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Lu J, Zhao Q, Wang L, Li J, Wang H, Lv L, Yuan M, Chen Q, Zhang Z, Luo D, Sheng S, Yuan K, Liu G, Liu M, Shi Y, Guo Y, Dong Z. MBNL2 promotes aging-related cardiac fibrosis via inhibited SUMOylation of Krüppel-like factor4. iScience 2024; 27:110163. [PMID: 38974966 PMCID: PMC11226984 DOI: 10.1016/j.isci.2024.110163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/06/2024] [Accepted: 05/29/2024] [Indexed: 07/09/2024] Open
Abstract
Aging-related cardiac fibrosis represents the principal pathological progression in cardiovascular aging. The Muscleblind-like splicing regulator 2 (MBNL2) has been unequivocally established as being associated with cardiovascular diseases. Nevertheless, its role in aging-related cardiac fibrosis remains unexplored. This investigation revealed an elevation of MBNL2 levels in the aged heart and senescent cardiac fibroblasts. Notably, the inhibition of MBNL2 demonstrated a capacity to mitigate H2O2-induced myofibroblast transformation and aging-related cardiac fibrosis. Further mechanistic exploration unveiled that aging heightened the expression of SENP1 and impeded the SUMO1 binding with KLF4, and SUMOylation of KLF4 effectively increased by the inhibition of MBNL2. Additionally, the inhibition of TGF-β1/SMAD3 signaling attenuated the impact of over-expression of MBNL2 in inducing senescence and cardiac fibrosis. MBNL2, by orchestrating SUMOylation of KLF4, upregulating the TGF-β1/SMAD3 signaling pathway, emerges as a significant promoter of aging-related cardiac fibrosis. This discovery identifies a novel regulatory target for managing aging-related cardiac fibrosis.
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Affiliation(s)
- Jing Lu
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Qi Zhao
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Lu Wang
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Jiahao Li
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Hongyan Wang
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Lin Lv
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
- Experimental Animal Center, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
| | - Meng Yuan
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Qiuyu Chen
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Zixin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Health Care Road, Nangang District, Harbin 150081, China
| | - Dankun Luo
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
| | - Siqi Sheng
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Keying Yuan
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Guannan Liu
- Department of Pharmacy, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Mingyu Liu
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Yuanqi Shi
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
| | - Yuanyuan Guo
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
- Department of Cardiology, Department of Geriatrics, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
| | - Zengxiang Dong
- The Key Laboratory of Cardiovascular Disease Acousto-Optic Electromagnetic Diagnosis and Treatment in Heilongjiang Province, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin150001, China
- NHC Key Laboratory of Cell Transplantation, The First Affiliated Hospital of Harbin Medical University, Youzheng Street, Nangang District, Harbin 150001, China
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Gu M, Wang Y, Yu Y. Ovarian fibrosis: molecular mechanisms and potential therapeutic targets. J Ovarian Res 2024; 17:139. [PMID: 38970048 PMCID: PMC11225137 DOI: 10.1186/s13048-024-01448-7] [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: 05/11/2024] [Accepted: 06/03/2024] [Indexed: 07/07/2024] Open
Abstract
Ovarian fibrosis, characterized by the excessive proliferation of ovarian fibroblasts and the accumulation of extracellular matrix (ECM), serves as one of the primary causes of ovarian dysfunction. Despite the critical role of ovarian fibrosis in maintaining the normal physiological function of the mammalian ovaries, research on this condition has been greatly underestimated, which leads to a lack of clinical treatment options for ovarian dysfunction caused by fibrosis. This review synthesizes recent research on the molecular mechanisms of ovarian fibrosis, encompassing TGF-β, extracellular matrix, inflammation, and other profibrotic factors contributing to abnormal ovarian fibrosis. Additionally, we summarize current treatment approaches for ovarian dysfunction targeting ovarian fibrosis, including antifibrotic drugs, stem cell transplantation, and exosomal therapies. The purpose of this review is to summarize the research progress on ovarian fibrosis and to propose potential therapeutic strategies targeting ovarian fibrosis for the treatment of ovarian dysfunction.
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Affiliation(s)
- Mengqing Gu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Ministry of Education, Beijing, 100191, China
- Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Yibo Wang
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Ministry of Education, Beijing, 100191, China.
- Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191, China.
- Institute of Obstetrics and Gynecology, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510150, China.
| | - Yang Yu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, Beijing, 100191, China.
- Key Laboratory of Assisted Reproduction (Peking University), Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Ministry of Education, Beijing, 100191, China.
- Clinical Stem Cell Research Center, Peking University Third Hospital, Beijing, 100191, China.
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
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Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
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Acharya P, Parkins S, Tranter M. RNA binding proteins as mediators of pathological cardiac remodeling. Front Cell Dev Biol 2024; 12:1368097. [PMID: 38818408 PMCID: PMC11137256 DOI: 10.3389/fcell.2024.1368097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
RNA binding proteins (RBPs) play a central in the post-transcriptional regulation of gene expression, which can account for up to 50% of all variations in protein expression within a cell. Following their binding to target RNAs, RBPs most typically confer changes in gene expression through modulation of alternative spicing, RNA stabilization/degradation, or ribosome loading/translation rate. All of these post-transcriptional regulatory processes have been shown to play a functional role in pathological cardiac remodeling, and a growing body of evidence is beginning to identify the mechanistic contribution of individual RBPs and their cardiac RNA targets. This review highlights the mechanisms of RBP-dependent post-transcriptional gene regulation in cardiomyocytes and fibroblasts and our current understanding of how RNA binding proteins functionally contribute to pathological cardiac remodeling.
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Affiliation(s)
- Pooja Acharya
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Sharon Parkins
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Department of Internal Medicine, Division of Cardiovascular Health and Disease, University of Cincinnati College of Medicine, Cincinnati, OH, United States
| | - Michael Tranter
- Department of Molecular Medicine and Therapeutics, The Ohio State University Wexner Medical Center, Columbus, OH, United States
- Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University Wexner Medical Center, Columbus, OH, United States
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Song J, Chen Y, Chen Y, Qiu M, Xiang W, Ke B, Fang X. Wnt/β-catenin Pathway Aggravates Renal Fibrosis by Activating PUM2 Transcription to Repress YME1L-mediated Mitochondrial Homeostasis. Biochem Genet 2024:10.1007/s10528-024-10756-y. [PMID: 38564095 DOI: 10.1007/s10528-024-10756-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024]
Abstract
Chronic kidney disease (CKD) affects more than 10% of people worldwide and is a leading cause of death. However, the pathogenesis of CKD remains elusive. The oxidative stress and mitochondrial membrane potential were detected using Enzyme-linked immunosorbent assay and JC-1 assay. Co-immunoprecipitation, dual-luciferase assay, chromatin IP, RNA IP and RNA pull-down were used to validate the interactions among genes. Exploiting a H2O2-induced fibrosis model in vitro, PUM2 expression was upregulated in Human kidney 2 cell (HK-2) cells, along with reduced cell viability, enhanced oxidative stress, impaired mitochondrial potential, and upregulated expressions of fibrosis-associated proteins. While PUM2 knockdown reversed the H2O2-induced injury in HK-2 cells. Mechanically, Wnt/β-catenin pathway activated PUM2 transcription via TCF4. It was further identified that Wnt/β-catenin pathway inhibited YME1L expression through PUM2-mediated destabilizing of its mRNA. PUM2 aggravated H2O2-induced oxidative stress, mitochondrial dysfunction, and renal fibrosis in HK-2 cell via suppressing YME1L expression. Our study revealed that Wnt/β-catenin aggravated renal fibrosis by activating PUM2 transcription to repress YME1L-mediated mitochondrial homeostasis, providing novel insights and potential therapeutic targets for the treatment of kidney fibrosis.
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Affiliation(s)
- Jianling Song
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yanxia Chen
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Yan Chen
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Minzi Qiu
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Wenliu Xiang
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Ben Ke
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
| | - Xiangdong Fang
- Department of Nephrology, The Second Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, 330006, Jiangxi, China.
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6
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Duan Y, Zhou M, Ye B, Yue K, Qiao F, Wang Y, Lai Q, Wu Y, Cao J, Wu Y, Wang X, Jing C. Hypoxia-induced miR-5100 promotes exosome-mediated activation of cancer-associated fibroblasts and metastasis of head and neck squamous cell carcinoma. Cell Death Dis 2024; 15:215. [PMID: 38485986 PMCID: PMC10940661 DOI: 10.1038/s41419-024-06587-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/18/2024]
Abstract
The invasion-metastasis cascade in head and neck squamous cell carcinoma (HNSCC) is predominantly caused by the interaction between tumor cells and tumor microenvironment, including hypoxia as well as stromal cells. However, the mechanism of hypoxia-activated tumor-stroma crosstalk in HNSCC metastasis remains to be deciphered. Here, we demonstrated that HIF1α was upregulated in HNSCC specimens compared with adjacent normal tissues, whose overexpression was associated with lymph node metastasis and predicted unfavorable prognosis. HIF1α expression correlated positively with the levels of miR-5100 as well as α-SMA, the marker of CAFs. Hypoxia/HIF1α regulated transcriptionally miR-5100 to promote the degradation of its target gene QKI, which acts as a tumor suppressor in HNSCC. Hypoxic HNSCC-derived exosomal miR-5100 promoted the activation of CAFs by orchestrating QKI/AKT/STAT3 axis, which further facilitated HNSCC metastasis. Additionally, miR-5100 derived from plasma exosomes indicated HNSCC malignant progression. In conclusion, our findings illuminate a novel HIF1α/miR-5100/QKI pathway in HNSCC metastasis, and suggest that miR-5100 might be a potential biomarker and therapeutic target for HNSCC.
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Affiliation(s)
- Yuansheng Duan
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Mengqian Zhou
- Department of Thyroid and Breast Surgery, The Second Hospital of Anhui Medical University, Anhui, 230601, China
| | - Beibei Ye
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Kai Yue
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Feng Qiao
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tianjin Medical University, Tianjin, 300070, China
| | - Yuxuan Wang
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Qingchuan Lai
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Yue Wu
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Jiayan Cao
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China
| | - Yansheng Wu
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China.
| | - Xudong Wang
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China.
| | - Chao Jing
- Department of Maxillofacial and Otorhinolaryngological Oncology, Tianjin Medical University Cancer Institute & Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Basic and Translational Medicine on Head & Neck Cancer, Tianjin, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin, 300060, China.
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Ma W, Tian Y, Shi L, Liang J, Ouyang Q, Li J, Chen H, Sun H, Ji H, Liu X, Huang W, Gao X, Jin X, Wang X, Liu Y, Yu Y, Guo X, Tian Y, Yang F, Li F, Wang N, Cai B. N-Acetyltransferase 10 represses Uqcr11 and Uqcrb independently of ac4C modification to promote heart regeneration. Nat Commun 2024; 15:2137. [PMID: 38459019 PMCID: PMC10923914 DOI: 10.1038/s41467-024-46458-7] [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: 05/12/2023] [Accepted: 02/27/2024] [Indexed: 03/10/2024] Open
Abstract
Translational control is crucial for protein production in various biological contexts. Here, we use Ribo-seq and RNA-seq to show that genes related to oxidative phosphorylation are translationally downregulated during heart regeneration. We find that Nat10 regulates the expression of Uqcr11 and Uqcrb mRNAs in mouse and human cardiomyocytes. In mice, overexpression of Nat10 in cardiomyocytes promotes cardiac regeneration and improves cardiac function after injury. Conversely, treating neonatal mice with Remodelin-a Nat10 pharmacological inhibitor-or genetically removing Nat10 from their cardiomyocytes both inhibit heart regeneration. Mechanistically, Nat10 suppresses the expression of Uqcr11 and Uqcrb independently of its ac4C enzyme activity. This suppression weakens mitochondrial respiration and enhances the glycolytic capacity of the cardiomyocytes, leading to metabolic reprogramming. We also observe that the expression of Nat10 is downregulated in the cardiomyocytes of P7 male pig hearts compared to P1 controls. The levels of Nat10 are also lower in female human failing hearts than non-failing hearts. We further identify the specific binding regions of Nat10, and validate the pro-proliferative effects of Nat10 in cardiomyocytes derived from human embryonic stem cells. Our findings indicate that Nat10 is an epigenetic regulator during heart regeneration and could potentially become a clinical target.
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Affiliation(s)
- Wenya Ma
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
- Institute of Clinical Pharmacy, NHC Key Laboratory of Cell Transplantation, the Heilongjiang Key Laboratory of Drug Research, Harbin Medical University, Harbin, China
| | - Yanan Tian
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Leping Shi
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Jing Liang
- Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
| | - Qimeng Ouyang
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Jianglong Li
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Hongyang Chen
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Hongyue Sun
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Haoyu Ji
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xu Liu
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Laboratory Medicine at The Fourth Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Wei Huang
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xinlu Gao
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xiaoyan Jin
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Xiuxiu Wang
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yining Liu
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Yang Yu
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Xiaofei Guo
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China
| | - Ye Tian
- Department of Pathophysiology and the Key Laboratory of Cardiovascular Pathophysiology, Harbin Medical University, Harbin, China
| | - Fan Yang
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Faqian Li
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN, USA
| | - Ning Wang
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China
| | - Benzhi Cai
- Department of Pharmacy at the Second Affiliated Hospital, Harbin Medical University, Harbin, China.
