1
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Gu X, Nardone C, Kamitaki N, Mao A, Elledge SJ, Greenberg ME. The midnolin-proteasome pathway catches proteins for ubiquitination-independent degradation. Science 2023; 381:eadh5021. [PMID: 37616343 PMCID: PMC10617673 DOI: 10.1126/science.adh5021] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 07/11/2023] [Indexed: 08/26/2023]
Abstract
Cells use ubiquitin to mark proteins for proteasomal degradation. Although the proteasome also eliminates proteins that are not ubiquitinated, how this occurs mechanistically is unclear. Here, we found that midnolin promoted the destruction of many nuclear proteins, including transcription factors encoded by the immediate-early genes. Diverse stimuli induced midnolin, and its overexpression was sufficient to cause the degradation of its targets by a mechanism that did not require ubiquitination. Instead, midnolin associated with the proteasome via an α helix, used its Catch domain to bind a region within substrates that can form a β strand, and used a ubiquitin-like domain to promote substrate destruction. Thus, midnolin contains three regions that function in concert to target a large set of nuclear proteins to the proteasome for degradation.
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Affiliation(s)
- Xin Gu
- Department of Neurobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Christopher Nardone
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nolan Kamitaki
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA
| | - Aoyue Mao
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Stephen J. Elledge
- Division of Genetics, Department of Medicine, Howard Hughes Medical Institute, Brigham and Women’s Hospital, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
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2
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Tearle JL, Arjunan SN, Tay SS, Colakoglu F, Cremasco J, Golo M, Biro M. Targeted Single-cell Isolation of Spontaneously Escaping Live Melanoma Cells for Comparative Transcriptomics. CANCER RESEARCH COMMUNICATIONS 2023; 3:1524-1537. [PMID: 37575281 PMCID: PMC10416804 DOI: 10.1158/2767-9764.crc-22-0305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 05/30/2023] [Accepted: 07/12/2023] [Indexed: 08/15/2023]
Abstract
Solid cancer cells escape the primary tumor mass by transitioning from an epithelial-like state to an invasive migratory state. As they escape, metastatic cancer cells employ interchangeable modes of invasion, transitioning between fibroblast-like mesenchymal movement to amoeboid migration, where cells display a rounded morphology and navigate the extracellular matrix in a protease-independent manner. However, the gene transcripts that orchestrate the switch between epithelial, mesenchymal, and amoeboid states remain incompletely mapped, mainly due to a lack of methodologies that allow the direct comparison of the transcriptomes of spontaneously invasive cancer cells in distinct migratory states. Here, we report a novel single-cell isolation technique that provides detailed three-dimensional data on melanoma growth and invasion, and enables the isolation of live, spontaneously invasive cancer cells with distinct morphologies and invasion parameters. Via the expression of a photoconvertible fluorescent protein, compact epithelial-like cells at the periphery of a melanoma mass, elongated cells in the process of leaving the mass, and rounded amoeboid cells invading away from the mass were tagged, isolated, and subjected to single-cell RNA sequencing. A total of 462 differentially expressed genes were identified, from which two candidate proteins were selected for further pharmacologic perturbation, yielding striking effects on tumor escape and invasion, in line with the predictions from the transcriptomics data. This work describes a novel, adaptable, and readily implementable method for the analysis of the earliest phases of tumor escape and metastasis, and its application to the identification of genes underpinning the invasiveness of malignant melanoma. Significance This work describes a readily implementable method that allows for the isolation of individual live tumor cells of interest for downstream analyses, and provides the single-cell transcriptomes of melanoma cells at distinct invasive states, both of which open avenues for in-depth investigations into the transcriptional regulation of the earliest phases of metastasis.
