Article
Multidisciplinary Sciences
Shilu Zhang, Saptarshi Pyne, Stefan Pietrzak, Spencer Halberg, Sunnie Grace McCalla, Alireza Fotuhi Siahpirani, Rupa Sridharan, Sushmita Roy
Summary: The authors developed a method called single-cell Multi-Task Network Inference (scMTNI) to accurately infer the dynamics of cell type-specific Gene Regulatory Networks (GRNs) from scRNA-seq and scATAC-seq datasets. This method can identify key regulators and accurately model network dynamics for diverse processes such as cellular reprogramming and differentiation.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Alexandre P. Marand, Zongliang Chen, Andrea Gallavotti, Robert J. Schmitz
Summary: By analyzing single-cell genomics data from six maize organs, researchers identified cis-regulatory factors and trans-regulatory factors, revealing the crucial role of cell-type-specific regulatory elements in gene expression regulation, and developed the single-cell analysis software Socrates for studying cis-regulatory variation in various species.
Article
Biochemistry & Molecular Biology
Chuandong Fan, Hongjoo An, Mohamed Sharif, Dongkyeong Kim, Yungki Park
Summary: Myrf is a pleiotropic membrane-bound transcription factor that is involved in various vital processes across different organisms. Recent studies have identified four de novo mutations in the MYRF gene associated with syndromic birth defects, with three causing haploinsufficiency and one exhibiting dominant negative functionality.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Biochemistry & Molecular Biology
Nathalia Almeida, Matthew W. H. Chung, Elena M. Drudi, Elise N. Engquist, Eva Hamrud, Abigail Isaacson, Victoria S. K. Tsang, Fiona M. Watt, Francesca M. Spagnoli
Summary: The interplay between extrinsic signaling and downstream gene networks controls cell identity, with transcription factor networks considered key determinants. The concept of the core regulatory circuit is proposed as a comprehensive framework for defining cellular identity and its connection to cell function in different contexts is discussed.
Article
Biology
Xiaochen Fan, V. Pragathi Masamsetti, Jane Q. J. Sun, Kasper Engholm-Keller, Pierre Osteil, Joshua Studdert, Mark E. Graham, Nicolas Fossat, Patrick P. L. Tam
Summary: The study identified the TWIST1-CRM module as crucial for NCC development, with its activity level influencing cell differentiation and migration potential. Loss of the module function results in abnormal cell fate choices.
Article
Oncology
Dylan L. Schaff, Shambhavi Singh, Kee-Beom Kim, Matthew D. Sutcliffe, Kwon-Sik Park, Kevin A. Janes
Summary: This study reveals that the single-cell regulatory heterogeneity of small-cell lung cancer becomes increasingly complex in the liver, a common metastatic site. Heterotypic interactions in the liver and lung may accelerate intratumor heterogeneity in small-cell lung cancer. These findings provide insights into the progression and complexity of small-cell lung cancer metastasis.
Article
Biochemistry & Molecular Biology
Shuze Wang, Mary P. Lee, Scott Jones, Jie Liu, Joerg Waldhaus
Summary: This study utilized single-cell omics approach to investigate the spatial formation of a lineage-specific regulatory landscape in hair cells, predicting cell type-specific functions of transcription factors and reconstructing gene regulatory networks. By clustering target genes, related transcription factors and their developmental functions were inferred. The study also revealed that gradual changes in the chromatin accessibility landscape lag behind the transcriptional identity of hair cells along the longitudinal axis of the organ.
Article
Gastroenterology & Hepatology
Ying Lu, Yangyang Li, Qi Liu, Na Tian, Peng Du, Fangming Zhu, Yichao Han, Xinnan Liu, Xisheng Liu, Xiao Peng, Xiaoxia Wang, Yuchen Wu, Lingfeng Tong, Yakui Li, Yemin Zhu, Lifang Wu, Ping Zhang, Ye Xu, Hanbei Chen, Bin Li, Xuemei Tong
Summary: In colorectal cancer, intratumoral regulatory T cells (Tregs) exhibit low activity of the MondoA-thioredoxin-interacting protein (TXNIP) axis and increased glucose uptake. While MondoA-deficient Tregs promoted Th1 responses in a subcutaneous colorectal cancer model, Treg-specific MondoA knockout mice were more susceptible to colorectal cancer induction.
Article
Biochemistry & Molecular Biology
Jian Sun, Yijun Lin, Nayoung Ha, Jianfei Zhang, Weiqi Wang, Xudong Wang, Qian Bian
Summary: In this study, researchers used single-cell RNA-Seq to investigate the transcriptional dynamics during mouse maxillary development. They identified distinct mesenchymal cell populations and their developmental trajectory, as well as key transcription factors associated with mesenchymal fate transitions. This study provides important insights for understanding craniofacial morphogenesis and abnormalities at a systems-level.
