Widespread Translational Control of Fibrosis in the Human Heart by RNA-Binding Proteins

Abstract

◼ fibrosis ◼ ribosome profiling ◼ RNAbinding proteins ◼ TGF-beta1 Sources of Funding, see page 949 BACKGROUND: Fibrosis is a common pathology in many cardiac disorders and is driven by the activation of resident fibroblasts. The global posttranscriptional mechanisms underlying fibroblast-to-myofibroblast conversion in the heart have not been explored. METHODS: Genome-wide changes of RNA transcription and translation during human cardiac fibroblast activation were monitored with RNA sequencing and ribosome profiling. We then used RNA-binding proteinbased analyses to identify translational regulators of fibrogenic genes. The integration with cardiac ribosome occupancy levels of 30 dilated cardiomyopathy patients demonstrates that these posttranscriptional mechanisms are also active in the diseased fibrotic human heart. RESULTS: We generated nucleotide-resolution translatome data during the transforming growth factor β1-driven cellular transition of human cardiac fibroblasts to myofibroblasts. This identified dynamic changes of RNA transcription and translation at several time points during the fibrotic response, revealing transient and early-responder genes. Remarkably, about one-third of all changes in gene expression in activated fibroblasts are subject to translational regulation, and dynamic variation in ribosome occupancy affects protein abundance independent of RNA levels. Targets of RNA-binding proteins were strongly enriched in posttranscriptionally regulated genes, suggesting genes such as MBNL2 can act as translational activators or repressors. Ribosome occupancy in the hearts of patients with dilated cardiomyopathy suggested the same posttranscriptional regulatory network was underlying cardiac fibrosis. Key network hubs include RNAbinding proteins such as Pumilio RNA binding family member 2 (PUM2) and Quaking (QKI) that work in concert to regulate the translation of target transcripts in human diseased hearts. Furthermore, silencing of both PUM2 and QKI inhibits the transition of fibroblasts toward profibrotic myofibroblasts in response to transforming growth factor β1. CONCLUSIONS: We reveal widespread translational effects of transforming growth factor β1 and define novel posttranscriptional regulatory networks that control the fibroblast-to-myofibroblast transition. These networks are active in human heart disease, and silencing of hub genes limits fibroblast activation. Our findings show the central importance of translational control in fibrosis and highlight novel pathogenic mechanisms in heart failure.

Transcontrol of cardiac mRNA translation in a protein length-dependent fashion

“…This locus furthermore co-localized with a highly replicated QTL for cardiac mass (Inomata et al, 2005;Siegel et al, 2003), for which a loss-of-function insertion in endonuclease G (Endog) was previously identified as a driver of cardiomyocyte hypertrophy and increased left-ventricular weight (McDermott-Roe et al, 2011). Among all genes associated with this master regulatory teQTL, we found strong enrichment for extracellular matrix (ECM) proteins (11 out of 25; GO:0031012; p adj = 3.32 × 10 -10 ) (Figure 2A and 2B), consistent with recent observations of strong translational control of fibrotic processes in human hearts (Chothani et al, 2019;Heesch et al, 2019).…”

deltaTE: Detection of Translationally Regulated Genes by Integrative Analysis of Ribo‐seq and RNA‐seq Data

“…However, this approach does not take into account the variance, low expression of RPFs or mRNA counts, or batch effects, severely compromising the accuracy of detection. Several other approaches to detect DTEGs by modeling changes in TE have Chothani et al (Chothani et al, 2019), four pair-wise comparisons)…”

“…However, in the presence of a batch effect or based on the data from Xiao et al (2016), TE is superior. To further verify that this effect is not confined to simulated data, we analyzed RNAseq and Ribo-seq data derived from our recent study on cardiac fibrosis (Chothani et al, 2019). This experiment contained cardiac fibroblasts from four different individuals, and, as a result, has a pronounced patient-related batch effect accounting for roughly 25% of the variance within the data.…”

Decreased MiR-30a promotes TGF-β1-mediated arachnoid fibrosis in post-hemorrhagic hydrocephalus

“…Other studies also showed that circulating miR-103a-3p leads to angiotensin II-induced renal inflammation and fibrosis through an SNRK/NF-κB/p65 regulatory axis. LncRNAAK081284, miR-489, and miR-455 influence cardiac fibrosis [ 39 , 40 , 41 ]. However, the roles of noncoding RNAs in arachnoid fibrosis and hydrocephalus remain unclear.…”