scholarly journals A molecular calcium integrator reveals a striatal cell-type driving aversion

2020 ◽  
Author(s):  
Christina K. Kim ◽  
Mateo I. Sanchez ◽  
Paul Hoerbelt ◽  
Lief E. Fenno ◽  
Robert C. Malenka ◽  
...  
Keyword(s):  
Nucleus Accumbens ◽  
Large Scale ◽  
Calcium Concentration ◽  
Modular Design ◽  
Cell Type ◽  
Neural Ensembles ◽  
Cellular Events ◽  
Large Scale Analysis ◽  
Genetic Tagging ◽  
A Cell

SUMMARYThe ability to record transient cellular events in the DNA or RNA of cells would enable precise, large-scale analysis, selection, and reprogramming of heterogeneous cell populations. Here we report a molecular technology for stable genetic tagging of cells that exhibit activity-related increases in intracellular calcium concentration (FLiCRE). We used FLiCRE to transcriptionally label activated neural ensembles in the nucleus accumbens of the mouse brain during brief stimulation of aversive inputs. Using single-cell RNA sequencing, we detected FLiCRE transcripts among the endogenous transcriptome, providing simultaneous readout of both cell-type and calcium activation history. We identified a cell-type in the nucleus accumbens activated downstream of long-range excitatory projections. Taking advantage of FLiCRE’s modular design, we expressed an optogenetic channel selectively in this cell-type, and showed that direct recruitment of this otherwise genetically-inaccessible population elicits behavioral aversion. The specificity and minute-resolution of FLiCRE enables molecularly-informed characterization, manipulation, and reprogramming of activated cellular ensembles.

scholarly journals ASCOT identifies key regulators of neuronal subtype-specific splicing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan P. Ling ◽  
Christopher Wilks ◽  
Rone Charles ◽  
Patrick J. Leavey ◽  
Devlina Ghosh ◽  
...  
Keyword(s):  
Rna Splicing ◽  
Large Scale ◽  
Splice Variants ◽  
Next Generation Sequencing Data ◽  
Data Sets ◽  
Cell Type ◽  
Sequencing Data ◽  
Large Scale Analysis ◽  
Cell Type Specific ◽  
Public Archives

AbstractPublic archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that uses annotation-free methods to rapidly analyze and visualize splice variants across tens of thousands of bulk and single-cell data sets in the public archive. To demonstrate the utility of ASCOT, we identify novel cell type-specific alternative exons across the nervous system and leverage ENCODE and GTEx data sets to study the unique splicing of photoreceptors. We find that PTBP1 knockdown and MSI1 and PCBP2 overexpression are sufficient to activate many photoreceptor-specific exons in HepG2 liver cancer cells. This work demonstrates how large-scale analysis of public RNA-Seq data sets can yield key insights into cell type-specific control of RNA splicing and underscores the importance of considering both annotated and unannotated splicing events.

scholarly journals Exploring the Landscape of Ectodomain Shedding by Quantitative Protein Terminomics

2020 ◽  
Author(s):  
Kazuya Tsumagari ◽  
Chih-Hsiang Chang ◽  
Yasushi Ishihama
Keyword(s):  
Membrane Proteins ◽  
Large Scale ◽  
Culture Media ◽  
Ectodomain Shedding ◽  
Cleavage Sites ◽  
Cell Type ◽  
Knowledge Based ◽  
A Cell ◽  
Cell Type Specific ◽  
Peptide Enrichment

AbstractEctodomain shedding is a proteolytic process that regulates the levels and functions of membrane proteins. Dysregulated shedding is linked to severe diseases, including cancer and Alzheimer’s disease. However, the exact cleavage sites of shedding substrates remain largely unknown. Here, we explore the landscape of ectodomain shedding by generating large-scale, cell-type-specific maps of shedding cleavage sites. By means of N- and C-terminal peptide enrichment and quantitative mass spectrometry, we quantified protein termini in the culture media of 10 human cell lines and identified 411 cleavage sites on the ectodomain of 132 membrane proteins whose proteolytic terminal fragments are downregulated in the presence of a broad-spectrum metalloprotease inhibitor. A major fraction of the presented cleavage sites was identified in a cell-type-specific manner, and mapped onto receptors, cell adhesion molecules, and protein kinases and phosphatases. We confidently identified 86 cleavage sites as metalloprotease substrates by means of knowledge-based scoring.

scholarly journals Cell type-specific changes in retinal ganglion cell function induced by rod death and cone reorganization in rats

2017 ◽  
Vol 118 (1) ◽  
pp. 434-454 ◽  
Author(s):  
Wan-Qing Yu ◽  
Norberto M. Grzywacz ◽  
Eun-Jin Lee ◽  
Greg D. Field
Keyword(s):  
Ganglion Cell ◽  
Spontaneous Activity ◽  
Retinal Ganglion Cell ◽  
Large Scale ◽  
Retinal Ganglion ◽  
Cell Type ◽  
Specific Manner ◽  
A Cell ◽  
Cell Type Specific ◽  
The Impact

We have determined the impact of rod death and cone reorganization on the spatiotemporal receptive fields (RFs) and spontaneous activity of distinct retinal ganglion cell (RGC) types. We compared RGC function between healthy and retinitis pigmentosa (RP) model rats (S334ter-3) at a time when nearly all rods were lost but cones remained. This allowed us to determine the impact of rod death on cone-mediated visual signaling, a relevant time point because the diagnosis of RP frequently occurs when patients are nightblind but daytime vision persists. Following rod death, functionally distinct RGC types persisted; this indicates that parallel processing of visual input remained largely intact. However, some properties of cone-mediated responses were altered ubiquitously across RGC types, such as prolonged temporal integration and reduced spatial RF area. Other properties changed in a cell type-specific manner, such as temporal RF shape (dynamics), spontaneous activity, and direction selectivity. These observations identify the extent of functional remodeling in the retina following rod death but before cone loss. They also indicate new potential challenges to restoring normal vision by replacing lost rod photoreceptors. NEW & NOTEWORTHY This study provides novel and therapeutically relevant insights to retinal function following rod death but before cone death. To determine changes in retinal output, we used a large-scale multielectrode array to simultaneously record from hundreds of retinal ganglion cells (RGCs). These recordings of large-scale neural activity revealed that following the death of all rods, functionally distinct RGCs remain. However, the receptive field properties and spontaneous activity of these RGCs are altered in a cell type-specific manner.

