scholarly journals Inferring the structures of signaling motifs from paired dynamic traces of single cells

2021 ◽  
Vol 17 (2) ◽  
pp. e1008657
Author(s):  
Raymond A. Haggerty ◽  
Jeremy E. Purvis
Keyword(s):  
Time Series ◽  
Single Cells ◽  
Underlying Mechanism ◽  
Repeated Measurements ◽  
Signaling Mechanism ◽  
Downstream Signaling ◽  
Signaling Dynamics ◽  
Functional Consequences ◽  
Averaging Time ◽  
Cell To Cell Variability

Individual cells show variability in their signaling dynamics that often correlates with phenotypic responses, indicating that cell-to-cell variability is not merely noise but can have functional consequences. Based on this observation, we reasoned that cell-to-cell variability under the same treatment condition could be explained in part by a single signaling motif that maps different upstream signals into a corresponding set of downstream responses. If this assumption holds, then repeated measurements of upstream and downstream signaling dynamics in a population of cells could provide information about the underlying signaling motif for a given pathway, even when no prior knowledge of that motif exists. To test these two hypotheses, we developed a computer algorithm called MISC (Motif Inference from Single Cells) that infers the underlying signaling motif from paired time-series measurements from individual cells. When applied to measurements of transcription factor and reporter gene expression in the yeast stress response, MISC predicted signaling motifs that were consistent with previous mechanistic models of transcription. The ability to detect the underlying mechanism became less certain when a cell’s upstream signal was randomly paired with another cell’s downstream response, demonstrating how averaging time-series measurements across a population obscures information about the underlying signaling mechanism. In some cases, motif predictions improved as more cells were added to the analysis. These results provide evidence that mechanistic information about cellular signaling networks can be systematically extracted from the dynamical patterns of single cells.

scholarly journals Inferring the structures of signaling motifs from paired dynamic traces of single cells

2019 ◽  
Author(s):  
R. A. Haggerty ◽  
Jeremy E. Purvis
Keyword(s):  
Time Series ◽  
Single Cell ◽  
Single Cells ◽  
Underlying Mechanism ◽  
Repeated Measurements ◽  
Signaling Networks ◽  
Molecular Signaling ◽  
Signaling Mechanism ◽  
Signaling Dynamics ◽  
Cell To Cell Variability

AbstractIndividual cells show variability in their signaling dynamics that often correlates with phenotypic responses, indicating that cell-to-cell variability is not merely noise but can have functional consequences. Based on this observation, we reasoned that cell-to-cell variability under the same treatment condition could be explained by a single signaling motif that deterministically maps different upstream signals into a corresponding set of downstream responses. If this assumption holds, then repeated measurements of upstream and downstream signaling dynamics in single cells could provide information about the underlying signaling motif for a given pathway, even when no prior knowledge of that motif exists. To test these two hypotheses, we developed a computer algorithm called MISC (Motif Inference from Single Cells) that infers the underlying signaling motif from paired time-series measurements from individual cells. When applied to measurements of transcription factor and reporter gene expression in the yeast stress response, MISC predicted signaling motifs that were consistent with previous mechanistic models of transcription. The ability to detect the underlying mechanism became less certain when a cell’s upstream signal was randomly paired with another cell’s downstream response, demonstrating how averaging time-series measurements across a population obscures information about the underlying signaling mechanism. In some cases, motif predictions improved as more cells were added to the analysis. These results provide evidence that mechanistic information about cellular signaling networks can be embedded within the dynamical patterns of single cells.Author SummaryCells use molecular signaling networks to translate dynamically changing stimuli into appropriate downstream responses. Specialized network structures, or motifs, allow cells to properly decode a variety of temporal input signals. In this paper, we present an algorithm that infers signaling motifs from multiple examples of an upstream signal paired with its downstream response in the same cell. We compare the predictive power of single-cell versus averaged time-series traces and the incremental benefit of adding more single-cell traces to the algorithm. We use this approach to understand how yeast respond to environmental stresses.

scholarly journals TRPV1 and PLC Participate in Histamine H4 Receptor-Induced Itch

