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Medicine, General & Internal
Yan Zhang, Quan Wang, Wei-Kang Yang, Yong-Si Wang, Qiao Zhou, Jie Lin, Xu-Xuan Wei, Tian Liang, Tongtong Liu, Wen-Tao Fan, Li Liang, You-Nian Xu
Summary: This study aimed to investigate the immune characteristics of TNBC using transcriptomic features and identify a novel prognostic biomarker. By analyzing the immune cell contents in tumor tissue and para-cancerous tissue, the researchers developed a new biomarker called Immune Infiltration Score (IIS). Results showed that IIS score can be used to evaluate the progression-free survival and prognosis of TNBC patients.
ANNALS OF MEDICINE
(2022)
Review
Biochemistry & Molecular Biology
Fuwen Yuan, William Hankey, Eric J. Wagner, Wei Li, Qianben Wang
Summary: Alternative polyadenylation (APA) is a molecular process that generates diversity at the 3' end of RNA polymerase II transcripts from over 60% of human genes, mainly occurring within the untranslated region (3'UTR), leading to significant impact on the regulatory potential of mRNA.
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Cell Biology
Yuan Huang, Xiaowei Wang, Yiran Zheng, Wei Chen, Yabing Zheng, Guangliang Li, Weiyang Lou, Xiaojia Wang
Summary: This study established a novel competing endogenous RNA network to predict prognosis in TNBC patients. Through differential gene expression analysis, key miRNAs, upregulated miRNAs, key lncRNAs, and others were identified, forming a complex network involving mRNAs, miRNAs, and lncRNAs.
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Oncology
Hao Zhang, Shuangli Zhu, Haiting Zhou, Rui Li, Xiaohui Xia, Huihua Xiong
Summary: This study found that the expression of Methylenetetrahydrofolate dehydrogenase 2 (MTHFD2) is upregulated in triple-negative breast cancer (TNBC) and is associated with poor prognosis. MTHFD2 is involved in various tumor-related processes and is closely related to immune cell infiltration. In vitro experiments showed that silencing MTHFD2 inhibits the proliferation, apoptosis, migration, and invasion of TNBC cells, and promotes ferroptosis. Therefore, MTHFD2 could serve as an important molecular biomarker for predicting prognosis and a potential therapeutic target in TNBC.
FRONTIERS IN ONCOLOGY
(2023)
Article
Biotechnology & Applied Microbiology
Zhenying Peng, Shuang Yu, Jingjing Meng, Kai-Hua Jia, Jialei Zhang, Xinguo Li, Wenwei Gao, Shubo Wan
Summary: The study found widespread alternative polyadenylation in peanut genes, crucial for peanut seed maturation. The AhACCA1 gene has four 3' UTRs, each showing tissue-specific expression patterns. Experimental evidence indicates that UTR2 has a stronger impact on gene expression regulation compared to the other UTRs.
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Oncology
Xiaowei Wang, Wenjia Su, Dabei Tang, Jing Jing, Jing Xiong, Yuwei Deng, Huili Liu, Wenjie Ma, Zhaoliang Liu, Qingyuan Zhang
Summary: Triple-negative breast cancer (TNBC) is a difficult-to-treat subtype of breast cancer, and the immune-related gene prognostic index (IRGPI) is significantly associated with immune cell compositions, tumor-infiltrating lymphocyte status, and PD-1/PD-L1 expression in the tumor-immune microenvironment. IRGPI shows promise as a biomarker for predicting patient survival and immune characteristics in TNBC.
Article
Biochemistry & Molecular Biology
Weiwei Jin, Qizhao Zhu, Yanbo Yang, Wenqian Yang, Dongyang Wang, Jiajun Yang, Xiaohui Niu, Debing Yu, Jing Gong
Summary: APA is a crucial post-transcriptional regulatory mechanism that impacts various biological processes in different species. A study systematically characterized APA profiles in 18 species using RNA sequencing data and developed a user-friendly database for further research and exploration.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Oncology
Wenting Peng, Caijin Lin, Shanshan Jing, Guanhua Su, Xi Jin, Genhong Di, Zhiming Shao
Summary: This study established clinical prognostic model, seven-gene signature, and combined model for predicting distant metastasis risk in lymph node-negative TNBC patients. The seven-gene signature showed significant differentiation of distant metastasis risk in both training and validation sets. The composite clinical and gene signature demonstrated improved prognostic accuracy compared to the clinical signature.
