Estimating Cell Type Composition using Isoform Expression One Gene at a Time

Biometrics ◽  
2021 ◽  
Author(s):  
Hillary M. Heiling ◽  
Douglas R. Wilson ◽  
Naim U. Rashid ◽  
Wei Sun ◽  
Joseph G. Ibrahim
Keyword(s):  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition ◽  
Isoform Expression

scholarly journals Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols

PLoS ONE ◽  
2016 ◽  
Vol 11 (1) ◽  
pp. e0147519 ◽  
Author(s):  
Yuh Shiwa ◽  
Tsuyoshi Hachiya ◽  
Ryohei Furukawa ◽  
Hideki Ohmomo ◽  
Kanako Ono ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Systematic Bias ◽  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition ◽  
Dna Collection

scholarly journals Seasonal changes in gene expression represent cell-type composition in whole blood

2014 ◽  
Vol 23 (10) ◽  
pp. 2721-2728 ◽  
Author(s):  
S. De Jong ◽  
M. Neeleman ◽  
J. J. Luykx ◽  
M. J. Ten Berg ◽  
E. Strengman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Whole Blood ◽  
Seasonal Changes ◽  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition

scholarly journals Assessing the Contribution of Relative Macrophage Frequencies to Subcutaneous Adipose Tissue

2021 ◽  
Vol 8 ◽  
Author(s):  
Marianthi Kalafati ◽  
Michael Lenz ◽  
Gökhan Ertaylan ◽  
Ilja C. W. Arts ◽  
Chris T. Evelo ◽  
...  
Keyword(s):  
Gene Expression ◽  
Adipose Tissue ◽  
Subcutaneous Adipose Tissue ◽  
Tissue Cell ◽  
Cell Type ◽  
Expression Of Genes ◽  
Cell Type Composition ◽  
Type Composition ◽  
Adipose Tissue Cell ◽  
Subcutaneous Adipose

Background: Macrophages play an important role in regulating adipose tissue function, while their frequencies in adipose tissue vary between individuals. Adipose tissue infiltration by high frequencies of macrophages has been linked to changes in adipokine levels and low-grade inflammation, frequently associated with the progression of obesity. The objective of this project was to assess the contribution of relative macrophage frequencies to the overall subcutaneous adipose tissue gene expression using publicly available datasets.Methods: Seven publicly available microarray gene expression datasets from human subcutaneous adipose tissue biopsies (n = 519) were used together with TissueDecoder to determine the adipose tissue cell-type composition of each sample. We divided the subjects in four groups based on their relative macrophage frequencies. Differential gene expression analysis between the high and low relative macrophage frequencies groups was performed, adjusting for sex and study. Finally, biological processes were identified using pathway enrichment and network analysis.Results: We observed lower frequencies of adipocytes and higher frequencies of adipose stem cells in individuals characterized by high macrophage frequencies. We additionally studied whether, within subcutaneous adipose tissue, interindividual differences in the relative frequencies of macrophages were reflected in transcriptional differences in metabolic and inflammatory pathways. Adipose tissue of individuals with high macrophage frequencies had a higher expression of genes involved in complement activation, chemotaxis, focal adhesion, and oxidative stress. Similarly, we observed a lower expression of genes involved in lipid metabolism, fatty acid synthesis, and oxidation and mitochondrial respiration.Conclusion: We present an approach that combines publicly available subcutaneous adipose tissue gene expression datasets with a deconvolution algorithm to calculate subcutaneous adipose tissue cell-type composition. The results showed the expected increased inflammation gene expression profile accompanied by decreased gene expression in pathways related to lipid metabolism and mitochondrial respiration in subcutaneous adipose tissue in individuals characterized by high macrophage frequencies. This approach demonstrates the hidden strength of reusing publicly available data to gain cell-type-specific insights into adipose tissue function.

scholarly journals Single nuclei sequencing of entire mammalian hearts: strain-dependent cell-type composition and velocity