2016 ◽  
Vol 2016 ◽  
pp. 1-9 ◽  
Author(s):  
Tunyu Jian ◽  
Niuniu Yang ◽  
Yan Yang ◽  
Chan Zhu ◽  
Xiaolin Yuan ◽  
...  
Keyword(s):  
Intracellular Signaling ◽  
Underlying Mechanism ◽  
Receptor Activation ◽  
Ruthenium Red ◽  
Drg Neurons ◽  
Histamine H4 Receptor ◽  
Signaling Mechanism ◽  
Downstream Signaling ◽  
Intracellular Ca ◽  
H4 Receptor

Histamine H4 receptor has been confirmed to play a role in evoking peripheral pruritus. However, the ionic and intracellular signaling mechanism of activation of H4 receptor on the dorsal root ganglion (DRG) neurons is still unknown. By using cell culture and calcium imaging, we studied the underlying mechanism of activation of H4 receptor on the DRG neuron. Immepip dihydrobromide (immepip)—a histamine H4 receptor special agonist under cutaneous injection—obviously induced itch behavior of mice. Immepip-induced scratching behavior could be blocked by TRPV1 antagonist AMG9810 and PLC pathway inhibitor U73122. Application of immepip (8.3–50 μM) could also induce a dose-dependent increase in intracellular Ca2+(Ca2+i) of DRG neurons. We found that 77.8% of the immepip-sensitized DRG neurons respond to the TRPV1 selective agonist capsaicin. U73122 could inhibit immepip-induced Ca2+responses. In addition, immepip-inducedCa2+iincrease could be blocked by ruthenium red, capsazepine, and AMG9810; however it could not be blocked by TRPA1 antagonist HC-030031. These results indicate that TRPV1 but not TRPA1 is the important ion channel to induce the DRG neurons’ responses in the downstream signaling pathway of histamine H4 receptor and suggest that TRPV1 may be involved in the mechanism of histamine-induced itch response by H4 receptor activation.

scholarly journals Mixed Models as a Tool for Comparing Groups of Time Series in Plant Sciences

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 362
Author(s):  
Ioannis Spyroglou ◽  
Jan Skalák ◽  
Veronika Balakhonova ◽  
Zuzana Benedikty ◽  
Alexandros G. Rigas ◽  
...  
Keyword(s):  
Time Series ◽  
Random Effects ◽  
Mixed Models ◽  
Mixed Model ◽  
Repeated Measurements ◽  
Time Series Models ◽  
Additional Time ◽  
Biotic Stresses ◽  
Viable Solution ◽  
Long Time

Plants adapt to continual changes in environmental conditions throughout their life spans. High-throughput phenotyping methods have been developed to noninvasively monitor the physiological responses to abiotic/biotic stresses on a scale spanning a long time, covering most of the vegetative and reproductive stages. However, some of the physiological events comprise almost immediate and very fast responses towards the changing environment which might be overlooked in long-term observations. Additionally, there are certain technical difficulties and restrictions in analyzing phenotyping data, especially when dealing with repeated measurements. In this study, a method for comparing means at different time points using generalized linear mixed models combined with classical time series models is presented. As an example, we use multiple chlorophyll time series measurements from different genotypes. The use of additional time series models as random effects is essential as the residuals of the initial mixed model may contain autocorrelations that bias the result. The nature of mixed models offers a viable solution as these can incorporate time series models for residuals as random effects. The results from analyzing chlorophyll content time series show that the autocorrelation is successfully eliminated from the residuals and incorporated into the final model. This allows the use of statistical inference.

scholarly journals Targeting the Calmodulin-Regulated ErbB/Grb7 Signaling Axis in Cancer Therapy

2013 ◽  
Vol 16 (2) ◽  
pp. 177 ◽  
Author(s):  
Antonio Villalobo ◽  
Irene García-Palmero ◽  
Silviya R. Stateva ◽  
Karim Jellali
Keyword(s):  
Cancer Therapy ◽  
Growth Factor Receptor ◽  
Adaptor Protein ◽  
Short Review ◽  
Receptor Protein ◽  
Pharmacological Intervention ◽  
Erbb Receptors ◽  
Aberrant Expression ◽  
Signaling Mechanism ◽  
Downstream Signaling

