MOLECULAR CELL
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2025
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IF 16.6
Jianfeng He,Yongyi Zhu,Zichao Tian,Mengqin Liu,Anmin Gao,Wangmi Fu,Fei Lu,Yutong Sun,Yajun Guo,Rongqing Pan,Yuchen Ji,Jianxiang Chen,Huasong Lu,Juan Lin,Xingguo Liang,Chun Kim,Chun Zhou,Huipeng Jiao
Z-DNA-binding protein 1 (ZBP1; also known as DAI or DLM-1) regulates cell death and inflammation by sensing left-handed double-helical nucleic acids, including Z-RNA and Z-DNA. However, the physiological conditions that generate Z-form nucleic acids (Z-NAs) and activate ZBP1-dependent signaling pathways remain largely elusive. In this study, we developed a probe, Zα-mFc, that specifically detected both Z-DNA and Z-RNA. Utilizing this probe, we discovered that inhibiting spliceosome causes nuclear accumulation of Z-RNA:DNA hybrids, which are sensed by ZBP1 via its Zα domains, triggering apoptosis and necroptosis in mammalian cells. Furthermore, we solved crystal structures of the human or mouse Zα1 domain complexed with a 6-bp RNA:DNA hybrid, revealing that the RNA:DNA hybrid adopts a left-handed conformation. Our findings demonstrate that the spliceosome acts as a checkpoint preventing accumulation of Z-RNA:DNA hybrids, which potentially function as endogenous ligands activating ZBP1-dependent cell death pathways.
研究领域:
分子生物学
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免疫学
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细胞生物学
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产品关联
DOI
PubMed
高影响因子
iScience
·
2022
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IF 6.107
Dawei Yang,Jie Yin,Liuqun Shan,Xingling Yi,Wei Zhang,Yongbin Ding
Summary Cancer cells tend to utilize aerobic glycolysis to generate energy and metabolites; the end product of aerobic glycolysis is lactate, which promotes lysine lactylation (Kla). Kla is a newly discovered histone post-translational modification (PTM) that plays important roles in regulating gene expression. However, Kla in non-histone mammalian proteins is unclear. Here, a comprehensive analysis of lactylated proteins in gastric cancer AGS cells was conducted. There were 2375 Kla sites found in 1014 proteins. Interestingly, KEGG pathway analysis showed that these proteins were significantly enriched in spliceosome function. In addition, Kla was more abundant in gastric tumors than in adjacent tissues, and high levels of Kla in gastric tumors were associated with poor prognosis. These results suggest that Kla could be a prognostic marker in gastric cancer. This lysine lactylome analysis in gastric cancer cells, the first of its kind, provides a valuable foundation for further studies of Kla.
研究领域:
癌症生物学
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蛋白质组学
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分子生物学
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生物化学
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DOI
PubMed
高影响因子
INTERNATIONAL IMMUNOPHARMACOLOGY
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2025
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IF 4.7
Dake Huang,Ke Shen,Li Gui,Qiongqiong Cao,Fangmei Yu,Yunxia Lu
Given resveratrol's (RES) potential as an anti-aging agent, this study explored its ability to inhibit the NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome through the miR-217/SIRT1 axis in senescent endothelial cells. Male C57BL/6 mice were administered a customized regular diet supplemented with 0.04 % RES for 64 consecutive weeks. Subsequently, the effects of RES on senescent human umbilical vein endothelial cells (HUVECs) induced by H 2 O 2 were evaluated. Gene expression analyses were conducted following SIRT1 knockdown in HUVECs treated with H 2 O 2 and RES, or transfected with miR-217 mimics and inhibitors. The study found that RES reduced body weight, improved endothelial function, enhanced SIRT1 expression, and suppressed the expression of miR-217, NADPH oxidase 4 (NOX4), and NLRP3 in the senescent thoracic aorta. Additionally, RES significantly reduced the expression of NOX4, X-box binding protein 1 spliced (XBP1s), and reactive oxygen species (ROS) production in a dose-dependent manner in senescent HUVECs. SIRT1 knockdown resulted in the activation of the NLRP3 inflammasome by upregulating NOX4 and XBP1s expression, an effect that was partially attenuated by RES pretreatment. RES also suppressed the expression of miR-217 induced by H 2 O 2 . The miR-217 mimic facilitated cellular senescence; however, RES mitigated this effect, which was further amplified by the miR-217 inhibitor.
