Article
Cell Biology
Xiaoqi Wang, Xiaobin Wu, Pei Zhang, Yuan Zhou, Jun Cai, Ling Jin
Summary: The adaptive immune response mediated by T cells plays a vital role in blood pressure elevation. This study identified four subsets of memory T cells in hypertensive patients and found that CD8 effector memory T cells have more biological functions. Subpopulation 1 of CD8 TEM cells was shown to contribute to blood pressure elevation, and marker genes CKS2, PLIN2, and CNBP were identified.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Martha B. Alvarez-Elizondo, Daphne Weihs
Summary: In this study, the invasiveness of CD44(+)ALDH(+) cancer stem-like cells (CSCs) was investigated using a rapid mechanobiology-based assay. It was found that CD44(+)ALDH(+) cells showed higher invasiveness and migratory capacity, suggesting their potential role in disease progression and as prognostic markers for recurrence and metastasis.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Article
Biology
Keiichiro Koiwai, Takashi Koyama, Soichiro Tsuda, Atsushi Toyoda, Kiyoshi Kikuchi, Hiroaki Suzuki, Ryuji Kawano
Summary: Crustacean aquaculture is expected to be a major source of fishery commodities in the near future. Hemocytes, key players of the immune system in shrimps, have been classified and their differentiation pathways predicted using single-cell RNA sequencing. A unified classification of shrimp hemocytes was provided, improving the understanding of its immune system.
Article
Biology
Linda K. Krasniewski, Papiya Chakraborty, Chang-Yi Cui, Krystyna Mazan-Mamczarz, Christopher Dunn, Yulan Piao, Jinshui Fan, Changyou Shi, Tonya Wallace, Cuong Nguyen, Isabelle A. Rathbun, Rachel Munk, Dimitrios Tsitsipatis, Supriyo De, Payel Sen, Luigi Ferrucci, Myriam Gorospe
Summary: By single-cell transcriptomic analysis, researchers identified 11 macrophage clusters in skeletal muscle, with four subgroups identified by membrane markers. Macrophages in old skeletal muscle showed increased proinflammatory and senescence-related traits.
Article
Multidisciplinary Sciences
Assaf Gottlieb, Naama Toledano-Furman, Karthik S. Prabhakara, Akshita Kumar, Henry W. Caplan, Supinder Bedi, Charles S. Cox, Scott D. Olson
Summary: This study conducted a temporal analysis of microglial cells in rats after traumatic brain injury (TBI), identifying sub-populations of microglia with different activation markers at different time points. These changes can help understand the progression of symptoms following TBI and redefine microglial subpopulations beyond the outdated M1/M2 paradigm.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Michael VanInsberghe, Jeroen van den Berg, Amanda Andersson-Rolf, Hans Clevers, Alexander van Oudenaarden
Summary: Single-cell sequencing methods have enabled in-depth analysis of cell diversity by focusing on sequencing genomes, epigenomes, and transcriptomes. However, measuring translation in individual cells remains a challenge. The technology described in this study achieves ribosome profiling with single-codon resolution, revealing ribosome pausing and diversity in translational processes among seemingly identical cells.
Article
Cell Biology
Jiamin Gao, Zhijian Li, Qinchen Lu, Jialing Zhong, Lixin Pan, Chao Feng, Shaomei Tang, Xi Wang, Yuting Tao, Jianyan Lin, Qiuyan Wang
Summary: This study constructed a tumor ecological landscape of 14 patients with hepatocellular carcinoma (HCC) and explored the interactions between tumor cells and the tumor microenvironment. The study found immune cell infiltration in the tumor tissues and specific cell subpopulations with potentially specific functions in the tumor microenvironment. The results have important implications for the treatment and prognosis of HCC.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Engineering, Mechanical
Cheng He, Zhonghua Li, Huan He, Jizhen Wang
Summary: A dynamic model updating approach is proposed in this study, considering thermal effects and uncertainties using a hierarchical strategy, and adjusting design parameter means and their covariance matrix based on a surrogate model. An inverse uncertainty propagation of mechanical system parameters under multiple physical fields is conducted, with thermal parameters and mechanical characteristics treated as temperature dependent.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2021)
Article
Immunology
Grace H. Attrill, Hansol Lee, Annie T. Tasker, Nurudeen A. Adegoke, Angela L. Ferguson, Ines Pires da Silva, Robyn P. M. Saw, John F. Thompson, Umaimainthan Palendira, Georgina Long, Peter M. Ferguson, Richard A. Scolyer, James S. Wilmott
Summary: This study characterizes the tumor immune microenvironment (TIME) in primary melanomas and identifies predictors of patient outcome. CD39+CD103+PD-1- CD8+ T-cell subset and B cells are associated with recurrence-free survival in primary melanoma.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Computer Science, Theory & Methods
Mark Tygert
Summary: Comparing differences in outcomes between subpopulations should consider the similarity of independent variables. Traditional binning methods may be arbitrary, but cumulative methods are more accurate in showing differences in results.
