Gene Expression Analysis of Neurons and Astrocytes Isolated by Laser Capture Microdissection from Frozen Human Brain Tissues

Genomic characteristics of adipose-derived stromal cells induced into neurons based on single-cell RNA sequencing

Adipose-derived stromal cells (ADSCs) can be induced to differentiate into neurons, representing the most promising avenue for cell therapy. However, the molecular mechanism and genomic characteristics of the differentiation of ADSCs into neurons remain poorly understood. In this study, cells from the adult ADSCs group, induction 1h, 3h, 5h, 6h, and 8h groups were selected for single-cell RNA sequencing (scRNA-Seq). Samples from these seven-time points were sequenced and analyzed. The expression of neuron marker genes, including NES, MAP2, TMEM59L, PTK2B, CHN1, DNM1, NRSN2, FBLN2, SCAMP1, SLC1A1, DLG4, CDK5, and ENO2, was found to be low in the ADSCs group, but highly expressed in differentiated cell clusters. The expression of stem cell marker genes, including CCND1, IL1B, MMP1, MMP3, MYO10, and BMP2, was the highest in the ADSCs cluster. This expression decreased significantly with the extension of induction time. Gene ontology (GO) enrichment analysis of upregulated genes in the induced samples showed that the biological processes related to neuronal differentiation and development, such as neuronal differentiation, projection, and apoptosis, were significantly upregulated with a longer induction time during cell cluster differentiation. The results of the cell communication analysis demonstrated the gradual formation of complex neural network connections between ADSC-derived neurons through receptor and ligand pairs at 5h after the induction of differentiation.

Human hippocampal astrocytes: Computational dissection of their transcriptome, sexual differences and exosomes across ageing and mild-cognitive impairment

The role of astrocytes in Alzheimer's disease is often disregarded. Hence, characterization of astrocytes along their early evolution toward Alzheimer would be greatly beneficial. However, due to their exquisite responsiveness, in vivo studies are difficult. So public microarray data of hippocampal homogenates from (healthy) young, (healthy) elder and elder with mild cognitive impairment (MCI) were subjected to re-analysis by a multi-step computational pipeline. Ontologies and pathway analyses were compared after determining the differential genes that, belonging to astrocytes, have splice forms. Likewise, the subset of molecules exportable to exosomes was also determined. The results showed that astrocyte's phenotypes changed significantly. While already 'activated' astrocytes were found in the younger group, major changes occurred during ageing (increased vascular remodelling and response to mechanical stimulus, diminished long-term potentiation and increased long-term depression). MCI's astrocytes showed some 'rejuvenated' features, but their sensitivity to shear stress was markedly lost. Importantly, most of the changes showed to be sex biassed. Men's astrocytes are enriched in a type 'endfeet-astrocytome', whereas women's astrocytes appear close to the 'scar-forming' type (prone to endothelial dysfunction, hypercholesterolemia, loss of glutamatergic synapses, Ca+2 dysregulation, hypoxia, oxidative stress and 'pro-coagulant' phenotype). In conclusion, the computational dissection of the networks based on the hippocampal gene isoforms provides a relevant proxy to in vivo astrocytes, also revealing the occurrence of sexual differences. Analyses of the astrocytic exosomes did not provide an acceptable approximation to the overall functioning of astrocytes in the hippocampus, probably due to the selective cellular mechanisms which charge the cargo molecules.

Molecular signatures underlying neurofibrillary tangle susceptibility in Alzheimer's disease

Tau aggregation in neurofibrillary tangles (NFTs) is closely associated with neurodegeneration and cognitive decline in Alzheimer's disease (AD). However, the molecular signatures that distinguish between aggregation-prone and aggregation-resistant cell states are unknown. We developed methods for the high-throughput isolation and transcriptome profiling of single somas with NFTs from the human AD brain, quantified the susceptibility of 20 neocortical subtypes for NFT formation and death, and identified both shared and cell-type-specific signatures. NFT-bearing neurons shared a marked upregulation of synaptic transmission-related genes, including a core set of 63 genes enriched for synaptic vesicle cycling. Oxidative phosphorylation and mitochondrial dysfunction were highly cell-type dependent. Apoptosis was only modestly enriched, and the susceptibilities of NFT-bearing and NFT-free neurons for death were highly similar. Our analysis suggests that NFTs represent cell-type-specific responses to stress and synaptic dysfunction. We provide a resource for biomarker discovery and the investigation of tau-dependent and tau-independent mechanisms of neurodegeneration.

