scholarly journals Conservation and divergence in cortical cellular organization between human and mouse revealed by single-cell transcriptome imaging

2021 ◽  
Author(s):  
Rongxin Fang ◽  
Chenglong Xia ◽  
Meng Zhang ◽  
Jiang He ◽  
Jennie Close ◽  
...  
Keyword(s):  
Single Cell ◽  
Neuronal Cell ◽  
Cell Interactions ◽  
Specific Cell ◽  
Interaction Patterns ◽  
Cellular Organization ◽  
Human Cortex ◽  
Spatially Resolved ◽  
Human And Mouse ◽  
Cell Cell

The human cerebral cortex has tremendous cellular diversity and complex cellular organization that are essential for brain function. How different types of cells are organized and interact with each other in the human cortex, and how cellular organizations and interaction patterns vary across species are, however, unclear. Here, we performed spatially resolved single-cell expression profiling of 4,000 genes in human middle and superior temporal gyrus using multiplexed error-robust fluorescence in situ hybridization (MERFISH). We identified >100 neuronal and non-neuronal cell populations with distinct transcriptional signatures, generated a molecularly defined and spatially resolved cell atlas of these brain regions, and analyzed cell-cell interactions in a cell-type-specific manner. Comparison with the mouse cortex showed conservation in the laminar organization of cells and substantial divergence in cell-cell interactions between human and mouse. Notably, our data revealed a drastic increase in interactions between neurons and non-neuronal cells in the human cortex, uncovered human-specific cell-cell interaction patterns, and identified potential ligand-receptor basis of microglia-neuron interactions.

scholarly journals Engineering reversible cell–cell interactions using enzymatically lipidated chemically self-assembled nanorings

2021 ◽  
Vol 12 (1) ◽  
pp. 331-340
Author(s):  
Yiao Wang ◽  
Ozgun Kilic ◽  
Clifford M. Csizmar ◽  
Sudhat Ashok ◽  
James L. Hougland ◽  
...  
Keyword(s):  
Cell Interactions ◽  
Specific Cell ◽  
Therapeutic Applications ◽  
Self Assembled ◽  
Cell Cell

Multicellular biology is dependent on the control of cell-cell interactions. The prenylated antigen-targeted CSANs provide a general approach for the regulation of specific cell-cell interactions and will be valuable for a plethora of fundamental and therapeutic applications.

scholarly journals Localization and site-specific cell–cell interactions of group 2 innate lymphoid cells

2021 ◽  
Author(s):  
Kiniwa Tsuyoshi ◽  
Kazuyo Moro
Keyword(s):  
Lipid Production ◽  
Allergic Diseases ◽  
Innate Lymphoid Cells ◽  
The Body ◽  
Cell Interactions ◽  
Lymphoid Cells ◽  
Specific Cell ◽  
Inflammatory Conditions ◽  
Group 2 ◽  
Cell Cell

Abstract Group 2 innate lymphoid cells (ILC2s) are novel lymphocytes discovered in 2010. Unlike T or B cells, ILC2s are activated nonspecifically by environmental factors and produce various cytokines, thus playing a role in tissue homeostasis, diseases including allergic diseases, and parasite elimination. ILC2s were first reported as cells abundantly present in fat-associated lymphoid clusters in adipose tissue. However, subsequent studies revealed their presence in various tissues throughout the body, acting as key players in tissue-specific diseases. Recent histologic analyses revealed that ILC2s are concentrated in specific regions in tissues, such as the lamina propria and perivascular regions, with their function being controlled by the surrounding cells, such as epithelial cells and other immune cells, via cytokine and lipid production or by cell–cell interactions through surface molecules. Especially, some stromal cells are identified as the niche cells for ILC2s, both in the steady state and under inflammatory conditions, through the production of IL-33 or extracellular-matrix factors. Additionally, peripheral neurons reportedly co-localize with ILC2s and alter their function directly through neurotransmitters. These findings suggest that the different localizations or different cell–cell interactions might affect the function of ILC2s. Furthermore, generally, ILC2s are thought to be tissue-resident cells; however, they occasionally migrate to other tissues and perform a new role; this supports the importance of the microenvironment for their function. We summarize here the current understanding of how the microenvironment controls ILC2 localization and function with the aim of promoting the development of novel diagnostic and therapeutic methods.