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Affiliation(s)
- Jacqueline L.E. Tearle
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- Present address: Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Satya N.V. Arjunan
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- Present address: Victor Chang Cardiac Research Institute, Darlinghurst, New South Wales, Australia
| | - Szun S. Tay
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Feyza Colakoglu
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - James Cremasco
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
- Present address: Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia
| | - Matteo Golo
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
| | - Maté Biro
- EMBL Australia, Single Molecule Science node, School of Biomedical Sciences, University of New South Wales, Sydney, Australia
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3
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Barman B, Kushwaha A, Thakur MK. Muscarinic Acetylcholine Receptors-Mediated Activation of PKC Restores the Hippocampal Immediate Early Gene Expression and CREB Phosphorylation in Scopolamine-Induced Amnesic Mice. Mol Neurobiol 2022; 59:5722-5733. [DOI: 10.1007/s12035-022-02940-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 06/23/2022] [Indexed: 10/17/2022]
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4
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Zhao M, Wang Y, Tan F, Liu L, Hou X, Fan C, Tang L, Mo Y, Wang Y, Yan Q, Gong Z, Li Z, Liao Q, Guo C, Huang H, Zeng X, Li G, Zeng Z, Xiong W, Wang F. Circular RNA circCCNB1 inhibits the migration and invasion of nasopharyngeal carcinoma through binding and stabilizing TJP1 mRNA. SCIENCE CHINA. LIFE SCIENCES 2022; 65:2233-2247. [PMID: 35471687 DOI: 10.1007/s11427-021-2089-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 03/12/2022] [Indexed: 10/18/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant tumor that usually occurs in people from Southeast Asia and Southern China. NPC is prone to migration and invasion, leading to poor prognosis. A large number of circular RNAs (circRNAs) exacerbate the process of metastasis in NPC; however, their underlying mechanisms remain unclear. We found that the circular RNA circCCNB1, encoded by the oncogene CCNB1, was downregulated in NPC biopsies and cell lines. In vitro assays show that circCCNB1 inhibits NPC cell migration and invasion. Moreover, circCCNB1 induces a protein, nuclear factor 90 (NF90), to bind and prolong the half-life of tight junction protein 1 (TJP1) mRNA. Upregulation of TJP1 enhances tight junctions between cancer cells and inhibits NPC cell migration and invasion. This study reveals a novel biological function of circCCNB1 in the migration and invasion of NPC by enhancing the tight junctions of cancer cells by binding to NF90 proteins and TJP1 mRNA, and may provide a potential therapeutic target for NPC.
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Affiliation(s)
- Mengyao Zhao
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Yian Wang
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Fenghua Tan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Lingyun Liu
- Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang, 421009, China
| | - Xiangchan Hou
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Chunmei Fan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Le Tang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Yongzhen Mo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Yumin Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Qijia Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, the Second Xiangya Hospital, Central South University, Changsha, 410011, China
| | - Zheng Li
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Qianjin Liao
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China
| | - Can Guo
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - He Huang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Xi Zeng
- Cancer Research Institute, Hengyang Medical College, University of South China, Hengyang, 421009, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China.,Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, the Third Xiangya Hospital, Central South University, Changsha, 410013, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China.,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410078, China. .,Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China.
| | - Fuyan Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Central South University, Changsha, 410083, China.
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5
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Lodde V, Floris M, Munk R, Martindale JL, Piredda D, Napodano CMP, Cucca F, Uzzau S, Abdelmohsen K, Gorospe M, Noh JH, Idda ML. Systematic identification of NF90 target RNAs by iCLIP analysis. Sci Rep 2022; 12:364. [PMID: 35013429 PMCID: PMC8748789 DOI: 10.1038/s41598-021-04101-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/01/2021] [Indexed: 12/26/2022] Open
Abstract
RNA-binding proteins (RBPs) interact with and determine the fate of many cellular RNAs directing numerous essential roles in cellular physiology. Nuclear Factor 90 (NF90) is an RBP encoded by the interleukin enhancer-binding factor 3 (ILF3) gene that has been found to influence RNA metabolism at several levels, including pre-RNA splicing, mRNA turnover, and translation. To systematically identify the RNAs that interact with NF90, we carried out iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) analysis in the human embryonic fibroblast cell line HEK-293. Interestingly, many of the identified RNAs encoded proteins involved in the response to viral infection and RNA metabolism. We validated a subset of targets and investigated the impact of NF90 on their expression levels. Two of the top targets, IRF3 and IRF9 mRNAs, encode the proteins IRF3 and IRF9, crucial regulators of the interferon pathway involved in the SARS-CoV-2 immune response. Our results support a role for NF90 in modulating key genes implicated in the immune response and offer insight into the immunological response to the SARS-CoV-2 infection.
