Disease-, region- and cell type specific diversity of α-synuclein carboxy terminal truncations in synucleinopathies

AbstractSynucleinopathies, including Parkinson’s disease (PD), Lewy body dementia (LBD), Alzheimer’s disease with amygdala restricted Lewy bodies (AD/ALB), and multiple system atrophy (MSA) comprise a spectrum of neurodegenerative disorders characterized by the presence of distinct pathological α-synuclein (αSyn) inclusions. Experimental and pathological studies support the notion that αSyn aggregates contribute to cellular demise and dysfunction with disease progression associated with a prion-like spread of αSyn aggregates via conformational templating. The initiating event(s) and factors that contribute to diverse forms of synucleinopathies remain poorly understood. A major post-translational modification of αSyn associated with pathological inclusions is a diverse array of specific truncations within the carboxy terminal region. While these modifications have been shown experimentally to induce and promote αSyn aggregation, little is known about their disease-, region- and cell type specific distribution. To this end, we generated a series of monoclonal antibodies specific to neo-epitopes in αSyn truncated after residues 103, 115, 119, 122, 125, and 129. Immunocytochemical investigations using these new tools revealed striking differences in the αSyn truncation pattern between different synucleinopathies, brain regions and specific cellular populations. In LBD, neuronal inclusions in the substantia nigra and amygdala were positive for αSyn cleaved after residues 103, 119, 122, and 125, but not 115. In contrast, in the same patients' brain αSyn cleaved at residue 115, as well as 103, 119 and 122 were abundant in the dorsal motor nucleus of the vagus. In patients with AD/ALB, these modifications were only weakly or not detected in amygdala αSyn inclusions. αSyn truncated at residues 103, 115, 119, and 125 was readily present in MSA glial cytoplasmic inclusions, but 122 cleaved αSyn was only weakly or not present. Conversely, MSA neuronal pathology in the pontine nuclei was strongly reactive to the αSyn x-122 neo-epitope but did not display any reactivity for αSyn 103 cleavage. These studies demonstrate significant disease-, region- and cell type specific differences in carboxy terminal αSyn processing associated with pathological inclusions that likely contributes to their distinct strain-like prion properties and promotes the diversity displayed in the degrees of these insidious diseases.

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Cortical structural differences in major depressive disorder correlate with cell type-specific transcriptional signatures

Nature Communications ◽

10.1038/s41467-021-21943-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Jiao Li ◽

Jakob Seidlitz ◽

John Suckling ◽

Feiyang Fan ◽

Gong-Jun Ji ◽

...

Keyword(s):

Gene Expression ◽

Major Depressive Disorder ◽

Depressive Disorder ◽

Structural Changes ◽

Brain Regions ◽

Cell Type ◽

Major Depressive ◽

Structural Differences ◽

Neuroimaging Data ◽

Cell Type Specific

AbstractMajor depressive disorder (MDD) has been shown to be associated with structural abnormalities in a variety of spatially diverse brain regions. However, the correlation between brain structural changes in MDD and gene expression is unclear. Here, we examine the link between brain-wide gene expression and morphometric changes in individuals with MDD, using neuroimaging data from two independent cohorts and a publicly available transcriptomic dataset. Morphometric similarity network (MSN) analysis shows replicable cortical structural differences in individuals with MDD compared to control subjects. Using human brain gene expression data, we observe that the expression of MDD-associated genes spatially correlates with MSN differences. Analysis of cell type-specific signature genes suggests that microglia and neuronal specific transcriptional changes account for most of the observed correlation with MDD-specific MSN differences. Collectively, our findings link molecular and structural changes relevant for MDD.

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The expression and localization of V-ATPase and cytokeratin 5 during postnatal development of the pig epididymis

Asian-Australasian Journal of Animal Sciences ◽

10.5713/ajas.19.0587 ◽

2020 ◽

Vol 33 (7) ◽

pp. 1077-1086 ◽

Cited By ~ 2

Author(s):

Yun-Jae Park ◽

Ji-Hyuk Kim ◽

Hack-Youn Kim ◽

Hee-Bok Park ◽

Juhui Choe ◽

...

