Article
Medicine, Research & Experimental
Xiang Zhou, Shuchen Zhang, Yiheng Zhao, Wenjing Wang, Hao Zhang
Summary: This study utilized a multi-omics approach to compare the transcriptomic, miRNA expression, and chromatin accessibility profiles between HF and control mice, providing mechanistic insights into the pathogenesis of pressure overload-induced HF.
Article
Biology
Shufang Cai, Bin Hu, Xiaoyu Wang, Tongni Liu, Zhuhu Lin, Xian Tong, Rong Xu, Meilin Chen, Tianqi Duo, Qi Zhu, Ziyun Liang, Enru Li, Yaosheng Chen, Jianhao Li, Xiaohong Liu, Delin Mo
Summary: In this study, the molecular and cellular dynamics of pig embryonic myogenesis were studied through single-cell resolution analysis of gene expression and chromatin accessibility. The differentiation trajectory of pig skeletal muscle development was identified, and critical regulators such as EGR1 and RHOB were identified through integrative analysis.
Review
Biology
Aidan S. Marshall, Nick S. Jones
Summary: Mitochondria, the powerhouse of the cell, exist in multiple copies in almost every cell, each with its own mtDNA. Mutations in mtDNA can lead to cell dysfunction and disease. Heteroplasmy, a state where cells harbor both wild type and variant mtDNA, can arise through inheritance or mutations throughout life.
Review
Biochemistry & Molecular Biology
Yulong Zhang, Siwen Xu, Zebin Wen, Jinyu Gao, Shuang Li, Sherman M. Weissman, Xinghua Pan
Summary: This article discusses the challenges of using single-cell sequencing with multiple samples and proposes sample-multiplexing approaches, including using variant features as sample markers for sample pooling and decoding. Additionally, other single-cell omics methods are introduced, along with selection guidelines.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Neurosciences
Anzhelika Koldaeva, Cary Zhang, Yu-Pei Huang, Janine Kristin Reinert, Seiya Mizuno, Fumihiro Sugiyama, Satoru Takahashi, Taha Soliman, Hiroaki Matsunami, Izumi Fukunaga
Summary: This study aimed to identify differentially expressed genes between MCs and TCs in the mouse olfactory system and ultimately generate a cell type-specific Cre-driver line. After validating potential markers, Pkib and Lbdh2 remained promising candidates. Using gene editing technology, a new inducible Cre-driver line was established and shown to effectively genetically label MCs.
JOURNAL OF NEUROSCIENCE
(2021)
Article
Genetics & Heredity
Yuge Wang, Xingzhi Sun, Hongyu Zhao
Summary: As single-cell chromatin accessibility profiling methods advance, scATAC-seq has become increasingly important in studying regulatory genomic regions and cell type annotation. This study evaluated the performance of five scATAC-seq annotation methods and found that bridge integration was the best method in terms of accuracy and scalability.
FRONTIERS IN GENETICS
(2022)
Article
Biochemistry & Molecular Biology
Joyce Tse, Tsz Ho Li, Jizhou Zhang, Alan Chun Kit Lee, Ivy Lee, Zhe Qu, Xiao Lin, Jerome Hui, Ting-Fung Chan
Summary: In this study, the role of a novel lncRNA in Drosophila leg development was investigated using single-cell analysis methods. The results revealed that this lncRNA has high expression in distal specific genes, suggesting its potential importance in leg development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Lejin Tian, Yunxiao Xie, Zhaobin Xie, Jasmine Tian, Weidong Tian
Summary: Here, we introduce AtacAnnoR, a two-round annotation method for scATAC-seq data that utilizes well-annotated scRNA-seq data as a reference. Through evaluation against six other methods on 11 benchmark datasets, AtacAnnoR demonstrates the highest mean accuracy and mean balanced accuracy, performing exceptionally well when unpaired scRNA-seq data is used as the reference. Moreover, AtacAnnoR incorporates a 'Combine and Discard' strategy to further enhance annotation accuracy when multiple reference annotations are available. AtacAnnoR is implemented as an R package and can be seamlessly integrated into popular scATAC-seq analysis pipelines.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Genetics & Heredity
Yang Chen, Yuping Zhang, James Y. H. Li, Zhengqing Ouyang
Summary: LISA2 is a fast and flexible trajectory learning method for single-cell data analysis, with two distinctive features: using specified leaves and root to reduce complexity for building developmental trajectory, and applicable for both transcriptomics and epigenomics data. LISA2 visualizes complex trajectories using 3D Landmark ISOmetric feature MAPping (L-ISOMAP).
