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Lu S, Di John Portela I, Martino N, Bossardi Ramos R, Salinero AE, Smith RM, Zuloaga KL, Adam AP. A transient brain endothelial translatome response to endotoxin is associated with mild cognitive changes post-shock in young mice. Neuroscience 2024; 555:194-204. [PMID: 39067684 DOI: 10.1016/j.neuroscience.2024.07.041] [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: 05/16/2024] [Revised: 07/10/2024] [Accepted: 07/23/2024] [Indexed: 07/30/2024]
Abstract
Sepsis-associated encephalopathy (SAE) is associated with increased risk of long-term cognitive impairment. SAE is driven, at least in part, by brain endothelial dysfunction in response to systemic cytokine signaling. However, the mechanisms driving SAE and its consequences remain largely unknown. Here, we performed translating ribosome affinity purification and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge. LPS induced a strong acute transcriptional response in the brain endothelium that partially correlates with the whole brain transcriptional response and suggested an endothelial-specific hypoxia response. Consistent with a crucial role for IL-6, loss of the main regulator of this pathway, SOCS3, leads to a broadening of the population of genes responsive to LPS, suggesting that an overactivation of the IL-6/JAK/STAT3 pathway leads to an increased transcriptional response that could explain our prior findings of severe brain injury in these mice. To identify any potential sequelae of this acute response, we performed brain TRAP-seq following a battery of behavioral tests in mice after apparent recovery. We found that the transcriptional response returns to baseline within days post-challenge, but reductions in gene expression regulating protein translation and respiratory electron transport remained. We observed that mice that recovered from the endotoxemic shock showed mild, sex-dependent cognitive impairment, suggesting that the acute brain injury led to sustained effects. A better understanding of the transcriptional and non-transcriptional changes in response to shock is needed in order to prevent and/or revert the devastating consequences of septic shock.
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Affiliation(s)
- Shuhan Lu
- Department of Molecular and Cellular Physiology, Albany Medical College, United States
| | - Iria Di John Portela
- Department of Molecular and Cellular Physiology, Albany Medical College, United States
| | - Nina Martino
- Department of Molecular and Cellular Physiology, Albany Medical College, United States
| | - Ramon Bossardi Ramos
- Department of Molecular and Cellular Physiology, Albany Medical College, United States
| | - Abigail E Salinero
- Department of Neuroscience & Experimental Therapeutics, Albany Medical College, United States
| | - Rachel M Smith
- Department of Neuroscience & Experimental Therapeutics, Albany Medical College, United States
| | - Kristen L Zuloaga
- Department of Neuroscience & Experimental Therapeutics, Albany Medical College, United States
| | - Alejandro P Adam
- Department of Molecular and Cellular Physiology, Albany Medical College, United States; Department of Ophthalmology, Albany Medical College, United States.
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2
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Artimagnella O, Maftei ES, Esposito M, Sanges R, Mallamaci A. Foxg1 regulates translation of neocortical neuronal genes, including the main NMDA receptor subunit gene, Grin1. BMC Biol 2024; 22:180. [PMID: 39183266 PMCID: PMC11346056 DOI: 10.1186/s12915-024-01979-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: 08/04/2023] [Accepted: 08/12/2024] [Indexed: 08/27/2024] Open
Abstract
BACKGROUND Mainly known as a transcription factor patterning the rostral brain and governing its histogenesis, FOXG1 has been also detected outside the nucleus; however, biological meaning of that has been only partially clarified. RESULTS Prompted by FOXG1 expression in cytoplasm of pallial neurons, we investigated its implication in translational control. We documented the impact of FOXG1 on ribosomal recruitment of Grin1-mRNA, encoding for the main subunit of NMDA receptor. Next, we showed that FOXG1 increases GRIN1 protein level by enhancing the translation of its mRNA, while not increasing its stability. Molecular mechanisms underlying this activity included FOXG1 interaction with EIF4E and, possibly, Grin1-mRNA. Besides, we found that, within murine neocortical cultures, de novo synthesis of GRIN1 undergoes a prominent and reversible, homeostatic regulation and FOXG1 is instrumental to that. Finally, by integrated analysis of multiple omic data, we inferred that FOXG1 is implicated in translational control of hundreds of neuronal genes, modulating ribosome engagement and progression. In a few selected cases, we experimentally verified such inference. CONCLUSIONS These findings point to FOXG1 as a key effector, potentially crucial to multi-scale temporal tuning of neocortical pyramid activity, an issue with profound physiological and neuropathological implications.
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Affiliation(s)
- Osvaldo Artimagnella
- Laboratory of Cerebral Cortex Development, SISSA, Via Bonomea 265, 34136, Trieste, Italy
- Present Address: IRCCS Centro Neurolesi "Bonino-Pulejo", Messina, Italy
| | - Elena Sabina Maftei
- Laboratory of Cerebral Cortex Development, SISSA, Via Bonomea 265, 34136, Trieste, Italy
| | - Mauro Esposito
- Laboratory of Computational Genomics, SISSA, via Bonomea 265, 34136, Trieste, Italy
- Present Address: Neomatrix SRL, Rome, Italy
| | - Remo Sanges
- Laboratory of Computational Genomics, SISSA, via Bonomea 265, 34136, Trieste, Italy
| | - Antonello Mallamaci
- Laboratory of Cerebral Cortex Development, SISSA, Via Bonomea 265, 34136, Trieste, Italy.
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3
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Nicholas SAE, Helming SR, Ménoret A, Pathoulas C, Xu MM, Hensel J, Kimble AL, Heineman B, Jellison ER, Reese B, Zhou B, Rodriguez-Oquendo A, Vella AT, Murphy PA. Endothelial Immunosuppression in Atherosclerosis : Translational Control by Elavl1/HuR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.605922. [PMID: 39131295 PMCID: PMC11312609 DOI: 10.1101/2024.08.02.605922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
Atherosclerotic plaques are defined by the accumulation of lipids and immune cells beneath the endothelium of the arterial intima. CD8 T cells are among the most abundant immune cell types in plaque, and conditions linked to their activation correlate with increased levels of cardiovascular disease. As lethal effectors of the immune response, CD8 T cell activation is suppressed at multiple levels. These checkpoints are critical in dampening autoimmune responses, and limiting damage in cardiovascular disease. Endothelial cells are well known for their role in recruiting CD8 T and other hematopoietic cells to low and disturbed flow (LDF) arterial regions that develop plaque, but whether they locally influence CD8 effector functions is unclear. Here, we show that endothelial cells can actively suppress CD8 T cell responses in settings of chronic plaque inflammation, but that this behavior is governed by expression of the RNA-binding protein Embryonic Lethal, Abnormal Vision-Like 1 (Elavl1). In response to immune cell recruitment in plaque, the endothelium dynamically shifts splicing of pre-mRNA and their translation to enhance expression of immune-regulatory proteins including C1q and CD27. This program is immuno-suppressive, and limited by Elavl1. We show this by Cdh5(PAC)-CreERT2-mediated deletion of Elavl1 (ECKO), and analysis of changes in translation by Translating Ribosome Affinity Purification (TRAP). In ECKO mice, the translational shift in chronic inflammation is enhanced, leading to increased ribosomal association of C1q components and other critical regulators of immune response and resulting in a ~70% reduction in plaque CD8 T cells. CITE-seq analysis of the remaining plaque T cells shows that they exhibit lower levels of markers associated with T cell receptor (TCR) signaling, survival, and activation. To understand whether the immunosuppressive mechanism occurred through failed CD8 recruitment or local modulation of T cell responses, we used a novel in vitro co-culture system to show that ECKO endothelial cells suppress CD8 T cell expansion-even in the presence of wild-type myeloid antigen-presenting cells, antigen-specific CD8 T cells, and antigen. Despite the induction of C1q mRNA by T cell co-culture in both wild-type and ECKO endothelial cells, we find C1q protein abundantly expressed only in co-culture with ECKO cells. Together, our data define a novel immune-suppressive transition in the endothelium, reminiscent of the transition of T cells to T-regs, and demonstrate the regulation of this process by Elavl1.
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Affiliation(s)
- Sarah-Anne E Nicholas
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
| | - Stephen R Helming
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
| | | | - Christopher Pathoulas
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
| | - Maria M Xu
- Department of Immunology, UCONN Health, Farmington, CT
| | - Jessica Hensel
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
| | - Amy L Kimble
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
| | - Brent Heineman
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
| | | | - Bo Reese
- Institute for Systems Genomics - Center for Genome Innovation, UCONN, Storrs, CT
| | - Beiyan Zhou
- Department of Immunology, UCONN Health, Farmington, CT
| | | | | | - Patrick A Murphy
- Center for Vascular Biology and Calhoun Cardiology Center, UCONN Health School of Medicine, Farmington, CT
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4
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Lu S, John Portela ID, Martino N, Ramos RB, Salinero AE, Smith RM, Zuloaga KL, Adam AP. A transient brain endothelial translatome response to endotoxin is associated with mild cognitive changes post-shock in young mice. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.03.583191. [PMID: 38496442 PMCID: PMC10942387 DOI: 10.1101/2024.03.03.583191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Sepsis-associated encephalopathy (SAE) is a common manifestation in septic patients that is associated with increased risk of long-term cognitive impairment. SAE is driven, at least in part, by brain endothelial dysfunction in response to systemic cytokine signaling. However, the mechanisms driving SAE and its consequences remain largely unknown. Here, we performed translating ribosome affinity purification and RNA-sequencing (TRAP-seq) from the brain endothelium to determine the transcriptional changes after an acute endotoxemic (LPS) challenge. LPS induced a strong acute transcriptional response in the brain endothelium that partially correlates with the whole brain transcriptional response and suggested an endothelial-specific hypoxia response. Consistent with a crucial role for IL-6, loss of the main regulator of this pathway, SOCS3, leads to a broadening of the population of genes responsive to LPS, suggesting that an overactivation of the IL-6/JAK/STAT3 pathway leads to an increased transcriptional response that could explain our prior findings of severe brain injury in these mice. To identify any potential sequelae of this acute response, we performed brain TRAP-seq following a battery of behavioral tests in mice after apparent recovery. We found that the transcriptional response returns to baseline within days post-challenge. Despite the transient nature of the response, we observed that mice that recovered from the endotoxemic shock showed mild, sex-dependent cognitive impairment, suggesting that the acute brain injury led to sustained, non-transcriptional effects. A better understanding of the transcriptional and non-transcriptional changes in response to shock is needed in order to prevent and/or revert the devastating consequences of septic shock. Abstract Figure
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He X, Yang T, Lu YW, Wu G, Dai G, Ma Q, Zhang M, Zhou H, Long T, Yan Y, Liang Z, Liu C, Pu WT, Dong Y, Ou J, Chen H, Mably JD, He J, Wang DZ, Huang ZP. The long noncoding RNA CARDINAL attenuates cardiac hypertrophy by modulating protein translation. J Clin Invest 2024; 134:e169112. [PMID: 38743498 PMCID: PMC11213465 DOI: 10.1172/jci169112] [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: 01/25/2023] [Accepted: 05/07/2024] [Indexed: 05/16/2024] Open
Abstract
One of the features of pathological cardiac hypertrophy is enhanced translation and protein synthesis. Translational inhibition has been shown to be an effective means of treating cardiac hypertrophy, although system-wide side effects are common. Regulators of translation, such as cardiac-specific long noncoding RNAs (lncRNAs), could provide new, more targeted therapeutic approaches to inhibit cardiac hypertrophy. Therefore, we generated mice lacking a previously identified lncRNA named CARDINAL to examine its cardiac function. We demonstrate that CARDINAL is a cardiac-specific, ribosome-associated lncRNA and show that its expression was induced in the heart upon pathological cardiac hypertrophy and that its deletion in mice exacerbated stress-induced cardiac hypertrophy and augmented protein translation. In contrast, overexpression of CARDINAL attenuated cardiac hypertrophy in vivo and in vitro and suppressed hypertrophy-induced protein translation. Mechanistically, CARDINAL interacted with developmentally regulated GTP-binding protein 1 (DRG1) and blocked its interaction with DRG family regulatory protein 1 (DFRP1); as a result, DRG1 was downregulated, thereby modulating the rate of protein translation in the heart in response to stress. This study provides evidence for the therapeutic potential of targeting cardiac-specific lncRNAs to suppress disease-induced translational changes and to treat cardiac hypertrophy and heart failure.
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Affiliation(s)
- Xin He
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Tiqun Yang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Yao Wei Lu
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gengze Wu
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Gang Dai
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Qing Ma
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Mingming Zhang
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Huimin Zhou
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Tianxin Long
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Youchen Yan
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Zhuomin Liang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Chen Liu
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Yugang Dong
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Jingsong Ou
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
- Division of Cardiac Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, Key Laboratory of Assisted Circulation and Vascular Diseases, Chinese Academy of Medical Sciences, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Hong Chen
- Vascular Biology Program, Department of Surgery, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - John D. Mably
- Center for Regenerative Medicine, USF Health Heart Institute and
| | - Jiangui He
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
| | - Da-Zhi Wang
- Department of Cardiology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Center for Regenerative Medicine, USF Health Heart Institute and
- Departments of Internal Medicine, Molecular Pharmacology and Physiology, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Zhan-Peng Huang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou, China
- Division of Cardiac Surgery, National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, Key Laboratory of Assisted Circulation and Vascular Diseases, Chinese Academy of Medical Sciences, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
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Sikder K, Phillips E, Zhong Z, Wang N, Saunders J, Mothy D, Kossenkov A, Schneider T, Nichtova Z, Csordas G, Margulies KB, Choi JC. Perinuclear damage from nuclear envelope deterioration elicits stress responses that contribute to LMNA cardiomyopathy. SCIENCE ADVANCES 2024; 10:eadh0798. [PMID: 38718107 PMCID: PMC11078192 DOI: 10.1126/sciadv.adh0798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 04/03/2024] [Indexed: 05/12/2024]
Abstract
Mutations in the LMNA gene encoding lamins A/C cause an array of tissue-selective diseases, with the heart being the most commonly affected organ. Despite progress in understanding the perturbations emanating from LMNA mutations, an integrative understanding of the pathogenesis underlying cardiac dysfunction remains elusive. Using a novel conditional deletion model capable of translatome profiling, we observed that cardiomyocyte-specific Lmna deletion in adult mice led to rapid cardiomyopathy with pathological remodeling. Before cardiac dysfunction, Lmna-deleted cardiomyocytes displayed nuclear abnormalities, Golgi dilation/fragmentation, and CREB3-mediated stress activation. Translatome profiling identified MED25 activation, a transcriptional cofactor that regulates Golgi stress. Autophagy is disrupted in the hearts of these mice, which can be recapitulated by disrupting the Golgi. Systemic administration of modulators of autophagy or ER stress significantly delayed cardiac dysfunction and prolonged survival. These studies support a hypothesis wherein stress responses emanating from the perinuclear space contribute to the LMNA cardiomyopathy development.
