RNA sequencing analysis in the transition from acute to chronic kidney injury with identification of Myoc as a marker of sustained kidney impairment
Authors: Fattah Hadi , Sriram Krishna , Insel Paul A. , Huang Winnie , Patel Rohit , Shigeoka Alana , Kasimsetty Sashi , Singh Prabhleen , McKay Dianne , Vallon Volker 
Published: June 2021

Background

Acute kidney injury (AKI) represents an acute decline in renal function and is associated with increased morbidity and mortality in all clinical settings. In most cases the kidneys recover but in some cases chronic kidney disease (CKD) develops. In order to better understand the transition from AKI to CKD or recovery, we performed RNA sequencing (RNA‐seq) analysis in a rodent AKI model over a 14 week period.

Methods

We induced ischemia/reperfusion (IR) injury by bilateral clamping of the renal arteries for 10, 15 or 20–25 minutes (min) in C57BL/6J males. On days 1, 3 and weeks (wks) 2 and 14 after reperfusion, we assayed plasma creatinine and GFR (by FITC‐sinistrin plasma elimination kinetics in awake mice, n= 4–5/group) and harvested kidneys for RNA‐seq (n= 3–5/group). RNA‐seq data were analyzed using R programming language to define transcript and differential gene expression profiles.

Results

A multidimensional scaling plot showed excellent clustering in the renal mRNA expression profile of individual samples for each group and time point. The post‐IR time points had prominent initial ischemia time‐dependent changes in gene expression followed by recovery tha,m.t was close to sham profiles at 14 wks but the 15 min IR profiles required more time than 10 min IR to match the sham profile (see Figure). Gene expression profiles in 20–25 min IR continued to move away from sham over time and the mice did not survive pass day 7. mRNA expression for established AKI biomarkers, such as KIM‐1, NGAL, Clusterin and Osteopontin, showed an initial ischemia time‐dependent rise followed by eventual normalization to sham levels despite plasma creatinine and GFR not obviously changing in 10 min IR versus sham, and GFR in 15 min IR at 14 weeks remaining about 30% below the values of 10 min IR or sham. Differential expression analysis revealed a potential novel kidney injury biomarker, Krt20, a member of the keratin family, which had an ischemia time‐dependent mRNA expression profile similar to the above listed biomarkers. Moreover, Myoc, a gene believed to be involved in cytoskeletal function, did not change initially in the 15 min IR group but showed a continuous sustained increase in mRNA expression over time, such that its level of expression was highest and ~20 fold above sham levels at 14 weeks after IR.

Conclusions

RNA‐seq after IR confirmed time‐dependent initial changes in established biomarkers of AKI as well as in the integrated renal mRNA expression profile. Hundreds of genes changed in response to modest renal ischemia (10 min IR) in the absence of robust changes in plasma creatinine or GFR. Recovery of established AKI biomarkers in the absence of GFR recovery indicated these markers do not capture sustained kidney impairment following AKI. The use of RNA‐seq identified Krt20 and Myoc as markers of acute and sustained kidney impairment, respectively, which may prove useful in assessing the transition from AKI to CKD in future studies.

Support or Funding Information

1) UAB UCSD O'Brien Center of Acute Kidney Injury Research NIH‐P30DK079337 2) NIH‐T32DK104717

This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.