1
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Mancino M, Lai G, De Grossi F, Cuomo A, Manganaro L, Butta GM, Ferrari I, Vicenzi E, Poli G, Pesce E, Oliveto S, Biffo S, Manfrini N. FAM46C Is an Interferon-Stimulated Gene That Inhibits Lentiviral Particle Production by Modulating Autophagy. Microbiol Spectr 2023; 11:e0521122. [PMID: 37358411 PMCID: PMC10434054 DOI: 10.1128/spectrum.05211-22] [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: 12/22/2022] [Accepted: 06/02/2023] [Indexed: 06/27/2023] Open
Abstract
FAM46C is a multiple myeloma (MM) tumor suppressor whose function is only starting to be elucidated. We recently showed that in MM cells FAM46C triggers apoptosis by inhibiting autophagy and altering intracellular trafficking and protein secretion. To date, both a physiological characterization of FAM46C role and an assessment of FAM46C-induced phenotypes outside of MM are lacking. Preliminary reports suggested an involvement of FAM46C with regulation of viral replication, but this was never confirmed. Here, we show that FAM46C is an interferon-stimulated gene and that the expression of wild-type FAM46C in HEK-293T cells, but not of its most frequently found mutant variants, inhibits the production of both HIV-1-derived and HIV-1 lentiviruses. We demonstrate that this effect does not require transcriptional regulation and does not depend on inhibition of either global or virus-specific translation but rather mostly relies on FAM46C-induced deregulation of autophagy, a pathway that we show to be required for efficient lentiviral particle production. These studies not only provide new insights on the physiological role of the FAM46C protein but also could help in implementing more efficient antiviral strategies on one side and lentiviral particle production approaches on the other. IMPORTANCE FAM46C role has been thoroughly investigated in MM, but studies characterizing its role outside of the tumoral environment are still lacking. Despite the success of antiretroviral therapy in suppressing HIV load to undetectable levels, there is currently no HIV cure, and treatment is lifelong. Indeed, HIV continues to be a major global public health issue. Here, we show that FAM46C expression in HEK-293T cells inhibits the production of both HIV and HIV-derived lentiviruses. We also demonstrate that such inhibitory effect relies, at least in part, on the well-established regulatory role that FAM46C exerts on autophagy. Deciphering the molecular mechanism underlying this regulation will not only facilitate the understanding of FAM46C physiological role but also give new insights on the interplay between HIV and the cellular environment.
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Affiliation(s)
- Marilena Mancino
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Giancarlo Lai
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | | | - Alessandro Cuomo
- Department of Experimental Oncology, IEO, European Institute of Oncology IRCCS, Milan, Italy
| | - Lara Manganaro
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Giacomo M. Butta
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Pharmacological and Biomolecular Sciences, University of Milan, Milan, Italy
| | - Ivan Ferrari
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
| | - Guido Poli
- Viral Pathogenesis and Biosafety Unit, San Raffaele Scientific Institute, Milan, Italy
- Vita-Salute San Raffaele University School of Medicine, Milan, Italy
| | - Elisa Pesce
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Stefania Oliveto
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
| | - Nicola Manfrini
- INGM, Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
- Department of Biosciences, University of Milan, Milan, Italy
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2
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Baghdadi H, Heidari R, Zavvar M, Ahmadi N, Shakouri Khomartash M, Vahidi M, Mohammadimehr M, Bashash D, Ghorbani M. Long Non-Coding RNA Signatures in Lymphopoiesis and Lymphoid Malignancies. Noncoding RNA 2023; 9:44. [PMID: 37624036 PMCID: PMC10458434 DOI: 10.3390/ncrna9040044] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/09/2023] [Accepted: 07/27/2023] [Indexed: 08/26/2023] Open
Abstract
Lymphoid cells play a critical role in the immune system, which includes three subgroups of T, B, and NK cells. Recognition of the complexity of the human genetics transcriptome in lymphopoiesis has revolutionized our understanding of the regulatory potential of RNA in normal lymphopoiesis and lymphoid malignancies. Long non-coding RNAs (lncRNAs) are a class of RNA molecules greater than 200 nucleotides in length. LncRNAs have recently attracted much attention due to their critical roles in various biological processes, including gene regulation, chromatin organization, and cell cycle control. LncRNAs can also be used for cell differentiation and cell fate, as their expression patterns are often specific to particular cell types or developmental stages. Additionally, lncRNAs have been implicated in lymphoid differentiation, such as regulating T-cell and B-cell development, and their expression has been linked to immune-associated diseases such as leukemia and lymphoma. In addition, lncRNAs have been investigated as potential biomarkers for diagnosis, prognosis, and therapeutic response to disease management. In this review, we provide an overview of the current knowledge about the regulatory role of lncRNAs in physiopathology processes during normal lymphopoiesis and lymphoid leukemia.
