Postmortem Human Brain Tissue Research Articles

Tau Activates Transposable Elements in Alzheimer’s Disease

SUMMARYAging and neurodegenerative disease are characterized by genomic instability in neurons, including aberrant activation and mobilization of transposable elements (TEs). Integrating studies of human postmortem brain tissue and Drosophila melanogaster models, we investigate TE activation in association with Tau pathology in Alzheimer’s disease (AD). Leveraging RNA sequencing from 636 human brains, we discover differential expression for several retrotransposons in association with neurofibrillary tangle burden and highlight evidence for global TE transcriptional activation among the long interspersed nuclear element 1 and endogenous retrovirus clades. In addition, we detect Tau-associated, active chromatin signatures at multiple HERV-Fc1 genomic loci. To determine whether Tau is sufficient to induce TE activation, we profile retrotransposons in Drosophila expressing human wild-type or mutant Tau throughout the brain. We discover heterogeneous response profiles, including both age- and genotype-dependent activation of TE expression by Tau. Our results implicate TE activation and associated genomic instability in Tau-mediated AD mechanisms.

Large inter- and intra-case variability of first generation tau PET ligand binding in neurodegenerative dementias

Imaging of pathological tau with positron emission tomography (PET) has the potential to allow early diagnosis of the dementias and monitoring of disease progression, including assessment of therapeutic interventions, in vivo. The first generation of tau PET tracers, including the carbazole flortaucipir and the 2-arylquinolines of the THK series, are now used in clinical research; however, concerns have been raised about off-target binding and low sensitivity.With the aim to determine the nature of tau pathology depicted by structurally distinct tau ligands we carried out a microscopic neuropathological evaluation in post-mortem human brain tissue of cases with primary and secondary tauopathies. Carbazole and 2-arylquinoline binding was only observed in cases with Alzheimer’s disease and one case with frontotemporal dementia and parkinsonism linked to chromosome 17 exhibiting a R406W MAPT mutation. In end stage Alzheimer’s disease cases, fluorescent imaging with the carbazole T726 and the 2-arylquinoline THK-5117 revealed high inter- and intra-case variability of tracer binding, and this was corroborated by quantitative phosphorimaging with the PET tracer [18F]THK-5117. Microscopic analysis of the pathological inclusions revealed that the fluorescent tracers preferentially bind to premature tau aggregates. Whilst T726 binding was limited to neuronal tau, THK-5117 additionally depicted neuritic tau. Neither tracer depicted tau in pre-symptomatic disease.Our results highlight limitations of the first generation of tau PET tracers, in particular lack of correlation between pathological tau load and tracer binding, limited sensitivity to tau in early disease, and high variability in tracer binding between and within cases. Concerns remain that these limitations may also affect the next generation tracers as they target the same high affinity binding site. Therefore, it is crucial to assess inter- and intra-subject correlation of tracer binding with pathological tau load in post-mortem tissue studies, and to rigorously assess novel tau PET tracers before translation into clinical studies.

T34. Dysregulated Inflammatory Related Gene Expression in the Dorsolateral Prefrontal of Individuals With PTSD

The inflammatory system plays a clear role in the pathophysiology of chronic mental and physical illnesses. Individuals with PTSD, depression, and other fear- and anxiety-related disorders exhibit alterations in circulating inflammatory marker levels, suggesting underlying dysfunction of the innate immune inflammatory system. The relationship between innate immune activation and PTSD has been investigated almost exclusively in the periphery, and has not been extensively explored in human postmortem PTSD brain tissue. Based on the known role of interleukin signaling in PTSD and depression, we investigated interleukin gene expression in the dorsolateral prefrontal cortex (dlPFC) using tissue from the newly established National PTSD Brain Bank (NPBB).

