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Chen HC, Wang J, Coffey RJ, Patton JG, Weaver AM, Shyr Y, Liu Q. EVPsort: An Atlas of Small ncRNA Profiling and Sorting in Extracellular Vesicles and Particles. J Mol Biol 2024:168571. [PMID: 38604528 DOI: 10.1016/j.jmb.2024.168571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 03/12/2024] [Accepted: 04/07/2024] [Indexed: 04/13/2024]
Abstract
Extracellular vesicles and particles (EVPs) play a crucial role in mediating cell-to-cell communication by transporting various molecular cargos, with small non-coding RNAs (ncRNAs) holding particular significance. A thorough investigation into the abundance and sorting mechanisms of ncRNA within EVPs is imperative for advancing their clinical applications. We have developed EVPsort, which not only provides an extensive overview of ncRNA profiling in 3,162 samples across various biofluids, cell lines, and disease contexts but also seamlessly integrates 19 external databases and tools. This integration encompasses information on associations between ncRNAs and RNA-binding proteins (RBPs), motifs, targets, pathways, diseases, and drugs. With its rich resources and powerful analysis tools, EVPsort extends its profiling capabilities to investigate ncRNA sorting, identify relevant RBPs and motifs, and assess functional implications. EVPsort stands as a pioneering database dedicated to comprehensively addressing both the abundance and sorting of ncRNA within EVPs. It is freely accessible at https://bioinfo.vanderbilt.edu/evpsort/.
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Affiliation(s)
- Hua-Chang Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Extracellular Vesicle Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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Qu S, Nelson H, Liu X, Semler E, Michell DL, Massick C, Franklin JL, Karijolich J, Weaver AM, Coffey RJ, Liu Q, Vickers KC, Patton JG. 5-Fluorouracil Treatment Represses Pseudouridine-Containing Small RNA Export into Extracellular Vesicles. bioRxiv 2024:2024.01.15.575751. [PMID: 38293013 PMCID: PMC10827090 DOI: 10.1101/2024.01.15.575751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
5-fluorouracil (5-FU) has been used for chemotherapy for colorectal and other cancers for over 50 years. The prevailing view of its mechanism of action is inhibition of thymidine synthase leading to defects in DNA replication and repair. However, 5-FU is also incorporated into RNA causing toxicity due to defects in RNA metabolism, inhibition of pseudouridine modification, and altered ribosome function. Here, we examine the impact of 5-FU on the expression and export of small RNAs (sRNAs) into small extracellular vesicles (sEVs). Moreover, we assess the role of 5-FU in regulation of post-transcriptional sRNA modifications (PTxM) using mass spectrometry approaches. EVs are secreted by all cells and contain a variety of proteins and RNAs that can function in cell-cell communication. PTxMs on cellular and extracellular sRNAs provide yet another layer of gene regulation. We found that treatment of the colorectal cancer (CRC) cell line DLD-1 with 5-FU led to surprising differential export of miRNA snRNA, and snoRNA transcripts. Strikingly, 5-FU treatment significantly decreased the levels of pseudouridine on both cellular and secreted EV sRNAs. In contrast, 5-FU exposure led to increased levels of cellular sRNAs containing a variety of methyl-modified bases. Our results suggest that 5-FU exposure leads to altered expression, base modifications, and mislocalization of EV base-modified sRNAs.
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Wang J, Chen HC, Sheng Q, Dawson TR, Coffey RJ, Patton JG, Weaver AM, Shyr Y, Liu Q. Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles. Cancers (Basel) 2023; 15:3446. [PMID: 37444556 PMCID: PMC10340377 DOI: 10.3390/cancers15133446] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/22/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
MOTIVATION Extracellular vesicles (EVs) are produced and released by most cells and are now recognized to play a role in intercellular communication through the delivery of molecular cargo, including proteins, lipids, and RNA. Small RNA sequencing (small RNA-seq) has been widely used to characterize the small RNA content in EVs. However, there is a lack of a systematic assessment of the quality, technical biases, RNA composition, and RNA biotypes enrichment for small RNA profiling of EVs across cell types, biofluids, and conditions. METHODS We collected and reanalyzed small RNA-seq datasets for 2756 samples from 83 studies involving 55 with EVs only and 28 with both EVs and matched donor cells. We assessed their quality by the total number of reads after adapter trimming, the overall alignment rate to the host and non-host genomes, and the proportional abundance of total small RNA and specific biotypes, such as miRNA, tRNA, rRNA, and Y RNA. RESULTS We found that EV extraction methods varied in their reproducibility in isolating small RNAs, with effects on small RNA composition. Comparing proportional abundances of RNA biotypes between EVs and matched donor cells, we discovered that rRNA and tRNA fragments were relatively enriched, but miRNAs and snoRNA were depleted in EVs. Except for the export of eight miRNAs being context-independent, the selective release of most miRNAs into EVs was study-specific. CONCLUSION This work guides quality control and the selection of EV isolation methods and enhances the interpretation of small RNA contents and preferential loading in EVs.
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Affiliation(s)
- Jing Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (H.-C.C.); (Q.S.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hua-Chang Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (H.-C.C.); (Q.S.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Quanhu Sheng
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (H.-C.C.); (Q.S.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - T. Renee Dawson
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (T.R.D.); (R.J.C.); (A.M.W.)
- Center for Extracellular Vesicle Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Robert J. Coffey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (T.R.D.); (R.J.C.); (A.M.W.)
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James G. Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA;
| | - Alissa M. Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; (T.R.D.); (R.J.C.); (A.M.W.)
- Center for Extracellular Vesicle Research, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Yu Shyr
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (H.-C.C.); (Q.S.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA; (J.W.); (H.-C.C.); (Q.S.)
- Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Konar G, Flickinger Z, Sharma S, Vallone K, Lyon C, Doshier C, Lyon W, Patton JG. Damage-induced senescent immune cells regulate regeneration of the zebrafish retina. bioRxiv 2023:2023.01.16.524296. [PMID: 36711649 PMCID: PMC9882244 DOI: 10.1101/2023.01.16.524296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Zebrafish spontaneously regenerate their retina in response to damage through the action of Müller glia. Even though Müller glia (MG) are conserved in higher vertebrates, the capacity to regenerate retinal damage is lost. Recent work has focused on the regulation of inflammation during tissue regeneration with precise temporal roles for macrophages and microglia. Senescent cells that have withdrawn from the cell cycle have mostly been implicated in aging, but are still metabolically active, releasing proinflammatory signaling molecules as part of the Senescence Associated Secretory Phenotype (SASP). Here, we discover that in response to retinal damage, a subset of cells expressing markers of microglia/macrophages also express markers of senescence. These cells display a temporal pattern of appearance and clearance during retina regeneration. Premature removal of senescent cells by senolytic treatment led to a decrease in proliferation and incomplete repair of the ganglion cell layer after NMDA damage. Our results demonstrate a role for modulation of senescent cell responses to balance inflammation, regeneration, plasticity, and repair as opposed to fibrosis and scarring.
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Affiliation(s)
| | | | - Shivani Sharma
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - Kyle Vallone
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - Charles Lyon
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - Claire Doshier
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - William Lyon
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
| | - James G. Patton
- Department of Biological Sciences, Vanderbilt University, Nashville TN, USA
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Barman B, Sung BH, Krystofiak E, Ping J, Ramirez M, Millis B, Allen R, Prasad N, Chetyrkin S, Calcutt MW, Vickers K, Patton JG, Liu Q, Weaver AM. VAP-A and its binding partner CERT drive biogenesis of RNA-containing extracellular vesicles at ER membrane contact sites. Dev Cell 2022; 57:974-994.e8. [PMID: 35421371 PMCID: PMC9075344 DOI: 10.1016/j.devcel.2022.03.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 01/11/2022] [Accepted: 03/17/2022] [Indexed: 12/12/2022]
Abstract
RNA transfer via extracellular vesicles (EVs) influences cell phenotypes; however, lack of information regarding biogenesis of RNA-containing EVs has limited progress in the field. Here, we identify endoplasmic reticulum membrane contact sites (ER MCSs) as platforms for the generation of RNA-containing EVs. We identify a subpopulation of small EVs that is highly enriched in RNA and regulated by the ER MCS linker protein VAP-A. Functionally, VAP-A-regulated EVs are critical for miR-100 transfer between cells and in vivo tumor formation. Lipid analysis of VAP-A-knockdown EVs revealed reductions in the EV biogenesis lipid ceramide. Knockdown of the VAP-A-binding ceramide transfer protein CERT led to similar defects in EV RNA content. Imaging experiments revealed that VAP-A promotes luminal filling of multivesicular bodies (MVBs), CERT localizes to MVBs, and the ceramide-generating enzyme neutral sphingomyelinase 2 colocalizes with VAP-A-positive ER. We propose that ceramide transfer via VAP-A-CERT linkages drives the biogenesis of a select RNA-containing EV population.
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Affiliation(s)
- Bahnisikha Barman
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Bong Hwan Sung
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Evan Krystofiak
- Vanderbilt University Cell Imaging Shared Resource, Nashville, TN, USA
| | - Jie Ping
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Marisol Ramirez
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Bryan Millis
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Biomedical Engineering, Vanderbilt Biophotonics Center, Vanderbilt School of Engineering, Nashville, TN, USA
| | - Ryan Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nripesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sergei Chetyrkin
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA
| | - M Wade Calcutt
- Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, USA; Department of Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Kasey Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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Liu H, Li D, Sun L, Qin H, Fan A, Meng L, Graves-Deal R, Glass SE, Franklin JL, Liu Q, Wang J, Yeatman TJ, Guo H, Zong H, Jin S, Chen Z, Deng T, Fang Y, Li C, Karijolich J, Patton JG, Wang X, Nie Y, Fan D, Coffey RJ, Zhao X, Lu Y. Interaction of lncRNA MIR100HG with hnRNPA2B1 facilitates m 6A-dependent stabilization of TCF7L2 mRNA and colorectal cancer progression. Mol Cancer 2022; 21:74. [PMID: 35279145 PMCID: PMC8917698 DOI: 10.1186/s12943-022-01555-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/02/2022] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Epithelial-to-mesenchymal transition (EMT) is a process linked to metastasis and drug resistance with non-coding RNAs (ncRNAs) playing pivotal roles. We previously showed that miR-100 and miR-125b, embedded within the third intron of the ncRNA host gene MIR100HG, confer resistance to cetuximab, an anti-epidermal growth factor receptor (EGFR) monoclonal antibody, in colorectal cancer (CRC). However, whether the MIR100HG transcript itself has a role in cetuximab resistance or EMT is unknown. METHODS The correlation between MIR100HG and EMT was analyzed by curating public CRC data repositories. The biological roles of MIR100HG in EMT, metastasis and cetuximab resistance in CRC were determined both in vitro and in vivo. The expression patterns of MIR100HG, hnRNPA2B1 and TCF7L2 in CRC specimens from patients who progressed on cetuximab and patients with metastatic disease were analyzed by RNAscope and immunohistochemical staining. RESULTS The expression of MIR100HG was strongly correlated with EMT markers and acted as a positive regulator of EMT. MIR100HG sustained cetuximab resistance and facilitated invasion and metastasis in CRC cells both in vitro and in vivo. hnRNPA2B1 was identified as a binding partner of MIR100HG. Mechanistically, MIR100HG maintained mRNA stability of TCF7L2, a major transcriptional coactivator of the Wnt/β-catenin signaling, by interacting with hnRNPA2B1. hnRNPA2B1 recognized the N6-methyladenosine (m6A) site of TCF7L2 mRNA in the presence of MIR100HG. TCF7L2, in turn, activated MIR100HG transcription, forming a feed forward regulatory loop. The MIR100HG/hnRNPA2B1/TCF7L2 axis was augmented in specimens from CRC patients who either developed local or distant metastasis or had disease progression that was associated with cetuximab resistance. CONCLUSIONS MIR100HG and hnRNPA2B1 interact to control the transcriptional activity of Wnt signaling in CRC via regulation of TCF7L2 mRNA stability. Our findings identified MIR100HG as a potent EMT inducer in CRC that may contribute to cetuximab resistance and metastasis by activation of a MIR100HG/hnRNPA2B1/TCF7L2 feedback loop.
