The expanding vistas of spatial transcriptomics

L Tian, F Chen, EZ Macosko - Nature Biotechnology, 2023 - nature.com
The formation and maintenance of tissue integrity requires complex, coordinated activities
by thousands of genes and their encoded products. Until recently, transcript levels could …

Mechanisms of kidney fibrosis and routes towards therapy

N Yamashita, R Kramann - Trends in Endocrinology & Metabolism, 2024 - cell.com
Kidney fibrosis is the final common pathway of virtually all chronic kidney diseases (CKDs)
and is therefore considered to be a promising therapeutic target for these conditions …

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 …

High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

MR Vahid, EL Brown, CB Steen, W Zhang… - Nature …, 2023 - nature.com
Recent studies have emphasized the importance of single-cell spatial biology, yet available
assays for spatial transcriptomics have limited gene recovery or low spatial resolution. Here …

An atlas of healthy and injured cell states and niches in the human kidney

BB Lake, R Menon, S Winfree, Q Hu, R Melo Ferreira… - Nature, 2023 - nature.com
Understanding kidney disease relies on defining the complexity of cell types and states, their
associated molecular profiles and interactions within tissue neighbourhoods. Here we …

A spatially anchored transcriptomic atlas of the human kidney papilla identifies significant immune injury in patients with stone disease

VH Canela, WS Bowen, RM Ferreira, F Syed… - Nature …, 2023 - nature.com
Kidney stone disease causes significant morbidity and increases health care utilization. In
this work, we decipher the cellular and molecular niche of the human renal papilla in …

STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping

K Clifton, M Anant, G Aihara, L Atta, OK Aimiuwu… - Nature …, 2023 - nature.com
Spatial transcriptomics (ST) technologies enable high throughput gene expression
characterization within thin tissue sections. However, comparing spatial observations across …

Spatially resolved transcriptomic analysis of acute kidney injury in a female murine model

EE Dixon, H Wu, Y Muto, PC Wilson… - Journal of the …, 2022 - journals.lww.com
Background Single-cell sequencing technologies have advanced our understanding of
kidney biology and disease, but the loss of spatial information in these datasets hinders our …

The role of cytokines in neutrophil development, tissue homing, function and plasticity in health and disease

M Tsioumpekou, D Krijgsman, JHW Leusen… - Cells, 2023 - mdpi.com
Neutrophils are crucial innate immune cells and comprise 50–70% of the white blood cell
population under homeostatic conditions. Upon infection and in cancer, blood neutrophil …

SPASCER: spatial transcriptomics annotation at single-cell resolution

Z Fan, Y Luo, H Lu, T Wang, YZ Feng… - Nucleic Acids …, 2023 - academic.oup.com
In recent years, the explosive growth of spatial technologies has enabled the
characterization of spatial heterogeneity of tissue architectures. Compared to traditional …