1
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Ohashi S, Nakamura M, Acharyya S, Inagaki M, Abe N, Kimura Y, Hashiya F, Abe H. Development and Comparison of 4-Thiouridine to Cytidine Base Conversion Reaction. ACS OMEGA 2024; 9:9300-9308. [PMID: 38434802 PMCID: PMC10905967 DOI: 10.1021/acsomega.3c08516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/14/2024] [Accepted: 02/01/2024] [Indexed: 03/05/2024]
Abstract
To study transcriptome dynamics without harming cells, it is essential to convert chemical bases. 4-Thiouridine (4sU) is a biocompatible uridine analogue that can be converted into a cytidine analogue. Although several reactions can convert 4sU into a cytidine analogue, few studies have compared the features of these reactions. In this study, we performed three reported base conversion reactions, including osmium tetroxide, iodoacetamide, and sodium periodate treatment, as well as a new reaction using 2,4-dinitrofluorobenzene. We compared the reaction time, conversion efficacy, and effects on reverse transcription. These reactions successfully converted 4sU into a cytidine analogue quantitatively using trinucleotides. However, the conversion efficacy and effect on reverse transcription vary depending on the reaction with the RNA transcript. OsO4 treatment followed by NH4Cl treatment showed the best base-conversion efficiency. Nevertheless, each reaction has its own advantages and disadvantages as a tool for studying the transcriptome. Therefore, it is crucial to select the appropriate reaction for the target of interest.
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Affiliation(s)
- Sana Ohashi
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Mayu Nakamura
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Susit Acharyya
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Masahito Inagaki
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Naoko Abe
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yasuaki Kimura
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Fumitaka Hashiya
- Research
Center for Material Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Hiroshi Abe
- Graduate
School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- Research
Center for Material Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- CREST, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
- Institute
for Glyco-core Research (iGCORE), Nagoya
University, Nagoya, Aichi 464-8602, Japan
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2
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Richard AC, Ma CY, Marioni JC, Griffiths GM. Cytotoxic T lymphocytes require transcription for infiltration but not target cell lysis. EMBO Rep 2023; 24:e57653. [PMID: 37860838 PMCID: PMC10626425 DOI: 10.15252/embr.202357653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/21/2023] Open
Abstract
Effector cytotoxic T lymphocytes (CTLs) are critical for ridding the body of infected or cancerous cells. CTL T cell receptor (TCR) ligation not only drives the delivery and release of cytolytic granules but also initiates a new wave of transcription. In order to address whether TCR-induced transcriptomic changes impact the ability of CTLs to kill, we asked which genes are expressed immediately after CTLs encounter targets and how CTL responses change when inhibiting transcription. Our data demonstrate that while expression of cytokines/chemokines and transcriptional machinery depend on transcription, cytotoxic protein expression and cytolytic activity are relatively robust to transcription blockade, with CTLs lysing nearby target cells for several hours after actinomycin D treatment. Monitoring CTL movement among target cells after inhibiting transcription demonstrates an infiltration defect that is not rectified by provision of exogenous cytokine/chemokine gradients, indicating a cell-intrinsic transcriptional requirement for infiltration. Together, our results reveal differential molecular control of CTL functions, separating recruitment and infiltration from cytolysis.
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Affiliation(s)
- Arianne C Richard
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- Present address:
Immunology ProgrammeThe Babraham InstituteCambridgeUK
| | - Claire Y Ma
- Cambridge Institute for Medical ResearchUniversity of CambridgeCambridgeUK
| | - John C Marioni
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUK
- European Molecular Biology LaboratoryEuropean Bioinformatics Institute (EMBL‐EBI)HinxtonUK
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3
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Deng S, Qian L, Liu L, Liu H, Xu Z, Liu Y, Wang Y, Chen L, Zhou Y. Circular RNA ARHGAP5 inhibits cisplatin resistance in cervical squamous cell carcinoma by interacting with AUF1. Cancer Sci 2023; 114:1582-1595. [PMID: 36632741 PMCID: PMC10067438 DOI: 10.1111/cas.15723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 12/12/2022] [Accepted: 12/20/2022] [Indexed: 01/13/2023] Open
Abstract
Cervical squamous cell carcinoma (CSCC) is one of the leading causes of cancer death in women worldwide. Patients with advanced cervical carcinoma always have a poor prognosis once resistant to cisplatin due to the lack of effective treatment. It is urgent to investigate the molecular mechanisms of cisplatin resistance. Circular RNAs (circRNAs) are known to exert their regulatory functions in a series of malignancies. However, their effects on CSCC remain to be elucidated. Here, we found that cytoplasmic circARHGAP5, derived from second and third exons of the ARHGAP5 gene, was downregulated in cisplatin-resistant tissues compared with normal cervix tissues and untreated cervical cancer tissues. In addition, experiments from overexpression/knockdown cell lines revealed that circARHGAP5 could inhibit cisplatin-mediated cell apoptosis in CSCC cells both in vitro and in vivo. Mechanistically, circARHGAP5 interacted with AU-rich element RNA-binding protein (AUF1) directly. Overexpression of AUF1 could also inhibit cell apoptosis mediated by cisplatin. Furthermore, we detected the potential targets of AUF1 related to the apoptotic pathway and found that bcl-2-like protein 11 (BIM) was not only negatively regulated by AUF1 but positively regulated by circARHGAP5, which indicated that BIM mRNA might be degraded by AUF1 and thereby inhibited tumor cell apoptosis. Collectively, our data indicated that circARHGAP5 directly bound to AUF1 and prevented AUF1 from interacting with BIM mRNA, thereby playing a pivotal role in cisplatin resistance in CSCC. Our study provides insights into overcoming cancer resistance to cisplatin treatment.
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Affiliation(s)
- Sisi Deng
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Lili Qian
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Luwen Liu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Hanyuan Liu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Zhihao Xu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yujie Liu
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Yingying Wang
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Liang Chen
- Department of Clinical LaboratoryThe First Affiliated Hospital of USTC, the CAS Key Laboratory of Innate Immunity and Chronic DiseaseSchool of Basic Medical SciencesDivision of Life Science and MedicineUniversity of Science and Technology of ChinaHefeiChina
| | - Ying Zhou
- Department of Obstetrics and GynecologyThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina
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4
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MicroRNAs in T Cell-Immunotherapy. Int J Mol Sci 2022; 24:ijms24010250. [PMID: 36613706 PMCID: PMC9820302 DOI: 10.3390/ijms24010250] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/06/2022] [Accepted: 12/15/2022] [Indexed: 12/28/2022] Open
Abstract
MicroRNAs (miRNAs) act as master regulators of gene expression in homeostasis and disease. Despite the rapidly growing body of evidence on the theranostic potential of restoring miRNA levels in pre-clinical models, the translation into clinics remains limited. Here, we review the current knowledge of miRNAs as T-cell targeting immunotherapeutic tools, and we offer an overview of the recent advances in miRNA delivery strategies, clinical trials and future perspectives in RNA interference technologies.
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5
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Matheson LS, Petkau G, Sáenz-Narciso B, D'Angeli V, McHugh J, Newman R, Munford H, West J, Chakraborty K, Roberts J, Łukasiak S, Díaz-Muñoz MD, Bell SE, Dimeloe S, Turner M. Multiomics analysis couples mRNA turnover and translational control of glutamine metabolism to the differentiation of the activated CD4 + T cell. Sci Rep 2022; 12:19657. [PMID: 36385275 PMCID: PMC9669047 DOI: 10.1038/s41598-022-24132-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/17/2022] Open
Abstract
The ZFP36 family of RNA-binding proteins acts post-transcriptionally to repress translation and promote RNA decay. Studies of genes and pathways regulated by the ZFP36 family in CD4+ T cells have focussed largely on cytokines, but their impact on metabolic reprogramming and differentiation is unclear. Using CD4+ T cells lacking Zfp36 and Zfp36l1, we combined the quantification of mRNA transcription, stability, abundance and translation with crosslinking immunoprecipitation and metabolic profiling to determine how they regulate T cell metabolism and differentiation. Our results suggest that ZFP36 and ZFP36L1 act directly to limit the expression of genes driving anabolic processes by two distinct routes: by targeting transcription factors and by targeting transcripts encoding rate-limiting enzymes. These enzymes span numerous metabolic pathways including glycolysis, one-carbon metabolism and glutaminolysis. Direct binding and repression of transcripts encoding glutamine transporter SLC38A2 correlated with increased cellular glutamine content in ZFP36/ZFP36L1-deficient T cells. Increased conversion of glutamine to α-ketoglutarate in these cells was consistent with direct binding of ZFP36/ZFP36L1 to Gls (encoding glutaminase) and Glud1 (encoding glutamate dehydrogenase). We propose that ZFP36 and ZFP36L1 as well as glutamine and α-ketoglutarate are limiting factors for the acquisition of the cytotoxic CD4+ T cell fate. Our data implicate ZFP36 and ZFP36L1 in limiting glutamine anaplerosis and differentiation of activated CD4+ T cells, likely mediated by direct binding to transcripts of critical genes that drive these processes.
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Affiliation(s)
- Louise S Matheson
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Georg Petkau
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Beatriz Sáenz-Narciso
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Vanessa D'Angeli
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: IONTAS, The Works, Unity Campus, Cambridge, CB22 3EF, UK
| | - Jessica McHugh
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Nature Reviews Rheumatology, The Campus, 4 Crinan Street, London, N1 9XW, UK
| | - Rebecca Newman
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Immunology Research Unit, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, Herts, UK
| | - Haydn Munford
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - James West
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, Jeffrey Cheah Biomedical Centre, University of Cambridge, Cambridge, CB2 0AW, UK
| | - Krishnendu Chakraborty
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Bioanalysis, Immunogenicity and Biomarkers (BIB), IVIVT, GSK, Stevenage, SG1 2NY, UK
| | - Jennie Roberts
- Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Sebastian Łukasiak
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Present Address: Discovery Biology, Discovery Science, R&D, AstraZeneca, Cambridge, UK
| | - Manuel D Díaz-Muñoz
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.,Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, BP3028, 31024, Toulouse, France
| | - Sarah E Bell
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Sarah Dimeloe
- Institute of Immunology and Immunotherapy, College of Medical and Dental Sciences, IBR, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Martin Turner
- Immunology Programme, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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6
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Nicolet BP, Wolkers MC. The relationship of mRNA with protein expression in CD8+ T cells associates with gene class and gene characteristics. PLoS One 2022; 17:e0276294. [PMID: 36260607 PMCID: PMC9581405 DOI: 10.1371/journal.pone.0276294] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 10/04/2022] [Indexed: 11/19/2022] Open
Abstract
T cells are key players in our defence against infections and malignancies. When T cells differentiate or become activated, they undergo substantial alterations in gene expression. Even though RNA expression levels are now well documented throughout different stages of T cells, it is not well understood how mRNA expression translates into the protein landscape. By combining paired RNA sequencing and mass spectrometry data of primary human CD8+ T cells, we report that mRNA expression is a poor proxy for the overall protein output, irrespective of the differentiation or activation status. Yet, gene class stratification revealed a function-specific correlation of mRNA with protein expression. This gene class-specific expression pattern associated with differences in gene characteristics such as sequence conservation and untranslated region (UTR) lengths. In addition, the presence of AU-rich elements in the 3'UTR associated with alterations in mRNA and protein abundance T cell activation dependent, gene class-specific manner. In conclusion, our study highlights the role of gene characteristics as a determinant for gene expression in T cells.
