scholarly journals Comprehensive mapping of the alternative polyadenylation site usage and its dynamics at single cell resolution

2021 ◽  
Author(s):  
Junliang Wang ◽  
Wei Chen ◽  
Wenhong Hou ◽  
Ni Hong ◽  
Hanbing Zhong ◽  
...  

AbstractAlternative polyadenylation (APA) plays an important role in post-transcriptional gene regulation such as transcript stability and translation efficiency. However, our knowledge about APA dynamics at single cell level is largely unexplored. Here we developed single cell polyadenylation sequencing (scPolyA-seq), a strand-specific approach for sequencing 3’ end of transcripts, to investigate the landscape of APA at single cell level. By analyzing several cell lines, we found many genes using multiple polyA sites in bulk data are prone to use only one polyA site in each single cell. Interestingly, cell cycle was significantly enriched in genes showing high variation of polyA site usages. We further identified 414 genes showing polyA site usage switch after cell synchronization. Genes showing cell cycle associated polyA site usage switch were grouped into 6 clusters, with cell phase specific functional categories enriched in each cluster. Furthermore, scPolyA-seq could facilitate study of APA in various biological processes.

2016 ◽  
Vol 130 (2) ◽  
pp. 512-520 ◽  
Author(s):  
Siang-Boon Koh ◽  
Patrice Mascalchi ◽  
Esther Rodriguez ◽  
Yao Lin ◽  
Duncan I. Jodrell ◽  
...  

2021 ◽  
Author(s):  
Sheng Zhu ◽  
Qiwei Lian ◽  
Wenbin Ye ◽  
Wei Qin ◽  
Zhe Wu ◽  
...  

Abstract Alternative polyadenylation (APA) is a widespread regulatory mechanism of transcript diversification in eukaryotes, which is increasingly recognized as an important layer for eukaryotic gene expression. Recent studies based on single-cell RNA-seq (scRNA-seq) have revealed cell-to-cell heterogeneity in APA usage and APA dynamics across different cell types in various tissues, biological processes and diseases. However, currently available APA databases were all collected from bulk 3′-seq and/or RNA-seq data, and no existing database has provided APA information at single-cell resolution. Here, we present a user-friendly database called scAPAdb (http://www.bmibig.cn/scAPAdb), which provides a comprehensive and manually curated atlas of poly(A) sites, APA events and poly(A) signals at the single-cell level. Currently, scAPAdb collects APA information from > 360 scRNA-seq experiments, covering six species including human, mouse and several other plant species. scAPAdb also provides batch download of data, and users can query the database through a variety of keywords such as gene identifier, gene function and accession number. scAPAdb would be a valuable and extendable resource for the study of cell-to-cell heterogeneity in APA isoform usages and APA-mediated gene regulation at the single-cell level under diverse cell types, tissues and species.


2020 ◽  
Author(s):  
Léonard Hérault ◽  
Mathilde Poplineau ◽  
Adrien Mazuel ◽  
Nadine Platet ◽  
Élisabeth Remy ◽  
...  

ABSTRACTHematopoietic stem cells (HSCs) are the guarantor of the proper functioning of hematopoiesis due to their incredible diversity of potential. During aging the heterogeneity of mouse HSCs evolves, which contributes to the deterioration of the immune system. Here we address the transcriptional plasticity of HSC upon aging at the single-cell resolution. Through the analysis of 15,000 young and aged transcriptomes, we reveal 15 clusters of HSCs unveiling rare and specific HSC abilities that change with age. Pseudotime ordering complemented with regulon analysis showed that the consecutive differentiation states of HSC are delayed upon aging. By analysing cell cycle at the single cell level we highlight an imbalance of cell cycle regulators of very immature aged HSC that may contribute to their accumulation in an undifferentiated state.Our results therefore establish a reference map of young and old mouse HSC differentiation and reveal a potential mechanism that delay aged HSC differentiation.


2013 ◽  
Vol 64 (1) ◽  
Author(s):  
Rachel J. Errington ◽  
Sally C. Chappell ◽  
Imtiaz A. Khan ◽  
Nuria Marquez ◽  
Marie Wiltshire ◽  
...  

2020 ◽  
Vol 12 (1) ◽  
Author(s):  
Hideyuki Takeshima ◽  
Yukie Yoda ◽  
Mika Wakabayashi ◽  
Naoko Hattori ◽  
Satoshi Yamashita ◽  
...  