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Affiliation(s)
- Hamed Baghdadi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
| | - Reza Heidari
- Research Center for Cancer Screening and Epidemiology, AJA University of Medical Sciences, Tehran 1411718541, Iran;
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mahdi Zavvar
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran 443614177, Iran;
| | - Nazanin Ahmadi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | | | - Mahmoud Vahidi
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Mojgan Mohammadimehr
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran 1985717443, Iran;
| | - Mahdi Ghorbani
- Department of Medical Laboratory Sciences, School of Allied Medical Sciences, AJA University of Medical Sciences, Tehran 1411718541, Iran; (H.B.); (M.V.); (M.M.)
- Medical Biotechnology Research Center, AJA University of Medical Sciences, Tehran 1411718541, Iran;
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3
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Xie M, Lee K, Lockhart JH, Cukras SD, Carvajal R, Beg AA, Flores ER, Teng M, Chung CH, Tan AC. TIMEx: tumor-immune microenvironment deconvolution web-portal for bulk transcriptomics using pan-cancer scRNA-seq signatures. Bioinformatics 2021; 37:3681-3683. [PMID: 33901274 PMCID: PMC11025676 DOI: 10.1093/bioinformatics/btab244] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 03/18/2021] [Accepted: 04/13/2021] [Indexed: 11/14/2022] Open
Abstract
SUMMARY The heterogeneous cell types of the tumor-immune microenvironment (TIME) play key roles in determining cancer progression, metastasis and response to treatment. We report the development of TIMEx, a novel TIME deconvolution method emphasizing on estimating infiltrating immune cells for bulk transcriptomics using pan-cancer single-cell RNA-seq signatures. We also implemented a comprehensive, user-friendly web-portal for users to evaluate TIMEx and other deconvolution methods with bulk transcriptomic profiles. AVAILABILITY AND IMPLEMENTATION TIMEx web-portal is freely accessible at http://timex.moffitt.org. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Mengyu Xie
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Kyubum Lee
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - John H Lockhart
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Scott D Cukras
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Rodrigo Carvajal
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Amer A Beg
- Department of Immunology H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Elsa R Flores
- Department of Molecular Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Mingxiang Teng
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
| | - Aik Choon Tan
- Department of Biostatistics and Bioinformatics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA
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4
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Kersy O, Salmon-Divon M, Shpilberg O, Hershkovitz-Rokah O. Non-Coding RNAs in Normal B-Cell Development and in Mantle Cell Lymphoma: From Molecular Mechanism to Biomarker and Therapeutic Agent Potential. Int J Mol Sci 2021; 22:ijms22179490. [PMID: 34502399 PMCID: PMC8430640 DOI: 10.3390/ijms22179490] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/23/2021] [Accepted: 08/29/2021] [Indexed: 12/27/2022] Open
Abstract
B-lymphocytes are essential for an efficient immune response against a variety of pathogens. A large fraction of hematologic malignancies are of B-cell origin, suggesting that the development and activation of B cells must be tightly regulated. In recent years, differentially expressed non-coding RNAs have been identified in mantle cell lymphoma (MCL) tumor samples as opposed to their naive, normal B-cell compartment. These aberrantly expressed molecules, specifically microRNAs (miRNAs), circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), have a role in cellular growth and survival pathways in various biological models. Here, we provide an overview of current knowledge on the role of non-coding RNAs and their relevant targets in B-cell development, activation and malignant transformation, summarizing the current understanding of the role of aberrant expression of non-coding RNAs in MCL pathobiology with perspectives for clinical use.
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Affiliation(s)
- Olga Kersy
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (O.K.); (M.S.-D.)
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv 6971028, Israel;
| | - Mali Salmon-Divon
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (O.K.); (M.S.-D.)
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel
| | - Ofer Shpilberg
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv 6971028, Israel;
- Adelson School of Medicine, Ariel University, Ariel 40700, Israel
- Institute of Hematology, Assuta Medical Centers, Tel-Aviv 6971028, Israel
| | - Oshrat Hershkovitz-Rokah
- Department of Molecular Biology, Faculty of Natural Sciences, Ariel University, Ariel 40700, Israel; (O.K.); (M.S.-D.)
