Review
Cell Biology
Ruchi Kumari, Parmjit Jat
Summary: Cellular senescence is a stable cell cycle arrest triggered in response to various stimuli, characterized by dynamic changes in senescent cells. It has both positive effects on tissue repair and anti-cancer mechanisms, but can also negatively impact organismal health. Multiple pathways, including p53/p21 and p16/pRB, play central roles in regulating this process.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Oncology
Sofia Zanotti, Bieke Decaesteker, Suzanne Vanhauwaert, Bram De Wilde, Winnok H. De Vos, Frank Speleman
Summary: Neuroblastoma, a common tumor in children under five, has poor treatment outcomes for high-risk cases and causes long-term side effects. Cellular senescence has been considered a barrier against tumorigenesis, but recent research suggests a more complex and reversible nature for this process, which may impact treatment strategies. Neuroblastoma cells in a senescent state may escape treatment and promote relapse, but senescence could also provide opportunities for new therapies.
BRITISH JOURNAL OF CANCER
(2022)
Article
Biochemistry & Molecular Biology
Jian-Xiang Liu, Dao-Lei Cui, Dan-Lei Yang, Jing-Ya Li, Zi-Yue Yang, Jin-Zhou Su, Cai-Xia Ren, You-Ya Niu, Ping Xiang
Summary: Tris (1-chloro-2-propyl) phosphate (TCPP) is a commonly detected organophosphorus flame retardant in the environment. This study investigated the detrimental effects of TCPP on human skin keratinocytes and found that it decreased cell viability, induced reactive oxygen species generation and DNA damage, arrested the cell cycle at the G1 phase, and caused cellular senescence through the p53-dependent DNA damage signal pathway.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Laureline Roger, Fanny Tomas, Veronique Gire
Summary: Cellular senescence is an essentially irreversible proliferative arrest state where cells release pro-inflammatory and proteolytic factors. Different types of senescent cells accumulate in various tissues and organs with unique functions. Understanding how cells undergo extensive changes to induce a common cellular state is crucial for cancer prevention and improving health during aging.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Virology
Xinna Wu, Xuqiang Zhou, Sanying Wang, Genxiang Mao
Summary: This paper reviews the relationship between DNA damage response, cellular senescence, and human cytomegalovirus, providing new insights for virus-induced senescence.
Review
Cell Biology
Xiurong Cai, Adrien Guillot, Hanyang Liu
Summary: With high morbidity and mortality, hepatocellular carcinoma (HCC) is a significant and increasing burden globally. The relapse-prone nature and drug resistance of HCC are attributed to various intracellular processes and extracellular interplay, which actively participate in tumor microenvironment remodeling. Cellular senescence, considered as a fail-safe program, plays a crucial role in the progression of chronic inflammatory liver diseases and carcinogenesis. The potential of senescence in affecting anti-cancer strategies is gaining attention in recent studies.
Review
Oncology
Shuai Xiao, Dongmin Qin, Xueyang Hou, Lingli Tian, Yeping Yu, Rui Zhang, Hao Lyu, Dong Guo, Xing-Zhen Chen, Cefan Zhou, Jingfeng Tang
Summary: Cellular senescence is a tumor-suppressive mechanism, but therapy-induced senescence may promote cancer cell survival and malignant transformation. Therefore, rapidly eliminating therapy-induced senescent cells is crucial.
FRONTIERS IN ONCOLOGY
(2023)
Review
Toxicology
Li You, Eugenie Nepovimova, Marian Valko, Qinghua Wu, Kamil Kuca
Summary: Mycotoxins induce oxidative stress, hypoxia, and cellular senescence, which are involved in immunosuppressive effects. Activation of senescence markers and cell cycle arrest pathways by mycotoxins further contribute to immunomodulatory effects.
ARCHIVES OF TOXICOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Herath Mudiyanselage Udari Lakmini Herath, Mei Jing Piao, Kyoung Ah Kang, Ao Xuan Zhen, Pincha Devage Sameera Madushan Fernando, Hee Kyoung Kang, Joo Mi Yi, Jin Won Hyun
Summary: This study revealed that hesperidin exhibits a protective effect on human HaCaT keratinocytes against PM2.5-induced cellular damage, cell cycle arrest, and cellular senescence. Hesperidin ameliorates PM2.5-induced mitochondrial damage, cell cycle arrest, and cellular senescence through the ROS/JNK pathway, and inhibits the activation of matrix metalloproteinases by suppressing activator protein 1 activation.
Article
Biochemistry & Molecular Biology
Theodoros Eleftheriadis, Georgios Pissas, Georgios Filippidis, Maria Efthymiadi, Vassilios Liakopoulos, Ioannis Stefanidis
Summary: Gliflozins, such as dapagliflozin, can inhibit cell senescence pathways and prevent renal tubular epithelial cell (RPTEC) senescence. High glucose induces oxidative stress and leads to a senescence-associated secretory phenotype. Dapagliflozin reduces glucose consumption and inhibits related pathways, effectively preventing cell senescence. Investigating the effects of gliflozins on cell senescence has potential significance for the treatment of diabetic nephropathy.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Cell Biology
Ashish Kumar, Kavitha Thirumurugan
Summary: Normal somatic cells undergo finite cellular divisions, but they can be arrested in response to various stressors such as oxidative stress, oncogene-induced abnormalities, genotoxic stress, and telomere attrition. Repair mechanisms are activated during the cell cycle pause caused by stress, and the nature of the stress determines whether repair or permanent arrest occurs. Quiescence allows damaged cells to repair and return to the cell cycle, while senescence is irreversible and leads to age-related disorders.