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Affiliation(s)
- Hao Liu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Danxiu Li
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Lina Sun
- The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, Liaoning, China
| | - Ahui Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Lingnan Meng
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Ramona Graves-Deal
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Sarah E Glass
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Jeffrey L Franklin
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA
| | - Qi Liu
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Jing Wang
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Timothy J Yeatman
- Departments of Surgery and Molecular Medicine, TGH Cancer Institute and University of South Florida, Tampa, FL, 33620, USA
| | - Hao Guo
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing, 210042, Jiangsu, China
| | - Hong Zong
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Shuilin Jin
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, 450052, Henan, China
| | - Zhiyu Chen
- Department of Medical Oncology, Fudan University Shanghai Cancer Center, Shanghai, 200032, China
| | - Ting Deng
- Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, 300060, China
| | - Ying Fang
- The Affiliated Children's Hospital of Xi'an Jiaotong University, Xi'an, 710003, China
| | - Cunxi Li
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, 100191, China
| | - John Karijolich
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Xin Wang
- Department of Gastroenterology, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710038, Shaanxi, China
| | - Yongzhan Nie
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China
| | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
| | - Robert J Coffey
- Departments of Medicine and Cell and Developmental Biology, Vanderbilt University Medical Center, 2213 Garland Ave, Nashville, TN, 37232, USA.
| | - Xiaodi Zhao
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
| | - Yuanyuan Lu
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 127 West Changle Rd, Xi'an, 710032, Shaanxi, China.
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Abner JJ, Franklin JL, Clement MA, Hinger SA, Allen RM, Liu X, Kellner S, Wu J, Karijolich J, Liu Q, Vickers KC, Dedon P, Weaver AM, Coffey RJ, Patton JG. Depletion of METTL3 alters cellular and extracellular levels of miRNAs containing m 6A consensus sequences. Heliyon 2021; 7:e08519. [PMID: 34934837 PMCID: PMC8654799 DOI: 10.1016/j.heliyon.2021.e08519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/02/2021] [Accepted: 11/29/2021] [Indexed: 12/21/2022] Open
Abstract
Extracellular vesicles (EVs) are capable of transferring cargo from donor to recipient cells, but precisely how cargo content is regulated for export is mostly unknown. For miRNA cargo, we previously showed that when compared to isogenic colorectal cancer (CRC) cells expressing wild-type KRAS, a distinct subset of miRNAs are differentially enriched in EVs from KRAS mutant active CRC cells, with miR-100 being one of the most enriched. The mechanisms that could explain how miR-100 and other miRNAs are differentially exported into EVs have not been fully elucidated. Here, we tested the effect of N6-methyladenosine (m6A) modification on miRNA export into EVs by depletion of METTL3 and ALKBH5, a writer and eraser of m6A modification, respectively. While the effects of ALKBH5 knockdown were quite modest, decreased levels of METTL3 led to reduced cellular and extracellular levels of a subset of miRNAs that contain consensus sequences for m6A modification. Functional testing of EVs prepared from cells expressing shRNAs against METTL3 showed that they were less capable of conferring colony growth in 3D to wild-type KRAS cells and were also largely incapable of conferring the spread of cetuximab resistance. Our data support a role for METTL3 modification on cellular miRNA levels and export of specific miRNAs.
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Affiliation(s)
- Jessica J. Abner
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Jeffrey L. Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Margaret A. Clement
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Scott A. Hinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ryan M. Allen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Xiao Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Stefanie Kellner
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Junzhou Wu
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Karijolich
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Kasey C. Vickers
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Peter Dedon
- Singapore-MIT Alliance for Research and Technology, Singapore
| | - Alissa M. Weaver
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Robert J. Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - James G. Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
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Nachtigall PG, Bovolenta LA, Patton JG, Fromm B, Lemke N, Pinhal D. A comparative analysis of heart microRNAs in vertebrates brings novel insights into the evolution of genetic regulatory networks. BMC Genomics 2021; 22:153. [PMID: 33663371 PMCID: PMC7931589 DOI: 10.1186/s12864-021-07441-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 02/12/2021] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND During vertebrate evolution, the heart has undergone remarkable changes that lead to morphophysiological differences in the fully formed heart of these species, such as chamber septation, heart rate frequency, blood pressure, and cardiac output volume. Despite these differences, the heart developmental process is guided by a core gene set conserved across vertebrates. Nonetheless, the regulatory mechanisms controlling the expression of genes involved in heart development and maintenance are largely uncharted. MicroRNAs (miRNAs) have been described as important regulatory elements in several biological processes, including heart biology. These small RNA molecules are broadly conserved in sequence and genomic context in metazoans. Mutations may occur in miRNAs and/or genes that contribute to the establishment of distinct repertoires of miRNA-target interactions, thereby favoring the differential control of gene expression and, consequently, the origin of novel phenotypes. In fact, several studies showed that miRNAs are integrated into genetic regulatory networks (GRNs) governing specific developmental programs and diseases. However, studies integrating miRNAs in vertebrate heart GRNs under an evolutionary perspective are still scarce. RESULTS We comprehensively examined and compared the heart miRNome of 20 species representatives of the five major vertebrate groups. We found 54 miRNA families with conserved expression and a variable number of miRNA families with group-specific expression in fishes, amphibians, reptiles, birds, and mammals. We also detected that conserved miRNAs present higher expression levels and a higher number of targets, whereas the group-specific miRNAs present lower expression levels and few targets. CONCLUSIONS Both the conserved and group-specific miRNAs can be considered modulators orchestrating the core and peripheral genes of heart GRNs of vertebrates, which can be related to the morphophysiological differences and similarities existing in the heart of distinct vertebrate groups. We propose a hypothesis to explain evolutionary differences in the putative functional roles of miRNAs in the heart GRNs analyzed. Furthermore, we present new insights into the molecular mechanisms that could be helping modulate the diversity of morphophysiology in the heart organ of vertebrate species.
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Affiliation(s)
- Pedro G Nachtigall
- Laboratório Especial de Toxinologia Aplicada (LETA), CeTICS, Instituto Butantan, São Paulo, Brazil. .,Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.
| | - Luiz A Bovolenta
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, USA
| | - Bastian Fromm
- Department of Molecular Biosciences, The Wenner-Gren Institute (MBW), Stockholm University, Stockholm, Sweden
| | - Ney Lemke
- Department of Biophysics and Pharmacology, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
| | - Danillo Pinhal
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil
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9
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Konar GJ, Ferguson C, Flickinger Z, Kent MR, Patton JG. miRNAs and Müller Glia Reprogramming During Retina Regeneration. Front Cell Dev Biol 2021; 8:632632. [PMID: 33537319 PMCID: PMC7848101 DOI: 10.3389/fcell.2020.632632] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
The use of model systems that are capable of robust, spontaneous retina regeneration has allowed for the identification of genetic pathways and components that are required for retina regeneration. Complemented by mouse models in which retina regeneration can be induced after forced expression of key factors, altered chromatin accessibility, or inhibition of kinase/signaling cascades, a clearer picture of the key regulatory events that control retina regeneration is emerging. In all cases, Müller glia (MG) serve as an adult retinal stem cell that must be reprogrammed to allow for regeneration, with the end goal being to understand why regenerative pathways are blocked in mammals, but spontaneous in other vertebrates such as zebrafish. miRNAs have emerged as key gene regulatory molecules that control both development and regeneration in vertebrates. Here, we focus on a small subset of miRNAs that control MG reprogramming during retina regeneration and have the potential to serve as therapeutic targets for treatment of visual disorders and damage.
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Affiliation(s)
- Gregory J Konar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Claire Ferguson
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Zachary Flickinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Matthew R Kent
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
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10
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Abstract
A potential treatment for retinal diseases is to induce an endogenous Müller glia (MG)-derived regenerative response to replace damaged neurons. In contrast to mammalian MG, zebrafish MG are capable of mediating spontaneous regeneration. We seek to define the mechanisms that enable retina regeneration in zebrafish in order to identify therapeutic targets to induce mammalian retina regeneration. We previously used pharmacological and genetic methods to inhibit gamma aminobutyric acid A (GABAA) receptors in undamaged zebrafish retinas and showed that such inhibition could induce initiation of retina regeneration, as measured by the dedifferentiation of MG and the appearance of MG-derived proliferating progenitor cells. Here, we show that inhibition of a pharmacologically distinct subset of GABAA receptors (GABAA-ρ) can also induce retina regeneration. Dual inhibition of both GABA receptor subtypes led to enhanced retina regeneration. Gene expression analyses indicate that inhibition of GABAA-ρ receptors induces a canonical retinal regenerative response. Our results support a model in which decreased levels of GABA, such as would occur after retinal cell death or damage, induce dedifferentiation of MG and the generation of proliferating progenitor cells during zebrafish retina regeneration. Animal experiments were approved by the Vanderbilt's Institutional Animal Care and Use Committee (Protocol M1800200) on January 29, 2019.