- Translational Research Lab, Assuta Medical Centers, Tel-Aviv 6971028, Israel;
- Correspondence: ; Tel.: +972-3-764-4094
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5
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Rodriguez PD, Paculova H, Kogut S, Heath J, Schjerven H, Frietze S. Non-Coding RNA Signatures of B-Cell Acute Lymphoblastic Leukemia. Int J Mol Sci 2021; 22:ijms22052683. [PMID: 33799946 PMCID: PMC7961854 DOI: 10.3390/ijms22052683] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 03/01/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a diverse class of non-protein coding transcripts that regulate critical cellular processes associated with cancer. Advances in RNA-sequencing (RNA-Seq) have led to the characterization of non-coding RNA expression across different types of human cancers. Through comprehensive RNA-Seq profiling, a growing number of studies demonstrate that ncRNAs, including long non-coding RNA (lncRNAs) and microRNAs (miRNA), play central roles in progenitor B-cell acute lymphoblastic leukemia (B-ALL) pathogenesis. Furthermore, due to their central roles in cellular homeostasis and their potential as biomarkers, the study of ncRNAs continues to provide new insight into the molecular mechanisms of B-ALL. This article reviews the ncRNA signatures reported for all B-ALL subtypes, focusing on technological developments in transcriptome profiling and recently discovered examples of ncRNAs with biologic and therapeutic relevance in B-ALL.
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Affiliation(s)
- Princess D. Rodriguez
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Hana Paculova
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Sophie Kogut
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
| | - Jessica Heath
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Department of Pediatrics, University of Vermont, Burlington, VT 05405, USA
| | - Hilde Schjerven
- Department of Laboratory Medicine, University of California, San Francisco, CA 94143, USA;
| | - Seth Frietze
- Department of Biomedical and Health Sciences, University of Vermont, Burlington, VT 05405, USA; (P.D.R.); (H.P.); (S.K.)
- The University of Vermont Cancer Center, University of Vermont, Burlington, VT 05405, USA;
- Department of Biochemistry, University of Vermont, Burlington, VT 05405, USA
- Correspondence:
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6
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Dutta A, Roy A, Chatterjee S. Long noncoding RNAs in cancer immunity: a new avenue in drug discovery. Drug Discov Today 2020; 26:264-272. [PMID: 32827755 DOI: 10.1016/j.drudis.2020.07.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 06/18/2020] [Accepted: 07/22/2020] [Indexed: 12/23/2022]
Abstract
The central role of the nonprotein-coding portion of the genome, such as long noncoding (lnc)RNAs is emerging as a hidden player manipulating the immune system in cancer. lncRNAs, in association with their interacting partners, regulate the expression of various immune system genes, which are perturbed during cancer. The tissue-specific expression of lncRNAs and their importance in cellular proliferation, the tumor microenvironment (TME), epithelial-mesenchymal transition (EMT), and modulation of the cells of the innate and adaptive immune system have novel therapeutic implications in establishing lncRNAs as biomarkers and targets to overcome cancer-associated immunosuppression. In this review, we establish and strengthen the link between lncRNAs and cancer immunity.
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Affiliation(s)
- Anindya Dutta
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
| | - Ananya Roy
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India
| | - Subhrangsu Chatterjee
- Department of Biophysics, Bose Institute, P-1/12, CIT Scheme VIIM, Kankurgachi, Kolkata 700054, West Bengal, India.
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7
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Manfrini N, Ricciardi S, Alfieri R, Ventura G, Calamita P, Favalli A, Biffo S. Ribosome profiling unveils translational regulation of metabolic enzymes in primary CD4 + Th1 cells. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2020; 109:103697. [PMID: 32330465 DOI: 10.1016/j.dci.2020.103697] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 04/06/2020] [Accepted: 04/06/2020] [Indexed: 05/22/2023]
Abstract
The transition from a naïve to an effector T cell is an essential event that requires metabolic reprogramming. We have recently demonstrated that the rapid metabolic changes that occur following stimulation of naïve T cells require the translation of preexisting mRNAs. Here, we provide evidence that translation regulates the metabolic asset of effector T cells. By performing ribosome profiling in human CD4+ Th1 cells, we show that the metabolism of glucose, fatty acids and pentose phosphates is regulated at the translational level. In Th1 cells, each pathway has at least one enzyme regulated at the translational level and selected enzymes have high translational efficiencies. mRNA expression does not predict protein expression. For instance, PKM2 mRNA is equally present in naïve T and Th1 cells, but the protein is abundant only in Th1. 5'-untranslated regions (UTRs) may partly account for this regulation. Overall we suggest that immunometabolism is controlled by translation.
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Affiliation(s)
- Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy
| | - Sara Ricciardi
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy
| | - Gabriele Ventura
- Department of Biological Sciences, University of Milan, Milan, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy
| | - Andrea Favalli
- Department of Biological Sciences, University of Milan, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Fondazione Romeo ed Enrica Invernizzi", Milano, Italy; Department of Biological Sciences, University of Milan, Milan, Italy.