Effect of Postmortem Interval and Years in Storage on RNA Quality of Tissue at a Repository of the NIH NeuroBioBank

Brain tissue from 1068 donors was analyzed for RNA quality as a function of postmortem interval (PMI) and years in storage. Approximately 83% of the cortical and cerebellar samples had an RNA integrity number (RIN) of 6 or greater, indicating their likely suitability for real-time quantitative polymerase chain reaction research. The average RIN value was independent of the PMI, up to at least 36 hours. The RNA quality for specific donated brains could not be predicted based on the PMI. Individual samples with a low PMI could have a poor RIN value, while a sample with a PMI over 36 hours may have a high RIN value. The RIN values for control brain donors, all of whom died suddenly and unexpectedly, were marginally higher than for individuals with clinical brain disorders. Polymerase chain reaction (PCR) analysis of samples confirmed that RIN values were more critical than PMI for determining suitability of tissue for molecular biological studies and samples should be matched by their RIN values rather than PMI. Importantly, PCR analysis established that tissue stored up to 23 years at −80°C yielded high-quality RNA. These results confirm that postmortem human brain tissue collected by brain and tissue banks over decades can serve as high quality material for the study of human disorders.

Forniceal deep brain stimulation induces gene expression and splicing changes that promote neurogenesis and plasticity

Clinical trials are currently underway to assess the efficacy of forniceal deep brain stimulation (DBS) for improvement of memory in Alzheimer's patients, and forniceal DBS has been shown to improve learning and memory in a mouse model of Rett syndrome (RTT), an intellectual disability disorder caused by loss-of-function mutations in MECP2. The mechanism of DBS benefits has been elusive, however, so we assessed changes in gene expression, splice isoforms, DNA methylation, and proteome following acute forniceal DBS in wild-type mice and mice lacking Mecp2. We found that DBS upregulates genes involved in synaptic function, cell survival, and neurogenesis and normalized expression of ~25% of the genes altered in Mecp2-null mice. Moreover, DBS induced expression of 17-24% of the genes downregulated in other intellectual disability mouse models and in post-mortem human brain tissue from patients with Major Depressive Disorder, suggesting forniceal DBS could benefit individuals with a variety of neuropsychiatric disorders.

Shaker-related voltage-gated potassium channels Kv1 in human hippocampus.

In this study, we investigated the tissue expression levels, alpha subunit composition and distribution of Shaker-related voltage-dependent potassium Kv1 channels in human hippocampus by combining western blotting experiments, toxin autoradiography, in vivo radioligand binding studies, immunoprecipitation and immunohistochemistry. Tissue expression of Kv1.1 and Kv1.2 α-subunits in human post-mortem brain tissue was confirmed in immunoblot analysis using a panel of specific monoclonal and polyclonal antibodies. Immunoprecipitation experiments using toxin-prelabeled Kv1 channels revealed that all toxin-sensitive Kv1 channels in human hippocampus contained either a Kv1.1 or Kv1.2 α-subunit with the majority being composed of Kv1.1/Kv1.2 heterotetramers. Receptor autoradiography suggested Kv1.1/Kv1.2 channel expression in the molecular layer of dentate gyrus. In accordance, immunohistochemical experiments also observed Kv1.1 and Kv1.2 α-subunits in the molecular layer of the dentate gyrus, in addition to the CA3 stratum lucidum and the CA1 stratum oriens. These findings indicate expression in axons and terminals of hippocampal pathways, namely the perforant path, the mossy fiber pathway and the Schaffer collaterals. Herein we present the first direct demonstration that Kv1.1 and Kv1.2 channel proteins are targeted to distinct compartments of the human hippocampal formation and that this expression pattern largely reflects their distribution profile in murine brain.

Global quantitative analysis of the human brain proteome in Alzheimer\u2019s and Parkinson\u2019s Disease

Patients with Alzheimer’s disease (AD) and Parkinson’s disease (PD) often have overlap in clinical presentation and brain neuropathology suggesting that these two diseases share common underlying mechanisms. Currently, the molecular pathways linking AD and PD are incompletely understood. Utilizing Tandem Mass Tag (TMT) isobaric labeling and synchronous precursor selection-based MS3 (SPS-MS3) mass spectrometry, we performed an unbiased quantitative proteomic analysis of post-mortem human brain tissues (n=80) from four different groups defined as controls, AD, PD, and co-morbid AD/PD cases across two brain regions (frontal cortex and anterior cingulate gyrus). In total, we identified 11 840 protein groups representing 10 230 gene symbols, which map to ~65% of the protein coding genes in brain. The utility of including two reference standards in each TMT 10-plex assay to assess intra- and inter-batch variance is also described. Ultimately, this comprehensive human brain proteomic dataset serves as a valuable resource for various research endeavors including, but not limited to, the identification of disease-specific protein signatures and molecular pathways that are common in AD and PD.

