Results 141 to 150 of about 81,661 (282)

Uncovering functional lncRNAs by scRNA-seq with ELATUS

Nature Communications
Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study at single-cell (sc) level is challenging due to their less accurate annotation and low expression compared to protein-coding genes.
Enrique Goñi, Aina Maria Mas, Jovanna Gonzalez, Amaya Abad, Marta Santisteban, Puri Fortes, Maite Huarte, Mikel Hernaez   +7 more
openaire   +3 more sources

Integrated Single‐Cell and Spatial Transcriptomics Reveal Cell‐Type‐Specific Immune Regulatory Networks in Maize Responding to Southern Corn Rust

Advanced Science, EarlyView.
By integrating single‐nuclei and spatial transcriptomics, this study presents a stereoscopic landscape of maize leaf to Puccinia polysora infection. Epidermal and mesophyll cells initiate primary defenses via RLPs/RLKs and jasmonic acid signaling. Cell‐cell communication analyses further reveal the underlying the dynamics of the underlying immune ...
Qiongqiong Wang, Xinyan Sun, Yingchao Sun, Zeqiang Cheng, Zixiang Cheng, Shengbo Han, Ying Feng, Wenbo Yang, Huimin Li, Meichen Zhu, Xiaoling Wu, Jinghua Zhang, Jihua Tang, Honglian Li, Yanyong Cao, Canxing Duan, Yan Shi   +16 more
wiley   +1 more source

scE2EGAE: enhancing single-cell RNA-Seq data analysis through an end-to-end cell-graph-learnable graph autoencoder with differentiable edge sampling

Biology Direct
Background: Single-cell RNA sequencing (scRNA-Seq) technology reveals biological processes and molecular-level genomic information among individual cells.
Shuo Wang, Yuanning Liu, Hao Zhang, Zhen Liu   +3 more
doaj   +1 more source

Super‐Enhancer‐Driven SOX4/SMAD3 Mediate Membrane Remodeling by Regulating Phospholipid Metabolism to Accelerate Leukemia Progression

Advanced Science, EarlyView.
Chronic myeloid leukemia blast phase (CML‐BP) poses a severe therapeutic challenge. This study reveals that the super‐enhancer‐driven transcription factors SOX4 and SMAD3 form a cooperative axis critical for disease progression. They co‐activate the oncogenic kinase AXL and promote phospholipid remodeling via LPCAT1 to facilitate its signaling ...
Enzhe Lou, Peilong Lai, Guanjie Peng, Bo Lu, Lizhen Jiang, Xinyue Li, Jinghong Chen, Ladi Mo, Qiong Mao, Haichuan Zhang, Jinxin Fang, Yi Meng, Aochu Liu, Yingyin Gao, Andong Huang, Wenhui Lin, Shiwen Hu, Zerong Guan, Xiaolan Ye, Zhenguo Liu, Liling Jiang, Yueyuan Zheng, Xianping Shi   +22 more
wiley   +1 more source

Microglial Fkbp5 Impairs Post‐Stroke Vascular Integrity and Regeneration by Promoting Yap1‐Mediated Glycolysis and Oxidative Phosphorylation

Advanced Science, EarlyView.
A post‐stroke perivascular niche of microglia characterized by low expression of M2 markers and elevated glycolysis, oxidative phosphorylation (OXPHOS), and phagocytic activity is identified, which is termed stroke‐activated vascular‐associated microglia (stroke‐VAM).
Yanan Li, Yanmei Qiu, Yunlei Yang, Yanhao Wei, Haokun Peng, Longhai Zeng, Pengcheng Li, Rentang Bi, Bo Hu   +8 more
wiley   +1 more source

Repertoire-based mapping and time-tracking of T helper cell subsets in scRNA-Seq

Frontiers in Immunology
IntroductionThe functional programs of CD4+ T helper (Th) cell clones play a central role in shaping immune responses to different challenges. While advances in single-cell RNA sequencing (scRNA-Seq) have significantly improved our understanding of the ...
Daniil K. Lukyanov, Daniil K. Lukyanov, Valeriia V. Kriukova, Kristin Ladell, Irina A. Shagina, Irina A. Shagina, Dmitry B. Staroverov, Dmitry B. Staroverov, Bella E. Minasian, Anna S. Fedosova, Pavel Shelyakin, Oleg N. Suchalko, Alexander Y. Komkov, Konstantin A. Blagodatskikh, Kelly L. Miners, Olga V. Britanova, Olga V. Britanova, Olga V. Britanova, Andre Franke, David A. Price, David A. Price, Dmitry M. Chudakov, Dmitry M. Chudakov, Dmitry M. Chudakov, Dmitry M. Chudakov, Dmitry M. Chudakov   +25 more
doaj   +1 more source