- Department of Pharmacology at College of Pharmacy (National Key Laboratory of Frigid Zone Cardiovascular Diseases, Key Laboratory of Cardiovascular Research, Ministry of Education), Harbin Medical University, Harbin, China.
- Institute of Clinical Pharmacy, NHC Key Laboratory of Cell Transplantation, the Heilongjiang Key Laboratory of Drug Research, Harbin Medical University, Harbin, China.
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8
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Göransson S, Strömblad S. Regulation of protein synthesis and stability by mechanical cues and its implications in cancer. Curr Opin Cell Biol 2024; 86:102304. [PMID: 38113713 DOI: 10.1016/j.ceb.2023.102304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 11/07/2023] [Accepted: 11/26/2023] [Indexed: 12/21/2023]
Abstract
Elevated tissue stiffness is a common feature of many solid tumors and the downstream mechanical signaling affects many cellular processes and contributes to cancer progression. Significant progress has been made in understanding how the mechanical properties of the matrix affect cancer cell behavior as well as transcription. However, how the same mechanical cues impact protein synthesis and stability and how this may contribute to disease is less well understood. Here, we present emerging evidence that cancer progression is frequently supported by gene regulation acting beyond the mRNA level and highlight some of the known crosstalk between this type of regulation and mechanotransduction in cancer as well as in other contexts. We suggest that future systematic approaches to define mechanosensitive translatomes and proteomes and how these are controlled may provide novel targets for cancer therapy.
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Affiliation(s)
- Sara Göransson
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden
| | - Staffan Strömblad
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-141 83 Huddinge, Sweden.
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9
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Dopkins N, Singh B, Michael S, Zhang P, Marston JL, Fei T, Singh M, Feschotte C, Collins N, Bendall ML, Nixon DF. Ribosomal profiling of human endogenous retroviruses in healthy tissues. BMC Genomics 2024; 25:5. [PMID: 38166631 PMCID: PMC10759522 DOI: 10.1186/s12864-023-09909-x] [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: 06/05/2023] [Accepted: 12/14/2023] [Indexed: 01/05/2024] Open
Abstract
Human endogenous retroviruses (HERVs) are the germline embedded proviral fragments of ancient retroviral infections that make up roughly 8% of the human genome. Our understanding of HERVs in physiology primarily surrounds their non-coding functions, while their protein coding capacity remains virtually uncharacterized. Therefore, we applied the bioinformatic pipeline "hervQuant" to high-resolution ribosomal profiling of healthy tissues to provide a comprehensive overview of translationally active HERVs. We find that HERVs account for 0.1-0.4% of all translation in distinct tissue-specific profiles. Collectively, our study further supports claims that HERVs are actively translated throughout healthy tissues to provide sequences of retroviral origin to the human proteome.
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Affiliation(s)
- Nicholas Dopkins
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA.
| | - Bhavya Singh
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Stephanie Michael
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Panpan Zhang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Jez L Marston
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Tongyi Fei
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Manvendra Singh
- Clinical Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
| | - Cedric Feschotte
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14850, USA
| | - Nicholas Collins
- Jill Roberts Institute for Research in Inflammatory Bowel Disease, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Matthew L Bendall
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
| | - Douglas F Nixon
- Division of Infectious Diseases, Department of Medicine, Weill Cornell Medicine, New York, NY, 10021, USA
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10
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Ruffenach G, Medzikovic L, Sun W, Hong J, Eghbali M. Functions of RNA-Binding Proteins in Cardiovascular Disease. Cells 2023; 12:2794. [PMID: 38132114 PMCID: PMC10742114 DOI: 10.3390/cells12242794] [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: 10/31/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
Gene expression is under tight regulation from the chromatin structure that regulates gene accessibility by the transcription machinery to protein degradation. At the transcript level, this regulation falls on RNA-binding proteins (RBPs). RBPs are a large and diverse class of proteins involved in all aspects of a transcript's lifecycle: splicing and maturation, localization, stability, and translation. In the past few years, our understanding of the role of RBPs in cardiovascular diseases has expanded. Here, we discuss the general structure and function of RBPs and the latest discoveries of their role in pulmonary and systemic cardiovascular diseases.
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Affiliation(s)
- Grégoire Ruffenach
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| | - Lejla Medzikovic
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| | - Wasila Sun
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
| | - Jason Hong
- Department of Pulmonary and Critical Care Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology, Division of Molecular Medicine, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA (W.S.)
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11
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Xie Y, Wang Q, Yang Y, Near D, Wang H, Colon M, Nguyen C, Slattery C, Keepers B, Farber G, Wang TW, Lee SH, Shih YYI, Liu J, Qian L. Translational landscape of direct cardiac reprogramming reveals a role of Ybx1 in repressing cardiac fate acquisition. NATURE CARDIOVASCULAR RESEARCH 2023; 2:1060-1077. [PMID: 38524149 PMCID: PMC10959502 DOI: 10.1038/s44161-023-00344-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 09/06/2023] [Indexed: 03/26/2024]
Abstract
Direct reprogramming of fibroblasts into induced cardiomyocytes holds great promise for heart regeneration. Although considerable progress has been made in understanding the transcriptional and epigenetic mechanisms of iCM reprogramming, its translational regulation remains largely unexplored. Here, we characterized the translational landscape of iCM reprogramming through integrative ribosome and transcriptomic profiling, and found extensive translatome repatterning during this process. Loss of function screening for translational regulators uncovered Ybx1 as a critical barrier to iCM induction. In a mouse model of myocardial infarction, removing Ybx1 enhanced in vivo reprogramming, resulting in improved heart function and reduced scar size. Mechanistically, Ybx1 depletion de-repressed the translation of its direct targets SRF and Baf60c, both of which mediated the effect of Ybx1 depletion on iCM generation. Furthermore, removal of Ybx1 allowed single factor Tbx5-mediated iCM conversion. In summary, this study revealed a new layer of regulatory mechanism that controls cardiac reprogramming at the translational level.
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Affiliation(s)
- Yifang Xie
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Qiaozi Wang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Yuchen Yang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - David Near
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Haofei Wang
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Marazzano Colon
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Christopher Nguyen
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Conor Slattery
- EIRNA Bio Ltd, BioInnovation Centre, Food Science and Technology Building, College Road, Cork, Ireland, T12 DP07
| | - Benjamin Keepers
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
| | - Gregory Farber
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
| | - Tzu-Wen Wang
- Departments of Neurology, University of North Carolina, Chapel Hill, NC 27599
| | - Sung-Ho Lee
- Departments of Neurology, University of North Carolina, Chapel Hill, NC 27599
| | - Yen-Yu Ian Shih
- Departments of Neurology, University of North Carolina, Chapel Hill, NC 27599
| | - Jiandong Liu
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
| | - Li Qian
- McAllister Heart Institute, University of North Carolina, Chapel Hill, NC 27599
- Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599
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12
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Hanquier Z, Misra J, Baxter R, Maiers JL. Stress and Liver Fibrogenesis: Understanding the Role and Regulation of Stress Response Pathways in Hepatic Stellate Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2023; 193:1363-1376. [PMID: 37422148 PMCID: PMC10548279 DOI: 10.1016/j.ajpath.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 05/24/2023] [Accepted: 06/06/2023] [Indexed: 07/10/2023]
Abstract
Stress response pathways are crucial for cells to adapt to physiological and pathologic conditions. Increased transcription and translation in response to stimuli place a strain on the cell, necessitating increased amino acid supply, protein production and folding, and disposal of misfolded proteins. Stress response pathways, such as the unfolded protein response (UPR) and the integrated stress response (ISR), allow cells to adapt to stress and restore homeostasis; however, their role and regulation in pathologic conditions, such as hepatic fibrogenesis, are unclear. Liver injury promotes fibrogenesis through activation of hepatic stellate cells (HSCs), which produce and secrete fibrogenic proteins to promote tissue repair. This process is exacerbated in chronic liver disease, leading to fibrosis and, if unchecked, cirrhosis. Fibrogenic HSCs exhibit activation of both the UPR and ISR, due in part to increased transcriptional and translational demands, and these stress responses play important roles in fibrogenesis. Targeting these pathways to limit fibrogenesis or promote HSC apoptosis is a potential antifibrotic strategy, but it is limited by our lack of mechanistic understanding of how the UPR and ISR regulate HSC activation and fibrogenesis. This article explores the role of the UPR and ISR in the progression of fibrogenesis, and highlights areas that require further investigation to better understand how the UPR and ISR can be targeted to limit hepatic fibrosis progression.
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Affiliation(s)
- Zachary Hanquier
- Department of Molecular and Medical Genetics, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jagannath Misra
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana
| | - Reese Baxter
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana
| | - Jessica L Maiers
- Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana.
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13
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Wang L, Zhou J, Kong L, Ying G, Sha J, Yi D, Zeng J, Xiong W, Wen T. Fibroblast-specific knockout of METTL1 attenuates myocardial infarction-induced cardiac fibrosis. Life Sci 2023; 329:121926. [PMID: 37437652 DOI: 10.1016/j.lfs.2023.121926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Cardiac fibrosis, a common pathology in inherited and acquired heart diseases, necessitates the identification of diagnostic and therapeutic targets. Methyltransferase Like 1 (METTL1), an enzyme responsible for RNA modification by methylating guanosine to form m7G, is an emerging area of research in understanding cellular processes and disease pathogenesis. Dysregulation of m7G modification has been implicated in various diseases. However, the role of METTL1 in cardiac fibrosis remains unclear. This study aimed to investigate the role of METTL1 in myocardial infarction-induced heart failure and cardiac fibrosis. Our findings demonstrate that elevated METTL1-mediated RNA m7G methylation is observed in cardiac fibrosis tissues and TGF-β1-induced cardiac fibroblast proliferation and myofibroblast transformation. Furthermore, fibroblast-specific knockout of METTL1 attenuated myocardial infarction-induced heart failure and cardiac fibrosis. Additionally, METTL1 knockout decreased m7G methylated fibrotic genes and impaired their translation efficiency. These results suggest a novel pro-fibrosis role of METTL1-mediated RNA m7G methylation, highlighting its potential as a therapeutic target in cardiac fibrosis.
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Affiliation(s)
- Liang Wang
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China
| | - Jiamin Zhou
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China
| | - Liming Kong
- Department of Outpatient clinic, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Guoqiu Ying
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China
| | - Juan Sha
- Department of Anesthesia and Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China
| | - Dasong Yi
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China
| | - Junyi Zeng
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China
| | - Wenjun Xiong
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China
| | - Tong Wen
- Department of Cardiology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi 330006, China; Hypertension Research Institute of Jiangxi Province, Nanchang, Jiangxi 330006, China.
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14
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Varma E, Burghaus J, Schwarzl T, Sekaran T, Gupta P, Górska AA, Hofmann C, Stroh C, Jürgensen L, Kamuf-Schenk V, Li X, Medert R, Leuschner F, Kmietczyk V, Freichel M, Katus HA, Hentze MW, Frey N, Völkers M. Translational control of Ybx1 expression regulates cardiac function in response to pressure overload in vivo. Basic Res Cardiol 2023; 118:25. [PMID: 37378715 PMCID: PMC10307726 DOI: 10.1007/s00395-023-00996-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 05/31/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023]
Abstract
RNA-protein interactions are central to cardiac function, but how activity of individual RNA-binding protein is regulated through signaling cascades in cardiomyocytes during heart failure development is largely unknown. The mechanistic target of rapamycin kinase is a central signaling hub that controls mRNA translation in cardiomyocytes; however, a direct link between mTOR signaling and RNA-binding proteins in the heart has not been established. Integrative transcriptome and translatome analysis revealed mTOR dependent translational upregulation of the RNA binding protein Ybx1 during early pathological remodeling independent of mRNA levels. Ybx1 is necessary for pathological cardiomyocyte growth by regulating protein synthesis. To identify the molecular mechanisms how Ybx1 regulates cellular growth and protein synthesis, we identified mRNAs bound to Ybx1. We discovered that eucaryotic elongation factor 2 (Eef2) mRNA is bound to Ybx1, and its translation is upregulated during cardiac hypertrophy dependent on Ybx1 expression. Eef2 itself is sufficient to drive pathological growth by increasing global protein translation. Finally, Ybx1 depletion in vivo preserved heart function during pathological cardiac hypertrophy. Thus, activation of mTORC1 links pathological signaling cascades to altered gene expression regulation by activation of Ybx1 which in turn promotes translation through increased expression of Eef2.
