NF-κB/AP-1-Targeted Inhibition of Macrophage-Mediated Inflammatory Responses by Depigmenting Compound AP736 Derived from Natural 1,3-Diphenylpropane Skeleton by Van Thai Ha, Heung Soo Beak, Eunji Kim, Kwang-Soo Baek, Muhammad Jahangir Hossen, Woo Seok Yang, Yong Kim, Jun Ho Kim, Sungjae Yang, Jeong-Hwan Kim, Yung Hyup Joo, Chang Seok Lee, Joonho Choi, Hong-Ju Shin, Sungyoul Hong, Song Seok Shin, Jae Youl Cho

“…Furthermore, AP736 also downregulated the expression of multiple inflammatory genes, such as inducible NO synthase (iNOS), cyclooxygenase- (COX-) 2, and interleukin- (IL-) 1β in LPS-treated RAW264.7 cells. Transcription factor analysis, including upstream signalling events, revealed that both NF-κB and AP-1 were targeted by AP736 via inhibition of the IKK/IκBα and IRAK1/TAK1 pathways. …”
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CYP3A5 promotes glioblastoma stemness and chemoresistance through fine-tuning NAD+/NADH ratio by Wentao Hu, Xiaoteng Cui, Hongyu Liu, Ze Li, Xu Chen, Qixue Wang, Guolu Zhang, Er Wen, Jinxin Lan, Junyi Chen, Jialin Liu, Chunsheng Kang, Ling Chen

“…This elevated expression of CYP3A5 is attributed to transcription factor STAT3 activated by EGFR signaling or TMZ treatment. …”
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Targeting the NOTCH2/ADAM10/TCF7L2 Axis‐Mediated Transcriptional Regulation of Wnt Pathway Suppresses Tumor Growth and Enhances Chemosensitivity in Colorectal Cancer by Zhen Xiang, Yiwei Wang, Xiao Ma, Shuzheng Song, Yuanqiao He, Jiamin Zhou, Longhai Feng, Su Yang, Yibin Wu, Bingran Yu, Guangkai Xia, Weiqi Xu, Yiming Zhao, Lu Wang

“…Abstract Wnt/β‐catenin/transcription factor (TCF) transcriptional activity plays an integral role in colorectal cancer (CRC) carcinogenesis. …”
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Characterization and functional analysis of conserved non-coding sequences among poaceae: insights into gene regulation and phenotypic variation in maize by Yi Luo, Hang Zhai, Xiu Zhong, Bo Yang, Yang Xu, Tianhong Liu, Qi Wang, Yang Zhou, Yan Mao, Yaxi Liu, Qi Tang, Yanli Lu, Yao Wang, Jie Xu

“…A significant enrichment of transcription factor binding sites was found within CNS sequences, including different transcription factors involved in abiotic stress response, such as OBP (OBF-BINDING PROTEIN) family and Adof1 (Encodes dof zinc finger protein). …”
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Comprehensive analysis of H3K27me3 LOCKs under different DNA methylation contexts reveal epigenetic redistribution in tumorigenesis by Yuan Liang, Mengni Liu, Bingyuan Liu, Benjamin Ziman, Guanjie Peng, Qiong Mao, Xingzhe Wang, Lizhen Jiang, De-Chen Lin, Yueyuan Zheng

“…Additionally, we find that genes upregulated in tumors following the loss of short LOCKs are typically poised promoter genes in normal cells, and their transcription is regulated by the ETS1 transcription factor. Conclusion These results provide new insights into the role of H3K27me3 LOCKs in cancer and underscore their potential impact on epigenetic regulation and disease mechanisms.…”
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Identifying health risk determinants and molecular targets in patients with idiopathic pulmonary fibrosis via combined differential and weighted gene co-expression analysis by Abu Tayab Moin, Md. Asad Ullah, Jannatul Ferdous Nipa, Mohammad Sheikh Farider Rahman, Afsana Emran, Md. Minhazul Islam, Swapnil Das, Tawsif Al Arian, Mohammad Mahfuz Enam Elahi, Mukta Akter, Umme Sadea Rahman, Arnab Halder, Shoaib Saikat, Mohammad Jakir Hosen

“…Regulatory analysis highlighted interactions with transcription factors and microRNAs, suggesting potential mechanisms driving IPF pathogenesis. …”
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Immunoregulatory programs in anti‐N‐methyl‐D‐aspartate receptor encephalitis identified by single‐cell multi‐omics analysis by Xinhui Li, Yicong Xu, Weixing Zhang, Zihao Chen, Dongjie Peng, Wenxu Ren, Zhongjie Tang, Huilu Li, Jin Xu, Yaqing Shu

