Article
Pharmacology & Pharmacy
Lucas Zhou, Abelardo D. Montalvo, Joseph M. Collins, Danxin Wang
Summary: UDP-glucuronosyltransferases (UGTs) are important drug metabolizing enzymes involved in the detoxification of endogenous and exogenous substances. This study comprehensively analyzed the transcriptome of 22 UGTs in different human tissues and regions, revealing large interindividual variability and differential UGT pool composition. Coexpression of UGTs, Cytochrome P450s, and transcription factors in the liver suggests potential coregulation or functional coordination. These findings provide a foundation for future studies on the regulation of UGT expression and activity.
PHARMACOLOGY RESEARCH & PERSPECTIVES
(2023)
Article
Biochemistry & Molecular Biology
Zhao Zhang, Wei Hong, Hang Ruan, Ying Jing, Shengli Li, Yaoming Liu, Jun Wang, Wenbo Li, Lixia Diao, Leng Han
Summary: This study characterized the landscape of eRNA expression in normal human tissues, identifying associations between eRNAs and traits such as gender, race, and age. A co-expression network was constructed to identify putative eRNA regulators and target genes across different tissues. The data portal HeRA provides a user-friendly platform for accessing and exploring eRNA expression profiles, trait-related associations, and co-expression networks.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Genetics & Heredity
Hui Yu, Yan Guo, Jingchun Chen, Xiangning Chen, Peilin Jia, Zhongming Zhao
Summary: Through transcriptomic analysis of schizophrenia, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and key genes and gene links in the disease.
Review
Cell Biology
Edda S. F. Matthees, Raphael S. Haider, Carsten Hoffmann, Julia Drube
Summary: This review discusses the regulatory mechanisms of G protein-coupled receptors (GPCRs) by GPCR kinases (GRKs) and beta-arrestins, highlighting the importance of direct GPCR-GRK interactions and tissue-specific expression of GRKs and beta-arrestins in influencing GPCR phosphorylation patterns. The analysis of expression data for GRKs and beta-arrestins in different tissues provides insights into the pathophysiological dysregulation of the GPCR/GRK/beta-arrestin system, indicating the potential key role of tissue-specific perspectives in understanding the individual impact of different GRK isoforms on GPCR regulation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biochemical Research Methods
Yue Fan, Huanhuan Zhu, Yanyi Song, Qinke Peng, Xiang Zhou
Summary: ECCO is presented as a simple and computationally scalable alternative to determine the optimal number of PEER factors for eQTL mapping studies, using joint analysis of differential expression and Mendelian randomization. It shows similar effectiveness to the standard approach in identifying the required number of PEER factors for eQTL mapping, but is two orders of magnitude faster. This computational scalability allows for optimized eQTL discovery across 48 GTEx tissues, resulting in a 5.89% power gain in the number of eGenes discovered compared to previous recommendations.
Article
Cell Biology
Xavier Hernandez-Alias, Hannah Benisty, Martin H. Schaefer, Luis Serrano
Summary: When viruses infect different tissues, they adjust their translational machinery to adapt to the specific host environment; research shows that there is a correspondence between the codon usage of viruses and the translational machinery of their specific tropism; this correspondence is mainly seen in early viral proteins, and it could be useful for the development of antiviral therapies and vaccines.
Article
Genetics & Heredity
Mette Viuff, Anne Skakkebaek, Emma B. Johannsen, Simon Chang, Steen Bonlykke Pedersen, Katrine Meyer Lauritsen, Mette Glavind Bulow Pedersen, Christian Trolle, Jesper Just, Claus H. Gravholt
Summary: This study comprehensively analyzed the effects of the X chromosome number on the transcriptome and methylome in blood, fat, and muscle tissue of individuals with sex chromosome aneuploidies (SCAs). It was found that X chromosome number globally affected the transcriptome and methylome in a tissue-specific manner. The study also identified different gene expression and methylation patterns between 45,X and 47,XXY, and observed a significant effect of sex in fat and muscle tissue. Additionally, the study found regulatory functions of Y chromosomal genes on X chromosomal genes.
Article
Pharmacology & Pharmacy
Wandong Zhang, Qing Yan Liu, Arsalan S. Haqqani, Ziying Liu, Caroline Sodja, Sonia Leclerc, Ewa Baumann, Christie E. Delaney, Eric Brunette, Danica B. Stanimirovic
Summary: This study investigates the expression patterns of ABC transporter genes in brain microvessels compared to peripheral tissues. The results show that most ABC transporters are more highly expressed in peripheral tissues than in human brain microvessels, while additional ABC transporters are enriched in rodent brain microvessels.