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Affiliation(s)
- Kunal Sikder
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Elizabeth Phillips
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Zhijiu Zhong
- Translational Research and Pathology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Nadan Wang
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Jasmine Saunders
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - David Mothy
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
| | - Andrew Kossenkov
- Bioinformatics Facility, The Wistar Institute Cancer Center, Philadelphia, PA, USA
| | - Timothy Schneider
- Mitocare, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Zuzana Nichtova
- Mitocare, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gyorgy Csordas
- Mitocare, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Kenneth B. Margulies
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jason C. Choi
- Center for Translational Medicine, Department of Medicine, Thomas Jefferson University, Philadelphia PA, USA
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7
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Kilfeather P, Khoo JH, Wagner K, Liang H, Caiazza MC, An Y, Zhang X, Chen X, Connor-Robson N, Shang Z, Wade-Martins R. Single-cell spatial transcriptomic and translatomic profiling of dopaminergic neurons in health, aging, and disease. Cell Rep 2024; 43:113784. [PMID: 38386560 DOI: 10.1016/j.celrep.2024.113784] [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: 04/12/2023] [Revised: 11/14/2023] [Accepted: 01/27/2024] [Indexed: 02/24/2024] Open
Abstract
The brain is spatially organized and contains unique cell types, each performing diverse functions and exhibiting differential susceptibility to neurodegeneration. This is exemplified in Parkinson's disease with the preferential loss of dopaminergic neurons of the substantia nigra pars compacta. Using a Parkinson's transgenic model, we conducted a single-cell spatial transcriptomic and dopaminergic neuron translatomic analysis of young and old mouse brains. Through the high resolving capacity of single-cell spatial transcriptomics, we provide a deep characterization of the expression features of dopaminergic neurons and 27 other cell types within their spatial context, identifying markers of healthy and aging cells, spanning Parkinson's relevant pathways. We integrate gene enrichment and genome-wide association study data to prioritize putative causative genes for disease investigation, identifying CASR as a regulator of dopaminergic calcium handling. These datasets represent the largest public resource for the investigation of spatial gene expression in brain cells in health, aging, and disease.
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Affiliation(s)
- Peter Kilfeather
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | | | - Katherina Wagner
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Maria Claudia Caiazza
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
| | - Yanru An
- BGI Research, 49276 Riga, Latvia
| | | | | | - Natalie Connor-Robson
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK
| | | | - Richard Wade-Martins
- Oxford Parkinson's Disease Centre and Department of Physiology, Anatomy and Genetics, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Kavli Institute for Nanoscience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, South Parks Road, Oxford OX1 3QU, UK; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA.
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Chen J, Zhang X, DeLaughter DM, Trembley MA, Saifee S, Xiao F, Chen J, Zhou P, Seidman CE, Seidman JG, Pu WT. Molecular and Spatial Signatures of Mouse Embryonic Endothelial Cells at Single-Cell Resolution. Circ Res 2024; 134:529-546. [PMID: 38348657 PMCID: PMC10906678 DOI: 10.1161/circresaha.123.323956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
BACKGROUND Mature endothelial cells (ECs) are heterogeneous, with subtypes defined by tissue origin and position within the vascular bed (ie, artery, capillary, vein, and lymphatic). How this heterogeneity is established during the development of the vascular system, especially arteriovenous specification of ECs, remains incompletely characterized. METHODS We used droplet-based single-cell RNA sequencing and multiplexed error-robust fluorescence in situ hybridization to define EC and EC progenitor subtypes from E9.5, E12.5, and E15.5 mouse embryos. We used trajectory inference to analyze the specification of arterial ECs (aECs) and venous ECs (vECs) from EC progenitors. Network analysis identified candidate transcriptional regulators of arteriovenous differentiation, which we tested by CRISPR (clustered regularly interspaced short palindromic repeats) loss of function in human-induced pluripotent stem cells undergoing directed differentiation to aECs or vECs (human-induced pluripotent stem cell-aECs or human-induced pluripotent stem cell-vECs). RESULTS From the single-cell transcriptomes of 7682 E9.5 to E15.5 ECs, we identified 19 EC subtypes, including Etv2+Bnip3+ EC progenitors. Spatial transcriptomic analysis of 15 448 ECs provided orthogonal validation of these EC subtypes and established their spatial distribution. Most embryonic ECs were grouped by their vascular-bed types, while ECs from the brain, heart, liver, and lung were grouped by their tissue origins. Arterial (Eln, Dkk2, Vegfc, and Egfl8), venous (Fam174b and Clec14a), and capillary (Kcne3) marker genes were identified. Compared with aECs, embryonic vECs and capillary ECs shared fewer markers than their adult counterparts. Early capillary ECs with venous characteristics functioned as a branch point for differentiation of aEC and vEC lineages. CONCLUSIONS Our results provide a spatiotemporal map of embryonic EC heterogeneity at single-cell resolution and demonstrate that the diversity of ECs in the embryo arises from both tissue origin and vascular-bed position. Developing aECs and vECs share common venous-featured capillary precursors and are regulated by distinct transcriptional regulatory networks.
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Affiliation(s)
- Jian Chen
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | | | | | - Shaila Saifee
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Feng Xiao
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Jiehui Chen
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Pingzhu Zhou
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
| | - Christine E. Seidman
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Cardiovascular Medicine, Brigham and Women’s Hospital, Boston, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | | | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, Boston, MA, USA
- Harvard Stem Cell Institute, Cambridge, MA, USA
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9
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Cochran JD, Leathers TA, Maldosevic E, Siejda KW, Vitello J, Lee H, Bradley LA, Young A, Jomaa A, Wolf MJ. Cell cycle specific, differentially tagged ribosomal proteins to measure phase specific transcriptomes from asynchronously cycling cells. Sci Rep 2024; 14:1623. [PMID: 38238470 PMCID: PMC10796924 DOI: 10.1038/s41598-024-52085-5] [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: 02/02/2023] [Accepted: 01/13/2024] [Indexed: 01/22/2024] Open
Abstract
Asynchronously cycling cells pose a challenge to the accurate characterization of phase-specific gene expression. Current strategies, including RNAseq, survey the steady state gene expression across the cell cycle and are inherently limited by their inability to resolve dynamic gene regulatory networks. Single cell RNAseq (scRNAseq) can identify different cell cycle transcriptomes if enough cycling cells are present, however some cells are not amenable to scRNAseq. Therefore, we merged two powerful strategies, the CDT1 and GMNN degrons used in Fluorescent Ubiquitination-based Cell Cycle Indicator (FUCCI) cell cycle sensors and the ribosomal protein epitope tagging used in RiboTrap/Tag technologies to isolate cell cycle phase-specific mRNA for sequencing. The resulting cell cycle dependent, tagged ribosomal proteins (ccTaggedRP) were differentially expressed during the cell cycle, had similar subcellular locations as endogenous ribosomal proteins, incorporated into ribosomes and polysomes, and facilitated the recovery of cell cycle phase-specific RNA for sequencing. ccTaggedRP has broad applications to investigate phase-specific gene expression in complex cell populations.
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Affiliation(s)
- Jesse D Cochran
- Medical Scientist Training Program, University of Virginia, Charlottesville, VA, USA
| | - Tess A Leathers
- Department of Anatomy, Physiology, and Cell Biology, University of California, Davis, USA
| | - Emir Maldosevic
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Klara W Siejda
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Julian Vitello
- Department of Biomedical Engineering, University of Virginia, Charlottesville, VA, USA
| | - Haesol Lee
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
| | - Leigh A Bradley
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Alex Young
- Department of Medicine, University of Virginia, Charlottesville, VA, USA
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA
| | - Ahmad Jomaa
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, USA
| | - Matthew J Wolf
- Department of Medicine, University of Virginia, Charlottesville, VA, USA.
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, USA.
- Division of Cardiology, University of Virginia, Medical Research Building 5 (MR5), Room G213, 415 Lane Road, Charlottesville, VA, 22908, USA.
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10
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Wilcox NS, Yarovinsky TO, Pandya P, Ramgolam VS, Moro A, Wu Y, Nicoli S, Hirschi KK, Bender JR. Distinct hypoxia-induced translational profiles of embryonic and adult-derived macrophages. iScience 2023; 26:107985. [PMID: 38047075 PMCID: PMC10690575 DOI: 10.1016/j.isci.2023.107985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 07/21/2023] [Accepted: 09/15/2023] [Indexed: 12/05/2023] Open
Abstract
Tissue resident macrophages are largely of embryonic (fetal liver) origin and long-lived, while bone marrow-derived macrophages (BMDM) are recruited following an acute perturbation, such as hypoxia in the setting of myocardial ischemia. Prior transcriptome analyses identified BMDM and fetal liver-derived macrophage (FLDM) differences at the RNA expression level. Posttranscriptional regulation determining mRNA stability and translation rate may override transcriptional signals in response to hypoxia. We profiled differentially regulated BMDM and FLDM transcripts in response to hypoxia at the level of mRNA translation. Using a translating ribosome affinity purification (TRAP) assay and RNA-seq, we identified non-overlapping transcripts with increased translation rate in BMDM (Ly6e, vimentin, PF4) and FLDM (Ccl7, Ccl2) after hypoxia. We further identified hypoxia-induced transcripts within these subsets that are regulated by the RNA-binding protein HuR. These findings define translational differences in macrophage subset gene expression programs, highlighting potential therapeutic targets in ischemic myocardium.
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Affiliation(s)
- Nicholas S. Wilcox
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Timur O. Yarovinsky
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Prakruti Pandya
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Vinod S. Ramgolam
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
| | - Albertomaria Moro
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Yinyu Wu
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Stefania Nicoli
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Karen K. Hirschi
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Genetics, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Jeffrey R. Bender
- Department of Internal Medicine, Section of Cardiovascular Medicine, Yale Cardiovascular Research Center, New Haven, CT USA
- Department of Immunobiology, and Yale University School of Medicine, New Haven, CT 06511, USA
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11
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Rizavi HS, Gavin HE, Krishnan HR, Gavin DP, Sharma RP. Ethanol- and PARP-Mediated Regulation of Ribosome-Associated Long Non-Coding RNA (lncRNA) in Pyramidal Neurons. Noncoding RNA 2023; 9:72. [PMID: 37987368 PMCID: PMC10661276 DOI: 10.3390/ncrna9060072] [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: 07/14/2023] [Revised: 10/23/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023] Open
Abstract
Although, by definition, long noncoding RNAs (lncRNAs) are not translated, they are sometimes associated with ribosomes. In fact, some estimates suggest the existence of more than 50 K lncRNA molecules that could encode for small peptides. We examined the effects of an ethanol and Poly-ADP Ribose Polymerase (PARP) inhibitor (ABT-888) on ribosome-bound lncRNAs. Mice were administered via intraperitoneal injection (i.p.) either normal saline (CTL) or ethanol (EtOH) twice a day for four consecutive days. On the fourth day, a sub-group of mice administered with ethanol also received ABT-888 (EtOH+ABT). Ribosome-bound lncRNAs in CaMKIIα-expressing pyramidal neurons were measured using the Translating Ribosome Affinity Purification (TRAP) technique. Our findings show that EtOH altered the attachment of 107 lncRNA transcripts, while EtOH+ABT altered 60 lncRNAs. Among these 60 lncRNAs, 49 were altered by both conditions, while EtOH+ABT uniquely altered the attachment of 11 lncRNA transcripts that EtOH alone did not affect. To validate these results, we selected eight lncRNAs (Mir124-2hg, 5430416N02Rik, Snhg17, Snhg12, Snhg1, Mir9-3hg, Gas5, and 1110038B12Rik) for qRT-PCR analysis. The current study demonstrates that ethanol-induced changes in lncRNA attachment to ribosomes can be mitigated by the addition of the PARP inhibitor ABT-888.
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Affiliation(s)
- Hooriyah S. Rizavi
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| | - Hannah E. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Harish R. Krishnan
- Center for Alcohol Research in Epigenetics, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA;
| | - David P. Gavin
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
| | - Rajiv P. Sharma
- Department of Psychiatry, University of Illinois at Chicago, Chicago, IL 60612, USA; (H.S.R.); (H.E.G.)
- Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
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12
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Gunduz-Cinar O, Castillo LI, Xia M, Van Leer E, Brockway ET, Pollack GA, Yasmin F, Bukalo O, Limoges A, Oreizi-Esfahani S, Kondev V, Báldi R, Dong A, Harvey-White J, Cinar R, Kunos G, Li Y, Zweifel LS, Patel S, Holmes A. A cortico-amygdala neural substrate for endocannabinoid modulation of fear extinction. Neuron 2023; 111:3053-3067.e10. [PMID: 37480845 PMCID: PMC10592324 DOI: 10.1016/j.neuron.2023.06.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 04/25/2023] [Accepted: 06/23/2023] [Indexed: 07/24/2023]
Abstract
Preclinical and clinical studies implicate endocannabinoids (eCBs) in fear extinction, but the underlying neural circuit basis of these actions is unclear. Here, we employed in vivo optogenetics, eCB biosensor imaging, ex vivo electrophysiology, and CRISPR-Cas9 gene editing in mice to examine whether basolateral amygdala (BLA)-projecting medial prefrontal cortex (mPFC) neurons represent a neural substrate for the effects of eCBs on extinction. We found that photoexcitation of mPFC axons in BLA during extinction mobilizes BLA eCBs. eCB biosensor imaging showed that eCBs exhibit a dynamic stimulus-specific pattern of activity at mPFC→BLA neurons that tracks extinction learning. Furthermore, using CRISPR-Cas9-mediated gene editing, we demonstrated that extinction memory formation involves eCB activity at cannabinoid CB1 receptors expressed at vmPFC→BLA synapses. Our findings reveal the temporal characteristics and a neural circuit basis of eCBs' effects on fear extinction and inform efforts to target the eCB system as a therapeutic approach in extinction-deficient neuropsychiatric disorders.