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8
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Amin V, Ağaç D, Barnes SD, Çobanoğlu MC. Accurate differential analysis of transcription factor activity from gene expression. Bioinformatics 2020; 35:5018-5029. [PMID: 31099391 DOI: 10.1093/bioinformatics/btz398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Revised: 04/02/2019] [Accepted: 05/08/2019] [Indexed: 12/17/2022] Open
Abstract
MOTIVATION Activity of transcriptional regulators is crucial in elucidating the mechanism of phenotypes. However regulatory activity hypotheses are difficult to experimentally test. Therefore, we need accurate and reliable computational methods for regulator activity inference. There is extensive work in this area, however, current methods have difficulty with one or more of the following: resolving activity of TFs with overlapping regulons, reflecting known regulatory relationships, or flexible modeling of TF activity over the regulon. RESULTS We present Effector and Perturbation Estimation Engine (EPEE), a method for differential analysis of transcription factor (TF) activity from gene expression data. EPEE addresses each of these principal challenges in the field. Firstly, EPEE collectively models all TF activity in a single multivariate model, thereby accounting for the intrinsic coupling among TFs that share targets, which is highly frequent. Secondly, EPEE incorporates context-specific TF-gene regulatory networks and therefore adapts the analysis to each biological context. Finally, EPEE can flexibly reflect different regulatory activity of a single TF among its potential targets. This allows the flexibility to implicitly recover other regulatory influences such as co-activators or repressors. We comparatively validated EPEE in 15 datasets from three well-studied contexts, namely immunology, cancer, and hematopoiesis. We show that addressing the aforementioned challenges enable EPEE to outperform alternative methods and reliably produce accurate results. AVAILABILITY AND IMPLEMENTATION https://github.com/Cobanoglu-Lab/EPEE. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Viren Amin
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Didem Ağaç
- Department of Immunology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Spencer D Barnes
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Murat Can Çobanoğlu
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
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9
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Hou Y, Zhang R, Sun X. Enhancer LncRNAs Influence Chromatin Interactions in Different Ways. Front Genet 2019; 10:936. [PMID: 31681405 PMCID: PMC6807612 DOI: 10.3389/fgene.2019.00936] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
More than 98% of the human genome does not encode proteins, and the vast majority of the noncoding regions have not been well studied. Some of these regions contain enhancers and functional non-coding RNAs. Previous research suggested that enhancer transcripts could be potent independent indicators of enhancer activity, and some enhancer lncRNAs (elncRNAs) have been proven to play critical roles in gene regulation. Here, we identified enhancer–promoter interactions from high-throughput chromosome conformation capture (Hi-C) data. We found that elncRNAs were highly enriched surrounding chromatin loop anchors. Additionally, the interaction frequency of elncRNA-associated enhancer–promoter pairs was significantly higher than the interaction frequency of other enhancer–promoter pairs, suggesting that elncRNAs may reinforce the interactions between enhancers and promoters. We also found that elncRNA expression levels were positively correlated with the interaction frequency of enhancer–promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Interestingly, G-quadruplexes were found to potentially mediate some enhancer–promoter interaction pairs, and the interaction frequency of these pairs was significantly higher than that of other enhancer–promoter pairs. We also found that the G-quadruplexes on enhancers were highly related to the expression of elncRNAs. G-quadruplexes located in the promoters of elncRNAs led to high expression of elncRNAs, whereas G-quadruplexes located in the gene bodies of elncRNAs generally resulted in low expression of elncRNAs.
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Affiliation(s)
- Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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10
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Wu Y, Chang YM, Stell AJ, Priestnall SL, Sharma E, Goulart MR, Gribben J, Xia D, Garden OA. Phenotypic characterisation of regulatory T cells in dogs reveals signature transcripts conserved in humans and mice. Sci Rep 2019; 9:13478. [PMID: 31530890 PMCID: PMC6748983 DOI: 10.1038/s41598-019-50065-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/05/2019] [Indexed: 12/12/2022] Open
Abstract
Regulatory T cells (Tregs) are a double-edged regulator of the immune system. Aberrations of Tregs correlate with pathogenesis of inflammatory, autoimmune and neoplastic disorders. Phenotypically and functionally distinct subsets of Tregs have been identified in humans and mice on the basis of their extensive portfolios of monoclonal antibodies (mAb) against Treg surface antigens. As an important veterinary species, dogs are increasingly recognised as an excellent model for many human diseases. However, insightful study of canine Tregs has been restrained by the limited availability of mAb. We therefore set out to characterise CD4+CD25high T cells isolated ex vivo from healthy dogs and showed that they possess a regulatory phenotype, function, and transcriptomic signature that resembles those of human and murine Tregs. By launching a cross-species comparison, we unveiled a conserved transcriptomic signature of Tregs and identified that transcript hip1 may have implications in Treg function.