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Affiliation(s)
- Benoît P. Nicolet
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Monika C. Wolkers
- Department of Hematopoiesis, Sanquin Research, Amsterdam, The Netherlands
- Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- * E-mail:
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7
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Salloum D, Singh K, Davidson NR, Cao L, Kuo D, Sanghvi VR, Jiang M, Lafoz MT, Viale A, Ratsch G, Wendel HG. A Rapid Translational Immune Response Program in CD8 Memory T Lymphocytes. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2022; 209:1189-1199. [PMID: 36002234 PMCID: PMC9492650 DOI: 10.4049/jimmunol.2100537] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 05/25/2022] [Indexed: 01/04/2023]
Abstract
The activation of memory T cells is a very rapid and concerted cellular response that requires coordination between cellular processes in different compartments and on different time scales. In this study, we use ribosome profiling and deep RNA sequencing to define the acute mRNA translation changes in CD8 memory T cells following initial activation events. We find that initial translation enables subsequent events of human and mouse T cell activation and expansion. Briefly, early events in the activation of Ag-experienced CD8 T cells are insensitive to transcriptional blockade with actinomycin D, and instead depend on the translation of pre-existing mRNAs and are blocked by cycloheximide. Ribosome profiling identifies ∼92 mRNAs that are recruited into ribosomes following CD8 T cell stimulation. These mRNAs typically have structured GC and pyrimidine-rich 5' untranslated regions and they encode key regulators of T cell activation and proliferation such as Notch1, Ifngr1, Il2rb, and serine metabolism enzymes Psat1 and Shmt2 (serine hydroxymethyltransferase 2), as well as translation factors eEF1a1 (eukaryotic elongation factor α1) and eEF2 (eukaryotic elongation factor 2). The increased production of receptors of IL-2 and IFN-γ precedes the activation of gene expression and augments cellular signals and T cell activation. Taken together, we identify an early RNA translation program that acts in a feed-forward manner to enable the rapid and dramatic process of CD8 memory T cell expansion and activation.
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Affiliation(s)
- Darin Salloum
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular Pharmacology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Bronx, NY
| | - Natalie R Davidson
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Linlin Cao
- Swiss Institute for Experimental Cancer Research, EPFL, Lausanne, Switzerland
| | - David Kuo
- Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY
| | - Viraj R Sanghvi
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY.,Department of Molecular and Cellular Pharmacology, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami FL
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Maria Tello Lafoz
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY; and
| | - Agnes Viale
- Integrated Genomics Operation, Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Gunnar Ratsch
- Department of Computer Science, ETH Zurich, Zurich, Switzerland.,Department of Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY;
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8
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Vieira TC, Oliveira EA, dos Santos BJ, Souza FR, Veloso ES, Nunes CB, Del Puerto HL, Cassali GD. COX-2 expression in mammary invasive micropapillary carcinoma is associated with prognostic factors and acts as a potential therapeutic target in comparative oncology. Front Vet Sci 2022; 9:983110. [PMID: 36172611 PMCID: PMC9510711 DOI: 10.3389/fvets.2022.983110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022] Open
Abstract
Pure human and canine mammary invasive micropapillary carcinoma is a rare malignant epithelial tumor accounting for 0.9 to 2% of all invasive mammary carcinomas and present a high rate of lymphatic invasion and metastasis, with unfavorable prognosis. Surgery and chemotherapy are standard treatments for almost all mammary cancer in both species, as well as hormonal and target therapies available for human patients. However, depending on the patient's clinical staging, satisfactory therapeutic results for invasive micropapillary carcinoma are a challenge due to its high capacity of invasion and metastasis. Cyclooxygenase-2 (COX-2) isoform is an important enzyme stimulated by cytokines, growth factors and oncogenes activation to synthetizes prostaglandins in inflammatory process. COX-2 overexpression is associated with angiogenesis and invasion and contributes to cancer development, disease progression, tumor recurrence and regional lymph node metastasis in human and canine mammary carcinomas. This enzyme can be targeted by non-steroidal anti-inflammatory drugs and its inhibition can reduce tumor growth and metastasis in several cancer types. Given the similarity between both species, the present study aims to elucidate the involvement of COX-2 mRNA and protein expression in canine (cIMPC) and human (hIMPC) pure invasive mammary micropapillary carcinoma, with clinicopathological and survival data. Twenty-nine cases of cIMPC and 17 cases of hIMPC were analyzed regarding histologic type, grade, age, tumor size, lymph node condition, extracapsular extension, inflammatory infiltrate and immunophenotype. When available, information on adjuvant treatment, recurrence, metastasis and overall survival were collected. The present study demonstrated COX-2 protein expression in 65.5% of cIMPC and 92.3% of hIMPC, and an association with more advanced histological grades in bitches and higher Ki67 in women. COX-2 mRNA expression was significantly higher in cIMPC than in hIMPC, and its expression was not associated with COX-2 protein expression in both species. COX-2 mRNA expression was associated with negative-ER hIMPC as well as higher Ki67. cIMPC demonstrated proportional early development, more regional metastasis, and a prevalence of negative estrogen receptor, than hIMPC. This is the first time COX-2 expression is associated with negative prognostic factors in both cIMPC and hIMPC, besides the overexpression of COX-2 protein in such unfavorable histological type, which suggests that COX-2 can act as a potential target in IMPC.
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Affiliation(s)
- Thaynan Cunha Vieira
- Laboratory of Comparative Oncology, Institute of Biological Sciences, Department of General Pathology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Evelyn Ane Oliveira
- Laboratory of Comparative Oncology, Institute of Biological Sciences, Department of General Pathology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bárbara Jaime dos Santos
- Laboratory of Breast Pathology, Medical School, Department of Pathological Anatomy, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Fernanda Rezende Souza
- Laboratory of Comparative Oncology, Institute of Biological Sciences, Department of General Pathology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Emerson Soares Veloso
- Laboratory of Cellular Behavior, Institute of Biological Sciences, Department of General Pathology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Cristiana Buzelin Nunes
- Laboratory of Breast Pathology, Medical School, Department of Pathological Anatomy, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Helen Lima Del Puerto
- Laboratory of Cellular Behavior, Institute of Biological Sciences, Department of General Pathology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Geovanni Dantas Cassali
- Laboratory of Comparative Oncology, Institute of Biological Sciences, Department of General Pathology, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- *Correspondence: Geovanni Dantas Cassali
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9
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Tan K, Stupack DG, Wilkinson MF. Nonsense-mediated RNA decay: an emerging modulator of malignancy. Nat Rev Cancer 2022; 22:437-451. [PMID: 35624152 PMCID: PMC11009036 DOI: 10.1038/s41568-022-00481-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/19/2022] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated RNA decay (NMD) is a highly conserved RNA turnover pathway that selectively degrades RNAs harbouring truncating mutations that prematurely terminate translation, including nonsense, frameshift and some splice-site mutations. Recent studies show that NMD shapes the mutational landscape of tumours by selecting for mutations that tend to downregulate the expression of tumour suppressor genes but not oncogenes. This suggests that NMD can benefit tumours, a notion further supported by the finding that mRNAs encoding immunogenic neoantigen peptides are typically targeted for decay by NMD. Together, this raises the possibility that NMD-inhibitory therapy could be of therapeutic benefit against many tumour types, including those with a high load of neoantigen-generating mutations. Complicating this scenario is the evidence that NMD can also be detrimental for many tumour types, and consequently tumours often have perturbed NMD. NMD may suppress tumour generation and progression by degrading subsets of specific normal mRNAs, including those encoding stress-response proteins, signalling factors and other proteins beneficial for tumours, as well as pro-tumour non-coding RNAs. Together, these findings suggest that NMD-modulatory therapy has the potential to provide widespread therapeutic benefit against diverse tumour types. However, whether NMD should be stimulated or repressed requires careful analysis of the tumour to be treated.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Dwayne G Stupack
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- UCSD Moores Cancer Center, University of California, San Diego, La Jolla, CA, USA.
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Diego, La Jolla, CA, USA.
- Institute of Genomic Medicine, University of California, San Diego, La Jolla, CA, USA.
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10
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Autin P, Deshayes S, Lea J, Boisgerault N, Dupré E, Labarrière N, Leguevel R, Fonteneau JF, Blanquart C, Fradin D. The DCMU Herbicide Shapes T-cell Functions By Modulating Micro-RNA Expression Profiles. Front Immunol 2022; 13:925241. [PMID: 35967413 PMCID: PMC9366666 DOI: 10.3389/fimmu.2022.925241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022] Open
Abstract
DCMU [N-(3,4-dichlorophenyl)-N-dimethylurea] or diuron is a widely used herbicide, which can cause adverse effects on human, especially on immune cells, due to their intrinsic properties and wide distribution. These cells are important for fighting not only against virus or bacteria but also against neoplastic cell development. We developed an approach that combines functional studies and miRNA and RNA sequencing data to evaluate the effects of DCMU on the human immune response against cancer, particularly the one carried out by CD8+ T cells. We found that DCMU modulates the expression of miRNA in a dose-dependent manner, leading to a specific pattern of gene expression and consequently to a diminished cytokine and granzyme B secretions. Using mimics or anti-miRs, we identified several miRNA, such as hsa-miR-3135b and hsa-miR-21-5p, that regulate these secretions. All these changes reduce the CD8+ T cells’ cytotoxic activity directed against cancer cells, in vitro and in vivo in a zebrafish model. To conclude, our study suggests that DCMU reduces T-cell abilities, participating thus to the establishment of an environment conducive to cancer development.
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Affiliation(s)
- Pierre Autin
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Sophie Deshayes
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Juliette Lea
- Université de Rennes, ImPACcell Plateform, BIOSIT, Rennes, France
| | - Nicolas Boisgerault
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Emilie Dupré
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Nathalie Labarrière
- Nantes Université, Univ Angers, INSERM, CNRS, Immunology and New Concepts in ImmunoTherapy, INCIT, UMR 1302/EMR6001, Nantes, France
| | - Rémy Leguevel
- Université de Rennes, ImPACcell Plateform, BIOSIT, Rennes, France
| | - Jean-François Fonteneau
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Christophe Blanquart
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
| | - Delphine Fradin
- Nantes Université, INSERM UMR1307, CNRS UMR6075, Université d’Angers, CRCI2NA, Nantes, France
- *Correspondence: Delphine Fradin,
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11
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Tan K, Wilkinson MF. Regulation of both transcription and RNA turnover contribute to germline specification. Nucleic Acids Res 2022; 50:7310-7325. [PMID: 35776114 PMCID: PMC9303369 DOI: 10.1093/nar/gkac542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/29/2022] [Accepted: 06/29/2022] [Indexed: 12/25/2022] Open
Abstract
The nuanced mechanisms driving primordial germ cells (PGC) specification remain incompletely understood since genome-wide transcriptional regulation in developing PGCs has previously only been defined indirectly. Here, using SLAMseq analysis, we determined genome-wide transcription rates during the differentiation of embryonic stem cells (ESCs) to form epiblast-like (EpiLC) cells and ultimately PGC-like cells (PGCLCs). This revealed thousands of genes undergoing bursts of transcriptional induction and rapid shut-off not detectable by RNAseq analysis. Our SLAMseq datasets also allowed us to infer RNA turnover rates, which revealed thousands of mRNAs stabilized and destabilized during PGCLC specification. mRNAs tend to be unstable in ESCs and then are progressively stabilized as they differentiate. For some classes of genes, mRNA turnover regulation collaborates with transcriptional regulation, but these processes oppose each other in a surprisingly high frequency of genes. To test whether regulated mRNA turnover has a physiological role in PGC development, we examined three genes that we found were regulated by RNA turnover: Sox2, Klf2 and Ccne1. Circumvention of their regulated RNA turnover severely impaired the ESC-to-EpiLC and EpiLC-to-PGCLC transitions. Our study demonstrates the functional importance of regulated RNA stability in germline development and provides a roadmap of transcriptional and post-transcriptional regulation during germline specification.
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Affiliation(s)
- Kun Tan
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Miles F Wilkinson
- Department of Obstetrics, Gynecology, and Reproductive Sciences, School of Medicine, University of California San Diego, La Jolla, CA 92093, USA
- Institute of Genomic Medicine (IGM), University of California San Diego, La Jolla, CA 92093, USA
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12
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Nicolet BP, Zandhuis ND, Lattanzio VM, Wolkers MC. Sequence determinants as key regulators in gene expression of T cells. Immunol Rev 2021; 304:10-29. [PMID: 34486113 PMCID: PMC9292449 DOI: 10.1111/imr.13021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/09/2021] [Accepted: 08/17/2021] [Indexed: 12/12/2022]
Abstract
T cell homeostasis, T cell differentiation, and T cell effector function rely on the constant fine-tuning of gene expression. To alter the T cell state, substantial remodeling of the proteome is required. This remodeling depends on the intricate interplay of regulatory mechanisms, including post-transcriptional gene regulation. In this review, we discuss how the sequence of a transcript influences these post-transcriptional events. In particular, we review how sequence determinants such as sequence conservation, GC content, and chemical modifications define the levels of the mRNA and the protein in a T cell. We describe the effect of different forms of alternative splicing on mRNA expression and protein production, and their effect on subcellular localization. In addition, we discuss the role of sequences and structures as binding hubs for miRNAs and RNA-binding proteins in T cells. The review thus highlights how the intimate interplay of post-transcriptional mechanisms dictate cellular fate decisions in T cells.
