This study uses spatial transcriptomics to identify CD8+ T cell-driven mechanisms of kidney damage in ICI-AIN, showing increased IFN-γ signaling and proinflammatory myeloid cell activation.

bioRxiv · Oct 31, 2025 · PreprintImmunology

The chromatin landscape of healthy and injured cell types in the human kidney

Debora L. Gisch, Michelle Brennan, Blue B. Lake, Jeannine M. Basta, Mark S. Keller, Ricardo Melo Ferreira, Shreeram Akilesh, Reetika R. Ghag, Charles Lu, Ying‐Hua Cheng, Kimberly S. Collins, Samir V. Parikh, Brad H. Rovin, Lynn Robbins, Lisa Stout, , Joana P. Gonçalves

The paper defines the chromatin landscape of healthy and injured kidney cells using multi-omics data, identifying regulatory elements and transcription factor networks involved in injury response.

Nature Communications · Jan 10, 2024Peer-reviewedMolecular Biology

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

Blue B. Lake, Rajasree Menon, Seth Winfree, Qiwen Hu, Ricardo Melo Ferreira, Kian Kalhor, Daria Barwinska, Edgar A. Otto, Michael J. Ferkowicz, Dinh H. Diep, Nongluk Plongthongkum, Amanda L. Knoten, Sarah M. Urata, Laura H. Mariani, Abhijit S. Naik, , Ljiljana Paša‐Tolić

The paper creates a high-resolution cellular atlas of healthy and injured kidney cell states and niches using single-cell and spatial technologies, identifying molecular signatures and pathways related to kidney injury.

Nature · Jul 19, 2023Peer-reviewedGenomics

High Resolution Slide-seqV2 Spatial Transcriptomics Enables Discovery of Disease-Specific Cell Neighborhoods and Pathways

Jamie L. Marshall, Teia Noel, Qingbo S. Wang, Haiqi Chen, Evan M. Murray, Ayshwarya Subramanian, Katherine A. Vernon, Silvana Bazúa‐Valenti, Katie Liguori, Keith H. Keller, Robert R. Stickels, Breanna Nicole McBean, Rowan M. Heneghan, Astrid Weins, Evan Z. Macosko, , Anna Greka

This study uses Slide-seqV2 to identify disease-specific cell neighborhoods and pathways in human and mouse kidneys.

iScience · Mar 16, 2022Peer-reviewedMolecular Biology

Obesity-instructed TREM2high macrophages identified by comparative analysis of diabetic mouse and human kidney at single cell resolution

Ayshwarya Subramanian, Katherine A. Vernon, Yiming Zhou, Jamie L. Marshall, Maria Alimova, Fan Zhang, Michal Slyper, Julia Waldman, Mónica S. Montesinos, Danielle Ashley Dionne, Lan Nguyễn, Michael S. Cuoco, Dan Dubinsky, Jason Purnell, Keith Heller, , Anna Greka

The paper identifies obesity-related TREM2high macrophages in diabetic mouse and human kidney through single-cell transcriptomics and cross-species comparison.

bioRxiv · May 30, 2021 · PreprintGenomics

RAAS blockade, kidney disease, and expression of ACE2, the entry receptor for SARS-CoV-2, in kidney epithelial and endothelial cells

Ayshwarya Subramanian, Katherine A. Vernon, Michal Slyper, Julia Waldman, Malte D. Luecken, Kirk Gosik, Dan Dubinsky, Michael S. Cuoco, Keith H. Keller, Jason Purnell, Lan Nguyễn, Danielle Ashley Dionne, Orit Rozenblatt–Rosen, Astrid Weins, Human Cell Atlas Lung Biological Network, , Anna Greka

The paper examines ACE2 expression in kidney cells in relation to RAAS blockers and age/sex, finding age-related differences and associations with drug use.

bioRxiv · Jun 23, 2020 · PreprintGenomics

Kidney organoid reproducibility across multiple human iPSC lines and diminished off target cells after transplantation revealed by single cell transcriptomics

Ayshwarya Subramanian, Eriene-Heidi Sidhom, Maheswarareddy Emani, Katherine A. Vernon, Nareh Sahakian, Yiming Zhou, Maria Kost‐Alimova, Michal Slyper, Julia Waldman, Danielle Ashley Dionne, Lan Nguyễn, Astrid Weins, Jamie L. Marshall, Orit Rozenblatt–Rosen, Aviv Regev, Anna Greka

The paper uses single-cell RNA-Seq to assess kidney organoid reproducibility across iPSC lines and shows transplantation reduces off-target cells.

Nature Communications · Nov 29, 2019Peer-reviewedGenomics