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Affiliation(s)
- Matthew R Kent
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Nergis Kara
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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11
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Hinger SA, Abner JJ, Franklin JL, Jeppesen DK, Coffey RJ, Patton JG. Rab13 regulates sEV secretion in mutant KRAS colorectal cancer cells. Sci Rep 2020; 10:15804. [PMID: 32978434 PMCID: PMC7519665 DOI: 10.1038/s41598-020-72503-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 08/26/2020] [Indexed: 12/17/2022] Open
Abstract
Small extracellular vesicles (sEVs), 50–150 nm in diameter, have been proposed to mediate cell–cell communication with important implications in tumor microenvironment interactions, tumor growth, and metastasis. We previously showed that mutant KRAS colorectal cancer (CRC) cells release sEVs containing Rab13 protein and mRNA. Previous work had shown that disruption of intracellular Rab13 trafficking inhibits epithelial cell proliferation and invasiveness. Here, we show that Rab13 additionally regulates the secretion of sEVs corresponding to both traditional exosomes and a novel subset of vesicles containing both β1-integrin and Rab13. We find that exposure of recipient cells to sEVs from KRAS mutant donor cells increases proliferation and tumorigenesis and that knockdown of Rab13 blocks these effects. Thus, Rab13 serves as both a cargo protein and as a regulator of sEV secretion. Our data support a model whereby Rab13 can mediate its effects on cell proliferation and invasiveness via autocrine and paracrine signaling.
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Affiliation(s)
- Scott A Hinger
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37235, USA.,Department of Physiology and Cell Biology, College of Medicine, The Ohio State University, Columbus, OH, 43210, USA
| | - Jessica J Abner
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Dennis K Jeppesen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37235, USA.,Veterans Affairs Medical Center, Nashville, TN, 37235, USA.,Vanderbilt University, Nashville, TN, 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN, 37235, USA.
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12
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Didiano D, Abner JJ, Hinger SA, Flickinger Z, Kent M, Clement MA, Balaiya S, Liu Q, Dai X, Levine EM, Patton JG. Induction of a proliferative response in the zebrafish retina by injection of extracellular vesicles. Exp Eye Res 2020; 200:108254. [PMID: 32961174 DOI: 10.1016/j.exer.2020.108254] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 08/26/2020] [Accepted: 09/14/2020] [Indexed: 12/18/2022]
Abstract
Ongoing research using cell transplantation and viral-mediated gene therapy has been making progress to restore vision by retinal repair, but targeted delivery and complete cellular integration remain challenging. An alternative approach is to induce endogenous Müller glia (MG) to regenerate lost neurons and photoreceptors, as occurs spontaneously in teleost fish and amphibians. Extracellular vesicles (EVs) can transfer protein and RNA cargo between cells serving as a novel means of cell-cell communication. We conducted an in vivo screen in zebrafish to identify sources of EVs that could induce MG to dedifferentiate and generate proliferating progenitor cells after intravitreal injection into otherwise undamaged zebrafish eyes. Small EVs (sEVs) from C6 glioma cells were the most consistent at inducing MG-derived proliferating cells. Ascl1a expression increased after intravitreal injection of C6 sEVs and knockdown of ascl1a inhibited the induction of proliferation. Proteomic and RNAseq analyses of EV cargo content were performed to begin to identify key factors that might target EVs to MG and initiate retina regeneration.
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Affiliation(s)
- Dominic Didiano
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Jessica J Abner
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Scott A Hinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Zachary Flickinger
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Matthew Kent
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Margaret A Clement
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Sankarathi Balaiya
- Department of Ophthalmology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Xiaozhuan Dai
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - Edward M Levine
- Department of Ophthalmology, Vanderbilt University Medical Center, Nashville, TN, 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
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13
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Kara N, Kent MR, Didiano D, Rajaram K, Zhao A, Summerbell ER, Patton JG. The miR-216a-Dot1l Regulatory Axis Is Necessary and Sufficient for Müller Glia Reprogramming during Retina Regeneration. Cell Rep 2020; 28:2037-2047.e4. [PMID: 31433981 PMCID: PMC6750267 DOI: 10.1016/j.celrep.2019.07.061] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 06/13/2019] [Accepted: 07/18/2019] [Indexed: 12/15/2022] Open
Abstract
Unlike the adult mammalian retina, Müller glia (MG) in the adult zebrafish retina are able to dedifferentiate into a ‘‘stem cell’’-like state and give rise to multipotent progenitor cells upon retinal damage. We show that miR-216a is downregulated in MG after constant intense light lesioning and that miR-216a suppression is necessary and sufficient for MG dedifferentiation and proliferation during retina regeneration. miR-216a targets the H3K79 methyltransferase Dot1l, which is upregulated in proliferating MG after retinal damage. Loss-of-function experiments show that Dot1l is necessary for MG reprogramming and mediates MG proliferation downstream of miR-216a. We further demonstrate that miR-216a and Dot1l regulate MG-mediated retina regeneration through canonical Wnt signaling. This article reports a regulatory mechanism upstream of Wnt signaling during retina regeneration and provides potential targets for enhancing regeneration in the adult mammalian retina. Unlike the adult mammalian retina, Müller glia in the adult zebrafish retina are able to reprogram into a stem cell-like state and give rise to multipotent progenitor cells upon retinal damage. Kara et al. show that miR-216a suppression stimulates Müller glia reprogramming through upregulation of the H3K79 methyltransferase Dot1l and activation of Wnt/β-catenin signaling.
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Affiliation(s)
- Nergis Kara
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Matthew R Kent
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Dominic Didiano
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Kamya Rajaram
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Anna Zhao
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Emily R Summerbell
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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14
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Weaver AM, Patton JG. Argonautes in Extracellular Vesicles: Artifact or Selected Cargo? Cancer Res 2019; 80:379-381. [PMID: 31784424 DOI: 10.1158/0008-5472.can-19-2782] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/18/2019] [Accepted: 11/19/2019] [Indexed: 01/19/2023]
Abstract
Argonaute-2 (Ago2) is a key component of the RNA-induced silencing complex that mediates downregulation of mRNA by miRNAs. Its presence in extracellular vesicles (EV) has been postulated to be important for the activity of EV-carried miRNA in modulating gene expression in recipient cells. However, whether it is in fact contained within EVs or is instead an extravesicular contaminant is controversial. In this opinion piece, we argue that the ability to detect Ago2 in EVs is a result of multiple factors, including cell source, cell signaling control of Ago2 trafficking to EVs, experimental conditions, and detection methods.
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Affiliation(s)
- Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee. .,Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James G Patton
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee.,Department of Ophthalmology and Visual Sciences, Vanderbilt University Medical Center, Nashville, Tennessee
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15
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Jeppesen DK, Fenix AM, Franklin JL, Higginbotham JN, Zhang Q, Zimmerman LJ, Liebler DC, Ping J, Liu Q, Evans R, Fissell WH, Patton JG, Rome LH, Burnette DT, Coffey RJ. Reassessment of Exosome Composition. Cell 2019; 177:428-445.e18. [PMID: 30951670 PMCID: PMC6664447 DOI: 10.1016/j.cell.2019.02.029] [Citation(s) in RCA: 1561] [Impact Index Per Article: 312.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 10/08/2018] [Accepted: 02/15/2019] [Indexed: 12/13/2022]
Abstract
The heterogeneity of small extracellular vesicles and presence of non-vesicular extracellular matter have led to debate about contents and functional properties of exosomes. Here, we employ high-resolution density gradient fractionation and direct immunoaffinity capture to precisely characterize the RNA, DNA, and protein constituents of exosomes and other non-vesicle material. Extracellular RNA, RNA-binding proteins, and other cellular proteins are differentially expressed in exosomes and non-vesicle compartments. Argonaute 1-4, glycolytic enzymes, and cytoskeletal proteins were not detected in exosomes. We identify annexin A1 as a specific marker for microvesicles that are shed directly from the plasma membrane. We further show that small extracellular vesicles are not vehicles of active DNA release. Instead, we propose a new model for active secretion of extracellular DNA through an autophagy- and multivesicular-endosome-dependent but exosome-independent mechanism. This study demonstrates the need for a reassessment of exosome composition and offers a framework for a clearer understanding of extracellular vesicle heterogeneity.
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Affiliation(s)
- Dennis K Jeppesen
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Aidan M Fenix
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Jeffrey L Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - James N Higginbotham
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qin Zhang
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Lisa J Zimmerman
- Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Daniel C Liebler
- Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jie Ping
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Rachel Evans
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - William H Fissell
- Division of Nephrology and Hypertension, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Leonard H Rome
- Department of Biological Chemistry, David Geffen School of Medicine and the California NanoSystems Institute, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Dylan T Burnette
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Veterans Affairs Medical Center, Nashville, TN 37232, USA.
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16
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Neitzel LR, Spencer ZT, Nayak A, Cselenyi CS, Benchabane H, Youngblood CQ, Zouaoui A, Ng V, Stephens L, Hann T, Patton JG, Robbins D, Ahmed Y, Lee E. Developmental regulation of Wnt signaling by Nagk and the UDP-GlcNAc salvage pathway. Mech Dev 2019; 156:20-31. [PMID: 30904594 DOI: 10.1016/j.mod.2019.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/15/2019] [Accepted: 03/18/2019] [Indexed: 11/19/2022]
Abstract
In a screen for human kinases that regulate Xenopus laevis embryogenesis, we identified Nagk and other components of the UDP-GlcNAc glycosylation salvage pathway as regulators of anteroposterior patterning and Wnt signaling. We find that the salvage pathway does not affect other major embryonic signaling pathways (Fgf, TGFβ, Notch, or Shh), thereby demonstrating specificity for Wnt signaling. We show that the role of the salvage pathway in Wnt signaling is evolutionarily conserved in zebrafish and Drosophila. Finally, we show that GlcNAc is essential for the growth of intestinal enteroids, which are highly dependent on Wnt signaling for growth and maintenance. We propose that the Wnt pathway is sensitive to alterations in the glycosylation state of a cell and acts as a nutritional sensor in order to couple growth/proliferation with its metabolic status. We also propose that the clinical manifestations observed in congenital disorders of glycosylation (CDG) in humans may be due, in part, to their effects on Wnt signaling during development.
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Affiliation(s)
- Leif R Neitzel
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Zachary T Spencer
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Anmada Nayak
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Christopher S Cselenyi
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Psychiatry, Columbia University Irving Medical Center, New York, NY 10032, USA
| | - Hassina Benchabane
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - CheyAnne Q Youngblood
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Department of Natural Science, Northeastern State University, Tahlequah, OK 74464, USA
| | - Alya Zouaoui
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Victoria Ng
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Leah Stephens
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Trevor Hann
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - David Robbins
- Sylvester Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Yashi Ahmed
- Department of Molecular and Systems Biology, Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth College, Hanover, NH 03755, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Program in Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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17
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Jimenez L, Yu H, McKenzie AJ, Franklin JL, Patton JG, Liu Q, Weaver AM. Quantitative Proteomic Analysis of Small and Large Extracellular Vesicles (EVs) Reveals Enrichment of Adhesion Proteins in Small EVs. J Proteome Res 2019; 18:947-959. [PMID: 30608700 DOI: 10.1021/acs.jproteome.8b00647] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Extracellular vesicles (EVs) are important mediators of cell-cell communication due to their cargo content of proteins, lipids, and RNAs. We previously reported that small EVs (SEVs) called exosomes promote directed and random cell motility, invasion, and serum-independent growth. In contrast, larger EVs (LEVs) were not active in those assays, but might have unique functional properties. In order to identify protein cargos that may contribute to different functions of SEVs and LEVs, we used isobaric tags for relative and absolute quantitation (iTRAQ)-liquid chromatography (LC) tandem mass spectrometry (MS) on EVs isolated from a colon cancer cell line. Bioinformatics analyses revealed that SEVs are enriched in proteins associated with cell-cell junctions, cell-matrix adhesion, exosome biogenesis machinery, and various signaling pathways. In contrast, LEVs are enriched in proteins associated with ribosome and RNA biogenesis, processing, and metabolism. Western blot analysis of EVs purified from two different cancer cell types confirmed the enrichment of cell-matrix and cell-cell adhesion proteins in SEVs. Consistent with those data, we found that cells exhibit enhanced adhesion to surfaces coated with SEVs compared to an equal protein concentration of LEVs. These data suggest that a major function of SEVs is to promote cellular adhesion.