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Affiliation(s)
- Benoit P. Nicolet
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Nordin D. Zandhuis
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - V. Maria Lattanzio
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
| | - Monika C. Wolkers
- Department of HematopoiesisSanquin Research and Landsteiner LaboratoryAmsterdam UMCUniversity of AmsterdamAmsterdamThe Netherlands
- Oncode InstituteUtrechtThe Netherlands
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13
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Divulging the Critical Role of HuR in Pancreatic Cancer as a Therapeutic Target and a Means to Overcome Chemoresistance. Cancers (Basel) 2021; 13:cancers13184634. [PMID: 34572861 PMCID: PMC8471481 DOI: 10.3390/cancers13184634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/10/2021] [Accepted: 09/14/2021] [Indexed: 12/21/2022] Open
Abstract
Simple Summary With pancreatic cancer incidence constantly rising, constituting one of the most lethal type of cancers worldwide, the need for discovering novel therapeutic targets and approaches becomes of the utmost importance. Meanwhile, modern eating habits, hyperadiposity, mutational burden affecting core signaling pathways and the unique tumor microenvironment of pancreatic cancer tissues intermingle and form a disease that is lethal and hard to treat. The importance of HuR in pancreatic cancer has repeatedly been observed and represents a key molecule in pancreatic carcinogenesis and chemoresistance. Therefore, creating and obtaining new therapeutic skills against HuR protein could prove to be the answer to pancreatic cancer therapy. Abstract Pancreatic cancer is set to become the most lethal and common type of cancer worldwide. This is partly attributed to the mutational burden that affects core signaling pathways and the crosstalk of tumor cells with their surrounding microenvironment, but it is also due to modern eating habits. Hyperadiposity along with the constant rise in metabolic syndrome’s incidence contribute to a state of metaflammation that impacts immune cells and causes them to shift towards an immunosuppressive phenotype that, ultimately, allows tumor cells to evade immune control. Unfortunately, among the conventional therapeutic modalities and the novel therapeutic agents introduced, pancreatic cancer still holds one of the lowest response rates to therapy. Human antigen R (HuR), an RNA binding protein (RBP), has been repeatedly found to be implicated in pancreatic carcinogenesis and chemotherapy resistance through the posttranscriptional binding and regulation of mRNA target genes. Additionally, its overexpression has been linked to adverse clinical outcomes, in terms of tumor grade, stage, lymph node status and metastasis. These properties suggest the prospective role that HuR’s therapeutic targeting can play in facilitating pancreatic neoplasia and could provide the means to overcome chemoresistance.
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14
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Moron-Lopez S, Bernal S, Wong JK, Martinez-Picado J, Yukl SA. ABX464 decreases the total HIV reservoir and HIV transcription initiation in CD4 + T cells from HIV-infected ART-suppressed individuals. Clin Infect Dis 2021; 74:2044-2049. [PMID: 34436569 DOI: 10.1093/cid/ciab733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Antiretroviral therapy (ART) intensification and disruption of latency have been suggested as strategies to eradicate HIV. ABX464 is a novel antiviral that inhibits HIV RNA biogenesis. We investigated the effect of ABX464 on HIV transcription and total and intact HIV DNA in CD4 + T cells from ART-suppressed participants enrolled in the ABIVAX-005 clinical trial (NCT02990325). METHODS Peripheral CD4 + T cells were available for analysis from nine ART-suppressed participants who were treated daily with 150mg of ABX464 for 4 weeks. Total and intact HIV DNA, and initiated, 5'elongated, unspliced, polyadenylated and multiply-spliced HIV transcripts, were quantified at weeks 0, 4 and 8 using droplet digital PCR. RESULTS We observed a significant decrease in total HIV DNA (p=0.008, median fold-change=0.8) and a lower median level of intact HIV DNA (p=n.s., median fold-change=0.8) after ABX464 treatment (wk 0 vs. 4). Moreover, we observed a decrease in initiated HIV RNA per million CD4 + T cells and per provirus (p=0.05, median fold-change=0.7; p=0.004, median fold-change=0.5, respectively), a trend towards a decrease in the 5'elongated HIV RNA per provirus (p=0.07, median fold-change=0.5), and a lower median level of unspliced HIV RNA (p=n.s., median fold-change=0.6), but no decrease in polyadenylated or multiply-spliced HIV RNA. CONCLUSION In this substudy, ABX464 had a dual effect of decreasing total HIV DNA (and possibly intact proviruses) and decreasing the amount of HIV transcription per provirus. To further characterize its specific mechanism of inhibiting HIV transcription, long-term administration of ABX464 should be studied in a larger cohort.
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Affiliation(s)
- Sara Moron-Lopez
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Silvia Bernal
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain
| | - Joseph K Wong
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Javier Martinez-Picado
- IrsiCaixa AIDS Research Institute, Badalona, Spain.,University of Vic-Central University of Catalonia (UVic-UCC), Vic, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Steven A Yukl
- Department of Medicine, San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
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15
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Hsieh HH, Chen YA, Chang YJ, Wang HH, Yu YH, Lin SW, Huang YJ, Lin S, Chang CJ. The functional characterization of phosphorylation of tristetraprolin at C-terminal NOT1-binding domain. JOURNAL OF INFLAMMATION-LONDON 2021; 18:22. [PMID: 34090459 PMCID: PMC8180021 DOI: 10.1186/s12950-021-00288-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 05/20/2021] [Indexed: 12/26/2022]
Abstract
Background Tristetraprolin (TTP) family proteins contain conserved tandem CCCH zinc-finger binding to AU-rich elements and C-terminal NOT1-binding domain. TTP is phosphorylated extensively in cells, and its mRNA destabilization activity is regulated by protein phosphorylation. Methods We generated an antibody against phospho-Serine316 located at the C-terminal NOT1-binding site and examined TTP phosphorylation in LPS-stimulated RAW264.7 cells. Knockout of TTP was created in RAW264.7 cells using CRISPR/Cas9 gene editing to explore TTP functions. Results We demonstrated that Ser316 was phosphorylated by p90 ribosomal S6 kinase 1 (RSK1) and p38-activated protein kinase (MK2) and dephosphorylated by Protein Phosphatase 2A (PP2A). A phosphorylation-mimic mutant of S316D resulted in dissociation with the CCR4-NOT deadenylase complex through weakening interaction with CNOT1. Furthermore, Ser316 and serines 52 and 178 were independently contributed to the CCR4-NOT complex recruitment in the immunoprecipitation assay using phosphor-mimic mutants. In RAW264.7 macrophages, TTP was induced, and Ser316 was phosphorylated through RSK1 and MK2 by LPS stimulation. Knockout of TTP resulted in TNFα mRNA increased due to mRNA stabilization. Overexpression of non-phosphorylated S316A TTP mutant can restore TTP activity and lead to TNFα mRNA decreased. GST pull-down and RNA pull-down analyses demonstrated that endogenous TTP with Ser316 phosphorylation decreased the interaction with CNOT1. Conclusions Our results suggest that the TTP-mediated mRNA stability is modulated by Ser316 phosphorylation via regulating the TTP interaction with the CCR4-NOT deadenylase complex. Supplementary Information The online version contains supplementary material available at 10.1186/s12950-021-00288-2.
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Affiliation(s)
- Hsin-Hui Hsieh
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Yen-An Chen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Hsin-Hui Wang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei, Taiwan.,Department of Pediatrics, Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan.,Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ya-Han Yu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yin-Jung Huang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Steven Lin
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan.,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Ching-Jin Chang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, No. 1 Sec 4 Roosevelt Rd, Taipei, 106, Taiwan. .,Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan.
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16
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Crittenden JR, Gipson TA, Smith AC, Bowden HA, Yildirim F, Fischer KB, Yim M, Housman DE, Graybiel AM. Striatal transcriptome changes linked to drug-induced repetitive behaviors. Eur J Neurosci 2021; 53:2450-2468. [PMID: 33759265 DOI: 10.1111/ejn.15116] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/23/2020] [Accepted: 01/09/2021] [Indexed: 11/30/2022]
Abstract
Disruptive or excessive repetitive motor patterns (stereotypies) are cardinal symptoms in numerous neuropsychiatric disorders. Stereotypies are also evoked by psychomotor stimulants such as amphetamine. The acquisition of motor sequences is paralleled by changes in activity patterns in the striatum, and stereotypies have been linked to abnormal plasticity in these reinforcement-related circuits. Here, we designed experiments in mice to identify transcriptomic changes that underlie striatal plasticity occurring alongside the development of drug-induced stereotypic behavior. We identified three schedules of amphetamine treatment inducing different degrees of stereotypy and used bulk RNAseq to compare striatal gene expression changes among groups of mice treated with the different drug-dose schedules and vehicle-treated, cage-mate controls. Mice were identified as naïve, sensitized, or tolerant to drug-induced stereotypy. All drug-treated groups exhibited expression changes in genes that encode members of the extracellular signal-regulated kinase (ERK) cascades known to regulate psychomotor stimulant responses. In the sensitized group with the most prolonged stereotypy, we found dysregulation of 20 genes that were not changed in other groups. Gene set enrichment analysis indicated highly significant overlap with genes regulated by neuregulin 1 (Nrg1). Nrg1 is known to be a schizophrenia and autism susceptibility gene that encodes a ligand for Erb-B receptors, which are involved in neuronal migration, myelination, and cell survival, including that of dopamine-containing neurons. Stimulant abuse is a risk factor for schizophrenia onset, and these two disorders share behavioral stereotypy phenotypes. Our results raise the possibility that drug-induced sensitization of the Nrg1 signaling pathway might underlie these links.
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Affiliation(s)
- Jill R Crittenden
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Theresa A Gipson
- Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anne C Smith
- Evelyn F. McKnight Brain Institute, University of Arizona, Tucson, AZ, USA
| | - Hilary A Bowden
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ferah Yildirim
- Department of Neuropsychiatry, Department of Psychiatry and Psychotherapy, and NeuroCure Cluster of Excellence, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Kyle B Fischer
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael Yim
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David E Housman
- Institute for Integrative Cancer Research, The Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ann M Graybiel
- McGovern Institute for Brain Research, The Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Brain and Cognitive Sciences, The Massachusetts Institute of Technology, Cambridge, MA, USA
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17
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Tian Y, Zeng Z, Li X, Wang Y, Chen R, Mattijssen S, Gaidamakov S, Wu Y, Maraia RJ, Peng W, Zhu J. Transcriptome-wide stability analysis uncovers LARP4-mediated NFκB1 mRNA stabilization during T cell activation. Nucleic Acids Res 2020; 48:8724-8739. [PMID: 32735645 PMCID: PMC7470963 DOI: 10.1093/nar/gkaa643] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 06/30/2020] [Accepted: 07/22/2020] [Indexed: 02/07/2023] Open
Abstract
T cell activation is a well-established model for studying cellular responses to exogenous stimulation. Motivated by our previous finding that intron retention (IR) could lead to transcript instability, in this study, we performed BruChase-Seq to experimentally monitor the expression dynamics of nascent transcripts in resting and activated CD4+ T cells. Computational modeling was then applied to quantify the stability of spliced and intron-retained transcripts on a genome-wide scale. Beyond substantiating that intron-retained transcripts were considerably less stable than spliced transcripts, we found a global stabilization of spliced mRNAs upon T cell activation, although the stability of intron-retained transcripts remained relatively constant. In addition, we identified that La-related protein 4 (LARP4), an RNA-binding protein (RBP) known to enhance mRNA stability, was involved in T cell activation-dependent mRNA stabilization. Knocking out Larp4 in mice destabilized Nfκb1 mRNAs and reduced secretion of interleukin-2 (IL2) and interferon-gamma (IFNγ), two factors critical for T cell proliferation and function. We propose that coordination between splicing regulation and mRNA stability may provide a novel paradigm to control spatiotemporal gene expression during T cell activation.
