Spatial biology of cancer evolution

Z Seferbekova, A Lomakin, LR Yates… - Nature Reviews …, 2023 - nature.com
The natural history of cancers can be understood through the lens of evolution given that the
driving forces of cancer development are mutation and selection of fitter clones. Cancer …

Principles and challenges of modeling temporal and spatial omics data

B Velten, O Stegle - Nature Methods, 2023 - nature.com
Studies with temporal or spatial resolution are crucial to understand the molecular dynamics
and spatial dependencies underlying a biological process or system. With advances in high …

A comprehensive benchmarking with practical guidelines for cellular deconvolution of spatial transcriptomics

H Li, J Zhou, Z Li, S Chen, X Liao, B Zhang… - Nature …, 2023 - nature.com
Spatial transcriptomics technologies are used to profile transcriptomes while preserving
spatial information, which enables high-resolution characterization of transcriptional patterns …

IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer

N Caronni, F La Terza, FM Vittoria, G Barbiera… - Nature, 2023 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to
therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour …

Modeling intercellular communication in tissues using spatial graphs of cells

DS Fischer, AC Schaar, FJ Theis - Nature Biotechnology, 2023 - nature.com
Abstract Models of intercellular communication in tissues are based on molecular profiles of
dissociated cells, are limited to receptor–ligand signaling and ignore spatial proximity in situ …

An integrated single cell and spatial transcriptomic map of human white adipose tissue

L Massier, J Jalkanen, M Elmastas, J Zhong… - Nature …, 2023 - nature.com
To date, single-cell studies of human white adipose tissue (WAT) have been based on small
cohort sizes and no cellular consensus nomenclature exists. Herein, we performed a …

Construction of a 3D whole organism spatial atlas by joint modelling of multiple slices with deep neural networks

G Wang, J Zhao, Y Yan, Y Wang, AR Wu… - Nature Machine …, 2023 - nature.com
Spatial transcriptomics (ST) technologies are revolutionizing the way to explore the spatial
architecture of tissues. Currently, ST data analysis is often restricted to a single two …

[HTML][HTML] Lymphatics act as a signaling hub to regulate intestinal stem cell activity

RE Niec, T Chu, M Schernthanner, S Gur-Cohen… - Cell stem cell, 2022 - cell.com
Barrier epithelia depend upon resident stem cells for homeostasis, defense, and repair.
Epithelial stem cells of small and large intestines (ISCs) respond to their local …

Integrated single-nucleus and spatial transcriptomics captures transitional states in soybean nodule maturation

Z Liu, X Kong, Y Long, S Liu, H Zhang, J Jia, W Cui… - Nature Plants, 2023 - nature.com
Legumes form symbiosis with rhizobium leading to the development of nitrogen-fixing
nodules. By integrating single-nucleus and spatial transcriptomics, we established a cell …

SPACEL: deep learning-based characterization of spatial transcriptome architectures

H Xu, S Wang, M Fang, S Luo, C Chen, S Wan… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies detect mRNA expression in single cells/spots
while preserving their two-dimensional (2D) spatial coordinates, allowing researchers to …