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Affiliation(s)
- Ozge Gunduz-Cinar
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.
| | - Laura I Castillo
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Maya Xia
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Elise Van Leer
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Emma T Brockway
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Gabrielle A Pollack
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Farhana Yasmin
- Northwestern Center for Psychiatric Neuroscience, Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Olena Bukalo
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Aaron Limoges
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Sarvar Oreizi-Esfahani
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Veronika Kondev
- Vanderbilt Brain Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rita Báldi
- Northwestern Center for Psychiatric Neuroscience, Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Ao Dong
- Peking University School of Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Judy Harvey-White
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Resat Cinar
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA; Section on Fibrotic Disorders, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - George Kunos
- Laboratory of Physiologic Studies, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA
| | - Yulong Li
- Peking University School of Life Sciences, PKU-IDG/McGovern Institute for Brain Research, Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Larry S Zweifel
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98195, USA; Department of Pharmacology, University of Washington, Seattle, WA 98195, USA
| | - Sachin Patel
- Northwestern Center for Psychiatric Neuroscience, Department of Psychiatry and Behavioral Sciences, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrew Holmes
- Laboratory of Behavioral and Genomic Neuroscience, National Institute on Alcohol Abuse and Alcoholism, NIH, Bethesda, MD 20892, USA.
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13
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Ramos RB, Martino N, Chuy D, Lu S, Zuo MXG, Balasubramanian U, Di John Portela I, Vincent PA, Adam AP. Shock drives a STAT3 and JunB-mediated coordinated transcriptional and DNA methylation response in the endothelium. J Cell Sci 2023; 136:jcs261323. [PMID: 37667913 PMCID: PMC10560554 DOI: 10.1242/jcs.261323] [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: 05/09/2023] [Accepted: 08/21/2023] [Indexed: 09/06/2023] Open
Abstract
Endothelial dysfunction is a crucial factor in promoting organ failure during septic shock. However, the underlying mechanisms are unknown. Here, we show that kidney injury after lipopolysaccharide (LPS) insult leads to strong endothelial transcriptional and epigenetic responses. Furthermore, SOCS3 loss leads to an aggravation of the responses, demonstrating a causal role for the STAT3-SOCS3 signaling axis in the acute endothelial response to LPS. Experiments in cultured endothelial cells demonstrate that IL-6 mediates this response. Furthermore, bioinformatics analysis of in vivo and in vitro transcriptomics and epigenetics suggests a role for STAT, AP1 and interferon regulatory family (IRF) transcription factors. Knockdown of STAT3 or the AP1 member JunB partially prevents the changes in gene expression, demonstrating a role for these transcription factors. In conclusion, endothelial cells respond with a coordinated response that depends on overactivated IL-6 signaling via STAT3, JunB and possibly other transcription factors. Our findings provide evidence for a critical role of IL-6 signaling in regulating shock-induced epigenetic changes and sustained endothelial activation, offering a new therapeutic target to limit vascular dysfunction.
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Affiliation(s)
- Ramon Bossardi Ramos
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Nina Martino
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Dareen Chuy
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Shuhan Lu
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Mei Xing G. Zuo
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Uma Balasubramanian
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Iria Di John Portela
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Peter A. Vincent
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
| | - Alejandro P. Adam
- Department of Molecular and Cellular Physiology, Albany Medical Center, Albany, NY 12208,USA
- Department of Ophthalmology, Albany Medical Center, Albany, NY 12208, USA
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14
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Sacharidou A, Chambliss K, Peng J, Barrera J, Tanigaki K, Luby-Phelps K, Özdemir İ, Khan S, Sirsi SR, Kim SH, Katzenellenbogen BS, Katzenellenbogen JA, Kanchwala M, Sathe AA, Lemoff A, Xing C, Hoyt K, Mineo C, Shaul PW. Endothelial ERα promotes glucose tolerance by enhancing endothelial insulin transport to skeletal muscle. Nat Commun 2023; 14:4989. [PMID: 37591837 PMCID: PMC10435471 DOI: 10.1038/s41467-023-40562-w] [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: 08/12/2021] [Accepted: 08/01/2023] [Indexed: 08/19/2023] Open
Abstract
The estrogen receptor (ER) designated ERα has actions in many cell and tissue types that impact glucose homeostasis. It is unknown if these include mechanisms in endothelial cells, which have the potential to influence relative obesity, and processes in adipose tissue and skeletal muscle that impact glucose control. Here we show that independent of impact on events in adipose tissue, endothelial ERα promotes glucose tolerance by enhancing endothelial insulin transport to skeletal muscle. Endothelial ERα-deficient male mice are glucose intolerant and insulin resistant, and in females the antidiabetogenic actions of estradiol (E2) are absent. The glucose dysregulation is due to impaired skeletal muscle glucose disposal that results from attenuated muscle insulin delivery. Endothelial ERα activation stimulates insulin transcytosis by skeletal muscle microvascular endothelial cells. Mechanistically this involves nuclear ERα-dependent upregulation of vesicular trafficking regulator sorting nexin 5 (SNX5) expression, and PI3 kinase activation that drives plasma membrane recruitment of SNX5. Thus, coupled nuclear and non-nuclear actions of ERα promote endothelial insulin transport to skeletal muscle to foster normal glucose homeostasis.
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Affiliation(s)
- Anastasia Sacharidou
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Ken Chambliss
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jun Peng
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Jose Barrera
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Keiji Tanigaki
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Katherine Luby-Phelps
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - İpek Özdemir
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Sohaib Khan
- University of Cincinnati Cancer Institute, Department of Cancer and Cell Biology, University of Cincinnati College of Medicine, Cincinnati, OH, 45219, USA
| | - Shashank R Sirsi
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Sung Hoon Kim
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Benita S Katzenellenbogen
- Departments of Physiology and Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Mohammed Kanchwala
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Adwait A Sathe
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Andrew Lemoff
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kenneth Hoyt
- Department of Bioengineering, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Chieko Mineo
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Philip W Shaul
- Center for Pulmonary and Vascular Biology, Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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15
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Ip CK, Rezitis J, Qi Y, Bajaj N, Koller J, Farzi A, Shi YC, Tasan R, Zhang L, Herzog H. Critical role of lateral habenula circuits in the control of stress-induced palatable food consumption. Neuron 2023; 111:2583-2600.e6. [PMID: 37295418 DOI: 10.1016/j.neuron.2023.05.010] [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: 06/12/2022] [Revised: 12/15/2022] [Accepted: 05/11/2023] [Indexed: 06/12/2023]
Abstract
Chronic stress fuels the consumption of palatable food and can enhance obesity development. While stress- and feeding-controlling pathways have been identified, how stress-induced feeding is orchestrated remains unknown. Here, we identify lateral habenula (LHb) Npy1r-expressing neurons as the critical node for promoting hedonic feeding under stress, since lack of Npy1r in these neurons alleviates the obesifying effects caused by combined stress and high fat feeding (HFDS) in mice. Mechanistically, this is due to a circuit originating from central amygdala NPY neurons, with the upregulation of NPY induced by HFDS initiating a dual inhibitory effect via Npy1r signaling onto LHb and lateral hypothalamus neurons, thereby reducing the homeostatic satiety effect through action on the downstream ventral tegmental area. Together, these results identify LHb-Npy1r neurons as a critical node to adapt the response to chronic stress by driving palatable food intake in an attempt to overcome the negative valence of stress.
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Affiliation(s)
- Chi Kin Ip
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
| | - Jemma Rezitis
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yue Qi
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Nikita Bajaj
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Julia Koller
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Aitak Farzi
- Division of Pharmacology, Otto Loewi Research Center, Medical University of Graz, 8010 Graz, Austria
| | - Yan-Chuan Shi
- Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia; Neuroendocrinology Group, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia
| | - Ramon Tasan
- Department of Pharmacology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Lei Zhang
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Herbert Herzog
- Neuroscience Division, Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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16
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Vasek MJ, Mueller SM, Fass SB, Deajon-Jackson JD, Liu Y, Crosby HW, Koester SK, Yi J, Li Q, Dougherty JD. Local translation in microglial processes is required for efficient phagocytosis. Nat Neurosci 2023; 26:1185-1195. [PMID: 37277487 PMCID: PMC10580685 DOI: 10.1038/s41593-023-01353-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/03/2023] [Indexed: 06/07/2023]
Abstract
Neurons, astrocytes and oligodendrocytes locally regulate protein translation within distal processes. Here, we tested whether there is regulated local translation within peripheral microglial processes (PeMPs) from mouse brain. We show that PeMPs contain ribosomes that engage in de novo protein synthesis, and these are associated with transcripts involved in pathogen defense, motility and phagocytosis. Using a live slice preparation, we further show that acute translation blockade impairs the formation of PeMP phagocytic cups, the localization of lysosomal proteins within them, and phagocytosis of apoptotic cells and pathogen-like particles. Finally, PeMPs severed from their somata exhibit and require de novo local protein synthesis to effectively surround pathogen-like particles. Collectively, these data argue for regulated local translation in PeMPs and indicate a need for new translation to support dynamic microglial functions.
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Affiliation(s)
- Michael J Vasek
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Shayna M Mueller
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Stuart B Fass
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jelani D Deajon-Jackson
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Yating Liu
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Haley W Crosby
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
| | - Sarah K Koester
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA
| | - Jiwon Yi
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA
- Division of Biology and Biomedical Sciences, Washington University School of Medicine, Saint Louis, MO, USA
| | - Qingyun Li
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA
- Department of Neuroscience, Washington University School of Medicine, Saint Louis, MO, USA
| | - Joseph D Dougherty
- Department of Genetics, Washington University School of Medicine, Saint Louis, MO, USA.
- Department of Psychiatry, Washington University School of Medicine, Saint Louis, MO, USA.
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17
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Sikder K, Phillips E, Zhong Z, Wang N, Saunders J, Mothy D, Kossenkov A, Schneider T, Nichtova Z, Csordas G, Margulies KB, Choi JC. Perinuclear damage from nuclear envelope deterioration elicits stress responses that contribute to LMNA cardiomyopathy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.14.528563. [PMID: 36824975 PMCID: PMC9949050 DOI: 10.1101/2023.02.14.528563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Mutations in the LMNA gene encoding nuclear lamins A/C cause a diverse array of tissue-selective diseases, with the heart being the most commonly affected organ. Despite progress in understanding the molecular perturbations emanating from LMNA mutations, an integrative understanding of the pathogenesis leading to cardiac dysfunction remains elusive. Using a novel cell-type specific Lmna deletion mouse model capable of translatome profiling, we found that cardiomyocyte-specific Lmna deletion in adult mice led to rapid cardiomyopathy with pathological remodeling. Prior to the onset of cardiac dysfunction, lamin A/C-depleted cardiomyocytes displayed nuclear envelope deterioration, golgi dilation/fragmentation, and CREB3-mediated golgi stress activation. Translatome profiling identified upregulation of Med25, a transcriptional co-factor that can selectively dampen UPR axes. Autophagy is disrupted in the hearts of these mice, which can be recapitulated by disrupting the golgi or inducing nuclear damage by increased matrix stiffness. Systemic administration of pharmacological modulators of autophagy or ER stress significantly improved the cardiac function. These studies support a hypothesis wherein stress responses emanating from the perinuclear space contribute to the development of LMNA cardiomyopathy. Teaser Interplay of stress responses underlying the development of LMNA cardiomyopathy.
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18
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Qi Y, Lee NJ, Ip CK, Enriquez R, Tasan R, Zhang L, Herzog H. Agrp-negative arcuate NPY neurons drive feeding under positive energy balance via altering leptin responsiveness in POMC neurons. Cell Metab 2023:S1550-4131(23)00177-8. [PMID: 37201523 DOI: 10.1016/j.cmet.2023.04.020] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/14/2022] [Accepted: 04/26/2023] [Indexed: 05/20/2023]
Abstract
Neuropeptide Y (NPY) in the arcuate nucleus (ARC) is known as one of the most critical regulators of feeding. However, how NPY promotes feeding under obese conditions is unclear. Here, we show that positive energy balance, induced by high-fat diet (HFD) or in genetically obese leptin-receptor-deficient mice, leads to elevated Npy2r expression especially on proopiomelanocortin (POMC) neurons, which also alters leptin responsiveness. Circuit mapping identified a subset of ARC agouti-related peptide (Agrp)-negative NPY neurons that control these Npy2r expressing POMC neurons. Chemogenetic activation of this newly discovered circuitry strongly drives feeding, while optogenetic inhibition reduces feeding. Consistent with that, lack of Npy2r on POMC neurons leads to reduced food intake and fat mass. This suggests that under energy surplus conditions, when ARC NPY levels generally drop, high-affinity NPY2R on POMC neurons is still able to drive food intake and enhance obesity development via NPY released predominantly from Agrp-negative NPY neurons.
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Affiliation(s)
- Yue Qi
- Neuroscience Division, Garvan Institute of Medical Research, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Nicola J Lee
- Neuroscience Division, Garvan Institute of Medical Research, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Chi Kin Ip
- Neuroscience Division, Garvan Institute of Medical Research, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia
| | - Ronaldo Enriquez
- Neuroscience Division, Garvan Institute of Medical Research, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia
| | - Ramon Tasan
- Department of Pharmacology, Medical University Innsbruck, Innsbruck, Austria
| | - Lei Zhang
- Neuroscience Division, Garvan Institute of Medical Research, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia.
| | - Herbert Herzog
- Neuroscience Division, Garvan Institute of Medical Research, St Vincent's Hospital, Darlinghurst, NSW 2010, Australia; St Vincent's Clinical School, UNSW Sydney, Sydney, NSW, Australia.
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19
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Thai LM, O’Reilly L, Reibe-Pal S, Sue N, Holliday H, Small L, Schmitz-Peiffer C, Dhenni R, Wang-Wei Tsai V, Norris N, Yau B, Zhang X, Lee K, Yan C, Shi YC, Kebede MA, Brink R, Cooney GJ, Irvine KM, Breit SN, Phan TG, Swarbrick A, Biden TJ. β-cell function is regulated by metabolic and epigenetic programming of islet-associated macrophages, involving Axl, Mertk, and TGFβ receptor signaling. iScience 2023; 26:106477. [PMID: 37091234 PMCID: PMC10113792 DOI: 10.1016/j.isci.2023.106477] [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: 09/27/2022] [Revised: 01/13/2023] [Accepted: 03/19/2023] [Indexed: 04/25/2023] Open
Abstract
We have exploited islet-associated macrophages (IAMs) as a model of resident macrophage function, focusing on more physiological conditions than the commonly used extremes of M1 (inflammation) versus M2 (tissue remodeling) polarization. Under steady state, murine IAMs are metabolically poised between aerobic glycolysis and oxidative phosphorylation, and thereby exert a brake on glucose-stimulated insulin secretion (GSIS). This is underpinned by epigenetic remodeling via the metabolically regulated histone demethylase Kdm5a. Conversely, GSIS is enhanced by engaging Axl receptors on IAMs, or by augmenting their oxidation of glucose. Following high-fat feeding, efferocytosis is stimulated in IAMs in conjunction with Mertk and TGFβ receptor signaling. This impairs GSIS and potentially contributes to β-cell failure in pre-diabetes. Thus, IAMs serve as relays in many more settings than currently appreciated, fine-tuning insulin secretion in response to dynamic changes in the external environment. Intervening in this nexus might represent a means of preserving β-cell function during metabolic disease.