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Affiliation(s)
- Valeria Lodde
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Matteo Floris
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute for Genetic and Biomedical Research (IRGB-CNR), Sassari, Italy
| | - Rachel Munk
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Jennifer L Martindale
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Davide Piredda
- Intensive Care Unit, Emergency Department, AOU Sassari, Sassari, Italy
| | | | - Francesco Cucca
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Institute for Genetic and Biomedical Research (IRGB-CNR), Sassari, Italy
| | - Sergio Uzzau
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
- Microbiology and Virology Unit, Diagnostic Department, AOU Sassari, Sassari, Italy
| | - Kotb Abdelmohsen
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Ji Heon Noh
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
- Department of Biochemistry, Chungnam National University, Daejeon, Korea
| | - M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA.
- Institute for Genetic and Biomedical Research (IRGB-CNR), Sassari, Italy.
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6
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Function of Circular RNAs in Fish and Their Potential Application as Biomarkers. Int J Mol Sci 2021; 22:ijms22137119. [PMID: 34281172 PMCID: PMC8268770 DOI: 10.3390/ijms22137119] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/16/2022] Open
Abstract
Circular RNAs (circRNAs) are an emerging class of regulatory RNAs with a covalently closed-loop structure formed during pre-mRNA splicing. Recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of novel approaches to their identification and functional characterization. CircRNAs are stable, developmentally regulated, and show tissue- and cell-type-specific expression across different taxonomic groups. They play a crucial role in regulating various biological processes at post-transcriptional and translational levels. However, the involvement of circRNAs in fish immunity has only recently been recognized. There is also broad evidence in mammals that the timely expression of circRNAs in muscle plays an essential role in growth regulation but our understanding of their expression and function in teleosts is still very limited. Here, we discuss the available knowledge about circRNAs and their role in growth and immunity in vertebrates from a comparative perspective, with emphasis on cultured teleost fish. We expect that the interest in teleost circRNAs will increase substantially soon, and we propose that they may be used as biomarkers for selective breeding of farmed fish, thus contributing to the sustainability of the aquaculture sector.
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7
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Magri K, Eftedal I, Petroni Magri V, Matity L, Azzopardi CP, Muscat S, Pace NP. Acute Effects on the Human Peripheral Blood Transcriptome of Decompression Sickness Secondary to Scuba Diving. Front Physiol 2021; 12:660402. [PMID: 34177613 PMCID: PMC8222921 DOI: 10.3389/fphys.2021.660402] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/12/2021] [Indexed: 01/22/2023] Open
Abstract
Decompression sickness (DCS) develops due to inert gas bubble formation in bodily tissues and in the circulation, leading to a wide range of potentially serious clinical manifestations. Its pathophysiology remains incompletely understood. In this study, we aim to explore changes in the human leukocyte transcriptome in divers with DCS compared to closely matched unaffected controls after uneventful diving. Cases (n = 7) were divers developing the typical cutis marmorata rash after diving with a confirmed clinical diagnosis of DCS. Controls (n = 6) were healthy divers who surfaced from a ≥25 msw dive without decompression violation or evidence of DCS. Blood was sampled at two separate time points-within 8 h of dive completion and 40-44 h later. Transcriptome analysis by RNA-Sequencing followed by bioinformatic analysis was carried out to identify differentially expressed genes and relate their function to biological pathways. In DCS cases, we identified enrichment of transcripts involved in acute inflammation, activation of innate immunity and free radical scavenging pathways, with specific upregulation of transcripts related to neutrophil function and degranulation. DCS-induced transcriptomic events were reversed at the second time point following exposure to hyperbaric oxygen. The observed changes are consistent with findings from animal models of DCS and highlight a continuum between the responses elicited by uneventful diving and diving complicated by DCS. This study sheds light on the inflammatory pathophysiology of DCS and the associated immune response. Such data may potentially be valuable in the search for novel treatments targeting this disease.