Profiling cell-type specific gene expression in post-mortem human brain samples through laser capture microdissection

The transcriptome of a cell constitutes an essential piece of cellular identity and contributes to the multifaceted complexity and heterogeneity of cell-types within the mammalian brain. Thus, while a wealth of studies have investigated transcriptomic alterations underlying the pathophysiology of diseases of the brain, their use of bulk-tissue homogenates makes it difficult to tease apart whether observed differences are explained by disease state or cellular composition. Cell-type-specific enrichment strategies are, therefore, crucial in the context of gene expression profiling. Laser capture microdissection (LCM) is one such strategy that allows for the capture of specific cell-types, or regions of interest, under microscopic visualization. In this review, we focus on using LCM for cell-type specific gene expression profiling in post-mortem human brain samples. We begin with a discussion of various LCM systems, followed by a walk-through of each step in the LCM to gene expression profiling workflow and a description of some of the limitations associated with LCM. Throughout the review, we highlight important considerations when using LCM with post-mortem human brain samples. Whenever applicable, commercially available kits that have proven successful in the context of LCM with post-mortem human brain samples are described.

Analysis of neuroendocrine clones in NSCLCs using an immuno-guided laser-capture microdissection-based approach

Clonal evolution and lineage plasticity are key contributors to tumor heterogeneity and response to treatment in cancer. However, capturing signal transduction events in coexisting clones remains challenging from a technical perspective. In this study, we developed and tested a signal-transduction-based workflow to isolate and profile coexisting clones within a complex cellular system like non-small cell lung cancers (NSCLCs). Cooccurring clones were isolated under immunohistochemical guidance using laser-capture microdissection, and cell signaling activation portraits were measured using the reverse-phase protein microarray. To increase the translational potential of this work and capture druggable vulnerabilities within different clones, we measured expression/activation of a panel of key drug targets and downstream substrates of FDA-approved or investigational agents. We isolated intermixed clones, including poorly represented ones (<5% of cells), within the tumor microecology and identified molecular characteristics uniquely attributable to cancer cells that undergo lineage plasticity and neuroendocrine transdifferentiation in NSCLCs.

Gene Expression Profiling of Mycosis Fungoides in Early and Tumor Stage-A Proof-of-Concept Study Using Laser Capture/Single Cell Microdissection and NanoString Analysis

A subset of patients with mycosis fungoides (MF) progress to the tumor stage, which correlates with a worse clinical outcome. The molecular events driving this progression are not well-understood. To identify the key molecular drivers, we performed gene expression profiling (GEP) using NanoString. Ten formalin-fixed/paraffin-embedded skin biopsies from six patients (six non-tumor and four tumor MF) were included; non-tumor and tumor samples were available in three patients. Laser capture/single cell microdissection of epidermotropic MF cells was used for non-tumor cases. We found that the RNA extracted from 700-800 single cells was consistently sufficient for GEP, provided that multiplexed target enrichment amplification was used. An un-supervised/hierarchical analysis revealed clustering of non-tumor and tumor cases. Many of the most upregulated or downregulated genes are implicated in the PI3K, RAS, cell cycle/apoptosis and MAPK pathways. Two of the targets, HMGA1 and PTPN11 (encodes SHP2), were validated using immunohistochemistry. HMGA1 was positive in six out of six non-tumor MF samples and negative in five out of five tumor MF samples. An opposite pattern was seen with SHP2. Our study has provided a proof-of-concept that single-cell microdissection/GEP can be applied to archival tissues. Some of our identified gene targets might be key drivers of the disease progression of MF.

Cellular and pathological heterogeneity of primary tauopathies

Microtubule-associated protein tau is abnormally aggregated in neuronal and glial cells in a range of neurodegenerative diseases that are collectively referred to as tauopathies. Multiple studies have suggested that pathological tau species may act as a seed that promotes aggregation of endogenous tau in naïve cells and contributes to propagation of tau pathology. While they share pathological tau aggregation as a common feature, tauopathies are distinct from one another with respect to predominant tau isoforms that accumulate and the selective vulnerability of brain regions and cell types that have tau inclusions. For instance, primary tauopathies present with glial tau pathology, while it is mostly neuronal in Alzheimer's disease (AD). Also, morphologies of tau inclusions can greatly vary even within the same cell type, suggesting distinct mechanisms or distinct tau conformers in each tauopathy. Neuropathological heterogeneity across tauopathies challenges our understanding of pathophysiology behind tau seeding and aggregation, as well as our efforts to develop effective therapeutic strategies for AD and other tauopathies. In this review, we describe diverse neuropathological features of tau inclusions in neurodegenerative tauopathies and discuss what has been learned from experimental studies with mouse models, advanced transcriptomics, and cryo-electron microscopy (cryo-EM) on the biology underlying cell type-specific tau pathology.