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Affiliation(s)
- Lizandra Jimenez
- Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States
| | - Hui Yu
- Department of Internal Medicine , University of New Mexico , Albuquerque , New Mexico 87131 , United States
| | - Andrew J McKenzie
- Sarah Cannon Research Institute , Nashville , Tennessee 37203 , United States
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Department of Medicine , Vanderbilt University Medical Center , Nashville , Tennessee 37212 , United States
| | - James G Patton
- Department of Biological Sciences , Vanderbilt University School of Medicine , Nashville , Tennessee 37212 , United States
| | - Qi Liu
- Department of Biostatistics , Vanderbilt University Medical Center , Nashville , Tennessee 37232 , United States
| | - Alissa M Weaver
- Department of Cell and Developmental Biology , Vanderbilt University School of Medicine , Nashville , Tennessee 37232 , United States.,Department of Pathology, Microbiology and Immunology , Vanderbilt University Medical Center , Nashville , Tennessee 37212 , United States
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18
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Hinger SA, Cha DJ, Franklin JL, Higginbotham JN, Dou Y, Ping J, Shu L, Prasad N, Levy S, Zhang B, Liu Q, Weaver AM, Coffey RJ, Patton JG. Diverse Long RNAs Are Differentially Sorted into Extracellular Vesicles Secreted by Colorectal Cancer Cells. Cell Rep 2018; 25:715-725.e4. [PMID: 30332650 PMCID: PMC6248336 DOI: 10.1016/j.celrep.2018.09.054] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/04/2018] [Accepted: 09/14/2018] [Indexed: 01/29/2023] Open
Abstract
The regulation and functional roles of secreted coding and long noncoding RNAs (lncRNAs; >200 nt) are largely unknown. We previously showed that mutant KRAS colorectal cancer (CRC) cells release extracellular vesicles (EVs) containing distinct proteomes, microRNAs (miRNAs), and circular RNAs. Here, we comprehensively identify diverse classes of CRC extracellular long RNAs secreted in EVs and demonstrate differential export of specific RNAs. Distinct noncoding RNAs, including antisense transcripts and transcripts derived from pseudogenes, are enriched in EVs compared to cellular profiles. We detected strong enrichment of Rab13 in mutant KRAS EVs and demonstrate functional delivery of Rab13 mRNA to recipient cells. To assay functional transfer of lncRNAs, we implemented a CRISPR/Cas9-based RNA-tracking system to monitor delivery to recipient cells. We show that gRNAs containing export signals from secreted RNAs can be transferred from donor to recipient cells. Our data support the existence of cellular mechanisms to selectively export diverse classes of RNA.
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Affiliation(s)
- Scott A Hinger
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Diana J Cha
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Veterans Affairs Medical Center, Nashville, TN 37235, USA
| | - James N Higginbotham
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Veterans Affairs Medical Center, Nashville, TN 37235, USA
| | - Yongchao Dou
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Jie Ping
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Lihua Shu
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | | | | | - Bing Zhang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Qi Liu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37235, USA; Veterans Affairs Medical Center, Nashville, TN 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, TN 37235, USA.
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19
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Pinhal D, Bovolenta LA, Moxon S, Oliveira AC, Nachtigall PG, Acencio ML, Patton JG, Hilsdorf AWS, Lemke N, Martins C. Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development. Sci Rep 2018; 8:8248. [PMID: 29844338 PMCID: PMC5974277 DOI: 10.1038/s41598-018-26607-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 05/15/2018] [Indexed: 12/11/2022] Open
Abstract
MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic organisms, as the fast-evolving cichlid fishes. Using RNA-seq and comparative genomics we carried out an in-depth report of miRNAs in Nile tilapia (Oreochromis niloticus), an emergent model organism to investigate evo-devo mechanisms. Five hundred known miRNAs and almost one hundred putative novel vertebrate miRNAs have been identified, many of which seem to be teleost-specific, cichlid-specific or tilapia-specific. Abundant miRNA isoforms (isomiRs) were identified with modifications in both 5p and 3p miRNA transcripts. Changes in arm usage (arm switching) of nine miRNAs were detected in early development, adult stage and even between male and female samples. We found an increasing complexity of miRNA expression during ontogenetic development, revealing a remarkable synchronism between the rate of new miRNAs recruitment and morphological changes. Overall, our results enlarge vertebrate miRNA collection and reveal a notable differential ratio of miRNA arms and isoforms influenced by sex and developmental life stage, providing a better picture of the evolutionary and spatiotemporal dynamics of miRNAs.
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Affiliation(s)
- Danillo Pinhal
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil.
| | - Luiz A Bovolenta
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia (UEA), Norwich Research Park, Norwich, United Kingdom
| | - Arthur C Oliveira
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Pedro G Nachtigall
- Department of Genetics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Marcio L Acencio
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - James G Patton
- Stevenson Center, Vanderbilt University, Nashville, TN, USA
| | | | - Ney Lemke
- Department of Physics and Biophysics, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
| | - Cesar Martins
- Department of Morphology, Institute of Biosciences of Botucatu, Sao Paulo State University (UNESP), Botucatu, SP, Brazil
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20
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Abstract
Antisense morpholino oligonucleotides have been commonly used in zebrafish to inhibit mRNA function, either by inhibiting pre-mRNA splicing or by blocking translation initiation. Even with the advent of genome editing by CRISP/Cas9 technology, morpholinos provide a useful and rapid tool to knockdown gene expression. This is especially true when dealing with multiple alleles and large gene families where genetic redundancy can complicate knockout of all family members. miRNAs are small noncoding RNAs that are often encoded in gene families and can display extensive genetic redundancy. This redundancy, plus their small size which can limit targeting by CRISPR/Cas9, makes morpholino-based strategies particularly attractive for inhibition of miRNA function. We provide the rationale, background, and methods to inhibit miRNA function with antisense morpholinos during early development and in the adult retina in zebrafish.
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Affiliation(s)
- Alex Sutton Flynt
- Department of Biological Sciences, University of Southern Mississippi, Hattiesburg, MS, USA
| | - Mahesh Rao
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN, 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN, 37235, USA.
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21
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Lu Y, Zhao X, Liu Q, Li C, Graves-Deal R, Cao Z, Singh B, Franklin JL, Wang J, Hu H, Wei T, Yang M, Yeatman TJ, Lee E, Saito-Diaz K, Hinger S, Patton JG, Chung CH, Emmrich S, Klusmann JH, Fan D, Coffey RJ. lncRNA MIR100HG-derived miR-100 and miR-125b mediate cetuximab resistance via Wnt/β-catenin signaling. Nat Med 2017; 23:1331-1341. [PMID: 29035371 PMCID: PMC5961502 DOI: 10.1038/nm.4424] [Citation(s) in RCA: 297] [Impact Index Per Article: 42.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 09/08/2017] [Indexed: 12/11/2022]
Abstract
De novo and acquired resistance, which are largely attributed to genetic alterations, are barriers to effective anti-epidermal-growth-factor-receptor (EGFR) therapy. To generate cetuximab-resistant cells, we exposed cetuximab-sensitive colorectal cancer cells to cetuximab in three-dimensional culture. Using whole-exome sequencing and transcriptional profiling, we found that the long non-coding RNA MIR100HG and two embedded microRNAs, miR-100 and miR-125b, were overexpressed in the absence of known genetic events linked to cetuximab resistance. MIR100HG, miR-100 and miR-125b overexpression was also observed in cetuximab-resistant colorectal cancer and head and neck squamous cell cancer cell lines and in tumors from colorectal cancer patients that progressed on cetuximab. miR-100 and miR-125b coordinately repressed five Wnt/β-catenin negative regulators, resulting in increased Wnt signaling, and Wnt inhibition in cetuximab-resistant cells restored cetuximab responsiveness. Our results describe a double-negative feedback loop between MIR100HG and the transcription factor GATA6, whereby GATA6 represses MIR100HG, but this repression is relieved by miR-125b targeting of GATA6. These findings identify a clinically actionable, epigenetic cause of cetuximab resistance.
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Affiliation(s)
- Yuanyuan Lu
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Xiaodi Zhao
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Qi Liu
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Cunxi Li
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Ramona Graves-Deal
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Zheng Cao
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Bhuminder Singh
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jeffrey L Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jing Wang
- Department of Biomedical Informatics and Center for Quantitative Sciences, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Huaying Hu
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Tianying Wei
- Jiaen Genetics Laboratory, Beijing Jiaen Hospital, Beijing, China, and Molecular Pathology, Cancer Research Center, Medical College of Xiamen University, Xiamen, China
| | - Mingli Yang
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, USA
| | - Timothy J Yeatman
- Gibbs Cancer Center & Research Institute, Spartanburg, South Carolina, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Kenyi Saito-Diaz
- Department of Cell and Developmental Biology and Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Scott Hinger
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | | | - Stephan Emmrich
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | | | - Daiming Fan
- State Key Laboratory of Cancer Biology, National Clinical Research Center for Digestive Diseases and Xijing Hospital of Digestive Diseases, Fourth Military Medical University, Xi'an, China
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, USA.,Department of Veterans Affairs Medical Center, Nashville, Tennessee, USA
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22
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Abstract
Cranial neural crest cells are a multipotent cell population that generate all the elements of the pharyngeal cartilage with differentiation into chondrocytes tightly regulated by temporal intracellular and extracellular cues. Here, we demonstrate a novel role for miR-27, a highly enriched microRNA in the pharyngeal arches, as a positive regulator of chondrogenesis. Knock down of miR-27 led to nearly complete loss of pharyngeal cartilage by attenuating proliferation and blocking differentiation of pre-chondrogenic cells. Focal adhesion kinase (FAK) is a key regulator in integrin-mediated extracellular matrix (ECM) adhesion and has been proposed to function as a negative regulator of chondrogenesis. We show that FAK is downregulated in the pharyngeal arches during chondrogenesis and is a direct target of miR-27. Suppressing the accumulation of FAK in miR-27 morphants partially rescued the severe pharyngeal cartilage defects observed upon knock down of miR-27. These data support a crucial role for miR-27 in promoting chondrogenic differentiation in the pharyngeal arches through regulation of FAK.