Signal transduction pathways essential for the survival and viability of the cell and that frequently present aberrant expression or function in tumors are attractive targets for pharmacological intervention in human cancers. In this short review we will describe the regulation exerted by the calcium-receptor protein calmodulin (CaM) on signaling routes involving the family of ErbB receptors - highlighting the epidermal growth factor receptor (EGFR/ErbB1) and ErbB2 - and the adaptor protein Grb7, a downstream signaling component of these receptors. The signaling mechanism of the ErbB/Grb7 axis and the regulation exerted by CaM on this pathway will be described. We will present a brief overview of the current efforts to inhibit the hyperactivity of ErbB receptors and Grb7 in tumors. The currently available information on targeting the CaM-binding site of these signaling proteins will be analyzed, and the pros and cons of directly targeting CaM versus the CaM-binding domain of the ErbB receptors and Grb7 as potential anti-cancer therapy will be discussed. This article is open to POST-PUBLICATION REVIEW. Registered readers (see “For Readers”) may comment by clicking on ABSTRACT on the issue’s contents page.

scholarly journals Haplotype-aware single-cell multiomics uncovers functional effects of somatic structural variation

2021 ◽  
Author(s):  
Hyobin Jeong ◽  
Karen Grimes ◽  
Peter-Martin Bruch ◽  
Tobias Rausch ◽  
Patrick Hasenfeld ◽  
...  
Keyword(s):  
Single Cell ◽  
Nucleosome Occupancy ◽  
Single Cells ◽  
Chromosomal Rearrangements ◽  
Regulatory Elements ◽  
Computational Method ◽  
Tumour Heterogeneity ◽  
Cancer Genomes ◽  
Functional Consequences ◽  
Oncogenic Transcription Factor

Somatic structural variants (SVs) are widespread in cancer genomes, however, their impact on tumorigenesis and intra-tumour heterogeneity is incompletely understood, since methods to functionally characterize the broad spectrum of SVs arising in cancerous single-cells are lacking. We present a computational method, scNOVA, that couples SV discovery with nucleosome occupancy analysis by haplotype-resolved single-cell sequencing, to systematically uncover SV effects on cis-regulatory elements and gene activity. Application to leukemias and cell lines uncovered SV outcomes at several loci, including dysregulated cancer-related pathways and mono-allelic oncogene expression near SV breakpoints. At the intra-patient level, we identified different yet overlapping subclonal SVs that converge on aberrant Wnt signaling. We also deconvoluted the effects of catastrophic chromosomal rearrangements resulting in oncogenic transcription factor dysregulation. scNOVA directly links SVs to their functional consequences, opening the door for single-cell multiomics of SVs in heterogeneous cell populations.

Hydra regeneration from recombined ectodermal and endodermal tissue. I. Epibolic ectodermal spreading is driven by cell intercalation

1996 ◽  
Vol 109 (4) ◽  
pp. 763-772 ◽  
Author(s):  
Y. Kishimoto ◽  
M. Murate ◽  
T. Sugiyama
Keyword(s):  
Contact Surface ◽  
Single Cells ◽  
Cell Interaction ◽  
Inhibitory Effect ◽  
Cell Aggregates ◽  
Signaling Mechanism ◽  
Initial Adhesion ◽  
Radial Cell ◽  
Epithelial Sheet ◽  
Cell Intercalation