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Affiliation(s)
- Le May Thai
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Liam O’Reilly
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Nancy Sue
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Holly Holliday
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Lewin Small
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Carsten Schmitz-Peiffer
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Rama Dhenni
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | | | - Nicholas Norris
- School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Belinda Yau
- Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Xuan Zhang
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Kailun Lee
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Chenxu Yan
- Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Yan-Chuan Shi
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Melkam A. Kebede
- School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | - Robert Brink
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Gregory J. Cooney
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- School of Medical Sciences, Charles Perkins Centre, University of Sydney, Sydney, NSW, Australia
| | | | - Samuel N. Breit
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Centre for Applied Medical Research, Sydney, NSW, Australia
| | - Tri G. Phan
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Alexander Swarbrick
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
| | - Trevor J. Biden
- Garvan Institute of Medical Research, Sydney, NSW, Australia
- St Vincent’s Clinical School, Faculty of Medicine, UNSW Sydney, Sydney, NSW, Australia
- Corresponding author
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20
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Zhou P, Zhang Y, Sethi I, Ye L, Trembley MA, Cao Y, Akerberg BN, Xiao F, Zhang X, Li K, Jardin BD, Mazumdar N, Ma Q, He A, Zhou B, Pu WT. GATA4 Regulates Developing Endocardium Through Interaction With ETS1. Circ Res 2022; 131:e152-e168. [PMID: 36263775 PMCID: PMC9669226 DOI: 10.1161/circresaha.120.318102] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 10/07/2022] [Indexed: 01/26/2023]
Abstract
BACKGROUND The pioneer transcription factor (TF) GATA4 (GATA Binding Protein 4) is expressed in multiple cardiovascular lineages and is essential for heart development. GATA4 lineage-specific occupancy in the developing heart underlies its lineage specific activities. Here, we characterized GATA4 chromatin occupancy in cardiomyocyte and endocardial lineages, dissected mechanisms that control lineage specific occupancy, and analyzed GATA4 regulation of endocardial gene expression. METHODS We mapped GATA4 chromatin occupancy in cardiomyocyte and endocardial cells of embryonic day 12.5 (E12.5) mouse heart using lineage specific, Cre-activated biotinylation of GATA4. Regulation of GATA4 pioneering activity was studied in cell lines stably overexpressing GATA4. GATA4 regulation of endocardial gene expression was analyzed using single cell RNA sequencing and luciferase reporter assays. RESULTS Cardiomyocyte-selective and endothelial-selective GATA4 occupied genomic regions had features of lineage specific enhancers. Footprints within cardiomyocyte- and endothelial-selective GATA4 regions were enriched for NKX2-5 (NK2 homeobox 5) and ETS1 (ETS Proto-Oncogene 1) motifs, respectively, and both of these TFs interacted with GATA4 in co-immunoprecipitation assays. In stable NIH3T3 cell lines expressing GATA4 with or without NKX2-5 or ETS1, the partner TFs re-directed GATA4 pioneer binding and augmented its ability to open previously inaccessible regions, with ETS1 displaying greater potency as a pioneer partner than NKX2-5. Single-cell RNA sequencing of embryonic hearts with endothelial cell-specific Gata4 inactivation identified Gata4-regulated endocardial genes, which were adjacent to GATA4-bound, endothelial regions enriched for both GATA4 and ETS1 motifs. In reporter assays, GATA4 and ETS1 cooperatively stimulated endothelial cell enhancer activity. CONCLUSIONS Lineage selective non-pioneer TFs NKX2-5 and ETS1 guide the activity of pioneer TF GATA4 to bind and open chromatin and create active enhancers and mechanistically link ETS1 interaction to GATA4 regulation of endocardial development.
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Affiliation(s)
- Pingzhu Zhou
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Yan Zhang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Isha Sethi
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Lincai Ye
- Department of Thoracic and Cardiovascular Surgery, Shanghai Children’s Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Michael A. Trembley
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Yangpo Cao
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Brynn N. Akerberg
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Feng Xiao
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Xiaoran Zhang
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Kai Li
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Blake D. Jardin
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Neil Mazumdar
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Qing Ma
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
| | - Aibin He
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Bin Zhou
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, China
| | - William T. Pu
- Department of Cardiology, Boston Children’s Hospital, 300 Longwood Ave., Boston, MA 02115
- Harvard Stem Cell Institute, 7 Divinity Avenue, Cambridge, MA 02138
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21
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Fox SN, McMeekin LJ, Savage CH, Joyce KL, Boas SM, Simmons MS, Farmer CB, Ryan J, Pereboeva L, Becker K, Auwerx J, Sudarshan S, Ma J, Lee A, Roberts RC, Crossman DK, Kralli A, Cowell RM. Estrogen-related receptor gamma regulates mitochondrial and synaptic genes and modulates vulnerability to synucleinopathy. NPJ Parkinsons Dis 2022; 8:106. [PMID: 35982091 PMCID: PMC9388660 DOI: 10.1038/s41531-022-00369-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
Many studies implicate mitochondrial dysfunction as a key contributor to cell loss in Parkinson disease (PD). Previous analyses of dopaminergic (DAergic) neurons from patients with Lewy-body pathology revealed a deficiency in nuclear-encoded genes for mitochondrial respiration, many of which are targets for the transcription factor estrogen-related receptor gamma (Esrrg/ERRγ). We demonstrate that deletion of ERRγ from DAergic neurons in adult mice was sufficient to cause a levodopa-responsive PD-like phenotype with reductions in mitochondrial gene expression and number, that partial deficiency of ERRγ hastens synuclein-mediated toxicity, and that ERRγ overexpression reduces inclusion load and delays synuclein-mediated cell loss. While ERRγ deletion did not fully recapitulate the transcriptional alterations observed in postmortem tissue, it caused reductions in genes involved in synaptic and mitochondrial function and autophagy. Altogether, these experiments suggest that ERRγ-deficient mice could provide a model for understanding the regulation of transcription in DAergic neurons and that amplifying ERRγ-mediated transcriptional programs should be considered as a strategy to promote DAergic maintenance in PD.
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Affiliation(s)
- S N Fox
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - L J McMeekin
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - C H Savage
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
| | - K L Joyce
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - S M Boas
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - M S Simmons
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - C B Farmer
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - J Ryan
- NeuroInitiative, LLC, Jacksonville, FL, 32207, USA
| | - L Pereboeva
- Department of Pediatrics, Infectious Disease, Neuroscience Vector and Virus Core, University of Alabama at Birmingham, Birmingham, AL, 35223, USA
| | - K Becker
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - J Auwerx
- Swiss Federal Institute of Technology Lausanne, Lausanne, Switzerland
| | - S Sudarshan
- Department of Urology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - J Ma
- Department of Neurodegenerative Science, Van Andel Institute, Grand Rapids, MI, 49503, USA
| | - A Lee
- NeuroInitiative, LLC, Jacksonville, FL, 32207, USA
| | - R C Roberts
- Department of Psychiatry and Behavioral Neurobiology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - D K Crossman
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL, 35294, USA
| | - A Kralli
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - R M Cowell
- Neuroscience Department, Drug Discovery Division, Southern Research, Birmingham, AL, 35205, USA.
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, 35294, USA.
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22
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Salussolia CL, Winden KD, Sahin M. Translating Ribosome Affinity Purification (TRAP) of Cell Type-specific mRNA from Mouse Brain Lysates. Bio Protoc 2022; 12:e4407. [PMID: 35800463 PMCID: PMC9090583 DOI: 10.21769/bioprotoc.4407] [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: 01/17/2022] [Accepted: 03/28/2022] [Indexed: 01/11/2023] Open
Abstract
Mammalian tissues are highly heterogenous and complex, posing a challenge in understanding the molecular mechanisms regulating protein expression within various tissues. Recent studies have shown that translation at the level of the ribosome is highly regulated, and can vary independently of gene expression observed at a transcriptome level, as well as between cell populations, contributing to the diversity of mammalian tissues. Earlier methods that analyzed gene expression at the level of translation, such as polysomal- or ribosomal-profiling, required large amounts of starting material to isolate enough RNA for analysis by microarray or RNA-sequencing. Thus, rare or less abundant cell types within tissues were not able to be properly studied with these methods. Translating ribosome affinity purification (TRAP) utilizes the incorporation of an eGFP-affinity tag on the large ribosome subunit, driven by expression of cell-type specific Cre-lox promoters, to allow for identification and capture of transcripts from actively translating ribosomes in a cell-specific manner. As a result, TRAP offers a unique opportunity to evaluate the entire mRNA translation profile within a specific cell type, and increase our understanding regarding the cellular complexity of mammalian tissues. Graphical abstract: Schematic demonstrating TRAP protocol for identifying ribosome-bound transcripts specifically within cerebellar Purkinje cells.
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Affiliation(s)
- Catherine L. Salussolia
- F.M. Kirby Neurobiology Center, Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kellen D. Winden
- F.M. Kirby Neurobiology Center, Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mustafa Sahin
- F.M. Kirby Neurobiology Center, Rosamund Stone Zander Translational Neuroscience Center, Department of Neurology, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
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23
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Van der Ent MA, Svilar D, Cleuren AC. Molecular analysis of vascular gene expression. Res Pract Thromb Haemost 2022; 6:e12718. [PMID: 35599705 PMCID: PMC9118339 DOI: 10.1002/rth2.12718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/17/2022] [Accepted: 04/12/2022] [Indexed: 12/04/2022] Open
Abstract
A State of the Art lecture entitled "Molecular Analysis of Vascular Gene Expression" was presented at the ISTH Congress in 2021. Endothelial cells (ECs) form a critical interface between the blood and underlying tissue environment, serving as a reactive barrier to maintain tissue homeostasis. ECs play an important role in not only coagulation, but also in the response to inflammation by connecting these two processes in the host defense against pathogens. Furthermore, ECs tailor their behavior to the needs of the microenvironment in which they reside, resulting in a broad display of EC phenotypes. While this heterogeneity has been acknowledged for decades, the contributing molecular mechanisms have only recently started to emerge due to technological advances. These include high-throughput sequencing combined with methods to isolate ECs directly from their native tissue environment, as well as sequencing samples at a high cellular resolution. In addition, the newest technologies simultaneously quantitate and visualize a multitude of RNA transcripts directly in tissue sections, thus providing spatial information. Understanding how ECs function in (patho)physiological conditions is crucial to develop new therapeutics as many diseases can directly affect the endothelium. Of particular relevance for thrombotic disorders, EC dysfunction can lead to a procoagulant, proinflammatory phenotype with increased vascular permeability that can result in coagulopathy and tissue damage, as seen in a number of infectious diseases, including sepsis and coronavirus disease 2019. In light of the current pandemic, we will summarize relevant new data on the latter topic presented during the 2021 ISTH Congress.
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Affiliation(s)
| | - David Svilar
- Department of PediatricsUniversity of MichiganAnn ArborMichiganUSA
- Life Sciences InstituteUniversity of MichiganAnn ArborMichiganUSA
| | - Audrey C.A. Cleuren
- Life Sciences InstituteUniversity of MichiganAnn ArborMichiganUSA
- Cardiovascular Biology Research ProgramOklahoma Medical Research FoundationOklahoma CityOklahomaUSA
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24
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Guo C, Zhang Y, Tan R, Tang Z, Lam CM, Ye X, Wang Z, Li X. Arid1a regulates bladder urothelium formation and maintenance. Dev Biol 2022; 485:61-69. [PMID: 35283102 PMCID: PMC10276770 DOI: 10.1016/j.ydbio.2022.02.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 11/22/2021] [Accepted: 02/19/2022] [Indexed: 12/12/2022]
Abstract
Epigenetic regulation of gene expression plays a central role in bladder urothelium development and maintenance. ATPase-dependent chromatin remodeling is a major epigenetic regulatory mechanism, but its role in the bladder has not been explored. Here, we show the functions of Arid1a, the largest subunit of the SWI/SNF or BAF chromatin remodeling ATPase complex, in embryonic and adult bladder urothelium. Knockout of Arid1a in urothelial progenitor cells significantly increases cell proliferation during bladder development. Deletion of Arid1a causes ectopic cell proliferation in the terminally differentiated superficial cells in adult mice. Consistently, gene-set enrichment analysis of differentially expressed genes demonstrates that the cell cycle-related pathways are significantly enriched in Arid1a knockouts. Gene-set of the polycomb repression complex 2 (PRC2) pathway is also enriched, suggesting that Arid1a antagonizes the PRC2-dependent epigenetic gene silencing program in the bladder. During acute cyclophosphamide-induced bladder injury, Arid1a knockouts develop hyperproliferative and hyperinflammatory phenotypes and exhibit a severe loss of urothelial cells. A Hallmark gene-set of the oxidative phosphorylation pathway is significantly reduced in Aria1a mutants before injury and is unexpectedly enriched during injury response. Together, this study uncovers functions of Arid1a in both bladder progenitor cells and the mature urothelium, suggesting its critical roles in urothelial development and regeneration.
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Affiliation(s)
- Chunming Guo
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA
| | - Yingsheng Zhang
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA
| | - Ruirong Tan
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA
| | - Zonghao Tang
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA
| | - Christa M Lam
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA
| | - Xing Ye
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA
| | - Zhong Wang
- Department of Cardiac Surgery Cardiovascular Research Center, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Xue Li
- Samuel Oschin Comprehensive Cancer Institute, Department of Medicine, Department of Biomedical Sciences, Cedars-Sinai Medical Center, 8700 Beverly Blvd, Davis 3089, Los Angeles, CA, 90048, USA.
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25
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Ribosome-Associated ncRNAs (rancRNAs) Adjust Translation and Shape Proteomes. Noncoding RNA 2022; 8:ncrna8020022. [PMID: 35314615 PMCID: PMC8938821 DOI: 10.3390/ncrna8020022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 12/02/2022] Open
Abstract
The regulation of protein synthesis is of extreme importance for cell survival in challenging environmental conditions. Modulating gene expression at the level of translation allows a swift and low-energy-cost response to external stimuli. In the last decade, an emerging class of regulatory ncRNAs, namely ribosome-associated non-coding RNAs (rancRNAs), has been discovered. These rancRNAs have proven to be efficient players in the regulation of translation as a first wave of stress adaptation by directly targeting the ribosome, the central enzyme of protein production. This underlying principle appears to be highly conserved, since rancRNAs are present in all three domains of life. Here, we review the major findings and mechanistic peculiarities of rancRNAs, a class of transcripts that is providing new and broader perspectives on the complexity of the ribosome and translation regulation.