A novel method to visualise the three-dimensional organisation of the human cerebral cortical vasculature.

Current tissue-clearing protocols for imaging in three dimensions (3D) are typically applied to optimally fixed, small-volume rodent brain tissue - which is not representative of the tissue found in diagnostic neuropathology laboratories. We present a method to visualise the cerebral cortical vasculature in 3D in human post-mortem brain tissue which had been preserved in formalin for many years. Tissue blocks of cerebral cortex from two control cases, two Alzheimer's brains and two cases from Alzheimer's patients immunised against Aβ42 were stained with fluorescent Lycopersicon esculentum agglutinin (Tomato lectin), dehydrated and cleared using an adapted three-dimensional imaging of solvent cleared organs (3DISCO) protocol to visualise the vascular endothelium. Tissue was imaged using light sheet and confocal microscopy and reconstructed in 3D using amira software. The method permits visualisation of the arrangement of the parallel penetrating cortical vasculature in the human brain. The presence of four vascular features including anastomosis, U-shaped vessels, spiralling and loops were revealed. In summary, we present a low cost and simple method to visualise the human cerebral vasculature in 3D compatible with prolonged fixation times (years), allowing study of vascular involvement in a range of normative and pathological states.

Functional coupling between adenosine A1 receptors and G-proteins in rat and postmortem human brain membranes determined with conventional guanosine-5'-O-(3-[35S]thio)triphosphate ([35S]GTPγS) binding or [35S]GTPγS/immunoprecipitation assay.

Adenosine signaling plays a complex role in multiple physiological processes in the brain, and its dysfunction has been implicated in pathophysiology of neuropsychiatric diseases such as schizophrenia and affective disorders. In the present study, the coupling between adenosine A1 receptor and G-protein was assessed by means of two [35S]GTPγS binding assays, i.e., conventional filtration method and [35S]GTPγS binding/immunoprecipitation in rat and human brain membranes. The latter method provides information about adenosine A1 receptor-mediated Gαi-3 activation in rat as well as human brain membranes. On the other hand, adenosine-stimulated [35S]GTPγS binding determined with conventional assay derives from functional activation of Gαi/o proteins (not restricted only to Gαi-3) coupled to adenosine A1 receptors. The determination of adenosine concentrations in the samples used in the present study indicates the possibility that the assay mixture under our experimental conditions contains residual endogenous adenosine at nanomolar concentrations, which was also suggested by the results on the effects of adenosine receptor antagonists on basal [35S]GTPγS binding level. The effects of adenosine deaminase (ADA) on basal binding also support the presence of adenosine. Nevertheless, the varied patterns of ADA discouraged us from adding ADA into assay medium routinely. The concentration-dependent increases elicited by adenosine were determined in 40 subjects without any neuropsychiatric disorders. The increases in %Emax values determined by conventional assay according to aging and postmortem delay should be taken into account in future studies focusing on the effects of psychiatric disorders on adenosine A1 receptor/G-protein interaction in postmortem human brain tissue.

A Common DIO2 Polymorphism and Alzheimer Disease Dementia in African and European Americans.

