Non-Coding RNA and CKD Progression
The burden of Chronic Kidney Disease (CKD) on the United States is very high with an estimated prevalence of 37 million. Decreased GFR is a powerful risk factor for cardiovascular outcomes and death. The total cost of managing CKD and its attendant complications are enormous. Kidney fibrosis is the final common pathway downstream of most renal injuries that contributes to progressive CKD. Prevention and reversal of kidney fibrosis are key strategies for the treatment of CKD that are likely to have a major impact on the progression of CKD.
Noncoding RNAs (ncRNA) such as long noncoding RNAs (lncRNA) and microRNAs (miRNA) play important roles in a wide range of biological processes. miRNAs regulate kidney fibrosis through direct repression and/or expression of matrix genes and through TGF-β signaling. LncRNAs modulate several physiological and pathogenic processes in the kidney. Importantly, targeting a lncRNA can control the expression of the host lncRNA, miRNAs, their targets and profibrotic genes.
Supported by the R01 grant from The National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) at the National Institutes of Health, this translational study is designed to discover ncRNAs as early biomarker of fibrosis, which could lead to targeted ncRNA-based therapies for CKD.
The aims of the study are as follows:
For Aim 1, we will employ an agnostic next-generation sequencing (NGS) to profile EncRNAs in blood and urine samples from a discovery cohort of 192 CRIC study participants exhibiting rapid progression of CKD and 191 study participants with slowest rate of loss of kidney function to characterize the circulating and urinary EncRNA profile associated with progression of CKD in CRIC study participants.
For Aim 2, we will replicate the top CKD progression-related circulating/urinary EncRNA discoveries (from Aim 1) in 3,088 CRIC study participants using quantitative RT-PCR.
For Aim 3, we will employ innovative in vitro experiments and in vivo gain and loss of function experiments in mouse models to identify targets and validate the functional significance of the EncRNA discoveries from human studies.
For Aim 4 we will verify the expression level of the top EncRNA discoveries in microdissected CKD kidney tissues. These samples will be chosen from ~1,600 samples form the kidney biorepository that are linked to clinical, histopathological and demographic information.
Non-coding RNA and CKD Progression
Acute kidney injury and microbiome
Acute kidney Injury (AKI) associated morbidity and mortality exerts a major clinical problem that involves multiple overlapping pathophysiological mechanisms. Understanding gut microbiota-kidney crosstalk during AKI or during recovery can prove to be a crucial step to improve patient outcomes.
With the R01 grant support from NIDDK (NIH) and in collaboration with Hamid Rabb (PI) from the Johns Hopkins University, we are examining the intestinal microbiota-kidney crosstalk in acute kidney.
Using mice models and human subjects we are aiming to identify microbial communities and metabolic components involved in the cross-talk to set the stage for novel therapeutics. Focusing on immune cell regulation and short-chain fatty acids/receptors signaling we hope to further our understanding the role of gut microbiota in initiation and progression of acute kidney injury.
Successful completion of these studies will help understand immunological effects of gut microbiota-kidney crosstalk and will open tremendous opportunity for novel treatment options involving SCFAs and targeting intestinal microbiota.
Cell free DNA Methylation Profile in Kidney Transplant Rejection
Long-term kidney allograft failure remains a major concern despite potent immunosuppression regimens. Protocol allograft biopsies at fixed time points from transplantation have provided insight into pathogenesis of allograft dysfunction and guided clinical management. However, transplant biopsy is used infrequently for surveillance because of the cost, logistics and potential complications.
Cell-free DNA (cfDNA) refers to fragments of DNA in the bloodstream that originate from cells undergoing cell injury and death. Donor-derived cfDNA (dcf-DNA) detected in the blood of transplant recipients has been proposed as a noninvasive marker for diagnosis of allograft rejection. We previously showed that DNA methylation is associated with progression of CKD. Epigenome could predict disease susceptibility and also specific epigenetic signature could be associated with disease states. Thus, serial determination of DNA methylation profile could provide invaluable insight and may be useful in identifying high risk subjects prone for rejection episodes. Since the effector cell types and target cells in acute cellular rejection (ACR), antibody mediated rejection (AMR) chronic allograft nephropathy (CAN) are different, determining methylation profile of cfDNA could be used as a diagnostic tool for non-invasive diagnosis of ACR, AMR and CAN.
In a longitudinal observational study we aim to characterize the DNA dcf-DNA methylation profile signature and explore their utility in the diagnosis of ACR, AMR and CAN. Genome-wide DNA methylation profile in kidney allograft will be assessed to interrogate 850,000 methylation sites in individuals with biopsy proven ACR, AMR CAN and individuals who never experienced rejection during the follow-up period (control).
Successful completion of the study will likely lead to the discovery of novel biomarkers for the identification of patients at risk for rejection and non-invasive diagnosis of ACR, AMR and CAR.