Widespread translational control of fibrosis in the human heart by RNA-binding proteins

Chothani, Sonia, Schäfer, Sebastian, Adami, Eleonora, Viswanathan, Sivakumar, Widjaja, Anissa A., Langley, Sarah R., Tan, Jessie, Wang, Mao, Quaife, Nicholas M., Jian Pua, Chee, D’agostino, Giuseppe, Guna Shekeran, Shamini, George, Benjamin L., Lim, Stella, Yiqun Cao, Elaine, Van Heesch, Sebastiaan, Witte, Franziska, Felkin, Leanne E., Christodoulou, Eleni G., Dong, Jinrui, Blachut, Susanne, Patone, Giannino, Barton, Paul J.r., Hubner, Norbert, Cook, Stuart A. and Rackham, Owen J.l. (2019) Widespread translational control of fibrosis in the human heart by RNA-binding proteins. Circulation, 140 (11), 937-951. (doi:10.1161/CIRCULATIONAHA.119.039596).

Abstract

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 protein-based 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 RNA-binding 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.

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Contributors

Author: Owen J.l. Rackham

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