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Affiliation(s)
- Yi Tian
- Department of Physics, George Washington University, Washington, DC 20052, USA
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Zhouhao Zeng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Xiang Li
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Yiyin Wang
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Runsen Chen
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Cardiothoracic Surgery, Children's Hospital of Nanjing Medical University, Nanjing 210008, China
| | - Sandy Mattijssen
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Sergei Gaidamakov
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University, Chongqing 400038, PR China
| | - Richard J Maraia
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Weiqun Peng
- Department of Physics, George Washington University, Washington, DC 20052, USA
| | - Jun Zhu
- Systems Biology Center, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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18
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Gagnon JD, Kageyama R, Shehata HM, Fassett MS, Mar DJ, Wigton EJ, Johansson K, Litterman AJ, Odorizzi P, Simeonov D, Laidlaw BJ, Panduro M, Patel S, Jeker LT, Feeney ME, McManus MT, Marson A, Matloubian M, Sanjabi S, Ansel KM. miR-15/16 Restrain Memory T Cell Differentiation, Cell Cycle, and Survival. Cell Rep 2020; 28:2169-2181.e4. [PMID: 31433990 PMCID: PMC6715152 DOI: 10.1016/j.celrep.2019.07.064] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 05/03/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022] Open
Abstract
Coordinate control of T cell proliferation, survival, and differentiation are essential for host protection from pathogens and cancer. Long-lived memory cells, whose precursors are formed during the initial immunological insult, provide protection from future encounters, and their generation is the goal of many vaccination strategies. microRNAs (miRNAs) are key nodes in regulatory networks that shape effective T cell responses through the fine-tuning of thousands of genes. Here, using compound conditional mutant mice to eliminate miR-15/16 family miRNAs in T cells, we show that miR-15/16 restrict T cell cycle, survival, and memory T cell differentiation. High throughput sequencing of RNA isolated by cross-linking immunoprecipitation of AGO2 combined with gene expression analysis in miR-15/16-deficient T cells indicates that these effects are mediated through the direct inhibition of an extensive network of target genes within pathways critical to cell cycle, survival, and memory.
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Affiliation(s)
- John D Gagnon
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Robin Kageyama
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Hesham M Shehata
- Virology and Immunology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - Marlys S Fassett
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Dermatology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Darryl J Mar
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Eric J Wigton
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Kristina Johansson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Adam J Litterman
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Pamela Odorizzi
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Dimitre Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Brian J Laidlaw
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Marisella Panduro
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Sana Patel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lukas T Jeker
- Diabetes Center and Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Pathology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Margaret E Feeney
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Diabetes Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Mehrdad Matloubian
- Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Shomyseh Sanjabi
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Virology and Immunology, Gladstone Institutes, San Francisco, CA 94158, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA; Sandler Asthma Basic Research Center, University of California, San Francisco, San Francisco, CA 94143, USA.
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19
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Hyjek‐Składanowska M, Bajczyk M, Gołębiewski M, Nuc P, Kołowerzo‐Lubnau A, Jarmołowski A, Smoliński DJ. Core spliceosomal Sm proteins as constituents of cytoplasmic mRNPs in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:1155-1173. [PMID: 32369637 PMCID: PMC7540296 DOI: 10.1111/tpj.14792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/13/2020] [Accepted: 04/21/2020] [Indexed: 05/15/2023]
Abstract
In recent years, research has increasingly focused on the key role of post-transcriptional regulation of messenger ribonucleoprotein (mRNP) function and turnover. As a result of the complexity and dynamic nature of mRNPs, the full composition of a single mRNP complex remains unrevealed and mRNPs are poorly described in plants. Here we identify canonical Sm proteins as part of the cytoplasmic mRNP complex, indicating their function in the post-transcriptional regulation of gene expression in plants. Sm proteins comprise an evolutionarily ancient family of small RNA-binding proteins involved in pre-mRNA splicing. The latest research indicates that Sm could also impact on mRNA at subsequent stages of its life cycle. In this work we show that in the microsporocyte cytoplasm of Larix decidua, the European larch, Sm proteins accumulate within distinct cytoplasmic bodies, also containing polyadenylated RNA. To date, several types of cytoplasmic bodies involved in the post-transcriptional regulation of gene expression have been described, mainly in animal cells. Their role and molecular composition in plants remain less well established, however. A total of 222 mRNA transcripts have been identified as cytoplasmic partners for Sm proteins. The specific colocalization of these mRNAs with Sm proteins within cytoplasmic bodies has been confirmed via microscopic analysis. The results from this work support the hypothesis, that evolutionarily conserved Sm proteins have been adapted to perform a whole repertoire of functions related to the post-transcriptional regulation of gene expression in Eukaryota. This adaptation presumably enabled them to coordinate the interdependent processes of splicing element assembly, mRNA maturation and processing, and mRNA translation regulation, and its degradation.
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Affiliation(s)
- Malwina Hyjek‐Składanowska
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Present address:
Laboratory of Protein StructureInternational Institute of Molecular and Cell Biology4 Trojdena St.02‐109WarsawPoland
| | - Mateusz Bajczyk
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Marcin Gołębiewski
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
- Department of Plant Physiology and BiotechnologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
| | - Przemysław Nuc
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Agnieszka Kołowerzo‐Lubnau
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
| | - Artur Jarmołowski
- Department of Gene ExpressionInstitute of Molecular Biology and BiotechnologyAdam Mickiewicz UniversityUmultowska 89Poznan61‐614Poland
| | - Dariusz Jan Smoliński
- Department of Cellular and Molecular BiologyNicolaus Copernicus UniveristyLwowska 187‐100TorunPoland
- Centre For Modern Interdisciplinary TechnologiesNicolaus Copernicus UniversityWilenska 487‐100TorunPoland
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20
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Portugal J. Insights into DNA-drug interactions in the era of omics. Biopolymers 2020; 112:e23385. [PMID: 32542701 DOI: 10.1002/bip.23385] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 05/23/2020] [Accepted: 05/25/2020] [Indexed: 01/07/2023]
Abstract
Despite the rise of sophisticated new targeting strategies in cancer chemotherapy, many classic DNA-binding drugs remain on the front line of the therapy against cancer. Based on examples primarily from the author's laboratory, this article reviews the capabilities of several DNA-binding drugs to alter gene expression. Research is ongoing about the molecular bases of the inhibition of gene expression and how alteration of the cellular transcriptome can commit cancer cells to die. The development of a variety of omic techniques allows us to gain insights into the effect of antitumor drugs. Genome-wide approaches provide unbiased genomic data that can facilitate a deeper understanding of the cellular response to DNA-binding drugs. Moreover, the results of large-scale genomic studies are gathered in publicly available databases that can be used in developing precision medicine in cancer treatment.
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Affiliation(s)
- José Portugal
- Instituto de Diagnóstico Ambiental y Estudios del Agua, CSIC, Barcelona, Spain
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21
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Papp B, Launay S, Gélébart P, Arbabian A, Enyedi A, Brouland JP, Carosella ED, Adle-Biassette H. Endoplasmic Reticulum Calcium Pumps and Tumor Cell Differentiation. Int J Mol Sci 2020; 21:ijms21093351. [PMID: 32397400 PMCID: PMC7247589 DOI: 10.3390/ijms21093351] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 12/21/2022] Open
Abstract
Endoplasmic reticulum (ER) calcium homeostasis plays an essential role in cellular calcium signaling, intra-ER protein chaperoning and maturation, as well as in the interaction of the ER with other organelles. Calcium is accumulated in the ER by sarco/endoplasmic reticulum calcium ATPases (SERCA enzymes) that generate by active, ATP-dependent transport, a several thousand-fold calcium ion concentration gradient between the cytosol (low nanomolar) and the ER lumen (high micromolar). SERCA enzymes are coded by three genes that by alternative splicing give rise to several isoforms, which can display isoform-specific calcium transport characteristics. SERCA expression levels and isoenzyme composition vary according to cell type, and this constitutes a mechanism whereby ER calcium homeostasis is adapted to the signaling and metabolic needs of the cell, depending on its phenotype, its state of activation and differentiation. As reviewed here, in several normal epithelial cell types including bronchial, mammary, gastric, colonic and choroid plexus epithelium, as well as in mature cells of hematopoietic origin such as pumps are simultaneously expressed, whereas in corresponding tumors and leukemias SERCA3 expression is selectively down-regulated. SERCA3 expression is restored during the pharmacologically induced differentiation of various cancer and leukemia cell types. SERCA3 is a useful marker for the study of cell differentiation, and the loss of SERCA3 expression constitutes a previously unrecognized example of the remodeling of calcium homeostasis in tumors.
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Affiliation(s)
- Bela Papp
- Institut National de la Santé et de la Recherche Médicale, UMR U976, Institut Saint-Louis, 75010 Paris, France
- Institut de Recherche Saint-Louis, Hôpital Saint-Louis, Université de Paris, 75010 Paris, France
- CEA, DRF-Institut Francois Jacob, Department of Hemato-Immunology Research, Hôpital Saint-Louis, 75010 Paris, France;
- Correspondence: or
| | - Sophie Launay
- EA481, UFR Santé, Université de Bourgogne Franche-Comté, 25000 Besançon, France;
| | - Pascal Gélébart
- Department of Clinical Science-Hematology Section, Haukeland University Hospital, University of Bergen, 5021 Bergen, Norway;
| | - Atousa Arbabian
- Laboratoire d’Innovation Vaccins, Institut Pasteur de Paris, 75015 Paris, France;
| | - Agnes Enyedi
- Second Department of Pathology, Semmelweis University, 1091 Budapest, Hungary;
| | - Jean-Philippe Brouland
- Institut Universitaire de Pathologie, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland;
| | - Edgardo D. Carosella
- CEA, DRF-Institut Francois Jacob, Department of Hemato-Immunology Research, Hôpital Saint-Louis, 75010 Paris, France;
| | - Homa Adle-Biassette
- AP-HP, Service d’Anatomie et Cytologie Pathologiques, Hôpital Lariboisière, 75010 Paris, France;
- Université de Paris, NeuroDiderot, Inserm UMR 1141, 75019 Paris, France
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22
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Abstract
MicroRNAs (miRNAs) are a class of short noncoding RNAs that play critical roles in the regulation of a broad range of biological processes. Like transcription factors, miRNAs exert their effects by modulating the expression of networks of genes that operate in common or convergent pathways. CD8+ T cells are critical agents of the adaptive immune system that provide protection from infection and cancer. Here, we review the important roles of miRNAs in the regulation of CD8+ T cell biology and provide perspectives on the broader emerging principles of miRNA function.
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Affiliation(s)
- John D Gagnon
- Sandler Asthma Basic Research Center, Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
| | - K Mark Ansel
- Sandler Asthma Basic Research Center, Department of Microbiology & Immunology, University of California San Francisco, San Francisco, CA, USA
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23
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Kulemzin SV, Matvienko DA, Sabirov AH, Sokratyan AM, Chernikova DS, Belovezhets TN, Chikaev AN, Taranin AV, Gorchakov AA. Design and analysis of stably integrated reporters for inducible transgene expression in human T cells and CAR NK-cell lines. BMC Med Genomics 2019; 12:44. [PMID: 30871576 PMCID: PMC6417161 DOI: 10.1186/s12920-019-0489-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Background Cytotoxic activity of T- and NK-cells can be efficiently retargeted against cancer cells using chimeric antigen receptors (CARs) and rTCRs. In the context of solid cancers, use of armored CAR T- and NK cells secreting additional anti-cancer molecules such as cytokines, chemokines, antibodies, BiTEs, inverted cytokine receptors, and checkpoint inhibitors, appears particularly promising, as this may help overcome immunosuppressive tumor microenvironment, attract bystander immune cells, and boost CAR T/NK-cell persistence. Placing the expression of such molecules under the transcriptional control downstream of CAR-mediated T/NK-cell activation offers the advantage of targeted delivery, high local concentration, and reduced toxicity. Several canonic DNA sequences that are known to function as activation-inducible promoters in human T and B cells have been described to date and typically encompass the multimers of NFkB and NFAT binding sites. However, relatively little is known about the DNA sequences that may function as activation-driven switches in the context of NK cells. We set out to compare the functionality of several activation-inducible promoters in primary human T cells, as well as in NK cell lines NK-92 and YT. Methods Lentiviral constructs were engineered to express two fluorescent reporters: mCherry under 4xNFAT, 2xNFkB, 5xNFkB, 10xNFkB, 30xNFkB promoters, as well as two variants of the CD69 promoter, and copGFP under the strong constitutive promoter of the human EF1a gene. Pseudotyped lentiviral particles obtained using these constructs were transduced into primary human T cells and NK-92 and YT cell lines expressing a CAR specific for PSMA. The transgenic cells obtained were activated by CD3/CD28 beads (T cells) or via a CAR (CAR-NK cell lines). Promoter activity before and after activation was assayed using FACS analysis. Results In T cells, the CD69 promoter encompassing CNS1 and CNS2 regions displayed the highest signal/noise ratio. Intriguingly, in the context of CAR-YT cell line neither of the seven promoters tested displayed acceptable activation profile. In CAR-NK-92 cells, the largest fold activation (which was modest) was achieved with the 10xNFkB and 30xNFkB promoters, however its expression was clearly leaky in “resting” non-activated cells. Conclusions Unlike in T cells, the robust activation-driven inducible expression of genetic cassettes in NK cells requires unbiased genome-wide identification of promoter sequences. Electronic supplementary material The online version of this article (10.1186/s12920-019-0489-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sergey V Kulemzin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Daria A Matvienko
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Artur H Sabirov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Arpine M Sokratyan
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Daria S Chernikova
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Tatyana N Belovezhets
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Anton N Chikaev
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia
| | - Aleksandr V Taranin
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Andrey A Gorchakov
- Institute of Molecular and Cellular Biology SB RAS, Novosibirsk, Russia. .,Novosibirsk State University, Novosibirsk, Russia.
