Exploring tissue architecture using spatial transcriptomics

A Rao, D Barkley, GS França, I Yanai - Nature, 2021 - nature.com
Deciphering the principles and mechanisms by which gene activity orchestrates complex
cellular arrangements in multicellular organisms has far-reaching implications for research …

Spatial components of molecular tissue biology

G Palla, DS Fischer, A Regev, FJ Theis - Nature Biotechnology, 2022 - nature.com
Methods for profiling RNA and protein expression in a spatially resolved manner are rapidly
evolving, making it possible to comprehensively characterize cells and tissues in health and …

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

B Li, W Zhang, C Guo, H Xu, L Li, M Fang, Y Hu… - Nature …, 2022 - nature.com
Spatial transcriptomics approaches have substantially advanced our capacity to detect the
spatial distribution of RNA transcripts in tissues, yet it remains challenging to characterize …

Spatially informed cell-type deconvolution for spatial transcriptomics

Y Ma, X Zhou - Nature biotechnology, 2022 - nature.com
Many spatially resolved transcriptomic technologies do not have single-cell resolution but
measure the average gene expression for each spot from a mixture of cells of potentially …

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 …

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 …

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 …

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 …

Clinical and translational values of spatial transcriptomics

L Zhang, D Chen, D Song, X Liu, Y Zhang… - … and Targeted Therapy, 2022 - nature.com
The combination of spatial transcriptomics (ST) and single cell RNA sequencing (scRNA-
seq) acts as a pivotal component to bridge the pathological phenomes of human tissues with …

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 …