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26
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Wang Y, Niu A, Pan Y, Cao S, Terker AS, Wang S, Fan X, Toth CL, Ramirez Solano MA, Michell DL, Contreras D, Allen RM, Zhu W, Sheng Q, Fogo AB, Vickers KC, Zhang MZ, Harris RC. Profile of Podocyte Translatome During Development of Type 2 and Type 1 Diabetic Nephropathy Using Podocyte-Specific TRAP mRNA RNA-seq. Diabetes 2021; 70:2377-2390. [PMID: 34233930 PMCID: PMC8576501 DOI: 10.2337/db21-0110] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/29/2021] [Indexed: 12/22/2022]
Abstract
Podocyte injury is important in development of diabetic nephropathy (DN). Although several studies have reported single-cell-based RNA sequencing (RNA-seq) of podocytes in type 1 DN (T1DN), the podocyte translating mRNA profile in type 2 DN (T2DN) has not previously been compared with that of T1DN. We analyzed the podocyte translatome in T2DN in podocin-Cre; Rosa26fsTRAP; eNOS-/-; db/db mice and compared it with that of streptozotocin-induced T1DN in podocin-Cre; Rosa26fsTRAP; eNOS-/- mice using translating ribosome affinity purification (TRAP) and RNA-seq. More than 125 genes were highly enriched in the podocyte ribosome. More podocyte TRAP genes were differentially expressed in T2DN than in T1DN. TGF-β signaling pathway genes were upregulated, while MAPK pathway genes were downregulated only in T2DN, while ATP binding and cAMP-mediated signaling genes were downregulated only in T1DN. Genes regulating actin filament organization and apoptosis increased, while genes regulating VEGFR signaling and glomerular basement membrane components decreased in both type 1 and type 2 diabetic podocytes. A number of diabetes-induced genes not previously linked to podocyte injury were confirmed in both mouse and human DN. On the basis of differences and similarities in the podocyte translatome in T2DN and T1DN, investigators can identify factors underlying the pathophysiology of DN and novel therapeutic targets to treat diabetes-induced podocyte injury.
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MESH Headings
- Animals
- Diabetes Mellitus, Experimental/genetics
- Diabetes Mellitus, Experimental/metabolism
- Diabetes Mellitus, Experimental/pathology
- Diabetes Mellitus, Type 1/complications
- Diabetes Mellitus, Type 1/genetics
- Diabetes Mellitus, Type 1/metabolism
- Diabetes Mellitus, Type 2/complications
- Diabetes Mellitus, Type 2/genetics
- Diabetes Mellitus, Type 2/metabolism
- Diabetic Nephropathies/genetics
- Diabetic Nephropathies/metabolism
- Diabetic Nephropathies/pathology
- Gene Expression Profiling
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Organ Specificity/genetics
- Podocytes/metabolism
- Podocytes/pathology
- Protein Biosynthesis/genetics
- Proteome/analysis
- Proteome/genetics
- Proteome/metabolism
- RNA, Messenger/analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA-Seq
- Sequence Analysis, RNA
- Streptozocin
- Transcriptome
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Affiliation(s)
- Yinqiu Wang
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Aolei Niu
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Yu Pan
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Shirong Cao
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Andrew S Terker
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Suwan Wang
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Xiaofeng Fan
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Cynthia L Toth
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Marisol A Ramirez Solano
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Danielle L Michell
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Danielle Contreras
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Ryan M Allen
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Wanying Zhu
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Quanhu Sheng
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Agnes B Fogo
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN
| | - Kasey C Vickers
- Division of Cardiovascular Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN
| | - Ming-Zhi Zhang
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
| | - Raymond C Harris
- Division of Nephrology and Hypertension, Vanderbilt University School of Medicine, Nashville, TN
- Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, TN
- Department of Veterans Affairs, Nashville, TN
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27
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Jang Y, Park YK, Lee JE, Wan D, Tran N, Gavrilova O, Ge K. MED1 is a lipogenesis coactivator required for postnatal adipose expansion. Genes Dev 2021; 35:713-728. [PMID: 33888555 PMCID: PMC8091974 DOI: 10.1101/gad.347583.120] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 03/16/2021] [Indexed: 12/28/2022]
Abstract
In this study, Jang et al. investigated the role of MED1 in adipose development and expansion in vivo, and they show that MED1 is not generally required for transcription during adipogenesisin culture and that MED1 is dispensable for adipose development in mice. Instead, MED1 is required for postnatal adipose expansion and the induction of fatty acid and triglyceride synthesis genes after pups switch diet from high-fat maternal milk to carbohydrate-based chow. Their findings identify a cell- and gene-specific regulatory role of MED1 as a lipogenesis coactivator required for postnatal adipose expansion. MED1 often serves as a surrogate of the general transcription coactivator complex Mediator for identifying active enhancers. MED1 is required for phenotypic conversion of fibroblasts to adipocytes in vitro, but its role in adipose development and expansion in vivo has not been reported. Here, we show that MED1 is not generally required for transcription during adipogenesis in culture and that MED1 is dispensable for adipose development in mice. Instead, MED1 is required for postnatal adipose expansion and the induction of fatty acid and triglyceride synthesis genes after pups switch diet from high-fat maternal milk to carbohydrate-based chow. During adipogenesis, MED1 is dispensable for induction of lineage-determining transcription factors (TFs) PPARγ and C/EBPα but is required for lipid accumulation in the late phase of differentiation. Mechanistically, MED1 controls the induction of lipogenesis genes by facilitating lipogenic TF ChREBP- and SREBP1a-dependent recruitment of Mediator to active enhancers. Together, our findings identify a cell- and gene-specific regulatory role of MED1 as a lipogenesis coactivator required for postnatal adipose expansion.
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Affiliation(s)
- Younghoon Jang
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Biology and Chemistry, Changwon National University, Changwon 51140, Korea
| | - Young-Kwon Park
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Ji-Eun Lee
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Danyang Wan
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Nhien Tran
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Oksana Gavrilova
- Mouse Metabolism Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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28
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Yan Y, Tang R, Li B, Cheng L, Ye S, Yang T, Han YC, Liu C, Dong Y, Qu LH, Lui KO, Yang JH, Huang ZP. The cardiac translational landscape reveals that micropeptides are new players involved in cardiomyocyte hypertrophy. Mol Ther 2021; 29:2253-2267. [PMID: 33677093 PMCID: PMC8261087 DOI: 10.1016/j.ymthe.2021.03.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Revised: 12/11/2020] [Accepted: 03/02/2021] [Indexed: 11/27/2022] Open
Abstract
Hypertrophic growth of cardiomyocytes is one of the major compensatory responses in the heart after physiological or pathological stimulation. Protein synthesis enhancement, which is mediated by the translation of messenger RNAs, is one of the main features of cardiomyocyte hypertrophy. Although the transcriptome shift caused by cardiac hypertrophy induced by different stimuli has been extensively investigated, translatome dynamics in this cellular process has been less studied. Here, we generated a nucleotide-resolution translatome as well as transcriptome data from isolated primary cardiomyocytes undergoing hypertrophy. More than 10,000 open reading frames (ORFs) were detected from the deep sequencing of ribosome-protected fragments (Ribo-seq), which orchestrated the shift of the translatome in hypertrophied cardiomyocytes. Our data suggest that rather than increase the translational rate of ribosomes, the increased efficiency of protein synthesis in cardiomyocyte hypertrophy was attributable to an increased quantity of ribosomes. In addition, more than 100 uncharacterized short ORFs (sORFs) were detected in long noncoding RNA genes from Ribo-seq with potential of micropeptide coding. In a random test of 15 candidates, the coding potential of 11 sORFs was experimentally supported. Three micropeptides were identified to regulate cardiomyocyte hypertrophy by modulating the activities of oxidative phosphorylation, the calcium signaling pathway, and the mitogen-activated protein kinase (MAPK) pathway. Our study provides a genome-wide overview of the translational controls behind cardiomyocyte hypertrophy and demonstrates an unrecognized role of micropeptides in cardiomyocyte biology.
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Affiliation(s)
- Youchen Yan
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Rong Tang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Bin Li
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Liangping Cheng
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Shangmei Ye
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Tiqun Yang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Yan-Chuang Han
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Chen Liu
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Yugang Dong
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China
| | - Liang-Hu Qu
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China
| | - Kathy O Lui
- Department of Chemical Pathology, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, Hong Kong SAR 999077, China
| | - Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, China.
| | - Zhan-Peng Huang
- Department of Cardiology, Center for Translational Medicine, Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China; NHC Key Laboratory of Assisted Circulation, Sun Yat-sen University, Guangzhou 510080, China; National-Guangdong Joint Engineering Laboratory for Diagnosis and Treatment of Vascular Diseases, Guangzhou 510080, China.
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29
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Maguire OA, Ackerman SE, Szwed SK, Maganti AV, Marchildon F, Huang X, Kramer DJ, Rosas-Villegas A, Gelfer RG, Turner LE, Ceballos V, Hejazi A, Samborska B, Rahbani JF, Dykstra CB, Annis MG, Luo JD, Carroll TS, Jiang CS, Dannenberg AJ, Siegel PM, Tersey SA, Mirmira RG, Kazak L, Cohen P. Creatine-mediated crosstalk between adipocytes and cancer cells regulates obesity-driven breast cancer. Cell Metab 2021; 33:499-512.e6. [PMID: 33596409 PMCID: PMC7954401 DOI: 10.1016/j.cmet.2021.01.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 11/24/2020] [Accepted: 01/27/2021] [Indexed: 01/08/2023]
Abstract
Obesity is a major risk factor for adverse outcomes in breast cancer; however, the underlying molecular mechanisms have not been elucidated. To investigate the role of crosstalk between mammary adipocytes and neoplastic cells in the tumor microenvironment (TME), we performed transcriptomic analysis of cancer cells and adjacent adipose tissue in a murine model of obesity-accelerated breast cancer and identified glycine amidinotransferase (Gatm) in adipocytes and Acsbg1 in cancer cells as required for obesity-driven tumor progression. Gatm is the rate-limiting enzyme in creatine biosynthesis, and deletion in adipocytes attenuated obesity-driven tumor growth. Similarly, genetic inhibition of creatine import into cancer cells reduced tumor growth in obesity. In parallel, breast cancer cells in obese animals upregulated the fatty acyl-CoA synthetase Acsbg1 to promote creatine-dependent tumor progression. These findings reveal key nodes in the crosstalk between adipocytes and cancer cells in the TME necessary for obesity-driven breast cancer progression.
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Affiliation(s)
- Olivia A Maguire
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-institutional MD-PhD Program, New York, NY 10065, USA
| | - Sarah E Ackerman
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA; AAAS Science and Technology Policy Fellow in the Office of Global Health, Health Workforce Branch, U.S. Agency for International Development, Washington, D.C. 20547, USA
| | - Sarah K Szwed
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-institutional MD-PhD Program, New York, NY 10065, USA
| | - Aarthi V Maganti
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - François Marchildon
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Xiaojing Huang
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA; Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daniel J Kramer
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA; Weill Cornell/Rockefeller/Sloan Kettering Tri-institutional MD-PhD Program, New York, NY 10065, USA
| | | | - Rebecca G Gelfer
- Weill Cornell/Rockefeller/Sloan Kettering Tri-institutional MD-PhD Program, New York, NY 10065, USA
| | - Lauren E Turner
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Victor Ceballos
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Asal Hejazi
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA
| | - Bozena Samborska
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G1Y6, Canada
| | - Janane F Rahbani
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G1Y6, Canada
| | - Christien B Dykstra
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G1Y6, Canada
| | - Matthew G Annis
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Thomas S Carroll
- Bioinformatics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Caroline S Jiang
- Rockefeller University Hospital, The Rockefeller University, New York, NY 10065, USA
| | - Andrew J Dannenberg
- Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Peter M Siegel
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G1Y6, Canada
| | - Sarah A Tersey
- Department of Medicine, The University of Chicago, Chicago, IL 60637, USA
| | | | - Lawrence Kazak
- Goodman Cancer Research Centre, McGill University, Montreal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montreal, QC H3G1Y6, Canada
| | - Paul Cohen
- Laboratory of Molecular Metabolism, The Rockefeller University, New York, NY 10065, USA.
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30
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Grieco SF, Qiao X, Johnston KG, Chen L, Nelson RR, Lai C, Holmes TC, Xu X. Neuregulin signaling mediates the acute and sustained antidepressant effects of subanesthetic ketamine. Transl Psychiatry 2021; 11:144. [PMID: 33627623 PMCID: PMC7904825 DOI: 10.1038/s41398-021-01255-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/09/2021] [Accepted: 02/01/2021] [Indexed: 01/03/2023] Open
Abstract
Subanesthetic ketamine evokes rapid antidepressant effects in human patients that persist long past ketamine's chemical half-life of ~2 h. Ketamine's sustained antidepressant action may be due to modulation of cortical plasticity. We find that ketamine ameliorates depression-like behavior in the forced swim test in adult mice, and this depends on parvalbumin-expressing (PV) neuron-directed neuregulin-1 (NRG1)/ErbB4 signaling. Ketamine rapidly downregulates NRG1 expression in PV inhibitory neurons in mouse medial prefrontal cortex (mPFC) following a single low-dose ketamine treatment. This NRG1 downregulation in PV neurons co-tracks with the decreases in synaptic inhibition to mPFC excitatory neurons for up to a week. This results from reduced synaptic excitation to PV neurons, and is blocked by exogenous NRG1 as well as by PV targeted ErbB4 receptor knockout. Thus, we conceptualize that ketamine's effects are mediated through rapid and sustained cortical disinhibition via PV-specific NRG1 signaling. Our findings reveal a novel neural plasticity-based mechanism for ketamine's acute and long-lasting antidepressant effects.
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Affiliation(s)
- Steven F. Grieco
- grid.266093.80000 0001 0668 7243Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275 USA
| | - Xin Qiao
- grid.266093.80000 0001 0668 7243Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275 USA
| | - Kevin G. Johnston
- grid.266093.80000 0001 0668 7243Department of Mathematics, University of California, Irvine, CA 92697-3875 USA
| | - Lujia Chen
- grid.266093.80000 0001 0668 7243Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275 USA
| | - Renetta R. Nelson
- grid.266093.80000 0001 0668 7243Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275 USA
| | - Cary Lai
- grid.411377.70000 0001 0790 959XDepartment of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405-7000 USA
| | - Todd C. Holmes
- grid.19006.3e0000 0000 9632 6718Department of Physiology and Biophysics, School of Medicine, Universityof California, Irvine, CA 92697- 4560 USA ,grid.266093.80000 0001 0668 7243The Center for Neural Circuit Mapping, University of California, Irvine, CA 92697 USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA, 92697-1275, USA. .,The Center for Neural Circuit Mapping, University of California, Irvine, CA, 92697, USA. .,Department of Biomedical Engineering, University of California, Irvine, CA, 92697-2715, USA. .,Department of Microbiology and Molecular Genetics, University of California, Irvine, CA, 92697-4025, USA. .,Department of Computer Science, University of California, Irvine, CA, 92697-3435, USA.
