Histologically resolved small RNA maps in primary focal segmental glomerulosclerosis indicate progressive changes within glomerular and tubulointerstitial regions Liang and Colleagues, Kidney Int., 2022 Abstract Pathological heterogeneity is common in clinical tissue specimens and complicates the interpretation of molecular data obtained from the specimen. As a typical example, a kidney biopsy specimen often contains glomeruli [...]
KrasG12D induces changes in chromatin territories that differentially impact early nuclear reprogramming in pancreatic cells Urrutia and Colleges, Genome Biol, 2021 Abstract Background: Pancreatic ductal adenocarcinoma initiation is most frequently caused by Kras mutations. Results: Here, we apply biological, biochemical, and network biology methods to validate GEMM-derived cell models using inducible KrasG12D expression. We describe the time-dependent, chromatin remodeling [...]
Whole-genome sequencing in diverse subjects identifies genetic correlates of leukocyte traits: The NHLBI TOPMed program Auer and colleagues, Am J Hum Genet, 2021 Many common and rare variants associated with hematologic traits have been discovered through imputation on large-scale reference panels. However, the majority of genome-wide association studies (GWASs) have been conducted in Europeans, and determining causal variants has [...]
Dietary Sodium Restriction Results in Tissue-Specific Changes in DNA Methylation in Humans Kidambi and colleagues. Hypertension. 2021 Dietary sodium affects blood pressure (BP) and vascular function. Animal studies suggest epigenetic changes (eg, DNA methylation) are involved. We hypothesized that sodium restriction induces methylation changes in T cells and arterioles in humans. Fifty subjects (49% women) [...]
KPT-330 Prevents Aortic Valve Calcification via a Novel C/EBPβ Signaling Pathway. Lincoln and colleagues. Circ Res. 2021 Rationale: Calcific aortic valve disease (CAVD) affects >5.2 million people in the United States. The only effective treatment is surgery, and this comes with complications and no guarantee of long-term success. Objective: Outcomes from pharmacological initiatives remain unsubstantiated [...]
miRNA551b-3p Activates an Oncostatin Signaling Module for the Progression of Triple-Negative Breast Cancer. Chaluvally-Raghavan and colleagues, Cell Rep. 2019 This publication is based on a genetic misfire of microRNA551b due to genomic amplification in breast and ovarian cancer, which promotes the aggressiveness and metastasis of cancer cells. MicroRNAs appeared to regulate cellular functions through having [...]
DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies. Liu and colleagues, Nucleic Acids Res. 2019. Although rapid progress has been made in computational approaches for prioritizing cancer driver genes, research is far from achieving the ultimate goal of discovering a complete catalog of genes truly associated with cancer. Driver gene lists predicted from these computational tools lack consistency and are prone to false positives. Here, we developed an [...]
MicroRNA-214-3p in the Kidney Contributes to the Development of Hypertension Liang and Colleagues, J Am Soc Nephrol. 2018 Abstract BACKGROUND: In spite of extensive study, the mechanisms for salt sensitivity of BP in humans and rodent models remain poorly understood. Several microRNAs (miRNAs) have been associated with hypertension, but few have been shown to contribute [...]
A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data Liu and Colleagues, Bioinformatics. 2018 Motivation: The rapid development of next-generation sequencing technology provides an opportunity to study genome-wide DNA methylation at single-base resolution. However, depletion of unmethylated cytosines brings challenges for aligning bisulfite-converted sequencing reads to a large reference. Software tools for [...]
miR-29 contributes to normal endothelial function and can restore it in cardiometabolic disorders. Liang and Colleagues, EMBO Mol Med. 2018 A team of scientists from multiple departments at MCW recently discovered a novel mechanism for vascular dysfunction in cardiometabolic disorders. They found the microRNA miR-29 was required for normal vascular function. Moreover, miR-29 could [...]