Cell-cell interaction and cell rearrangement were examined in the process of epithelial sheet formation during regeneration from hydra cell aggregates. The ectodermal and endodermal epithelial cell layers of Hydra magnipapillata were separated by procaine treatment. Each of the separated layers was then dissociated into single cells and reaggregated to produce ectodermal or endodermal cell aggregates. When the two aggregate types were recombined, a firm adhesion was quickly established between them. This was followed by a vigorous spreading of the ectodermal epithelial cells as a thin layer over the endoderm in a manner similar to the ‘epiboly’ in some developing embryos. Cell movement in this spreading process was examined using fluorescent dyestaining. It revealed that cells initially located in the inside of the aggregate migrated to intercalate themselves among the cells originally present in the contact surface. This radial cell intercalation took place continuously in the contact surface of both the ectodermal and endodermal aggregates, and produced a rapid growth of the contact surface, eventually leading to complete envelopment of the entire endoderm by the ectoderm. The resulting structure was a small sphere having a two-layered epithelial organization as in normal hydra. This sphere regenerated into a complete hydra a few days later. A tryptic extract of hydra membrane fraction specifically inhibited the ectodermal spreading over the endoderm, but not the initial adhesion or the later regeneration processes. These observations suggest that radial cell intercalation at the contact surface plays a crucial role in producing ectodermal spreading and establishing epithelial sheet organization in the recombined aggregates. The intercalation is presumably activated by a signal exchange through the contact surface. The inhibitory effect of the membrane extract suggests that it contains a factor that is involved in some way in this signaling mechanism.

scholarly journals Mevalonate metabolism–dependent protein geranylgeranylation regulates thymocyte egress

2019 ◽  
Vol 217 (2) ◽  
Author(s):  
Xingrong Du ◽  
Hu Zeng ◽  
Shaofeng Liu ◽  
Cliff Guy ◽  
Yogesh Dhungana ◽  
...  
Keyword(s):  
T Cell ◽  
Similar Process ◽  
Immune Homeostasis ◽  
T Cell Homeostasis ◽  
Protein Prenylation ◽  
Critical Determinant ◽  
Cell Homeostasis ◽  
Signaling Mechanism ◽  
Downstream Signaling

Thymocyte egress is a critical determinant of T cell homeostasis and adaptive immunity. Despite the roles of G protein–coupled receptors in thymocyte emigration, the downstream signaling mechanism remains poorly defined. Here, we report the discrete roles for the two branches of mevalonate metabolism–fueled protein prenylation pathway in thymocyte egress and immune homeostasis. The protein geranylgeranyltransferase Pggt1b is up-regulated in single-positive thymocytes, and loss of Pggt1b leads to marked defects in thymocyte egress and T cell lymphopenia in peripheral lymphoid organs in vivo. Mechanistically, Pggt1b bridges sphingosine-1-phosphate and chemokine-induced migratory signals with the activation of Cdc42 and Pak signaling and mevalonate-dependent thymocyte trafficking. In contrast, the farnesyltransferase Fntb, which mediates a biochemically similar process of protein farnesylation, is dispensable for thymocyte egress but contributes to peripheral T cell homeostasis. Collectively, our studies establish context-dependent effects of protein prenylation and unique roles of geranylgeranylation in thymic egress and highlight that the interplay between cellular metabolism and posttranslational modification underlies immune homeostasis.

scholarly journals Internalization of B Cell Receptors in Human EU12μHC+Immature B Cells Specifically Alters Downstream Signaling Events

2013 ◽  
Vol 2013 ◽  
pp. 1-9
Author(s):  
Jing Liu ◽  
Wanqin Xie ◽  
Miles D. Lange ◽  
Sang Yong Hong ◽  
Kaihong Su ◽  
...  
Keyword(s):  
B Cells ◽  
Cell Surface ◽  
B Cell ◽  
Cell Fate ◽  
Cell Activation ◽  
Underlying Mechanism ◽  
Cell Fate Decisions ◽  
Downstream Signaling ◽  
Signaling Events ◽  
Immature B Cells

It has been recognized for a long time that engagement of B cell antigen receptors (BCRs) on immature B cells or mature B cells leads to completely opposite cell fate decisions. The underlying mechanism remains unclear. Here, we show that crosslinking of BCRs on human EU12μHC+immature B cells resulted in complete internalization of cell surface BCRs. After loss of cell surface BCRs, restimulation of EU12μHC+cells showed impaired Ca2+flux, delayed SYK phosphorylation, and decreased CD19 and FOXO1 phosphorylation, which differ from those in mature Daudi or Ramos B cells with partial internalization of BCRs. In contrast, sustained phosphorylation and reactivation of ERK upon restimulation were observed in the EU12μHC+cells after BCR internalization. Taken together, these results show that complete internalization of cell surface BCRs in EU12μHC+cells specifically alters the downstream signaling events, which may favor receptor editing versus cell activation.

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