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31
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Wu J, Venkata Subbaiah KC, Jiang F, Hedaya O, Mohan A, Yang T, Welle K, Ghaemmaghami S, Tang WHW, Small E, Yan C, Yao P. MicroRNA-574 regulates FAM210A expression and influences pathological cardiac remodeling. EMBO Mol Med 2021; 13:e12710. [PMID: 33369227 PMCID: PMC7863409 DOI: 10.15252/emmm.202012710] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 11/17/2020] [Accepted: 11/19/2020] [Indexed: 12/23/2022] Open
Abstract
Aberrant expression of mitochondrial proteins impairs cardiac function and causes heart disease. The mechanism of regulation of mitochondria encoded protein expression during cardiac disease, however, remains underexplored. Here, we show that multiple pathogenic cardiac stressors induce the expression of miR-574 guide and passenger strands (miR-574-5p/3p) in both humans and mice. miR-574 knockout mice exhibit severe cardiac disorder under different pathogenic cardiac stresses while miR-574-5p/3p mimics that are delivered systematically using nanoparticles reduce cardiac pathogenesis under disease insults. Transcriptomic analysis of miR-574-null hearts uncovers family with sequence similarity 210 member A (FAM210A) as a common target mRNA of miR-574-5p and miR-574-3p. The interactome capture analysis suggests that FAM210A interacts with mitochondrial translation elongation factor EF-Tu. Manipulating miR-574-5p/3p or FAM210A expression changes the protein expression of mitochondrial-encoded electron transport chain (ETC) genes but not nuclear-encoded mitochondrial ETC genes in both human AC16 cardiomyocyte cells and miR-574-null murine hearts. Together, we discovered that miR-574 regulates FAM210A expression and modulates mitochondrial-encoded protein expression, which may influence cardiac remodeling in heart failure.
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Affiliation(s)
- Jiangbin Wu
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Kadiam C Venkata Subbaiah
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Feng Jiang
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
- Department of Biochemistry & BiophysicsUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Omar Hedaya
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
- Department of Biochemistry & BiophysicsUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Amy Mohan
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Tingting Yang
- Department of OphthalmologyColumbia UniversityNew YorkNYUSA
| | - Kevin Welle
- Mass Spectrometry Resource LabUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Sina Ghaemmaghami
- Mass Spectrometry Resource LabUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | | | - Eric Small
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Chen Yan
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
| | - Peng Yao
- Department of MedicineAab Cardiovascular Research InstituteUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
- Department of Biochemistry & BiophysicsUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
- The Center for RNA BiologyUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
- The Center for Biomedical InformaticsUniversity of Rochester School of Medicine & DentistryRochester, New YorkNYUSA
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32
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Zeng C, Hamada M. Detection and Characterization of Ribosome-Associated Long Noncoding RNAs. Methods Mol Biol 2021; 2254:179-194. [PMID: 33326076 DOI: 10.1007/978-1-0716-1158-6_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Ribosome profiling shows potential for studying the function of long noncoding RNAs (lncRNAs). We introduce a bioinformatics pipeline for detecting ribosome-associated lncRNAs (ribo-lncRNAs) from ribosome profiling data. Further, we describe a machine-learning approach for the characterization of ribo-lncRNAs based on their sequence features. Scripts for ribo-lncRNA analysis can be accessed at ( https://ribolnc.hamadalab.com/ ).
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Affiliation(s)
- Chao Zeng
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan.,Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Michiaki Hamada
- AIST-Waseda University Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), Tokyo, Japan. .,Faculty of Science and Engineering, Waseda University, Tokyo, Japan. .,Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan. .,Institute for Medical-oriented Structural Biology, Waseda University, Tokyo, Japan. .,Graduate School of Medicine, Nippon Medical School, Tokyo, Japan.
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33
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Serotonin receptor 4 in the hippocampus modulates mood and anxiety. Mol Psychiatry 2021; 26:2334-2349. [PMID: 33441982 PMCID: PMC8275670 DOI: 10.1038/s41380-020-00994-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/02/2020] [Accepted: 12/09/2020] [Indexed: 12/26/2022]
Abstract
Serotonin receptor 4 (5-HT4R) plays an important role in regulating mood, anxiety, and cognition, and drugs that activate this receptor have fast-acting antidepressant (AD)-like effects in preclinical models. However, 5-HT4R is widely expressed throughout the central nervous system (CNS) and periphery, making it difficult to pinpoint the cell types and circuits underlying its effects. Therefore, we generated a Cre-dependent 5-HT4R knockout mouse line to dissect the function of 5-HT4R in specific brain regions and cell types. We show that the loss of functional 5-HT4R specifically from excitatory neurons of hippocampus led to robust AD-like behavioral responses and an elevation in baseline anxiety. 5-HT4R was necessary to maintain the proper excitability of dentate gyrus (DG) granule cells and cell type-specific molecular profiling revealed a dysregulation of genes necessary for normal neural function and plasticity in cells lacking 5-HT4R. These adaptations were accompanied by an increase in the number of immature neurons in ventral, but not dorsal, dentate gyrus, indicating a broad impact of 5-HT4R loss on the local cellular environment. This study is the first to use conditional genetic targeting to demonstrate a direct role for hippocampal 5-HT4R signaling in modulating mood and anxiety. Our findings also underscore the need for cell type-based approaches to elucidate the complex action of neuromodulatory systems on distinct neural circuits.
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34
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Lim SL, Rodriguez-Ortiz CJ, Hsu HW, Wu J, Zumkehr J, Kilian J, Vidal J, Ayata P, Kitazawa M. Chronic copper exposure directs microglia towards degenerative expression signatures in wild-type and J20 mouse model of Alzheimer's disease. J Trace Elem Med Biol 2020; 62:126578. [PMID: 32599538 PMCID: PMC7655674 DOI: 10.1016/j.jtemb.2020.126578] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/24/2020] [Accepted: 06/05/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Copper (Cu) is an essential metal mediating a variety of vital biological reactions with its redox property. Its dyshomeostasis has been associated with accelerated cognitive decline and neurodegenerative disorders, such as Alzheimer's disease (AD). However, underlying neurotoxic mechanisms elicited by dysregulated Cu remain largely elusive. We and others previously demonstrated that exposure to Cu in drinking water significantly exacerbated pathological hallmarks of AD and pro-inflammatory activation of microglia, coupled with impaired phagocytic capacity, in mouse models of AD. METHODS In the present study, we extended our investigation to evaluate whether chronic Cu exposure to wild-type (WT) and J20 mouse model of AD perturbs homeostatic dynamics of microglia and contributes to accelerated transformation of microglia towards degenerative phenotypes that are closely associated with neurodegeneration. We further looked for evidence of alterations in the microglial morphology and spatial memory of the Cu-exposed mice to assess the extent of the Cu toxicity. RESULTS We find that chronic Cu exposure to pre-pathological J20 mice upregulates the translation of degenerative genes and represses homeostatic genes within microglia even in the absence amyloid-beta plaques. We also observe similar expression signatures in Cu-exposed WT mice, suggesting that excess Cu exposure alone could lead to perturbed microglial homeostatic phenotypes and contribute to accelerated cognitive decline. CONCLUSION Our findings highlight the risk of chronic Cu exposure on cognitive decline and altered microglia activation towards degenerative phenotypes. These changes may represent one of the key mechanisms linking Cu exposure or its dyshomeostasis to an increased risk for AD.
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Affiliation(s)
- Siok Lam Lim
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Carlos J Rodriguez-Ortiz
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Heng-Wei Hsu
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Jie Wu
- Department of Biological Chemistry, University of California, Irvine, CA, USA
| | - Joannee Zumkehr
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Jason Kilian
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Janielle Vidal
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA
| | - Pinar Ayata
- Nash Family Department of Neuroscience, Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, NY, USA
| | - Masashi Kitazawa
- Center for Occupational and Environmental Health, Department of Medicine, University of California, Irvine, CA, USA.
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RPL-4 and RPL-9 ̶Mediated Ribosome Purifications Facilitate the Efficient Analysis of Gene Expression in Caenorhabditis elegans Germ Cells. G3-GENES GENOMES GENETICS 2020; 10:4063-4069. [PMID: 32883755 PMCID: PMC7642943 DOI: 10.1534/g3.120.401644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
In many organisms, tissue complexity and cellular diversity create a barrier that can hinder our understanding of gene expression programs. To address this problem, methods have been developed that allow for easy isolation of translated mRNAs from genetically defined cell populations. A prominent example is the Translating Ribosome Affinity Purification method also called TRAP. Here, ribosome associated mRNAs are isolated via purification of the ribosomal protein RPL10A/uL1, which is expressed under the control of a tissue specific promoter. Originally developed to investigate gene expression in mouse neurons, it has by now been adopted to many different organisms and tissues. Interestingly, TRAP has never been used successfully to analyze mRNA translation in germ cells. Employing a combination of genetic and biochemical approaches, I assessed several ribosomal proteins for their suitability for TRAP using the Caenorhabditis elegans germline as a target tissue. Surprisingly, I found that RPL10A/uL1 is not the ideal ribosomal component to perform such an analysis in germ cells. Instead other proteins such as RPL4/uL4 or RPL9/eL6 are much better suited for this task. Tagged variants of these proteins are well expressed in germ cells, integrated into translating ribosomes and do not influence germ cell functions. Furthermore, germ cell-specific mRNAs are much more efficiently co-purified with RPL4/uL4 and RPL9/uL6 compared to RPL10A/uL1. This study provides a solid basis upon which future germ cell TRAP experiments can be built, and it highlights the need for rigorous testing when adopting such methods to a new biological system.
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Tavares-Ferreira D, Ray PR, Sankaranarayanan I, Mejia GL, Wangzhou A, Shiers S, Uttarkar R, Megat S, Barragan-Iglesias P, Dussor G, Akopian AN, Price TJ. Sex Differences in Nociceptor Translatomes Contribute to Divergent Prostaglandin Signaling in Male and Female Mice. Biol Psychiatry 2020; 91:129-140. [PMID: 33309016 PMCID: PMC8019688 DOI: 10.1016/j.biopsych.2020.09.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND There are clinically relevant sex differences in acute and chronic pain mechanisms, but we are only beginning to understand their mechanistic basis. Transcriptome analyses of rodent whole dorsal root ganglion (DRG) have revealed sex differences, mostly in immune cells. We examined the transcriptome and translatome of the mouse DRG with the goal of identifying sex differences. METHODS We used translating ribosome affinity purification sequencing and behavioral pharmacology to test the hypothesis that in Nav1.8-positive neurons, most of which are nociceptors, translatomes would differ by sex. RESULTS We found 80 genes with sex differential expression in the whole DRG transcriptome and 66 genes whose messenger RNAs were sex differentially actively translated (translatome). We also identified different motifs in the 3' untranslated region of messenger RNAs that were sex differentially translated. In further validation studies, we focused on Ptgds, which was increased in the translatome of female mice. The messenger RNA encodes the prostaglandin PGD2 synthesizing enzyme. We observed increased PTGDS protein and PGD2 in female mouse DRG. The PTGDS inhibitor AT-56 caused intense pain behaviors in male mice but was only effective at high doses in female mice. Conversely, female mice responded more robustly to another major prostaglandin, PGE2, than did male mice. PTGDS protein expression was also higher in female cortical neurons, suggesting that DRG findings may be generalizable to other nervous system structures. CONCLUSIONS Our results demonstrate sex differences in nociceptor-enriched translatomes and reveal unexpected sex differences in one of the oldest known nociceptive signaling molecule families, the prostaglandins.
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Affiliation(s)
- Diana Tavares-Ferreira
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | - Pradipta R. Ray
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | | | - Galo L. Mejia
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | - Andi Wangzhou
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | - Stephanie Shiers
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | - Ruta Uttarkar
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | - Salim Megat
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | | | - Gregory Dussor
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies
| | - Armen N. Akopian
- University of Texas Health San Antonio, Department of Endodontics
| | - Theodore J. Price
- University of Texas at Dallas, Department of Neuroscience and Center for Advanced Pain Studies,correspondence to Theodore J Price – , 800 W Campbell Rd, Richardson TX 75080, USA, 972-883-4311
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Scheckel C, Imeri M, Schwarz P, Aguzzi A. Ribosomal profiling during prion disease uncovers progressive translational derangement in glia but not in neurons. eLife 2020; 9:62911. [PMID: 32960170 PMCID: PMC7527237 DOI: 10.7554/elife.62911] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 09/16/2020] [Indexed: 01/19/2023] Open
Abstract
Prion diseases are caused by PrPSc, a self-replicating pathologically misfolded protein that exerts toxicity predominantly in the brain. The administration of PrPSc causes a robust, reproducible and specific disease manifestation. Here, we have applied a combination of translating ribosome affinity purification and ribosome profiling to identify biologically relevant prion-induced changes during disease progression in a cell-type-specific and genome-wide manner. Terminally diseased mice with severe neurological symptoms showed extensive alterations in astrocytes and microglia. Surprisingly, we detected only minor changes in the translational profiles of neurons. Prion-induced alterations in glia overlapped with those identified in other neurodegenerative diseases, suggesting that similar events occur in a broad spectrum of pathologies. Our results suggest that aberrant translation within glia may suffice to cause severe neurological symptoms and may even be the primary driver of prion disease.