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Affiliation(s)
- Nergis Kara
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Chunyao Wei
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - Alexander C Commanday
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, United States.
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23
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Rao MB, Didiano D, Patton JG. Neurotransmitter-Regulated Regeneration in the Zebrafish Retina. Stem Cell Reports 2017; 8:831-842. [PMID: 28285877 PMCID: PMC5390103 DOI: 10.1016/j.stemcr.2017.02.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 02/08/2017] [Accepted: 02/08/2017] [Indexed: 01/26/2023] Open
Abstract
Current efforts to repair damaged or diseased mammalian retinas are inefficient and largely incapable of fully restoring vision. Conversely, the zebrafish retina is capable of spontaneous regeneration upon damage using Müller glia (MG)-derived progenitors. Understanding how zebrafish MG initiate regeneration may help develop new treatments that prompt mammalian retinas to regenerate. We show that inhibition of γ-aminobutyric acid (GABA) signaling facilitates initiation of MG proliferation. GABA levels decrease following damage, and MG are positioned to detect decreased ambient levels and undergo dedifferentiation. Using pharmacological and genetic approaches, we demonstrate that GABAA receptor inhibition stimulates regeneration in undamaged retinas while activation inhibits regeneration in damaged retinas.
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Affiliation(s)
- Mahesh B Rao
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN 37235, USA
| | - Dominic Didiano
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, 2325 Stevenson Center, Box 1820 Station B, Nashville, TN 37235, USA.
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24
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Khuansuwan S, Clanton JA, Dean BJ, Patton JG, Gamse JT. A transcription factor network controls cell migration and fate decisions in the developing zebrafish pineal complex. Development 2016; 143:2641-50. [PMID: 27317804 PMCID: PMC4958332 DOI: 10.1242/dev.131680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 06/02/2016] [Indexed: 11/20/2022]
Abstract
The zebrafish pineal complex consists of four cell types (rod and cone photoreceptors, projection neurons and parapineal neurons) that are derived from a single pineal complex anlage. After specification, parapineal neurons migrate unilaterally away from the rest of the pineal complex whereas rods, cones and projection neurons are non-migratory. The transcription factor Tbx2b is important for both the correct number and migration of parapineal neurons. We find that two additional transcription factors, Flh and Nr2e3, negatively regulate parapineal formation. Flh induces non-migratory neuron fates and limits the extent of parapineal specification, in part by activation of Nr2e3 expression. Tbx2b is positively regulated by Flh, but opposes Flh action during specification of parapineal neurons. Loss of parapineal neuron specification in Tbx2b-deficient embryos can be partially rescued by loss of Nr2e3 or Flh function; however, parapineal migration absolutely requires Tbx2b activity. We conclude that cell specification and migration in the pineal complex are regulated by a network of at least three transcription factors. Summary: Cell fate specification and migration in the zebrafish pineal complex are regulated by a network of at least three transcription factors: Tbx2b, Flh and Nr2e3.
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Affiliation(s)
- Sataree Khuansuwan
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Joshua A Clanton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Benjamin J Dean
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
| | - Joshua T Gamse
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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25
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Broadus MR, Chen TW, Neitzel LR, Ng VH, Jodoin JN, Lee LA, Salic A, Robbins DJ, Capobianco AJ, Patton JG, Huppert SS, Lee E. Identification of a Paralog-Specific Notch1 Intracellular Domain Degron. Cell Rep 2016; 15:1920-9. [PMID: 27210761 DOI: 10.1016/j.celrep.2016.04.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 03/14/2016] [Accepted: 04/19/2016] [Indexed: 01/13/2023] Open
Abstract
Upon Notch pathway activation, the receptor is cleaved to release the Notch intracellular domain (NICD), which translocates to the nucleus to activate gene transcription. Using Xenopus egg extracts, we have identified a Notch1-specific destruction signal (N1-Box). We show that mutations in the N1-Box inhibit NICD1 degradation and that the N1-Box is transferable for the promotion of degradation of heterologous proteins in Xenopus egg extracts and in cultured human cells. Mutation of the N1-Box enhances Notch1 activity in cultured human cells and zebrafish embryos. Human cancer mutations within the N1-Box enhance Notch1 signaling in transgenic zebrafish, highlighting the physiological relevance of this destruction signal. We find that binding of the Notch nuclear factor, CSL, to the N1-Box blocks NICD1 turnover. Our studies reveal a mechanism by which degradation of NICD1 is regulated by the N1-Box to minimize stochastic flux and to establish a threshold for Notch1 pathway activation.
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Affiliation(s)
- Matthew R Broadus
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tony W Chen
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Leif R Neitzel
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Victoria H Ng
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jeanne N Jodoin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Laura A Lee
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Adrian Salic
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - David J Robbins
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - Anthony J Capobianco
- Molecular Oncology Program, Division of Surgical Oncology, Dewitt Daughtry Family Department of Surgery, University of Miami, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, Miller School of Medicine, University of Miami, Miami, FL 33136, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Stacey S Huppert
- Division of Gastroenterology, Hepatology, and Nutrition, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Ingram Cancer Center, Vanderbilt Medical Center, Nashville, TN 37232, USA.
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26
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McKenzie AJ, Hoshino D, Hong NH, Cha DJ, Franklin JL, Coffey RJ, Patton JG, Weaver AM. KRAS-MEK Signaling Controls Ago2 Sorting into Exosomes. Cell Rep 2016; 15:978-987. [PMID: 27117408 PMCID: PMC4857875 DOI: 10.1016/j.celrep.2016.03.085] [Citation(s) in RCA: 292] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Revised: 02/06/2016] [Accepted: 03/24/2016] [Indexed: 01/19/2023] Open
Abstract
Secretion of RNAs in extracellular vesicles is a newly recognized form of intercellular communication. A potential regulatory protein for microRNA (miRNA) secretion is the critical RNA-induced silencing complex (RISC) component Argonaute 2 (Ago2). Here, we use isogenic colon cancer cell lines to show that overactivity of KRAS due to mutation inhibits localization of Ago2 to multivesicular endosomes (MVEs) and decreases Ago2 secretion in exosomes. Mechanistically, inhibition of mitogen-activated protein kinase kinases (MEKs) I and II, but not Akt, reverses the effect of the activating KRAS mutation and leads to increased Ago2-MVE association and increased exosomal secretion of Ago2. Analysis of cells expressing mutant Ago2 constructs revealed that phosphorylation of Ago2 on serine 387 prevents Ago2-MVE interactions and reduces Ago2 secretion into exosomes. Furthermore, regulation of Ago2 exosomal sorting controls the levels of three candidate miRNAs in exosomes. These data identify a key regulatory signaling event that controls Ago2 secretion in exosomes.
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Affiliation(s)
- Andrew J McKenzie
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Daisuke Hoshino
- Division of Cancer Cell Research, Kanagawa Cancer Center, Yokohama 241-8515, Japan
| | - Nan Hyung Hong
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Diana J Cha
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Jeffrey L Franklin
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - Robert J Coffey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Veterans Affairs Medical Center, Nashville, TN 37232, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Alissa M Weaver
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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27
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Patton JG, Franklin JL, Weaver AM, Vickers K, Zhang B, Coffey RJ, Ansel KM, Blelloch R, Goga A, Huang B, L'Etoille N, Raffai RL, Lai CP, Krichevsky AM, Mateescu B, Greiner VJ, Hunter C, Voinnet O, McManus MT. Biogenesis, delivery, and function of extracellular RNA. J Extracell Vesicles 2015; 4:27494. [PMID: 26320939 PMCID: PMC4553266 DOI: 10.3402/jev.v4.27494] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Revised: 04/08/2015] [Accepted: 05/03/2015] [Indexed: 01/08/2023] Open
Abstract
The Extracellular RNA (exRNA) Communication Consortium was launched by the National Institutes of Health to focus on the extent to which RNA might function in a non-cell-autonomous manner. With the availability of increasingly sensitive tools, small amounts of RNA can be detected in serum, plasma, and other bodily fluids. The exact mechanism(s) by which RNA can be secreted from cells and the mechanisms for the delivery and uptake by recipient cells remain to be determined. This review will summarize current knowledge about the biogenesis and delivery of exRNA and outline projects seeking to understand the functional impact of exRNA.
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Affiliation(s)
- James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA;
| | - Jeffrey L Franklin
- VA Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - Alissa M Weaver
- VA Medical Center, Nashville, TN, USA.,Department of Cancer Biology, Vanderbilt University, Nashville, TN, USA
| | - Kasey Vickers
- Department of Cardiology, Vanderbilt University, Nashville, TN, USA
| | - Bing Zhang
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Robert J Coffey
- VA Medical Center, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, USA.,Department of Medicine, Vanderbilt University, Nashville, TN, USA
| | - K Mark Ansel
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA.,Sandler Asthma Basic Research Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Andrei Goga
- Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA, USA.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Noelle L'Etoille
- Department of Cell & Tissue Biology, University of California San Francisco, San Francisco, CA, USA
| | - Robert L Raffai
- Department of Surgery, University of California San Francisco, San Francisco, CA, USA.,VA Medical Center, San Francisco, CA, USA
| | - Charles P Lai
- Department of Neurology, Massachusetts General Hospital, Charlestown, MA, USA
| | - Anna M Krichevsky
- Department of Neurology, Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA, USA.,Harvard Medical School, Boston, MA, USA
| | - Bogdan Mateescu
- Swiss Federal Institute of Technology Zürich (ETH Zürich), Zürich, Switzerland
| | - Vanille J Greiner
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA.,Diabetes Center, University of California San Francisco, San Francisco, CA, USA
| | | | - Olivier Voinnet
- Swiss Federal Institute of Technology Zürich (ETH Zürich), Zürich, Switzerland
| | - Michael T McManus
- Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA.,Diabetes Center, University of California San Francisco, San Francisco, CA, USA
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28
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Cha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG. KRAS-dependent sorting of miRNA to exosomes. eLife 2015; 4:e07197. [PMID: 26132860 PMCID: PMC4510696 DOI: 10.7554/elife.07197] [Citation(s) in RCA: 263] [Impact Index Per Article: 29.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 06/29/2015] [Indexed: 12/13/2022] Open
Abstract
Mutant KRAS colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment. To test whether exosomal RNAs also contribute to changes in gene expression in recipient cells, and whether mutant KRAS might regulate the composition of secreted microRNAs (miRNAs), we compared small RNAs of cells and matched exosomes from isogenic CRC cell lines differing only in KRAS status. We show that exosomal profiles are distinct from cellular profiles, and mutant exosomes cluster separately from wild-type KRAS exosomes. miR-10b was selectively increased in wild-type exosomes, while miR-100 was increased in mutant exosomes. Neutral sphingomyelinase inhibition caused accumulation of miR-100 only in mutant cells, suggesting KRAS-dependent miRNA export. In Transwell co-culture experiments, mutant donor cells conferred miR-100-mediated target repression in wild-type-recipient cells. These findings suggest that extracellular miRNAs can function in target cells and uncover a potential new mode of action for mutant KRAS in CRC.