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24
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Russo J, Mundell CT, Charley PA, Wilusz C, Wilusz J. Engineered viral RNA decay intermediates to assess XRN1-mediated decay. Methods 2018; 155:116-123. [PMID: 30521847 DOI: 10.1016/j.ymeth.2018.11.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 01/23/2023] Open
Abstract
Both RNA synthesis and decay must be balanced within a cell to achieve proper gene expression. Additionally, modulation of RNA decay specifically offers the cell an opportunity to rapidly reshape the transcriptome in response to specific stimuli or cues. Therefore, it is critical to understand the underlying mechanisms through which RNA decay contribute to gene expression homeostasis. Cell-free reconstitution approaches have been used successfully to reveal mechanisms associated with numerous post-transcriptional RNA processes. Historically, it has been difficult to examine all aspects of RNA decay in such an in vitro setting due, in part, to limitations on the ability to resolve larger RNAs through denaturing polyacrylamide gels. Thus, in vitro systems to study RNA decay rely on smaller, less biologically relevant RNA fragments. Herein, we present an approach to more confidently examine RNA decay parameters of large mRNA size transcripts through the inclusion of an engineered XRN1-resistant reporter RNA (xrRNA). By placing a 67 nucleotide xrRNA near the 3' end of any in vitro transcribed RNA with variable size or sequence context, investigators can observe the accumulation of the xrRNA as a readout of exoribonuclease-mediated 5'-3' decay. This approach may allow in vitro RNA decay assays to include full biologically relevant mRNA/mRNPs, extending their utility and allow improved experimental design considerations to promote biologically relevant outcomes.
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Affiliation(s)
- Joseph Russo
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States
| | - Cary T Mundell
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States; Program in Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80525, United States
| | - Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States
| | - Carol Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States; Program in Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80525, United States
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, CO 80525, United States; Program in Cell & Molecular Biology, Colorado State University, Fort Collins, CO 80525, United States.
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25
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Deng C, Lv X, Li J, Liu Y, Du G, Amaro RL, Liu L. Synthetic repetitive extragenic palindromic (REP) sequence as an efficient mRNA stabilizer for protein production and metabolic engineering in prokaryotic cells. Biotechnol Bioeng 2018; 116:5-18. [DOI: 10.1002/bit.26841] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 08/24/2018] [Accepted: 09/14/2018] [Indexed: 12/13/2022]
Affiliation(s)
- Chen Deng
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Jianghua Li
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
| | | | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
- Key Laboratory of Industrial Biotechnology; Ministry of Education, Jiangnan University; Wuxi China
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26
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Yamada T, Akimitsu N. Contributions of regulated transcription and mRNA decay to the dynamics of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 10:e1508. [PMID: 30276972 DOI: 10.1002/wrna.1508] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 12/21/2022]
Abstract
Organisms have acquired sophisticated regulatory networks that control gene expression in response to cellular perturbations. Understanding of the mechanisms underlying the coordinated changes in gene expression in response to external and internal stimuli is a fundamental issue in biology. Recent advances in high-throughput technologies have enabled the measurement of diverse biological information, including gene expression levels, kinetics of gene expression, and interactions among gene expression regulatory molecules. By coupling these technologies with quantitative modeling, we can now uncover the biological roles and mechanisms of gene regulation at the system level. This review consists of two parts. First, we focus on the methods using uridine analogs that measure synthesis and decay rates of RNAs, which demonstrate how cells dynamically change the regulation of gene expression in response to both internal and external cues. Second, we discuss the underlying mechanisms of these changes in kinetics, including the functions of transcription factors and RNA-binding proteins. Overall, this review will help to clarify a system-level view of gene expression programs in cells. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Turnover and Surveillance > Regulation of RNA Stability RNA Methods > RNA Analyses in vitro and In Silico.
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Affiliation(s)
- Toshimichi Yamada
- Department of Molecular and Cellular Biochemistry, Meiji Pharmaceutical University, Tokyo, Japan
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27
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Jung E, Seong Y, Jeon B, Kwon YS, Song H. MicroRNAs of miR-17-92 cluster increase gene expression by targeting mRNA-destabilization pathways. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2018; 1861:603-612. [PMID: 29935344 DOI: 10.1016/j.bbagrm.2018.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 05/27/2018] [Accepted: 06/15/2018] [Indexed: 01/07/2023]
Abstract
MicroRNAs (miRNAs) of the miR-17-92 cluster are overexpressed in human cancers, and their enforced expression is tumorigenic in mouse models. A number of genes are reported to be targets of these miRNAs and are implicated in their tumorigenic potential. However, the mode of action by miRNAs suggests that global analysis of their targets is required to understand their cellular roles. In this study, we globally analyzed AGO2-bound mRNAs and found that the miR-17-92 miRNAs coherently repress multiple targets involved in the destabilization of mRNA. While the miRNAs repress the expression of their targets, they increase stability and lengthen the poly-A tails of non-target mRNAs. Furthermore, the expression of BTG3, TOB1, CSNK1A1 and ANKRD52 is negatively correlated with the expression of the miR-17-92 cluster in cancer cell lines. Our results suggest that the miR-17-92 miRNAs promote tumorigenesis not only by repression of key regulators, but also by posttranscriptional increases of global gene expression.
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Affiliation(s)
- Eunsun Jung
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Youngmo Seong
- Department of Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea
| | - Bohyun Jeon
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea
| | - Young-Soo Kwon
- Department of Bioscience & Biotechnology, Sejong University, Seoul 05006, Republic of Korea.
| | - Hoseok Song
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Republic of Korea.
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28
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Brody JR, Dixon DA. Complex HuR function in pancreatic cancer cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1469. [PMID: 29452455 DOI: 10.1002/wrna.1469] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/02/2018] [Accepted: 01/09/2018] [Indexed: 12/30/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is one of the most lethal cancers with dismal patient outcomes. The underlying core genetic drivers of disease have been identified in human tumor specimens and described in genetically engineered mouse models. These genetic drivers of PDAC include KRAS signaling, TP53 mutations, and genetic loss of the SMAD4 tumor suppressor protein. Beyond the known mutational landscape of PDAC genomes, alternative disrupted targets that extend beyond conventional genetic mutations have been elusive and understudied in the context of PDAC cell therapeutic resistance and survival. This last point is important because PDAC tumors have a unique and complex tumor microenvironment that includes hypoxic and nutrient-deprived niches that could select for cell populations that garner therapeutic resistance, explaining tumor heterogeneity in regards to response to different therapies. We and others have embarked in a line of investigation focused on the key molecular mechanism of posttranscriptional gene regulation that is altered in PDAC cells and supports this pro-survival phenotype intrinsic to PDAC cells. Specifically, the key regulator of this mechanism is a RNA-binding protein, HuR (ELAVL1), first described in cancer nearly two decades ago. Herein, we will provide a brief overview of the work demonstrating the importance of this RNA-binding protein in PDAC biology and then provide insight into ongoing work developing therapeutic strategies aimed at targeting this molecule in PDAC cells. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Jonathan R Brody
- Division of Surgical Research, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Jefferson Pancreas, Biliary and Related Cancer Center, Jefferson Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Dan A Dixon
- Department of Cancer Biology and University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, Kansas
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29
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West SM, Mecenas D, Gutwein M, Aristizábal-Corrales D, Piano F, Gunsalus KC. Developmental dynamics of gene expression and alternative polyadenylation in the Caenorhabditis elegans germline. Genome Biol 2018; 19:8. [PMID: 29368663 PMCID: PMC5784609 DOI: 10.1186/s13059-017-1369-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 12/03/2017] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND The 3' untranslated regions (UTRs) of mRNAs play a major role in post-transcriptional regulation of gene expression. Selection of transcript cleavage and polyadenylation sites is a dynamic process that produces multiple transcript isoforms for the same gene within and across different cell types. Using LITE-Seq, a new quantitative method to capture transcript 3' ends expressed in vivo, we have characterized sex- and cell type-specific transcriptome-wide changes in gene expression and 3'UTR diversity in Caenorhabditis elegans germline cells undergoing proliferation and differentiation. RESULTS We show that nearly half of germline transcripts are alternatively polyadenylated, that differential regulation of endogenous 3'UTR variants is common, and that alternative isoforms direct distinct spatiotemporal protein expression patterns in vivo. Dynamic expression profiling also reveals temporal regulation of X-linked gene expression, selective stabilization of transcripts, and strong evidence for a novel developmental program that promotes nucleolar dissolution in oocytes. We show that the RNA-binding protein NCL-1/Brat is a posttranscriptional regulator of numerous ribosome-related transcripts that acts through specific U-rich binding motifs to down-regulate mRNAs encoding ribosomal protein subunits, rRNA processing factors, and tRNA synthetases. CONCLUSIONS These results highlight the pervasive nature and functional potential of patterned gene and isoform expression during early animal development.
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Affiliation(s)
- Sean M West
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Desirea Mecenas
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Michelle Gutwein
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - David Aristizábal-Corrales
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA
| | - Fabio Piano
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
| | - Kristin C Gunsalus
- Center for Genomics & Systems Biology, Department of Biology, New York University, New York, NY, 10012, USA.
- Center for Genomics & Systems Biology, NYU Abu Dhabi, P.O. Box 129188, Saadiyat Island, Abu Dhabi, United Arab Emirates.
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30
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Mitra M, Lee HN, Coller HA. Determining Genome-wide Transcript Decay Rates in Proliferating and Quiescent Human Fibroblasts. J Vis Exp 2018. [PMID: 29364236 DOI: 10.3791/56423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Quiescence is a temporary, reversible state in which cells have ceased cell division, but retain the capacity to proliferate. Multiple studies, including ours, have demonstrated that quiescence is associated with widespread changes in gene expression. Some of these changes occur through changes in the level or activity of proliferation-associated transcription factors, such as E2F and MYC. We have demonstrated that mRNA decay can also contribute to changes in gene expression between proliferating and quiescent cells. In this protocol, we describe the procedure for establishing proliferating and quiescent cultures of human dermal foreskin fibroblasts. We then describe the procedures for inhibiting new transcription in proliferating and quiescent cells with Actinomycin D (ActD). ActD treatment represents a straightforward and reproducible approach to dissociating new transcription from transcript decay. A disadvantage of ActD treatment is that the time course must be limited to a short time frame because ActD affects cell viability. Transcript levels are monitored over time to determine transcript decay rates. This procedure allows for the identification of genes and isoforms that exhibit differential decay in proliferating versus quiescent fibroblasts.
