Article
Immunology
Min Feng, Luc Swevers, Jingchen Sun
Summary: This article highlights the importance of using high-throughput single cell technologies, such as scRNA-seq, to study the subtypes of insect hemocytes. After genetic analysis in Drosophila, the authors analyzed the differentiation and functions of different cell clusters in Bombyx and identified characteristic marker genes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Fuping Qian, Guanyun Wei, Yajing Gao, Xin Wang, Jie Gong, Chao Guo, Xiaoning Wang, Xu Zhang, Jinxiang Zhao, Cheng Wang, Mengting Xu, Yuebo Hu, Guoli Yin, Jiahui Kang, Renjie Chai, Gangcai Xie, Dong Liu
Summary: Hair cells are essential for hearing and balance, and understanding their molecular characteristics and gene expression can provide insights into their formation and function. This study used single-cell RNA sequencing to identify three subtypes of hair cells in zebrafish and discovered specific genes associated with each subtype.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Shaoyi Cai, Zhiyou Chen, Heng Tang, Siyan Meng, Liang Tao, Qin Wang
Summary: This study identified the crucial role of FKBP1A in GBM and its underlying molecular mechanism, showing that upregulated FKBP1A promotes GBM cell death through the apoptosis pathway, thereby inhibiting GBM growth.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Andrew E. Teschendorff, Alok K. Maity, Xue Hu, Chen Weiyan, Matthias Lechner
Summary: The study introduces a new single-cell potency measurement method CCAT, which can accurately estimate the potency of millions of cells in a short period of time, showing significant improvement over existing methods. Experimental results demonstrate that CCAT has advantages in accuracy, computational cost, and handling missing data.
Article
Biochemistry & Molecular Biology
Sloan A. Lewis, Brianna M. Doratt, Suhas Sureshchandra, Allen Jankeel, Natali Newman, Weining Shen, Kathleen A. Grant, Ilhem Messaoudi
Summary: This study investigates the effects of long-term alcohol drinking on the immunological landscape of the lung using a rhesus macaque model. The results show that chronic alcohol drinking leads to heightened inflammatory state in alveolar macrophages, accompanied by changes in gene regulation, antimicrobial defenses, and cellular functions. These findings provide novel insights into the mechanisms underlying increased susceptibility to infection in patients with alcohol use disorders.
AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY
(2022)
Article
Immunology
Sloan A. Lewis, Suhas Sureshchandra, Brianna Doratt, Vanessa A. Jimenez, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Summary: Chronic heavy drinking can alter classical monocyte subset composition, leading to a hyper-inflammatory response to LPS but a compromised response to pathogens. This dysregulated inflammatory response may increase susceptibility to infections and impair wound healing.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Yu Chen, Shuqin Zhang
Summary: This paper introduces a new automatic cell type annotation method, ACAM, which provides more accurate annotation results through representative cluster identification, representative cluster annotation using marker genes, and classification of the remaining cells.
Article
Biochemistry & Molecular Biology
Xianhui Ruan, Yue Huang, Lin Geng, Mengran Tian, Yu Liu, Mei Tao, Xiangqian Zheng, Peng Li, Min Zhao
Summary: Single-cell transcriptome sequencing provides higher resolution for cellular differences in papillary thyroid carcinoma. Through integrative analysis of two datasets, we identified 31 consistently differentially expressed genes across multiple cell types, which are related to adaptive immune response and autoimmune thyroid diseases. Experimental validation suggests that KRT7 may be a potential biomarker for PTC epithelial cells.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Critical Care Medicine
Zefang Sun, Tao Zhang, Caihong Ning, Dingcheng Shen, Wenwu Pei, Rui Zhou, Shuai Zhu, Gengwen Huang
Summary: This study investigated the association between Helicobacter pylori infection and gastric cancer using gene expression profiling and single-cell RNA sequencing. The results showed a significant correlation between H. pylori infection and gastric cancer development. Furthermore, the study found that H. pylori infection could induce gastric cancer cells to enhance their invasion and metastasis abilities by expressing specific genes.
Article
Oncology
Yuanshuai Su, Chen Xue, Xinyu Gu, Wankun Wang, Yu Sun, Renfang Zhang, Lanjuan Li
Summary: This study constructed a TAM-related gene model that is associated with the prognosis and immunotherapeutic response of hepatocellular carcinoma (HCC) patients by analyzing single-cell transcriptomic data. The model can predict patient survival and response to immunotherapy, and characterize the immune landscape and tumor immune escape status.
FRONTIERS IN ONCOLOGY
(2023)
Article
Multidisciplinary Sciences
Eliza Duvall, Cecil M. Benitez, Krissie Tellez, Martin Enge, Philip T. Pauerstein, Lingyu Li, Songjoon Baek, Stephen R. Quake, Jason P. Smith, Nathan C. Sheffield, Seung K. Kim, H. Efsun Arda
Summary: This paper describes the molecular analysis of mouse pancreatic endocrine cell differentiation using single-cell transcriptomics, chromatin accessibility assays, and cytometry-based cell purification. The researchers uncover transcription factor networks that regulate pancreatic cell development and suggest the transcription factor Neurog3 may be important for specifying the pancreatic endocrine lineage. These findings have implications for improving diabetes therapy through replacement endocrine cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Engineering, Environmental
Jie Meng, Wen-Xiong Wang
Summary: In this study, the responses of different cell populations of hemocytes in oysters under copper exposure were investigated using single-cell transcriptome profiling. The results showed that different cell types had heterogeneous responses to copper, with the granulocyte being the most important responsive cell type and displaying heterogeneity responses of its two subtypes. These findings have significant implications for understanding the impact of copper contamination on oysters.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2022)
Article
Genetics & Heredity
Jian Sun, Jianfei Zhang, Qian Bian, Xudong Wang
Summary: The transcription factor Dlx2 is crucial for craniomaxillofacial development, and dysregulation of its expression can lead to malformation in mice. Through various analyses including RNA-Seq and CUT & Tag, the study provides comprehensive insights into the effects of Dlx2 overexpression on maxillary processes during early development. The results demonstrate considerable changes in the transcriptome, with genes involved in RNA metabolism and neuronal development being significantly affected. Additionally, it is revealed that Dlx2 overexpression restricts cell proliferation and induces precocious differentiation, potentially contributing to craniomaxillofacial defects.
FRONTIERS IN GENETICS
(2023)
Article
Biochemistry & Molecular Biology
Hong Ma, Ziqing Liu, Yuchen Yang, Dong Feng, Yanhan Dong, Tiffany A. Garbutt, Zhiyuan Hu, Li Wang, Changfei Luan, Cynthia D. Cooper, Yun Li, Joshua D. Welch, Li Qian, Jiandong Liu
Summary: Single-cell transcriptomic analysis reveals the diversity and subpopulation distribution of non-cardiomyocytes during cardiac regeneration, with macrophages playing a key role in activating fibroblast and endothelial cell subpopulations. The study also identifies dynamic transitions between macrophage functional states and factors associated with mRNA processing and transcriptional regulation. A blueprint for interrogating the molecular and cellular basis of cardiac regeneration is provided.
Article
Biochemical Research Methods
Ruiqing Zheng, Ziwei Xu, Yanping Zeng, Edwin Wang, Min Li
Summary: This study proposed a cell potency inference method, SPIDE, based on cell-specific network entropy, which accurately identifies key cellular stages and quantifies the differentiation potency of cells along a differentiation pathway. Results showed consistent conclusions with real cell differentiation potency on most datasets, and SPIDE accurately recovers the continuous changes of potency during cell differentiation.