RNA binding protein 24 deletion disrupts global alternative splicing and causes dilated cardiomyopathy

Abstract

RNA splicing contributes to a broad spectrum of posttranscriptional gene regulation during normal development, as well as pathological manifestation of heart diseases. However, the functional role and regulation of splicing in heart failure remain poorly understood. RNA binding protein (RBP), a major component of the splicing machinery, is a critical factor in this process. RNA binding motif protein 24 (RBM24) is a tissue-specific RBP which is highly expressed in human and mouse heart. Previous studies demonstrated the functional role of RBM24 in the embryonic heart development. However, the role of RBM24 in postnatal heart development and heart disease has not been investigated. In this paper, using conditional RBM24 knockout mice, we demonstrated that ablation of RBM24 in postnatal heart led to rapidly progressive dilated cardiomyopathy (DCM), heart failure, and postnatal lethality. Global splicing profiling revealed that RBM24 regulated a network of genes related to cardiac function and diseases. Knockout of RBM24 resulted in misregulation of these splicing transitions which contributed to the subsequent development of cardiomyopathy. Notably, our analysis identified RBM24 as a splice factor that determined the splicing switch of a subset of genes in the sacomeric Z-disc complex, including Titin, the major disease gene of DCM and heart failure. Together, this study identifies regulation of RNA splicing by RBM24 as a potent player in remodeling of heart during postnatal development, and provides novel mechanistic insights to the pathogenesis of DCM.

Keywords

RNA binding protein / RBM24 / dilated cardiomyopathy / alternative splicing / heart failure

References

[1] Anderson BR, Granzier HL (2012) Titin-based tension in the cardiac sarcomere: molecular origin and physiological adaptations. Prog Biophys Mol Biol 110(2–3):204–217

[2] Arimura T, Takeya R, Ishikawa T, Yamano T, Matsuo A, Tatsumi T, Nomura T, Sumimoto H, Kimura A (2013) Dilated cardiomyopathy-associated FHOD3 variant impairs the ability to induce activation of transcription factor serum response factor. Circ J 77(12):2990–2996

[3] Benz PM, Merkel CJ, Offner K, Abeßer M, Ullrich M, Fischer T, Bayer B, Wagner H, Gambaryan S, Ursitti JA (2013) Mena/VASP and alphaII-Spectrin complexes regulate cytoplasmic actin networks in cardiomyocytes and protect from conduction abnormalities and dilated cardiomyopathy. Cell Commun Signal 11:56

[4] Beqqali A, Bollen IAE, Rasmussen TB, van den Hoogenhof MM, van Deutekom HWM, Schafer S, Haas J, Meder B, Sørensen KE, van Oort RJ (2016) A mutation in the glutamate-rich region of RNA-binding motif protein 20 causes dilated cardiomyopathy through missplicing of titin and impaired Frank-Starling mechanism. Cardiovasc Res 112(1):452–463

[5] Bienengraeber M, Olson TM, Selivanov VA, Kathmann EC, O’Cochlain F, Gao F, Karger AB, Ballew JD, Hodgson DM, Zingman LV (2004) ABCC9 mutations identified in human dilated cardiomyopathy disrupt catalytic KATP channel gating. Nat Genet 36(4):382–387

[6] Blech-Hermoni Y, Ladd AN (2013) RNA binding proteins in the regulation of heart development. Int J Biochem Cell Biol 45(11):2467–2478

[7] Cheng G, Takahashi M, Shunmugavel A, Wallenborn JG, DePaoli-Roach AA, Gergs U, Neumann J, Kuppuswamy D, Menick DR, Cooper G (2010) Basis for MAP4 dephosphorylation-related microtubule network densification in pressure overload cardiac hypertrophy. J Biol Chem 285(49):38125–38140

[8] Cooper TA (2005) Alternative splicing regulation impacts heart development. Cell 120(1):1–2

[9] Gao C, Ren S, Lee JH, Qiu J, Chapski DJ, Rau CD, Zhou Y, Abdellatif M, Nakano A, Vondriska TM (2016) RBFox1-mediated RNA splicing regulates cardiac hypertrophy and heart failure. J Clin Invest 126(1):195–206

[10] Gregorio CC, Trombitás K, Centner T, Kolmerer B, Stier G, Kunke K, Suzuki K, Obermayr F, Herrmann B, Granzier H (1998) The NH2 terminus of titin spans the Z-disc: its interaction with a novel 19-kD ligand (T-cap) is required for sarcomeric integrity. J Cell Biol 143(4):1013–1027

[11] Guo W, Schafer S, Greaser ML, Radke MH, Liss M, Govindarajan T, Maatz H, Schulz H, Li S, Parrish AM (2012) RBM20, a gene for hereditary cardiomyopathy, regulates titin splicing. Nat Med 18(5):766–773

[12] Hallegger M, Llorian M, Smith CW (2010) Alternative splicing: global insights. FEBS J 277(4):856–866

[13] Kalsotra A, Cooper TA (2011) Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet 12(10):715–729

[14] Knöll R, Hoshijima M, Hoffman HM, Person V, Lorenzen-Schmidt I, Bang ML, Hayashi T, Shiga N, Yasukawa H, Schaper W (2002) The cardiac mechanical stretch sensor machinery involves a Z disc complex that is defective in a subset of human dilated cardiomyopathy. Cell 111(7):943–955

[15] Kong SW, Hu YW, Ho JW, Ikeda S, Polster S, John R, Hall JL, Bisping E, Pieske B, dos Remedios CG (2010) Heart failureassociated changes in RNA splicing of sarcomere genes. Circ Cardiovasc Genet 3(2):138–146