JOURNAL OF GENETICS AND GENOMICS
(2023)
Article
Multidisciplinary Sciences
Michael W. Dorrity, Cristina M. Alexandre, Morgan O. Hamm, Anna-Lena Vigil, Stanley Fields, Christine Queitsch, Josh T. Cuperus
Summary: The study reports the regulatory landscape of Arabidopsis thaliana roots at single-cell resolution and identifies thousands of differentially accessible sites. It finds that a cell's regulatory landscape and transcriptome independently capture cell type identity, and leveraging this information to integrate data helps characterize developmental progression and cell division. The approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
NATURE COMMUNICATIONS
(2021)
Review
Cell Biology
Trine V. Dam, Nicolaj I. Toft, Lars Grontved
Summary: The prevalence of non-alcoholic fatty liver disease (NAFLD) is increasing rapidly. There are difficulties in diagnosing and treating NAFLD. Further insight into disease mechanisms and gene regulatory mechanisms associated with tissue remodeling is needed. Mapping the cis-regulatory genome and single-cell analysis are emerging technologies that provide more possibilities for research.
Article
Multidisciplinary Sciences
Benjamin P. Hurrell, Doumet Georges Helou, Emily Howard, Jacob D. Painter, Pedram Shafiei-Jahani, Arlene H. Sharpe, Omid Akbari
Summary: Regulatory T (Treg) cells play a critical role in limiting immune responses to allergens. This study demonstrates the importance of the immune suppression signal from PD-L2 in modulating Treg cell metabolism and function, thus leading to the proper induction of respiratory tolerance in mice. It is shown that PD-L2 deficiency prevents the induction of tolerance to ovalbumin and control of airway hyperreactivity, primarily by limiting the numbers and function of pTreg cells. The study also reveals that PD-1/PD-L2 interactions increase iTreg numbers and stability. Additionally, the study uncovers the molecular mechanisms underlying the metabolic defects in pTregs lacking PD-L2, including decreased Tricarboxylic Acid (TCA) cycle function and ATP production. The findings highlight the significance of the PD-1/PD-L2 axis in regulating Treg cell stability and suppressive functions, suggesting potential therapeutic targets for mucosal immunotherapy.
NATURE COMMUNICATIONS
(2022)
Article
Veterinary Sciences
Dawei Wei, Sayed Haidar Abbas Raza, Xingping Wang, Rajwali Khan, Zhaoxiong Lei, Guijie Zhang, Jiupan Zhang, Zhuoma Luoreng, Yun Ma, Muna O. Alamoudi, Bandar Hamad Aloufi, Ahmed Mohajja Alshammari, Ayman Hassan Abd El-Aziz, Majid Alhomrani, Abdulhakeem S. Alamri
Summary: This study investigated the tissue expression patterns and functional promoter of bovine LATS1, and identified the key transcription factors in the core promoter region. It revealed the regulatory mechanisms of bovine LATS1 transcription in mediating skeletal muscle growth. Bovine LATS1 was highly expressed in the longissimus thoracis and upregulated in infancy muscle.
FRONTIERS IN VETERINARY SCIENCE
(2022)
Article
Immunology
Si-Yu Yang, Jie Long, Meng-Xing Huang, Pan-Yue Luo, Zhen-Hua Bian, Ya-Fei Xu, Cheng-Bo Wang, Shu-Han Yang, Liang Li, Carlo Selmi, M. Eric Gershwin, Zhi-Bin Zhao, Zhe-Xiong Lian
Summary: Regulatory B cells (Breg) are immunosuppressive cells with different subsets identified in various organs. This study used high-throughput single-cell RNA sequencing and B-cell receptor sequencing to define the phenotype of Breg cells. The research revealed organ-specific subsets of Breg cells, with non-B10 Breg cells exhibiting unique immunosuppressive properties linked to TGF-beta pathway activation.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Ruth-Love Yeboah, Charmaine U. Pira, Matthew Shankel, Allen M. Cooper, Endika Haro, Van-Dai Ly, Kenrick Wysong, Michael Zhang, Nicole Sandoval, Kerby C. Oberg
Summary: The expression of Gdf5 during elbow joint development is regulated by multiple transcription factors, including Fox, Sox, and Lmx1b. Binding sites for Fox and Sox are required for enhancer activity, while binding sites for Lmx1b have a repressive effect. Osr2 does not affect GARR activity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)