Metabolism-Based Gene Differences in Neurons Expressing Hyperphosphorylated AT8- Positive (AT8+) Tau in Alzheimer's Disease

Metabolic adaptations in the brain are critical to the establishment and maintenance of normal cellular functions and to the pathological responses to disease processes. Here, we have focused on specific metabolic pathways that are involved in immune-mediated neuronal processes in brain using isolated neurons derived from human autopsy brain sections of normal individuals and individuals diagnosed as Alzheimer's disease (AD). Laser capture microscopy was used to select specific cell types in immune-stained thin brain sections followed by NanoString technology to identify and quantify differences in mRNA levels between age-matched control and AD neuronal samples. Comparisons were also made between neurons isolated from AD brain sections expressing pathogenic hyperphosphorylated AT8- positive (AT8+) tau and non-AT8+ AD neurons using double labeling techniques. The mRNA expression data showed unique patterns of metabolic pathway expression between the subtypes of captured neurons that involved membrane based solute transporters, redox factors, and arginine and methionine metabolic pathways. We also identified the expression levels of a novel metabolic gene, Radical-S-Adenosyl Domain1 (RSAD1) and its corresponding protein, Rsad1, that impact methionine usage and radical based reactions. Immunohistochemistry was used to identify specific protein expression levels and their cellular location in NeuN+ and AT8+ neurons. APOE4 vs APOE3 genotype-specific and sex-specific gene expression differences in these metabolic pathways were also observed when comparing neurons from individuals with AD to age-matched individuals.

Laser Capture Microdissection-Based RNA Microsequencing Reveals Optic Nerve Crush-Related Early mRNA Alterations in Retinal Ganglion Cell Layer

Purpose

To establish a method of laser capture microdissection (LCM) and RNA microsequencing for exploring optic nerve crush (ONC)–related early mRNA alterations in retinal ganglion cell (RGC) layer.

Methods

An LCM protocol was developed using retinal tissue sections to obtain high-quality RNA for microsequencing. Cells in the RGC layer were collected by laser pressure catapulting (LPC) using a PALM Zeiss UV LCM system. The effect of section thickness and slide type on tissue capture success and RNA yield and the integrity after LCM were evaluated. The optimal LCM protocol was used to explore ONC-related early mRNA alterations in the RGC layer. Candidate genes were validated by real-time polymerase chain reaction of the RGC layer tissue dissected by “cut and LPC” using the same LCM system.

Results

We successfully established an optimal LCM protocol using 30-µm–thick retinal tissue sections mounted on glass slides and laser pressure catapulting (LPC) to collect cells in the RGC layer and to obtain high-quality RNA for microsequencing. On the basis of our protocol, we identified 8744 differentially expressed genes that were involved in ONC-related early mRNA alterations in the RGC layer. Candidate genes included Atf3, Lgals3, LOC102551701, Plaur, Tmem140, and Maml1.

Conclusions

The LCM-based single-cell RNA sequencing allowed a new sight into the early mRNA changes of RGCs highlighting new molecules associated to ONC.

Translational Relevance

This technique will be helpful for more accurate transcriptome analysis of clinical pathological samples of ophthalmology and provide important reference for the discovery of new pathological diagnosis indicators and drug development targets.

Identification of Molecular Signatures in Neural Differentiation and Neurological Diseases Using Digital Color-Coded Molecular Barcoding

Human pluripotent stem cells (PSCs), including embryonic stem cells and induced pluripotent stem cells, represent powerful tools for disease modeling and for therapeutic applications. PSCs are particularly useful for the study of development and diseases of the nervous system. However, generating in vitro models that recapitulate the architecture and the full variety of subtypes of cells that make the complexity of our brain remains a challenge. In order to fully exploit the potential of PSCs, advanced methods that facilitate the identification of molecular signatures in neural differentiation and neurological diseases are highly demanded. Here, we review the literature on the development and application of digital color-coded molecular barcoding as a potential tool for standardizing PSC research and applications in neuroscience. We will also describe relevant examples of the use of this technique for the characterization of the heterogeneous composition of the brain tumor glioblastoma multiforme.