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Affiliation(s)
- Claudia Scheckel
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Marigona Imeri
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Petra Schwarz
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
| | - Adriano Aguzzi
- Institute of Neuropathology, University of Zurich, Zurich, Switzerland
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Grieco SF, Qiao X, Zheng X, Liu Y, Chen L, Zhang H, Yu Z, Gavornik JP, Lai C, Gandhi SP, Holmes TC, Xu X. Subanesthetic Ketamine Reactivates Adult Cortical Plasticity to Restore Vision from Amblyopia. Curr Biol 2020; 30:3591-3603.e8. [PMID: 32822611 PMCID: PMC7925140 DOI: 10.1016/j.cub.2020.07.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/07/2020] [Accepted: 07/01/2020] [Indexed: 12/09/2022]
Abstract
Subanesthetic ketamine evokes rapid and long-lasting antidepressant effects in human patients. The mechanism for ketamine's effects remains elusive, but ketamine may broadly modulate brain plasticity processes. We show that single-dose ketamine reactivates adult mouse visual cortical plasticity and promotes functional recovery of visual acuity defects from amblyopia. Ketamine specifically induces downregulation of neuregulin-1 (NRG1) expression in parvalbumin-expressing (PV) inhibitory neurons in mouse visual cortex. NRG1 downregulation in PV neurons co-tracks both the fast onset and sustained decreases in synaptic inhibition to excitatory neurons, along with reduced synaptic excitation to PV neurons in vitro and in vivo following a single ketamine treatment. These effects are blocked by exogenous NRG1 as well as PV targeted receptor knockout. Thus, ketamine reactivation of adult visual cortical plasticity is mediated through rapid and sustained cortical disinhibition via downregulation of PV-specific NRG1 signaling. Our findings reveal the neural plasticity-based mechanism for ketamine-mediated functional recovery from adult amblyopia.
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Affiliation(s)
- Steven F Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, USA
| | - Xin Qiao
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, USA
| | - Xiaoting Zheng
- Department of Neurobiology and Behavior, School of Biology, University of California, Irvine, CA 92697-1275, USA
| | - Yongjun Liu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, USA; Key Laboratory of Pollinating Insect Biology, Institute of Agricultural Research, Chinese Academy of Agricultural Sciences, Beijing 100093, China
| | - Lujia Chen
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, USA
| | - Hai Zhang
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, USA
| | - Zhaoxia Yu
- Department of Statistics, University of California, Irvine, CA 92697-1250, USA
| | | | - Cary Lai
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405-7000, USA
| | - Sunil P Gandhi
- Department of Neurobiology and Behavior, School of Biology, University of California, Irvine, CA 92697-1275, USA
| | - Todd C Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, CA 92697- 4560, USA
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, CA 92697-1275, USA; Department of Biomedical Engineering, University of California, Irvine, CA 92697-2715, USA; Department of Microbiology and Molecular Genetics, University of California, Irvine, CA 92697-4025, USA.
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Yang LM, Stout L, Rauchman M, Ornitz DM. Analysis of FGF20-regulated genes in organ of Corti progenitors by translating ribosome affinity purification. Dev Dyn 2020; 249:1217-1242. [PMID: 32492250 DOI: 10.1002/dvdy.211] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Understanding the mechanisms that regulate hair cell (HC) differentiation in the organ of Corti (OC) is essential to designing genetic therapies for hearing loss due to HC loss or damage. We have previously identified Fibroblast Growth Factor 20 (FGF20) as having a key role in HC and supporting cell differentiation in the mouse OC. To investigate the genetic landscape regulated by FGF20 signaling in OC progenitors, we employ Translating Ribosome Affinity Purification combined with Next Generation RNA Sequencing (TRAPseq) in the Fgf20 lineage. RESULTS We show that TRAPseq targeting OC progenitors effectively enriched for RNA from this rare cell population. TRAPseq identified differentially expressed genes (DEGs) downstream of FGF20, including Etv4, Etv5, Etv1, Dusp6, Hey1, Hey2, Heyl, Tectb, Fat3, Cpxm2, Sall1, Sall3, and cell cycle regulators such as Cdc20. Analysis of Cdc20 conditional-null mice identified decreased cochlea length, while analysis of Sall1-null and Sall1-ΔZn2-10 mice, which harbor a mutation that causes Townes-Brocks syndrome, identified a decrease in outer hair cell number. CONCLUSIONS We present two datasets: genes with enriched expression in OC progenitors, and DEGs downstream of FGF20 in the embryonic day 14.5 cochlea. We validate select DEGs via in situ hybridization and in vivo functional studies in mice.
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Affiliation(s)
- Lu M Yang
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Lisa Stout
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Michael Rauchman
- Division of Nephrology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - David M Ornitz
- Department of Developmental Biology, Washington University School of Medicine, St. Louis, Missouri, USA
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Comparison of RNA isolation procedures for analysis of adult murine brain and spinal cord astrocytes. J Neurosci Methods 2020; 333:108545. [PMID: 31821821 DOI: 10.1016/j.jneumeth.2019.108545] [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: 08/28/2019] [Revised: 11/25/2019] [Accepted: 12/06/2019] [Indexed: 11/23/2022]
Abstract
BACKGROUND Molecular analyses of cell populations and single cells have been instrumental in the advancement of our understanding of the physiology and pathologic processes of the nervous system. However, the limitation of these methods is the dependence on a gentle, efficient and specific enrichment procedure for the target cell population. In particular, this has been challenging for tightly interconnected cells, for example central nervous system (CNS) endogenous cells such as astrocytes. NEW METHOD Here we adopted one of the most common methods of cell extraction, namely, enzymatic tissue digestion followed by fluorescence-activated cell sorting (FACS) of individual cells. We evaluated different enzymatic/mechanical tissue dissociation procedures and analyzed different astrocyte lineage transgenic models. Furthermore, we compared the cell extraction efficiency from spinal cord vs. brain. RESULTS Enzymatic digestion of CNS tissue of Glast-CreERT2x tdTomatofl/fl or Aldh1l1-CreERT2x tdTomatofl/fl followed by FACS resulted in highly purified astrocytes. Automated tissue digestion strongly improved the isolated cell numbers. Aldh1l1-CreERT2 identified more astrocytes than Glast-CreERT2; isolation from brain yields higher numbers than from spinal cord. COMPARISON WITH EXISTING METHODS We compared the efficiency and purity of the enzymatic dissociation/FACS approach with a more modern procedure consisting of tissue homogenization followed by translating ribosome affinity purification (TRAP). CONCLUSION We found that both methods result in highly enriched astrocytic RNA. However, only TRAP isolation resulted in reliably detectable RNA concentrations from spinal cord tissue on a single animal level. Depending on the aim of the study both methods have advantages and disadvantages but both are acceptable for astrocytic RNA analysis.
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Guo Q, Zhang Y, Zhang S, Jin J, Pang S, Wu X, Zhang W, Bi X, Zhang Y, Zhang Q, Jiang F. Genome-wide translational reprogramming of genes important for myocyte functions in overload-induced heart failure. Biochim Biophys Acta Mol Basis Dis 2019; 1866:165649. [PMID: 31870714 DOI: 10.1016/j.bbadis.2019.165649] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 12/22/2022]
Abstract
Genome-wide changes in gene translational efficiency during the development of heart failure are poorly understood. We tested the hypothesis that aberrant changes in translational efficiency of cardiac genes are associated with the development of myocyte decompensation in response to persistent stress stimuli. We demonstrated that chronic pressure overload in mice resulted in a genome-wide reprogramming of translational efficiency, with >50% of the translatome exhibiting decreased translational efficiencies during the transition from myocardial compensation to decompensation. Importantly, these translationally repressed genes included those involved in angiogenesis and energy metabolism. Moreover, we showed that the stress-induced translational reprogramming was accompanied by persistent activation of the eukaryotic initiation factor 2α (eIF2α)-mediated stress response pathway. Counteracting the endogenous eIF2α functions by cardiac-specific overexpression of an eIF2α-S51A mutant ameliorated the development of myocyte decompensation, with concomitant improvements in translation of cardiac functional genes and increases in angiogenic responses. These data suggest that the mismatch between transcription and translation of the cardiac genes with essential functions may represent a novel molecular mechanism underlying the development of myocyte decompensation in response to chronic stress stimuli, and the eIF2α pathway may be a viable therapeutic target for recovering the optimal translation of the repressed cardiac genes.
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Affiliation(s)
- Qianqian Guo
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Yongtao Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China; Department of Physiology and Pathophysiology, School of Basic Medicine, Shandong University, Jinan, Shandong Province, China; Department of Cardiology, Affiliated Hospital of Qingdao University, Qingdao, Shandong Province, China
| | - Shucui Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Jiajia Jin
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Shu Pang
- Department of Physiology and Pathophysiology, School of Basic Medicine, Shandong University, Jinan, Shandong Province, China
| | - Xiao Wu
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Wencheng Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaolei Bi
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China; Department of Cardiology, Qingdao Municipal Hospital, Qingdao, Shandong Province, China
| | - Yun Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China
| | - Qunye Zhang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China.
| | - Fan Jiang
- Key Laboratory of Cardiovascular Remodeling and Function Research, Chinese Ministry of Education, Chinese National Health Commission and Chinese Academy of Medical Sciences, and The State and Shandong Province Joint Key Laboratory of Translational Cardiovascular Medicine, Department of Cardiology, Qilu Hospital of Shandong University, Jinan, China; Department of Physiology and Pathophysiology, School of Basic Medicine, Shandong University, Jinan, Shandong Province, China.
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The in vivo endothelial cell translatome is highly heterogeneous across vascular beds. Proc Natl Acad Sci U S A 2019; 116:23618-23624. [PMID: 31712416 DOI: 10.1073/pnas.1912409116] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Endothelial cells (ECs) are highly specialized across vascular beds. However, given their interspersed anatomic distribution, comprehensive characterization of the molecular basis for this heterogeneity in vivo has been limited. By applying endothelial-specific translating ribosome affinity purification (EC-TRAP) combined with high-throughput RNA sequencing analysis, we identified pan EC-enriched genes and tissue-specific EC transcripts, which include both established markers and genes previously unappreciated for their presence in ECs. In addition, EC-TRAP limits changes in gene expression after EC isolation and in vitro expansion, as well as rapid vascular bed-specific shifts in EC gene expression profiles as a result of the enzymatic tissue dissociation required to generate single-cell suspensions for fluorescence-activated cell sorting or single-cell RNA sequencing analysis. Comparison of our EC-TRAP with published single-cell RNA sequencing data further demonstrates considerably greater sensitivity of EC-TRAP for the detection of low abundant transcripts. Application of EC-TRAP to examine the in vivo host response to lipopolysaccharide (LPS) revealed the induction of gene expression programs associated with a native defense response, with marked differences across vascular beds. Furthermore, comparative analysis of whole-tissue and TRAP-selected mRNAs identified LPS-induced differences that would not have been detected by whole-tissue analysis alone. Together, these data provide a resource for the analysis of EC-specific gene expression programs across heterogeneous vascular beds under both physiologic and pathologic conditions.
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Wu H, Lai CF, Chang-Panesso M, Humphreys BD. Proximal Tubule Translational Profiling during Kidney Fibrosis Reveals Proinflammatory and Long Noncoding RNA Expression Patterns with Sexual Dimorphism. J Am Soc Nephrol 2019; 31:23-38. [PMID: 31537650 DOI: 10.1681/asn.2019040337] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/01/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Proximal tubule injury can initiate CKD, with progression rates that are approximately 50% faster in males versus females. The precise transcriptional changes in this nephron segment during fibrosis and potential differences between sexes remain undefined. METHODS We generated mice with proximal tubule-specific expression of an L10a ribosomal subunit protein fused with enhanced green fluorescent protein. We performed unilateral ureteral obstruction surgery on four male and three female mice to induce inflammation and fibrosis, collected proximal tubule-specific and bulk cortex mRNA at day 5 or 10, and sequenced samples to a depth of 30 million reads. We applied computational methods to identify sex-biased and shared molecular responses to fibrotic injury, including up- and downregulated long noncoding RNAs (lncRNAs) and transcriptional regulators, and used in situ hybridization to validate critical genes and pathways. RESULTS We identified >17,000 genes in each proximal tubule group, including 145 G-protein-coupled receptors. More than 700 transcripts were differentially expressed in the proximal tubule of males versus females. The >4000 genes displaying altered expression during fibrosis were enriched for proinflammatory and profibrotic pathways. Our identification of nearly 150 differentially expressed proximal tubule lncRNAs during fibrosis suggests they may have unanticipated regulatory roles. Network analysis prioritized proinflammatory and profibrotic transcription factors such as Irf1, Nfkb1, and Stat3 as drivers of fibrosis progression. CONCLUSIONS This comprehensive transcriptomic map of the proximal tubule revealed sexually dimorphic gene expression that may reflect sex-related disparities in CKD, proinflammatory gene modules, and previously unappreciated proximal tubule-specific bidirectional lncRNA regulation.
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Affiliation(s)
- Haojia Wu
- Division of Nephrology.,Departments of Medicine and
| | - Chun-Fu Lai
- Division of Nephrology.,Departments of Medicine and.,Renal Division, Department of Internal Medicine, National Taiwan University Hospital, Taipai, Taiwan
| | | | - Benjamin D Humphreys
- Division of Nephrology, .,Departments of Medicine and.,Developmental Biology, Washington University in St. Louis School of Medicine, St. Louis, Missouri; and
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Grieco SF, Wang G, Mahapatra A, Lai C, Holmes TC, Xu X. Neuregulin and ErbB expression is regulated by development and sensory experience in mouse visual cortex. J Comp Neurol 2019; 528:419-432. [PMID: 31454079 PMCID: PMC6901715 DOI: 10.1002/cne.24762] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/22/2019] [Accepted: 08/14/2019] [Indexed: 01/14/2023]
Abstract
Neuregulins (NRGs) are protein ligands that impact neural development and circuit function. NRGs signal through the ErbB receptor tyrosine kinase family. NRG1/ErbB4 signaling in parvalbumin-expressing (PV) inhibitory interneurons is critical for visual cortical plasticity. There are multiple types of NRGs and ErbBs that can potentially contribute to visual cortical plasticity at different developmental stages. Thus, it is important to understand the normal developmental expression profiles of NRGs and ErbBs in specific neuron types in the visual cortex, and to study whether and how their expression changes in PV inhibitory neurons and excitatory neurons track with sensory perturbation. Cell type-specific translating ribosome affinity purification and qPCR was used to compare mRNA expression of nrg1,2,3,4 and erbB1,2,3,4 in PV and excitatory neurons in mouse visual cortex. We show that the expression of nrg1 and nrg3 decreases in PV neurons at the critical period peak, postnatal day 28 (P28) after monocular deprivation and dark rearing, and in the adult cortex (at P104) after 2-week long dark exposure. In contrast, nrg1 expression by excitatory neurons is unchanged at P28 and P104 following sensory deprivation, whereas nrg3 expression by excitatory neurons shows changes depending on the age and the mode of sensory deprivation. ErbB4 expression in PV neurons remains consistently high and does not appear to change in response to sensory deprivation. These data provide new important details of cell type-specific NRG/ErbB expression in the visual cortex and support that NRG1/ErbB4 signaling is implicated in both critical period and adult visual cortical plasticity.