Keyword(s):

Epithelial Cells ◽

Expression Patterns ◽

Basal Cells ◽

Cell Type ◽

Clear Cells ◽

Specific Distribution ◽

Cytokeratin 5 ◽

Cell Type Specific ◽

Immunofluorescence Labeling ◽

And Storage

Objective: We examined the localization and expression of H<sup>+ pumping vacuolar ATPase (V-ATPase) and cytokeratin 5 (KRT5) in the epididymis of pigs, expressed in clear and basal cells, respectively, during postnatal development.Methods: Epididymides were obtained from pigs at 1, 7, 21, 60, 120, and 180 days of age; we observed the localization and expression patterns of V-ATPase and KRT5 in the different regions of these organs, namely, the caput, corpus, and cauda. The differentiation of epididymal epithelial cells was determined by immunofluorescence labeling using cell-type-specific markers and observed using confocal microscopy.Results: At postnatal day 5 (PND5), the localization of clear cells commenced migration from the cauda toward the caput. Although at PND120, goblet-shaped clear cells were detected along the entire length of the epididymis, those labeled for V-ATPase had disappeared from the corpus to cauda and were maintained only in the caput epididymis in adult pigs. In contrast, whereas basal cells labeled for KRT5 were only present in the vas deferens at birth, they were detected in all regions of the epididymis at PND60. These cells were localized at the base of the epithelium; however, no basal cells characterized by luminally extending cell projections were observed in any of the adult epididymides examined.Conclusion: The differentiation of clear and basal cells progressively initiates in a retrograde manner from the cauda to the caput epididymis. The cell-type-specific distribution and localization of the epithelial cells play important roles in establishing a unique luminal environment for sperm maturation and storage in the pig epididymis.

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Using multiple measurements of tissue to estimate subject- and cell-type-specific gene expression

Bioinformatics ◽

10.1093/bioinformatics/btz619 ◽

2019 ◽

Vol 36 (3) ◽

pp. 782-788 ◽

Cited By ~ 6

Author(s):

Jiebiao Wang ◽

Bernie Devlin ◽

Kathryn Roeder

Keyword(s):

Gene Expression ◽

Empirical Bayes ◽

Brain Regions ◽

Tissue Level ◽

Supplementary Information ◽

Specific Gene ◽

Expression Data ◽

Cell Type ◽

Multiple Measurements ◽

Cell Type Specific

Abstract Motivation Patterns of gene expression, quantified at the level of tissue or cells, can inform on etiology of disease. There are now rich resources for tissue-level (bulk) gene expression data, which have been collected from thousands of subjects, and resources involving single-cell RNA-sequencing (scRNA-seq) data are expanding rapidly. The latter yields cell type information, although the data can be noisy and typically are derived from a small number of subjects. Results Complementing these approaches, we develop a method to estimate subject- and cell-type-specific (CTS) gene expression from tissue using an empirical Bayes method that borrows information across multiple measurements of the same tissue per subject (e.g. multiple regions of the brain). Analyzing expression data from multiple brain regions from the Genotype-Tissue Expression project (GTEx) reveals CTS expression, which then permits downstream analyses, such as identification of CTS expression Quantitative Trait Loci (eQTL). Availability and implementation We implement this method as an R package MIND, hosted on https://github.com/randel/MIND. Supplementary information Supplementary data are available at Bioinformatics online.

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The carboxy-terminal transactivation domain of Oct-4 acquires cell specificity through the POU domain.

Molecular and Cellular Biology ◽

10.1128/mcb.17.1.154 ◽

1997 ◽

Vol 17 (1) ◽

pp. 154-162 ◽

Cited By ~ 67

Author(s):

A Brehm ◽

K Ohbo ◽

H Schöler

Keyword(s):

Dna Binding ◽

Cell Lines ◽

Regulatory Mechanism ◽

Cell Types ◽

Binding Domain ◽

Dna Binding Domain ◽

Cell Type ◽

Pou Domain ◽

Cell Type Specific ◽

Carboxy Terminal

The POU transcription factor Oct-4 is expressed in totipotent and pluripotent cells of the early mouse embryo and the germ cell lineage. Transactivation capacities of regions flanking the DNA binding domain of Oct-4 were analyzed in undifferentiated and differentiated cell lines. The amino- and carboxy-terminal regions (N domain and C domain) fused to the Gal4 DNA binding domain both functioned as transactivation domains in all cell lines tested. However, the C domain failed to activate transcription in some cell lines in the context of the native protein. The underlying regulatory mechanism appears to involve the POU domain of Oct-4 and can discriminate between different POU domains, since constructs in which the C domain was instead fused to the POU domain of Pit-1 were again equally active in all cell lines. These results indicate that the C domain is subject to cell-type-specific regulation mediated by the Oct-4 POU domain. Phosphopeptide analysis revealed that the cell-type-specific difference of C-domain activity correlates with a difference in Oct-4 phosphorylation status. Since Oct-4 is expressed in a variety of distinct cell types during murine embryogenesis, these results suggest an additional regulatory mechanism for determining Oct-4 function in rapidly changing cell types during development.