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Affiliation(s)
- Mithun Mitra
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles; Department of Biological Chemistry, David Geffen School of Medicine
| | - Ha Neul Lee
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles; Department of Biological Chemistry, David Geffen School of Medicine; Molecular Biology Institute Interdepartmental Program, University of California, Los Angeles
| | - Hilary A Coller
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles; Department of Biological Chemistry, David Geffen School of Medicine; Molecular Biology Institute Interdepartmental Program, University of California, Los Angeles;
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31
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Charley PA, Wilusz CJ, Wilusz J. Identification of phlebovirus and arenavirus RNA sequences that stall and repress the exoribonuclease XRN1. J Biol Chem 2017; 293:285-295. [PMID: 29118186 DOI: 10.1074/jbc.m117.805796] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 11/06/2017] [Indexed: 12/22/2022] Open
Abstract
Regulated mRNA decay plays a vital role in determining both the level and quality of cellular gene expression. Viral RNAs must successfully evade this host RNA decay machinery to establish a productive infection. One way for RNA viruses to accomplish this is to target the cellular exoribonuclease XRN1, because this enzyme is accessible in the cytoplasm and plays a major role in mRNA decay. Members of the Flaviviridae use RNA structures in their 5'- or 3'-untranslated regions to stall and repress XRN1, effectively stabilizing viral RNAs while also causing significant dysregulation of host cell mRNA stability. Here, we use a series of biochemical assays to demonstrate that the 3'-terminal portion of the nucleocapsid (N) mRNA of Rift Valley fever virus, a phlebovirus of the Bunyaviridae family, also can effectively stall and repress XRN1. The region responsible for impeding XRN1 includes a G-rich portion that likely forms a G-quadruplex structure. The 3'-terminal portions of ambisense-derived transcripts of multiple arenaviruses also stalled XRN1. Therefore, we conclude that RNAs from two additional families of mammalian RNA viruses stall and repress XRN1. This observation. emphasizes the importance and commonality of this viral strategy to interfere with the 5'-to-3'-exoribonuclease component of the cytoplasmic RNA decay machinery.
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Affiliation(s)
- Phillida A Charley
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Carol J Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado 80523.
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32
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Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods 2017; 14:955-958. [PMID: 28846088 PMCID: PMC5623139 DOI: 10.1038/nmeth.4407] [Citation(s) in RCA: 620] [Impact Index Per Article: 88.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 07/13/2017] [Indexed: 11/20/2022]
Abstract
Single-nucleus RNA sequencing (sNuc-seq) profiles RNA from tissues that are preserved or cannot be dissociated, but it does not provide high throughput. Here, we develop DroNc-seq: massively parallel sNuc-seq with droplet technology. We profile 39,111 nuclei from mouse and human archived brain samples to demonstrate sensitive, efficient, and unbiased classification of cell types, paving the way for systematic charting of cell atlases.
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Affiliation(s)
- Naomi Habib
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
- Broad Institute of MIT and Harvard, Cambridge MA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
MA
| | | | - Anindita Basu
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Tyler Burks
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
| | - Karthik Shekhar
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
| | - Matan Hofree
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
| | - Sourav R. Choudhury
- Broad Institute of MIT and Harvard, Cambridge MA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
MA
| | | | | | | | - David A Weitz
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
- Department of Physics, Harvard University, Cambridge, MA
| | | | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge MA
- McGovern Institute, Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge
MA
| | - Aviv Regev
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge MA
- Howard Hughes Medical Institute, Department of Biology, Koch Institute of Integrative Cancer Research, Massachusetts
Institute of Technology, Cambridge MA
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Sharma S, Poetz F, Bruer M, Ly-Hartig TBN, Schott J, Séraphin B, Stoecklin G. Acetylation-Dependent Control of Global Poly(A) RNA Degradation by CBP/p300 and HDAC1/2. Mol Cell 2017; 63:927-38. [PMID: 27635759 DOI: 10.1016/j.molcel.2016.08.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 05/09/2016] [Accepted: 08/24/2016] [Indexed: 12/31/2022]
Abstract
Acetylation of histones and transcription-related factors is known to exert epigenetic and transcriptional control of gene expression. Here we report that histone acetyltransferases (HATs) and histone deacetylases (HDACs) also regulate gene expression at the posttranscriptional level by controlling poly(A) RNA stability. Inhibition of HDAC1 and HDAC2 induces massive and widespread degradation of normally stable poly(A) RNA in mammalian and Drosophila cells. Acetylation-induced RNA decay depends on the HATs p300 and CBP, which acetylate the exoribonuclease CAF1a, a catalytic subunit of the CCR4-CAF1-NOT deadenlyase complex and thereby contribute to accelerating poly(A) RNA degradation. Taking adipocyte differentiation as a model, we observe global stabilization of poly(A) RNA during differentiation, concomitant with loss of CBP/p300 expression. Our study uncovers reversible acetylation as a fundamental switch by which HATs and HDACs control the overall turnover of poly(A) RNA.
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Affiliation(s)
- Sahil Sharma
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Fabian Poetz
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Marius Bruer
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Thi Bach Nga Ly-Hartig
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Johanna Schott
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch, France; Centre National de Recherche Scientifique (CNRS) UMR 7104, 67404 Illkirch, France; INSERM U964, 67404 Illkirch, France; Université de Strasbourg, 67404 Illkirch, France
| | - Georg Stoecklin
- Division of Biochemistry, Center for Biomedicine and Medical Technology Mannheim (CBTM), Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany; Center for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
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Techasintana P, Ellis JS, Glascock J, Gubin MM, Ridenhour SE, Magee JD, Hart ML, Yao P, Zhou H, Whitney MS, Franklin CL, Martindale JL, Gorospe M, Davis WJ, Fox PL, Li X, Atasoy U. The RNA-Binding Protein HuR Posttranscriptionally Regulates IL-2 Homeostasis and CD4 + Th2 Differentiation. Immunohorizons 2017; 1:109-123. [PMID: 30035254 PMCID: PMC6052877 DOI: 10.4049/immunohorizons.1700017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Posttranscriptional gene regulation by RNA-binding proteins, such as HuR (elavl1), fine-tune gene expression in T cells, leading to powerful effects on immune responses. HuR can stabilize target mRNAs and/or promote translation by interacting with their 3' untranslated region adenylate and uridylate-rich elements. It was previously demonstrated that HuR facilitates Th2 cytokine expression by mRNA stabilization. However, its effects upon IL-2 homeostasis and CD4+ Th2 differentiation are not as well understood. We found that optimal translation of Il2ra (CD25) required interaction of its mRNA with HuR. Conditional HuR knockout in CD4+ T cells resulted in loss of IL-2 homeostasis and defects in JAK-STAT signaling, Th2 differentiation, and cytokine production. HuR-knockout CD4+ T cells from OVA-immunized mice also failed to proliferate in response to Ag. These results demonstrate that HuR plays a pivotal role in maintaining normal IL-2 homeostasis and initiating CD4+ Th2 differentiation.
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Affiliation(s)
- Patsharaporn Techasintana
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Jason S. Ellis
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Jacqueline Glascock
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Matthew M. Gubin
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Suzanne E. Ridenhour
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Joseph D. Magee
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
| | - Marcia L. Hart
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201
| | - Peng Yao
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Hao Zhou
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Maryln S. Whitney
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201
| | - Craig L. Franklin
- Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201
| | | | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging, Baltimore, MD 21224
| | - Wade J. Davis
- Department of Biostatistics, University of Missouri, Columbia, MO 65212
| | - Paul L. Fox
- Department of Cellular and Molecular Medicine, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Xiaoxia Li
- Department of Immunology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH 44195
| | - Ulus Atasoy
- Department of Surgery, University of Missouri, Columbia, MO 65212
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65212
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Loupasakis K, Kuo D, Sokhi UK, Sohn C, Syracuse B, Giannopoulou EG, Park SH, Kang H, Rätsch G, Ivashkiv LB, Kalliolias GD. Tumor Necrosis Factor dynamically regulates the mRNA stabilome in rheumatoid arthritis fibroblast-like synoviocytes. PLoS One 2017; 12:e0179762. [PMID: 28708839 PMCID: PMC5510804 DOI: 10.1371/journal.pone.0179762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 06/02/2017] [Indexed: 12/29/2022] Open
Abstract
During rheumatoid arthritis (RA), Tumor Necrosis Factor (TNF) activates fibroblast-like synoviocytes (FLS) inducing in a temporal order a constellation of genes, which perpetuate synovial inflammation. Although the molecular mechanisms regulating TNF-induced transcription are well characterized, little is known about the impact of mRNA stability on gene expression and the impact of TNF on decay rates of mRNA transcripts in FLS. To address these issues we performed RNA sequencing and genome-wide analysis of the mRNA stabilome in RA FLS. We found that TNF induces a biphasic gene expression program: initially, the inducible transcriptome consists primarily of unstable transcripts but progressively switches and becomes dominated by very stable transcripts. This temporal switch is due to: a) TNF-induced prolonged stabilization of previously unstable transcripts that enables progressive transcript accumulation over days and b) sustained expression and late induction of very stable transcripts. TNF-induced mRNA stabilization in RA FLS occurs during the late phase of TNF response, is MAPK-dependent, and involves several genes with pathogenic potential such as IL6, CXCL1, CXCL3, CXCL8/IL8, CCL2, and PTGS2. These results provide the first insights into genome-wide regulation of mRNA stability in RA FLS and highlight the potential contribution of dynamic regulation of the mRNA stabilome by TNF to chronic synovitis.
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Affiliation(s)
- Konstantinos Loupasakis
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - David Kuo
- Graduate Program in Physiology, Biophysics and Systems Biology, Weill Cornell Graduate School of Medical Sciences, New York, United States of America
- Computational Biology Program, Sloan Kettering Institute, New York, United States of America
| | - Upneet K. Sokhi
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Christopher Sohn
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Bethany Syracuse
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Eugenia G. Giannopoulou
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, United States of America
| | - Sung Ho Park
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - Hyelim Kang
- Biological Sciences Department, New York City College of Technology, City University of New York, Brooklyn, United States of America
| | - Gunnar Rätsch
- Computational Biology Program, Sloan Kettering Institute, New York, United States of America
- Department of Computer Science, ETH Zürich, Zürich, Switzerland
| | - Lionel B. Ivashkiv
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
| | - George D. Kalliolias
- Arthritis and Tissue Degeneration Program and David Z. Rosensweig Genomics Research Center, Hospital for Special Surgery, New York, United States of America
- * E-mail:
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36
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Cardoso FM, Tomkova M, Petrovajova D, Bubanova M, Ragac O, Hornakova T. New and cost effective cell-based assay for Dialyzed Leukocyte Extract (DLE)-induced Jurkat cells proliferation under azathioprine treatment. J Pharm Biomed Anal 2017; 138:100-108. [PMID: 28189890 DOI: 10.1016/j.jpba.2017.01.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 01/23/2017] [Accepted: 01/26/2017] [Indexed: 11/16/2022]
Abstract
The human Dialyzed Leukocyte Extract (DLE) is a heterogeneous mix of oligopeptides of <10kDa, extracted from leukocytes of healthy donors. There is significant clinical evidence of improvement using DLE during treatment of allergies, cancer,immunodeficiencies, and in mycotic and viral infections. Nevertheless, the DLE exact nature and mechanism of action have been elusive for more than 50 years. DLE biological activity testing is necessary in DLE production and quality control. Both in vitro and in vivo assays exist: E-rosette test, induction of delayed type hypersensitivity in mice, leukocyte migration and IFN-γ secretion. The animal-origin materials and in vivo assays convey a considerable logistic, ethic and economic burden, meanwhile the available in vitro assays have been reported with limited reproducibility and sometimes contradictory results. Here we are reporting a new DLE biological activity cell-based assay. The A20 and Jurkat cell lines were treated with (+Aza) or without (-Aza) azathioprine, DLE (+DLE) or both (+Aza/+DLE). After 72h, the cell proliferation was analyzed by the MTT or BrdU incorporation assays. In +Aza/+DLE treated cells, we observed a significant higher proliferation, when compared with +Aza/-DLE. In the absence of Aza, cells did not present any proliferation difference between -DLE or +DLE treatments. Both assays, MTT and BrdU showed similar results, being the MTT test more cost effective and we select it for validation as DLE biological assay using Jurkat cells only. We tested three different lyophilized DLE batches and we found consistent results with acceptable assay reproducibility and linearity. The DLE capacity for rescuing Jurkat cell proliferation during +Aza treatment was consistent using different liquid and lyophilized DLE batches, presenting also consistent chromatographic profiles. Finally, DLE treatment in Jurkat cells did not result into significant IL-2 of IFN-γ secretion, and known lymphocyte proliferative drugs failed to rescue Jurkat cells viability in presence of +Aza, as +DLE treatment did in our MTT assay. In conclusion, our new cell-based MTT assay has excellent DLE biological activity consistency, robustness and is cost effective, presenting important advantages over previous DLE activity in vitro and in vivo assays.