FRONTIERS IN GENETICS
(2021)
Article
Ophthalmology
Joseph Collin, Rachel Queen, Darin Zerti, David H. Steel, Claire Bowen, Manoj Parulekar, Majlinda Lako
Summary: This study identified cone precursors as the predominant cell type in Rb tumors, with the G2/M subset determined as the cell type of origin. scATAC-Seq analysis revealed two Rb-enriched cone subclusters characterized by activation of specific signaling pathways, allowing proliferating cone precursors to evade cell cycle arrest and apoptosis. These findings highlight the heterogeneity of Rb tumors and suggest potential molecular targets for new treatment strategies.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2021)
Article
Multidisciplinary Sciences
Zhenhua Li, Quanli Yang, Xin Tang, Yiming Chen, Shanshan Wang, Xiaojie Qi, Yawen Zhang, Zonghua Liu, Jing Luo, Hui Liu, Yongbing Ba, Lianxia Guo, Baojian Wu, Fang Huang, Guangchao Cao, Zhinan Yin
Summary: This study explores the heterogeneity of gamma delta T cells in different tissues and uncovers potential regulatory mechanisms. It identifies a novel subset of immature gamma delta T cells localized to the thymus and validates the circadian transcription factor NR1D1 as a negative regulator of gamma delta T17 cell differentiation.
Article
Ophthalmology
Zhao-Jing Lu, Jin-Guo Ye, Dong-Liang Wang, Meng-Ke Li, Qi-Kai Zhang, Zhong Liu, Yan-Jing Huang, Cai-Neng Pan, Yu-Heng Lin, Zhuo-Xing Shi, Ying-Feng Zheng
Summary: This study utilizes single-cell multi-omics analysis to investigate the gene regulatory profiles of mouse corneal epithelial cells. It reveals that cell type-specific accessible regions are mainly located at distal regions, indicating the crucial roles of distal regulatory elements in determining the diversity of corneal epithelial cells. The study also identifies key transcription factors, including NFI family members, Rarg, and Elf3, driving corneal epithelial cell differentiation.
INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE
(2023)
Article
Immunology
Shun Li, Bin Wu, Yun Ling, Mingquan Guo, Boyin Qin, Xiaonan Ren, Chao Wang, Hua Yang, Lixiang Chen, Yixin Liao, Yang Liu, Xiuhua Peng, Chunhua Xu, Zhenyan Wang, Yinzhong Shen, Jun Chen, Li Liu, Bowen Niu, Mengmin Zhu, Lingling Liu, Feng Li, Tongyu Zhu, Zhaoqin Zhu, Xiaohui Zhou, Hongzhou Lu
Summary: The study revealed significant changes in epigenetic chromatin accessibility and transcriptomic immune profiles of T cells in patients with COVID-19, including enrichment of inflammatory pathways and altered gene expressions. Decreased Th1 cells in CD4(+) T cells, and upregulated activation markers in CD8(+) T cells, suggest that T-cell inflammatory states with defective functions in CD4(+) T cells of severely ill/critical patients may play a crucial role in determining the pathogenesis and recovery from COVID-19.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Cell Biology
Kai Hu, Haibo Liu, Nathan D. Lawson, Lihua Julie Zhu
Summary: This article introduces the development of a comprehensive analysis pipeline called scATACpipe for single-cell ATAC-seq (scATAC-seq) data. The pipeline enables extensive analysis including quality assessment, preprocessing, dimension reduction, clustering, peak calling, differential accessibility inference, integration with scRNA-seq data, and generates comprehensive HTML reports and visualization files.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Review
Cell Biology
Alecia-Jane Twigger, Walid T. Khaled
Summary: Understanding the complexity and heterogeneity of mammary cell subpopulations is crucial for uncovering the mechanisms of breast cancer development. Advances in single cell technologies have provided researchers with more data, revealing the differentiation potential of mammary cell subtypes.
SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
(2021)
Editorial Material
Urology & Nephrology
Bilal A. Naved, Joseph Bonventre, Jeffrey A. Hubbell, Neil A. Hukriede, Benjamin D. Humphreys, Carl Kesselman, M. Todd Valerius, Andrew P. McMahon, Stuart J. Shankland, Jason A. Wertheim, Michael J. White, Mark P. de Caestecker, Iain A. Drummond
Summary: Acute kidney injury is a serious global health issue with millions of individuals affected and significant mortality rates. The (Re)Building a Kidney (RBK) consortium is focused on studying endogenous kidney repair mechanisms and generating new kidney tissue. This review provides an update on RBK studies of nephron repair and addresses important questions regarding the cellular sources and drivers of repair. Additionally, it highlights the importance of RBK in promoting the development of therapeutics and provides a guide to their open access data hub.
KIDNEY INTERNATIONAL
(2022)
Article
Biotechnology & Applied Microbiology
Minori Tamai, Shinichi Fujisawa, Thao T. T. Nguyen, Chiaki Komatsu, Keiko Kagami, Kenji Kamimoto, Kohei Omachi, Shin Kasai, Daisuke Harama, Atsushi Watanabe, Koshi Akahane, Kumiko Goi, Kazuhito Naka, Tadashi Kaname, Takanori Teshima, Takeshi Inukai
Summary: The Philadelphia chromosome, generated by aberrant ligation between the BCR and ABL1 genes, is the first translocation identified in leukemia. Simultaneous double-strand breaks at the breakpoints of these genes have been found to be the initiation events for Ph+ leukemia and lead to the fusion of BCR and ABL1.
CANCER GENE THERAPY
(2023)
Article
Urology & Nephrology
Mark E. Rosenberg, Sharon Anderson, Samira S. Farouk, Keisha L. Gibson, Robert S. Hoover, Benjamin D. Humphreys, Janis M. Orlowski, Suneel M. Udani, Joshua S. Waitzman, Melissa West, Tod Ibrahim
Summary: The American Society of Nephrology (ASN) Task Force on the Future of Nephrology was established to address training requirements and improve the quality of care in nephrology. The task force developed 10 recommendations to promote equitable care, highlight the value of nephrology, and enhance nephrology education. This report reviews the process, rationale, and details of these recommendations.
CLINICAL JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Article
Urology & Nephrology
Yasuhiro Yoshimura, Yoshiharu Muto, Kohei Omachi, Jeffrey H. Miner, Benjamin D. Humphreys
Summary: This study reveals the regulatory mechanisms of HNF4A and HNF4G during human proximal tubule differentiation. The experimental strategy can be applied more broadly to investigate transcriptional regulation in human kidney development.
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Editorial Material
Urology & Nephrology
Benjamin D. Humphreys
JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY
(2023)
Article
Urology & Nephrology
Jun Kuwazuru, Mary Ann Suico, Kohei Omachi, Haruka Kojima, Misato Kamura, Shota Kaseda, Teppei Kawahara, Yuki Hitora, Hikaru Kato, Sachiko Tsukamoto, Mikiyo Wada, Toshifumi Asano, Shunsuke Kotani, Makoto Nakajima, Shogo Misumi, Yuya Sannomiya, Jun Horizono, Yuimi Koyama, Aimi Owaki, Tsuyoshi Shuto, Hirofumi Kai
Summary: This study provides a novel therapeutic candidate, alisporivir, for Alport syndrome (AS) by enhancing the secretion of mutant 345(IV) and reveals the importance of cyclophilin D in this process. It suggests that alisporivir could be a safer option than cyclosporin A for AS treatment.
Article
Urology & Nephrology
Kohei Omachi, Colin O'Carroll, Jeffrey H. Miner
Summary: This study investigated the effects of PPARd agonist REN001 in a mouse model of Alport syndrome. The results showed that REN001 reduced proteinuria, decreased BUN levels, and improved renal inflammation and fibrosis. The combination of REN001 with ACEis may have additive effects to attenuate renal injury and slow disease progression.