Article
Biochemical Research Methods
Zhi-Hua Du, Yang-Han Wu, Yu-An Huang, Jie Chen, Gui-Qing Pan, Lun Hu, Zhu-Hong You, Jian-Qiang Li
Summary: This study introduces a graph attention-based autoencoder model to predict TF-target gene interactions, which shows excellent prediction performance on a real dataset.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Cell Biology
Chih-Chien Wang, Jen-Jie Weng, Hsiang-Cheng Chen, Meng-Chang Lee, Pi-Shao Ko, Sui-Lung Su
Summary: This study identified SNPs of TFBSs influencing osteoporosis and validated the association between the rs130347 genotype and downstream gene expression. The findings provide new insights into the genetic basis of osteoporosis and suggest that this strategy can be expanded to other diseases for personalized precision medicine.
Article
Neurosciences
Kaiyue Zhao, Li Zeng, Zhongdi Cai, Mimin Liu, Ting Sun, Zhuorong Li, Rui Liu
Summary: This study investigated the potential mechanism and biomarkers of vascular dementia (VaD) through studying the miRNA, TF, and their co-regulatory networks in the cortex of rats. The results revealed differentially expressed miRNAs, TFs, and genes in VaD rats, indicating their involvement in various signaling pathways and biological processes.
FRONTIERS IN NEUROSCIENCE
(2022)
Article
Endocrinology & Metabolism
Qianqian Dong, Ziqi Han, Limin Tian
Summary: The study identified DE mRNAs, DE miRNAs, and DE circRNAs associated with postmenopausal osteoporosis (PMOP) and found that these genes were mainly related to inflammatory responses. Through gene enrichment analysis, the potential roles and related signaling pathways of these genes in the development of osteoporosis were determined.
FRONTIERS IN ENDOCRINOLOGY
(2022)
Article
Biochemical Research Methods
Yu-An Huang, Gui-Qing Pan, Jia Wang, Jian-Qiang Li, Jie Chen, Yang-Han Wu
Summary: The proposed deep learning model HGETGI shows high prediction performance in identifying TF-target gene interactions, with successful case studies on two important TFs. The method has the potential to be feasible and effective for large-scale predictions in biomedical research.
Article
Multidisciplinary Sciences
Eui Jung Moon, Stephano S. Mello, Caiyun G. Li, Jen-Tsan Chi, Kaushik Thakkar, Jacob G. Kirkland, Edward L. Lagory, Ik Jae Lee, Anh N. Diep, Yu Miao, Marjan Rafat, Marta Vilalta, Laura Castellini, Adam J. Krieg, Edward E. Graves, Laura D. Attardi, Amato J. Giaccia
Summary: This study identified MAFF as a critical regulator of tumor invasion in breast cancer, activating the IL11/STAT3 pathway.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Harish K. Datta, Marianne K. Kringen, Stephen P. Tuck, Georgia Salpingidou, Ole K. Olstad, Kaare M. Gautvik, Simon J. Cockell, Vigdis T. Gautvik, Michael Prediger, Jun Jie Wu, Mark A. Birch, Sjur Reppe
Summary: Mechanical loading plays a significant role in bone density and architecture. The study demonstrates that the transcriptional factor ZIC1 is strongly associated with genes characteristically associated with bone cells. The findings also suggest a link between mechanical stress and epigenetic control of gene expression, with implications for bone pathophysiology.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Hansaim Lim, Lei Xie
Summary: The WINTF algorithm predicts unobserved target genes for TFs using protein-protein interaction networks and known but noisy, incomplete, and biased TF-gene associations, outperforming other matrix factorization-based algorithms and tri-factorization methods in TF-gene association prediction.
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
(2021)
Review
Pharmacology & Pharmacy
Ju-Xian Song, Jia Liu, Yimin Jiang, Zi-Ying Wang, Min Li
Summary: TFEB as a master regulator of the autophagy-lysosomal pathway holds therapeutic potential for neurodegenerative disorders, with small molecules identified as TFEB activators showing promise in protecting against these diseases. Research is ongoing and the development of specific and potent TFEB activators with ideal brain bioavailability could provide a method for treating neurodegenerative disorders.
DRUG DISCOVERY TODAY
(2021)
Article
Biochemistry & Molecular Biology
Jemma G. Gasperoni, Jarrad N. Fuller, Charbel Darido, Tomasz Wilanowski, Sebastian Dworkin
Summary: Grainyhead-like (GRHL) factors are critical transcription factors that regulate cellular behaviors during development and in cancer. Identifying and studying the target genes of these factors are essential for discovering potential targets for disease diagnosis, drug discovery, and therapeutic strategies.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Pharmacology & Pharmacy
Jingmin Che, Jiancheng Yang, Bin Zhao, Peng Shang
Summary: HO-1 plays a crucial role in osteoporosis by regulating mechanisms such as inflammation and oxidative stress to slow the progression of the disease. Therapies targeting HO-1 may offer new potential treatment options for osteoporosis.
EUROPEAN JOURNAL OF PHARMACOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Yanjiao Zhang, Xinyi Fang, Jiahua Wei, Runyu Miao, Haoran Wu, Kaile Ma, Jiaxing Tian
Summary: PDX-1 plays a crucial role in pancreatic development and the pathogenesis of diabetes. Overexpression of PDX-1 regulates pancreatic development and promotes beta-cell differentiation and insulin secretion. The absence of PDX-1 increases susceptibility to diabetes.
Article
Genetics & Heredity
Changhong Chen, Fei Hu, Shichang Miao, Liping Sun, Yajun Jiao, Mingwei Xu, Xin Huang, Ying Yang, Rongkui Zhou
Summary: This study revealed that osteoclast differentiation is promoted by KLF7 through inhibiting HO-1, thereby facilitating osteoporosis. This finding enriches the understanding of the pathogenesis of osteoporosis and provides a basis for the development of new treatment methods.
FRONTIERS IN GENETICS
(2022)
Article
Biotechnology & Applied Microbiology
Changsheng Wang, Xiaobo Zhang, Rongsheng Chen, Xitian Zhu, Nancheng Lian
Summary: In this study, the involvement of the EGR1-mediated METTL3/m6A/CHI3L1 axis in osteoporosis was investigated. The findings revealed that EGR1 promotes METTL3 transcription to increase the m6A modification on CHI3L1, leading to the differentiation of osteoclasts and the development of osteoporosis.
Review
Oncology
Francesca Lorenzin, Francesca Demichelis
Summary: In addition to its role in development and in the vascular and hematopoietic systems, ERG plays a central role in prostate cancer. Inhibiting ERG activity may be a significant step in improving treatment efficacy for patients with ERG-positive prostate tumors.