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Affiliation(s)
- Steven F Grieco
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, California
| | - Gina Wang
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, California
| | - Ananya Mahapatra
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, California
| | - Cary Lai
- Department of Psychological and Brain Sciences, Indiana University, Bloomington, Indiana
| | - Todd C Holmes
- Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, California
| | - Xiangmin Xu
- Department of Anatomy and Neurobiology, School of Medicine, University of California, Irvine, California.,Department of Biomedical Engineering, University of California, Irvine, California
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Doroudgar S, Hofmann C, Boileau E, Malone B, Riechert E, Gorska AA, Jakobi T, Sandmann C, Jürgensen L, Kmietczyk V, Malovrh E, Burghaus J, Rettel M, Stein F, Younesi F, Friedrich UA, Mauz V, Backs J, Kramer G, Katus HA, Dieterich C, Völkers M. Monitoring Cell-Type-Specific Gene Expression Using Ribosome Profiling In Vivo During Cardiac Hemodynamic Stress. Circ Res 2019; 125:431-448. [PMID: 31284834 PMCID: PMC6690133 DOI: 10.1161/circresaha.119.314817] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Supplemental Digital Content is available in the text. Rationale: Gene expression profiles have been mainly determined by analysis of transcript abundance. However, these analyses cannot capture posttranscriptional gene expression control at the level of translation, which is a key step in the regulation of gene expression, as evidenced by the fact that transcript levels often poorly correlate with protein levels. Furthermore, genome-wide transcript profiling of distinct cell types is challenging due to the fact that lysates from tissues always represent a mixture of cells. Objectives: This study aimed to develop a new experimental method that overcomes both limitations and to apply this method to perform a genome-wide analysis of gene expression on the translational level in response to pressure overload. Methods and Results: By combining ribosome profiling (Ribo-seq) with a ribosome-tagging approach (Ribo-tag), it was possible to determine the translated transcriptome in specific cell types from the heart. After pressure overload, we monitored the cardiac myocyte translatome by purifying tagged cardiac myocyte ribosomes from cardiac lysates and subjecting the ribosome-protected mRNA fragments to deep sequencing. We identified subsets of mRNAs that are regulated at the translational level and found that translational control determines early changes in gene expression in response to cardiac stress in cardiac myocytes. Translationally controlled transcripts are associated with specific biological processes related to translation, protein quality control, and metabolism. Mechanistically, Ribo-seq allowed for the identification of upstream open reading frames in transcripts, which we predict to be important regulators of translation. Conclusions: This method has the potential to (1) provide a new tool for studying cell-specific gene expression at the level of translation in tissues, (2) reveal new therapeutic targets to prevent cellular remodeling, and (3) trigger follow-up studies that address both, the molecular mechanisms involved in the posttranscriptional control of gene expression in cardiac cells, and the protective functions of proteins expressed in response to cellular stress.
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Affiliation(s)
- Shirin Doroudgar
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Christoph Hofmann
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Etienne Boileau
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Brandon Malone
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Eva Riechert
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Agnieszka A Gorska
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Tobias Jakobi
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Clara Sandmann
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Lonny Jürgensen
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Vivien Kmietczyk
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Ellen Malovrh
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Jana Burghaus
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Mandy Rettel
- Proteomics Core Facility, EMBL Heidelberg, Germany (M.R., F.S.)
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Germany (M.R., F.S.)
| | - Fereshteh Younesi
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Ulrike A Friedrich
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Germany (G.K., U.A.F.)
| | - Victoria Mauz
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Institute of Experimental Cardiology, Heidelberg, Germany (V.M., J. Backs)
| | - Johannes Backs
- DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Institute of Experimental Cardiology, Heidelberg, Germany (V.M., J. Backs)
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH) and German Cancer Research Center (DKFZ), Center for Molecular Biology of Heidelberg University (ZMBH) and German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, Germany (G.K., U.A.F.)
| | - Hugo A Katus
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
| | - Christoph Dieterich
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.).,Section of Bioinformatics and Systems Cardiology and Klaus Tschira Institute for Integrative Computational Cardiology, University of Heidelberg, Germany (E.B., B.M., T.J., C.D.)
| | - Mirko Völkers
- From the Department of Cardiology, Angiology, and Pneumology, Internal Medicine III, Heidelberg University Hospital (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., H.A.K., C.D., M.V.).,DZHK (German Center for Cardiovascular Research), Partner Site Heidelberg/Mannheim, Germany (S.D., C.H., E.B., B.M., E.R., A.A.G., T.J., C.S., L.J., V.K., E.M., J. Burghaus, F.Y., V.M., J. Backs, H.A.K., C.D., M.V.)
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Ip CK, Zhang L, Farzi A, Qi Y, Clarke I, Reed F, Shi YC, Enriquez R, Dayas C, Graham B, Begg D, Brüning JC, Lee NJ, Hernandez-Sanchez D, Gopalasingam G, Koller J, Tasan R, Sperk G, Herzog H. Amygdala NPY Circuits Promote the Development of Accelerated Obesity under Chronic Stress Conditions. Cell Metab 2019; 30:111-128.e6. [PMID: 31031093 DOI: 10.1016/j.cmet.2019.04.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 02/16/2019] [Accepted: 04/02/2019] [Indexed: 12/22/2022]
Abstract
Neuropeptide Y (NPY) exerts a powerful orexigenic effect in the hypothalamus. However, extra-hypothalamic nuclei also produce NPY, but its influence on energy homeostasis is unclear. Here we uncover a previously unknown feeding stimulatory pathway that is activated under conditions of stress in combination with calorie-dense food; NPY neurons in the central amygdala are responsible for an exacerbated response to a combined stress and high-fat-diet intervention. Central amygdala NPY neuron-specific Npy overexpression mimics the obese phenotype seen in a combined stress and high-fat-diet model, which is prevented by the selective ablation of Npy. Using food intake and energy expenditure as readouts, we demonstrate that selective activation of central amygdala NPY neurons results in increased food intake and decreased energy expenditure. Mechanistically, it is the diminished insulin signaling capacity on central amygdala NPY neurons under combined stress and high-fat-diet conditions that leads to the exaggerated development of obesity.
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Affiliation(s)
- Chi Kin Ip
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Lei Zhang
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Aitak Farzi
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yue Qi
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Ireni Clarke
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Felicia Reed
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Yan-Chuan Shi
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Ronaldo Enriquez
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Chris Dayas
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Bret Graham
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, NSW, Australia
| | - Denovan Begg
- School of Psychology, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jens C Brüning
- Max Planck Institute for Metabolism Research, Cologne, Germany
| | - Nicola J Lee
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia
| | - Diana Hernandez-Sanchez
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gopana Gopalasingam
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Julia Koller
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Ramon Tasan
- Department of Pharmacology, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Günther Sperk
- Department of Pharmacology, Medical University Innsbruck, Innsbruck 6020, Austria
| | - Herbert Herzog
- Neuroscience Division, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia; Faculty of Medicine, University of New South Wales, Sydney, NSW 2052, Australia.
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Good AL, Cannon CE, Haemmerle MW, Yang J, Stanescu DE, Doliba NM, Birnbaum MJ, Stoffers DA. JUND regulates pancreatic β cell survival during metabolic stress. Mol Metab 2019; 25:95-106. [PMID: 31023625 PMCID: PMC6600134 DOI: 10.1016/j.molmet.2019.04.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 04/01/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVE In type 2 diabetes (T2D), oxidative stress contributes to the dysfunction and loss of pancreatic β cells. A highly conserved feature of the cellular response to stress is the regulation of mRNA translation; however, the genes regulated at the level of translation are often overlooked due to the convenience of RNA sequencing technologies. Our goal is to investigate translational regulation in β cells as a means to uncover novel factors and pathways pertinent to cellular adaptation and survival during T2D-associated conditions. METHODS Translating ribosome affinity purification (TRAP) followed by RNA-seq or RT-qPCR was used to identify changes in the ribosome occupancy of mRNAs in Min6 cells. Gene depletion studies used lentiviral delivery of shRNAs to primary mouse islets or CRISPR-Cas9 to Min6 cells. Oxidative stress and apoptosis were measured in primary islets using cell-permeable dyes with fluorescence readouts of oxidation and activated cleaved caspase-3 and-7, respectively. Gene expression was assessed by RNA-seq, RT-qPCR, and western blot. ChIP-qPCR was used to determine chromatin enrichment. RESULTS TRAP-seq in a PDX1-deficiency model of β cell dysfunction uncovered a cohort of genes regulated at the level of mRNA translation, including the transcription factor JUND. Using a panel of diabetes-associated stressors, JUND was found to be upregulated in mouse islets cultured with high concentrations of glucose and free fatty acid, but not after treatment with hydrogen peroxide or thapsigargin. This induction of JUND could be attributed to increased mRNA translation. JUND was also upregulated in islets from diabetic db/db mice and in human islets treated with high glucose and free fatty acid. Depletion of JUND in primary islets reduced oxidative stress and apoptosis in β cells during metabolic stress. Transcriptome assessment identified a cohort of genes, including pro-oxidant and pro-inflammatory genes, regulated by JUND that are commonly dysregulated in models of β cell dysfunction, consistent with a maladaptive role for JUND in islets. CONCLUSIONS A translation-centric approach uncovered JUND as a stress-responsive factor in β cells that contributes to redox imbalance and apoptosis during pathophysiologically relevant stress.
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Affiliation(s)
- Austin L Good
- Institute for Diabetes, Obesity, and Metabolism and the Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Corey E Cannon
- Institute for Diabetes, Obesity, and Metabolism and the Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Matthew W Haemmerle
- Institute for Diabetes, Obesity, and Metabolism and the Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Juxiang Yang
- Division of Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Diana E Stanescu
- Division of Endocrinology, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Nicolai M Doliba
- Institute for Diabetes, Obesity, and Metabolism and the Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Morris J Birnbaum
- Institute for Diabetes, Obesity, and Metabolism and the Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Doris A Stoffers
- Institute for Diabetes, Obesity, and Metabolism and the Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Differences between Dorsal Root and Trigeminal Ganglion Nociceptors in Mice Revealed by Translational Profiling. J Neurosci 2019; 39:6829-6847. [PMID: 31253755 DOI: 10.1523/jneurosci.2663-18.2019] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 06/19/2019] [Accepted: 06/20/2019] [Indexed: 01/08/2023] Open
Abstract
Nociceptors located in the trigeminal ganglion (TG) and DRG are the primary sensors of damaging or potentially damaging stimuli for the head and body, respectively, and are key drivers of chronic pain states. While nociceptors in these two tissues show a high degree of functional similarity, there are important differences in their development lineages, their functional connections to the CNS, and recent genome-wide analyses of gene expression suggest that they possess some unique genomic signatures. Here, we used translating ribosome affinity purification to comprehensively characterize and compare mRNA translation in Scn10a-positive nociceptors in the TG and DRG of male and female mice. This unbiased method independently confirms several findings of differences between TG and DRG nociceptors described in the literature but also suggests preferential utilization of key signaling pathways. Most prominently, we provide evidence that translational efficiency in mechanistic target of rapamycin (mTOR)-related genes is higher in the TG compared with DRG, whereas several genes associated with the negative regulator of mTOR, AMP-activated protein kinase, have higher translational efficiency in DRG nociceptors. Using capsaicin as a sensitizing stimulus, we show that behavioral responses are greater in the TG region and this effect is completely reversible with mTOR inhibition. These findings have implications for the relative capacity of these nociceptors to be sensitized upon injury. Together, our data provide a comprehensive, comparative view of transcriptome and translatome activity in TG and DRG nociceptors that enhances our understanding of nociceptor biology.SIGNIFICANCE STATEMENT The DRG and trigeminal ganglion (TG) provide sensory information from the body and head, respectively. Nociceptors in these tissues are critical first neurons in the pain pathway. Injury to peripheral neurons in these tissues can cause chronic pain. Interestingly, clinical and preclinical findings support the conclusion that injury to TG neurons is more likely to cause chronic pain and chronic pain in the TG area is more intense and more difficult to treat. We used translating ribosome affinity purification technology to gain new insight into potential differences in the translatomes of DRG and TG neurons. Our findings demonstrate previously unrecognized differences between TG and DRG nociceptors that provide new insight into how injury may differentially drive plasticity states in nociceptors in these two tissues.
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Abstract
Understanding adipogenesis, the process of adipocyte development, may provide new ways to treat obesity and related metabolic diseases. Adipogenesis is controlled by coordinated actions of lineage-determining transcription factors and epigenomic regulators. Peroxisome proliferator-activated receptor gamma (PPARγ) and C/EBPα are master "adipogenic" transcription factors. In recent years, a growing number of studies have reported the identification of novel transcriptional and epigenomic regulators of adipogenesis. However, many of these novel regulators have not been validated in adipocyte development in vivo and their working mechanisms are often far from clear. In this minireview, we discuss recent advances in transcriptional and epigenomic regulation of adipogenesis, with a focus on factors and mechanisms shared by both white adipogenesis and brown adipogenesis. Studies on the transcriptional regulation of adipogenesis highlight the importance of investigating adipocyte differentiation in vivo rather than drawing conclusions based on knockdown experiments in cell culture. Advances in understanding of epigenomic regulation of adipogenesis have revealed critical roles of histone methylation/demethylation, histone acetylation/deacetylation, chromatin remodeling, DNA methylation, and microRNAs in adipocyte differentiation. We also discuss future research directions that may help identify novel factors and mechanisms regulating adipogenesis.
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50
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Zimmerman CA, Huey EL, Ahn JS, Beutler LR, Tan CL, Kosar S, Bai L, Chen Y, Corpuz TV, Madisen L, Zeng H, Knight ZA. A gut-to-brain signal of fluid osmolarity controls thirst satiation. Nature 2019; 568:98-102. [PMID: 30918408 PMCID: PMC6483081 DOI: 10.1038/s41586-019-1066-x] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 03/04/2019] [Indexed: 12/03/2022]
Affiliation(s)
- Christopher A Zimmerman
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Erica L Huey
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Graduate Program in Neuroscience, Harvard Medical School, Boston, MA, USA
| | - Jamie S Ahn
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,California Northstate University College of Medicine, Elk Grove, CA, USA
| | - Lisa R Beutler
- Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Chan Lek Tan
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Department of Neuroscience, Genentech Inc., South San Francisco, CA, USA
| | - Seher Kosar
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | - Ling Bai
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | - Yiming Chen
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA.,Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA, USA
| | - Timothy V Corpuz
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA.,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA
| | | | - Hongkui Zeng
- Allen Institute for Brain Science, Seattle, WA, USA
| | - Zachary A Knight
- Department of Physiology, University of California San Francisco, San Francisco, CA, USA. .,Kavli Institute for Fundamental Neuroscience, University of California San Francisco, San Francisco, CA, USA. .,Neuroscience Graduate Program, University of California San Francisco, San Francisco, CA, USA. .,Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA, USA.
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