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Affiliation(s)
- Ying Wu
- Royal Veterinary College, London, UK
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | | | - Eshita Sharma
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Michelle R Goulart
- Royal Veterinary College, London, UK
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - John Gribben
- Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Dong Xia
- Royal Veterinary College, London, UK
| | - Oliver A Garden
- Royal Veterinary College, London, UK.
- School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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11
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Finotello F, Mayer C, Plattner C, Laschober G, Rieder D, Hackl H, Krogsdam A, Loncova Z, Posch W, Wilflingseder D, Sopper S, Ijsselsteijn M, Brouwer TP, Johnson D, Xu Y, Wang Y, Sanders ME, Estrada MV, Ericsson-Gonzalez P, Charoentong P, Balko J, de Miranda NFDCC, Trajanoski Z. Molecular and pharmacological modulators of the tumor immune contexture revealed by deconvolution of RNA-seq data. Genome Med 2019; 11:34. [PMID: 31126321 PMCID: PMC6534875 DOI: 10.1186/s13073-019-0638-6] [Citation(s) in RCA: 664] [Impact Index Per Article: 132.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 04/09/2019] [Indexed: 12/26/2022] Open
Abstract
We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients' responses to checkpoint blockers.Availability: quanTIseq is available at http://icbi.at/quantiseq .
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Affiliation(s)
- Francesca Finotello
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Clemens Mayer
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Christina Plattner
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Gerhard Laschober
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Dietmar Rieder
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Hubert Hackl
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Anne Krogsdam
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Zuzana Loncova
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria
| | - Wilfried Posch
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Doris Wilflingseder
- Division of Hygiene and Medical Microbiology, Medical University of Innsbruck, Innsbruck, Austria
| | - Sieghart Sopper
- Department of Haematology and Oncology, Medical University of Innsbruck, Innsbruck, Austria
| | - Marieke Ijsselsteijn
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Thomas P Brouwer
- Department of Pathology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Douglas Johnson
- Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yu Wang
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Melinda E Sanders
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Monica V Estrada
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Paula Ericsson-Gonzalez
- Department Pathology Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Pornpimol Charoentong
- Department of Medical Oncology and Internal Medicine VI, National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
- Division of Translational Immunotherapy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Justin Balko
- Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Zlatko Trajanoski
- Biocenter, Division of Bioinformatics, Medical University of Innsbruck, Innrain 80, Innsbruck, Austria.
- Austrian Drug Screening Institute, Innrain 66A, Innsbruck, Austria.
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12
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Ricciardi S, Manfrini N, Alfieri R, Calamita P, Crosti MC, Gallo S, Müller R, Pagani M, Abrignani S, Biffo S. The Translational Machinery of Human CD4 + T Cells Is Poised for Activation and Controls the Switch from Quiescence to Metabolic Remodeling. Cell Metab 2018; 28:895-906.e5. [PMID: 30197303 PMCID: PMC6773601 DOI: 10.1016/j.cmet.2018.08.009] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 03/24/2018] [Accepted: 08/07/2018] [Indexed: 12/13/2022]
Abstract
Naive T cells respond to T cell receptor (TCR) activation by leaving quiescence, remodeling metabolism, initiating expansion, and differentiating toward effector T cells. The molecular mechanisms coordinating the naive to effector transition are central to the functioning of the immune system, but remain elusive. Here, we discover that T cells fulfill this transitional process through translational control. Naive cells accumulate untranslated mRNAs encoding for glycolysis and fatty acid synthesis factors and possess a translational machinery poised for immediate protein synthesis. Upon TCR engagement, activation of the translational machinery leads to synthesis of GLUT1 protein to drive glucose entry. Subsequently, translation of ACC1 mRNA completes metabolic reprogramming toward an effector phenotype. Notably, inhibition of the eIF4F complex abrogates lymphocyte metabolic activation and differentiation, suggesting ACC1 to be a key regulatory node. Thus, our results demonstrate that translation is a direct mediator of T cell metabolism and indicate translation factors as targets for novel immunotherapeutic approaches.
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Affiliation(s)
- Sara Ricciardi
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Bioscience Department, Università degli Studi di Milano, Milan, Italy
| | - Nicola Manfrini
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Roberta Alfieri
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Piera Calamita
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Bioscience Department, Università degli Studi di Milano, Milan, Italy
| | - Maria Cristina Crosti
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Simone Gallo
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Center for Infection Research and Department of Pharmacy, Saarland University Campus, Building C2.3, Saarbrücken 66123, Germany
| | - Massimiliano Pagani
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
| | - Sergio Abrignani
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Milan, Italy
| | - Stefano Biffo
- INGM, National Institute of Molecular Genetics, "Romeo ed Enrica Invernizzi", Via Francesco Sforza 35, Milan 20122, Italy; Bioscience Department, Università degli Studi di Milano, Milan, Italy.