Abstract 3391: Dissecting intratumoral cell-cell interactions in myeloid reprogramming by single cell RNA-seq

2019 ◽  
Author(s):  
Qianqian Song ◽  
Gregory A. Hawkins ◽  
Leonard Wudel ◽  
Ping-Chieh Chou ◽  
Elizabeth Forbes ◽  
...  
Keyword(s):  
Single Cell ◽  
Cell Interactions ◽  
Rna Seq ◽  
Cell Cell

scholarly journals Identifying signaling genes in spatial single-cell expression data

2020 ◽  
Author(s):  
Dongshunyi Li ◽  
Jun Ding ◽  
Ziv Bar-Joseph
Keyword(s):  
Single Cell ◽  
Cell Interactions ◽  
Excitatory Neuron ◽  
Expression Data ◽  
Mixture Of Experts ◽  
Prediction Of Response ◽  
Technological Advances ◽  
A Cell ◽  
Cell Expression ◽  
Cell Cell

Abstract Motivation Recent technological advances enable the profiling of spatial single-cell expression data. Such data present a unique opportunity to study cell–cell interactions and the signaling genes that mediate them. However, most current methods for the analysis of these data focus on unsupervised descriptive modeling, making it hard to identify key signaling genes and quantitatively assess their impact. Results We developed a Mixture of Experts for Spatial Signaling genes Identification (MESSI) method to identify active signaling genes within and between cells. The mixture of experts strategy enables MESSI to subdivide cells into subtypes. MESSI relies on multi-task learning using information from neighboring cells to improve the prediction of response genes within a cell. Applying the methods to three spatial single-cell expression datasets, we show that MESSI accurately predicts the levels of response genes, improving upon prior methods and provides useful biological insights about key signaling genes and subtypes of excitatory neuron cells. Availability and implementation MESSI is available at: https://github.com/doraadong/MESSI

scholarly journals Single-Cell Transcriptomic Map of the Human and Mouse Bladders

2019 ◽  
Vol 30 (11) ◽  
pp. 2159-2176 ◽  
Author(s):  
Zhenyuan Yu ◽  
Jinling Liao ◽  
Yang Chen ◽  
Chunlin Zou ◽  
Haiying Zhang ◽  
...  
Keyword(s):  
Bladder Cancer ◽  
Epithelial Cells ◽  
Single Cell ◽  
Cell Types ◽  
Specific Cell ◽  
Human Bladder ◽  
Healthy Human ◽  
Bladder Cell ◽  
Bladder Cells ◽  
Human And Mouse

BackgroundHaving a comprehensive map of the cellular anatomy of the normal human bladder is vital to understanding the cellular origins of benign bladder disease and bladder cancer.MethodsWe used single-cell RNA sequencing (scRNA-seq) of 12,423 cells from healthy human bladder tissue samples taken from patients with bladder cancer and 12,884 cells from mouse bladders to classify bladder cell types and their underlying functions.ResultsWe created a single-cell transcriptomic map of human and mouse bladders, including 16 clusters of human bladder cells and 15 clusters of mouse bladder cells. The homology and heterogeneity of human and mouse bladder cell types were compared and both conservative and heterogeneous aspects of human and mouse bladder evolution were identified. We also discovered two novel types of human bladder cells. One type is ADRA2A+ and HRH2+ interstitial cells which may be associated with nerve conduction and allergic reactions. The other type is TNNT1+ epithelial cells that may be involved with bladder emptying. We verify these TNNT1+ epithelial cells also occur in rat and mouse bladders.ConclusionsThis transcriptomic map provides a resource for studying bladder cell types, specific cell markers, signaling receptors, and genes that will help us to learn more about the relationship between bladder cell types and diseases.