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Affiliation(s)
- Kurt Magri
- Hyperbaric Unit, Department of Medicine, Mater Dei Hospital, Msida, Malta
| | - Ingrid Eftedal
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, Trondheim, Norway
- Faculty of Nursing and Health Sciences, Nord University, Bodø, Norway
| | - Vanessa Petroni Magri
- Department of Clinical Pharmacology and Therapeutics, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
| | - Lyubisa Matity
- Hyperbaric Unit, Department of Medicine, Mater Dei Hospital, Msida, Malta
| | | | - Stephen Muscat
- Hyperbaric Unit, Department of Medicine, Mater Dei Hospital, Msida, Malta
| | - Nikolai Paul Pace
- Centre for Molecular Medicine and Biobanking, Faculty of Medicine and Surgery, University of Malta, Msida, Malta
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8
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Nazitto R, Amon LM, Mast FD, Aitchison JD, Aderem A, Johnson JS, Diercks AH. ILF3 Is a Negative Transcriptional Regulator of Innate Immune Responses and Myeloid Dendritic Cell Maturation. THE JOURNAL OF IMMUNOLOGY 2021; 206:2949-2965. [PMID: 34031149 DOI: 10.4049/jimmunol.2001235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/31/2021] [Indexed: 12/31/2022]
Abstract
APCs such as myeloid dendritic cells (DCs) are key sentinels of the innate immune system. In response to pathogen recognition and innate immune stimulation, DCs transition from an immature to a mature state that is characterized by widespread changes in host gene expression, which include the upregulation of cytokines, chemokines, and costimulatory factors to protect against infection. Several transcription factors are known to drive these gene expression changes, but the mechanisms that negatively regulate DC maturation are less well understood. In this study, we identify the transcription factor IL enhancer binding factor 3 (ILF3) as a negative regulator of innate immune responses and DC maturation. Depletion of ILF3 in primary human monocyte-derived DCs led to increased expression of maturation markers and potentiated innate responses during stimulation with viral mimetics or classic innate agonists. Conversely, overexpression of short or long ILF3 isoforms (NF90 and NF110) suppressed DC maturation and innate immune responses. Through mutagenesis experiments, we found that a nuclear localization sequence in ILF3, and not its dual dsRNA-binding domains, was required for this function. Mutation of the domain associated with zinc finger motif of ILF3's NF110 isoform blocked its ability to suppress DC maturation. Moreover, RNA-sequencing analysis indicated that ILF3 regulates genes associated with cholesterol homeostasis in addition to genes associated with DC maturation. Together, our data establish ILF3 as a transcriptional regulator that restrains DC maturation and limits innate immune responses through a mechanism that may intersect with lipid metabolism.
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Affiliation(s)
- Rodolfo Nazitto
- Department of Immunology, University of Washington School of Medicine, Seattle, WA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Lynn M Amon
- Center for Infectious Disease Research, Seattle, WA; and
| | - Fred D Mast
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - John D Aitchison
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Alan Aderem
- Department of Immunology, University of Washington School of Medicine, Seattle, WA.,Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA
| | - Jarrod S Johnson
- Center for Infectious Disease Research, Seattle, WA; and.,Department of Biochemistry, University of Utah, Salt Lake City, UT
| | - Alan H Diercks
- Department of Immunology, University of Washington School of Medicine, Seattle, WA;
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9
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Tsai H, Zeng X, Liu L, Xin S, Wu Y, Xu Z, Zhang H, Liu G, Bi Z, Su D, Yang M, Tao Y, Wang C, Zhao J, Eriksson JE, Deng W, Cheng F, Chen H. NF45/NF90-mediated rDNA transcription provides a novel target for immunosuppressant development. EMBO Mol Med 2021; 13:e12834. [PMID: 33555115 PMCID: PMC7933818 DOI: 10.15252/emmm.202012834] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 12/26/2020] [Accepted: 01/04/2021] [Indexed: 12/31/2022] Open
Abstract
Herein, we demonstrate that NFAT, a key regulator of the immune response, translocates from cytoplasm to nucleolus and interacts with NF45/NF90 complex to collaboratively promote rDNA transcription via triggering the directly binding of NF45/NF90 to the ARRE2-like sequences in rDNA promoter upon T-cell activation in vitro. The elevated pre-rRNA level of T cells is also observed in both mouse heart or skin transplantation models and in kidney transplanted patients. Importantly, T-cell activation can be significantly suppressed by inhibiting NF45/NF90-dependent rDNA transcription. Amazingly, CX5461, a rDNA transcription-specific inhibitor, outperformed FK506, the most commonly used immunosuppressant, both in terms of potency and off-target activity (i.e., toxicity), as demonstrated by a series of skin and heart allograft models. Collectively, this reveals NF45/NF90-mediated rDNA transcription as a novel signaling pathway essential for T-cell activation and as a new target for the development of safe and effective immunosuppressants.