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Affiliation(s)
- Eshita Varma
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Jana Burghaus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Thomas Schwarzl
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Thileepan Sekaran
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Parul Gupta
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Agnieszka A Górska
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Christoph Hofmann
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Claudia Stroh
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Lonny Jürgensen
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Verena Kamuf-Schenk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Xue Li
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Rebekka Medert
- Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Florian Leuschner
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Vivien Kmietczyk
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Marc Freichel
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
- Institute of Pharmacology, University Hospital Heidelberg, University of Heidelberg, Im Neuenheimer Feld 366, 69120, Heidelberg, Germany
| | - Hugo A Katus
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Norbert Frey
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany
| | - Mirko Völkers
- Department of Internal Medicine III (Cardiology, Angiology, and Pneumology), Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, 69120, Heidelberg, Germany.
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15
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Liu W, Yuan Q, Cao S, Wang G, Liu X, Xia Y, Bian Y, Xu F, Chen Y. Review: Acetylation Mechanisms andTargeted Therapies in Cardiac Fibrosis. Pharmacol Res 2023; 193:106815. [PMID: 37290541 DOI: 10.1016/j.phrs.2023.106815] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Cardiac fibrosis is a common pathophysiological remodeling process that occurs in a variety of cardiovascular diseases and greatly influences heart structure and function, progressively leading to the development of heart failure. However, to date, few effective therapies for cardiac fibrosis exist. Abnormal proliferation, differentiation, and migration of cardiac fibroblasts are responsible for the excessive deposition of extracellular matrix in the myocardium. Acetylation, a widespread and reversible protein post-translational modification, plays an important role in the development of cardiac fibrosis by adding acetyl groups to lysine residues. Many acetyltransferases and deacetylases regulate the dynamic alterations of acetylation in cardiac fibrosis, regulating a range of pathogenic conditions including oxidative stress, mitochondrial dysfunction, and energy metabolism disturbance. In this review, we demonstrate the critical roles that acetylation modifications caused by different types of pathological injury play in cardiac fibrosis. Furthermore, we propose therapeutic acetylation-targeting strategies for the prevention and treatment of patients with cardiac fibrosis.
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Affiliation(s)
- Weikang Liu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Qiuhuan Yuan
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Shengchuan Cao
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Guoying Wang
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Xiangguo Liu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Yanan Xia
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China
| | - Yuan Bian
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China.
| | - Feng Xu
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China.
| | - Yuguo Chen
- Department of Emergency Medicine, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Clinical Research Center for Emergency and Critical Care Medicine, Institute of Emergency and Critical Care Medicine of Shandong University, Chest Pain Center, Qilu Hospital of Shandong University, Jinan, China; Shandong Provincial Engineering Laboratory for Emergency and Critical Care Medicine, Key Laboratory of Cardiopulmonary-Cerebral Resuscitation Research of Shandong Province, Key Laboratory of Emergency and Critical Care Medicine of Shandong Province, Qilu Hospital of Shandong University, Jinan, China; The Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese Ministry of Health and Chinese Academy of Medical Sciences; The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine; Qilu Hospital of Shandong University, Jinan, China; NMPA Key Laboratory for Clinical Research and Evaluation of Innovative Drug, Qilu Hospital of Shandong University, Jinan, China.
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16
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Jia M, Rosas L, Kapetanaki MG, Tabib T, Sebrat J, Cruz T, Bondonese A, Mora AL, Lafyatis R, Rojas M, Benos PV. Early events marking lung fibroblast transition to profibrotic state in idiopathic pulmonary fibrosis. Respir Res 2023; 24:116. [PMID: 37085855 PMCID: PMC10122312 DOI: 10.1186/s12931-023-02419-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 04/12/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Idiopathic Pulmonary Fibrosis (IPF) is an age-associated progressive lung disease with accumulation of scar tissue impairing gas exchange. Previous high-throughput studies elucidated the role of cellular heterogeneity and molecular pathways in advanced disease. However, critical pathogenic pathways occurring in the transition of fibroblasts from normal to profibrotic have been largely overlooked. METHODS We used single cell transcriptomics (scRNA-seq) from lungs of healthy controls and IPF patients (lower and upper lobes). We identified fibroblast subclusters, genes and pathways associated with early disease. Immunofluorescence assays validated the role of MOXD1 early in fibrosis. RESULTS We identified four distinct fibroblast subgroups, including one marking the normal-to-profibrotic state transition. Our results show for the first time that global downregulation of ribosomal proteins and significant upregulation of the majority of copper-binding proteins, including MOXD1, mark the IPF transition. We find no significant differences in gene expression in IPF upper and lower lobe samples, which were selected to have low and high degree of fibrosis, respectively. CONCLUSIONS Early events during IPF onset in fibroblasts include dysregulation of ribosomal and copper-binding proteins. Fibroblasts in early stage IPF may have already acquired a profibrotic phenotype while hallmarks of advanced disease, including fibroblast foci and honeycomb formation, are still not evident. The new transitional fibroblasts we discover could prove very important for studying the role of fibroblast plasticity in disease progression and help develop early diagnosis tools and therapeutic interventions targeting earlier disease states.
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Affiliation(s)
- Minxue Jia
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon University – University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, USA
| | - Lorena Rosas
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Maria G. Kapetanaki
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
| | - Tracy Tabib
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - John Sebrat
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Tamara Cruz
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Anna Bondonese
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
| | - Ana L. Mora
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Robert Lafyatis
- Division of Rheumatology and Clinical Immunology, Department of Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Mauricio Rojas
- Department of Internal Medicine, Division Pulmonary, Critical Care and Sleep Medicine, The Ohio State University, Columbus, USA
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, USA
| | - Panayiotis V. Benos
- Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, USA
- Joint Carnegie Mellon University – University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, USA
- Department of Epidemiology, University of Florida, 2004 Mowry Rd, Gainesville, FL 32610 USA
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17
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Nelson AR, Bugg D, Davis J, Saucerman JJ. Network model integrated with multi-omic data predicts MBNL1 signals that drive myofibroblast activation. iScience 2023; 26:106502. [PMID: 37091233 PMCID: PMC10119756 DOI: 10.1016/j.isci.2023.106502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 01/09/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
RNA-binding protein muscleblind-like1 (MBNL1) was recently identified as a central regulator of cardiac wound healing and myofibroblast activation. To identify putative MBNL1 targets, we integrated multiple genome-wide screens with a fibroblast network model. We expanded the model to include putative MBNL1-target interactions and recapitulated published experimental results to validate new signaling modules. We prioritized 14 MBNL1 targets and developed novel fibroblast signaling modules for p38 MAPK, Hippo, Runx1, and Sox9 pathways. We experimentally validated MBNL1 regulation of p38 expression in mouse cardiac fibroblasts. Using the expanded fibroblast model, we predicted a hierarchy of MBNL1 regulated pathways with strong influence on αSMA expression. This study lays a foundation to explore the network mechanisms of MBNL1 signaling central to fibrosis.
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Affiliation(s)
- Anders R. Nelson
- Department of Pharmacology, University of Virginia, 1340 Jefferson Park Avenue, Pinn Hall, 5th Floor, PO Box 800735, Charlottesville, VA 22908-0735, USA
| | - Darrian Bugg
- Department of Lab Medicine & Pathology, University of Washington, 1959 NE Pacific Street Box 357470, Seattle, WA 98195, USA
| | - Jennifer Davis
- Department of Lab Medicine & Pathology, University of Washington, 1959 NE Pacific Street Box 357470, Seattle, WA 98195, USA
- Department of Bioengineering, University of Washington, PO Box 355061, Seattle, WA 98195-5061, USA
- Institute for Stem Cell & Regenerative Medicine, University of Washington, 850 Republican Street, PO Box 358056, Seattle, WA 98109, USA
| | - Jeffrey J. Saucerman
- Department of Biomedical Engineering, University of Virginia, PO Box 800759, Charlottesville, VA 22903 , USA
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18
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Chen W, Pilling D, Gomer RH. The mRNA-binding protein DDX3 mediates TGF-β1 upregulation of translation and promotes pulmonary fibrosis. JCI Insight 2023; 8:e167566. [PMID: 36821384 PMCID: PMC10132153 DOI: 10.1172/jci.insight.167566] [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: 11/28/2022] [Accepted: 02/17/2023] [Indexed: 02/24/2023] Open
Abstract
Pulmonary fibrosis is potentiated by a positive feedback loop involving the extracellular sialidase enzyme neuraminidase 3 (NEU3) causing release of active TGF-β1 and TGF-β1 upregulating NEU3 by increasing translation without affecting mRNA levels. In this report, we elucidate the TGF-β1 upregulation of the translation mechanism. In human lung fibroblasts, TGF-β1 increased levels of proteins, including NEU3, by increasing translation of the encoding mRNAs without significantly affecting levels of these mRNAs. A total of 180 of these mRNAs shared a common 20-nucleotide motif. Deletion of this motif from NEU3 mRNA eliminated the TGF-β1 upregulation of NEU3 translation, while insertion of this motif in 2 mRNAs insensitive to TGF-β1 caused TGF-β1 to upregulate their translation. RNA-binding proteins including DEAD box helicase 3, X-linked (DDX3), bind the RNA motif, and TGF-β1 regulates their protein levels and/or binding to the motif. We found that DDX3 was upregulated in the fibrotic lesions in patients with pulmonary fibrosis, and inhibiting DDX3 in fibroblasts reduced TGF-β1 upregulation of NEU3 levels. In the mouse bleomycin model of pulmonary fibrosis, injections of the DDX3 inhibitor RK-33 potentiated survival and reduced lung inflammation, fibrosis, and tissue levels of DDX3, TGF-β1, and NEU3. These results suggest that inhibiting an mRNA-binding protein that mediates TGF-β1 upregulation of translation can reduce pulmonary fibrosis.
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19
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Chen S, Niu S, Wang W, Zhao X, Pan Y, Qiao L, Yang K, Liu J, Liu W. Overexpression of the QKI Gene Promotes Differentiation of Goat Myoblasts into Myotubes. Animals (Basel) 2023; 13:ani13040725. [PMID: 36830512 PMCID: PMC9952742 DOI: 10.3390/ani13040725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/01/2023] [Accepted: 02/12/2023] [Indexed: 02/22/2023] Open
Abstract
The QKI genes encode RNA-binding proteins regulating cell proliferation, differentiation, and apoptosis. The Goat QKI has six isoforms, but their roles in myogenesis are unclear. In this study, the six isoforms of the QKI gene were overexpressed in goat myoblast. Immunofluorescence, qPCR and Western blot were used to evaluate the effect of QKI on the differentiation of goat myoblast. An RNA-Seq was performed on the cells with the gain of the function from the major isoforms to screen differentially expressed genes (DEGs). The results show that six isoforms had different degrees of deletion in exons 6 and 7, and caused the appearance of different types of encoded amino acids. The expression levels of the QKI-1 and QKI-5 groups were upregulated in the biceps femoris and latissimus dorsi muscle tissues compared with those of the QKI-4, QKI-7, QKI-3 and QKI-6 groups. After 6 d of myoblast differentiation, QKI-5 and the myogenic differentiators MyoG, MyoD, and MyHC were upregulated. Compared to the negative control group, QKI promoted myotube differentiation and the myoblasts overexpressing QKI-5 formed large, abundant myotubes. In summary, we identified that the overexpression of the QKI gene promotes goat-myoblast differentiation and that QKI-5 is the major isoform, with a key role. The RNA-Seq screened 76 upregulated and 123 downregulated DEGs between the negative control and the QKI-5-overexpressing goat myoblasts after d 6 of differentiation. The GO and KEGG analyses associated the downregulated DEGs with muscle-related biological functions. Only the pathways related to muscle growth and development were enriched. This study provides a theoretical basis for further exploring the regulatory mechanism of QKI in skeletal-muscle development in goats.
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20
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Badaoui M, Sobolewski C, Luscher A, Bacchetta M, Köhler T, van Delden C, Foti M, Chanson M. Targeting HuR-Vav3 mRNA interaction prevents Pseudomonas aeruginosa adhesion to the cystic fibrosis airway epithelium. JCI Insight 2023; 8:161961. [PMID: 36602863 PMCID: PMC9977432 DOI: 10.1172/jci.insight.161961] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 12/21/2022] [Indexed: 01/06/2023] Open
Abstract
Cystic fibrosis (CF) is characterized by chronic bacterial infections leading to progressive bronchiectasis and respiratory failure. Pseudomonas aeruginosa (Pa) is the predominant opportunistic pathogen infecting the CF airways. The guanine nucleotide exchange factor Vav3 plays a critical role in Pa adhesion to the CF airways by inducing luminal fibronectin deposition that favors bacteria trapping. Here we report that Vav3 overexpression in CF is caused by upregulation of the mRNA-stabilizing protein HuR. We found that HuR accumulates in the cytoplasm of CF airway epithelial cells and that it binds to and stabilizes Vav3 mRNA. Interestingly, disruption of the HuR-Vav3 mRNA interaction improved the CF epithelial integrity, inhibited the formation of the fibronectin-made bacterial docking platforms, and prevented Pa adhesion to the CF airway epithelium. These findings indicate that targeting HuR represents a promising antiadhesive approach in CF that can prevent initial stages of Pa infection in a context of emergence of multidrug-resistant pathogens.