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Affiliation(s)
- Diana J Cha
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, United States
- Vanderbilt University, Nashville, United States
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States
- Affairs Medical Center, Nashville, United States
| | - Yongchao Dou
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States
| | - Qi Liu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States
| | - James N Higginbotham
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States
| | | | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, United States
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, United States
| | - Kasey Vickers
- Department of Cardiology, Vanderbilt University Medical Center, Nashville, United States
| | - Nirpesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Bing Zhang
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
- Department of Medicine, Vanderbilt University Medical Center, Nashville, United States
- Affairs Medical Center, Nashville, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, United States
- Vanderbilt University, Nashville, United States
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29
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Cha DJ, Franklin JL, Dou Y, Liu Q, Higginbotham JN, Demory Beckler M, Weaver AM, Vickers K, Prasad N, Levy S, Zhang B, Coffey RJ, Patton JG. KRAS-dependent sorting of miRNA to exosomes. eLife 2015. [PMID: 26132860 DOI: 10.7554/elife07197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutant KRAS colorectal cancer (CRC) cells release protein-laden exosomes that can alter the tumor microenvironment. To test whether exosomal RNAs also contribute to changes in gene expression in recipient cells, and whether mutant KRAS might regulate the composition of secreted microRNAs (miRNAs), we compared small RNAs of cells and matched exosomes from isogenic CRC cell lines differing only in KRAS status. We show that exosomal profiles are distinct from cellular profiles, and mutant exosomes cluster separately from wild-type KRAS exosomes. miR-10b was selectively increased in wild-type exosomes, while miR-100 was increased in mutant exosomes. Neutral sphingomyelinase inhibition caused accumulation of miR-100 only in mutant cells, suggesting KRAS-dependent miRNA export. In Transwell co-culture experiments, mutant donor cells conferred miR-100-mediated target repression in wild-type-recipient cells. These findings suggest that extracellular miRNAs can function in target cells and uncover a potential new mode of action for mutant KRAS in CRC.
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Affiliation(s)
- Diana J Cha
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, United States
| | - Jeffrey L Franklin
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
| | - Yongchao Dou
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States
| | - Qi Liu
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States
| | - James N Higginbotham
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
| | | | - Alissa M Weaver
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
| | - Kasey Vickers
- Department of Cardiology, Vanderbilt University Medical Center, Nashville, United States
| | - Nirpesh Prasad
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Shawn Levy
- HudsonAlpha Institute for Biotechnology, Huntsville, United States
| | - Bing Zhang
- Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, United States
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University Medical Center, Nashville, United States
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University Medical Center, Nashville, United States
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30
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Yin L, Maddison LA, Li M, Kara N, LaFave MC, Varshney GK, Burgess SM, Patton JG, Chen W. Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs. Genetics 2015; 200:431-41. [PMID: 25855067 PMCID: PMC4492370 DOI: 10.1534/genetics.115.176917] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 04/06/2015] [Indexed: 12/13/2022] Open
Abstract
Determining the mechanism of gene function is greatly enhanced using conditional mutagenesis. However, generating engineered conditional alleles is inefficient and has only been widely used in mice. Importantly, multiplex conditional mutagenesis requires extensive breeding. Here we demonstrate a system for one-generation multiplex conditional mutagenesis in zebrafish (Danio rerio) using transgenic expression of both cas9 and multiple single guide RNAs (sgRNAs). We describe five distinct zebrafish U6 promoters for sgRNA expression and demonstrate efficient multiplex biallelic inactivation of tyrosinase and insulin receptor a and b, resulting in defects in pigmentation and glucose homeostasis. Furthermore, we demonstrate temporal and tissue-specific mutagenesis using transgenic expression of Cas9. Heat-shock-inducible expression of cas9 allows temporal control of tyr mutagenesis. Liver-specific expression of cas9 disrupts insulin receptor a and b, causing fasting hypoglycemia and postprandial hyperglycemia. We also show that delivery of sgRNAs targeting ascl1a into the eye leads to impaired damage-induced photoreceptor regeneration. Our findings suggest that CRISPR/Cas9-based conditional mutagenesis in zebrafish is not only feasible but rapid and straightforward.
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Affiliation(s)
- Linlin Yin
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Lisette A Maddison
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Mingyu Li
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
| | - Nergis Kara
- Department of Biological Science, Vanderbilt University, Nashville, Tennessee 37240
| | - Matthew C LaFave
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Gaurav K Varshney
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Shawn M Burgess
- Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - James G Patton
- Department of Biological Science, Vanderbilt University, Nashville, Tennessee 37240
| | - Wenbiao Chen
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232
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Olena AF, Rao MB, Thatcher EJ, Wu SY, Patton JG. miR-216a regulates snx5, a novel notch signaling pathway component, during zebrafish retinal development. Dev Biol 2015; 400:72-81. [PMID: 25645681 DOI: 10.1016/j.ydbio.2015.01.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 01/14/2015] [Accepted: 01/17/2015] [Indexed: 01/13/2023]
Abstract
Precise regulation of Notch signaling is essential for normal vertebrate development. Mind bomb (Mib) is a ubiquitin ligase that is required for activation of Notch by Notch׳s ligand, Delta. Sorting Nexin 5 (SNX5) co-localizes with Mib and Delta complexes and has been shown to directly bind to Mib. We show that microRNA-216a (miR-216a) is expressed in the retina during early development and regulates snx5 to precisely regulate Notch signaling. miR-216a and snx5 have complementary expression patterns. Knocking down miR-216a and/or overexpression of snx5 resulted in increased Notch activation. Conversely, knocking down snx5 and/or miR-216a overexpression caused a decrease in Notch activation. We propose a model in which SNX5, precisely controlled by miR-216a, is a vital partner of Mib in promoting endocytosis of Delta and subsequent activation of Notch signaling.
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Affiliation(s)
- Abigail F Olena
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | - Mahesh B Rao
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | | | - Shu-Yu Wu
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN
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Rajaram K, Harding RL, Bailey T, Patton JG, Hyde DR. Dynamic miRNA expression patterns during retinal regeneration in zebrafish: reduced dicer or miRNA expression suppresses proliferation of Müller glia-derived neuronal progenitor cells. Dev Dyn 2014; 243:1591-605. [PMID: 25220904 DOI: 10.1002/dvdy.24188] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 08/06/2014] [Accepted: 08/26/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Adult zebrafish spontaneously regenerate their retinas after damage. Although a number of genes and signaling pathways involved in regeneration have been identified, the exact mechanisms regulating various aspects of regeneration are unclear. microRNAs (miRNAs) were examined for their potential roles in regulating zebrafish retinal regeneration. RESULTS To investigate the requirement of miRNAs during zebrafish retinal regeneration, we knocked down the expression of Dicer in retinas prior to light-induced damage. Reduced Dicer expression significantly decreased the number of proliferating Müller glia-derived neuronal progenitor cells during regeneration. To identify individual miRNAs with roles in neuronal progenitor cell proliferation, we collected retinas at different stages of light damage and performed small RNA high-throughput sequencing. We identified subsets of miRNAs that were differentially expressed during active regeneration but returned to basal levels once regeneration was completed. We then knocked down five different miRNAs that increased in expression and assessed the effects on retinal regeneration. Reduction of miR-142b and miR-146a expression significantly reduced INL proliferation at 51 h of light treatment, while knockdown of miR-7a, miR-27c, and miR-31 expression significantly reduced INL proliferation at 72 h of constant light. CONCLUSIONS miRNAs exhibit dynamic expression profiles during retinal regeneration and are necessary for neuronal progenitor cell proliferation.
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Affiliation(s)
- Kamya Rajaram
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee
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Rajaram K, Summerbell ER, Patton JG. Technical brief: Constant intense light exposure to lesion and initiate regeneration in normally pigmented zebrafish. Mol Vis 2014; 20:1075-84. [PMID: 25324680 PMCID: PMC4119235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/29/2014] [Indexed: 11/23/2022] Open
Abstract
Zebrafish are capable of robust and spontaneous regeneration of injured retina. Constant intense light exposure to adult albino zebrafish specifically causes apoptosis of rod and cone photoreceptor cells and is an excellent model to study the molecular mechanisms underlying photoreceptor regeneration. However, this paradigm has only been applied to lesion zebrafish of the nonpigmented albino genetic background, which precludes the use of numerous transgenic reporter lines that are widely used to study regeneration. Here, we explored the effectiveness of constant intense light exposure in causing photoreceptor apoptosis and stimulating regeneration in normally pigmented zebrafish retinas. We show that constant intense light exposure causes widespread photoreceptor damage in the dorsal-central retinas of pigmented zebrafish. Photoreceptor loss triggers dedifferentiation and proliferation of Müller glia as well as progenitor cell proliferation. We also demonstrate that the timeline of regeneration response is comparable between the albino and the pigmented retinas.
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Rajaram K, Harding RL, Hyde DR, Patton JG. miR-203 regulates progenitor cell proliferation during adult zebrafish retina regeneration. Dev Biol 2014; 392:393-403. [PMID: 24858486 DOI: 10.1016/j.ydbio.2014.05.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 05/06/2014] [Accepted: 05/07/2014] [Indexed: 02/04/2023]
Abstract
Damage of the zebrafish retina triggers a spontaneous regeneration response that is initiated by Müller Glia (MG) dedifferentiation and asymmetric cell division to produce multipotent progenitor cells. Subsequent expansion of the progenitor pool by proliferation is critical for retina regeneration. Pax6b expression in the progenitor cells is necessary for their proliferation, but exact regulation of its expression is unclear. Here, we show that miR-203 is downregulated during regeneration in proliferating progenitor cells. Elevated miR-203 levels inhibit progenitor cell expansion without affecting MG dedifferentiation or progenitor cell generation. Using GFP-reporter assays and gain and loss of function experiments in the retina, we show that miR-203 expression must be suppressed to allow pax6b expression and subsequent progenitor cell proliferation.
