The Transcription Factor <i>SUB1</i> Is a Master Regulator of the Macrophage TLR Response in Atherosclerosis

Huang, Rongzhong; Hu, Zicheng; Chen, Hong; Cao, Yu; Li, Hongrong; Zhang, Hong; Li, Yongyong; Liang, Liwen; Feng, Yuxing; Wang, Ying; Kong, Zerui; Melgiri, ND; Jiang, Lihong; Li, Xingsheng; Du, Jianlin; Chen, Yunqing

doi:10.1002/advs.202004162

Cited by 12 publications

(4 citation statements)

References 58 publications

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“…S1b includes Ndufa4 and Sub1 (Fig. 3f), markers for macrophage differentiation [30,31]. S1c includes Irf8, Cst3 and Cts (Fig.…”

Section: Resultsmentioning

confidence: 99%

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

Gao

Wang

et al. 2023

Preprint

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Single-cell sequencing has provided a means of quantifying cellular omic phenotypes. Identifying cell-type-specific feature genes is a crucial aspect of understanding cellular heterogeneity. Over the past decade, many methods have been developed to identify feature genes; however, these methods either depend on dubious cell clustering or fail to provide subpopulation-specific markers. We introduce SifiNet, a robust and accurate approach for identifying marker gene sets based on gene co-expression network topology. The identified gene sets facilitate the calculation of cellular gene set enrichment scores and cell annotation, and can reveal potential transitional relationships between cell subpopulations. SifiNet outperforms state-of-the-art methods in marker gene set identification and cell-type annotation accuracy. It is applicable to both single-cell RNA sequencing (scRNA-seq) and single-cell ATAC sequencing (scATAC-seq) data. We have applied SifiNet to various experimental studies, successfully identifying novel gene markers, annotating cells with complex heterogeneity, and uncovering intriguing cell developmental trajectories.

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“…S1b includes Ndufa4 and Sub1 (Fig. 3f), markers for macrophage differentiation [30,31]. S1c includes Irf8, Cst3 and Cts (Fig.…”

Section: Resultsmentioning

confidence: 99%

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

Gao

Wang

et al. 2023

Preprint

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“…By using the model of PC4 knockout in mice, it has been found that loss of PC4 results in early embryo lethality, indicating an essential role of PC4 in embryonic development [ 38 ]. In addition, conditional knockout mice models showed defects in the development of the nervous system [ 38 ] or impairment of inflammatory response [ 39 ]. In addition, an overexpression of PC4 results in the malignant transformation of normal cells in several cancer models, indicating that PC4 has a role in tumorigenesis [ 40 , 41 , 42 ].…”

Section: Discussionmentioning

confidence: 99%

The Catalytic Subunit of Schizosaccharomyces pombe CK2 (Cka1) Negatively Regulates RNA Polymerase II Transcription through Phosphorylation of Positive Cofactor 4 (PC4)

Rojas

Urbina

Solari

et al. 2022

IJMS

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Positive cofactor 4 (PC4) is a transcriptional coactivator that plays important roles in transcription and DNA replication. In mammals, PC4 is phosphorylated by CK2, and this event downregulates its RNA polymerase II (RNAPII) coactivator function. This work describes the effect of fission yeast PC4 phosphorylation on RNAPII transcription in a cell extract, which closely resembles the cellular context. We found that fission yeast PC4 is strongly phosphorylated by the catalytic subunit of CK2 (Cka1), while the regulatory subunit (Ckb1) downregulates the PC4 phosphorylation. The addition of Cka1 to an in vitro transcription assay can diminish the basal transcription from the Ad-MLP promoter; however, the addition of recombinant fission yeast PC4 or Ckb1 can stimulate the basal transcription in a cell extract. Fission yeast PC4 is phosphorylated in a domain which has consensus phosphorylation sites for CK2, and two serine residues were identified as critical for CK2 phosphorylation. Mutation of one of the serine residues in PC4 does not completely abolish the phosphorylation; however, when the two serine residues are mutated, CK2 is no longer able to phosphorylate PC4. The mutant which is not phosphorylated is able to stimulate transcription even though it is previously phosphorylated by Cka1, while the wild type and the point mutant are inactivated by Cka1 phosphorylation, and they cannot stimulate transcription by RNAPII in cell extracts. Those results demonstrate that CK2 can regulate the coactivator function of fission yeast PC4 and suggests that this event could be important in vivo as well.

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“…AS is a chronic progressive and inflammatory artery disease with an intricate pathogenesis, in which dyslipidaemia is the main risk factor, and oxidative stress is a key initiating factor [ 60 ]. Endothelial cell dysfunction or death is affected by intracellular lipid peroxides and participates in the regulation of AS [ 61 ].…”

Section: Asmentioning

confidence: 99%

Emerging roles of ferroptosis in cardiovascular diseases

et al. 2022

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The mechanism of cardiovascular diseases (CVDs) is complex and threatens human health. Cardiomyocyte death is an important participant in the pathophysiological basis of CVDs. Ferroptosis is a new type of iron-dependent programmed cell death caused by excessive accumulation of iron-dependent lipid peroxides and reactive oxygen species (ROS) and abnormal iron metabolism. Ferroptosis differs from other known cell death pathways, such as apoptosis, necrosis, necroptosis, autophagy and pyroptosis. Several compounds have been shown to induce or inhibit ferroptosis by regulating related key factors or signalling pathways. Recent studies have confirmed that ferroptosis is associated with the development of diverse CVDs and may be a potential therapeutic drug target for CVDs. In this review, we summarize the characteristics and related mechanisms of ferroptosis and focus on its role in CVDs, with the goal of inspiring novel treatment strategies.

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The Transcription Factor SUB1 Is a Master Regulator of the Macrophage TLR Response in Atherosclerosis

Cited by 12 publications

References 58 publications

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

The Catalytic Subunit of Schizosaccharomyces pombe CK2 (Cka1) Negatively Regulates RNA Polymerase II Transcription through Phosphorylation of Positive Cofactor 4 (PC4)

Emerging roles of ferroptosis in cardiovascular diseases

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