The Role of MicroRNAs in Repair Processes in Multiple Sclerosis

Multiple sclerosis (MS) is an autoimmune disorder characterised by demyelination of central nervous system neurons with subsequent damage, cell death and disability. While mechanisms exist in the CNS to repair this damage, they are disrupted in MS and currently there are no treatments to address this deficit. In recent years, increasing attention has been paid to the influence of the small, non-coding RNA molecules, microRNAs (miRNAs), in autoimmune disorders, including MS. In this review, we examine the role of miRNAs in remyelination in the different cell types that contribute to MS. We focus on key miRNAs that have a central role in mediating the repair process, along with several more that play either secondary or inhibitory roles in one or more aspects. Finally, we consider the current state of miRNAs as therapeutic targets in MS, acknowledging current challenges and potential strategies to overcome them in developing effective novel therapeutics to enhance repair mechanisms in MS.

Tissue-selective regulation of protein homeostasis and unfolded protein response signalling in sporadic ALS

Amyotrophic lateral sclerosis (ALS) is a disorder that affects motor neurons in motor cortex and spinal cord, and the degeneration of both neuronal populations is a critical feature of the disease. Abnormalities in protein homeostasis (proteostasis) are well established in ALS. However, they have been investigated mostly in spinal cord but less so in motor cortex. Herein, we monitored the unfolded protein (UPR) and heat shock response (HSR), two major proteostasis regulatory pathways, in human post‐mortem tissue derived from the motor cortex of sporadic ALS (SALS) and compared them to those occurring in spinal cord. Although the UPR was activated in both tissues, specific expression of select UPR target genes, such as PDIs, was observed in motor cortex of SALS cases strongly correlating with oligodendrocyte markers. Moreover, we found that endoplasmic reticulum‐associated degradation (ERAD) and HSR genes, which were activated predominately in spinal cord, correlated with the expression of neuronal markers. Our results indicate that proteostasis is strongly and selectively activated in SALS motor cortex and spinal cord where subsets of these genes are associated with specific cell type. This study expands our understanding of convergent molecular mechanisms occurring in motor cortex and spinal cord and highlights cell type–specific contributions.

Proteomic Approaches to Decipher Mechanisms Underlying Pathogenesis in Multiple Sclerosis Patients

Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS). The cause of MS is unknown, with no effective therapies available to halt the progressive neurological disability. Development of new and improvement of existing therapeutic strategies therefore require a better understanding of MS pathogenesis, especially during the progressive phase of the disease. This can be achieved through development of biomarkers that can help to identify disease pathophysiology and monitor disease progression. Proteomics is a powerful and promising tool to accelerate biomarker detection and contribute to novel therapeutics. In this review, an overview of how proteomic technology using CNS tissues and biofluids from MS patients has provided important clues to the pathogenesis of MS is provided. Current publications, pitfalls, as well as directions of future research involving proteomic approaches to understand the pathogenesis of MS are discussed.

Genetics of human brain evolution

During the course of evolution the human brain has increased in size and complexity, ultimately these differences are the result of changes at the genetic level. Identifying and characterizing molecular evolution requires an understanding of both the genetic underpinning of the system as well as the comparative genetic tools to identify signatures of selection. This chapter aims to describe our current understanding of the genetics of human brain evolution. Primarily this is the story of the evolution of the human brain since our last common ape ancestor, but where relevant we will also discuss changes that are unique to the primate brain (compared to other mammals) or various other lineages in the evolution of humans more generally. It will focus on genetic changes that both directly affected the development and function of the brain as well as those that have indirectly influenced brain evolution through both prenatal and postnatal environment. This review is not meant to be exhaustive, but rather to begin to construct a general framework for understanding the full array of data being generated.

Fluorescence-Activated Cell Sorting and NanoString Profiling of Single Neural Crest Cells and Pigment Cells

Neural crest cells are an important class of multipotent stem cells, generating highly diverse derivatives. Understanding the gene regulatory networks underlying this process is of great interest, but the highly migratory and thus widely dispersed nature of the differentiating cells makes isolation of cells difficult. Fluorescence-activated cell sorting (FACS) of transgenically labelled neural crest-derived cells after disaggregation of embryos is well-suited to purifying these cells. However, their diverse differentiation means that transcriptional analysis at single cell resolution is necessary to dissect the gene regulatory networks at play. NanoString technology provides a method for highly sensitive, quantitative transcriptional profiling for a pre-defined set of genes of interest. Here we provide a detailed protocol for FACS purification of neural crest-derived cells, sorted as single cells into a multi-well plate, and their subsequent NanoString profiling, using a predetermined gene set focused on pigment cells.

