Diabetic kidney disease (DKD) is a serious disease that presents a major health problem worldwide. There is a desperate need to explore novel biomarkers to further facilitate the early diagnosis and effective treatment in DKD patients so that to prevent them to develop end-stage renal disease (ESRD). However, most of regulation mechanisms at genetic level in DKD still remain unclear. In this work-in-progress paper, we describe our innovative methodologies that integrate biological, statistics, and computational approaches to investigate important roles performed by regulations among microRNAs (miRs), long non-coding RNAs (lncRNAs), and messenger RNAs (mRNAs) in DKD. We conducted a series of experiments and identified a list of miRs and lncRNAs as potential novel biomarkers, along with the set of target genes regulated by discovered miRs. Our initial analysis results are promising in better understanding regulation mechanisms of miRs and lncRNAs on the pathogenesis and progression of DKD.