scholarly journals Spatial analysis of ligand-receptor interactions in skin cancer at genome-wide and single-cell resolution

2020 ◽  
Author(s):  
M Tran ◽  
S Yoon ◽  
ST Min ◽  
S Andersen ◽  
K Devitt ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Single Cell ◽  
Molecular Mechanisms ◽  
Digital Pcr ◽  
Droplet Digital Pcr ◽  
Cell Interactions ◽  
Genome Wide ◽  
Receptor Interactions ◽  
Cell Cell

AbstractThe ability to study cancer-immune cell communication across the whole tumor section without tissue dissociation is important to understand molecular mechanisms of cancer immunotherapy and drug targets. Current experimental methods such as immunohistochemistry allow researchers to investigate a small number of cells or a limited number of ligand-receptor pairs at tissue scale with limited cellular resolution. In this work, we developed a powerful experimental and analytical pipeline that allows for the genome-wide discovery and targeted validation of cellular communication. By profiling thousands of genes, spatial transcriptomic and single-cell RNA sequencing data show genes that are possibly involved in interactions. The expression of the candidate genes could be visualized by single-molecule in situ hybridization and droplet digital PCR. We developed a computational pipeline called STRISH that enables us to quantitatively model cell-cell interactions by automatically scanning for local expression of RNAscope data to recapitulate an interaction landscape across the whole tissue. Furthermore, we showed the strong correlation of microscopic RNAscope imaging data analyzed by STRISH with the gene expression values measured by droplet digital PCR. We validated the unique ability of this approach to discover new cell-cell interactions in situ through analysis of two types of cancer, basal cell carcinoma and squamous cell carcinoma. We expect that the approach described here will help to discover and validate ligand receptor interactions in different biological contexts such as immune-cancer cell interactions within a tumor.

scholarly journals Growth kinetics and power laws indicate distinct mechanisms of cell-cell interactions in the aggregation process

2021 ◽  
Author(s):  
Debangana Mukhopadhyay ◽  
Rumi De
Keyword(s):  
Growth Kinetics ◽  
Single Cells ◽  
Domain Size ◽  
Power Laws ◽  
Theoretical Work ◽  
Cell Interactions ◽  
Specific Cell ◽  
Aggregation Process ◽  
Chemical Signalling ◽  
Cell Cell

Cellular aggregation is a complex process orchestrated by various kinds of interactions depending on its environments. Different interactions give rise to different pathways of cellular rearrangement and the development of specialized tissues. To distinguish the underlying mechanisms, in this theoretical work, we investigate the spontaneous emergence of tissue patterns from an ensemble of single cells on a substrate following three leading pathways of cell-cell interactions, namely, direct cell adhesion contacts, matrix mediated mechanical interaction, and chemical signalling. Our analysis shows that the growth kinetics of the aggregation process is distinctly different for each pathway and bears the signature of the specific cell-cell interactions. Interestingly, we find that the average domain size and the mass of the clusters exhibit a power law growth in time under certain interaction mechanisms hitherto unexplored. Further, as observed in experiments, the cluster size distribution can be characterized by stretched exponential functions showing distinct cellular organization processes.

scholarly journals Examining Cell-Cell Interactions in the Kidney Using AFM Single-Cell Force Spectroscopy

2019 ◽  
pp. 189-201 ◽  
Author(s):  
Eleftherios Siamantouras ◽  
Claire E. Hills ◽  
Kuo-Kang Liu ◽  
Paul E. Squires
Keyword(s):  
Single Cell ◽  
Force Spectroscopy ◽  
Cell Interactions ◽  
Cell Force ◽  
Cell Cell
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