A common single nucleotide polymorphism in DIO2, Thr92AlaD2, has been associated with a transcriptome typically found in neurodegenerative diseases in postmortem human brain tissue. To determine whether Thr92AlaD2 is associated with incident Alzheimer disease (AD). Population-based study; human brain tissue microarray. Community-based cohorts from Chicago and northeastern Illinois and religious clergymen from across the United States constituted the primary population. A representative sample of the U.S. population was used for secondary analyses. 3054 African Americans (AAs) and 9304 European Americans (EAs). Incident AD. In the primary population, AAs with Thr92AlaD2 had 1.3 times [95% confidence interval (CI), 1.02 to 1.68; P = 0.048] greater odds of developing AD. AAs from a second population with Thr92AlaD2 showed a trend toward increased odds of dementia (odds ratio, 1.33; 95% CI, 0.99 to 1.78; P = 0.06) and 1.35 times greater odds of developing cognitive impairment not demented (CIND; 95% CI, 1.09 to 1.67; P = 0.006). Meta-analysis showed that AAs with Thr92AlaD2 had 1.3 times increased odds of developing AD/dementia (95% CI, 1.07 to 1.58; P = 0.008). In EAs, no association was found between Thr92AlaD2 and AD, dementia, or CIND. Microarray of AA brain tissue identified transcriptional patterns linked to AD pathogenesis. Thr92AlaD2 was associated with molecular markers known to underlie AD pathogenesis in AAs, translating to an observed phenotype of increased odds of developing AD/dementia in AAs in these populations. Thr92AlaD2 might represent one factor contributing to racial discrepancies in incident AD.

Endogenous Alpha-Synuclein Analysis using Single-Molecule Pull-Down Assay

Parkinson's disease (PD) is the second most common neurodegenerative disease, but molecular mechanisms underlying PD pathogenesis remain unclear. Alpha-synuclein (α-SYN) and its oligomeric species are implicated as a key player in Parkinson's disease. Thus, the determination of α-SYN expression levels and its oligomerization states is crucial to understand PD. However, it has been challenging to analyze them quantitatively because of the limited amount of specimens and the lack of techniques that are insensitive to the size and conformation of α-SYN oligomers. Here, we demonstrated quantitative analysis of endogenous α-SYN taken from postmortem human brain tissue using a single-molecule pull-down (SiMPull) assay. The SiMPull assay probes immunoprecipitated proteins, which are then tagged with a fluorescent molecule for imaging and detection. By utilizing in vivo crosslinking, we preserved the native oligomerization state of the α-SYN proteins. Our results showed that the tissue lysates from the substantia nigra of a human PD brain showed 3.3-fold higher number of α-SYN molecules and 2.4-fold higher oligomeric population compared to a healthy brain. Our technique is a powerful diagnostic tool for the detection of various neurodegenerative diseases, such as Parkinson's disease and Alzheimer's disease, and can be used to analyze various biospecimens not limited to post mortem brain tissue.

Neurochemical Characterization of PSA-NCAM+ Cells in the Human Brain and Phenotypic Quantification in Alzheimer’s Disease Entorhinal Cortex

Polysialylated neural cell adhesion molecule (PSA-NCAM) is widely expressed in the adult human brain and facilitates structural remodeling of cells through steric inhibition of intercellular NCAM adhesion. We previously showed that PSA-NCAM immunoreactivity is decreased in the entorhinal cortex in Alzheimer’s disease (AD). Based on available evidence, we hypothesized that a loss of PSA-NCAM+ interneurons may underlie this reduction. PSA-NCAM expression by interneurons has previously been described in the human medial prefrontal cortex. Here we used postmortem human brain tissue to provide further evidence of PSA-NCAM+ interneurons throughout the human hippocampal formation and additional cortical regions. Furthermore, PSA-NCAM+ cell populations were assessed in the entorhinal cortex of normal and AD cases using fluorescent double labeling and manual cell counting. We found a significant decrease in the number of PSA-NCAM+ cells per mm2 in layer II and V of the entorhinal cortex, supporting our previous description of reduced PSA-NCAM immunoreactivity. Additionally, we found a significant decrease in the proportion of PSA-NCAM+ cells that co-labeled with NeuN and parvalbumin, but no change in the proportion that co-labeled with calbindin or calretinin. These results demonstrate that PSA-NCAM is expressed by a variety of interneuron populations throughout the brain. Furthermore, that loss of PSA-NCAM expression by NeuN+ cells predominantly contributes to the reduced PSA-NCAM immunoreactivity in the AD entorhinal cortex.