FRONTIERS IN ONCOLOGY
(2021)
Article
Oncology
Weihua Jiang, Xiao-Liang Xing, Chenguang Zhang, Lina Yi, Wenting Xu, Jianghua Ou, Ning Zhu
Summary: The study found that the expression of MET and FASN in TNBC patients is closely related to clinical pathological characteristics and prognosis, with positive expression significantly correlated with lymph node metastasis, pathological TNM, and pathological Stage. The combined use of MET and FASN can better predict the survival condition of patients.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Si-Yuan Zhu, Ding Ma, Zhi-Ming Shao, Ke-Da Yu
Summary: The study found that in patients with triple-negative breast cancer, the immune-inflamed tumor subtype may be associated with longer RFS in node-positive patients and pT2-3 stage tumor patients. However, in terms of treatment efficacy, there was no significant difference in RFS between the two regimens for either hot or cold tumor phenotypes.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Oncology
Meng Li, Junnan Xu, Cui Jiang, Jingyan Zhang, Tao Sun
Summary: This study explored the significance of peripheral blood lymphocytes and clinicopathological factors in triple-negative breast cancer (TNBC). The results showed that the peripheral CD4+ T lymphocyte level is associated with treatment response and prognosis. This study provides important reference for the treatment and prognosis of TNBC patients.
FRONTIERS IN ONCOLOGY
(2022)
Article
Oncology
Marine Lemesle, Marine Geoffroy, Fabien Alpy, Catherine-Laure Tomasetto, Sandra Kuntz, Isabelle Grillier-Vuissoz
Summary: This study investigated the role of CLDN1 in triple-negative breast cancer (TNBC) and found that CLDN1 can increase the sensitivity of TNBC cells to chemotherapy drugs. The findings support the use of CLDN1 as a predictive marker for chemotherapy response in TNBC.
Review
Medicine, Research & Experimental
Yu-Long Lan, Jianmin Zhang
Summary: RNA modification is a crucial form of regulation in cancer biology, with untranslated region-alternative polyadenylation (UTR-APA) potentially playing a key role in the pathogenesis of glioma. Less targeted strategies, such as inhibitors of UTR-APA regulators, may have superior therapeutic effects in glioma treatment.
BIOMEDICINE & PHARMACOTHERAPY
(2021)
Article
Biotechnology & Applied Microbiology
Siyu Liu, Xiaobin Cao, Jing Li, Jingjing Liu
Summary: This study investigated whether the transcription factor ZNF503 and GATA3 could serve as prognostic markers in triple-negative breast cancer (TNBC). The results showed that the ratio index ZNF503/GATA3 could be a novel prognostic biomarker in TNBC. The combination of ZNF503 and GATA3 significantly improved the predictive ability of clinical outcomes in TNBC patients.
Editorial Material
Chemistry, Multidisciplinary
Alexandre de Nonneville, Pascal Finetti, Daniel Birnbaum, Emilie Mamessier, Francois Bertucci
Summary: This study demonstrates the critical role of WEE1 in triple negative breast cancer, its pejorative prognostic value, and its correlation with biomarkers of sensitivity to WEE1 inhibitors.