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Affiliation(s)
| | | | - Alexandre Luscher
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | | | - Thilo Köhler
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
| | - Christian van Delden
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Switzerland
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21
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Quaife NM, Chothani S, Schulz JF, Lindberg EL, Vanezis K, Adami E, O'Fee K, Greiner J, Litviňuková M, van Heesch S, Whiffin N, Hubner N, Schafer S, Rackham O, Cook SA, Barton PJR. LINC01013 Is a Determinant of Fibroblast Activation and Encodes a Novel Fibroblast-Activating Micropeptide. J Cardiovasc Transl Res 2023; 16:77-85. [PMID: 35759180 PMCID: PMC9944705 DOI: 10.1007/s12265-022-10288-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/09/2022] [Indexed: 10/17/2022]
Abstract
Myocardial fibrosis confers an almost threefold mortality risk in heart disease. There are no prognostic therapies and novel therapeutic targets are needed. Many thousands of unannotated small open reading frames (smORFs) have been identified across the genome with potential to produce micropeptides (< 100 amino acids). We sought to investigate the role of smORFs in myocardial fibroblast activation.Analysis of human cardiac atrial fibroblasts (HCFs) stimulated with profibrotic TGFβ1 using RNA sequencing (RNA-Seq) and ribosome profiling (Ribo-Seq) identified long intergenic non-coding RNA LINC01013 as TGFβ1 responsive and containing an actively translated smORF. Knockdown of LINC01013 using siRNA reduced expression of profibrotic markers at baseline and blunted their response to TGFβ1. In contrast, overexpression of a codon-optimised smORF invoked a profibrotic response comparable to that seen with TGFβ1 treatment, whilst FLAG-tagged peptide associated with the mitochondria.Together, these data support a novel LINC01013 smORF micropeptide-mediated mechanism of fibroblast activation. TGFβ1 stimulation of atrial fibroblasts induces expression of LINC01013, whose knockdown reduces fibroblast activation. Overexpression of a smORF contained within LINC01013 localises to mitochondria and activates fibroblasts.
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Affiliation(s)
- N M Quaife
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - S Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - J F Schulz
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
| | - E L Lindberg
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - K Vanezis
- National Heart and Lung Institute, Imperial College London, London, UK
- MRC London Institute of Medical Sciences, London, UK
| | - E Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - K O'Fee
- MRC London Institute of Medical Sciences, London, UK
| | - J Greiner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - M Litviňuková
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - S van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
| | - N Whiffin
- National Heart and Lung Institute, Imperial College London, London, UK
- Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, Guy's and St Thomas NHS Foundation Trust, London, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - N Hubner
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Center for Cardiovascular Research), partner site Berlin, Berlin, Germany
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - S Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - O Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - S A Cook
- MRC London Institute of Medical Sciences, London, UK
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
- National Heart Centre Singapore, Singapore, Singapore
| | - P J R Barton
- National Heart and Lung Institute, Imperial College London, London, UK.
- MRC London Institute of Medical Sciences, London, UK.
- Cardiovascular Research Centre, Royal Brompton and Harefield Hospitals, Guy's and St Thomas NHS Foundation Trust, London, UK.
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22
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Ma CX, Wei ZR, Sun T, Yang MH, Sun YQ, Kai KL, Shi JC, Zhou MJ, Wang ZW, Chen J, Li W, Wang TQ, Zhang SF, Xue L, Zhang M, Yin Q, Zang MX. Circ-sh3rf3/GATA-4/miR-29a regulatory axis in fibroblast-myofibroblast differentiation and myocardial fibrosis. Cell Mol Life Sci 2023; 80:50. [PMID: 36694058 PMCID: PMC11072806 DOI: 10.1007/s00018-023-04699-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/21/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023]
Abstract
The transdifferentiation from cardiac fibroblasts to myofibroblasts is an important event in the initiation of cardiac fibrosis. However, the underlying mechanism is not fully understood. Circ-sh3rf3 (circular RNA SH3 domain containing Ring Finger 3) is a novel circular RNA which was induced in hypertrophied ventricles by isoproterenol hydrochloride, and our work has established that it is a potential regulator in cardiac hypertrophy, but whether circ-sh3rf3 plays a role in cardiac fibrosis remains unclear, especially in the conversion of cardiac fibroblasts into myofibroblasts. Here, we found that circ-sh3rf3 was down-regulated in isoproterenol-treated rat cardiac fibroblasts and cardiomyocytes as well as during fibroblast differentiation into myofibroblasts. We further confirmed that circ-sh3rf3 could interact with GATA-4 proteins and reduce the expression of GATA-4, which in turn abolishes GATA-4 repression of miR-29a expression and thus up-regulates miR-29a expression, thereby inhibiting fibroblast-myofibroblast differentiation and myocardial fibrosis. Our work has established a novel Circ-sh3rf3/GATA-4/miR-29a regulatory cascade in fibroblast-myofibroblast differentiation and myocardial fibrosis, which provides a new therapeutic target for myocardial fibrosis.
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Affiliation(s)
- Cai-Xia Ma
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Zhi-Ru Wei
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Tong Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Ming-Hui Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Yu-Qie Sun
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Kun-Lun Kai
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Jia-Chen Shi
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Meng-Jiao Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Zi-Wei Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Jing Chen
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Wei Li
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Tian-Qi Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Shan-Feng Zhang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China
| | - Lixiang Xue
- Medical Research Center, Peking University Third Hospital, 49 Huayuan North Road, Beijing, 100191, China
| | - Min Zhang
- Cardiovascular Division, Department of Cardiology, King's College London British Heart Foundation Centre of Research Excellence, London, UK
| | - Qianqian Yin
- Medical Research Center, Peking University Third Hospital, 49 Huayuan North Road, Beijing, 100191, China.
| | - Ming-Xi Zang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Zhengzhou University, Ke Xue Da Dao 100, Zheng Zhou, 450001, China.
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23
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Mehta Z, Touma M. Post-Transcriptional Modification by Alternative Splicing and Pathogenic Splicing Variants in Cardiovascular Development and Congenital Heart Defects. Int J Mol Sci 2023; 24:ijms24021555. [PMID: 36675070 PMCID: PMC9862068 DOI: 10.3390/ijms24021555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Advancements in genomics, bioinformatics, and genome editing have uncovered new dimensions in gene regulation. Post-transcriptional modifications by the alternative splicing of mRNA transcripts are critical regulatory mechanisms of mammalian gene expression. In the heart, there is an expanding interest in elucidating the role of alternative splicing in transcriptome regulation. Substantial efforts were directed toward investigating this process in heart development and failure. However, few studies shed light on alternative splicing products and their dysregulation in congenital heart defects (CHDs). While elegant reports showed the crucial roles of RNA binding proteins (RBPs) in orchestrating splicing transitions during heart development and failure, the impact of RBPs dysregulation or genetic variation on CHDs has not been fully addressed. Herein, we review the current understanding of alternative splicing and RBPs' roles in heart development and CHDs. Wediscuss the impact of perinatal splicing transition and its dysregulation in CHDs. We further summarize the discoveries made of causal splicing variants in key transcription factors that are implicated in CHDs. An improved understanding of the roles of alternative splicing in heart development and CHDs may potentially inform novel preventive and therapeutic advancements for newborn infants with CHDs.
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Affiliation(s)
- Zubin Mehta
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Marlin Touma
- Neonatal/Congenital Heart Laboratory, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Children’s Discovery and Innovation Institute, Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Eli and Edythe Broad Stem Cell Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Correspondence:
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24
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Chothani S, Ho L, Schafer S, Rackham O. Discovering microproteins: making the most of ribosome profiling data. RNA Biol 2023; 20:943-954. [PMID: 38013207 PMCID: PMC10730196 DOI: 10.1080/15476286.2023.2279845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
Building a reference set of protein-coding open reading frames (ORFs) has revolutionized biological process discovery and understanding. Traditionally, gene models have been confirmed using cDNA sequencing and encoded translated regions inferred using sequence-based detection of start and stop combinations longer than 100 amino-acids to prevent false positives. This has led to small ORFs (smORFs) and their encoded proteins left un-annotated. Ribo-seq allows deciphering translated regions from untranslated irrespective of the length. In this review, we describe the power of Ribo-seq data in detection of smORFs while discussing the major challenge posed by data-quality, -depth and -sparseness in identifying the start and end of smORF translation. In particular, we outline smORF cataloguing efforts in humans and the large differences that have arisen due to variation in data, methods and assumptions. Although current versions of smORF reference sets can already be used as a powerful tool for hypothesis generation, we recommend that future editions should consider these data limitations and adopt unified processing for the community to establish a canonical catalogue of translated smORFs.
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Affiliation(s)
- Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
| | - Owen Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore
- School of Biological Sciences, University of Southampton, Southampton, UK
- The Alan Turing Institute, The British Library, London, UK
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25
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Zou S, Khoo BL. Subtyping based on immune cell fractions reveal heterogeneity of cardiac fibrosis in end-stage heart failure. Front Immunol 2023; 14:1053793. [PMID: 36875078 PMCID: PMC9975711 DOI: 10.3389/fimmu.2023.1053793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Background A central issue hindering the development of effective anti-fibrosis drugs for heart failure is the unclear interrelationship between fibrosis and the immune cells. This study aims at providing precise subtyping of heart failure based on immune cell fractions, elaborating their differences in fibrotic mechanisms, and proposing a biomarker panel for evaluating intrinsic features of patients' physiological statuses through subtype classification, thereby promoting the precision medicine for cardiac fibrosis. Methods We inferred immune cell type abundance of the ventricular samples by a computational method (CIBERSORTx) based on ventricular tissue samples from 103 patients with heart failure, and applied K-means clustering to divide patients into two subtypes based on their immune cell type abundance. We also designed a novel analytic strategy: Large-Scale Functional Score and Association Analysis (LAFSAA), to study fibrotic mechanisms in the two subtypes. Results Two subtypes of immune cell fractions: pro-inflammatory and pro-remodeling subtypes, were identified. LAFSAA identified 11 subtype-specific pro-fibrotic functional gene sets as the basis for personalised targeted treatments. Based on feature selection, a 30-gene biomarker panel (ImmunCard30) established for diagnosing patient subtypes achieved high classification performance, with the area under the receiver operator characteristic curve corresponding to 0.954 and 0.803 for the discovery and validation sets, respectively. Conclusion Patients with the two subtypes of cardiac immune cell fractions were likely having different fibrotic mechanisms. Patients' subtypes can be predicted based on the ImmunCard30 biomarker panel. We envision that our unique stratification strategy revealed in this study will unravel advance diagnostic techniques for personalised anti-fibrotic therapy.
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Affiliation(s)
- Shangjie Zou
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.,Hong Kong Center for Cerebro-Cardiovascular Health Engineering (COCHE), Hong Kong, Hong Kong SAR, China
| | - Bee Luan Khoo
- Department of Biomedical Engineering, City University of Hong Kong, Hong Kong, Hong Kong SAR, China.,Hong Kong Center for Cerebro-Cardiovascular Health Engineering (COCHE), Hong Kong, Hong Kong SAR, China.,Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong-Shenzhen Futian Research Institute, Shenzhen, China
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26
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Fang Q, Wang J, Wei J, Long X, Wang Y, He J, Yuan X, Du J. Transcriptomic profile analysis of the left atrium in spontaneously hypertensive rats in the early stage. Front Pharmacol 2022; 13:989636. [PMID: 36324689 PMCID: PMC9620422 DOI: 10.3389/fphar.2022.989636] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/28/2022] [Indexed: 11/19/2022] Open
Abstract
Left atrial remodeling, characterized by enlargement and hypertrophy of the left atrium and increased fibrosis, was accompanied by an increased incidence of atrial fibrillation. While before morphological changes at the early stage of hypertension, how overloaded hypertension influences the transcriptomic profile of the left atrium remains unclear. Therefore, RNA-sequencing was performed to define the RNA expressing profiles of left atrium in spontaneously hypertensive rats (SHRs) and normotensive Wistar-Kyoto (WKY) rats as a control group. We also compared the changes in the RNA expression profiles in SHRs treated with an angiotensin receptor blocker (ARB) and angiotensin receptor-neprilysin inhibitor (ARNI) to assess the distinct effects on the left atrium. In total, 1,558 differentially expressed genes were found in the left atrium between WKY rats and SHRs. Bioinformatics analysis showed that these mRNAs could regulate upstream pathways in atrial remodeling through atrial fibrosis, inflammation, electrical remodeling, and cardiac metabolism. The regulated transcripts detected in the left atrial tissue in both the ARB-treated and ARNI-treated groups were related to metabolism. In contrast to the ARB-treated rates, the transcripts in ARNI-treated rats were mapped to the cyclic guanosine monophosphate-protein kinase G signaling pathway.
