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Verma SK, Kuyumcu-Martinez MN. RNA binding proteins in cardiovascular development and disease. Curr Top Dev Biol 2024; 156:51-119. [PMID: 38556427 DOI: 10.1016/bs.ctdb.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/02/2024]
Abstract
Congenital heart disease (CHD) is the most common birth defect affecting>1.35 million newborn babies worldwide. CHD can lead to prenatal, neonatal, postnatal lethality or life-long cardiac complications. RNA binding protein (RBP) mutations or variants are emerging as contributors to CHDs. RBPs are wizards of gene regulation and are major contributors to mRNA and protein landscape. However, not much is known about RBPs in the developing heart and their contributions to CHD. In this chapter, we will discuss our current knowledge about specific RBPs implicated in CHDs. We are in an exciting era to study RBPs using the currently available and highly successful RNA-based therapies and methodologies. Understanding how RBPs shape the developing heart will unveil their contributions to CHD. Identifying their target RNAs in the embryonic heart will ultimately lead to RNA-based treatments for congenital heart disease.
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Affiliation(s)
- Sunil K Verma
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States.
| | - Muge N Kuyumcu-Martinez
- Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine Charlottesville, VA, United States; Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA, United States; University of Virginia Cancer Center, Charlottesville, VA, United States.
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Bajpai AK, Gu Q, Orgil BO, Alberson NR, Towbin JA, Martinez HR, Lu L, Purevjav E. Exploring the Regulation and Function of Rpl3l in the Development of Early-Onset Dilated Cardiomyopathy and Congestive Heart Failure Using Systems Genetics Approach. Genes (Basel) 2023; 15:53. [PMID: 38254943 PMCID: PMC10815855 DOI: 10.3390/genes15010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 12/25/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
BACKGROUND Cardiomyopathies, diseases affecting the myocardium, are common causes of congestive heart failure (CHF) and sudden cardiac death. Recently, biallelic variants in ribosomal protein L3-like (RPL3L) have been reported to be associated with severe neonatal dilated cardiomyopathy (DCM) and CHF. This study employs a systems genetics approach to gain understanding of the regulatory mechanisms underlying the role of RPL3L in DCM. METHODS Genetic correlation, expression quantitative trait loci (eQTL) mapping, differential expression analysis and comparative functional analysis were performed using cardiac gene expression data from the patients and murine genetic reference populations (GRPs) of BXD mice (recombinant inbred strains from a cross of C57BL/6J and DBA/2J mice). Additionally, immune infiltration analysis was performed to understand the relationship between DCM, immune cells and RPL3L expression. RESULTS Systems genetics analysis identified high expression of Rpl3l mRNA, which ranged from 11.31 to 12.16 across murine GRPs of BXD mice, with an ~1.8-fold difference. Pathways such as "diabetic cardiomyopathy", "focal adhesion", "oxidative phosphorylation" and "DCM" were significantly associated with Rpl3l. eQTL mapping suggested Myl4 (Chr 11) and Sdha (Chr 13) as the upstream regulators of Rpl3l. The mRNA expression of Rpl3l, Myl4 and Sdha was significantly correlated with multiple echocardiography traits in BXD mice. Immune infiltration analysis revealed a significant association of RPL3L and SDHA with seven immune cells (CD4, CD8-naive T cell, CD8 T cell, macrophages, cytotoxic T cell, gamma delta T cell and exhausted T cell) that were also differentially infiltrated between heart samples obtained from DCM patients and normal individuals. CONCLUSIONS RPL3L is highly expressed in the heart tissue of humans and mice. Expression of Rpl3l and its upstream regulators, Myl4 and Sdha, correlate with multiple cardiac function traits in murine GRPs of BXD mice, while RPL3L and SDHA correlate with immune cell infiltration in DCM patient hearts, suggesting important roles for RPL3L in DCM and CHF pathogenesis via immune inflammation, necessitating experimental validations of Myl4 and Sdha in Rpl3l regulation.
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Affiliation(s)
- Akhilesh K. Bajpai
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Qingqing Gu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Buyan-Ochir Orgil
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Neely R. Alberson
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Jeffrey A. Towbin
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
- Cardiology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Hugo R. Martinez
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
| | - Lu Lu
- Department of Genetics, Genomics and Informatics, University of Tennessee Health Science Center, Memphis, TN 38103, USA; (A.K.B.); (Q.G.)
| | - Enkhsaikhan Purevjav
- The Heart Institute, Le Bonheur Children’s Hospital, University of Tennessee Health and Science Center, Memphis, TN 38103, USA; (B.-O.O.); (N.R.A.); (J.A.T.); (H.R.M.)