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13
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Dahl M, Kristensen LS, Grønbæk K. Long Non-Coding RNAs Guide the Fine-Tuning of Gene Regulation in B-Cell Development and Malignancy. Int J Mol Sci 2018; 19:E2475. [PMID: 30134619 PMCID: PMC6165225 DOI: 10.3390/ijms19092475] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 08/16/2018] [Accepted: 08/20/2018] [Indexed: 12/13/2022] Open
Abstract
With the introduction of next generation sequencing methods, such as RNA sequencing, it has become apparent that alterations in the non-coding regions of our genome are important in the development of cancer. Particularly interesting is the class of long non-coding RNAs (lncRNAs), including the recently described subclass of circular RNAs (circRNAs), which display tissue- and cell-type specific expression patterns and exert diverse regulatory functions in the cells. B-cells undergo complex and tightly regulated processes in order to develop from antigen naïve cells residing in the bone marrow to the highly diverse and competent effector cells circulating in peripheral blood. These processes include V(D)J recombination, rapid proliferation, somatic hypermutation and clonal selection, posing a risk of malignant transformation at each step. The aim of this review is to provide insight into how lncRNAs including circRNAs, participate in normal B-cell differentiation, and how deregulation of these molecules is involved in the development of B-cell malignancies. We describe the prognostic value and functional significance of specific deregulated lncRNAs in diseases such as acute lymphoblastic leukemia, chronic lymphocytic leukemia, mantle cell lymphoma, diffuse large B-cell lymphoma, follicular lymphoma, Burkitt lymphoma and multiple myeloma, and we provide an overview of the current knowledge on the role of circRNAs in these diseases.
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MESH Headings
- B-Lymphocytes/immunology
- B-Lymphocytes/pathology
- Burkitt Lymphoma/genetics
- Burkitt Lymphoma/immunology
- Burkitt Lymphoma/pathology
- Cell Differentiation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/pathology
- Gene Expression Regulation, Neoplastic
- Humans
- Leukemia, Lymphocytic, Chronic, B-Cell/genetics
- Leukemia, Lymphocytic, Chronic, B-Cell/immunology
- Leukemia, Lymphocytic, Chronic, B-Cell/pathology
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/immunology
- Lymphoma, Follicular/pathology
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Mantle-Cell/genetics
- Lymphoma, Mantle-Cell/immunology
- Lymphoma, Mantle-Cell/pathology
- Multiple Myeloma/genetics
- Multiple Myeloma/immunology
- Multiple Myeloma/pathology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/immunology
- Precursor Cell Lymphoblastic Leukemia-Lymphoma/pathology
- RNA/genetics
- RNA/immunology
- RNA, Circular
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/immunology
- Signal Transduction
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Affiliation(s)
- Mette Dahl
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
- Biotech Research and Innovation Centre, BRIC, Copenhagen University, DK-2100 Copenhagen, Denmark.
| | - Lasse Sommer Kristensen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, DK-8000 Aarhus, Denmark.
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus, Denmark.
| | - Kirsten Grønbæk
- Department of Hematology, Rigshospitalet, Copenhagen University Hospital, DK-2100 Copenhagen, Denmark.
- Biotech Research and Innovation Centre, BRIC, Copenhagen University, DK-2100 Copenhagen, Denmark.
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14
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Chakravarthy A, Furness A, Joshi K, Ghorani E, Ford K, Ward MJ, King EV, Lechner M, Marafioti T, Quezada SA, Thomas GJ, Feber A, Fenton TR. Pan-cancer deconvolution of tumour composition using DNA methylation. Nat Commun 2018; 9:3220. [PMID: 30104673 PMCID: PMC6089972 DOI: 10.1038/s41467-018-05570-1] [Citation(s) in RCA: 169] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 07/10/2018] [Indexed: 12/17/2022] Open
Abstract
The nature and extent of immune cell infiltration into solid tumours are key determinants of therapeutic response. Here, using a DNA methylation-based approach to tumour cell fraction deconvolution, we report the integrated analysis of tumour composition and genomics across a wide spectrum of solid cancers. Initially studying head and neck squamous cell carcinoma, we identify two distinct tumour subgroups: 'immune hot' and 'immune cold', which display differing prognosis, mutation burden, cytokine signalling, cytolytic activity and oncogenic driver events. We demonstrate the existence of such tumour subgroups pan-cancer, link clonal-neoantigen burden to cytotoxic T-lymphocyte infiltration, and show that transcriptional signatures of hot tumours are selectively engaged in immunotherapy responders. We also find that treatment-naive hot tumours are markedly enriched for known immune-resistance genomic alterations, potentially explaining the heterogeneity of immunotherapy response and prognosis seen within this group. Finally, we define a catalogue of mediators of active antitumour immunity, deriving candidate biomarkers and potential targets for precision immunotherapy.