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Affiliation(s)
- Qinghua Fang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jing Wang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiangjun Wei
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xianglin Long
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yao Wang
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jiacheng He
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xin Yuan
- Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianlin Du
- Department of Cardiology, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- *Correspondence: Jianlin Du,
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27
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Li J, Zhang X, Ren P, Wu Y, Wang Y, Zhou W, Wang Z, Chao P. Landscape of RNA-binding proteins in diagnostic utility, immune cell infiltration and PANoptosis features of heart failure. Front Genet 2022; 13:1004163. [PMID: 36313471 PMCID: PMC9614340 DOI: 10.3389/fgene.2022.1004163] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 09/27/2022] [Indexed: 11/13/2022] Open
Abstract
Objective: Heart failure remains a global public health problem linked to rising morbidity and mortality. RNA-binding proteins (RBPs) are crucial regulators in post-transcriptionally determining gene expression. Our study aimed to comprehensively elucidate the diagnostic utility and biological roles of RBPs in heart failure. Methods: Genomic data of human failing and nonfailing left ventricular myocardium specimens were retrieved from the GEO datasets. Heart failure-specific RBPs were screened with differential expression analyses, and RBP-based subtypes were clustered with consensus clustering approach. GSEA was implemented for comparing KEGG pathways across subtypes. RBP-based subtype-related genes were screened with WGCNA. Afterwards, characteristic genes were selected through integrating LASSO and SVM-RFE approaches. A nomogram based on characteristic genes was established and verified through calibration curve, decision curve and clinical impact curve analyses. The abundance of immune cell types was estimated with CIBERSORT approach. Results: Heart failure-specific RBPs were determined, which were remarkably linked to RNA metabolism process. Three RBP-based subtypes (namely C1, C2, C3) were established, characterized by distinct pathway activities and PANoptosis gene levels. C2 subtype presented the highest abundance of immune cells, followed by C1 and C3. Afterwards, ten characteristic genes were selected, which enabled to reliably diagnose heart failure risk. The characteristic gene-based nomogram enabled to accurately predict risk of heart failure, with the excellent clinical utility. Additionally, characteristic genes correlated to immune cell infiltration and PANoptosis genes. Conclusion: Our findings comprehensively described the roles of RBPs in heart failure. Further research is required for verifying the effectiveness of RBP-based subtypes and characteristic genes in heart failure.
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Affiliation(s)
- Jie Li
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Xueqin Zhang
- Department of Nephrology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Peng Ren
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yu Wu
- Department of Medical Administration, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Yaoguo Wang
- Department of Information Center, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
| | - Wenzheng Zhou
- Department of Orthopaedics, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Zhao Wang
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
| | - Peng Chao
- Department of Cardiology, People’s Hospital of Xinjiang Uygur Autonomous Region, Urumqi, China
- *Correspondence: Wenzheng Zhou, ; Zhao Wang, ; Peng Chao,
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28
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Manfredi-Lozano M, Leysen V, Adamo M, Paiva I, Rovera R, Pignat JM, Timzoura FE, Candlish M, Eddarkaoui S, Malone SA, Silva MSB, Trova S, Imbernon M, Decoster L, Cotellessa L, Tena-Sempere M, Claret M, Paoloni-Giacobino A, Plassard D, Paccou E, Vionnet N, Acierno J, Maceski AM, Lutti A, Pfrieger F, Rasika S, Santoni F, Boehm U, Ciofi P, Buée L, Haddjeri N, Boutillier AL, Kuhle J, Messina A, Draganski B, Giacobini P, Pitteloud N, Prevot V. GnRH replacement rescues cognition in Down syndrome. Science 2022; 377:eabq4515. [PMID: 36048943 PMCID: PMC7613827 DOI: 10.1126/science.abq4515] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
At the present time, no viable treatment exists for cognitive and olfactory deficits in Down syndrome (DS). We show in a DS model (Ts65Dn mice) that these progressive nonreproductive neurological symptoms closely parallel a postpubertal decrease in hypothalamic as well as extrahypothalamic expression of a master molecule that controls reproduction-gonadotropin-releasing hormone (GnRH)-and appear related to an imbalance in a microRNA-gene network known to regulate GnRH neuron maturation together with altered hippocampal synaptic transmission. Epigenetic, cellular, chemogenetic, and pharmacological interventions that restore physiological GnRH levels abolish olfactory and cognitive defects in Ts65Dn mice, whereas pulsatile GnRH therapy improves cognition and brain connectivity in adult DS patients. GnRH thus plays a crucial role in olfaction and cognition, and pulsatile GnRH therapy holds promise to improve cognitive deficits in DS.
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Affiliation(s)
- Maria Manfredi-Lozano
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Valerie Leysen
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Michela Adamo
- Department of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland,Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland
| | - Isabel Paiva
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, Université de Strasbourg-CNRS, Strasbourg, France
| | - Renaud Rovera
- Univ. Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, Bron 69500, France
| | - Jean-Michel Pignat
- Department of Clinical Neurosciences, Neurorehabilitation Unit, University Hospital CHUV, Lausanne, Switzerland
| | - Fatima Ezzahra Timzoura
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Michael Candlish
- Experimental Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, 66421, Homburg, Germany
| | - Sabiha Eddarkaoui
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France
| | - Samuel A. Malone
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Mauro S. B. Silva
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Sara Trova
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Monica Imbernon
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Laurine Decoster
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Ludovica Cotellessa
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Manuel Tena-Sempere
- Univ. Cordoba, IMIBC/HURS, CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, Cordoba, Spain
| | - Marc Claret
- Neuronal Control of Metabolism Laboratory, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; Centro de Investigación Biomédica en Red (CIBER) de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), 08036 Barcelona, Spain
| | - Ariane Paoloni-Giacobino
- Department of Genetic Medicine, University Hospitals of Geneva, 4 rue Gabrielle-Perret-Gentil, 1211, Genève 14, Switzerland
| | - Damien Plassard
- CNRS UMR 7104, INSERM U1258, GenomEast Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), Université de Strasbourg, Illkirch, France
| | - Emmanuelle Paccou
- Department of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Nathalie Vionnet
- Department of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - James Acierno
- Department of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland
| | - Aleksandra Maleska Maceski
- Neurologic Clinic and Polyclinic, MS Centre and Research Centre for Clinical Neuroimmunology and Neuroscience Basel; University Hospital Basel, University of Basel, Basel Switzerland
| | - Antoine Lutti
- Laboratory for Research in Neuroimaging LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Switzerland
| | - Frank Pfrieger
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives, 67000 Strasbourg, France
| | - S. Rasika
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Federico Santoni
- Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland
| | - Ulrich Boehm
- Experimental Pharmacology, Center for Molecular Signaling (PZMS), Saarland University School of Medicine, 66421, Homburg, Germany
| | - Philippe Ciofi
- Univ. Bordeaux, Inserm, U1215, Neurocentre Magendie, Bordeaux, France
| | - Luc Buée
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France
| | - Nasser Haddjeri
- Univ. Lyon, Université Claude Bernard Lyon 1, Inserm, Stem Cell and Brain Research Institute U1208, Bron 69500, France
| | - Anne-Laurence Boutillier
- Laboratoire de Neurosciences Cognitives et Adaptatives (LNCA), UMR 7364, Université de Strasbourg-CNRS, Strasbourg, France
| | - Jens Kuhle
- Neurologic Clinic and Polyclinic, MS Centre and Research Centre for Clinical Neuroimmunology and Neuroscience Basel; University Hospital Basel, University of Basel, Basel Switzerland
| | - Andrea Messina
- Department of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland,Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland
| | - Bogdan Draganski
- Laboratory for Research in Neuroimaging LREN, Centre for Research in Neurosciences, Department of Clinical Neurosciences, Lausanne University Hospital and University of Lausanne, Switzerland,Neurology Department, Max-Planck-Institute for Human Cognitive and Brain Sciences, Leipzig, Germany
| | - Paolo Giacobini
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France
| | - Nelly Pitteloud
- Department of Endocrinology, Diabetology, and Metabolism, Lausanne University Hospital, 1011 Lausanne, Switzerland,Faculty of Biology and Medicine, University of Lausanne, Lausanne 1005, Switzerland,Correspondence to: and (+33 612903876)
| | - Vincent Prevot
- Univ. Lille, Inserm, CHU Lille, Lille Neuroscience & Cognition, UMR-S 1172, LabexDistAlz, Lille, France,Laboratory of Development and Plasticity of the Neuroendocrine Brain, FHU 1000 days for health, EGID, Lille, France,Correspondence to: and (+33 612903876)
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29
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Abstract
Heart regenerative medicine has been gradually evolving from a view of the heart as a nonregenerative organ with terminally differentiated cardiac muscle cells. Understanding the biology of the heart during homeostasis and in response to injuries has led to the realization that cellular communication between all cardiac cell types holds great promise for treatments. Indeed, recent studies highlight new disease-reversion concepts in addition to cardiomyocyte renewal, such as matrix- and vascular-targeted therapies, and immunotherapy with a focus on inflammation and fibrosis. In this review, we will discuss the cross-talk within the cardiac microenvironment and how specific therapies aim to target the hostile cardiac milieu under pathological conditions.
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Affiliation(s)
- Eldad Tzahor
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Stefanie Dimmeler
- Institute of Cardiovascular Regeneration, Center of Molecular Medicine, Goethe University Frankfurt, 60594 Frankfurt, Germany.,Cardiopulmonary Institute, Goethe University Frankfurt, Frankfurt, Germany.,German Center for Cardiovascular Research, RheinMain, Frankfurt, Germany
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30
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Cornelius VA, Naderi-Meshkin H, Kelaini S, Margariti A. RNA-Binding Proteins: Emerging Therapeutics for Vascular Dysfunction. Cells 2022; 11:2494. [PMID: 36010571 PMCID: PMC9407011 DOI: 10.3390/cells11162494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 12/02/2022] Open
Abstract
Vascular diseases account for a significant number of deaths worldwide, with cardiovascular diseases remaining the leading cause of mortality. This ongoing, ever-increasing burden has made the need for an effective treatment strategy a global priority. Recent advances in regenerative medicine, largely the derivation and use of induced pluripotent stem cell (iPSC) technologies as disease models, have provided powerful tools to study the different cell types that comprise the vascular system, allowing for a greater understanding of the molecular mechanisms behind vascular health. iPSC disease models consequently offer an exciting strategy to deepen our understanding of disease as well as develop new therapeutic avenues with clinical translation. Both transcriptional and post-transcriptional mechanisms are widely accepted to have fundamental roles in orchestrating responses to vascular damage. Recently, iPSC technologies have increased our understanding of RNA-binding proteins (RBPs) in controlling gene expression and cellular functions, providing an insight into the onset and progression of vascular dysfunction. Revelations of such roles within vascular disease states have therefore allowed for a greater clarification of disease mechanisms, aiding the development of novel therapeutic interventions. Here, we discuss newly discovered roles of RBPs within the cardio-vasculature aided by iPSC technologies, as well as examine their therapeutic potential, with a particular focus on the Quaking family of isoforms.
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Affiliation(s)
| | | | | | - Andriana Margariti
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
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31
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Widjaja AA, Chothani S, Viswanathan S, Goh JWT, Lim WW, Cook SA. IL11 Stimulates IL33 Expression and Proinflammatory Fibroblast Activation across Tissues. Int J Mol Sci 2022; 23:ijms23168900. [PMID: 36012165 PMCID: PMC9408968 DOI: 10.3390/ijms23168900] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 01/16/2023] Open
Abstract
Interleukin 11 (IL11) is upregulated in inflammatory conditions, where it is mostly believed to have anti-inflammatory activity. However, recent studies suggest instead that IL11 promotes inflammation by activating fibroblasts. Here, we assessed whether IL11 is pro- or anti-inflammatory in fibroblasts. Primary cultures of human kidney, lung or skin fibroblasts were stimulated with IL11 that resulted in the transient phosphorylation of signal transducer and activator of transcription 3 (STAT3) and the sustained activation of extracellular signal-regulated protein kinases (ERK). RNA sequencing over a time course of IL11 stimulation revealed a robust but short-lived transcriptional response that was enriched for gene set hallmarks of inflammation and characterized by the upregulation of SERPINB2, TNFRSF18, Interleukin 33 (IL33), CCL20, IL1RL1, CXCL3/5/8, ICAM1 and IL11 itself. IL33 was the most upregulated signaling factor (38-fold, p = 9.8 × 10-5), and IL1RL1, its cognate receptor, was similarly increased (18-fold, p = 1.1 × 10-34). In proteomic studies, IL11 triggered a proinflammatory secretome with the notable upregulation of IL8, IL6, MCP1, CCL20 and CXCL1/5/6, which are important chemotaxins for neutrophils, monocytes, and lymphocytes. IL11 induced IL33 expression across fibroblast types, and the inhibition of STAT3 but not of MEK/ERK prevented this. These data establish IL11 as pro-inflammatory with specific importance for priming the IL33 alarmin response in inflammatory fibroblasts across tissues.
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Affiliation(s)
- Anissa A. Widjaja
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
- Correspondence: (A.A.W.); (S.A.C.)
| | - Sonia Chothani
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Sivakumar Viswanathan
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Joyce Wei Ting Goh
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
| | - Wei-Wen Lim
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
| | - Stuart A. Cook
- Cardiovascular and Metabolic Disorders Program, Duke-National University of Singapore Medical School, Singapore 169857, Singapore
- National Heart Research Institute Singapore, National Heart Centre Singapore, Singapore 169609, Singapore
- MRC-London Institute of Medical Sciences, Hammersmith Hospital Campus, London SW7 2AZ, UK
- Correspondence: (A.A.W.); (S.A.C.)