Article
Multidisciplinary Sciences
Yanxiang Deng, Marek Bartosovic, Sai Ma, Di Zhang, Petra Kukanja, Yang Xiao, Graham Su, Yang Liu, Xiaoyu Qin, Gorazd B. Rosoklija, Andrew J. Dwork, J. John Mann, Mina L. Xu, Stephanie Halene, Joseph E. Craft, Kam W. Leong, Maura Boldrini, Goncalo Castelo-Branco, Rong Fan
Summary: This study presents a new method for spatial chromatin accessibility profiling in tissues, allowing researchers to explore the spatial epigenetic information at the cellular level and genome scale. The technology has been successfully applied to understand gene regulators in the development of the central nervous system and immune cell types in tonsil tissue. This advancement in spatial biology improves our understanding of cell identity, cell state, and cell fate decision in relation to epigenetic underpinnings in development and disease.
Article
Biochemical Research Methods
Moran Sharon, Ekaterina Vinogradov, Chanan M. Argov, Or Lazarescu, Yazeed Zoabi, Idan Hekselman, Esti Yeger-Lotem
Summary: The study introduces a method called Tissue-Process Activity (TiPA), which identifies preferentially active or underexpressed processes in specific contexts by comparing the expression levels of process genes between contexts. The results show that TiPA outperforms other methods and provides insights into the genotype-phenotype relationships of hereditary diseases and the functionality of cell types.
Article
Multidisciplinary Sciences
P. Ostheim, S. W. Alemu, A. Tichy, I Sirak, M. Davidkova, M. Markova Stastna, G. Kultova, S. Schuele, T. Paunesku, G. Woloschak, S. A. Ghandhi, S. A. Amundson, M. Haimerl, C. Stroszczynski, M. Port, M. Abend
Summary: In this study, RNA was isolated from human whole saliva using selective cDNA synthesis and adjusted RNA input. The findings provide important information for gene expression analysis in human saliva.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Pei F. Lai, Kaiyu Lei, Xiaoyu Zhan, Gavin Sooranna, Jonathan K. H. Li, Ektoras X. Georgiou, Ananya Das, Natasha Singh, Qiye Li, Zachary Stanfield, Guojie Zhang, Rachel M. Tribe, Sam Mesiano, Mark R. Johnson
Summary: The study found that early labor and ROM have a significant impact on myometrial transcriptome, possibly due to limitations of bulk RNA-seq and the importance of processes other than gene transcription at the onset of labor. Additional integrative analysis with refined clinical classification and alternative omics approaches is needed to fully understand the critical transcriptomic changes during labor onset.
Article
Biochemistry & Molecular Biology
Qin Li, Hongyan Lai, Yuchen Li, Bing Chen, Siyuan Chen, Yan Li, Zhaohui Huang, Zhiqiang Meng, Peng Wang, Zhixiang Hu, Shenglin Huang
Summary: Splicing is a crucial step in RNA processing for multi-exon genes, and RJunBase is a new database that contains different types of RNA splice junctions derived from non-cancerous and cancerous tissues. This database allows researchers to visualize gene-level splicing patterns and junction-level expression profiles, as well as demonstrate unannotated and tumor-specific junctions, aiding in the discovery of new splicing-associated targets and the identification of potential neoepitopes for cancer treatment.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemical Research Methods
Daniel Osorio, James J. Cai
Summary: The study found that the average mtDNA% in human scRNA-seq data is significantly higher than in mouse tissues. While the 5% threshold performs well for distinguishing between healthy and low-quality cells in mouse tissues, it may not be accurate for human tissues. Omitting or using a suboptimal mtDNA% threshold in scRNA-seq data analysis could lead to erroneous biological interpretations.
Article
Genetics & Heredity
Ammarah Ghaffar, Dale R. Nyholt
Summary: We developed a method named GIDEE to prioritize trait-relevant tissues by combining GWAS summary statistic data with tissue-specific eQTL data. The best-performing GIDEE method ranked the known trait-relevant tissue first multiple times across nine training datasets. Application of the GIDEE approach to test datasets provided important prioritization of tissues relevant to the trait's regulatory architecture.
FRONTIERS IN GENETICS
(2023)