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Affiliation(s)
- F M Cardoso
- R&D Department, Imuna Pharm a. s., Jarková 17, 082 22 Šarišské Michaľany, Slovak Republic.
| | - M Tomkova
- R&D Department, Imuna Pharm a. s., Jarková 17, 082 22 Šarišské Michaľany, Slovak Republic
| | - D Petrovajova
- R&D Department, Imuna Pharm a. s., Jarková 17, 082 22 Šarišské Michaľany, Slovak Republic
| | - M Bubanova
- R&D Department, Imuna Pharm a. s., Jarková 17, 082 22 Šarišské Michaľany, Slovak Republic
| | - O Ragac
- R&D Department, Imuna Pharm a. s., Jarková 17, 082 22 Šarišské Michaľany, Slovak Republic
| | - T Hornakova
- R&D Department, Imuna Pharm a. s., Jarková 17, 082 22 Šarišské Michaľany, Slovak Republic; Olomouc University Social Health Institute (OUSHI), Univerzitní 22, 771 11 Olomouc, Czech Republic
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37
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MDH2 is an RNA binding protein involved in downregulation of sodium channel Scn1a expression under seizure condition. Biochim Biophys Acta Mol Basis Dis 2017; 1863:1492-1499. [PMID: 28433711 DOI: 10.1016/j.bbadis.2017.04.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/31/2017] [Accepted: 04/18/2017] [Indexed: 12/13/2022]
Abstract
Voltage-gated sodium channel α-subunit type I (NaV1.1, encoded by SCN1A gene) plays a critical role in the excitability of brain. Downregulation of SCN1A expression is associated with epilepsy, a common neurological disorder characterized by recurrent seizures. Here we reveal a novel role of malate dehydrogenase 2 (MDH2) in the posttranscriptional regulation of SCN1A expression under seizure condition. We identified that MDH2 was an RNA binding protein that could bind two of the four conserved regions in the 3' UTRs of SCN1A. We further showed that knockdown of MDH2 or inactivation of MDH2 activity in HEK-293 cells increased the reporter gene expression through the 3' UTR of SCN1A, and MDH2 overexpression decreased gene expression by affecting mRNA stability. In the hippocampus of seizure mice, the upregulation of MDH2 expression contributed to the decrease of the NaV1.1 levels at posttranscriptional level. In addition, we showed that the H2O2 levels increased in the hippocampus of the seizure mice, and H2O2 could promote the binding of MDH2 to the binding sites of Scn1a gene, whereas β-mercaptoethanol decreased the binding capability, indicating an important effect of the seizure-induced oxidation on the MDH2-mediated downregulation of Scn1a expression. Taken together, these data suggest that MDH2, functioning as an RNA-binding protein, is involved in the posttranscriptional downregulation of SCN1A expression under seizure condition.
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38
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Michel M, Demel C, Zacher B, Schwalb B, Krebs S, Blum H, Gagneur J, Cramer P. TT-seq captures enhancer landscapes immediately after T-cell stimulation. Mol Syst Biol 2017; 13:920. [PMID: 28270558 PMCID: PMC5371733 DOI: 10.15252/msb.20167507] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
To monitor transcriptional regulation in human cells, rapid changes in enhancer and promoter activity must be captured with high sensitivity and temporal resolution. Here, we show that the recently established protocol TT-seq ("transient transcriptome sequencing") can monitor rapid changes in transcription from enhancers and promoters during the immediate response of T cells to ionomycin and phorbol 12-myristate 13-acetate (PMA). TT-seq maps eRNAs and mRNAs every 5 min after T-cell stimulation with high sensitivity and identifies many new primary response genes. TT-seq reveals that the synthesis of 1,601 eRNAs and 650 mRNAs changes significantly within only 15 min after stimulation, when standard RNA-seq does not detect differentially expressed genes. Transcription of enhancers that are primed for activation by nucleosome depletion can occur immediately and simultaneously with transcription of target gene promoters. Our results indicate that enhancer transcription is a good proxy for enhancer regulatory activity in target gene activation, and establish TT-seq as a tool for monitoring the dynamics of enhancer landscapes and transcription programs during cellular responses and differentiation.
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Affiliation(s)
- Margaux Michel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Carina Demel
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Benedikt Zacher
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Björn Schwalb
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Krebs
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Helmut Blum
- Gene Center Munich, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Julien Gagneur
- Department of Informatics, Technische Universität München, Garching, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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39
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Galectin-3 is a non-classic RNA binding protein that stabilizes the mucin MUC4 mRNA in the cytoplasm of cancer cells. Sci Rep 2017; 7:43927. [PMID: 28262838 PMCID: PMC5338267 DOI: 10.1038/srep43927] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/01/2017] [Indexed: 12/22/2022] Open
Abstract
Pancreatic cancer cells express high levels of MUC1, MUC4 and MUC16 mRNAs that encode membrane-bound mucins. These mRNAs share unusual features such as a long half-life. However, it remains unknown how mucin mRNA stability is regulated. Galectin-3 (Gal-3) is an endogenous lectin playing important biological functions in epithelial cells. Gal-3 is encoded by LGALS3 which is up-regulated in pancreatic cancer. Despite the absence of a RNA-recognition motif, Gal-3 interacts indirectly with pre-mRNAs in the nucleus and promotes constitutive splicing. However a broader role of Gal-3 in mRNA fate is unexplored. We report herein that Gal-3 increases MUC4 mRNA stability through an intermediate, hnRNP-L which binds to a conserved CA repeat element in the 3′UTR in a Gal-3 dependent manner and also controls Muc4 mRNA levels in epithelial tissues of Gal3−/− mice. Gal-3 interacts with hnRNP-L in the cytoplasm, especially during cell mitosis, but only partly associates with protein markers of P-Bodies or Stress Granules. By RNA-IP plus RNA-seq analysis and imaging, we demonstrate that Gal-3 binds to mature spliced MUC4 mRNA in the perinuclear region, probably in hnRNP-L-containing RNA granules. Our findings highlight a new role for Gal-3 as a non-classic RNA-binding protein that regulates MUC4 mRNA post-transcriptionally.
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40
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Metabolic labeling and recovery of nascent RNA to accurately quantify mRNA stability. Methods 2017; 120:39-48. [PMID: 28219744 DOI: 10.1016/j.ymeth.2017.02.003] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 02/10/2017] [Accepted: 02/14/2017] [Indexed: 12/26/2022] Open
Abstract
Changes in the rate of mRNA decay are closely coordinated with transcriptional changes and together these events have profound effects on gene expression during development and disease. Traditional approaches to assess mRNA decay have relied on inhibition of transcription, which can alter mRNA decay rates and confound interpretation. More recently, metabolic labeling combined with chemical modification and fractionation of labeled RNAs has allowed the isolation of nascent transcripts and the subsequent calculation of mRNA decay rates. This approach has been widely adopted for measuring mRNA half-lives on a global scale, but has proven challenging to use for analysis of single genes. We present a series of normalization and quality assurance steps to be used in combination with 4-thiouridine pulse labeling of cultured eukaryotic cells. Importantly, we demonstrate how the relative amount of 4sU-labeled nascent RNA influences accurate quantification. The approach described facilitates reproducible measurement of individual mRNA half-lives using 4-thiouridine and could be adapted for use with other nucleoside analogs.
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41
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Johnson EL, Robinson DG, Coller HA. Widespread changes in mRNA stability contribute to quiescence-specific gene expression patterns in a fibroblast model of quiescence. BMC Genomics 2017; 18:123. [PMID: 28143407 PMCID: PMC5286691 DOI: 10.1186/s12864-017-3521-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/26/2017] [Indexed: 01/29/2023] Open
Abstract
Background Quiescence, reversible exit from the cell division cycle, is characterized by large-scale changes in steady-state gene expression, yet mechanisms controlling these changes are in need of further elucidation. In order to characterize the effects of post-transcriptional control on the quiescent transcriptome in human fibroblasts, we determined mRNA decay rates for over 10,000 genes using a transcription shut-off time-course. Results We found that ~500 of the genes monitored exhibited significant changes in decay rate upon quiescence induction. Genes involved in RNA processing and ribosome biogenesis were destabilized with quiescence, while genes involved in the developmental process were stabilized with quiescence. Moreover, extracellular matrix genes demonstrated an upregulation of gene expression that corresponded with a stabilization of these transcripts. Additionally, targets of a quiescence-associated microRNA (miR-29) were significantly enriched in the fraction of transcripts that were stabilized during quiescence. Conclusion Coordinated stability changes in clusters of genes with important functions in fibroblast quiescence maintenance are highly correlated with quiescence gene expression patterns. Analysis of miR-29 target decay rates suggests that microRNA-induced changes in RNA stability are important contributors to the quiescence gene expression program in fibroblasts. The identification of multiple stability-related gene clusters suggests that other posttranscriptional regulators of transcript stability may contribute to the coordination of quiescence gene expression. Such regulators may ultimately prove to be valuable targets for therapeutics that target proliferative cells, for instance, in cancer or fibrosis. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3521-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elizabeth L Johnson
- Department of Molecular Biology, Princeton University, Princeton, NJ, 08544, USA
| | - David G Robinson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, 08544, USA
| | - Hilary A Coller
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA. .,Department of Biological Chemistry, David Geffen School of Medicine, Los Angeles, CA, 90095, USA.
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THZ1 targeting CDK7 suppresses STAT transcriptional activity and sensitizes T-cell lymphomas to BCL2 inhibitors. Nat Commun 2017; 8:14290. [PMID: 28134252 PMCID: PMC5290269 DOI: 10.1038/ncomms14290] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 12/14/2016] [Indexed: 12/29/2022] Open
Abstract
Peripheral T-cell lymphomas (PTCL) are aggressive diseases with poor response to chemotherapy and dismal survival. Identification of effective strategies to target PTCL biology represents an urgent need. Here we report that PTCL are sensitive to transcription-targeting drugs, and, in particular, to THZ1, a covalent inhibitor of cyclin-dependent kinase 7 (CDK7). The STAT-signalling pathway is highly vulnerable to THZ1 even in PTCL cells that carry the activating STAT3 mutation Y640F. In mutant cells, CDK7 inhibition decreases STAT3 chromatin binding and expression of highly transcribed target genes like MYC, PIM1, MCL1, CD30, IL2RA, CDC25A and IL4R. In surviving cells, THZ1 decreases the expression of STAT-regulated anti-apoptotic BH3 family members MCL1 and BCL-XL sensitizing PTCL cells to BH3 mimetic drugs. Accordingly, the combination of THZ1 and the BH3 mimetic obatoclax improves lymphoma growth control in a primary PTCL ex vivo culture and in two STAT3-mutant PTCL xenografts, delineating a potential targeted agent-based therapeutic option for these patients. T-cell lymphomas are aggressive diseases associated with poor outcome. Here, the authors show that the THZ1, a CDK7 inhibitor, suppresses STAT transcriptional activity leading to apoptosis and sensitization to BCL2 inhibitors in T-cell lymphomas.
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43
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Ferizi M, Aneja MK, Balmayor ER, Badieyan ZS, Mykhaylyk O, Rudolph C, Plank C. Human cellular CYBA UTR sequences increase mRNA translation without affecting the half-life of recombinant RNA transcripts. Sci Rep 2016; 6:39149. [PMID: 27974853 PMCID: PMC5156912 DOI: 10.1038/srep39149] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 11/18/2016] [Indexed: 12/24/2022] Open
Abstract
Modified nucleotide chemistries that increase the half-life (T1/2) of transfected recombinant mRNA and the use of non-native 5'- and 3'-untranslated region (UTR) sequences that enhance protein translation are advancing the prospects of transcript therapy. To this end, a set of UTR sequences that are present in mRNAs with long cellular T1/2 were synthesized and cloned as five different recombinant sequence set combinations as upstream 5'-UTR and/or downstream 3'-UTR regions flanking a reporter gene. Initial screening in two different cell systems in vitro revealed that cytochrome b-245 alpha chain (CYBA) combinations performed the best among all other UTR combinations and were characterized in detail. The presence or absence of CYBA UTRs had no impact on the mRNA stability of transfected mRNAs, but appeared to enhance the productivity of transfected transcripts based on the measurement of mRNA and protein levels in cells. When CYBA UTRs were fused to human bone morphogenetic protein 2 (hBMP2) coding sequence, the recombinant mRNA transcripts upon transfection produced higher levels of protein as compared to control transcripts. Moreover, transfection of human adipose mesenchymal stem cells with recombinant hBMP2-CYBA UTR transcripts induced bone differentiation demonstrating the osteogenic and therapeutic potential for transcript therapy based on hybrid UTR designs.