Article
Cell Biology
Li-Bin Gao, Ya-Hong Wang, Zhi-Hua Liu, Yu Sun, Peng Cai, Qing Jing
Summary: The study demonstrated that the small molecule SR9009 effectively suppresses the senescence-associated secretory phenotype (SASP) by activating the NRF2 pathway, preventing cellular senescence. It also showed efficacy in inhibiting cellular aging and inflammation in mouse models.
Article
Biochemistry & Molecular Biology
Thu-Huyen Pham, Hyo-Min Park, Jinju Kim, Jin-Tae Hong, Do-Young Yoon
Summary: IL-32θ exerts anti-proliferative effects in breast cancer cells, inducing permanent senescence and chromosomal instability, which may lead to resistance to doxorubicin (DR). Targeting IL-32θ in combination with DR treatment may not be suitable for treating metastatic breast cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Jingfeng Liu, Xiaofei Huang, Dandan Liu, Kaiyuan Ji, Cheng Tao, Ren Zhang, Jian Chen
Summary: In this study, we demonstrated that DMB inhibits NSCLC progression by inducing cell cycle arrest and triggering cellular senescence through downregulating the c-Myc/HIF-1 alpha pathway. We also found that DMB suppresses cell migration by inhibiting epithelial-mesenchymal transition (EMT) and accelerates senescence by suppressing HIF-1 alpha expression in NSCLC cells. Additionally, DMB decreases c-Myc expression, an upstream regulator of HIF-1 alpha.
Article
Cell Biology
Xin Li, Zhiguo Niu, Chen Sun, Shu Zhuo, Huijie Yang, Xiao Yang, Yun Liu, Cheng Yan, Zhongbo Li, Qi Cao, Guimei Ji, Yinlu Ding, Ting Zhuang, Jian Zhu
Summary: The tumor suppressor P53 plays a critical role in preventing breast cancer. RNF187, a ubiquitin ligase, has been found to regulate the P53 signaling pathway and promote breast cancer growth while inhibiting cell apoptosis. The expression of RNF187 is correlated with breast cancer survival only in the P53 wild-type groups. Further experiments reveal that RNF187 interacts with P53 and facilitates its degradation by promoting polyubiquitination, independent of MDM2.
CELL DEATH & DISEASE
(2022)
Article
Biochemical Research Methods
Tao Hu, Shixiong Xu, Lei Wei, Xuegong Zhang, Xiaowo Wang
Summary: Recent advances in long-term time-lapse microscopy have enabled researchers to quantify cell behavior and molecular dynamics with ease. However, the lack of user-friendly software tools optimized for customized research remains a major challenge. CellTracker is a highly integrated graphical user interface software that automates cell segmentation and tracking in time-lapse microscopy images, offering features such as project management, image pre-processing, and statistical analysis.
Article
Biochemistry & Molecular Biology
Shengquan Chen, Qiao Liu, Xuejian Cui, Zhanying Feng, Chunquan Li, Xiaowo Wang, Xuegong Zhang, Yong Wang, Rui Jiang
Summary: OpenAnnotate is the first web server developed to efficiently annotate openness of massive genomic regions across various biosample types, tissues, and biological systems. It provides user-friendly functionalities, ultra-efficient calculation, real-time browsing, and intuitive visualization.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Wei Zhang, Lei Wei, Jiaqi Huang, Bixi Zhong, Jiaqi Li, Hanwen Xu, Shuying He, Yu Liu, Juhong Liu, Hairong Lv, Xiaowo Wang
Summary: cfDNApipe is an easy-to-use and systematic python package for cfDNA whole-genome sequencing and whole-genome bisulfite sequencing data analysis, covering the entire analysis pipeline, quality control, and statistical analysis.
Article
Biochemical Research Methods
Wei Zhang, Hanwen Xu, Rong Qiao, Bixi Zhong, Xianglin Zhang, Jin Gu, Xuegong Zhang, Lei Wei, Xiaowo Wang
Summary: ARIC is a promising algorithm for deconvolution of bulk data, accurately estimating cell type proportions from gene expression or DNA methylation data, with a focus on rare cell types.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Hematology
Xiaofei Zhang, Tingting Cong, Lei Wei, Bixi Zhong, Xiaowo Wang, Jin Sun, Shuxia Wang, Meng Michelle Xu, Ping Zhu, Hong Jiang, Jianwei Wang
Summary: This study identified the role of m6A RNA modification in regulating the reconstitution capacity of HSC. Ythdf3 and Mettl3 regulate HSC by controlling the translation process of Ccnd1.