Abstract Background Epigenetic reprogramming using DNA demethylating drugs is a promising approach for cancer therapy, but its efficacy is highly dependent on the dosing regimen. Low-dose treatment for a prolonged period shows a remarkable therapeutic efficacy, despite its small demethylating effect. Here, we aimed to explore the mechanisms of how such low-dose treatment shows this remarkable efficacy by focusing on epigenetic reprograming at the single-cell level. Methods Expression profiles in HCT116 cells treated with decitabine (DAC) were analyzed by single-cell RNA-sequencing (scRNA-seq). Functional consequences and DNA demethylation at the single-cell level were analyzed using cloned HCT116 cells after DAC treatment. Results scRNA-seq revealed that DAC-treated cells had highly diverse expression profiles at the single-cell level, and tumor-suppressor genes, endogenous retroviruses, and interferon-stimulated genes were upregulated in random fractions of cells. DNA methylation analysis of cloned HCT116 cells revealed that, while only partial reduction of DNA methylation levels was observed in bulk cells, complete demethylation of specific cancer-related genes, such as cell cycle regulation, WNT pathway, p53 pathway, and TGF-β pathway, was observed, depending upon clones. Functionally, a clone with complete demethylation of CDKN2A (p16) had a larger fraction of cells with tetraploid than parental cells, indicating induction of cellular senescence due to normalization of cell cycle regulation. Conclusions Epigenetic reprogramming of specific cancer-related pathways at the single-cell level is likely to underlie the remarkable efficacy of low-dose DNA demethylating therapy.


Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 1723-1723
Author(s):  
Cristina Pina ◽  
Tariq Enver

Abstract Human cord blood-derived CD133+G0 cells are a primitive population highly enriched in hematopoietic stem cells (HSC). We used this population to investigate the molecular characteristics of primitive human HSC, and, in particular, to unveil how different cell fates of quiescence, self-renewal and lineage commitment and differentiation are regulated at the molecular level. We isolated cord blood CD133+ cells in the G0 and G1 compartments of the cell cycle on the basis of low or high RNA content, respectively, as detected by Pyronin Y staining. More than 98% of the CD133+G0 cells were Ki67-negative, and at least 90% did not express CD38, thus confirming the quiescent and primitive status of the cells. Consistent with earlier findings showing that CD133+G0 cells have the highest reported frequency of LTC-IC (1), our quiescent population presented a significantly higher frequency of LTC-IC when compared to CD133+G1 cells. We further showed that CD133+G0 cells had significantly higher colony-forming capacity in progenitor assays and a higher CFU-Mix content. Initial RT-PCR analysis revealed that while both compartments express the erythroid marker beta-globin, myeloid MPO and lymphoid IL7R can only be observed in CD133+G1 cells. This suggests a hierarchy of commitment decisions in relation to cell cycle that places the erythroid signature upstream of myelo-lymphoid differentiation and may be in agreement with revised models of the hematopoietic differentiation tree recently proposed in mouse (2). This hypothesis is currently being assessed at the single-cell level. We next compared the overall gene expression programmes of CD133+G0 and G1 populations using global profiling. Consistent with the sorting criteria, CD133+G1-enriched transcripts have a comparatively higher frequency of cell cycle, protein synthesis and RNA processing, and metabolism-associated genes, which underlines the robustness of the data. The CD133+G1 population is associated with a lymphoid signature, including immunoglobulin heavy and light chains, and the SLAM family member CD48, which is consistent with the revised hierarchy of commitment decisions discussed above. Functional categories comparatively over-represented amongst CD133+G0-enriched genes include transcriptional regulation and signal transduction, suggesting that primitive quiescent HSC are ready to respond to a variety of cues that modulate alternative fate decisions. Since the transcriptional profile of a given population of cells may not reflect the transcriptional profile of each individual cell, we are currently analyzing the expression patterns of CD133+G0-enriched transcription factors (TF) at the single-cell level. This approach may help define subpopulations of cells with unique molecular signatures and suggest functional subcompartments within an otherwise heterogeneous population of primitive hematopoietic cells.


Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 785-785
Author(s):  
Paul S. Hole ◽  
Sara Davies ◽  
Chinmay R Munje ◽  
Sandra Kreuser ◽  
Robert K. Hills ◽  
...  