“…Differential gene expression analysis, transcription factor activity profiling, and cell‐cell communication modeling were performed to elucidate the immune mechanisms underlying the disease. …”
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Mendelian randomization and multiomics comprehensively reveal the causal relationship and potential mechanism between atrial fibrillation and gastric cancer by Zhao Sicheng, Zhao Sicheng, Zhang Jingcheng, Zhang Jingcheng, Zhang Shuo, Zhang Shuo, Lou Jiaheng, Lou Jiaheng, Cai Yan, Cai Yan, Bai Xing, Bai Xing, Jiang Tao, Jiang Tao, Jiang Tao, Zhang Guangji, Zhang Guangji, Zhang Guangji

“…Through single-cell sequencing data analysis, fibroblast subpopulations associated with the key gene set are identified in GC, showing significant correlations with cancer progression and inflammation regulation pathways. Transcription factor analysis and developmental trajectory analysis reveal the potential role of fibroblasts in GC development. …”
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3-Hydroxyanthranic acid inhibits growth of oral squamous carcinoma cells through growth arrest and DNA damage inducible alpha by Guifang Gan, Xinxia Zhou, Qiaoping Zheng, Xianfu Gao, Xu Chen, Han Zhang, Jinghao Liu, Zhaopeng Shi, Fuxiang Chen

“…RNA-seq indicated that 3-HAA significantly increased GADD45A expression. 3-HAA promoted transcription of GADD45A by transcription factor YY1. Knockdown of GADD45A significantly reversed 3-HAA-induced growth inhibition of OSCC cells in vivo and in vitro. …”
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Genetic disruption of Blimp-1 drastically augments the antitumor efficacy of BCMA-targeting CAR T cells by Anthony M. Battram, Joan Mañé-Pujol, David F. Moreno, Aina Oliver-Caldés, Judit Carpio, Oriol Cardus, Luis Gerardo Rodríguez-Lobato, Álvaro Urbano-Ispizua, Carlos Fernández de Larrea

“…To improve long-term efficacy, we used CRISPR/CRISPR-associated protein 9-mediated gene editing to ablate the expression of the transcription factor Blimp-1. Blimp-1 knockout (KO) CAR T cells displayed a memory-like phenotype compared with control (Mock) CAR T cells, but had reduced effector function, with a striking loss of granzyme B. …”
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Ferroptosis-related genes participate in the microglia-induced neuroinflammation of spinal cord injury via NF-κB signaling: evidence from integrated single-cell and spatial transcr... by Siqiao Wang, Li Yang, Zhourui Wu, Chen Li, Shaoke Wang, Zhihui Xiao, Bei Ma, Rongrong Zhu, Liming Cheng

“…Protein–protein interaction and microRNA-mRNA-transcription factor regulatory networks were constructed based on Search Tool for the Retrieval of Interacting Genes (STRING) and NetworkAnalyst, respectively, which were validated by chromatin immunoprecipitation followed by sequencing (ChIP-seq). …”
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Genome-Wide Comprehensive Identification and In Silico Characterization of Lectin Receptor-Like Kinase Gene Family in Barley (Hordeum vulgare L.) by Fee Faysal Ahmed, Farah Sumaiya Dola, Md Shohel Ul Islam, Fatema Tuz Zohra, Nasrin Akter, Shaikh Mizanur Rahman, Md. Abdur Rauf Sarkar

“…The regulatory network analysis identified 29 transcription factor families (TFFs), with seven major TFFs including bZIP, C2H2, ERF, MIKC_MADS, MYB, NAC, and WRKY participating in the regulation of HvlecRLK gene functions. …”
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Characterizing tumor biology and immune microenvironment in high-grade serous ovarian cancer via single-cell RNA sequencing: insights for targeted and personalized immunotherapy st... by Fu Zhao, Fu Zhao, Xiaojing Jiang, Yumeng Li, Tianjiao Huang, Zhikai Xiahou, Wenyang Nie, Qian Li

“…The CellChat software package predicted cellular communication between malignant cell subtypes and other cells, while pySCENIC analysis was utilized to identify transcription factor regulatory networks within malignant cell subtypes. …”
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SMARCA4 deficiency in small cell lung cancer: A case report and narrative review of the literature by Andreas M. Matthaiou, Ioannis Tomos, Nikoleta Bizymi, Ioannis Vamvakaris, Nektarios Anagnostopoulos, Aikaterini Papadopoulou, Kalliopi Angelou, Grigoris Stratakos, Adamantia Liapikou