JOURNAL OF BIG DATA
(2021)
Article
Computer Science, Artificial Intelligence
Zi Wang, Yichi Xu, Dali Wang, Jiawei Yang, Zhirong Bao
Summary: This study utilizes deep reinforcement learning to infer cell-cell interactions and collective cell behaviors from 3D time-lapse images, revealing a novel migration mechanism in embryogenesis.
NATURE MACHINE INTELLIGENCE
(2022)
Article
Oncology
Xiaonan Wang, Carlotta Peticone, Ekaterini Kotsopoulou, Berthold Gottgens, Fernando J. Calero-Nieto
Summary: This study used single-cell transcriptomic analysis to characterize the molecular features of CAR T cell activation, revealing several subpopulations of cells in CAR products with reproducible cellular composition across donors. Targeted data interrogation also showed that a small proportion of antigen-responding CAR-expressing cells exhibited exhaustion signatures with known markers and previously unassociated genes.
Article
Immunology
Fuquan Wang, Ming Chen, Jiamin Ma, Chenchen Wang, Jingxu Wang, Haifa Xia, Dingyu Zhang, Shanglong Yao
Summary: This study used single-cell RNA sequencing to investigate cellular changes in sepsis-induced lung injury. The results showed that sepsis alters the composition of all cellular compartments, especially neutrophils, monocytes, T cells, endothelial, and fibroblast populations. By integrating bulk sequencing and single-cell data with the Scissors-method, the researchers identified cell subpopulations that are most associated with the septic lung injury phenotype. Function analysis further revealed the important role of these phenotype-related cell subpopulations in septic lung injury.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Yipeng Gao, Lei Li, Christopher Amos, Wei Li
Summary: Alternative polyadenylation (APA) plays a significant role in post-transcriptional regulation in various cellular processes, but the heterogeneity of APA among individual cells remains largely unknown. A new bioinformatics algorithm, scDaPars, has been introduced to accurately quantify APA events at single-cell and single-gene resolution, allowing for a better understanding of cellular heterogeneity at the post-transcriptional APA level. This approach not only reveals cell-type-specific APA regulation in cancer and human endoderm differentiation data, but also identifies cell subpopulations that are otherwise invisible to conventional gene expression analysis.
Article
Multidisciplinary Sciences
Christopher J. Hanley, Sara Waise, Matthew J. Ellis, Maria A. Lopez, Wai Y. Pun, Julian Taylor, Rachel Parker, Lucy M. Kimbley, Serena J. Chee, Emily C. Shaw, Jonathan West, Aiman Alzetani, Edwin Woo, Christian H. Ottensmeier, Matthew J. J. Rose-Zerilli, Gareth J. Thomas
Summary: Through single cell RNA-sequencing, multiplexed immunohistochemistry, and digital cytometry, three major fibroblast subpopulations in non-small cell lung cancer are identified and characterised. These subpopulations include adventitial, alveolar, and myofibroblasts. Myofibroblasts are associated with poor overall survival rates in lung adenocarcinomas, while their presence in squamous carcinomas does not have a prognostic value. These findings have important implications for the development of fibroblast-targeting strategies in cancer therapy.
NATURE COMMUNICATIONS
(2023)