scholarly journals Single-cell transcriptomics analysis showing functional heterogeneity in decidual stromal cells during labor

2020 ◽  
pp. jim-2020-001616
Author(s):  
Jingrui Huang ◽  
Yingming Xie ◽  
Qiaozhen Peng ◽  
Weinan Wang ◽  
Chenlin Pei ◽  
...  
Keyword(s):  
Single Cell ◽  
Stromal Cells ◽  
Atp Synthesis ◽  
Sequencing Analysis ◽  
Activator Protein 1 ◽  
Oxygen Homeostasis ◽  
Substrate Adhesion ◽  
Before And After ◽  
Cell Substrate Adhesion ◽  
Labor Onset

To investigate the heterogeneity of decidual stromal cells (DSCs) and their functional alterations during delivery, we conducted single-cell RNA sequencing analysis to characterize the transcriptomic profiles of DSCs before and after labor onset. According to their transcriptomic profiles, DSCs (6382 cells) were clustered into five subgroups with different functions. Similar to stromal cells, cells in cluster 1 were involved in cell substrate adhesion. On the other hand, cells in clusters 2 and 3 were enriched in signal transduction-related genes. Labor onset led to significant alterations in many pathways, including the activator protein 1 pathway (all clusters), as well as in the response to lipopolysaccharide (clusters 1–3). The downregulated genes were involved in coagulation, ATP synthesis, and oxygen homeostasis, possibly reflecting the oxygen and energy balance during delivery. Our findings highlight that peripartum DSCs are heterogeneous and play multiple roles in labor.

scholarly journals Common and Unique Transcription Signatures of YAP and TAZ in Gastric Cancer Cells

Cancers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3667
Author(s):  
Yaelim Lee ◽  
Megan Finch-Edmondson ◽  
Hamizah Cognart ◽  
Bowen Zhu ◽  
Haiwei Song ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Cancer Cells ◽  
Dominant Role ◽  
Sequencing Analysis ◽  
Gastric Cancer Cells ◽  
Transcriptional Targets ◽  
Substrate Adhesion ◽  
Cell Substrate ◽  
And Function ◽  
Cell Substrate Adhesion

YAP and its paralog TAZ are the nuclear effectors of the Hippo tumour-suppressor pathway, and function as transcriptional co-activators to control gene expression in response to mechanical cues. To identify both common and unique transcriptional targets of YAP and TAZ in gastric cancer cells, we carried out RNA-sequencing analysis of overexpressed YAP or TAZ in the corresponding paralogous gene-knockouts (KOs), TAZ KO or YAP KO, respectively. Gene Ontology (GO) analysis of the YAP/TAZ-transcriptional targets revealed activation of genes involved in platelet biology and lipoprotein particle formation as targets that are common for both YAP and TAZ. However, the GO terms for cell-substrate junction were a unique function of YAP. Further, we found that YAP was indispensable for the gastric cancer cells to re-establish cell-substrate junctions on a rigid surface following prolonged culture on a soft substrate. Collectively, our study not only identifies common and unique transcriptional signatures of YAP and TAZ in gastric cancer cells but also reveals a dominant role for YAP over TAZ in the control of cell-substrate adhesion.

scholarly journals Probing single-cell metabolism reveals prognostic value of highly metabolically active circulating stromal cells in prostate cancer

2020 ◽  
Vol 6 (40) ◽  
pp. eaaz3849
Author(s):  
Francesca Rivello ◽  
Kinga Matuła ◽  
Aigars Piruska ◽  
Minke Smits ◽  
Niven Mehra ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Single Cell ◽  
Cancer Patients ◽  
Stromal Cells ◽  
Metastatic Prostate Cancer ◽  
Epithelial To Mesenchymal Transition ◽  
Therapy Response ◽  
Sequencing Analysis ◽  
Label Free ◽  
Mesenchymal Transition

Despite their important role in metastatic disease, no general method to detect circulating stromal cells (CStCs) exists. Here, we present the Metabolic Assay-Chip (MA-Chip) as a label-free, droplet-based microfluidic approach allowing single-cell extracellular pH measurement for the detection and isolation of highly metabolically active cells (hm-cells) from the tumor microenvironment. Single-cell mRNA-sequencing analysis of the hm-cells from metastatic prostate cancer patients revealed that approximately 10% were canonical EpCAM+ hm-CTCs, 3% were EpCAM− hm-CTCs with up-regulation of prostate-related genes, and 87% were hm-CStCs with profiles characteristic for cancer-associated fibroblasts, mesenchymal stem cells, and endothelial cells. Kaplan-Meier analysis shows that metastatic prostate cancer patients with more than five hm-cells have a significantly poorer survival probability than those with zero to five hm-cells. Thus, prevalence of hm-cells is a prognosticator of poor outcome in prostate cancer, and a potentially predictive and therapy response biomarker for agents cotargeting stromal components and preventing epithelial-to-mesenchymal transition.