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32
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Chothani SP, Adami E, Widjaja AA, Langley SR, Viswanathan S, Pua CJ, Zhihao NT, Harmston N, D'Agostino G, Whiffin N, Mao W, Ouyang JF, Lim WW, Lim S, Lee CQE, Grubman A, Chen J, Kovalik JP, Tryggvason K, Polo JM, Ho L, Cook SA, Rackham OJL, Schafer S. A high-resolution map of human RNA translation. Mol Cell 2022; 82:2885-2899.e8. [PMID: 35841888 DOI: 10.1016/j.molcel.2022.06.023] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 03/10/2022] [Accepted: 06/15/2022] [Indexed: 10/17/2022]
Abstract
Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.
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Affiliation(s)
- Sonia P Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Eleonora Adami
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Anissa A Widjaja
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Sarah R Langley
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Sivakumar Viswanathan
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Chee Jian Pua
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Nevin Tham Zhihao
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nathan Harmston
- Program in Cancer and Stem Cell Biology, Duke-NUS Medical School, Singapore 169857, Singapore; Science Division, Yale-NUS College, Singapore 138527, Singapore
| | - Giuseppe D'Agostino
- Lee Kong Chian School of Medicine, Nanyang Technological University, Clinical Sciences Building, Singapore 308232, Singapore
| | - Nicola Whiffin
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Wang Mao
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - John F Ouyang
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Wei Wen Lim
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Shiqi Lim
- National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore
| | - Cheryl Q E Lee
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Alexandra Grubman
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Joseph Chen
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - J P Kovalik
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Karl Tryggvason
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Jose M Polo
- Department of Anatomy and Developmental Biology, Monash University, Wellington Road, Clayton, VIC 3800, Australia; Development and Stem Cells Program, Monash Biomedicine Discovery Institute, Wellington Road, Clayton, VIC 3800, Australia; Australian Regenerative Medicine Institute, Monash University, Wellington Road, Clayton, VIC 3800, Australia
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore
| | - Stuart A Cook
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore; London Institute of Medical Sciences, London W12 ONN, UK
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; School of Biological Sciences, University of Southampton, Southampton, UK.
| | - Sebastian Schafer
- Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore 169857, Singapore; National Heart Research Institute Singapore (NHRIS), National Heart Centre Singapore, Singapore 169609, Singapore.
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Albaradei S, Albaradei A, Alsaedi A, Uludag M, Thafar MA, Gojobori T, Essack M, Gao X. MetastaSite: Predicting metastasis to different sites using deep learning with gene expression data. Front Mol Biosci 2022; 9:913602. [PMID: 35936793 PMCID: PMC9353773 DOI: 10.3389/fmolb.2022.913602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 06/29/2022] [Indexed: 12/03/2022] Open
Abstract
Deep learning has massive potential in predicting phenotype from different omics profiles. However, deep neural networks are viewed as black boxes, providing predictions without explanation. Therefore, the requirements for these models to become interpretable are increasing, especially in the medical field. Here we propose a computational framework that takes the gene expression profile of any primary cancer sample and predicts whether patients’ samples are primary (localized) or metastasized to the brain, bone, lung, or liver based on deep learning architecture. Specifically, we first constructed an AutoEncoder framework to learn the non-linear relationship between genes, and then DeepLIFT was applied to calculate genes’ importance scores. Next, to mine the top essential genes that can distinguish the primary and metastasized tumors, we iteratively added ten top-ranked genes based upon their importance score to train a DNN model. Then we trained a final multi-class DNN that uses the output from the previous part as an input and predicts whether samples are primary or metastasized to the brain, bone, lung, or liver. The prediction performances ranged from AUC of 0.93–0.82. We further designed the model’s workflow to provide a second functionality beyond metastasis site prediction, i.e., to identify the biological functions that the DL model uses to perform the prediction. To our knowledge, this is the first multi-class DNN model developed for the generic prediction of metastasis to various sites.
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Affiliation(s)
- Somayah Albaradei
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Faculty of Computing and Information Technology, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Asim Alsaedi
- King Saud Bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
- King Abdulaziz Medical City, Jeddah, Saudi Arabia
| | - Mahmut Uludag
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Maha A. Thafar
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- College of Computers and Information Technology, Taif University, Taif, Saudi Arabia
| | - Takashi Gojobori
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Magbubah Essack
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magbubah Essack, ; Xin Gao,
| | - Xin Gao
- Computer Electrical and Mathematical Sciences and Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- *Correspondence: Magbubah Essack, ; Xin Gao,
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Kerouanton B, Schäfer S, Ho L, Chothani S, Rackham OJL. CLIPreg: Constructing translational regulatory networks from CLIP-, Ribo- and RNA-seq. Bioinformatics 2022; 38:3651-3653. [PMID: 35652722 DOI: 10.1093/bioinformatics/btac363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/19/2022] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION The creation and analysis of gene regulatory networks have been the focus of bioinformatics research and underpins much of what is known about gene regulation. However, as a result of a bias in the availability of data-types that are collected, the vast majority of gene regulatory network resources and tools have focused on either transcriptional regulation or protein-protein interactions. This has left other areas of regulation, for instance, translational regulation, vastly underrepresented despite them having been shown to play a critical role in both health and disease. RESULTS In order to address this we have developed CLIPreg, a package that integrates RNA, Ribo and CLIP- sequencing data in order to construct translational regulatory networks coordinated by RNA-binding proteins and micro-RNAs. This is the first tool of its type to be created, allowing for detailed investigation into a previously unseen layer of regulation. AVAILABILITY AND IMPLEMENTATION CLIPreg is available at https://github.com/SGDDNB/CLIPreg.
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Affiliation(s)
- Baptiste Kerouanton
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Sebastian Schäfer
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Lena Ho
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Sonia Chothani
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Owen J L Rackham
- Program in Cardiovascular and Metabolic Disorders, Duke-NUS Medical School, Singapore 169857, Singapore
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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He Y, Chen Y, Yao L, Wang J, Sha X, Wang Y. The Inflamm-Aging Model Identifies Key Risk Factors in Atherosclerosis. Front Genet 2022; 13:865827. [PMID: 35706446 PMCID: PMC9191626 DOI: 10.3389/fgene.2022.865827] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Accepted: 04/26/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Atherosclerosis, one of the main threats to human life and health, is driven by abnormal inflammation (i.e., chronic inflammation or oxidative stress) during accelerated aging. Many studies have shown that inflamm-aging exerts a significant impact on the occurrence of atherosclerosis, particularly by inducing an immune homeostasis imbalance. However, the potential mechanism by which inflamm-aging induces atherosclerosis needs to be studied more thoroughly, and there is currently a lack of powerful prediction models.Methods: First, an improved inflamm-aging prediction model was constructed by integrating aging, inflammation, and disease markers with the help of machine learning methods; then, inflamm-aging scores were calculated. In addition, the causal relationship between aging and disease was identified using Mendelian randomization. A series of risk factors were also identified by causal analysis, sensitivity analysis, and network analysis.Results: Our results revealed an accelerated inflamm-aging pattern in atherosclerosis and suggested a causal relationship between inflamm-aging and atherosclerosis. Mechanisms involving inflammation, nutritional balance, vascular homeostasis, and oxidative stress were found to be driving factors of atherosclerosis in the context of inflamm-aging.Conclusion: In summary, we developed a model integrating crucial risk factors in inflamm-aging and atherosclerosis. Our computation pipeline could be used to explore potential mechanisms of related diseases.
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Affiliation(s)
- Yudan He
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yao Chen
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Lilin Yao
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Junyi Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Xianzheng Sha
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
| | - Yin Wang
- Department of Biomedical Engineering, School of Intelligent Sciences, China Medical University, Shenyang, China
- Tumor Etiology and Screening Department of Cancer Institute and General Surgery, The First Affiliated Hospital of China Medical University, Shenyang, China
- *Correspondence: Yin Wang,
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Liu Y, Xu X, Lei W, Hou Y, Zhang Y, Tang R, Yang Z, Tian Y, Zhu Y, Wang C, Deng C, Zhang S, Yang Y. The NLRP3 inflammasome in fibrosis and aging: The known unknowns. Ageing Res Rev 2022; 79:101638. [PMID: 35525426 DOI: 10.1016/j.arr.2022.101638] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 03/27/2022] [Accepted: 05/01/2022] [Indexed: 11/28/2022]
Abstract
Aging-related diseases such as cancer, cardiovascular diseases, diabetes, and neurodegenerative diseases are often accompanied by fibrosis. The NLRP3 inflammasome triggers the inflammatory response and subsequently promotes fibrosis through pathogen-associated molecular patterns (PAMPs). In this review, we first introduce the general background and specific mechanism of NLRP3 in fibrosis. Second, we investigate the role of NLRP3 in fibrosis in different organs/tissues. Third, we discuss the relationship between NLRP3 and fibrosis during aging. In summary, this review describes the latest progress on the roles of NLRP3 in fibrosis and aging and reveals the possibility of NLRP3 as an antifibrotic and anti-aging treatment target.
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Affiliation(s)
- Yanqing Liu
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Xuezeng Xu
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Wangrui Lei
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yuxuan Hou
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yan Zhang
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Ran Tang
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Zhi Yang
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Ye Tian
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Yanli Zhu
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Changyu Wang
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China
| | - Chao Deng
- Department of Cardiovascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shaofei Zhang
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China.
| | - Yang Yang
- Department of Cardiology, Xi'an No.3 Hospital, School of Life Sciences and Medicine, Northwest University, Xi'an, China; Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education. School of Life Sciences and Medicine, Northwest University, Xi'an, China.
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Morin C, Moyret-Lalle C, Mertani HC, Diaz JJ, Marcel V. Heterogeneity and dynamic of EMT through the plasticity of ribosome and mRNA translation. Biochim Biophys Acta Rev Cancer 2022; 1877:188718. [PMID: 35304296 DOI: 10.1016/j.bbcan.2022.188718] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 03/02/2022] [Accepted: 03/11/2022] [Indexed: 02/06/2023]
Abstract
Growing evidence exposes translation and its translational machinery as key players in establishing and maintaining physiological and pathological biological processes. Examining translation may not only provide new biological insight but also identify novel innovative therapeutic targets in several fields of biology, including that of epithelial-to-mesenchymal transition (EMT). EMT is currently considered as a dynamic and reversible transdifferentiation process sustaining the transition from an epithelial to mesenchymal phenotype, known to be mainly driven by transcriptional reprogramming. However, it seems that the characterization of EMT plasticity is challenging, relying exclusively on transcriptomic and epigenetic approaches. Indeed, heterogeneity in EMT programs was reported to depend on the biological context. Here, by reviewing the involvement of translational control, translational machinery and ribosome biogenesis characterizing the different types of EMT, from embryonic and adult physiological to pathological contexts, we discuss the added value of integrating translational control and its machinery to depict the heterogeneity and dynamics of EMT programs.
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Affiliation(s)
- Chloé Morin
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Caroline Moyret-Lalle
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Hichem C Mertani
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Jean-Jacques Diaz
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France
| | - Virginie Marcel
- Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Université de Lyon, Université Claude Bernard Lyon 1, Centre Léon Bérard, F-69373 Lyon Cedex 08, France; Institut Convergence PLAsCAN, 69373 Lyon cedex 08, France; DevWeCan Labex Laboratory, 69373 Lyon cedex 08, France.
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Bugg D, Bailey LRJ, Bretherton RC, Beach KE, Reichardt IM, Robeson KZ, Reese AC, Gunaje J, Flint G, DeForest CA, Stempien-Otero A, Davis J. MBNL1 drives dynamic transitions between fibroblasts and myofibroblasts in cardiac wound healing. Cell Stem Cell 2022; 29:419-433.e10. [PMID: 35176223 PMCID: PMC8929295 DOI: 10.1016/j.stem.2022.01.012] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 11/30/2021] [Accepted: 01/24/2022] [Indexed: 12/18/2022]
Abstract
Dynamic fibroblast to myofibroblast state transitions underlie the heart's fibrotic response. Because transcriptome maturation by muscleblind-like 1 (MBNL1) promotes differentiated cell states, this study investigated whether tactical control of MBNL1 activity could alter myofibroblast activity and fibrotic outcomes. In healthy mice, cardiac fibroblast-specific overexpression of MBNL1 transitioned the fibroblast transcriptome to that of a myofibroblast and after injury promoted myocyte remodeling and scar maturation. Both fibroblast- and myofibroblast-specific loss of MBNL1 limited scar production and stabilization, which was ascribed to negligible myofibroblast activity. The combination of MBNL1 deletion and injury caused quiescent fibroblasts to expand and adopt features of cardiac mesenchymal stem cells, whereas transgenic MBNL1 expression blocked fibroblast proliferation and drove the population into a mature myofibroblast state. These data suggest MBNL1 is a post-transcriptional switch, controlling fibroblast state plasticity during cardiac wound healing.