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Affiliation(s)
- Kamya Rajaram
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Rachel L Harding
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - David R Hyde
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - James G Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
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Noto JM, Piazuelo MB, Chaturvedi R, Bartel CA, Thatcher EJ, Delgado A, Romero-Gallo J, Wilson KT, Correa P, Patton JG, Peek RM. Strain-specific suppression of microRNA-320 by carcinogenic Helicobacter pylori promotes expression of the antiapoptotic protein Mcl-1. Am J Physiol Gastrointest Liver Physiol 2013; 305:G786-96. [PMID: 24136787 PMCID: PMC3882435 DOI: 10.1152/ajpgi.00279.2013] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Helicobacter pylori is the strongest risk factor for gastric cancer, and strains harboring the cag pathogenicity island, which translocates the oncoprotein CagA into host cells, further augment cancer risk. We previously reported that in vivo adaptation of a noncarcinogenic H. pylori strain (B128) generated a derivative strain (7.13) with the ability to induce adenocarcinoma, providing a unique opportunity to define mechanisms that mediate gastric carcinogenesis. MicroRNAs (miRNAs) are small noncoding RNAs that regulate expression of oncogenes or tumor suppressors and are frequently dysregulated in carcinogenesis. To identify miRNAs and their targets involved in H. pylori-mediated carcinogenesis, miRNA microarrays were performed on RNA isolated from gastric epithelial cells cocultured with H. pylori strains B128, 7.13, or a 7.13 cagA(-) isogenic mutant. Among 61 miRNAs differentially expressed in a cagA-dependent manner, the tumor suppressor miR-320 was significantly downregulated by strain 7.13. Since miR-320 negatively regulates the antiapoptotic protein Mcl-1, we demonstrated that H. pylori significantly induced Mcl-1 expression in a cagA-dependent manner and that suppression of Mcl-1 results in increased apoptosis. To extend these results, mice were challenged with H. pylori strain 7.13 or its cagA(-) mutant; consistent with cell culture data, H. pylori induced Mcl-1 expression in a cagA-dependent manner. In human subjects, cag(+) strains induced significantly higher levels of Mcl-1 than cag(-) strains, and Mcl-1 expression levels paralleled the severity of neoplastic lesions. Collectively, these results indicate that H. pylori suppresses miR-320, upregulates Mcl-1, and decreases apoptosis in a cagA-dependent manner, which likely confers an increased risk for gastric carcinogenesis.
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Affiliation(s)
- Jennifer M. Noto
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee;
| | - M. Blanca Piazuelo
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee;
| | - Rupesh Chaturvedi
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee;
| | - Courtney A. Bartel
- 2Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee;
| | | | - Alberto Delgado
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee;
| | - Judith Romero-Gallo
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee;
| | - Keith T. Wilson
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee; ,3Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee; ,4Department of Pathology, Microbiology, and Immunology, Vanderbilt University, Nashville, Tennessee; and ,5Veterans Affairs Tennessee Valley Healthcare System, Nashville, Tennessee
| | - Pelayo Correa
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee;
| | - James G. Patton
- 2Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee;
| | - Richard M. Peek
- 1Department of Medicine, Division of Gastroenterology, Vanderbilt University, Nashville, Tennessee; ,3Department of Cancer Biology, Vanderbilt University, Nashville, Tennessee;
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Wei C, Thatcher EJ, Olena AF, Cha DJ, Perdigoto AL, Marshall AF, Carter BD, Broadie K, Patton JG. miR-153 regulates SNAP-25, synaptic transmission, and neuronal development. PLoS One 2013; 8:e57080. [PMID: 23451149 PMCID: PMC3581580 DOI: 10.1371/journal.pone.0057080] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Accepted: 01/16/2013] [Indexed: 01/01/2023] Open
Abstract
SNAP-25 is a core component of the trimeric SNARE complex mediating vesicle exocytosis during membrane addition for neuronal growth, neuropeptide/growth factor secretion, and neurotransmitter release during synaptic transmission. Here, we report a novel microRNA mechanism of SNAP-25 regulation controlling motor neuron development, neurosecretion, synaptic activity, and movement in zebrafish. Loss of miR-153 causes overexpression of SNAP-25 and consequent hyperactive movement in early zebrafish embryos. Conversely, overexpression of miR-153 causes SNAP-25 down regulation resulting in near complete paralysis, mimicking the effects of treatment with Botulinum neurotoxin. miR-153-dependent changes in synaptic activity at the neuromuscular junction are consistent with the observed movement defects. Underlying the movement defects, perturbation of miR-153 function causes dramatic developmental changes in motor neuron patterning and branching. Together, our results indicate that precise control of SNAP-25 expression by miR-153 is critically important for proper neuronal patterning as well as neurotransmission.
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Affiliation(s)
- Chunyao Wei
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Elizabeth J. Thatcher
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Abigail F. Olena
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Diana J. Cha
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Ana L. Perdigoto
- Department of Biochemistry, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Andrew F. Marshall
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Bruce D. Carter
- Department of Biochemistry, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - Kendal Broadie
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
| | - James G. Patton
- Department of Biological Sciences, Vanderbilt University and Medical School, Nashville, Tennessee, United States of America
- * E-mail:
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Abstract
During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function for most of these noncoding RNAs remain largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small noncoding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized next-generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 198 known miRNAs within 122 different miRNA families and eight novel miRNAs were determined. Significant sequence variation was observed at the 5' and 3'ends of miRNAs, with most extra nucleotides added at the 3' end in a nontemplate directed manner. For the miR-430 family, the addition of adenosine and uracil residues is developmentally regulated and may play a role in miRNA stability during the maternal zygotic transition. Similar modification at the 3' ends of a large number of miRNAs suggests widespread regulation of stability during early development. Beside miRNAs, we also identified a large and unexpectedly diverse set of piRNAs expressed during early development.
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Affiliation(s)
- Chunyao Wei
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Leonidas Salichos
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Carli M. Wittgrove
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
| | - James G. Patton
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA
- Corresponding author.E-mail .
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Li N, Wei C, Olena AF, Patton JG. Regulation of endoderm formation and left-right asymmetry by miR-92 during early zebrafish development. Development 2011; 138:1817-26. [PMID: 21447552 DOI: 10.1242/dev.056697] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
microRNAs (miRNAs) are a family of 21-23 nucleotide endogenous non-coding RNAs that post-transcriptionally regulate gene expression in a sequence-specific manner. Typically, miRNAs downregulate target genes by recognizing and recruiting protein complexes to 3'UTRs, followed by translation repression or mRNA degradation. miR-92 is a well-studied oncogene in mammalian systems. Here, using zebrafish as a model system, we uncovered a novel tissue-inductive role for miR-92 during early vertebrate development. Overexpression resulted in reduced endoderm formation during gastrulation with consequent cardia and viscera bifida. By contrast, depletion of miR-92 increased endoderm formation, which led to abnormal Kupffer's vesicle development and left-right patterning defects. Using target prediction algorithms and reporter constructs, we show that gata5 is a target of miR-92. Alteration of gata5 levels reciprocally mirrored the effects of gain and loss of function of miR-92. Moreover, genetic epistasis experiments showed that miR-92-mediated defects could be substantially suppressed by modulating gata5 levels. We propose that miR-92 is a critical regulator of endoderm formation and left-right asymmetry during early zebrafish development and provide the first evidence for a regulatory function for gata5 in the formation of Kupffer's vesicle and left-right patterning.
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Affiliation(s)
- Nan Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Abstract
Previous work led to the hypothesis that SRrp86, a related member of the SR protein superfamily, can interact with and modulate the activity of other SR proteins. Here, we sought to test this hypothesis by examining the effect of changing SRrp86 concentrations on overall alternative splicing patterns. SpliceArrays were used to examine 9,854 splicing events in wild-type cells, cells overexpressing SRrp86, and cells treated with siRNAs to knockdown SRrp86. From among the 500 splicing events exhibiting altered splicing under these conditions, the splicing of c-Jun and IκBβ were validated as being regulated by SRrp86 resulting in altered regulation of their downstream targets. In both cases, functionally distinct isoforms were generated that demonstrate the role SRrp86 plays in controlling alternative splicing.
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Affiliation(s)
- Amanda S Solis
- Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
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40
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Abstract
A number of lower vertebrates including urodele amphibians and teleost fish are remarkably adept at repairing and regenerating damaged tissues and organs. Freshwater planarians are even more amazing, capable of regenerating entire body plans from small amputated fragments. In contrast, mammalian regenerative capacity is quite limited but of intense interest, especially related to human health and disease. For those organisms capable of robust regeneration, a common theme is the use of stem cells to replace complex tissues. Key questions remain as to the origin of these cells, whether there are pools of such cells that migrate to injured regions or whether they are generated on site. Beyond their origin, how are the genetic pathways that enable differentiation into multiple cell types and tissues regulated? microRNAs (miRNAs) are small noncoding RNAs that have recently been shown to play important roles in controlling stem cell self-renewal, proliferation and differentiation. Some of these are thought to be required to maintain "stemness". Here, we summarize recent work on the role of miRNAs in stem cells and their roles during regeneration.
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Abstract
The response to osmotic stress in developing zebrafish embryos requires proper apical patterning and trafficking of transmembrane ion transporters in ionocytes, specialized cells of the epidermis. The miR-8 family of miRNAs plays a key role in this process by precisely regulating the activity of NHERF1, a regulator of sodium hydrogen exchange that also serves as an adaptor protein linked to the actin cytoskeleton. We have discovered that NHERF1 activity is also coupled to Planar Cell Polarity (PCP) signaling in the zebrafish epidermis. Loss of NHERF1 in wild type fish disrupts actin organization but the observed defects can be largely restored when combined with mutants in the PCP pathway. We propose that proper apical patterning depends on input and coordination between PCP signaling and the response to stress.
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Affiliation(s)
- Alex S Flynt
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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Abstract
microRNAs (miRNAs) are small ( approximately 22 nt) noncoding RNAs that have been shown to regulate gene expression post-transcriptionally. They function by pairing with the 3' UTR of target mRNAs and repressing translation or by targeting the mRNA for degradation. miRNAs are involved in diverse aspects of development, maintenance, and disease, and are largely evolutionarily conserved in metazoans. Searching the genomes of organisms from viruses to worms to humans has revealed potentially thousands of miRNA genes. Understanding the patterns of genomic organization between species cannot only help to refine tools to identify new miRNAs, but also provide insight into miRNA biogenesis and function.