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Affiliation(s)
- Mehrije Ferizi
- Institute of Molecular Immunology- Experimental Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
- Ethris GmbH, Planegg, 82152, Germany
| | | | - Elizabeth R. Balmayor
- Experimental Trauma Surgery, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Zohreh Sadat Badieyan
- Institute of Molecular Immunology- Experimental Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
| | - Olga Mykhaylyk
- Institute of Molecular Immunology- Experimental Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
- Ethris GmbH, Planegg, 82152, Germany
| | | | - Christian Plank
- Institute of Molecular Immunology- Experimental Oncology, Klinikum rechts der Isar, Technische Universität München, Munich, 81675, Germany
- Ethris GmbH, Planegg, 82152, Germany
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La Porta J, Matus-Nicodemos R, Valentín-Acevedo A, Covey LR. The RNA-Binding Protein, Polypyrimidine Tract-Binding Protein 1 (PTBP1) Is a Key Regulator of CD4 T Cell Activation. PLoS One 2016; 11:e0158708. [PMID: 27513449 PMCID: PMC4981342 DOI: 10.1371/journal.pone.0158708] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 06/21/2016] [Indexed: 02/07/2023] Open
Abstract
We have previously shown that the RNA binding protein, polypyrimidine tract-binding protein (PTBP1) plays a critical role in regulating the expression of CD40L in activated CD4 T cells. This is achieved mechanistically through message stabilization at late times of activation as well as by altered distribution of CD40L mRNA within distinct cellular compartments. PTBP1 has been implicated in many different processes, however whether PTBP1 plays a broader role in CD4 T cell activation is not known. To examine this question, experiments were designed to introduce shRNA into primary human CD4 T cells to achieve decreased, but not complete ablation of PTBP1 expression. Analyses of shPTB-expressing CD4 T cells revealed multiple processes including cell proliferation, activation-induced cell death and expression of activation markers and cytokines that were regulated in part by PTBP1 expression. Although there was an overall decrease in the steady-state level of several activation genes, only IL-2 and CD40L appeared to be regulated by PTBP1 at the level of RNA decay suggesting that PTBP1 is critical at different regulatory steps of expression that is gene-specific. Importantly, even though the IL-2 protein levels were reduced in cells with lowered PTBP1, the steady-state level of IL-2 mRNA was significantly higher in these cells suggesting a block at the translational level. Evaluation of T cell activation in shPTB-expressing T cells revealed that PTBP1 was linked primarily to the activation of the PLCγ1/ERK1/2 and the NF-κB pathways. Overall, our results reveal the importance of this critical RNA binding protein in multiple steps of T cell activation.
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Affiliation(s)
- James La Porta
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Rodrigo Matus-Nicodemos
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Aníbal Valentín-Acevedo
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, New Jersey, United States of America
| | - Lori R. Covey
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, New Jersey, United States of America
- * E-mail:
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Targeted mRNA Decay by RNA Binding Protein AUF1 Regulates Adult Muscle Stem Cell Fate, Promoting Skeletal Muscle Integrity. Cell Rep 2016; 16:1379-1390. [PMID: 27452471 DOI: 10.1016/j.celrep.2016.06.095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 05/26/2016] [Accepted: 06/29/2016] [Indexed: 12/16/2022] Open
Abstract
Following skeletal muscle injury, muscle stem cells (satellite cells) are activated, proliferate, and differentiate to form myofibers. We show that mRNA-decay protein AUF1 regulates satellite cell function through targeted degradation of specific mRNAs containing 3' AU-rich elements (AREs). auf1(-/-) mice undergo accelerated skeletal muscle wasting with age and impaired skeletal muscle repair following injury. Satellite cell mRNA analysis and regeneration studies demonstrate that auf1(-/-) satellite cell self-renewal is impaired due to increased stability and overexpression of ARE-mRNAs, including cell-autonomous overexpression of matrix metalloprotease MMP9. Secreted MMP9 degrades the skeletal muscle matrix, preventing satellite-cell-mediated regeneration and return to quiescence. Blocking MMP9 activity in auf1(-/-) mice restores skeletal muscle repair and maintenance of the satellite cell population. Control of ARE-mRNA decay by AUF1 represents a mechanism for adult stem cell regulation and is implicated in human skeletal muscle wasting diseases.
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Istomine R, Pavey N, Piccirillo CA. Posttranscriptional and Translational Control of Gene Regulation in CD4+ T Cell Subsets. THE JOURNAL OF IMMUNOLOGY 2016; 196:533-40. [PMID: 26747571 DOI: 10.4049/jimmunol.1501337] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The immune system is under strict regulatory control to ensure homeostasis of inflammatory responses, lying dormant when not needed but quick to act when called upon. Small changes in gene expression can lead to drastic changes in lineage commitment, cellular function, and immunity. Conventional assessment of these changes centered on the analysis of mRNA levels through a variety of methodologies, including microarrays. However, mRNA synthesis does not always correlate directly to protein synthesis and downstream functional activity. Work conducted in recent years has begun to shed light on the various posttranscriptional changes that occur in response to a dynamic external environment that a given cell type encounters. We provide a critical review of key posttranscriptional mechanisms (i.e., microRNA) and translational mechanisms of regulation of gene expression in the immune system, with a particular emphasis on these regulatory processes in various CD4(+) T cell subsets.
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Affiliation(s)
- Roman Istomine
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;Translational Immunology Unit, Program in Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada; andFederation of Clinical Immunology Societies Center of Excellence, McGill University and the Research Institute of the McGill University Health Center, Montreal, Quebec H3H 2R9, Canada
| | - Nils Pavey
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;Translational Immunology Unit, Program in Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada; andFederation of Clinical Immunology Societies Center of Excellence, McGill University and the Research Institute of the McGill University Health Center, Montreal, Quebec H3H 2R9, Canada
| | - Ciriaco A Piccirillo
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec H3A 2B4, Canada;Translational Immunology Unit, Program in Infectious Disease and Immunity in Global Health, Research Institute of the McGill University Health Center, Montreal, Quebec H4A 3J1, Canada; andFederation of Clinical Immunology Societies Center of Excellence, McGill University and the Research Institute of the McGill University Health Center, Montreal, Quebec H3H 2R9, Canada
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Affiliation(s)
- Carola G. Vinuesa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia;
| | - Michelle A. Linterman
- Lymphocyte Signalling and Development Institute Strategic Programme, Babraham Institute, Cambridge CB22 3AT, United Kingdom;
| | - Di Yu
- Laboratory for Molecular Immunomodulation, Department of Biochemistry and Molecular Biology, and Center for Inflammatory Diseases, Monash University, Melbourne, Victoria 3800, Australia;
| | - Ian C.M. MacLennan
- School of Immunity and Infection, University of Birmingham, Birmingham B15 2TT, United Kingdom
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48
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Morón-López S, Gómez-Mora E, Salgado M, Ouchi D, Puertas MC, Urrea V, Navarro J, Jou A, Pérez M, Tural C, Clotet B, Montaner LJ, Blanco J, Crespo M, Martinez-Picado J. Short-term Treatment With Interferon Alfa Diminishes Expression of HIV-1 and Reduces CD4+ T-Cell Activation in Patients Coinfected With HIV and Hepatitis C Virus and Receiving Antiretroviral Therapy. J Infect Dis 2015; 213:1008-12. [PMID: 26525407 DOI: 10.1093/infdis/jiv521] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2015] [Accepted: 10/22/2015] [Indexed: 11/12/2022] Open
Abstract
Long-term treatment with interferon (IFN) alfa plus ribavirin decreases the proviral human immunodeficiency virus type 1 (HIV) DNA level. However, the short-term impact of IFN alfa on persistent HIV and its effects on immune activation after antiretroviral therapy remain unknown. Our study showed that the cell-associated HIV RNA level and CD4(+) T-cell activation decreased in the IFN group (n = 10). No changes were detected in levels of residual plasma viremia, replication-competent reservoirs, proviral DNA, or 2-long-terminal repeat circles, although APOBEC3G, TRIM5α, BST2, and TRIM22 were upregulated in the IFN group. These data suggest that short-term treatment with IFN alfa combined with RBV decreases HIV expression, in part through inhibition of HIV transcription by TRIM22 and decrease in T-cell activation.
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Affiliation(s)
- Sara Morón-López
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona
| | - Elisabet Gómez-Mora
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona
| | - Maria Salgado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona
| | - Dan Ouchi
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona
| | - Maria C Puertas
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona
| | - Víctor Urrea
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona
| | - Jordi Navarro
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron
| | - Antoni Jou
- Fundació Lluita Contra la SIDA, Badalona
| | - Mercedes Pérez
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron
| | | | - Bonaventura Clotet
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona Fundació Lluita Contra la SIDA, Badalona Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | | | - Julià Blanco
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
| | - Manuel Crespo
- Infectious Diseases Department, Hospital Universitari Vall d'Hebron
| | - Javier Martinez-Picado
- AIDS Research Institute IrsiCaixa, Institut d'Investigació en Cièncias de la Salut Germans Trias i Pujol, Universitat Autònoma de Barcelona Institució Catalana de Recerca i Estudis Avançats, Barcelona Universitat de Vic-Universitat Central de Catalunya, Vic, Spain
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49
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Blackinton JG, Keene JD. Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation. Nucleic Acids Res 2015; 44:426-36. [PMID: 26490963 PMCID: PMC4705648 DOI: 10.1093/nar/gkv1066] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/05/2015] [Indexed: 01/30/2023] Open
Abstract
Global mRNA abundance depends on the balance of synthesis and decay of a population of mRNAs. To account for this balance during activation of T cells, we used metabolic labeling to quantify the contributions of RNA transcription and decay over a 4 h time course during activation of leukemia-derived Jurkat T cells. While prior studies suggested more than half of the changes in mRNA abundance were due to RNA stability, we found a smaller but more interesting population of mRNAs changed stability. These mRNAs clustered into functionally related subpopulations that included replicative histones, ribosomal biogenesis and cell motility functions. We then applied a novel analysis based on integrating global protein-RNA binding with concurrent changes in RNA stability at specific time points following activation. This analysis demonstrated robust stabilization of mRNAs by the HuR RNA-binding protein 4 h after activation. Our unexpected findings demonstrate that the temporal regulation of mRNA stability coordinates vital cellular pathways and is in part controlled by the HuR RNA binding protein in Jurkat T cells following activation.
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Affiliation(s)
- Jeff G Blackinton
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
| | - Jack D Keene
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA
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50
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Jiang SH, Shen N, Vinuesa CG. Posttranscriptional T cell gene regulation to limit Tfh cells and autoimmunity. Curr Opin Immunol 2015; 37:21-7. [PMID: 26432764 DOI: 10.1016/j.coi.2015.09.003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 08/23/2015] [Accepted: 09/10/2015] [Indexed: 01/06/2023]
Abstract
T follicular helper (Tfh) cells are crucial to induce protective extrafollicular and germinal center antibody responses against protein antigens. Over the last decade, control of Tfh cell numbers has emerged as an important regulatory checkpoint which, when perturbed, may lead to production of autoantibodies. Recent progress in understanding how Tfh cells are kept limiting has revealed an important role for posttranscriptional control of gene expression mediated by microRNAs such as miR-17 ∼ 92, miR-155 and miR-146a, and the RNA-binding proteins Roquin and Regnase. Additionally, T cell microRNAs dysregulated in patients with systemic lupus erythematosus have been shown to influence processes such as DNA hypomethylation, IL-2 and CCL5 secretion, and Treg function, which contribute to autoantibody formation and tissue damage.
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Affiliation(s)
- Simon H Jiang
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research and Centre for Personalised Immunology, Australian National University, Canberra, Australia; Department of Renal Medicine, The Canberra Hospital, Canberra, Australia; China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, China and Australian National University, Australia.
| | - Nan Shen
- China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, China and Australian National University, Australia; Joint Molecular Rheumatology Laboratory of the Institute of Health Sciences and Shanghai Renji Hospital, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Carola G Vinuesa
- Department of Immunology and Infectious Disease, John Curtin School of Medical Research and Centre for Personalised Immunology, Australian National University, Canberra, Australia; China Australia Centre for Personalised Immunology, Shanghai Renji Hospital, China and Australian National University, Australia.
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