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Affiliation(s)
- Darrian Bugg
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Logan R J Bailey
- Molecular & Cellular Biology, University of Washington, Seattle, WA 98195, USA
| | - Ross C Bretherton
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Kylie E Beach
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | | | - Kalen Z Robeson
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Anna C Reese
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Jagadambika Gunaje
- Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Galina Flint
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA
| | - Cole A DeForest
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, USA; Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
| | | | - Jennifer Davis
- Department of Bioengineering, University of Washington, Seattle, WA 98105, USA; Department of Lab Medicine & Pathology, University of Washington, Seattle, WA 98195, USA; Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98109, USA.
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Zhou Y, Ng DY, Richards AM, Wang P. Loss of full-length pumilio 1 abrogates miRNA-221-induced gene p27 silencing-mediated cell proliferation in the heart. MOLECULAR THERAPY - NUCLEIC ACIDS 2022; 27:456-470. [PMID: 35036057 PMCID: PMC8728526 DOI: 10.1016/j.omtn.2021.12.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 12/09/2021] [Indexed: 12/02/2022]
Abstract
Upregulated expression of microRNA (miR)-221 is associated with downregulation of p27 and subsequent increased cell proliferation in a variety of human cancers. It is unknown whether miR-221 mimics could trigger neoplastic cellular proliferation. In vitro, we demonstrated miR-221 significantly downregulates the expression of P27 and increases proliferation of H9c2 and cardiac fibroblasts. The knockdown of PUM1 but not PUM2 abolished such effects by miR-221, as verified by RT-qPCR and western blot, direct binding of p27 3′ UTR by luciferase reporter assay and cell proliferation by Ki67. In vivo expression of P27 in the rat liver, heart, kidney, spleen, and muscle were not affected by miR-221 at 1 and 4 mg/kg and concurrently full-length (FL) PUM1 (140 kDa) was not detected. Instead, isoforms of 105 and 90 kDa were observed and generated through alternative RNA slicing verified by cDNA cloning and sequencing and cathepsin K cleavage confirmed by studies with the inhibitor odanacatib. This is the first study to address the possible pro-proliferative effects of miR-221 mimic therapeutics in cardiovascular applications. Loss of FL PUM1 expression is a key factor abrogating miR-221-mediated p27 regulation, although other concurrent mechanisms cannot be excluded. Our findings provide essential insights into the context-dependent nature of miRNA functionality.
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In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. PLoS Comput Biol 2022; 18:e1009918. [PMID: 35226669 PMCID: PMC8912908 DOI: 10.1371/journal.pcbi.1009918] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 03/10/2022] [Accepted: 02/10/2022] [Indexed: 01/03/2023] Open
Abstract
Reactivation of fetal-specific genes and isoforms occurs during heart failure. However, the underlying molecular mechanisms and the extent to which the fetal program switch occurs remains unclear. Limitations hindering transcriptome-wide analyses of alternative splicing differences (i.e. isoform switching) in cardiovascular system (CVS) tissues between fetal, healthy adult and heart failure have included both cellular heterogeneity across bulk RNA-seq samples and limited availability of fetal tissue for research. To overcome these limitations, we have deconvoluted the cellular compositions of 996 RNA-seq samples representing heart failure, healthy adult (heart and arteria), and fetal-like (iPSC-derived cardiovascular progenitor cells) CVS tissues. Comparison of the expression profiles revealed that reactivation of fetal-specific RNA-binding proteins (RBPs), and the accompanied re-expression of 1,523 fetal-specific isoforms, contribute to the transcriptome differences between heart failure and healthy adult heart. Of note, isoforms for 20 different RBPs were among those that reverted in heart failure to the fetal-like expression pattern. We determined that, compared with adult-specific isoforms, fetal-specific isoforms encode proteins that tend to have more functions, are more likely to harbor RBP binding sites, have canonical sequences at their splice sites, and contain typical upstream polypyrimidine tracts. Our study suggests that compared with healthy adult, fetal cardiac tissue requires stricter transcriptional regulation, and that during heart failure reversion to this stricter transcriptional regulation occurs. Furthermore, we provide a resource of cardiac developmental stage-specific and heart failure-associated genes and isoforms, which are largely unexplored and can be exploited to investigate novel therapeutics for heart failure. Heart failure is a chronic condition in which the heart does not pump enough blood. It has been shown that in heart failure, the adult heart reverts to a fetal-like metabolic state and oxygen consumption. Additionally, genes and isoforms that are expressed in the heart only during fetal development (i.e. not in the healthy adult heart) are turned on in heart failure. However, the underlying molecular mechanisms and the extent to which the switch to a fetal gene program occurs remains unclear. In this study, we initially characterized the differences between the fetal and adult heart transcriptomes (entire set of expressed genes and isoforms). We found that RNA binding proteins (RBPs), a family of genes that regulate multiple aspects of a transcript’s maturation, including transcription, splicing and post-transcriptional modifications, play a central role in the differences between fetal and adult heart tissues. We observed that many RBPs that are only expressed in the heart during fetal development become reactivated in heart failure, resulting in the expression of 1,523 fetal-specific isoforms. These findings suggest that reactivation of fetal-specific RBPs in heart failure drives a transcriptome-wide switch to expression of fetal-specific isoforms; and hence that RBPs could potentially serve as novel therapeutic targets.
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Li H, Li K, Zhu Q, Tang Z, Wang Z. Transcriptomic analysis of bladder tissue in a rat model of ketamine-induced bladder fibrosis. Neurourol Urodyn 2022; 41:765-776. [PMID: 35170809 DOI: 10.1002/nau.24892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 11/10/2022]
Abstract
INTRODUCTION Ketamine-induced cystitis (KIC) is a disease caused by ketamine that can cause lower urinary tract symptoms (LUTS). Its end-stage is bladder contracture, which is related to bladder fibrosis and poses a serious burden to patient lives. METHODS We established a KIC model in female Sprague Dawley rats and verified bladder fibrosis in the model by Masson trichrome staining and western blot analysis. The bladders of the rats from the ketamine and control groups were used to perform transcriptome analysis. In particular, association analysis with metabolomics was also used to determine the potential mechanisms of ketamine-induced bladder fibrosis. RESULTS A total of 685 differentially expressed messenger RNAs, 71 differentially expressed long noncoding RNAs, 23 differentially expressed microRNAs, and 68 differentially expressed circular RNAs were identified. We found that ribosome, Wnt signaling, vascular endothelial growth factor signaling, cytoskeleton organization, and cytoskeletal protein binding may be potential pathways in ketamine-induced bladder fibrosis as identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. In addition, the mitogen-activated protein kinase pathway appeared to be closely related to the development of ketamine-induced bladder fibrosis according to association analysis. CONCLUSIONS In this study, using transcriptomic and correlation analyses of metabolomics, we identified pathways that may be potential targets for the prevention and treatment of ketamine-induced bladder fibrosis.
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Affiliation(s)
- Haozhen Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Department of Urology, The second hospital of Dalian medical university, Dalian, Liaoning, China
| | - Kaixuan Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Provincial Laboratory for Diagnosis and Treatment of Genitourinary System Disease, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Quan Zhu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Provincial Laboratory for Diagnosis and Treatment of Genitourinary System Disease, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhengyan Tang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Provincial Laboratory for Diagnosis and Treatment of Genitourinary System Disease, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhao Wang
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China.,Provincial Laboratory for Diagnosis and Treatment of Genitourinary System Disease, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
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Inhibition of Src improves cardiac fibrosis in AngII-induced hypertrophy by regulating the expression of galectin-3. Microvasc Res 2022; 142:104347. [DOI: 10.1016/j.mvr.2022.104347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 12/15/2022]
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Ilieva M, Miller HE, Agarwal A, Paulus GK, Madsen JH, Bishop AJR, Kauppinen S, Uchida S. FibroDB: Expression Analysis of Protein-Coding and Long Non-Coding RNA Genes in Fibrosis. Noncoding RNA 2022; 8:ncrna8010013. [PMID: 35202087 PMCID: PMC8877069 DOI: 10.3390/ncrna8010013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 01/25/2022] [Accepted: 01/27/2022] [Indexed: 02/06/2023] Open
Abstract
Most long non-coding RNAs (lncRNAs) are expressed at lower levels than protein-coding genes and their expression is often restricted to specific cell types, certain time points during development, and various stress and disease conditions, respectively. To revisit this long-held concept, we focused on fibroblasts, a common cell type in various organs and tissues. Using fibroblasts and changes in their expression profiles during fibrosis as a model system, we show that the overall expression level of lncRNA genes is significantly lower than that of protein-coding genes. Furthermore, we identified lncRNA genes whose expression is upregulated during fibrosis. Using dermal fibroblasts as a model, we performed loss-of-function experiments and show that the knockdown of the lncRNAs LINC00622 and LINC01711 result in gene expression changes associated with cellular and inflammatory responses, respectively. Since there are no lncRNA databases focused on fibroblasts and fibrosis, we built a web application, FibroDB, to further promote functional and mechanistic studies of fibrotic lncRNAs.
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Affiliation(s)
- Mirolyuba Ilieva
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.); (S.K.)
| | - Henry E. Miller
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA; (H.E.M.); (A.J.R.B.)
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- Bioinformatics Research Network, Atlanta, GA 30317, USA; (A.A.); (G.K.P.)
| | - Arav Agarwal
- Bioinformatics Research Network, Atlanta, GA 30317, USA; (A.A.); (G.K.P.)
- Language Technologies Institute, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Gabriela K. Paulus
- Bioinformatics Research Network, Atlanta, GA 30317, USA; (A.A.); (G.K.P.)
- Osthus GmbH, 52068 Aachen, Germany
| | - Jens Hedelund Madsen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.); (S.K.)
| | - Alexander J. R. Bishop
- Department of Cell Systems and Anatomy, UT Health San Antonio, San Antonio, TX 78229, USA; (H.E.M.); (A.J.R.B.)
- Greehey Children’s Cancer Research Institute, UT Health San Antonio, San Antonio, TX 78229, USA
- May’s Cancer Center, UT Health San Antonio, San Antonio, TX 78229, USA
| | - Sakari Kauppinen
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.); (S.K.)
| | - Shizuka Uchida
- Center for RNA Medicine, Department of Clinical Medicine, Aalborg University, DK-2450 Copenhagen, Denmark; (M.I.); (J.H.M.); (S.K.)
- Correspondence: or
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Zhu H, Zhang Y, Zhang C, Xie Z. RNA-Binding Profiles of CKAP4 as an RNA-Binding Protein in Myocardial Tissues. Front Cardiovasc Med 2022; 8:773573. [PMID: 35004889 PMCID: PMC8733325 DOI: 10.3389/fcvm.2021.773573] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/29/2021] [Indexed: 01/08/2023] Open
Abstract
Background: Pathological tissue remodeling such as fibrosis is developed in various cardiac diseases. As one of cardiac activated-myofibroblast protein markers, CKAP4 may be involved in this process and the mechanisms have not been explored. Methods: We assumed that CKAP4 held a role in the regulation of cardiac fibrotic remodeling as an RNA-binding protein. Using improved RNA immunoprecipitation and sequencing (iRIP-seq), we sought to analyze the RNAs bound by CKAP4 in normal atrial muscle (IP1 group) and remodeling fibrotic atrial muscle (IP2 group) from patients with cardiac valvular disease. Quantitative PCR and Western blotting were applied to identify CKAP4 mRNA and protein expression levels in human right atrium samples. Results: iRIP-seq was successfully performed, CKAP4-bound RNAs were characterized. By statistically analyzing the distribution of binding peaks in various regions on the reference human genome, we found that the reads of IP samples were mainly distributed in the intergenic and intron regions implying that CKAP4 is more inclined to combine non-coding RNAs. There were 913 overlapping binding peaks between the IP1 and IP2 groups. The top five binding motifs were obtained by HOMER, in which GGGAU was the binding sequence that appeared simultaneously in both IP groups. Binding peak-related gene cluster enrichment analysis demonstrated these genes were mainly involved in biological processes such as signal transduction, protein phosphorylation, axonal guidance, and cell connection. The signal pathways ranking most varied in the IP2 group compared to the IP1 group were relating to mitotic cell cycle, protein ubiquitination and nerve growth factor receptors. More impressively, peak analysis revealed the lncRNA-binding features of CKAP4 in both IP groups. Furthermore, qPCR verified CKAP4 differentially bound lncRNAs including LINC00504, FLJ22447, RP11-326N17.2, and HELLPAR in remodeling myocardial tissues when compared with normal myocardial tissues. Finally, the expression of CKAP4 is down-regulated in human remodeling fibrotic atrium. Conclusions: We reveal certain RNA-binding features of CKAP4 suggesting a relevant role as an unconventional RNA-binding protein in cardiac remodeling process. Deeper structural and functional analysis will be helpful to enrich the regulatory network of cardiac remodeling and to identify potential therapeutic targets.