2020 ◽  
Vol 116 (7) ◽  
pp. 1249-1251
Author(s):  
Markus Wolfien ◽  
Anne-Marie Galow ◽  
Paula Müller ◽  
Madeleine Bartsch ◽  
Ronald M Brunner ◽  
...  
Keyword(s):  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition ◽  
Dependent Cell ◽  
Strain Dependent

scholarly journals Altered testicular cell type composition in males of two outbred mouse lines selected for high fertility

Andrology ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. 1419-1427
Author(s):  
Marten Michaelis ◽  
Alexander Sobczak ◽  
Carolin Ludwig ◽  
Hana Marvanová ◽  
Martina Langhammer ◽  
...  
Keyword(s):  
High Fertility ◽  
Cell Type ◽  
Testicular Cell ◽  
Cell Type Composition ◽  
Type Composition ◽  
Outbred Mouse ◽  
Mouse Lines

scholarly journals ITGA6+ Human Testicular Cell Populations Acquire a Mesenchymal Rather than Germ Cell Transcriptional Signature during Long-Term Culture

2020 ◽  
Vol 21 (21) ◽  
pp. 8269
Author(s):  
Robert B. Struijk ◽  
Callista L. Mulder ◽  
Saskia K. M. van Daalen ◽  
Cindy M. de Winter-Korver ◽  
Aldo Jongejan ◽  
...  
Keyword(s):  
Germ Cell ◽  
Cell Sorting ◽  
In Vitro Propagation ◽  
Cell Type ◽  
Testicular Cell ◽  
Testicular Cells ◽  
Cell Type Composition ◽  
Type Composition

Autologous spermatogonial stem cell transplantation is an experimental technique aimed at restoring fertility in infertile men. Although effective in animal models, in vitro propagation of human spermatogonia prior to transplantation has proven to be difficult. A major limiting factor is endogenous somatic testicular cell overgrowth during long-term culture. This makes the culture both inefficient and necessitates highly specific cell sorting strategies in order to enrich cultured germ cell fractions prior to transplantation. Here, we employed RNA-Seq to determine cell type composition in sorted integrin alpha-6 (ITGA6+) primary human testicular cells (n = 4 donors) cultured for up to two months, using differential gene expression and cell deconvolution analyses. Our data and analyses reveal that long-term cultured ITGA6+ testicular cells are composed mainly of cells expressing markers of peritubular myoid cells, (progenitor) Leydig cells, fibroblasts and mesenchymal stromal cells and only a limited percentage of spermatogonial cells as compared to their uncultured counterparts. These findings provide valuable insights into the cell type composition of cultured human ITGA6+ testicular cells during in vitro propagation and may serve as a basis for optimizing future cell sorting strategies as well as optimizing the current human testicular cell culture system for clinical use.

scholarly journals Transit-amplifying cells coordinate changes in intestinal epithelial cell-type composition

2019 ◽  
Author(s):  
Laura E. Sanman ◽  
Ina W. Chen ◽  
Jake M. Bieber ◽  
Veronica Steri ◽  
Byron Hann ◽  
...  
Keyword(s):  
Quantitative Imaging ◽  
Cell Types ◽  
Culture Conditions ◽  
Tissue Cell ◽  
Specific Cell ◽  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition ◽  
Coordinate Changes

AbstractRenewing tissues have the remarkable ability to continually produce both proliferative progenitor and specialized differentiated cell-types. How are complex milieus of microenvironmental signals interpreted to coordinate tissue cell-type composition? Here, we develop a high-throughput approach that combines organoid technology and quantitative imaging to address this question in the context of the intestinal epithelium. Using this approach, we comprehensively survey enteroid responses to individual and paired perturbations to eight epithelial signaling pathways. We uncover culture conditions that enrich for specific cell-types, including Lgr5+ stem and enteroendocrine cells. We analyze interactions between perturbations and dissect mechanisms underlying an unexpected mutual antagonism between EGFR and IL-4 signals. Finally, we show that, across diverse perturbations, modulating proliferation of transit-amplifying cells also consistently changes the composition of differentiated secretory and absorptive cell-types. This property is conserved in vivo and can arise from differential amplification of secretory and absorptive progenitor cells. Taken together, the observations highlight an underappreciated role for transit-amplifying cells in which proliferation of these short-lived progenitors provides a lineage-based mechanism for tuning differentiated cell-type composition.

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