scholarly journals A self-exciting point process to study multicellular spatial signaling patterns

2021 ◽  
Vol 118 (32) ◽  
pp. e2026123118
Author(s):  
Archit Verma ◽  
Siddhartha G. Jena ◽  
Danielle R. Isakov ◽  
Kazuhiro Aoki ◽  
Jared E. Toettcher ◽  
...  

Multicellular organisms rely on spatial signaling among cells to drive their organization, development, and response to stimuli. Several models have been proposed to capture the behavior of spatial signaling in multicellular systems, but existing approaches fail to capture both the autonomous behavior of single cells and the interactions of a cell with its neighbors simultaneously. We propose a spatiotemporal model of dynamic cell signaling based on Hawkes processes—self-exciting point processes—that model the signaling processes within a cell and spatial couplings between cells. With this cellular point process (CPP), we capture both the single-cell pathway activation rate and the magnitude and duration of signaling between cells relative to their spatial location. Furthermore, our model captures tissues composed of heterogeneous cell types with different bursting rates and signaling behaviors across multiple signaling proteins. We apply our model to epithelial cell systems that exhibit a range of autonomous and spatial signaling behaviors basally and under pharmacological exposure. Our model identifies known drug-induced signaling deficits, characterizes signaling changes across a wound front, and generalizes to multichannel observations.

2020 ◽  
Author(s):  
Archit Verma ◽  
Siddhartha G. Jena ◽  
Danielle R. Isakov ◽  
Kazuhiro Aoki ◽  
Jared E. Toettcher ◽  
...  

Multi-cellular organisms rely on spatial signaling among cells to drive their organization, development, and response to stimuli. Several models have been proposed to capture the behavior of spatial signaling in multi-cellular systems, but existing approaches fail to capture both the autonomous behavior of single cells and the interactions of a cell with its neighbors simultaneously. We propose a spatiotemporal model of dynamic cell signaling based on Hawkes processes—self-exciting point processes—that model the signaling processes within a cell and spatial couplings between cells. With this cellular point process (CPP) model, we capture both the single-cell protein bursting rate and the magnitude and duration of signaling between cells relative to spatial locations. Furthermore, our model captures tissues composed of heterogeneous cell types with different bursting rates and signaling behaviors across multiple signaling proteins. We apply our model to epithelial cell systems that exhibit a range of autonomous and spatial signaling behaviors basally and under pharmacological exposure. Our model identifies known drug-induced signaling deficits, characterizes differences in signaling across a wound front, and generalizes to multi-channel observations.


1966 ◽  
Vol 166 (1004) ◽  
pp. 358-368 ◽  

The work which I have been asked to review began a little over a year ago with an experiment which I made in collaboration with Dr J. F. Watkins (Harris & Watkins 1965). We showed that an animal virus, killed by irradiation with ultraviolet light, could be used to fuse together cells derived from mouse and man to produce artificial man-mouse hybrid cells. The idea of using viruses in this way has its origins in observations which go back for more than a century. (For a review of the relevant literature see Harris, Watkins, Ford & Schoefl 1966). Many diseases have long been known to be associated with lesions in which multi-nucleate cells are found. In the medical literature of the nineteenth century there is a protracted and vigorous controversy about the mode of formation of these cells. Multinucleate cells are commonly found in the lesions produced by certain pathogenic viruses and, during the last decade, it has become clear that in at least some cases the virus produces the multinucleate cell by fusing single cells together. It was thus a very small step to attempt to see whether a virus could be used to fuse together cells of different kinds, and whether the resulting hybrid cells, if they were formed, would survive. And since the survival of the hybrid cells might be jeopardized by infection with a living virus, the virus was killed before the cells were treated with it. In the event, it turned out that viruses, inactivated by ultraviolet light, could be used to provide a general method for fusing together both differentiated and undifferentiated cells from different species and even different orders of vertebrate. The resulting interspecific hybrid cells survived for long periods and proved in some cases to be capable of multiplication. They thus offered interesting possibilities for the study of nucleo-cytoplasmic relationships and lent themselves to experiments of a kind which had not hitherto been feasible. It is these experiments which I propose to discuss. The virus used in this work was the ‘Sendai’ virus, a member of the para-influenza group of myxoviruses; other members of this group of viruses have since been used by other workers. Sendai virus was chosen because it had been shown by Okada (1958, 1962) that animal tumour cells in suspension could be rapidly fused together by high concentrations of this virus. The virus was irradiated with doses of ultraviolet light which reduced its infectivity by at least 10 6 ; but the dead virus retained its ability to fuse cells together. The two cell types studied in the first instance were the HeLa cell (a cell of human origin which has been grown for many years in artificial culture) and the Ehrlich ascites cell (a tumour which grows as a cell suspension in the peritoneal cavity of the mouse). These two cell types were chosen for a number of technical reasons, but mainly because their nuclei were easily distinguishable on morphological grounds. When a suspension containing a mixture of the two cell types is treated with the dead virus under appropriate conditions the cells clump together, and, during the ensuing 20 to 30 min, at 37 °C, the cell surfaces at the points of contact between the cells undergo dissolution. This process results in the progressive coalescence of the cytoplasms of neighbouring cells, so that multinucleate cells containing varying numbers of nuclei are formed.