Abstract The serine/ threonine kinase, p38MAPK is activated by phosphorylation in response to a variety of cellular stresses including oxidative stress. Prolonged p38MAPK activation drives cell-cycle arrest and apoptosis; and in HSC activation of p38MAPK leads to a loss of reconstituting capacity (Ito et al, Nat.Med. 2006;12:446-451). In cancer, p38MAPK responses are often attenuated and cancer models suggest that this is a necessary adaptation for transformation (Dolado et al, Cancer Cell 2007;11:191-205). Previously we have shown that 60% of acute myeloid leukemia (AML) patients constitutively generate significantly more extracellular reactive oxygen species (ROS) than normal hematopoietic CD34+ cells (Hole et al, Blood 2013;122:3322-3330). Despite this, AML blasts showed low or absent p38MAPK phosphorylation; even in patients generating high levels of ROS. Here we examine p38MAPK activation at the single cell level in primary AML blasts using flow cytometry. We challenged AML blasts with a dose of hydrogen peroxide (H2O2) sufficient to completely activate p38MAPK in normal CD34+ cells (1 mM for 30 min), where the threshold for activation was defined as the 95th percentile of basal p38MAPK activation in unstimulated cells. Attenuated responses to H2O2 were seen in 14/15 (93%) of patients; where 16-95% of the total blast population failed to activate p38MAPK. These non-responding cells are hereafter termed “Δpp38MAPK cells” and were absent in normal CD34+ cells (p < 0.01; Figure 1). Examination of a panel of 6 AML cell lines showed that each of the lines contained Δpp38MAPK cells at different frequencies: MV4-11 (10%); HL60 (10%); KG-1 (15%), U937 (30%), NB4 (50%), THP-1 (65%). Further analysis showed that Δpp38MAPK cells were not distinguished by cell cycle phase, immunophenotype or reduced viability in either cell lines or AML blasts. These data suggest that nearly all AML patients harbor a population of blasts which have developed resistance to p38MAPK activation. We reasoned that failure to respond could arise either through defective p38MAPK signaling or because of enhanced anti-oxidative protection in a subpopulation of cells. To investigate the latter, we labelled cells with the lipophilic oxidation probe, C11 -BODIPY or the cytosolic oxidant probe, CM-DCFDA and monitored the oxidative response to H2O2 at the single cell level in the AML cell lines: KG-1, MV4-11 and THP-1. In each case C11 -BODIPY oxidation exactly matched the heterogeneous profile of p38MAPK activation in these cells, whereas CM-DCFDA showed only homogeneous responses to H2O2 induction. These data show that Δpp38MAPK cells are defined by an enhanced membrane-associated anti-oxidant capacity and we are currently analyzing this resistant subpopulation to identify the molecules responsible. To examine whether p38MAPK responsiveness influenced responsiveness to pro-oxidant drugs, we selected KG-1 and THP-1 cells (as representative examples of strong and weak p38MAPK responses respectively) and tested their sensitivity to the pro-oxidant drugs, phenethyl isothiocyanate (PEITC) and buthionine sulfoximine (BSO). We found that the IC50 was higher for THP-1 for both PEITC (KG-1 = 0.6µM; THP-1 = 7.5µM) and BSO (KG-1 = 50µM; THP-1 = 70µM), indicating that the p38MAPK responsiveness limits the effectiveness of pro-oxidant drugs. We next examined whether promoting p38MAPK activation could augment the effects of these pro-oxidants. We used the p38MAPK activator 2-benzylidene-3-(cyclohexylamino)-1-indanone (BCI), which promotes activation of p38MAPK via inhibition of a p38MAPK phosphatase, DUSP1. This compound weakly promoted phosphorylation of p38MAPK in THP-1 cells and consistent with this, had no effect on the efficacy of these compounds in these cells. However, BCI potently activated p38MAPK in KG-1 cells and showed synergy with BSO in this context (CI = 0.3; Figure 2) indicating that where BCI is effective in activating p38MAPK it can promote the effectiveness of pro-oxidant drugs. In summary, we show for the first time that AML patients almost universally display attenuated p38MAPK responses in all or part of the blast population and we suggest that this trait may be selected for to maintain self-renewing potential under the pro-oxidative conditions found in the leukemic marrow. Further we show that by manipulating p38MAPK activity, we can augment the potency of the pro-oxidant compound BSO. Figure 1 Figure 1. Figure 2 Figure 2. Disclosures No relevant conflicts of interest to declare.


2020 ◽  
Vol 19 ◽  
pp. 153303382095703
Author(s):  
Wenqian Zhang ◽  
Tong Li ◽  
Bin Hu ◽  
Hui Li

Objective: This study aimed to explore PLEK2 expression profile, its prognostic value, and the potential genomic alterations associated with its dysregulation in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Materials and methods: Data from The Cancer Genome Atlas (TCGA), The Genotype-Tissue Expression (GTEx), and Kaplan-Meier plotter were used in combination for bioinformatic analysis. Results: PLEK2 mRNA was significantly upregulated in both LUAD and LUSC compared with their respective normal controls. PLEK2 upregulation showed independent prognostic value in progression-free survival (PFS) (HR: 1.169, 95%CI: 1.033 -1.322, p = 0.014). PLEK2 mRNA expression was positively correlated with invasion, cell cycle, DNA damage, and DNA repair of LUAD cells at the single-cell level. Genomic analysis showed that gene-level amplification might not directly lead to increased PLEK2 expression. Methylation profile analysis found 4 CpG sites (cg12199376, cg14437634, cg17641252, and cg06724236) had at least a weakly negative correlation with PLEK2 expression, among which cg12199376, cg14437634 and cg17641252 locate around the first exon of the gene. Conclusions: Increased PLEK2 expression might be a specific prognostic biomarker of poor PFS in LUAD patients. Its expression had significant positive correlations with invasion, cell cycle, DNA damage, and DNA repair of LUAD cells at the single-cell level. Promoter hypomethylation might be a potential mechanism leading to its upregulation.


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