Results 41 to 50 of about 3,101 (214)

Research progress of spatial transcriptomics and its applications in bone research

Kouqiang hemian waike zazhi
The structural and functional heterogeneity of cells in bone tissue is closely related to their spatial location. Spatial transcriptomics can simultaneously obtain location information and transcriptome changes of spatial units within tissues.
CHEN Yongliang, WANG Zuolin
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Spatially resolved transcriptomic profiling of degraded and challenging fresh frozen samples

Nature Communications, 2023
Spatial transcriptomics relies on RNA quality, which is variable and dependent on sample handling, storage, and/or intrinsic factors. Here, authors present a genome-wide spatial gene expression profiling method called RNA Rescue Spatial Transcriptomics ...
Reza Mirzazadeh, Zaneta Andrusivova, Ludvig Larsson, Phillip T. Newton, Leire Alonso Galicia, Xesús M. Abalo, Mahtab Avijgan, Linda Kvastad, Alexandre Denadai-Souza, Nathalie Stakenborg, Alexandra B. Firsova, Alia Shamikh, Aleksandra Jurek, Niklas Schultz, Monica Nistér, Christos Samakovlis, Guy Boeckxstaens, Joakim Lundeberg   +17 more
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EDNRB‐dependent endothelin signaling reduces proliferation and promotes proneural‐to‐mesenchymal transition in gliomas

Molecular Oncology, EarlyView.
Glioma cells mainly express the endothelin receptor EDNRB, while EDNRA is restricted to a perivascular tumor subpopulation. Endothelin signaling reduces glioma cell proliferation while promoting migration and a proneural‐to‐mesenchymal transition associated with poor prognosis. This pathway activates Ca2+, K+, ERK, and STAT3 signalings and is regulated
Donovan Pineau, Leonor Garcia, Hugo Arnold, Antonija Hanžek, Maialen Arrieta, Laurent R Gauthier, Christine Granotier‐Beckers, François D Boussin, Amaury Herbet, Marie Hautière, Valentin Asei‐Ceschino, Clémentin Jacques, Laura Brard, Thomas Harnois, Valérie Coronas, Bruno Constantin, Aurélien Chatelier, Jean Chemin, Serge Urbach, Martial Seveno, Szimonetta Hideg, Chantal Ripoll, Kasandra Aguilar‐Cázarez, Min Zheng, Guo‐Hao Huang, Sheng‐Qing Lv, Lei Zhang, Philippe Rondard, Laurent Prezeau, Jean‐Philippe Pin, Hugues Duffau, Luc Bauchet, Valérie Rigau, Franck Denat, Charles Truillet, Didier Boquet, Jean‐Philippe Hugnot   +36 more
wiley   +1 more source

Combining spatial transcriptomics with tissue morphology

Nature Communications
Spatial transcriptomics has transformed our understanding of tissue architecture by preserving the spatial context of gene expression patterns. Simultaneously, advances in imaging AI have enabled extraction of morphological features describing the tissue.
Eduard Chelebian, Christophe Avenel, Carolina Wählby   +2 more
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Spatial Transcriptomics for Tumor Heterogeneity Analysis

Frontiers in Genetics, 2022
The molecular heterogeneity of cancer is one of the major causes of drug resistance that leads to treatment failure. Thus, better understanding the heterogeneity of cancer will contribute to more precise diagnosis and improved patient outcomes.
Qiongyu Li, Xinya Zhang, Rongqin Ke
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Interrogating the immune landscape of microsatellite stable RAS‐mutated colon cancer

Molecular Oncology, EarlyView.
COLOSSUS project RAS‐mutated MSS colon cancer study explored transcriptomics and immune cell density by immunohistochemistry (IHC), Immunoscore (IS), ISIC/TuLIS scores, mutation counts, and detected different prevalences but similar microenvironment composition across immune markers with clinical relevance for future immunotherapy combination ...
Rodrigo Dienstmann, Eduardo García‐Galea, Alice O'Farrell, Zak Kinsella, Maxime Meylan, Florent Petitprez, Ingrid Arijs, Tom Venken, Hari Ps, Adrian Lärkeryd, Ian Miller, Janick Selves, Nadja Meindl‐Beinker, Fiorella Ruiz‐Pace, Elena Élez, Raquel Comas‐Navarro, Frank Lincoln, Dirk Fey, Gift Nyamundanda, Aoife Nolan, Joern Lewin, Raquel Perez‐Lopez, Jonathan Briody, Kathleen Bennett, Walter Kolch, David Matallanas, Alexander Kel, Enrique Arenas, Joaquín Arribas, Bart Ghesquière, Josep Tabernero, Julie Meilleroux, Deborah McNamara, Ray McDermott, Marvin Lim, Mary O'Reilly, Brian Bird, Lisa Stack, Lucia Moloney, Patrick Morris, Keith Egan, Maciej Milewski, Lars Scheuer, Joachim Behringer, Georg Bolz, Ramon Salazar, Cristina Santos, Andrea Ruiz, Orla Casey, Verena Murphy, Matthias Ebert, Livio Trusolino, Diether Lambrechts, Anguraj Sadanandam, Catherine Sautès‐Fridman, Jochen Prehn, Paolo Nuciforo, Jacques Fieschi, Florence Monville, Darran O'Connor, Wolf Fridman, Annette Byrne   +61 more
wiley   +1 more source

Graph attention automatic encoder based on contrastive learning for domain recognition of spatial transcriptomics

Communications Biology
Spatial transcriptomics is an emerging technology that enables the profiling of gene expression in tissues while preserving spatial location information.
Tianqi Wang, Huitong Zhu, Yunlan Zhou, Weihong Ding, Weichao Ding, Liangxiu Han, Xueqin Zhang   +6 more
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Nova-ST: Nano-patterned ultra-dense platform for spatial transcriptomics

Cell Reports: Methods
Summary: Spatial transcriptomics workflows using barcoded capture arrays are commonly used for resolving gene expression in tissues. However, existing techniques are either limited by capture array density or are cost prohibitive for large-scale atlasing.
Suresh Poovathingal, Kristofer Davie, Lars E. Borm, Roel Vandepoel, Nicolas Poulvellarie, Annelien Verfaillie, Nikky Corthout, Stein Aerts   +7 more
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Deciphering transcriptional plasticity in pancreatic ductal adenocarcinoma reveals alterations in sensory neuron innervation

Molecular Oncology, EarlyView.
Pancreatic sensory neurons innervating healthy and PDAC tissue were retrogradely labeled and profiled by single‐cell RNA sequencing. Tumor‐associated innervation showed a dominant neurofilament‐positive subtype, altered mitochondrial gene signatures, and reduced non‐peptidergic neurons.
Elena Genova, Michele Montrone, Uday Rangaswamy, Francesco Diversi, Irene Schiavo, Denise Ferrarini, Roberta Di Florio, Irene Longo, Michele Coscia, Nicola Zamboni, Giorgia Demontis, Lisa Veghini, Vincenzo Corbo, Remo Sanges, Paul Heppenstall   +14 more
wiley   +1 more source

HiSTaR: identifying spatial domains with hierarchical spatial transcriptomics variational autoencoder

Journal of Translational Medicine
Background The development of spatial transcriptomics (ST) has enabled biologists to measure transcriptome data on an entire tissue and retain spatial information.
Junhua Yu, Jiaqi Yuan, Qianbei Yi, Zheng Ye, Peng Xu, Wenbin Liu   +5 more
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