“…SMARCA2 and SMARCA4 deficiency is frequent in solid predominant adenocarcinomas and tumors with low levels of bronchial epithelial markers, including thyroid transcription factor 1. A rare case of SMARCA4 deficiency in small cell lung cancer is described. …”
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m6A demethylase CpALKBH regulates CpZap1 mRNA stability to modulate the development and virulence of chestnut blight fungus by Lijiu Zhao, Xiangyu Wei, Fengyue Chen, Baoshan Chen, Ru Li

“…Additionally, CpZap1—a transcription factor—was identified as a downstream target of CpALKBH demethylase based on RNA sequencing analysis. …”
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Altered chromatin landscape and 3D interactions associated with primary constitutional MLH1 epimutations by Paula Climent-Cantó, Marc Subirana-Granés, Mireia Ramos-Rodríguez, Estela Dámaso, Fátima Marín, Covadonga Vara, Beatriz Pérez-González, Helena Raurell, Elisabet Munté, José Luis Soto, Ángel Alonso, GiWon Shin, Hanlee Ji, Megan Hitchins, Gabriel Capellá, Lorenzo Pasquali, Marta Pineda

“…Of note, rare genetic alterations potentially affecting transcription factor binding sites were found in the promoter-contacting region of CME carriers. …”
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Computational identification of anti-cancer compounds targeting the RNA-binding domain of human FOX-1 protein (RBFOX1) by Muhammad Tahir ul Qamar, Pablo Sanz-Jimenez, Shaima Rabeea Banoon, Xi-Tong Zhu, Fahad M. Aldakheel, Nahlah Makki Almansour, Leen A. Aldaiji, Wafa Abdullah I. Al-Megrin, Faisal Ahmad

“…The transcription factor RBFOX1 is essential for cellular proliferation and has shown upregulation in many human cancers. …”
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Genome-wide association mapping of biochemical traits and its correlation with MYMIV resistance in mungbean (Vigna radiata L. Wilczek) by Manju Kohli, Hina Bansal, Muraleedhar Aski, Gyan P. Mishra, B. R. Shashidhar, Anirban Roy, Soma Gupta, Subodh K. Sinha, Brijesh Kumar Mishra, Nikki Kumari, Atul Kumar, Ranjeet Ranjan Kumar, Ramakrishnan M. Nair, Harsh Kumar Dikshit

“…The key candidate genes include VRADI09G06940 (YMD resistance, TIR-NBS-LRR class, chr. 9), VRADI01G05030 [flavonoid biosynthesis; MYB65 transcription factor (TF); chr. 1], VRADI03G07600 (phenol biosynthesis; GATA TF 16; chr. 3), VRADI04G08470 (ascorbic acid; heat shock protein 70 kDa protein; chr. 4), VRADI04G07510 (FRAP; subtilisin-like protease SBT1.9; chr. 4), and VRADI05G02870 (DPPH; vacuolar protein sorting-associated protein 2; chr. 5). …”
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<i>CaHY5</i> Mediates UV-B Induced Anthocyanin Biosynthesis in Purple Pepper by Xiang Zhang, Yunrong Mo, Huidan Zhou, Mengjuan Li, Hong Cheng, Pingping Li, Ruihao Zhang, Yaoyao Huang, Yanyan Wang, Junqiang Xu, Jingjing Liao, Qiaoli Xie, Kai Zhao, Minghua Deng, Junheng Lv

“…In this study, we identified the transcription factor <i>CaHY5</i>, which mediates UV-B signaling, and demonstrated its regulatory role in anthocyanin biosynthesis in purple pepper (<i>Capsicum annuum</i> L.). …”
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m6A Reader PRRC2A Promotes Colorectal Cancer Progression via CK1ε‐Mediated Activation of WNT and YAP Signaling Pathways by Xi Wu, Shiyang Wang, Yuwei Pan, Mengzhen Li, Manyu Song, Hanfu Zhang, Min Deng, Xu Yang, Jiuzhi Xu, Shuo Zhang, Jinhua Zhang, Fengchao Wang, Maksim V. Plikus, Cong Lv, Lu Yu, Zhengquan Yu

“…Interestingly, PRRC2A is directly regulated by the transcription factor ATF1 in its promoter. In summary, the work reveals a novel mechanism by which m6A reader PRRC2A promotes colorectal cancer progression via CK1ε and aberrant upregulation of WNT and YAP signaling. …”
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