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Affiliation(s)
- Hong Zhu
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Yanfeng Zhang
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Chengliang Zhang
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhongshang Xie
- Department of Cardiovascular Surgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
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45
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Schneider-Lunitz V, Ruiz-Orera J, Hubner N, van Heesch S. Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes. PLoS Comput Biol 2021; 17:e1009658. [PMID: 34879078 PMCID: PMC8687540 DOI: 10.1371/journal.pcbi.1009658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/20/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulation in vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Like the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8—all identified as multifunctional RBPs by our analysis—selectively influence target translation rates depending on 5’ UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression. The lifecycle of an RNA molecule is controlled by hundreds of proteins that can bind RNA, also known as RNA-binding proteins (RBPs). These proteins recognize landing sites within the RNA and guide the RNA’s transcription from DNA, its processing into a mature messenger RNA, its translation into protein, or its degradation once the RNA is no longer needed. Although we now mechanistically understand how certain RBPs regulate these processes, for many RBP-target interactions the consequences imposed by RNA binding are not well understood. For 143 RBPs with known RNA binding positions, the authors of the current study investigated how RNA molecules responded to fluctuations in the expression levels of these RBPs, across each of 80 human hearts. Using statistical approaches, they could show that many RBPs influenced stages of the RNA lifecycle that they were not known to be involved in. Some RBPs turned out to be true "all-rounders" of RNA metabolism: they controlled the RNA transcript levels of some genes, whereas they influenced the translation rates of others. This unexpected multifunctionality unveiled previously hidden aspects of the everyday RNA-binding protein working life.
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Affiliation(s)
- Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- * E-mail: (NH); (SvH)
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- * E-mail: (NH); (SvH)
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Li Y, Shi Y, He Y, Li X, Yang J. RNA binding Motif protein-38 regulates myocardial hypertrophy in LXR-α-dependent lipogenesis pathway. Bioengineered 2021; 12:9655-9667. [PMID: 34854353 PMCID: PMC8809983 DOI: 10.1080/21655979.2021.1977552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Myocardial hypertrophy is a pathological thickening of the myocardium, leading to various ailments, such as myocardial infarction and heart failure. RBM38 is critical in modulating mRNA translation for multiple protective activities such as p53 tumor repressor and p21 kinase cell cycle inhibitors. Liver X receptors (LXR-α) agonists reduce cellular hypertrophy initiated by various hypertrophic stimuli as lipopolysaccharides and Ang II. This research investigates the possible cooperation between RBM38 and LXR-α and mechanisms in modulating myocardial hypertrophy. H9C2 cells were treated with PE, TNF-α, and AngII to induce myocardial hypertrophy. RBM38 and LXR- α were overexpressed or silenced in H9C2 cells, and hypertrophy markers (ANF and Myh7) were determined with Western blot and RT-qPCR. Binding assays were done through RNA immunoprecipitation. H&E and Rhodamine-labeled phalloidin staining assays were used to assess the relative cell surface change. The results demonstrated RBM38 downregulation in in vitro models of myocardial hypertrophy. Modulation of RBM38 expression also exerted inverse effects on myocardial hypertrophy markers. Further observations also showed that LXR-α expression regulates the myocardial hypertrophy markers in H9C2 cells and RBM38 binds with LXR-α mRNA, consequently inhibiting LXR-α expression. Finally, overexpression of RBM38 rescues Angiotensin II-induced myocardial hypertrophy by regulating LXR-α dependent lipogenesis pathway. In conclusion, RBM38 Overexpression rescues Angiotensin II-induced myocardial hypertrophy by regulating LXR-α dependent lipogenesis pathway.
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Affiliation(s)
- Yao Li
- Department of Cardiovascular Medicine, Baoji People's Hospital, Baoji City, Shaanxi Province, China
| | - Yanhu Shi
- Department of Cardiology, Baoji Chinese Medicine Hospital, Baoji City, Shaanxi Province, China
| | - Yaoli He
- Department of Geriatric Cardio-cerebrovascular Diseases, Baoji Central Hospital, Baoji City, Shaanxi Province, China
| | - Xiaoming Li
- Department of Cardiovascular Medicine, Baoji Central Hospital, Baoji City, Shaanxi Province, China
| | - Junlu Yang
- Department of Cardiovascular Medicine, Baoji Chinese Medicine Hospital, Baoji City, Shaanxi Province, China
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47
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Palano G, Foinquinos A, Müllers E. In vitro Assays and Imaging Methods for Drug Discovery for Cardiac Fibrosis. Front Physiol 2021; 12:697270. [PMID: 34305651 PMCID: PMC8298031 DOI: 10.3389/fphys.2021.697270] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/07/2021] [Indexed: 12/20/2022] Open
Abstract
As a result of stress, injury, or aging, cardiac fibrosis is characterized by excessive deposition of extracellular matrix (ECM) components resulting in pathological remodeling, tissue stiffening, ventricular dilatation, and cardiac dysfunction that contribute to heart failure (HF) and eventually death. Currently, there are no effective therapies specifically targeting cardiac fibrosis, partially due to limited understanding of the pathological mechanisms and the lack of predictive in vitro models for high-throughput screening of antifibrotic compounds. The use of more relevant cell models, three-dimensional (3D) models, and coculture systems, together with high-content imaging (HCI) and machine learning (ML)-based image analysis, is expected to improve predictivity and throughput of in vitro models for cardiac fibrosis. In this review, we present an overview of available in vitro assays for cardiac fibrosis. We highlight the potential of more physiological 3D cardiac organoids and coculture systems and discuss HCI and automated artificial intelligence (AI)-based image analysis as key methods able to capture the complexity of cardiac fibrosis in vitro. As 3D and coculture models will soon be sufficiently mature for application in large-scale preclinical drug discovery, we expect the combination of more relevant models and high-content analysis to greatly increase translation from in vitro to in vivo models and facilitate the discovery of novel targets and drugs against cardiac fibrosis.
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Affiliation(s)
- Giorgia Palano
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Ariana Foinquinos
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Erik Müllers
- Bioscience Cardiovascular, Research and Early Development, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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48
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Witte F, Ruiz-Orera J, Mattioli CC, Blachut S, Adami E, Schulz JF, Schneider-Lunitz V, Hummel O, Patone G, Mücke MB, Šilhavý J, Heinig M, Bottolo L, Sanchis D, Vingron M, Chekulaeva M, Pravenec M, Hubner N, van Heesch S. A trans locus causes a ribosomopathy in hypertrophic hearts that affects mRNA translation in a protein length-dependent fashion. Genome Biol 2021; 22:191. [PMID: 34183069 PMCID: PMC8240307 DOI: 10.1186/s13059-021-02397-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 06/02/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Little is known about the impact of trans-acting genetic variation on the rates with which proteins are synthesized by ribosomes. Here, we investigate the influence of such distant genetic loci on the efficiency of mRNA translation and define their contribution to the development of complex disease phenotypes within a panel of rat recombinant inbred lines. RESULTS We identify several tissue-specific master regulatory hotspots that each control the translation rates of multiple proteins. One of these loci is restricted to hypertrophic hearts, where it drives a translatome-wide and protein length-dependent change in translational efficiency, altering the stoichiometric translation rates of sarcomere proteins. Mechanistic dissection of this locus across multiple congenic lines points to a translation machinery defect, characterized by marked differences in polysome profiles and misregulation of the small nucleolar RNA SNORA48. Strikingly, from yeast to humans, we observe reproducible protein length-dependent shifts in translational efficiency as a conserved hallmark of translation machinery mutants, including those that cause ribosomopathies. Depending on the factor mutated, a pre-existing negative correlation between protein length and translation rates could either be enhanced or reduced, which we propose to result from mRNA-specific imbalances in canonical translation initiation and reinitiation rates. CONCLUSIONS We show that distant genetic control of mRNA translation is abundant in mammalian tissues, exemplified by a single genomic locus that triggers a translation-driven molecular mechanism. Our work illustrates the complexity through which genetic variation can drive phenotypic variability between individuals and thereby contribute to complex disease.
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Affiliation(s)
- Franziska Witte
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: NUVISAN ICB GmbH, Lead Discovery-Structrual Biology, 13353, Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Camilla Ciolli Mattioli
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
- Present Address: Department of Biological Regulation, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Susanne Blachut
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Eleonora Adami
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- Present Address: Program in Cardiovascular and Metabolic Disorders, Duke-National University of Singapore, Singapore, 169857, Singapore
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Oliver Hummel
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Giannino Patone
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
| | - Michael Benedikt Mücke
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany
- Charité-Universitätsmedizin, 10117, Berlin, Germany
| | - Jan Šilhavý
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Matthias Heinig
- Institute of Computational Biology (ICB), HMGU, Ingolstaedter Landstr. 1, 85764 Neuherberg, Munich, Germany
- Department of Informatics, Technische Universitaet Muenchen (TUM), Boltzmannstr. 3, 85748 Garching, Munich, Germany
| | - Leonardo Bottolo
- Department of Medical Genetics, University of Cambridge, Cambridge, CB2 0QQ, UK
- The Alan Turing Institute, London, NW1 2DB, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, UK
| | - Daniel Sanchis
- Institut de Recerca Biomedica de Lleida (IRBLLEIDA), Universitat de Lleida, Edifici Biomedicina-I. Av. Rovira Roure, 80, 25198, Lleida, Spain
| | - Martin Vingron
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany
| | - Marina Chekulaeva
- Berlin Institute for Medical Systems Biology (BIMSB), Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 10115, Berlin, Germany
| | - Michal Pravenec
- Institute of Physiology of the Czech Academy of Sciences, 4, 142 20, Praha, Czech Republic
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, 13347, Berlin, Germany.
- Charité-Universitätsmedizin, 10117, Berlin, Germany.
| | - Sebastiaan van Heesch
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125, Berlin, Germany.
- Present Address: The Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands.
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Chen X, Yin J, Cao D, Xiao D, Zhou Z, Liu Y, Shou W. The Emerging Roles of the RNA Binding Protein QKI in Cardiovascular Development and Function. Front Cell Dev Biol 2021; 9:668659. [PMID: 34222237 PMCID: PMC8242579 DOI: 10.3389/fcell.2021.668659] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/10/2021] [Indexed: 12/30/2022] Open
Abstract
RNA binding proteins (RBPs) have a broad biological and physiological function and are critical in regulating pre-mRNA posttranscriptional processing, intracellular migration, and mRNA stability. QKI, also known as Quaking, is a member of the signal transduction and activation of RNA (STAR) family, which also belongs to the heterogeneous nuclear ribonucleoprotein K- (hnRNP K-) homology domain protein family. There are three major alternatively spliced isoforms, QKI-5, QKI-6, and QKI-7, differing in carboxy-terminal domains. They share a common RNA binding property, but each isoform can regulate pre-mRNA splicing, transportation or stability differently in a unique cell type-specific manner. Previously, QKI has been known for its important role in contributing to neurological disorders. A series of recent work has further demonstrated that QKI has important roles in much broader biological systems, such as cardiovascular development, monocyte to macrophage differentiation, bone metabolism, and cancer progression. In this mini-review, we will focus on discussing the emerging roles of QKI in regulating cardiac and vascular development and function and its potential link to cardiovascular pathophysiology.
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Affiliation(s)
- Xinyun Chen
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Jianwen Yin
- Department of Foot, Ankle and Hand Surgery, Shenzhen Second People’s Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Dayan Cao
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Deyong Xiao
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Zhongjun Zhou
- Faculty of Medicine, School of Biomedical Sciences, The University of Hong Kong, Hong Kong
| | - Ying Liu
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Weinian Shou
- Department of Pediatrics, Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
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Reconstruction of the miR-506-Quaking axis in Idiopathic Pulmonary Fibrosis using integrative multi-source bioinformatics. Sci Rep 2021; 11:12456. [PMID: 34127686 PMCID: PMC8203802 DOI: 10.1038/s41598-021-89531-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/21/2021] [Indexed: 12/17/2022] Open
Abstract
The family of RNA-binding proteins (RBP) functions as a crucial regulator of multiple biological processes and diseases. However, RBP function in the clinical setting of idiopathic pulmonary fibrosis (IPF) is still unknown. We developed a practical in silico screening approach for the characterization of RBPs using multi-sources data information and comparative molecular network bioinformatics followed by wet-lab validation studies. Data mining of bulk RNA-Sequencing data of tissues of patients with IPF identified Quaking (QKI) as a significant downregulated RBP. Cell-type specific expression was confirmed by single-cell RNA-Sequencing analysis of IPF patient data. We systematically analyzed the molecular interaction network around QKI and its functional interplay with microRNAs (miRs) in human lung fibroblasts and discovered a novel regulatory miR-506-QKI axis contributing to the pathogenesis of IPF. The in silico results were validated by in-house experiments applying model systems of miR and lung biology. This study supports an understanding of the intrinsic molecular mechanisms of IPF regulated by the miR-506-QKI axis. Initially applied to human lung disease, the herein presented integrative in silico data mining approach can be adapted to other disease entities, underlining its practical relevance in RBP research.
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