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Affiliation(s)
- Hsiang‐i Tsai
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Xiaobin Zeng
- Center Lab of Longhua Branch and Department of Infectious DiseaseShenzhen People's Hospital2 Clinical Medical College of Jinan UniversityShenzhenChina
- Guangdong Provincial Key Laboratory of Regional Immunity and DiseasesMedicine School of Shenzhen UniversityShenzhenChina
| | - Longshan Liu
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Shengchang Xin
- State Key Laboratory of Coordination ChemistryInstitute of Chemistry and Biomedical SciencesSchool of Life SciencesNanjing UniversityNanjingChina
| | - Yingyi Wu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Zhanxue Xu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Huanxi Zhang
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Gan Liu
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Zirong Bi
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Dandan Su
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Min Yang
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Yijing Tao
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Changxi Wang
- Organ Transplant CentermThe First Affiliated HospitalSun Yat‐sen UniversityGuangzhouChina
| | - Jing Zhao
- State Key Laboratory of Coordination ChemistryInstitute of Chemistry and Biomedical SciencesSchool of Life SciencesNanjing UniversityNanjingChina
| | - John E Eriksson
- Cell BiologyBiosciencesFaculty of Science and EngineeringÅbo Akademi UniversityTurkuFinland
- Turku Centre for BiotechnologyUniversity of Turku and Åbo Akademi UniversityTurkuFinland
| | - Wenbin Deng
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Fang Cheng
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
| | - Hongbo Chen
- School of Pharmaceutical Sciences (Shenzhen)Sun Yat‐Sen UniversityShenzhenChina
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10
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Sun Q, Hao Q, Lin YC, Song YJ, Bangru S, Arif W, Tripathi V, Zhang Y, Cho JH, Freier SM, Jenkins LM, Ma J, Yoon JH, Kalsotra A, Lal A, Prasanth SG, Prasanth KV. Antagonism between splicing and microprocessor complex dictates the serum-induced processing of lnc- MIRHG for efficient cell cycle reentry. RNA (NEW YORK, N.Y.) 2020; 26:1603-1620. [PMID: 32675111 PMCID: PMC7566567 DOI: 10.1261/rna.075309.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 07/08/2020] [Indexed: 05/03/2023]
Abstract
Cellular quiescence and cell cycle reentry regulate vital biological processes such as cellular development and tissue homeostasis and are controlled by precise regulation of gene expression. The roles of long noncoding RNAs (lncRNAs) during these processes remain to be elucidated. By performing genome-wide transcriptome analyses, we identify differential expression of several hundreds of lncRNAs, including a significant number of the less-characterized class of microRNA-host-gene (MIRHG) lncRNAs or lnc-MIRHGs, during cellular quiescence and cell cycle reentry in human diploid fibroblasts. We observe that MIR222HG lncRNA displays serum-stimulated RNA processing due to enhanced splicing of the host nascent pri-MIR222HG transcript. The pre-mRNA splicing factor SRSF1 negatively regulates the microprocessor-catalyzed cleavage of pri-miR-222, thereby increasing the cellular pool of the mature MIR222HG Association of SRSF1 to pri-MIR222HG, including to a mini-exon, which partially overlaps with the primary miR-222 precursor, promotes serum-stimulated splicing over microRNA processing of MIR222HG Further, we observe that the increased levels of spliced MIR222HG in serum-stimulated cells promote the cell cycle reentry post quiescence in a microRNA-independent manner. MIR222HG interacts with DNM3OS, another lncRNA whose expression is elevated upon serum-stimulation, and promotes cell cycle reentry. The double-stranded RNA binding protein ILF3/2 complex facilitates MIR222HG:DNM3OS RNP complex assembly, thereby promoting DNM3OS RNA stability. Our study identifies a novel mechanism whereby competition between the splicing and microprocessor machinery modulates the serum-induced RNA processing of MIR222HG, which dictates cell cycle reentry.
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Affiliation(s)
- Qinyu Sun
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Qinyu Hao
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yo-Chuen Lin
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - You Jin Song
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Waqar Arif
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Vidisha Tripathi
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Zhang
- School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Jung-Hyun Cho
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Susan M Freier
- Ionis Pharmaceuticals Inc., Carlsbad, California 92008, USA
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland 20892, USA
| | - Jian Ma
- School of Computer Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, USA
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, South Carolina 29425, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland 20892, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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