[16] Lara-Pezzi E, Gómez-Salinero J, Gatto A, García-Pavía P (2013) The alternative heart: impact of alternative splicing in heart disease. J Cardiovasc Transl Res 6(6):945–955

[17] LeMasters KE, Blech-Hermoni Y, Stillwagon SJ, Vajda NA, Ladd AN (2012) Loss of muscleblind-like 1 promotes invasive mesenchyme formation in endocardial cushions by stimulating autocrine TGFbeta3. BMC Dev Biol 12:22

[18] Lin Y, Tan KT, Liu J, Kong X, Huang Z, Xu XQ (2017) Global profiling of Rbm24 bound RNAs uncovers a multi-tasking RNA binding protein. Int J Biochem Cell Biol 94:10–21

[19] Liu J, Kong X, Lee YM, Zhang MK, Guo LY, Lin Y, Lim TK, Lin Q, Xu XQ (2017a) Stk38 modulates Rbm24 protein stability to regulate sarcomere assembly in cardiomyocytes. Sci Rep 7:44870

[20] Liu JS, Fan LL, Zhang H, Liu X, Huang H, Tao LJ, Xia K, Xiang R (2017b) Whole-exome sequencing identifies two novel TTN mutations in Chinese families with dilated cardiomyopathy. Cardiology 136(1):10–14

[21] Mayr JA, Merkel O, Kohlwein SD, Gebhardt BR, Böhles H, Fötschl U, Koch J, Jaksch M, Lochmüller H, Horváth R (2007) Mitochondrial phosphate-carrier deficiency: a novel disorder of oxidative phosphorylation. Am J Hum Genet 80(3):478–484

[22] Ong SB, Kalkhoran SB, Hernández-Reséndiz S, Samangouei P, Ong SG, Hausenloy DJ (2017) Mitochondrial-shaping proteins in cardiac health and disease—the long and the short of it! Cardiovasc Drugs Ther 31(1):87–107

[23] Poon KL, Tan KT, Wei YY, Ng CP, Colman A, Korzh V, Xu XQ (2012) RNA-binding protein RBM24 is required for sarcomere assembly and heart contractility. Cardiovasc Res 94(3):418–427

[24] Purevjav E, Varela J, Morgado M, Kearney DL, Li H, Taylor MD, Arimura T, Moncman CL, McKenna W, Murphy RT (2010) Nebulette mutations are associated with dilated cardiomyopathy and endocardial fibroelastosis. J Am Coll Cardiol 56(18):1493–1502

[25] Ray D, Kazan H, Cook KB, Weirauch MT, Najafabadi HS, Li X, Gueroussov S, Albu M, Zheng H, Yang A (2013) A compendium of RNA-binding motifs for decoding gene regulation. Nature 499(7457):172–177

[26] Roberts AM, Ware JS, Herman DS, Schafer S, Baksi J, Bick AG, Buchan RJ, Walsh R, John S, Wilkinson S (2015) Integrated allelic, transcriptional, and phenomic dissection of the cardiac effects of titin truncations in health and disease. Sci Transl Med 7(270):270–276

[27] Tayal U, Prasad S, Cook SA (2017) Genetics and genomics of dilated cardiomyopathy and systolic heart failure. Genome Med 9(1):20

[28] Wang J, Xu N, Feng X, Hou N, Zhang J, Cheng X, Chen Y, Zhang Y, Yang X (2005) Targeted disruption of Smad4 in cardiomyocytes results in cardiac hypertrophy and heart failure. Circ Res 97(8):821–828

[29] Wei C, Qiu J, Zhou Y, Xue Y, Hu J, Ouyang K, Banerjee I, Zhang C, Chen B, Li H (2015) Repression of the central splicing regulator RBFox2 is functionally linked to pressure overloadinduced heart failure. Cell Rep 10:1521–1533

[30] Weintraub RG, Semsarian C, Macdonald P (2017) Dilated cardiomyopathy. Lancet 16:31713–31715

[31] Wells QS, Becker JR, Su YR, Mosley JD, Weeke P, D’Aoust L, Ausborn NL, Ramirez AH, Pfotenhauer JP, Naftilan AJ (2013) Whole exome sequencing identifies a causal RBM20 mutation in a large pedigree with familial dilated cardiomyopathy. Circ Cardiovasc Genet 6(4):317–326

[32] Xu XQ, Soo SY, Sun W, Zweigerdt R (2009) Global expression profile of highly enriched cardiomyocytes derived from human embryonic stem cells. Stem Cells 27(9):2163–2174

[33] Xu XQ, Zweigerdt R, Xu XQ, Zweigerdt R, Soo SY, Ngoh ZX, Tham SC, Wang ST, Graichen R, Davidson B (2008) Highly enriched cardiomyocytes from human embryonic stem cells. Cytotherapy 10(4):376–389

[34] Yang J, Hung L-H, Licht T, Kostin S, Looso M, Khrameeva E, Bindereif A, Schneider A, Braun T (2014) RBM24 is a major regulator of muscle-specific alternative splicing. Dev Cell 31(1):87–99

[35] Zhang T, Lin Y, Liu J, Zhang ZG, Fu W, Guo LY, Pan L, Kong X, Zhang MK, Lu YH (2016) Rbm24 regulates alternative splicing switch in embryonic stem cell cardiac lineage differentiation. Stem Cells 34(7):1776–1789

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