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Affiliation(s)
- Ankur Chakravarthy
- Department of Oncology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
- Princess Margaret Cancer Centre, Toronto, ON, M5G 2C4, Canada
| | - Andrew Furness
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Kroopa Joshi
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Ehsan Ghorani
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Kirsty Ford
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Matthew J Ward
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Emma V King
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Matt Lechner
- Department of Oncology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Teresa Marafioti
- Department of Pathology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Sergio A Quezada
- Department of Haematology, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Gareth J Thomas
- Cancer Sciences Unit, University of Southampton, Tremona Road, Southampton, SO16 6YD, UK
| | - Andrew Feber
- Division of Surgery and Interventional Science, University College London, London, WC1E 6BT, UK
| | - Tim R Fenton
- School of Biosciences, University of Kent, Canterbury, CT2 7NJ, UK.
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15
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Wang J, Lin F, Wan Z, Sun X, Lu Y, Huang J, Wang F, Zeng Y, Chen YH, Shi Y, Zheng W, Li Z, Xiong C, Liu W. Profiling the origin, dynamics, and function of traction force in B cell activation. Sci Signal 2018; 11:11/542/eaai9192. [PMID: 30087179 DOI: 10.1126/scisignal.aai9192] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
B lymphocytes use B cell receptors (BCRs) to recognize membrane-bound antigens to further initiate cell spreading and contraction responses during B cell activation. We combined traction force microscopy and live-cell imaging to profile the origin, dynamics, and function of traction force generation in these responses. We showed that B cell activation required the generation of 10 to 20 nN of traction force when encountering antigens presented by substrates with stiffness values from 0.5 to 1 kPa, which mimic the rigidity of antigen-presenting cells in vivo. Perturbation experiments revealed that F-actin remodeling and myosin- and dynein-mediated contractility contributed to traction force generation and B cell activation. Moreover, membrane-proximal BCR signaling molecules (including Lyn, Syk, Btk, PLC-γ2, BLNK, and Vav3) and adaptor molecules (Grb2, Cbl, and Dok-3) linking BCR microclusters and motor proteins were also required for the sustained generation of these traction forces. We found a positive correlation between the strength of the traction force and the mean fluorescence intensity of the BCR microclusters. Furthermore, we demonstrated that isotype-switched memory B cells expressing immunoglobulin G (IgG)-BCRs generated greater traction forces than did mature naïve B cells expressing IgM-BCRs during B cell activation. Last, we observed that primary B cells from patients with rheumatoid arthritis generated greater traction forces than did B cells from healthy donors in response to antigen stimulation. Together, these data delineate the origin, dynamics, and function of traction force during B cell activation.
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Affiliation(s)
- Junyi Wang
- China Ministry of Education Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Feng Lin
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing 100871, China
| | - Zhengpeng Wan
- China Ministry of Education Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Xiaolin Sun
- Department of Rheumatology and Immunology, Clinical Immunology Center, Peking University People's Hospital, Beijing, China
| | - Yun Lu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianyong Huang
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing 100871, China
| | - Fei Wang
- Chengdu Institute of Biology, Chinese Academy of Sciences, No. 9 Section 4, Renmin South Road, Chengdu 610041, China
| | - Yingyue Zeng
- School of Life Science, Liaoning University, Shenyang 110036, China
| | - Ying-Hua Chen
- China Ministry of Education Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Yan Shi
- Center for Life Sciences, Department of Basic Medical Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China
| | - Wenjie Zheng
- Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China
| | - Zhanguo Li
- Department of Rheumatology and Immunology, Clinical Immunology Center, Peking University People's Hospital, Beijing, China
| | - Chunyang Xiong
- Department of Mechanics and Engineering Science, College of Engineering, Peking University, Beijing 100871, China. .,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Wanli Liu
- China Ministry of Education Key Laboratory of Protein Sciences, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Life Sciences, Institute for Immunology, Tsinghua University, Beijing 100084, China. .,Beijing Key Lab for Immunological Research on Chronic Diseases, Beijing 100084, China
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16
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Salviano-Silva A, Lobo-Alves SC, Almeida RCD, Malheiros D, Petzl-Erler ML. Besides Pathology: Long Non-Coding RNA in Cell and Tissue Homeostasis. Noncoding RNA 2018; 4:ncrna4010003. [PMID: 29657300 PMCID: PMC5890390 DOI: 10.3390/ncrna4010003] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 12/12/2022] Open
Abstract
A significant proportion of mammalian genomes corresponds to genes that transcribe long non-coding RNAs (lncRNAs). Throughout the last decade, the number of studies concerning the roles played by lncRNAs in different biological processes has increased considerably. This intense interest in lncRNAs has produced a major shift in our understanding of gene and genome regulation and structure. It became apparent that lncRNAs regulate gene expression through several mechanisms. These RNAs function as transcriptional or post-transcriptional regulators through binding to histone-modifying complexes, to DNA, to transcription factors and other DNA binding proteins, to RNA polymerase II, to mRNA, or through the modulation of microRNA or enzyme function. Often, the lncRNA transcription itself rather than the lncRNA product appears to be regulatory. In this review, we highlight studies identifying lncRNAs in the homeostasis of various cell and tissue types or demonstrating their effects in the expression of protein-coding or other non-coding RNA genes.