研究领域:
分子生物学
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老年医学
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心血管病学
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细胞衰老
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信号转导
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氧化应激
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RNA干扰
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药理学
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产品关联
DOI
PubMed
高影响因子
Frontiers in Oncology
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2022
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IF 5.738
Youfu Zhang,Xuyang Wang,Huaxiang Wang,Yi Jiang,Zhidan Xu,Laibang Luo
Background Elevated Small Nuclear Ribonucleoprotein Polypeptide A ( SNRPA ) can enhance tumor cell growth and proliferation in various cancers. However, rarely studies focus on the comprehensive analysis of SNRPA in hepatocellular carcinoma (HCC). Methods TCGA and GEO databases were used to analyze the mRNA expression of SNRPA in HCC. Protein expression of SNAPA was validated using immunohistochemistry. Stably transfected HCC cells were used to investigate the role of SNRPA in the progression of HCC. The functional enrichment analysis was utilized for the biological function prediction. The CIBERSORT and ssGSEA algorithms were used to evaluate the composition of the tumor microenvironment and immunocyte infiltration ratio. Results The SNRPA expression was upregulated in HCC and positively correlated with tumor stage and grade. SNRPA overexpression were independent risk factors for poor overall survival (OS) and recurrence-free survival (RFS). In patients with early-stage disease, low alpha-fetoprotein expression, and better differentiation, SNRPA still exhibited the excellent prognostic value. Knockdown of SNRPA inhibited the proliferation and migration while promoting the apoptosis of HCC cells. Higher methylation of the CpG site cg16596691 correlated with longer OS in HCC patients. Genes co-expressed with SNRPA were overexpressed in HCC and correlated with shorter OS. The GO and KEGG enrichment analysis showed that SNRPA expression was related to mRNA splicing, spliceosome signaling. GSEA demonstrated that the main enrichment pathway of SNRPA-related differential genes was spliceosome signaling, cell cycle signaling, P53 signaling pathway, T cell receptor signaling pathway, natural killer cell-mediated signaling. CIBERSORT and ssGSEA algorithm revealed that SNRPA was mainly associated with the higher proportion of CD8+T cells, T cells follicular helper, T cells regulatory, Macrophages M0, and the lower proportion of T cells CD4 memory resting, NK cells resting, Monocytes, and Mast cells resting. Conclusion Elevated SNRPA enhances tumor cell proliferation and correlated with poor prognosis and immune infiltrates in patients with HCC.
研究领域:
肿瘤学
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分子生物学
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免疫学
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生物信息学
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产品关联
DOI
PubMed
高影响因子
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
·
2024
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IF 2.5
Luyu Qi,Jun Zhu,Zhongyi Cheng,Zhiyi Yuan,Wulin Qi,JiaHuan Wu,Yifeng Qin,Jingbo Yang,Tao Luo,Minkun Wang,Yejing Weng,Jianzhong Shao
Protein phosphorylation, a widely occurring and significant post-translational modification, is integral to various biological processes. We previously utilized a protein affinity probe to identify genes damaged by cisplatin, revealing that it inflicts substantial damage on protein kinase and protein phosphatase genes. In this study, we investigated cisplatin-induced alterations in the global proteome and phosphoproteome of A549 cells. Employing Fe-IMAC beads and tyrosine phosphorylation enrichment antibodies, we identified 6944 protein groups and 18,274 phosphorylation sites on 4915 proteins across three biological replicates of both cisplatin-treated A549 cells and control cells. Among these, 730 tyrosine phosphorylation sites were identified—marking the most substantial discovery of such sites in A549 cells following cisplatin treatment. Bioinformatics analysis indicated that the proteins exhibiting significant phosphorylation level changes predominantly involved in RNA processing, modification, transcription, translation, and the spliceosome. This suggests that cisplatin-induced damage to protein kinases and phosphatases may disrupt the normal function of these proteins, consequently impairing DNA replication, RNA translation, and shearing, ultimately culminating in tumor cell death. Moreover, we cross-referenced our proteomic data with our previously obtained cisplatin-damaged genes, observing that the majority of down-regulated proteins derived from cisplatin-induced gene damage. The data are available on ProteomeXchange under the identifier PXD053902.
