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Acute Kidney Injury Markers Found With Single-Cell Transcriptomics, Proteomics


NEW YORK – With a combination of single-cell transcriptomics and plasma proteomics, a team led by researchers at Johns Hopkins has identified maladaptive repair processes in acute kidney injury (AKI) that correspond with progression to more severe kidney disease.

AKI has been linked to sharp increases in both chronic kidney disease development and risk of in-hospital patient death, researchers from Johns Hopkins University School of Medicine, Yale School of Medicine, the University of Pittsburgh, and elsewhere explained in a Science Translational Medicine paper on Wednesday. Even so, potential causes of AKI complications have been incompletely understood.

Based on past studies in mouse models, the team suspected that a subset of cells in the kidney's proximal tubule structures fail to repair fully after an injury, leading to a "maladaptive" state marked by inflammation and scarring, or fibrosis — a hypothesis they set out to explore in humans using single-nucleus RNA sequencing on 120,985 kidney cells from 17 biopsied patients with AKI and seven individuals without.

With the single-cell data, the team put together half a dozen expression-based clusters corresponding with kidney, stromal, and immune cells subclusters in individuals with or without AKI. In addition to healthy proximal tubule cell subclusters, the transcriptomic profiles pointed to the presence of proximal tubule cells with features linked to dedifferentiation and higher-than-usual activity in pro-inflammatory and profibrotic activity.

The researchers went on to tease out the transcriptomic regulatory structures and transcription factors contributing to healthy kidney cells or to maladaptive expression shifts after injury, which included an upregulation in genes involved in processes ranging from stress response or injury to cellular proliferation.

Together, the results revealed maladaptive proximal tubule repair in at least some of the study's AKI-affected participants, who were part of the Kidney Precision Medicine Project.

"Our study investigated the kidney transcriptome in patients who developed acute kidney injury (AKI) in the hospital and found that maladaptive repair of injured proximal tubule is a common response to injury in diverse etiologies of AKI," Chirag Parikh, a researcher at Johns Hopkins University School of Medicine and the senior author of the study, said in an email.

After flagging transcriptomic and regulatory features linked to maladaptive proximal tubule repair, the investigators set out to find potential blood plasma markers for severe AKI in two situations that can increase the risk of AKI: heart surgery and marathon running.

Using SomaLogic SomaScan aptamer assays, the researchers assessed blood plasma samples from 322 adult cardiac surgery patients, focusing on proteins that corresponded to genes that were upregulated or downregulated in maladaptive proximal tubule cells in the transcriptomic stage of the study.

From 122 proteins with enhanced blood plasma levels post-surgery, they noted that 39 proteins turned up at higher levels in the subset of cardiac surgery patients who developed severe AKI. On the other hand, 38 of the 192 proteins showing reduced plasma levels after surgery tracked with the development of advanced AKI.

Through validation testing on samples from 68 pediatric patients who underwent cardiac surgery for congenital heart disease repair and from 39 post-marathon runners deemed to be at high risk for exercise-related AKI, the team narrowed in on a handful of plasma protein markers for severe AKI.

Those markers, which included enhanced transforming growth factor-beta2, collagen type XXIII-alpha1, and X-linked neuroligin 4 protein levels and lower-than-usual levels of plasminogen, ectonucleotide pyrophosphatase/phosphodiesterase 6, and protein C, were also tied to kidney atrophy in the researchers' RT-PCR analyses of kidney samples from mouse models of kidney toxicity or injury that progressed to scarring or atrophy of the organ.

"[T]hese markers of maladaptive repair are strongly associated with adverse outcomes after AKI, such as progression to severe AKI after cardiac surgery," Parikh explained.

Beyond their potential utility for identifying individuals with maladaptive repair after AKI, the availability of blood-based markers is expected to inform future efforts to find and evaluate therapeutic strategies for treating or preventing AKI complications.

"When a candidate therapeutic emerges," Parikh wrote, "the noninvasive biomarkers from our study can be used as pharmacodynamic endpoints in early clinical development, evaluating its efficacy, and as prognostic enrichment to identify patients who will more likely benefit from drugs targeting maladaptive repair."