Author(s):  
Yan Zhang ◽  
Yaru Zhang ◽  
Jun Hu ◽  
Ji Zhang ◽  
Fangjie Guo ◽  
...  

ABSTRACTThe most fundamental challenge in current single-cell RNA-seq data analysis is functional interpretation and annotation of cell clusters. The biological pathways in distinct cell types have different activation patterns, which facilitates understanding cell functions in single-cell transcriptomics. However, no effective web tool has been implemented for single-cell transcriptomic data analysis based on prior biological pathway knowledge. Here, we introduce scTPA (http://sctpa.bio-data.cn/sctpa), which is a web-based platform providing pathway-based analysis of single-cell RNA-seq data in human and mouse. scTPA incorporates four widely-used gene set enrichment methods to estimate the pathway activation scores of single cells based on a collection of available biological pathways with different functional and taxonomic classifications. The clustering analysis and cell-type-specific activation pathway identification were provided for the functional interpretation of cell types from pathway-oriented perspective. An intuitive interface allows users to conveniently visualize and download single-cell pathway signatures. Together, scTPA is a comprehensive tool to identify pathway activation signatures for dissecting single cell heterogeneity.


1992 ◽  
Vol 119 (5) ◽  
pp. 1371-1380 ◽  
Author(s):  
R I Pennell ◽  
L Janniche ◽  
G N Scofield ◽  
H Booij ◽  
S C de Vries ◽  
...  

We have located a novel carbohydrate epitope in the cell walls of certain single cells in embryogenic, but not in non-embryogenic, suspension cultures of carrot. Expression of this epitope, recognized by the mAb JIM8, is regulated during initiation, proliferation, and prolonged growth of suspension cultures such that changes in the abundance of JIM8-reactive cells always precede equivalent changes in embryogenic potential. Therefore, a direct correlation exists between the presence of the JIM8-reactive cell wall epitope and somatic embryo formation. The JIM8-reactive cell wall epitope is expressed in the cell walls of three types of single cells and one type of cell cluster. One of the single cell types seems able to follow one of two phytohormone-controlled developmental pathways, either a cell elongation pathway that eventually leads to cell death, or a cell division pathway that gives rise to proembryogenic masses. We demonstrate that all JIM8-reactive cell types in embryogenic carrot suspension cultures are developmentally related, and that the switch by one of them to somatic embryogenesis is accompanied by the immediate dissipation of the JIM8-reactive cell wall epitope. The cell wall carbohydrate epitope recognized by JIM8 therefore represents a cell wall marker for a very early transitional cell state in the developmental pathway to carrot somatic embryogenesis.


2018 ◽  
Author(s):  
Changlin Wan ◽  
Wennan Chang ◽  
Yu Zhang ◽  
Fenil Shah ◽  
Xiaoyu Lu ◽  
...  

ABSTRACTA key challenge in modeling single-cell RNA-seq (scRNA-seq) data is to capture the diverse gene expression states regulated by different transcriptional regulatory inputs across single cells, which is further complicated by a large number of observed zero and low expressions. We developed a left truncated mixture Gaussian (LTMG) model that stems from the kinetic relationships between the transcriptional regulatory inputs and metabolism of mRNA and gene expression abundance in a cell. LTMG infers the expression multi-modalities across single cell entities, representing a gene’s diverse expression states; meanwhile the dropouts and low expressions are treated as left truncated, specifically representing an expression state that is under suppression. We demonstrated that LTMG has significantly better goodness of fitting on an extensive number of single-cell data sets, comparing to three other state of the art models. In addition, our systems kinetic approach of handling the low and zero expressions and correctness of the identified multimodality are validated on several independent experimental data sets. Application on data of complex tissues demonstrated the capability of LTMG in extracting varied expression states specific to cell types or cell functions. Based on LTMG, a differential gene expression test and a co-regulation module identification method, namely LTMG-DGE and LTMG-GCR, are further developed. We experimentally validated that LTMG-DGE is equipped with higher sensitivity and specificity in detecting differentially expressed genes, compared with other five popular methods, and that LTMG-GCR is capable to retrieve the gene co-regulation modules corresponding to perturbed transcriptional regulations. A user-friendly R package with all the analysis power is available at https://github.com/zy26/LTMGSCA.