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Highly efficient and super-bright neurocircuit tracing using vector mixing-based virus cocktail

10.1101/705772 ◽

2019 ◽

Cited By ~ 2

Author(s):

Pei Sun ◽

Sen Jin ◽

Sijue Tao ◽

Junjun Wang ◽

Anan Li ◽

...

Keyword(s):

Brain Function ◽

Individual Cell ◽

Brain Regions ◽

Cell Type ◽

Current Standard ◽

Functional Studies ◽

Highly Efficient ◽

Order Of Magnitude ◽

Cell Type Specific ◽

Dependent Vector

ABSTRACTMapping the detailed cell-type-specific input networks and neuronal projectomes are essential to understand brain function in normal and pathological states. However, several properties of current tracing systems, including labeling sensitivity, trans-synaptic efficiencies, reproducibility among different individuals and different Cre-driver animals, still remained unsatisfactory. Here, we developed MAP-ENVIVIDERS, a recombinase system-dependent vector mixing-based strategy for highly efficient neurocircuit tracing. MAP-ENVIVIDERS enhanced tracing efficiency of input networks across the whole brain, with over 10-fold improvement in diverse previously poor-labeled input brain regions and particularly, up to 70-fold enhancement in brainstem compared with the current standard rabies-virus-mediated systems. MAP-ENVIVIDERS was over 10-fold more sensitive for cell-type-specific labeling than previous strategies, enabling us to capture individual cell-type-specific neurons with extremely complex axonal branches and presynaptic axonal boutons, both about one order of magnitude than previously reported and considered. MAP-ENVIVIDERS provides powerful tools for deconstructing novel input/output circuitry towards functional studies and disorders-related mechanisms.

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Cell-type specific distribution of chloride transporters in the rat suprachiasmatic nucleus

Neuroscience ◽

10.1016/j.neuroscience.2009.11.040 ◽

2010 ◽

Vol 165 (4) ◽

pp. 1519-1537 ◽

Cited By ~ 39

Author(s):

M.A. Belenky ◽

P.J. Sollars ◽

D.B. Mount ◽

S.L. Alper ◽

Y. Yarom ◽

...

Keyword(s):

Suprachiasmatic Nucleus ◽

Cell Type ◽

Specific Distribution ◽

Cell Type Specific

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Acoustically Targeted Chemogenetics for Noninvasive Control of Neural Circuits

10.1101/241406 ◽

2018 ◽

Cited By ~ 2

Author(s):

Jerzy O. Szablowski ◽

Brian Lue ◽

Audrey Lee-Gosselin ◽

Dina Malounda ◽

Mikhail G. Shapiro

Keyword(s):

Neural Circuits ◽

Brain Regions ◽

Cell Type ◽

Spatial Targeting ◽

Temporal Specificity ◽

Cell Type Specific ◽

Orally Bioavailable ◽

G Protein Coupled ◽

The Brain ◽

Spatial Cell

ABSTRACTNeurological and psychiatric diseases often involve the dysfunction of specific neural circuits in particular regions of the brain. Existing treatments, including drugs and implantable brain stimulators, aim to modulate the activity of these circuits, but are typically not cell type-specific, lack spatial targeting or require invasive procedures. Here, we introduce an approach to modulating neural circuits noninvasively with spatial, cell-type and temporal specificity. This approach, called acoustically targeted chemogenetics, or ATAC, uses transient ultrasonic opening of the blood brain barrier to transduce neurons at specific locations in the brain with virally-encoded engineered G-protein-coupled receptors, which subsequently respond to systemically administered bio-inert compounds to activate or inhibit the activity of these neurons. We demonstrate this concept in mice by using ATAC to noninvasively modify and subsequently activate or inhibit excitatory neurons within the hippocampus, showing that this enables pharmacological control of memory formation. This technology allows a brief, noninvasive procedure to make one or more specific brain regions capable of being selectively modulated using orally bioavailable compounds, thereby overcoming some of the key limitations of conventional brain therapies.

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Mass Cytometry for Multivariate Organoid Signalling Analysis

10.21203/rs.2.16232/v2 ◽

2020 ◽

Author(s):

Xiao Qin ◽

Jahangir Sufi ◽

Petra Vlckova ◽

Pelagia Kyriakidou ◽

Sophie E. Acton ◽

...