Enrichment of schizophrenia heritability in both neuronal and glia cell regulatory elements

Genome-wide association studies have identified over 100 robust risk loci for schizophrenia with thousands of variants mediating genetic heritability, the majority of which reside in non-coding regions. Analytical approaches have shown this heritability is strongly enriched at variants within regulatory elements identified from human post-mortem brain tissue. However, bulk post-mortem brain tissue has a heterogeneous cell composition, making biological interpretations difficult. We sought to refine the cell types mediating schizophrenia heritability by separating neuronal and glial signals using data from: (1) NeuN-sorted post-mortem brain and (2) cell culture systems. Schizophrenia heritability was partitioned using linkage disequilbrium (LD) score regression. Variants within genomic regions marked by H3K4me3 (marker of active promoters) from NeuN-positive (neuronal) and NeuN-negative (non-neuronal) cells explained a significant amount of schizophrenia heritability (P = 1.38 × 10−10 and P = 7.97 × 10−10). However, variants located in H3K4me3 sites specific to NeuN-positive (neuronal) cells were enriched (P = 3.13 × 10−4), while those specific to NeuN-negative (non-neuronal) cells were not (P = 0.470). Data from cell culture systems mimicked this pattern of association. We show the previously observed enrichment of heritability from variants at brain H3K4me3 sites is mediated by both neuronal and non-neuronal brain cell types. However, only neuronal cell populations showed a unique contribution driven by cell-type specific regulatory elements. Cell culture systems recapitulate disease relevant gene-regulatory landscapes, validating them as a tool for future investigation of genetic mechanisms underlying schizophrenia. Identifying the cell types in which risk variants operate will greatly increase our understanding of schizophrenia pathobiology and aid in the development of novel model systems and therapies.

Chapter 17 - Epigenetic analysis of human postmortem brain tissue

Epigenomic profiles have been mapped across a broad range of brain regions and developmental contexts in postmortem human brain tissues, illuminating our understanding of epigenetic regulation in neural function and plasticity across the life course. Importantly, disease-associated epigenetic alterations in postmortem brain have provided compelling insights into the gene-regulatory architecture underlying neurobiologic disease susceptibility and pathogenesis. However, the use of postmortem brain tissues for molecular analyses warrants careful consideration of key technical and biologic factors that may confound epigenetic analyses. In this chapter, we describe the predominant forms of epigenetic regulation (DNA modifications, chromatin structure, and noncoding RNA expression) and discuss the various methodologies used to assess each epigenetic mark. In addition, we provide an overview of existing epigenetic studies using human brain tissues as well as highlight the various challenges and considerations for epigenomic profiling in human postmortem brain samples.

Flow cytometric evaluation of crude synaptosome preparation as a way to study synaptic alteration in neurodegenerative diseases.

Neurodegenerative diseases, the most common among them Alzheimer's disease (AD) and Lewy body disease (LBD), are a group of progressive incurable illnesses. In both AD and LBD, abundant evidence points to the synapse as the critical and early focus of pathological changes. Here we present a method for the isolation and flow cytometric analysis of synaptosomes prepared from postmortem human brain tissue, which we also applied to animal models, including mice and nonhuman primates. The use of flow cytometry for analysis allows for relatively fast and efficient examination of thousands of synaptosome particles in a matter of minutes, and also makes it possible to use crude, rather than purified, synaptosomal preparation, thus conserving tissue resources. We have applied this method to study synaptic alteration in several brain regions in human research participants and animal models.

Chapter 18 - Laser microdissection and gene expression profiling in the human postmortem brain

Laser microdissection in combination with gene expression profiling using postmortem human brain tissue provides a powerful approach to interrogating cell type-specific pathologies within neural circuits that are known to be dysfunctional in neuropsychiatric disorders. The success of these experiments critically depends on a number of factors, such as the cellular purity of the sample, the quality of the RNA, the methodologies of data normalization and computational data analysis, and how data are interpreted. Data obtained from these experiments should be validated at the protein level. Furthermore, from the perspective of disease mechanism discovery, it would be ideal to investigate whether manipulation of the expression of genes identified as differentially expressed can rescue or ameliorate the neurobiologic or behavioral phenotypes associated with the specific disease. Thus, the ultimate value of this approach rests upon the fact that the generation of novel disease-related pathophysiologic hypotheses may lead to deeper understanding of disease mechanisms and possible development of effective targeted treatments.