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Biochemistry & Molecular Biology
Lei Wang, Ling Yao, Yi-Zi Zheng, Qing Xu, Xiu-Ping Liu, Xin Hu, Peng Wang, Zhi-Ming Shao
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
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Biochemistry & Molecular Biology
Hongyuan Chang, Yuwei Liu, Mengzhu Xue, Haiyue Liu, Shaowei Du, Liwen Zhang, Peng Wang
NUCLEIC ACIDS RESEARCH
(2016)
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Multidisciplinary Sciences
Mengzhu Xue, Haiyue Liu, Liwen Zhang, Hongyuan Chang, Yuwei Liu, Shaowei Du, Yingqun Yang, Peng Wang
NATURE COMMUNICATIONS
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Oncology
Yi-Zi Zheng, Meng-Zhu Xue, Hong-Jie Shen, Xiao-Guang Li, Ding Ma, Yue Gong, Yi-Rong Liu, Feng Qiao, Hong-Yan Xie, Bi Lian, Wei-Li Sun, Hai-Yun Zhao, Ling Yao, Wen-Jia Zuo, Da-Qiang Li, Peng Wang, Xin Hu, Zhi-Ming Shao
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Biochemical Research Methods
Peng Wang, John Sidney, Yohan Kim, Alessandro Sette, Ole Lund, Morten Nielsen, Bjoern Peters
BMC BIOINFORMATICS
(2010)
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Immunology
Daniel Mucida, Mohammad Mushtaq Husain, Sawako Muroi, Femke van Wijk, Ryo Shinnakasu, Yoshinori Naoe, Bernardo Sgarbi Reis, Yujun Huang, Florence Lambolez, Michael Docherty, Antoine Attinger, Jr-Wen Shui, Gisen Kim, Christopher J. Lena, Shinya Sakaguchi, Chizuko Miyamoto, Peng Wang, Koji Atarashi, Yunji Park, Toshinori Nakayama, Kenya Honda, Wilfried Ellmeier, Mitchell Kronenberg, Ichiro Taniuchi, Hilde Cheroutre
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Multidisciplinary Sciences
Li Li, Duolin Wang, Mengzhu Xue, Xianqiang Mi, Yanchun Liang, Peng Wang
SCIENTIFIC REPORTS
(2014)
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Biochemical Research Methods
Peng Wang, John Sidney, Courtney Dow, Bianca Mothe, Alessandro Sette, Bjoern Peters
PLOS COMPUTATIONAL BIOLOGY
(2008)
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Oncology
Yi-Zhou Jiang, Ding Ma, Chen Suo, Jinxiu Shi, Mengzhu Xue, Xin Hu, Yi Xiao, Ke-Da Yu, Yi-Rong Liu, Ying Yu, Yuanting Zheng, Xiangnan Li, Chenhui Zhang, Pengchen Hu, Jing Zhang, Qi Hua, Jiyang Zhang, Wanwan Hou, Luyao Ren, Ding Bao, Bingying Li, Jingcheng Yang, Ling Yao, Wen-Jia Zuo, Shen Zhao, Yue Gong, Yi-Xing Ren, Ya-Xin Zhao, Yun-Song Yang, Zhenmin Niu, Zhi-Gang Cao, Daniel G. Stover, Claire Verschraegen, Virginia Kaklamani, Anneleen Daemen, John R. Benson, Kazuaki Takabe, Fan Bai, Da-Qiang Li, Peng Wang, Leming Shi, Wei Huang, Zhi-Ming Shao
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Oncology
Yi Xiao, Ding Ma, Shen Zhao, Chen Suo, Jinxiu Shi, Meng-Zhu Xue, Miao Ruan, Hai Wang, Jingjing Zhao, Qin Li, Peng Wang, Leming Shi, Wen-Tao Yang, Wei Huang, Xin Hu, Ke-Da Yu, Shenglin Huang, Francois Bertucci, Yi-Zhou Jiang, Zhi-Ming Shao
CLINICAL CANCER RESEARCH
(2019)
Article
Multidisciplinary Sciences
Ke Zhang, Wanwan Feng, Peng Wang
Summary: The authors develop a highly scalable method, scGCO, to identify genes whose expression values form spatial patterns from spatial transcriptomics data.
NATURE COMMUNICATIONS
(2022)
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Biochemical Research Methods
Peng Wang, Alexander A. Morgan, Qing Zhang, Alessandro Sette, Bjoern Peters
BMC BIOINFORMATICS
(2007)