研究领域:
癌症生物学
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分子生物学
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蛋白质组学
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磷酸蛋白质组学
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生物信息学
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产品关联
DOI
PubMed
高影响因子
ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY
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2020
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IF 4.872
Hui Hao,Yao Dang,Sheng Chen,Qian Sun,Ren Kong,Shiyang Cheng,Chunsheng Liu
Triphenyl phosphate (TPHP) is one of the most widely used organophosphate flame retardants (OPFRs) and is frequently detected in a variety of environmental media. Previous studies reported that TPHP had toxic effects on vertebrates, but little toxic information was available in lower trophic aquatic organisms which were more sensitive to the exposure of many toxic substances. In this study, protozoa Tetrahymena thermophila ( T. thermophila ) were exposed to 0, 0.01, 0.17 or 2.35 mg/L TPHP for 5 days to study the effects of sub-chronic exposure on theoretical population, cell viability, cell size and number of cilia. Additionally, the effects of TPHP on gene transcription were assessed by transcriptome sequencing technique (RNA-Seq). Cell viability and number of cilia were significantly reduced in all TPHP exposure groups compared with the control. In addition, exposure to 0.17 or 2.35 mg/L TPHP significantly reduced the theoretical population, circumference and body width, and there was a significant decrease in body length in the 2.35 mg/L exposure group. Comparative transcriptome sequencing identified a total of 4105 up- and 4487 down-regulated genes after exposure to 2.35 mg/L TPHP for 5 days compared with the control. KEGG analysis showed that dysfunction of pathways associated with ribosome, spliceosome, phagosome, proteasome and protein processing in endoplasmic reticulum in this study might be responsible for the toxicity of T. thermophila caused by TPHP. In general, the results indicated that TPHP had an adverse effect on the protozoa T. thermophila .
研究领域:
环境毒理学
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分子生物学
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水生毒理学
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DOI
PubMed
高影响因子
PeerJ
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2024
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IF 2.3
Mengxiang Du,Shengwei Huang,Zihan Huang,Lijuan Qian,Yang Gui,Jing Hu,Yujun Sun
Although Morchella esculenta (L.) Pers. is an edible and nutritious mushroom with significant selenium (Se)-enriched potential, its biological response to selenium stimuli remains unclear. This study explored the effect of selenium on mushroom growth and the global gene expression profiles of M. esculenta . While 5 µg mL −1 selenite treatment slightly promoted mycelia growth and mushroom yield, 10 µg mL −1 significantly inhibited growth. Based on comparative transcriptome analysis, samples treated with 5 µg mL −1 and 10 µg mL −1 of Se contained 16,061 (452 upregulated and 15,609 downregulated) and 14,155 differentially expressed genes (DEGs; 800 upregulated and 13,355 downregulated), respectively. Moreover, DEGs were mainly enriched in the cell cycle, meiosis, aminoacyl-tRNA biosynthesis, spliceosome, protein processing in endoplasmic reticulum pathway, and mRNA surveillance pathway in both selenium-treated groups. Among these, MFS substrate transporter and aspartate aminotransferase genes potentially involved in Se metabolism and those linked to redox homeostasis were significantly upregulated, while genes involved in isoflavone biosynthesis and flavonoid metabolism were significantly downregulated. Gene expression levels increased alongside selenite treatment concentration, suggesting that high Se concentrations promoted M. esculenta detoxification. These results can be used to thoroughly explain the potential detoxification and Se enrichment processes in M. esculenta and edible fungi.
研究领域:
真菌学
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转录组学
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分子生物学
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营养学
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产品关联
DOI
PubMed
高影响因子
危险品化学品经营许可证（带存储）