Evidence map›Paper›PMID 42323650›Full record

ArticleGenome biology2026

Spatiotemporal transcriptomic analysis during cold ischemic injury to the murine kidney reveals compartment-specific changes.

Srujan Singh, Shishir Kumar Patel, Ryo Matsuura, Dee Velazquez, Zhaoli Sun, Sanjeev Noel, Hamid Rabb, Jean Fan

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In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed
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1 · What the graph read from it

What it found

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2 · The registry

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3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

8 authors.

Srujan SinghCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
Shishir Kumar PatelDepartment of Medicine, Johns Hopkins University, Baltimore, MD, USA.
Ryo MatsuuraDepartment of Medicine, Johns Hopkins University, Baltimore, MD, USA.
Dee VelazquezCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA.
Zhaoli SunDepartment of Surgery, Johns Hopkins University, Baltimore, MD, USA.
Sanjeev NoelDepartment of Medicine, Johns Hopkins University, Baltimore, MD, USA.
Hamid RabbDepartment of Medicine, Johns Hopkins University, Baltimore, MD, USA. hrabb1@jhmi.edu.
Jean FanCenter for Computational Biology, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, USA. jeanfan@jhu.edu.

Funding

Resource Development CoreU54DK137331 · NIDDK · JOHNS HOPKINS UNIVERSITY · PI JOSEF CORESH · 2023 to 2026
$4.3M
Acute kidney injury and microbiomeR01DK123342 · NIDDK · JOHNS HOPKINS UNIVERSITY · PI RABB, HAMID · 2020 to 2024
$3.0M
Computational methods for delineating subcellular and cellular spatial transcriptional heterogeneity along developmental trajectoriesR35GM142889 · NIGMS · JOHNS HOPKINS UNIVERSITY · PI FAN, JEAN · 2021 to 2025
$2.0M
TIGIT in acute kidney injury and repairR01DK132278 · NIDDK · JOHNS HOPKINS UNIVERSITY · PI Sanjeev Noel · 2023 to 2026
$1.9M
National Science Foundation 2047611NIDDK NIH HHS R01 DK123342NIDDK NIH HHS R01 DK132278NIDDK NIH HHS R01DK132278, R01DK123342, U54DK137331NIDDK NIH HHS U54 DK137331NIGMS NIH HHS R35 GM142889NIGMS NIH HHS R35-GM142889
6 · The paper itself

Abstract

backgroundKidney transplantation is the preferred treatment strategy for end-stage kidney disease. Deceased donor kidneys usually undergo cold storage until kidney transplantation, leading to cold ischemia injury that may contribute to poor graft outcomes. However, the molecular characterization of potential mechanisms of cold ischemia injury remains incomplete.

resultsTo bridge this knowledge gap, we leverage 10x Visium spatial transcriptomic technology to perform full transcriptome profiling of murine kidneys subject to varying durations of cold ischemia typical in a deceased donor kidney transplant setting. We develop a computational workflow to identify and compare spatiotemporal transcriptomic changes that accompany the injury pathophysiology in a tissue compartment-specific manner. We identify proportional enrichment of oxidative phosphorylation (OXPHOS) genes with increasing duration of cold ischemia injury within the oxygen-lean inner medulla region, suggestive of atypical metabolic presentation. This is distinct in cold ischemia injury tissue compared to warm ischemia-reperfusion kidney injury tissue. Spatiotemporal trends are validated by qPCR and immunofluorescence in a larger cohort of mice.

conclusionsAltogether, our spatiotemporal transcriptomic analysis identifies coordinated molecular changes within metabolic pathways such as OXPHOS deep within the cold ischemic kidney, highlighting the need for increased attention to the inner medulla and potential opportunities for new insights beyond those available from superficial biopsy-focused tissue examination.

Indexed as

Cold IschemiaKidneyReperfusion InjuryTranscriptomeAnimalsGene Expression ProfilingKidney TransplantationMaleMiceMice, Inbred C57BLOxidative PhosphorylationSpatial TranscriptomicsCold ischemiaKidney transplantSpatial transcriptomicsWarm ischemia

Identifiers

PMID42323650
PMCPMC13531896

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.