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 …

How many cell types are in the kidney and what do they do?

MS Balzer, T Rohacs, K Susztak - Annual review of physiology, 2022 - annualreviews.org
The kidney maintains electrolyte, water, and acid-base balance, eliminates foreign and
waste compounds, regulates blood pressure, and secretes hormones. There are at least 16 …

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 …

Spatial transcriptomics at subspot resolution with BayesSpace

E Zhao, MR Stone, X Ren, J Guenthoer… - Nature …, 2021 - nature.com
Recent spatial gene expression technologies enable comprehensive measurement of
transcriptomic profiles while retaining spatial context. However, existing analysis methods …

[HTML][HTML] 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 …

[HTML][HTML] 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 …

Spatial charting of single-cell transcriptomes in tissues

R Wei, S He, S Bai, E Sei, M Hu, A Thompson… - Nature …, 2022 - nature.com
Single-cell RNA sequencing methods can profile the transcriptomes of single cells but
cannot preserve spatial information. Conversely, spatial transcriptomics assays can profile …

[HTML][HTML] Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury

RM Ferreira, AR Sabo, S Winfree, KS Collins… - JCI insight, 2021 - ncbi.nlm.nih.gov
Single-cell sequencing studies have characterized the transcriptomic signature of cell types
within the kidney. However, the spatial distribution of acute kidney injury (AKI) is regional …

[HTML][HTML] 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 …

[HTML][HTML] Intrinsic TGF-β signaling attenuates proximal tubule mitochondrial injury and inflammation in chronic kidney disease

M Kayhan, J Vouillamoz, DG Rodriguez… - Nature …, 2023 - nature.com
Excessive TGF-β signaling and mitochondrial dysfunction fuel chronic kidney disease (CKD)
progression. However, inhibiting TGF-β failed to impede CKD in humans. The proximal …