Cell Type-Specific Laser Capture Microdissection for Gene Expression Profiling in the Human Brain.

Cell type-specific laser microdissection technologies in combination with molecular techniques to determine gene expression profiles have become powerful tools to gain insight into the neurobiological basis of neural circuit disturbances in various neurologic or psychiatric diseases. To identify specific cell populations in human postmortem brain tissue, one can use the inherent properties of the cells, such as pigmentation and morphology or their structural composition through immunohistochemistry (IHC). Here, we describe the isolation of homogeneous neurons and oligodendrocytes and the extraction of high-quality RNA from these cells in human postmortem brain using a combination of rapid IHC, Nissl staining, or simple morphology with Laser Capture Microdissection (LCM), or Laser Microdissection (LMD).

Chapter 11 - Brain donation at autopsy: clinical characterization and toxicologic analyses

The study of postmortem human brain tissue is central to the advancement of neurobiologic studies of psychiatric and neurologic illnesses, particularly the study of brain-specific isoforms and molecules. Due to tissue demands, especially pertaining to brain regions strongly implicated in the pathophysiology of neuropsychiatric disorders, the success and future of this research depend on the availability of high-quality brain specimens from large numbers of subjects, including nonpsychiatric controls, both of which may be obtained from brain banks. In this chapter, we elaborate on the need for and acquisition of well-curated and properly diagnosed postmortem human brains, relying upon our experience with the Human Brain and Tissue Repository located at the Lieber Institute for Brain Development in Baltimore, MD. We explain the advantages of sourcing postmortem human tissue from medical examiner offices, which provide access to cases of all ages, both with and without central nervous system disorders. Neuropathology analyses and toxicologic screenings, along with autopsy reports and extensive interviews with family members and treating physicians, are invaluable to the diagnoses of postmortem cases. Ultimately, the study of psychiatric and neurologic disorders is the study of brain disease, and accordingly, there is no substitution for human brain tissue.

Chapter 4 - The NIH NeuroBioBank: creating opportunities for human brain research

The National Institutes of Health (NIH) NeuroBioBank is a federally funded research resource for human neurologic diseases and disorders. This chapter will discuss the principles that guided the creation of the NIH NeuroBioBank and the rationale for the resource model selected. In addition, we will describe some performance metrics in the first 2 years and highlight recent advances in biomedical neuroscience that could only have been achieved using postmortem human tissues. The NIH NeuroBioBank was created in order to increase availability of high-quality postmortem human brain tissues to the research community across a broad spectrum of neurologic diseases and disorders, and to achieve economies of scale over previous funding and organizational models. In addition, we aim to increase public awareness about the value of human tissue donation for research by providing web-based information to the public and through active outreach to disease advocacy communities. Studies with human brain tissue have led to a rapid increase in our knowledge of the biologic differences between humans and are bridging the divide between humans and model organisms. Studies of human brain are beginning to give us a glimpse not only into what makes us uniquely human as well as how individual biology may be connected to health and disease.

Chapter 7 - A new viewpoint: running a nonprofit brain bank as a business

It has become clear over the past decades that studying postmortem human brain tissue is one of the most effective ways to increase our knowledge of the pathogenesis and etiology of neuropathologic and psychiatric diseases. Many breakthroughs in neuroscience have depended on the availability of human brain tissue. However, the process of brain banking presents many different challenges, including the high cost that is associated with collecting the samples and with providing the diagnostics, storage, and distribution. Funding is generally from research and facility grants and donations but all are irregular, uncertain, and only cover the costs for a determined period of time. For professional brain banks with extensive prospective donor programs and that are open-access it can be very beneficial to draft a business plan to achieve long-term sustainability. Such a business plan should identify the interests of the stakeholders and address the implementation of cost efficiency and cost recovery systems.