Keyword(s):

Single Cell ◽

High Throughput ◽

Single Cell Analysis ◽

Cell Type ◽

Mass Cytometry ◽

Post Translational Modification ◽

Specific Analysis ◽

Cell Type Specific ◽

Tissue Models

Abstract Organoids are powerful biomimetic tissue models. Despite their increasing popularity, no existing methods are suitable for cell-type specific analysis of post-translational modification (PTM) signalling networks in organoids. Here we report a multivariate mass cytometry (MC) protocol for single-cell analysis of cell-type specific PTM signalling in organoid monocultures and organoids co-cultured with stromal and immune cells. Thiol-reactive Organoid Barcoding in situ (TOBis) was developed to facilitate high-throughput comparison of signalling networks between organoid cultures. Taken together, our protocol enables high-throughput multivariate PTM signalling analysis of healthy and cancerous organoids at the single-cell level.

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Single-Cell Signalling Analysis of Heterocellular Organoids

10.1101/659896 ◽

2019 ◽

Cited By ~ 2

Author(s):

Xiao Qin ◽

Jahangir Sufi ◽

Petra Vlckova ◽

Pelagia Kyriakidou ◽

Sophie E. Acton ◽

...

Keyword(s):

Single Cell ◽

High Throughput ◽

Single Cell Analysis ◽

Cell Signalling ◽

Tumour Microenvironment ◽

Cell Type ◽

Mass Cytometry ◽

Post Translational Modification ◽

Stromal Fibroblasts ◽

Cell Type Specific

Organoids are powerful biomimetic tissue models. Despite their widespread adoption, methods to analyse cell-type specific post-translational modification (PTM) signalling networks in organoids are absent. Here we report multivariate single-cell analysis of cell-type specific signalling networks in organoids and organoid co-cultures. Simultaneous measurement of 28 PTMs in >1 million single small intestinal organoid cells by mass cytometry reveals cell-type and cell-state specific signalling networks in stem, Paneth, enteroendocrine, tuft, goblet cells, and enterocytes. Integrating single-cell PTM analysis with Thiol-reactive Organoid Barcoding in situ (TOBis) enables high-throughput comparison of signalling networks between organoid cultures. Multivariate cell-type specific PTM analysis of colorectal cancer tumour microenvironment organoids reveals that shApc, KrasG12D, and Trp53R172H cell-autonomously mimic signalling states normally induced by stromal fibroblasts and macrophages. These results demonstrate how standard mass cytometry workflows can be modified to perform high-throughput multivariate cell-type specific signalling analysis of healthy and cancerous organoids.

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Addiction-associated genetic variants implicate brain cell type- and region-specific cis-regulatory elements in addiction neurobiology

10.1101/2020.09.29.318329 ◽

2020 ◽

Cited By ~ 1

Author(s):

Chaitanya Srinivasan ◽

BaDoi N. Phan ◽

Alyssa J. Lawler ◽

Easwaran Ramamurthy ◽

Michael Kleyman ◽

...

Keyword(s):

Genetic Variants ◽

Cell Types ◽

Regulatory Elements ◽

Brain Regions ◽

Open Chromatin ◽

Genome Wide Association Studies ◽

Cell Type ◽

Coding Regions ◽

Cell Type Specific ◽

The Impact

ABSTRACTRecent large genome-wide association studies (GWAS) have identified multiple confident risk loci linked to addiction-associated behavioral traits. Genetic variants linked to addiction-associated traits lie largely in non-coding regions of the genome, likely disrupting cis-regulatory element (CRE) function. CREs tend to be highly cell type-specific and may contribute to the functional development of the neural circuits underlying addiction. Yet, a systematic approach for predicting the impact of risk variants on the CREs of specific cell populations is lacking. To dissect the cell types and brain regions underlying addiction-associated traits, we applied LD score regression to compare GWAS to genomic regions collected from human and mouse assays for open chromatin, which is associated with CRE activity. We found enrichment of addiction-associated variants in putative regulatory elements marked by open chromatin in neuronal (NeuN+) nuclei collected from multiple prefrontal cortical areas and striatal regions known to play major roles in reward and addiction. To further dissect the cell type-specific basis of addiction-associated traits, we also identified enrichments in human orthologs of open chromatin regions of mouse neuron subtypes: cortical excitatory, PV, D1, and D2. Lastly, we developed machine learning models from mouse cell type-specific regions of open chromatin to further dissect human NeuN+ open chromatin regions into cortical excitatory or striatal D1 and D2 neurons and predict the functional impact of addiction-associated genetic variants. Our results suggest that different neuron subtypes within the reward system play distinct roles in the variety of traits that contribute to addiction.Significance StatementOur study on cell types and brain regions contributing to heritability of addiction-associated traits suggests that the conserved non-coding regions within cortical excitatory and striatal medium spiny neurons contribute to genetic predisposition for nicotine, alcohol, and cannabis use behaviors. This computational framework can flexibly integrate epigenomic data across species to screen for putative causal variants in a cell type- and tissue-specific manner across numerous complex traits.

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