scholarly journals HDAC3 Activity within the Nucleus Accumbens Regulates Cocaine-induced Plasticity and Behavior in a Cell-Type Specific Manner

2021 ◽  
pp. JN-RM-2829-20
Author(s):  
RR Campbell ◽  
EA Kramár ◽  
L Pham ◽  
JH Beardwood ◽  
AS Augustynski ◽  
...  
Keyword(s):  
Nucleus Accumbens ◽  
Cell Type ◽  
Specific Manner ◽  
A Cell ◽  
Cell Type Specific ◽  
And Behavior

scholarly journals CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

Science ◽  
2016 ◽  
Vol 355 (6320) ◽  
pp. eaah7111 ◽  
Author(s):  
S. John Liu ◽  
Max A. Horlbeck ◽  
Seung Woo Cho ◽  
Harjus S. Birk ◽  
Martina Malatesta ◽  
...  
Keyword(s):  
Cell Lines ◽  
Noncoding Rna ◽  
Large Scale ◽  
Cellular Growth ◽  
Transcriptional Networks ◽  
Cell Type ◽  
Cell Type Specificity ◽  
A Cell ◽  
Induced Pluripotent ◽  
Transformed Cell Lines

The human genome produces thousands of long noncoding RNAs (lncRNAs)—transcripts >200 nucleotides long that do not encode proteins. Although critical roles in normal biology and disease have been revealed for a subset of lncRNAs, the function of the vast majority remains untested. We developed a CRISPR interference (CRISPRi) platform targeting 16,401 lncRNA loci in seven diverse cell lines, including six transformed cell lines and human induced pluripotent stem cells (iPSCs). Large-scale screening identified 499 lncRNA loci required for robust cellular growth, of which 89% showed growth-modifying function exclusively in one cell type. We further found that lncRNA knockdown can perturb complex transcriptional networks in a cell type–specific manner. These data underscore the functional importance and cell type specificity of many lncRNAs.

scholarly journals Multiplex recording of cellular events over time on CRISPR biological tape

Science ◽  
2017 ◽  
Vol 358 (6369) ◽  
pp. 1457-1461 ◽  
Author(s):  
Ravi U. Sheth ◽  
Sung Sun Yim ◽  
Felix L. Wu ◽  
Harris H. Wang
Keyword(s):  
Cell Population ◽  
Large Scale ◽  
Environmental Changes ◽  
Biological Information ◽  
Cellular Events ◽  
Biological Signals ◽  
A Cell ◽  
Temporal Measurement ◽  
New Applications ◽  
Over Time

Although dynamics underlie many biological processes, our ability to robustly and accurately profile time-varying biological signals and regulatory programs remains limited. Here we describe a framework for storing temporal biological information directly in the genomes of a cell population. We developed a “biological tape recorder” in which biological signals trigger intracellular DNA production that is then recorded by the CRISPR-Cas adaptation system. This approach enables stable recording over multiple days and accurate reconstruction of temporal and lineage information by sequencing CRISPR arrays. We further demonstrate a multiplexing strategy to simultaneously record the temporal availability of three metabolites (copper, trehalose, and fucose) in the environment of a cell population over time. This work enables the temporal measurement of dynamic cellular states and environmental changes and suggests new applications for chronicling biological events on a large scale.

Dendritic cells of the human epidermis: immuno-electron microscopic studies of la antigen reactivity

1978 ◽  
Vol 36 (2) ◽  
pp. 644-645
Author(s):  
G. Rowden ◽  
M. G. Lewis ◽  
T. M. Phillips
Keyword(s):  
Dendritic Cells ◽  
Langerhans Cells ◽  
Cell Types ◽  
Cell Type ◽  
Electron Microscopic ◽  
La Antigen ◽  
Microscopic Studies ◽  
A Cell ◽  
C3 Receptors ◽  
Antigen Reactivity

Langerhans cells of mammalian stratified squamous epithelial have proven to be an enigma since their discovery in 1868. These dendritic suprabasal cells have been considered as related to melanocytes either as effete cells, or as post divisional products. Although grafting experiments seemed to demonstrate the independence of the cell types, much confusion still exists. The presence in the epidermis of a cell type with morphological features seemingly shared by melanocytes and Langerhans cells has been especially troublesome. This so called "indeterminate", or " -dendritic cell" lacks both Langerhans cells granules and melanosomes, yet it is clearly not a keratinocyte. Suggestions have been made that it is related to either Langerhans cells or melanocyte. Recent studies have unequivocally demonstrated that Langerhans cells are independent cells with immune function. They display Fc and C3 receptors on their surface as well as la (immune region associated) antigens.

IFIH1-deficiency results in a cell-type specific alteration of autophagic activity in response to S. typhimurium

2017 ◽  
Vol 55 (05) ◽  
pp. e28-e56
Author(s):  
S Macheiner ◽  
R Gerner ◽  
A Pfister ◽  
A Moschen ◽  
H Tilg
Keyword(s):  
Cell Type ◽  
A Cell ◽  
Cell Type Specific ◽  
Autophagic Activity ◽  
Specific Alteration
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