Neocortical Microdissection at Columnar and Laminar Resolution for Molecular Interrogation

The heterogeneous organization of the mammalian neocortex poses a challenge for elucidating the molecular mechanisms underlying its physiological processes. Although high-throughput molecular methods are increasingly deployed in neuroscience, their anatomical specificity is often lacking. In this unit, we introduce a targeted microdissection technique that enables extraction of high-quality RNA and proteins at high anatomical resolution from acutely prepared brain slices. We exemplify its utility by isolating single cortical columns and laminae from the mouse primary somatosensory (barrel) cortex. Tissues can be isolated from living slices in minutes, and the extracted RNA and protein are of sufficient quantity and quality to be used for RNA sequencing and mass spectrometry. This technique will help to increase the anatomical specificity of molecular studies of the neocortex, and the brain in general, as it is applicable to any brain structure that can be identified using optical landmarks in living slices. © 2018 by John Wiley & Sons, Inc.

Cell-Specific RNA Quantification in Human SN DA Neurons from Heterogeneous Post-mortem Midbrain Samples by UV-Laser Microdissection and RT-qPCR

Cell specificity of gene expression analysis is from particular relevance when the abundance of target cells is not homogeneous in the compared tissue samples, like it is the case, e.g., when comparing brain tissues from controls and in neurodegenerative disease states. While single-cell gene expression profiling is already a methodological challenge per se, it becomes even more prone to artifacts when analyzing individual cells from human post-mortem samples. Not only because human samples can never be matched as precisely as those from animal models, but also, because the RNA-quality that can be obtained from human samples usually displays a high range of variability. Here, we detail our most actual method for combining contact-free UV-laser microdissection (UV-LMD) with reverse transcription and quantitative PCR (RT-qPCR) that addresses all these issues. We specifically optimized our protocols to quantify and compare mRNA as well as miRNA levels in human neurons from post-mortem brain tissue. As human post-mortem tissue samples are never perfectly matched (e.g., in respect to distinct donor ages and RNA integrity numbers RIN), we refined data analysis by applying a linear mixed effects model to RT-qPCR data, which allows dissecting and subtracting linear contributions of distinct confounders on detected gene expression levels (i.e., RIN, age). All these issues were considered for comparative gene expression analysis in dopamine (DA) midbrain neurons of the Substantia nigra (SN) from controls and Parkinson's disease (PD) specimens, as the preferential degeneration of SN DA neurons in the pathological hallmark of PD. By utilizing the here-described protocol we identified that a variety of genes-encoding for ion channels, dopamine metabolism proteins, and PARK gene products-display a transcriptional dysregulation in remaining human SN DA neurons from PD brains compared to those of controls. We show that the linear mixed effects model allows further stratification of RT-qPCR data, as it indicated that differential gene expression of some genes was rather correlated with different ages of the analyzed human brain samples than with the disease state.

Laser microdissection: A powerful tool for genomics at cell level

Laser microdissection (LM) has become widely democratized over the last fifteen years. Instruments have evolved to offer more powerful and efficient lasers as well as new options for sample collection and preparation. Technological evolutions have also focused on the post-microdissection analysis capabilities, opening up investigations in all disciplines of experimental and clinical biology, thanks to the advent of new high-throughput methods of genome analysis, including RNAseq and proteomics, now globally known as microgenomics, i.e. analysis of biomolecules at the cell level. In spite of the advances these rapidly developing methods have allowed, the workflow for sampling and collection by LM remains a critical step in insuring sample integrity in terms of histology (accurate cell identification) and biochemistry (reliable analyzes of biomolecules). In this review, we describe the sample processing as well as the strengths and limiting factors of LM applied to the specific selection of one or more cells of interest from a heterogeneous tissue. We will see how the latest developments in protocols and methods have made LM a powerful and sometimes essential tool for genomic and proteomic analyzes of tiny amounts of biomolecules extracted from few cells isolated from a complex tissue, in their physiological context, thus offering new opportunities for understanding fundamental physiological and/or patho-physiological processes.

Neuropathology of suicide: recent findings and future directions

Suicide is a major public health concern and a leading cause of death in most societies. Suicidal behaviour is complex and heterogeneous, likely resulting from several causes. It associates with multiple factors, including psychopathology, personality traits, early-life adversity and stressful life events, among others. Over the past decades, studies in fields ranging from neuroanatomy, genetics and molecular psychiatry have led to a model whereby behavioural dysregulation, including suicidal behaviour (SB), develops as a function of biological adaptations in key brain systems. More recently, the unravelling of the unique epigenetic processes that occur in the brain has opened promising avenues in suicide research. The present review explores the various facets of the current knowledge on suicidality and discusses how the rapidly evolving field of neurobehavioural epigenetics may fuel our ability to understand, and potentially prevent, SB.