aβ in the human inferior temporal cortex (ITC) during late-stage AD, which we further investigated at cellular resolution with combined immunofluorescence and single molecule fluorescent in situ hybridization (smFISH). The study provides a data analysis workflow for Visium-SPG, and the data represent a proof-of-principal for the power of multi-omic profiling in identifying changes in molecular dynamics that are spatially-associated with pathology in the human brain. We provide the scientific community with web-based, interactive resources to access the datasets of the spatially resolved AD-related transcriptomes at https://research.libd.org/Visium_SPG_AD/.

Small RNA Profiles of Brain Tissue-Derived Extracellular Vesicles in Alzheimer's Disease.

Extracellular vesicles (EVs) and non-coding RNAs (ncRNAs) are emerging contributors to Alzheimer's disease (AD) pathophysiology. Differential abundance of ncRNAs carried by EVs may provide valuable insights into underlying disease mechanisms. Brain tissue-derived EVs (bdEVs) are particularly relevant, as they may offer valuable insights about the tissue of origin. However, there is limited research on diverse ncRNA species in bdEVs in AD. This study explored whether the non-coding RNA composition of EVs isolated from post-mortem brain tissue is related to AD pathogenesis. bdEVs from age-matched late-stage AD patients (n = 23) and controls (n = 10) that had been separated and characterized in our previous study were used for RNA extraction, small RNA sequencing, and qPCR verification. Significant differences of non-coding RNAs between AD and controls were found, especially for miRNAs and tRNAs. AD pathology-related miRNA and tRNA differences of bdEVs partially matched expression differences in source brain tissues. AD pathology had a more prominent association than biological sex with bdEV miRNA and tRNA components in late-stage AD brains. Our study provides further evidence that EV non-coding RNAs from human brain tissue, including but not limited to miRNAs, may be altered and contribute to AD pathogenesis.

Advancing Towards Physiologically Relevant Models of the Brain: Three-Dimensional Human Induced Pluripotent Stem Cell (hiPSC)-Based Cell Culture Systems in Neuroscience

One of the biggest challenges in the field of neurological disorders is the limited availability of freshly dissected human brain tissue. Therefore, the use of human induced pluripotent stem cells (hiPSCs) is important to develop human brain-like models to study the interaction of different brain cell types in health and disease. For physiologically relevant disease modeling, three-dimensional (3D) cell culture systems are of great importance because they provide a more representative in vivo-like micro-environment to the cells. The field of 3D cell culture systems using diverse hiPSC-derived cells is growing and gets steadily advanced. However, to this day, there is no cell culture model available that includes all brain cell types. Here, we review the latest improvements of 3D hiPSC-based cell culture systems in the field of neuroscience. We focus on innovations for the generation of neurons, astrocytes, oligodendrocytes, microglia as well as endothelial cells and pericytes.

IL-12 sensing in neurons induces neuroprotective CNS tissue adaptation and attenuates neuroinflammation in mice.

Interleukin-12 (IL-12) is a potent driver of type 1 immunity. Paradoxically, in autoimmune conditions, including of the CNS, IL-12 reduces inflammation. The underlying mechanism behind these opposing properties and the involved cellular players remain elusive. Here we map IL-12 receptor (IL-12R) expression to NK and T cells as well as neurons and oligodendrocytes. Conditionally ablating the IL-12R across these cell types in adult mice and assessing their susceptibility to experimental autoimmune encephalomyelitis revealed that the neuroprotective role of IL-12 is mediated by neuroectoderm-derived cells, specifically neurons, and not immune cells. In human brain tissue from donors with multiple sclerosis, we observe an IL-12R distribution comparable to mice, suggesting similar mechanisms in mice and humans. Combining flow cytometry, bulk and single-nucleus RNA sequencing, we reveal an IL-12-induced neuroprotective tissue adaption preventing early neurodegeneration and sustaining trophic factor release during neuroinflammation, thereby maintaining CNS integrity in mice.