Signal Transduction to and from Adhesion Molecules

Gomperts, Bastien D.

doi:10.1016/b978-0-12-369441-6.00013-1

Cited by 2 publications

(2 citation statements)

References 106 publications

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“…Cells do not interact directly with material surface because the materials are always covered by either body fluid or culture medium . Fibronectin (FN) was chosen as a protein model because it is a major component of extracellular matrix which contains cell binding domain to facilitate cell adhesion process …”

Section: Resultsmentioning

confidence: 99%

Oxygen Plasma Etching of Silk Fibroin Alters Surface Stiffness: A Cell-Substrate Interaction Study

Amornsudthiwat

Damrongsakkul

2014

Plasma Process. Polym.

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Oxygen plasma etching was used to treat silk fibroin (SF). The plasma exposure removed a significant amount of SF but left behind most surface properties close to their original state. However, nano-indenter measurements revealed a substantial increase in surface modulus of swollen SF from 62 to 500 kPa. This allowed oxygen plasma etching as a potential tool to investigate the impact of surface stiffness on cell-substrate interaction. Mouse fibroblasts (L929) and human mesenchymal stem cells (hMSC) were employed as distinct model cases. In vitro results revealed that the increased stiffness of plasma-treated SF affected only L929 adhesion, not hMSC. L929 cell attachment and spreading were better on the stiffer surface than the untreated surface, while hMSC could spread well on all SF surfaces.

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Section: Resultsmentioning

confidence: 99%

Oxygen Plasma Etching of Silk Fibroin Alters Surface Stiffness: A Cell-Substrate Interaction Study

Amornsudthiwat

Damrongsakkul

2014

Plasma Process. Polym.

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“…Since CD45 plays a key role in T cell activation [50], this may suggest that CD8 T cells upregulate this surface protein to mount a strong cytotoxic response over roughly two weeks following COVID-19 symptom onset. ICAM2, a gene whose protein products functions in leukocyte migration [51], was among the 6 most highly up-regulated genes in samples from COVID-19 patient serum [52]. We show that this gene is expressed above baseline and decreases linearly through time; however, its expression continues to decrease below baseline between day 10 and 15 post-symptom onset.…”

Section: Discussionmentioning

confidence: 83%

Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs

O’Leary,

Zheng

2023

Preprint

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BackgroundBy resolving cellular heterogeneity in a biological sample, single cell RNA sequencing (scRNA-seq) can detect gene expression and its dynamics in different cell types. Its application to time-series samples can thus identify temporal genetic programs active in different cell types, for example, immune cells’ responses to viral infection. However, current scRNA-seq analysis need improvement. Two issues are related to data generation. One is that the number of genes detected in each cell is relatively low especially when currently popular dropseq-based technology is used for analyzing thousands of cells or more. The other is the lack of sufficient replicates (often 1-2) due to high cost of library preparation and sequencing. The third issue lies in the data analysis –-usage of individual cells as independent sampling data points leads to inflated statistics.MethodsTo address these issues, we explore a new data analysis framework, specifically whether “metacells” that are carefully constructed to maintain cellular heterogeneity within individual cell types (or clusters) can be used as “replicates” for statistical methods requiring multiple replicates. Toward this, we applied SEACells to a time-series scRNA-seq dataset from peripheral blood mononuclear cells (PBMCs) after SARS-Cov-2 infection to construct metacells, which were then used in maSigPro for quadratic regression to find significantly differentially expressed genes (DEGs) over time, followed by clustering analysis of the expression velocity trends.ResultsWe found that metacells generated using the SEACells algorithm retained greater between-cell variance and produced more biologically meaningful results compared to metacells generated from random cells. Quadratic regression revealed significant DEGs through time that have been previously annotated in the SARS-CoV2 infection response pathway. It also identified significant genes that have not been annotated in this pathway, which were compared to baseline expression and showed unique expression patterns through time.ConclusionsThe results demonstrated that this strategy could overcome the limitation of 1-2 replicates, as it correctly identified the known ISG15 interferon response program in almost all PBMC cell types. Its application further led to the uncovering of additional and more cell type-specific gene expression programs that potentially modulate different levels of host response after infection.

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Signal Transduction to and from Adhesion Molecules

Cited by 2 publications

References 106 publications

Oxygen Plasma Etching of Silk Fibroin Alters Surface Stiffness: A Cell-Substrate Interaction Study

Oxygen Plasma Etching of Silk Fibroin Alters Surface Stiffness: A Cell-Substrate Interaction Study

Metacell-based differential expression analysis identifies cell type specific temporal gene response programs in COVID-19 patient PBMCs

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