Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing

Wu, Wanying; Zhang, Jinyang; Cao, Xiaofei; Cai, Zhengyi; Zhao, Fangqing

doi:10.1038/s41467-022-30963-8

Cited by 40 publications

(20 citation statements)

References 87 publications

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“…Most recently, an analysis of single-cell full-length transcriptome has provided a resource of circRNA expression in different cell types. 37 This data resource demonstrated that circ-PTPN22 was expressed in regulatory and central memory T cells, whereas circ-ADAMTS6 was expressed in multiple types of stromal cells. These results add to our observation that host genes were co-expressed with circ-PTPN22 and circ-ADAMTS6 and were highly expressed in regulatory T cells, CD8 + T cells, and endothelial cells, respectively ( Figures 4 C and 4E).…”

Section: Discussionmentioning

confidence: 83%

Exosomal circ-PTPN22 and circ-ADAMTS6 mark T cell exhaustion and neutrophil extracellular traps in Asian intrahepatic cholangiocarcinoma

Wang¹,

Wang²,

Wu³

et al. 2023

Molecular Therapy - Nucleic Acids

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Section: Discussionmentioning

confidence: 83%

Exosomal circ-PTPN22 and circ-ADAMTS6 mark T cell exhaustion and neutrophil extracellular traps in Asian intrahepatic cholangiocarcinoma

Wang¹,

Wang²,

Wu³

et al. 2023

Molecular Therapy - Nucleic Acids

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“…These models were based on reports on the characteristics of blood serum profiling in high-fat-fed mice, rats, monkeys, and humans with obesity models [ 48 , 49 , 50 , 51 , 52 , 53 ]. Blood serum factors in obesity are important mediators in the onset of neurodegenerative diseases since the blood-brain barrier (BBB) is disrupted or loosened in obesity conditions, and consequently, blood serum factors can be delivered into brain tissue resulting in memory loss [ 54 , 55 , 56 ]. Other studies also showed that the blood serum in obese contains higher pro-inflammatory cytokine levels, such as TNF-α and IL-6, leading to neuroinflammation and spatial memory loss [ 57 , 58 ].…”

Section: Discussionmentioning

confidence: 99%

Profiling and Cellular Analyses of Obesity-Related circRNAs in Neurons and Glia under Obesity-like In Vitro Conditions

Yoon

Lim

et al. 2023

IJMS

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Recent evidence indicates that the pathogenesis of neurodegenerative diseases, including Alzheimer’s disease, is associated with metabolic disorders such as diabetes and obesity. Various circular RNAs (circRNAs) have been found in brain tissues and recent studies have suggested that circRNAs are related to neuropathological mechanisms in the brain. However, there is a lack of interest in the involvement of circRNAs in metabolic imbalance-related neuropathological problems until now. Herein we profiled and analyzed diverse circRNAs in mouse brain cell lines (Neuro-2A neurons, BV-2 microglia, and C8-D1a astrocytes) exposed to obesity-related in vitro conditions (high glucose, high insulin, and high levels of tumor necrosis factor-alpha, interleukin 6, palmitic acid, linoleic acid, and cholesterol). We observed that various circRNAs were differentially expressed according to cell types with many of these circRNAs conserved in humans. After suppressing the expression of these circRNAs using siRNAs, we observed that these circRNAs regulate genes related to inflammatory responses, formation of synaptic vesicles, synaptic density, and fatty acid oxidation in neurons; scavenger receptors in microglia; and fatty acid signaling, inflammatory signaling cyto that may play important roles in metabolic disorders associated with neurodegenerative diseases.

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“…For example, Ji et al detected 71,112, 77,812, and 56,769 full-length circRNAs from 17 human, 13 macaque, and 14 mouse tissue samples, respectively [ 63 ]. It is worth noting that a total of 139,643 human and 214,747 mouse circRNAs were identified from 171 full-length single-cell RNA-seq datasets [ 64 ]. Meanwhile, 6519 circRNAs full-length circRNAs were studied in rice ( Oryza sativa ) and they were conserved in another 46 plant species [ 65 ].…”

Section: Discussionmentioning

confidence: 99%

Identification of circRNAs Associated with Adipogenesis Based on RNA-Seq Data in Pigs

Wang

Xing

et al. 2022

Genes

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Adipocytes or fat cells play a vital role in the storage and release of energy in pigs, and many circular RNAs (circRNAs) have emerged as important regulators in various tissues and cell types in pigs. However, the spatio-temporal expression pattern of circRNAs between different adipose deposition breeds remains elusive. In this study, RNA sequencing (RNA-seq) produced transcriptome profiles of Western Landrace (lean-type) and Chinese Songliao black pigs (obese-type) with different thicknesses of subcutaneous fat tissues and were used to identify circRNAs involved in the regulation of adipogenesis. Gene expression analysis revealed 883 circRNAs, among which 26 and 11 circRNAs were differentially expressed between Landrace vs. Songliao pigs and high- vs. low-thickness groups, respectively. We also analyzed the interaction between circRNAs and microRNAs (miRNAs) and constructed their interaction network in adipogenesis; gene ontology classification and pathway analysis revealed two vital circRNAs, with the majority of their target genes enriched in biological functions such as fatty acids biosynthesis, fatty acid metabolism, and Wnt/TGF-β signaling pathways. These candidate circRNAs can be taken as potential targets for further experimental studies. Our results show that circRNAs are dynamically expressed and provide a valuable basis for understanding the molecular mechanism of circRNAs in pig adipose biology.

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Exploring the cellular landscape of circular RNAs using full-length single-cell RNA sequencing

Cited by 40 publications

References 87 publications

Exosomal circ-PTPN22 and circ-ADAMTS6 mark T cell exhaustion and neutrophil extracellular traps in Asian intrahepatic cholangiocarcinoma

Exosomal circ-PTPN22 and circ-ADAMTS6 mark T cell exhaustion and neutrophil extracellular traps in Asian intrahepatic cholangiocarcinoma

Profiling and Cellular Analyses of Obesity-Related circRNAs in Neurons and Glia under Obesity-like In Vitro Conditions

Identification of circRNAs Associated with Adipogenesis Based on RNA-Seq Data in Pigs

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