scholarly journals Uncovering transcriptional dark matter via gene annotation independent single-cell RNA sequencing analysis

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Michael F. Z. Wang ◽  
Madhav Mantri ◽  
Shao-Pei Chou ◽  
Gaetano J. Scuderi ◽  
David W. McKellar ◽  
...  
Keyword(s):  
Single Cell ◽  
Genome Annotation ◽  
Gene Annotation ◽  
Active Regions ◽  
Sequencing Analysis ◽  
Biologically Relevant ◽  
Mole Rat ◽  
Genome Annotations ◽  
Cell Expression ◽  
High Quality Genome

AbstractConventional scRNA-seq expression analyses rely on the availability of a high quality genome annotation. Yet, as we show here with scRNA-seq experiments and analyses spanning human, mouse, chicken, mole rat, lemur and sea urchin, genome annotations are often incomplete, in particular for organisms that are not routinely studied. To overcome this hurdle, we created a scRNA-seq analysis routine that recovers biologically relevant transcriptional activity beyond the scope of the best available genome annotation by performing scRNA-seq analysis on any region in the genome for which transcriptional products are detected. Our tool generates a single-cell expression matrix for all transcriptionally active regions (TARs), performs single-cell TAR expression analysis to identify biologically significant TARs, and then annotates TARs using gene homology analysis. This procedure uses single-cell expression analyses as a filter to direct annotation efforts to biologically significant transcripts and thereby uncovers biology to which scRNA-seq would otherwise be in the dark.

scholarly journals Regulation of cell-substrate adhesion by proteoglycans immobilized on extracellular substrates

1989 ◽  
Vol 264 (14) ◽  
pp. 8012-8018 ◽  
Author(s):  
M Yamagata ◽  
S Suzuki ◽  
S K Akiyama ◽  
K M Yamada ◽  
K Kimata
Keyword(s):  
Substrate Adhesion ◽  
Cell Substrate ◽  
Cell Substrate Adhesion

scholarly journals A GTPase controls cell-substrate adhesion in Xenopus XTC fibroblasts.

1992 ◽  
Vol 118 (5) ◽  
pp. 1235-1244 ◽  
Author(s):  
M H Symons ◽  
T J Mitchison
Keyword(s):  
Control Cell ◽  
Response To Treatment ◽  
Nucleotide Analogs ◽  
Cell Contractility ◽  
Cell Rounding ◽  
Substrate Adhesion ◽  
Cell Substrate ◽  
Adhesive Interactions ◽  
Cell Substrate Adhesion ◽  
Gamma S

Cell-substrate adhesion is crucial at various stages of development and for the maintenance of normal tissues. Little is known about the regulation of these adhesive interactions. To investigate the role of GTPases in the control of cell morphology and cell-substrate adhesion we have injected guanine nucleotide analogs into Xenopus XTC fibroblasts. Injection of GTP gamma S inhibited ruffling and increased spreading, suggesting an increase in adhesion. To further investigate this, we made use of GRGDSP, a peptide which inhibits binding of integrins to vitronectin and fibronectin. XTC fibroblasts injected with non-hydrolyzable analogs of GTP took much more time to round up than mock-injected cells in response to treatment with GRGDSP, while GDP beta S-injected cells rounded up in less time than controls. Injection with GTP gamma S did not inhibit cell rounding induced by trypsin however, showing that cell contractility is not significantly affected by the activation of GTPases. These data provide evidence for the existence of a GTPase which can control cell-substrate adhesion from the cytoplasm. Treatment of XTC fibroblasts with the phorbol ester 12-o-tetradecanoylphorbol-13-acetate reduced cell spreading and accelerated cell rounding in response to GRGDSP, which is essentially opposite to the effect exerted by non-hydrolyzable GTP analogs. These results suggest the existence of at least two distinct pathways controlling cell-substrate adhesion in XTC fibroblasts, one depending on a GTPase and another one involving protein kinase C.

Sign in / Sign up

Export Citation Format

Share Document