- Children’s Foundation Research Institute, Le Bonheur Children’s Hospital, Memphis, TN 38103, USA
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Baldwin TA, Teuber JP, Kuwabara Y, Subramani A, Lin SCJ, Kanisicak O, Vagnozzi RJ, Zhang W, Brody MJ, Molkentin JD. Palmitoylation-dependent regulation of cardiomyocyte Rac1 signaling activity and minor effects on cardiac hypertrophy. J Biol Chem 2023; 299:105426. [PMID: 37926281 PMCID: PMC10716590 DOI: 10.1016/j.jbc.2023.105426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/28/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023] Open
Abstract
S-palmitoylation is a reversible lipid modification catalyzed by 23 S-acyltransferases with a conserved zinc finger aspartate-histidine-histidine-cysteine (zDHHC) domain that facilitates targeting of proteins to specific intracellular membranes. Here we performed a gain-of-function screen in the mouse and identified the Golgi-localized enzymes zDHHC3 and zDHHC7 as regulators of cardiac hypertrophy. Cardiomyocyte-specific transgenic mice overexpressing zDHHC3 show cardiac disease, and S-acyl proteomics identified the small GTPase Rac1 as a novel substrate of zDHHC3. Notably, cardiomyopathy and congestive heart failure in zDHHC3 transgenic mice is preceded by enhanced Rac1 S-palmitoylation, membrane localization, activity, downstream hypertrophic signaling, and concomitant induction of all Rho family small GTPases whereas mice overexpressing an enzymatically dead zDHHC3 mutant show no discernible effect. However, loss of Rac1 or other identified zDHHC3 targets Gαq/11 or galectin-1 does not diminish zDHHC3-induced cardiomyopathy, suggesting multiple effectors and pathways promoting decompensation with sustained zDHHC3 activity. Genetic deletion of Zdhhc3 in combination with Zdhhc7 reduces cardiac hypertrophy during the early response to pressure overload stimulation but not over longer time periods. Indeed, cardiac hypertrophy in response to 2 weeks of angiotensin-II infusion is not diminished by Zdhhc3/7 deletion, again suggesting other S-acyltransferases or signaling mechanisms compensate to promote hypertrophic signaling. Taken together, these data indicate that the activity of zDHHC3 and zDHHC7 at the cardiomyocyte Golgi promote Rac1 signaling and maladaptive cardiac remodeling, but redundant signaling effectors compensate to maintain cardiac hypertrophy with sustained pathological stimulation in the absence of zDHHC3/7.
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Affiliation(s)
- Tanya A Baldwin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - James P Teuber
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Yasuhide Kuwabara
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Araskumar Subramani
- Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA
| | - Suh-Chin J Lin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Onur Kanisicak
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pathology, University of Cincinnati, Cincinnati, Ohio, USA
| | - Ronald J Vagnozzi
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Division of Cardiology, Department of Medicine, Consortium for Fibrosis Research & Translation, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Weiqi Zhang
- Laboratory of Molecular Psychiatry, Department of Mental Health, University of Münster, Münster, Germany
| | - Matthew J Brody
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA; Department of Pharmacology, University of Michigan, Ann Arbor, Michigan, USA; Division of Cardiovascular Medicine, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA.
| | - Jeffery D Molkentin
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.
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Shiraishi C, Matsumoto A, Ichihara K, Yamamoto T, Yokoyama T, Mizoo T, Hatano A, Matsumoto M, Tanaka Y, Matsuura-Suzuki E, Iwasaki S, Matsushima S, Tsutsui H, Nakayama KI. RPL3L-containing ribosomes determine translation elongation dynamics required for cardiac function. Nat Commun 2023; 14:2131. [PMID: 37080962 PMCID: PMC10119107 DOI: 10.1038/s41467-023-37838-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 04/03/2023] [Indexed: 04/22/2023] Open
Abstract
Although several ribosomal protein paralogs are expressed in a tissue-specific manner, how these proteins affect translation and why they are required only in certain tissues have remained unclear. Here we show that RPL3L, a paralog of RPL3 specifically expressed in heart and skeletal muscle, influences translation elongation dynamics. Deficiency of RPL3L-containing ribosomes in RPL3L knockout male mice resulted in impaired cardiac contractility. Ribosome occupancy at mRNA codons was found to be altered in the RPL3L-deficient heart, and the changes were negatively correlated with those observed in myoblasts overexpressing RPL3L. RPL3L-containing ribosomes were less prone to collisions compared with RPL3-containing canonical ribosomes. Although the loss of RPL3L-containing ribosomes altered translation elongation dynamics for the entire transcriptome, its effects were most pronounced for transcripts related to cardiac muscle contraction and dilated cardiomyopathy, with the abundance of the encoded proteins being correspondingly decreased. Our results provide further insight into the mechanisms and physiological relevance of tissue-specific translational regulation.
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Affiliation(s)
- Chisa Shiraishi
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Akinobu Matsumoto
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
| | - Kazuya Ichihara
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Taishi Yamamoto
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Takeshi Yokoyama
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Taisuke Mizoo
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Atsushi Hatano
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Masaki Matsumoto
- Department of Omics and Systems Biology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Niigata, 951-8510, Japan
| | - Yoshikazu Tanaka
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, 980-8577, Japan
| | - Eriko Matsuura-Suzuki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama, 351-0198, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba, 277-8561, Japan
| | - Shouji Matsushima
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Hiroyuki Tsutsui
- Department of Cardiovascular Medicine, Faculty of Medical Sciences, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan
| | - Keiichi I Nakayama
- Division of Cell Biology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Fukuoka, 812-8582, Japan.
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