Article
Biochemistry & Molecular Biology
Yanhong Wu, Qifan Hu, Shicheng Wang, Changyi Liu, Yiran Shan, Wenbo Guo, Rui Jiang, Xiaowo Wang, Jin Gu
Summary: In this study, a feature selection method called Highly Regional Genes (HRG) is proposed based on the cell-cell similarity network to identify informative genes that exhibit regional expression patterns. The HRG method demonstrates high accuracy and robustness compared to other unsupervised methods, and it improves the performance of cell clustering and gene correlation analysis.
JOURNAL OF GENETICS AND GENOMICS
(2022)
Article
Biochemical Research Methods
Lekang Yuan, Zhen Xie, Ye Wang, Xiaowo Wang
Summary: This study presents DeSP, a simulation pipeline for DNA storage errors, which systematically optimizes encoding redundancy by simulating errors generated in different stages. The simulation results are consistent with the in vitro experiments.
BMC BIOINFORMATICS
(2022)
Article
Multidisciplinary Sciences
Sijie Chen, Yanting Luo, Haoxiang Gao, Fanhong Li, Yixin Chen, Jiaqi Li, Renke You, Minsheng Hao, Haiyang Bian, Xi Xi, Wenrui Li, Weiyu Li, Mingli Ye, Qiuchen Meng, Ziheng Zou, Chen Li, Haochen Li, Yangyuan Zhang, Yanfei Cui, Lei Wei, Fufeng Chen, Xiaowo Wang, Hairong Lv, Kui Hua, Rui Jiang, Xuegong Zhang
Summary: The accumulation of massive single-cell omics data has provided abundant resources for building biomolecular atlases of human organs or the entire body. In this study, a unified informatics framework was developed for seamless cell-centric data assembly, resulting in the construction of the human Ensemble Cell Atlas (hECA) that includes 1,093,299 labeled human cells from 116 published datasets, covering 38 organs and 11 systems. The application of cell-centric assembly methods led to the development of new techniques for targeted data retrieval, multi-view representations of biological entities, and automatic annotation generation, demonstrating the great potential of the cell-centric ensemble atlas.
Article
Biochemical Research Methods
Xianglin Zhang, Xiaowo Wang
Summary: In this study, we proposed a method named MeConcord to measure the local methylation concordance across reads and CpG sites. MeConcord showed stable and efficient performance in distinguishing different methylation patterns and their associations with genomic characteristics.
Correction
Biochemical Research Methods
Lekang Yuan, Zhen Xie, Ye Wang, Xiaowo Wang
BMC BIOINFORMATICS
(2022)
Article
Biochemical Research Methods
Xianglin Zhang, Xiaodong Jia, Bixi Zhong, Lei Wei, Jiaqi Li, Wei Zhang, Huan Fang, Yanda Li, Yinying Lu, Xiaowo Wang
Summary: This study designed a specific mapping strategy to investigate the methylation patterns of ribosomal DNA (rDNA) and found that rDNA methylation profiles can serve as biomarkers for cancer detection with good performances.
BRIEFINGS IN BIOINFORMATICS
(2022)
Review
Biology
Xian-En Zhang, Chenli Liu, Junbiao Dai, Yingjin Yuan, Caixia Gao, Yan Feng, Bian Wu, Ping Wei, Chun You, Xiaowo Wang, Tong Si
Summary: Synthetic biology provides a new paradigm (build to learn) for life science research and opens up the future of biotechnology (build to use). This article discusses the advances in various principles and technologies in synthetic biology, including genome synthesis and assembly, DNA storage, gene editing, molecular evolution, de novo design of functional proteins, cell and gene circuit engineering, cell-free synthetic biology, AI-aided synthetic biology, and biofoundries. The concept of quantitative synthetic biology, which aims to increase accuracy and predictability in rational design, is also introduced. The article concludes that as enabling technologies continue to develop and core theories mature, synthetic biology will establish its own disciplinary system.
SCIENCE CHINA-LIFE SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Xin Zhang, Pengbo Wang, Yi Yang, Xin Gao, Yu Tang, Ying Luo, Xiangbing Deng, Yongyang Yu, Lanlan Zhang, Yan Zhang
Summary: This study investigated the mechanism of the impact of depression on Crohn's disease (CD) and found that monocytes/macrophages in blood and intestine play significant roles in both depression and CD. These cells mediate the effects of depression on CD through modulation of CD4+ T lymphocyte differentiation, epithelial barrier dysfunction, phagocytic ability, and cytokine production.
SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY
(2023)
Article
Genetics & Heredity
Tao Hu, Lei Wei, Shuailin Li, Tianrun Cheng, Xuegong Zhang, Xiaowo Wang
Summary: This study demonstrates evidence that miRNAs can reduce gene expression noise in mouse cells at the mRNA level, with key features such as miRNA expression level, target number, target pool abundance, and miRNA-target interaction strength contributing to noise repression. miRNAs work cooperatively in cell type-specific subnetworks to synergistically repress target noise, providing resistance to extrinsic fluctuations through accelerated degradation and elevated transcriptional activation of miRNA targets. Through integrated analysis of single-cell RNA and miRNA expression profiles, miRNAs are shown to be important post-transcriptional regulators for reducing gene expression noise and conferring robustness to biological processes.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