2010 ◽  
Vol 10 (2) ◽  
pp. 150-155 ◽  
Author(s):  
Wonhee Jang ◽  
Richard H. Gomer

ABSTRACT Much remains to be understood about how a group of cells break symmetry and differentiate into distinct cell types. The simple eukaryote Dictyostelium discoideum is an excellent model system for studying questions such as cell type differentiation. Dictyostelium cells grow as single cells. When the cells starve, they aggregate to develop into a multicellular structure with only two main cell types: spore and stalk. There has been a longstanding controversy as to how a cell makes the initial choice of becoming a spore or stalk cell. In this review, we describe how the controversy arose and how a consensus developed around a model in which initial cell type choice in Dictyostelium is dependent on the cell cycle phase that a cell happens to be in at the time that it starves.


2017 ◽  
Vol 114 (10) ◽  
pp. E1866-E1874 ◽  
Author(s):  
Yuhong Cao ◽  
Martin Hjort ◽  
Haodong Chen ◽  
Fikri Birey ◽  
Sergio A. Leal-Ortiz ◽  
...  

Here, we report a method for time-resolved, longitudinal extraction and quantitative measurement of intracellular proteins and mRNA from a variety of cell types. Cytosolic contents were repeatedly sampled from the same cell or population of cells for more than 5 d through a cell-culture substrate, incorporating hollow 150-nm-diameter nanostraws (NS) within a defined sampling region. Once extracted, the cellular contents were analyzed with conventional methods, including fluorescence, enzymatic assays (ELISA), and quantitative real-time PCR. This process was nondestructive with >95% cell viability after sampling, enabling long-term analysis. It is important to note that the measured quantities from the cell extract were found to constitute a statistically significant representation of the actual contents within the cells. Of 48 mRNA sequences analyzed from a population of cardiomyocytes derived from human induced pluripotent stem cells (hiPSC-CMs), 41 were accurately quantified. The NS platform samples from a select subpopulation of cells within a larger culture, allowing native cell-to-cell contact and communication even during vigorous activity such as cardiomyocyte beating. This platform was applied both to cell lines and to primary cells, including CHO cells, hiPSC-CMs, and human astrocytes derived in 3D cortical spheroids. By tracking the same cell or group of cells over time, this method offers an avenue to understand dynamic cell behavior, including processes such as induced pluripotency and differentiation.


2014 ◽  
Vol 25 (3) ◽  
pp. 368-379 ◽  
Author(s):  
Neelanjan Vishnu ◽  
Muhammad Jadoon Khan ◽  
Felix Karsten ◽  
Lukas N. Groschner ◽  
Markus Waldeck-Weiermair ◽  
...  

Multiple functions of the endoplasmic reticulum (ER) essentially depend on ATP within this organelle. However, little is known about ER ATP dynamics and the regulation of ER ATP import. Here we describe real-time recordings of ER ATP fluxes in single cells using an ER-targeted, genetically encoded ATP sensor. In vitro experiments prove that the ATP sensor is both Ca2+and redox insensitive, which makes it possible to monitor Ca2+-coupled ER ATP dynamics specifically. The approach uncovers a cell type–specific regulation of ER ATP homeostasis in different cell types. Moreover, we show that intracellular Ca2+release is coupled to an increase of ATP within the ER. The Ca2+-coupled ER ATP increase is independent of the mode of Ca2+mobilization and controlled by the rate of ATP biosynthesis. Furthermore, the energy stress sensor, AMP-activated protein kinase, is essential for the ATP increase that occurs in response to Ca2+depletion of the organelle. Our data highlight a novel Ca2+-controlled process that supplies the ER with additional energy upon cell stimulation.


2018 ◽  
Author(s):  
Ruei-Jiun Hung ◽  
Yanhui Hu ◽  
Rory Kirchner ◽  
Fangge Li ◽  
Chiwei Xu ◽  
...  

AbstractStudies of the adult Drosophila midgut have provided a number of insights on cell type diversity, stem cell regeneration, tissue homeostasis and cell fate decision. Advances in single-cell RNA sequencing (scRNA-seq) provide opportunities to identify new cell types and molecular features. We used inDrop to characterize the transcriptome of midgut epithelial cells and identified 12 distinct clusters representing intestinal stem cells (ISCs), enteroblasts (EBs), enteroendocrine cells (EEs), enterocytes (ECs) from different regions, and cardia. This unbiased approach recovered 90% of the known ISCs/EBs markers, highlighting the high quality of the dataset. Gene set enrichment analysis in conjunction with electron micrographs revealed that ISCs are enriched in free ribosomes and possess mitochondria with fewer cristae. We demonstrate that a subset of EEs in the middle region of the midgut expresses the progenitor marker esg and that individual EEs are capable of expressing up to 4 different gut hormone peptides. We also show that the transcription factor klumpfuss (klu) is expressed in EBs and functions to suppress EE formation. Lastly, we provide a web-based resource for visualization of gene expression in single cells. Altogether, our study provides a comprehensive resource for addressing novel functions of genes in the midgut epithelium.


Author(s):  
G. Rowden ◽  
M. G. Lewis ◽  
T. M. Phillips

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.


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