Abstract: SA-PO1039
Profiling of Urinary RNA Biomarkers for CKD with Nanopore Sequencing
Session Information
- Pathology and Lab Medicine - II
November 04, 2023 | Location: Exhibit Hall, Pennsylvania Convention Center
Abstract Time: 10:00 AM - 12:00 PM
Category: Pathology and Lab Medicine
- 1800 Pathology and Lab Medicine
Authors
- Mackenzie, Morgan Elena, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States
- Roumelioti, Maria-Eleni, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States
- Schmidt, Darren W., University of New Mexico School of Medicine, Albuquerque, New Mexico, United States
- Argyropoulos, Christos, University of New Mexico School of Medicine, Albuquerque, New Mexico, United States
Background
There is a need to develop new biomarkers of kidney dysfunction & damage that are more informative than the estimated glomerular filtration rate (eGFR) & urine albumin to creatinine ratio (UACR). While RNAseq is increasingly being used for biomarker discovery, there are few reports of applications of 3rd generation sequencing platforms (Nanopore) to CKD.
Methods
Urinary RNA from participants in the COMPASS study (PMC5830321) with variable kidney function & UACR was isolated to make cDNA libraries with a novel pipeline for Nanopore sequencing (PALS-NS, https://www.biorxiv.org/content/10.1101/2022.12.16.520507v1). RNA counts were normalized via Analysis of Variance and analyzed via negative binomial mixed effects models (NBMEM, PMC5499834).
Results
19 cDNA libraries were made from the initial and follow up (12 mo) samples of 7 pts (6F), aged 54 ± 22 yrs with SBP 132 ± 15 mmHg, UACR 48 ± 73 mg/g, eGFR was assessed via the 2021 CKD Epi formulas for Creat (74 ± 35), Beta 2 microglobulin (65.5 ± 30), Creat/Cystatin (86.53 ± 39).
Protein coding and long non coding (lncRNA) RNAs were the most frequently encountered RNA species (14-20% and 8-9% respectively).
Correlation of the counts between follow up & baseline samples was high (>0.89). NBME estimates of the effects of eGFR on counts were correlated highly with each other, correlated moderately with UACR and not correlated with SBP[fig]. Term analysis mapped the differentially expressed RNAs (>70% lncRNA) to trascriptional factors and the lysine degradation pathway (including several lysine methyltransferases) that has been recently implicated in the pathogenesis of CKD (PMC9283537) and podocyte injury (PMC9086358).
Conclusion
Nanopore sequencing provides a cheap, portable, platform for novel RNA biomarker discovery & quantification in CKD.
Funding
- Other NIH Support – Dialysis Clinic Inc, #C-3765