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 …

Spatial transcriptomics in health and disease

S Jain, MT Eadon - Nature Reviews Nephrology, 2024 - nature.com
The ability to localize hundreds of macromolecules to discrete locations, structures and cell
types in a tissue is a powerful approach to understand the cellular and spatial organization …

Spatiotemporal immune atlas of a clinical-grade gene-edited pig-to-human kidney xenotransplant

MD Cheung, R Asiimwe, EN Erman, CF Fucile… - Nature …, 2024 - nature.com
Pig-to-human xenotransplantation is rapidly approaching the clinical arena; however, it is
unclear which immunomodulatory regimens will effectively control human immune …

3d ground truth annotations of nuclei in 3d microscopy volumes

A Chen, L Wu, S Winfree, KW Dunn, P Salama, EJ Delp - bioRxiv, 2022 - biorxiv.org
In this paper we describe a set of 3D microscopy volumes we have partially manually
annotated. We describe the volumes annotated and the tools and processes we use to …

Acute kidney injury results in long-term alterations of kidney lymphatics in mice

G Ghajar-Rahimi, D Barwinska… - American Journal …, 2024 - journals.physiology.org
The long-term effects of a single episode of acute kidney injury (AKI) induced by bilateral
ischemia-reperfusion injury (BIRI) on kidney lymphatic dynamics are not known. The …

High-throughput image analysis with deep learning captures heterogeneity and spatial relationships after kidney injury

MC McElliott, A Al-Suraimi, AC Telang… - Scientific Reports, 2023 - nature.com
Recovery from acute kidney injury can vary widely in patients and in animal models.
Immunofluorescence staining can provide spatial information about heterogeneous injury …

Two distinct phenotypes of calcium oxalate stone formers could imply different long-term risks for renal function

JC Williams Jr, WS Bowen, JE Lingeman, M Rivera… - Urolithiasis, 2024 - Springer
Endoscopic and biopsy findings have identified two distinct phenotypes among individuals
with calcium oxalate (CaOx) kidney stones. The first type has normal renal papillae but …

Defining protein expression in the kidney at large scale: from antibody validation to cytometry analysis

AR Sabo, S Winfree… - American Journal of …, 2023 - journals.physiology.org
The kidney is a complex organ and a key regulator of homeostasis. It comprises various
functional units (nephrons, vasculature, and interstitium) that are organized spatially, so that …

Tissue cytometry with machine learning in kidney: From small specimens to big data

TM El-Achkar, S Winfree, N Talukder… - Frontiers in …, 2022 - frontiersin.org
Advances in cellular and molecular interrogation of kidney tissue have ushered a new era of
understanding the pathogenesis of kidney disease and potentially identifying molecular …

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

VH Canela, WS Bowen, RM Ferreira, JE Lingeman… - bioRxiv, 2022 - biorxiv.org
Kidney stone disease causes significant morbidity and increases health care utilization. The
pathogenesis of stone disease is not completely understood, due in part to the poor …