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Affiliation(s)
- Abigail F Olena
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, USA
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Hamid R, Phillips JA, Holladay C, Cogan JD, Austin ED, Backeljauw PF, Travers SH, Patton JG. A molecular basis for variation in clinical severity of isolated growth hormone deficiency type II. J Clin Endocrinol Metab 2009; 94:4728-34. [PMID: 19837935 PMCID: PMC2795644 DOI: 10.1210/jc.2009-0746] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
CONTEXT Dominant-negative GH1 mutations cause familial isolated growth hormone deficiency type II (IGHD II), which is characterized by GH deficiency, occasional multiple anterior pituitary hormone deficiencies, and anterior pituitary hypoplasia. The basis of the variable expression and progression of IGHD II among relatives who share the same GH1 mutation is poorly understood. OBJECTIVE We hypothesized that the cellular ratios of mutant/normal GH1 transcripts would correlate with the severity of the IGHD II phenotype. We determined the relative amounts of mutant and normal GH1 transcripts in cell lines and correlated transcript ratios with severity. DESIGN AND PATIENTS Members of the same IGHD II kindred were genotyped for the GH1 E3+1 G/A mutation by DNA sequencing. Ratios of their 17.5-kDa (mutant)/22-kDa (normal) GH1 transcripts were determined in cultured lymphocytes (CLs), and these ratios were correlated with height sd scores obtained before GH replacement therapy. RESULTS Ratios of 17.5-/22-kDa GH1 transcripts in CLs from family members with the same IGHD II mutation correlated with differences in their height SD scores. CONCLUSIONS Our findings suggest that expression levels of both the mutant and normal GH1 allele are important in the pathogenesis of IGHD II, that the ratio of mutant/normal transcripts may be a predictive marker of the penetrance and severity of IGHD II, and that CLs may be useful as surrogates to study GH1 transcript expression of subjects whose anterior pituitary cells are not available.
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Affiliation(s)
- Rizwan Hamid
- Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-2578, USA.
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Qiu R, Liu K, Liu Y, Mo W, Flynt AS, Patton JG, Kar A, Wu JY, He R. The role of miR-124a in early development of the Xenopus eye. Mech Dev 2009; 126:804-16. [PMID: 19703558 DOI: 10.1016/j.mod.2009.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2008] [Revised: 07/27/2009] [Accepted: 08/17/2009] [Indexed: 11/25/2022]
Abstract
It has been reported that miR-124a is abundant in the central nervous system including the eye, and is related to neurogenesis in several species. However, the role of miR-124a in the eye remains unclear. In this study, we show that the expression of miR-124a in Xenopus laevis begins along the neural fold, including the protruding eye anlagen, at a low level at around stage 18; its expression level gradually increases in the neural tube and the eye as embryos develop into later stages and then maintains at a high level in eye to adult stages. Microinjection of a miR-124a precursor at the 8-cell stage leads to malformation of the optic nerve and optic cup, indicating the importance of maintaining low levels of miR-124a during early embryonic development. In addition, miR-124a overexpression markedly down regulates the expression of its predicted targets Lhx2, Hairy2, Gli3, NeuroD1 and Otx2 in/around the eye anlagen, and the interaction of miR-124a with the 3' UTR of Lhx2 represses gene expression as shown by luciferase assays. Moreover, excess miR-124a inhibits cell proliferation in the eye of Xenopus embryos during retinogenesis. These results indicate that miR-124a acts as a post-transcriptional regulator in the genetic network controlling eye morphogenesis and neurogenesis. The mechanism of miR-124a's early interaction with the genetic network may also persist in its later role in the maturing and adult eye and brain.
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Affiliation(s)
- Rong Qiu
- The State Key Laboratory of Brain and Cognitive Science, Institute of Biophysics, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
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Abstract
MicroRNAs (miRNAs) are highly conserved small RNAs that act as translational regulators of gene expression, exerting their influence by selectively targeting mRNAs bearing complementary sequence elements. These RNAs function in diverse aspects of animal development and physiology. Because of an ability to act as rapid responders at the level of translation, miRNAs may also influence stress response. In this study, we show that the miR-8 family of miRNAs regulates osmoregulation in zebrafish embryos. Ionocytes, which are a specialized cell type scattered throughout the epidermis, are responsible for pH and ion homeostasis during early development before gill formation. The highly conserved miR-8 family is expressed in ionocytes and enables precise control of ion transport by modulating the expression of Nherf1, which is a regulator of apical trafficking of transmembrane ion transporters. Ultimately, disruption of miR-8 family member function leads to an inability to respond to osmotic stress and blocks the ability to properly traffic and/or cluster transmembrane glycoproteins at the apical surface of ionocytes.
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Affiliation(s)
- Alex S Flynt
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Solis AS, Peng R, Crawford JB, Phillips JA, Patton JG. Growth hormone deficiency and splicing fidelity: two serine/arginine-rich proteins, ASF/SF2 and SC35, act antagonistically. J Biol Chem 2008; 283:23619-26. [PMID: 18586677 DOI: 10.1074/jbc.m710175200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The majority of mutations that cause isolated growth hormone deficiency type II are the result of aberrant splicing of transcripts encoding human growth hormone. Such mutations increase skipping of exon 3 and encode a 17.5-kDa protein that acts as a dominant negative to block secretion of full-length protein produced from unaffected alleles. Previously, we identified a splicing regulatory element in exon 3 (exonic splicing enhancer 2 (ESE2)), but we had not determined the molecular mechanism by which this element prevents exon skipping. Here, we show that two members of the serine/arginine-rich (SR) protein superfamily (ASF/SF2 and SC35) act antagonistically to regulate exon 3 splicing. ASF/SF2 activates exon 3 inclusion, but SC35, acting through a region just downstream of ESE2, can block such activation. These findings explain the disease-causing mechanism of a patient mutation in ESE2 that creates a functional SC35-binding site that then acts synergistically with the downstream SC35 site to produce pathological levels of exon 3 skipping. Although the precedent for SR proteins acting as repressors is established, this is the first example of a patient mutation that creates a site through which an SR protein represses splicing.
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Affiliation(s)
- Amanda S Solis
- Department of Biological Sciences, Vanderbilt University, 2301 Vanderbilt Pl., Nashville, TN 37235, USA
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Li N, Flynt AS, Kim HR, Solnica-Krezel L, Patton JG. Dispatched Homolog 2 is targeted by miR-214 through a combination of three weak microRNA recognition sites. Nucleic Acids Res 2008; 36:4277-85. [PMID: 18583362 PMCID: PMC2490740 DOI: 10.1093/nar/gkn388] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression by inhibiting translation of target mRNAs through pairing with miRNA recognition elements (MREs), usually in 3′ UTRs. Because pairing is imperfect, identification of bona fide mRNA targets presents a challenge. Most target recognition algorithms strongly emphasize pairing between nucleotides 2–8 of the miRNA (the ‘seed’ sequence) and the mRNA but adjacent sequences and the local context of the 3′ UTR also affect targeting. Here, we show that dispatched 2 is a target of miR-214. In zebrafish, dispatched 2 is expressed in the telencephalon and ventral hindbrain and is essential for normal zebrafish development. Regulation of dispatched 2 by miR-214 is via pairing with three, noncanonical, weak MREs. By comparing the repression capacity of GFP reporters containing different dispatched 2 sequences, we found that a combination of weak sites, which lack canonical seed pairing, can effectively target an mRNA for silencing. This finding underscores the challenge that prediction algorithms face and emphasizes the need to experimentally validate predicted MREs.
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Affiliation(s)
- Nan Li
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
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Shariat N, Holladay CD, Cleary RK, Phillips JA, Patton JG. Isolated growth hormone deficiency type II caused by a point mutation that alters both splice site strength and splicing enhancer function. Clin Genet 2008; 74:539-45. [PMID: 18554279 DOI: 10.1111/j.1399-0004.2008.01042.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A heterozygous single base mutation in the human growth hormone (GH) gene (GH-1) was identified in a family presenting with isolated GH deficiency type II (IGHD II). Affected individuals have a guanine to adenine transition at the first nucleotide of exon 3 (E3+1 G-->A) that results in exon skipping and production of a dominant-negative 17.5-kDa isoform. We show that the mechanistic basis for exon skipping is due to the unique position of this mutation because it weakens the 3' splice site and simultaneously disrupts a splicing enhancer located within the first seven bases of exon 3. A G-->T mutation at this same position not only affects splicing but also results in a premature stop codon for those transcripts that include exon 3. Thus, mutations that alter the first nucleotide of exon 3 illustrate the various mechanisms by which changes in sequence can cause disease: splice site selection, splicing enhancer function, messenger RNA decay, missense mutations, and nonsense mutations. For IGHD II, only exon skipping leads to production of the dominant-negative isoform, with increasing skipping correlating with increasing disease severity.
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Affiliation(s)
- N Shariat
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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Abstract
Background microRNAs (miRNAs) are small (~22 nt) non-coding RNAs that regulate cell movement, specification, and development. Expression of miRNAs is highly regulated, both spatially and temporally. Based on direct cloning, sequence conservation, and predicted secondary structures, a large number of miRNAs have been identified in higher eukaryotic genomes but whether these RNAs are simply a subset of a much larger number of noncoding RNA families is unknown. This is especially true in zebrafish where genome sequencing and annotation is not yet complete. Results We analyzed the zebrafish genome to identify the number and location of proven and predicted miRNAs resulting in the identification of 35 new miRNAs. We then grouped all 415 zebrafish miRNAs into families based on seed sequence identity as a means to identify possible functional redundancy. Based on genomic location and expression analysis, we also identified those miRNAs that are likely to be encoded as part of polycistronic transcripts. Lastly, as a resource, we compiled existing zebrafish miRNA expression data and, where possible, listed all experimentally proven mRNA targets. Conclusion Current analysis indicates the zebrafish genome encodes 415 miRNAs which can be grouped into 44 families. The largest of these families (the miR-430 family) contains 72 members largely clustered in two main locations along chromosome 4. Thus far, most zebrafish miRNAs exhibit tissue specific patterns of expression.
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Shariat N, Ryther RCC, Phillips JA, Robinson ICAF, Patton JG. Rescue of pituitary function in a mouse model of isolated growth hormone deficiency type II by RNA interference. Endocrinology 2008; 149:580-6. [PMID: 18006625 PMCID: PMC2219309 DOI: 10.1210/en.2007-1360] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Splicing mutations in the human GH (hGH) gene (GH-1) that cause skipping of exon 3 result in a form of GH deficiency termed isolated GH deficiency type II (IGHD II). The GH-1 gene contains five exons; constitutive splicing produces the wild-type 22-kDa hormone, whereas skipping of exon 3 results in transcripts encoding a 17.5-kDa isoform that acts as a dominant-negative to block secretion of the wild-type hormone. Common characteristics of IGHD II include short stature due to impaired bone elongation, growth, and, in severe cases, anterior pituitary hypoplasia. Typically, IGHD II is treated by sc delivery of hGH, which can rescue stature but, unfortunately, does not inhibit pituitary hypoplasia. Direct destruction of transcripts encoding the dominant-negative 17.5-kDa isoform should both rescue stature and prevent hypoplasia. Here, we have used delivery of short hairpin RNAs to rescue a murine model of IGHD II by specifically targeting transcripts encoding the 17.5-kDa isoform using RNA interference. To our knowledge, this is the first example where a short hairpin RNA has been expressed to specifically degrade an incorrectly spliced transcript and rescue a dominant-negative disease phenotype in vivo.
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Affiliation(s)
- Nikki Shariat
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37235, USA
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