Chromatin establishes an immature version of neuronal protocadherin selection during the naive-to-primed conversion of pluripotent stem cells. [PDF]

, 2019
In the mammalian genome, the clustered protocadherin (cPCDH) locus provides a paradigm for stochastic gene expression with the potential to generate a unique cPCDH combination in every neuron.
Allegue, Catarina, Almenar-Queralt, Angels, Bohaciakova, Dasa, Chaves, Rodrigo S, Chen, Andrew G, Dittrich, Marcus, Driscoll, Shawn P, El Hajj, Nady, Fong, Lauren K, Garcia-Bassets, Ivan, Goldstein, Lawrence SB, Hruska-Plochan, Marian, Kim, Hong Sook, Kohlnhofer, Bridget, Ma, Qi, Mackintosh, Carlos, Marsala, Martin, Merkurjev, Daria, Navarro, Michael, Tadokoro, Takahiro, Woodruff, Grace, Young, Jessica E   +21 more
core  

Spatial Profiling Reveals Distinct Molecular and Immune Evolution of Mouse Lung Adenocarcinoma Precancers with or Without Carcinogen Exposure

Advanced Science, EarlyView.
Tumor evolution in lung adenocarcinoma is shaped by genetic alterations and spatial immune dynamics. By integrating whole‐exome sequencing, imaging mass cytometry, and spatial transcriptomics across two mouse models, this study reveals how mutational burden, immune infiltration, and cell–state interactions evolve during early and late carcinogenesis ...
Bo Zhu, Muhammad Aminu, Pingjun Chen, Jian‐Rong Li, Chuanpeng Dong, Chenyang Li, Yanhua Tian, Shao‐Wei Lu, Hong Chen, Chenxi Ma, Xin Hu, Jie Ye, Andrew Y. Liu, Beibei Huang, Frank R. Rojas, Parra Cuentas. Edwin Roger, Ou Shi, Monique B. Nilsson, Alissa Poteete, Khaja B. Khan, Wei Lu, Luisa M. Solis Soto, Junya Fujimoto, Cara Haymaker, Ignacio I. Wistuba, Zhubo Wei, Linghua Wang, Don L. Gibbons, Ken Chen, Alexandre Reuben, Jason M. Schenkel, John V. Heymach, Chao Cheng, Jia Wu, Jianjun Zhang   +34 more
wiley   +1 more source

Single-cell analysis of cardiogenesis reveals basis for organ-level developmental defects. [PDF]

, 2019
Organogenesis involves integration of diverse cell types; dysregulation of cell-type-specific gene networks results in birth defects, which affect 5% of live births.
de Soysa, T Yvanka, Del Sol, Antonio, Gifford, Casey A, Huang, Yu, Okawa, Satoshi, Ranade, Sanjeev S, Ravichandran, Srikanth, Salunga, Hazel T, Schricker, Amelia, Srivastava, Deepak   +9 more
core  

PBRM1 Deficiency Reshapes an Immune Suppressive Microenvironment Through Epigenetic Tuning of PBRM1‐KDM5C‐IL6 Axis in ccRCC

Advanced Science, EarlyView.
PBRM1 ranks as the second most commonly mutated gene in ccRCC. This study reveals that PBRM1 loss promotes an immunosuppressive microenvironment by elevating M2 TAMs via the KDM5C–IL‐6 axis. These M2 TAMs, along with CAFs, form a barrier that excludes CD8+ T cells. Targeting IL‐6 synergizes with anti‐PD1 therapy, offering a promising strategy for PBRM1‐
Wenjiao Xia, Hongru Wang, Yu Dong, Zitong Yang, Yiyang Zhou, Zhinan Xia, Qinchen Li, Liangliang Ren, Yichun Zheng, Junliang Yan, Dongmei Ma, Zhi Chen, Xingang Cui, Guixin Zhu, Cheng Zhang   +14 more
wiley   +1 more source