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Affiliation(s)
- Amanda Salviano-Silva
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Caixa Postal 19071, Brazil.
| | - Sara Cristina Lobo-Alves
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Caixa Postal 19071, Brazil.
| | - Rodrigo Coutinho de Almeida
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Caixa Postal 19071, Brazil.
| | - Danielle Malheiros
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Caixa Postal 19071, Brazil.
| | - Maria Luiza Petzl-Erler
- Laboratory of Human Molecular Genetics, Department of Genetics, Universidade Federal do Paraná, Curitiba 81531-980, Caixa Postal 19071, Brazil.
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17
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Massolt ET, Meima ME, Swagemakers SMA, Leeuwenburgh S, van den Hout-van Vroonhoven MCGM, Brigante G, Kam BLR, van der Spek PJ, van IJcken WFJ, Visser TJ, Peeters RP, Visser WE. Thyroid State Regulates Gene Expression in Human Whole Blood. J Clin Endocrinol Metab 2018; 103:169-178. [PMID: 29069456 DOI: 10.1210/jc.2017-01144] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 10/16/2017] [Indexed: 02/03/2023]
Abstract
CONTEXT Despite the well-recognized clinical features resulting from insufficient or excessive thyroid hormone (TH) levels in humans, it is largely unknown which genes are regulated by TH in human tissues. OBJECTIVE To study the effect of TH on human gene expression profiles in whole blood, mainly consisting of T3 receptor (TR) α-expressing cells. METHODS We performed next-generation RNA sequencing on whole blood samples from eight athyroid patients (four females) on and after 4 weeks off levothyroxine replacement. Gene expression changes were analyzed through paired differential expression analysis and confirmed in a validation cohort. Weighted gene coexpression network analysis (WGCNA) was applied to identify thyroid state-related networks. RESULTS We detected 486 differentially expressed genes (fold-change >1.5; multiple testing corrected P value < 0.05), of which 76% were positively and 24% were negatively regulated. Gene ontology (GO) enrichment analysis revealed that three biological processes were significantly overrepresented, of which the process translational elongation showed the highest fold enrichment (7.3-fold, P = 1.8 × 10-6). WGCNA analysis independently identified various gene clusters that correlated with thyroid state. Further GO analysis suggested that thyroid state affects platelet function. CONCLUSIONS Changes in thyroid state regulate numerous genes in human whole blood, predominantly TRα-expressing leukocytes. In addition, TH may regulate gene transcripts in platelets.
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Affiliation(s)
- Elske T Massolt
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Marcel E Meima
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | | | - Selmar Leeuwenburgh
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | | | - Giulia Brigante
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Boen L R Kam
- Department of Nuclear Medicine, Erasmus MC, Rotterdam, the Netherlands
| | | | | | - Theo J Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - Robin P Peeters
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
| | - W Edward Visser
- Department of Internal Medicine, Erasmus MC, Rotterdam, the Netherlands
- Academic Center for Thyroid Diseases, Erasmus MC, Rotterdam, the Netherlands
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18
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Manfrini N, Ricciardi S, Miluzio A, Fedeli M, Scagliola A, Gallo S, Brina D, Adler T, Busch DH, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Biffo S. High levels of eukaryotic Initiation Factor 6 (eIF6) are required for immune system homeostasis and for steering the glycolytic flux of TCR-stimulated CD4 + T cells in both mice and humans. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2017; 77:69-76. [PMID: 28743432 DOI: 10.1016/j.dci.2017.07.022] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 07/21/2017] [Accepted: 07/21/2017] [Indexed: 06/07/2023]
Abstract
Eukaryotic Initiation Factor 6 (eIF6) is required for 60S ribosomal subunit biogenesis and efficient initiation of translation. Intriguingly, in both mice and humans, endogenous levels of eIF6 are detrimental as they act as tumor and obesity facilitators, raising the question on the evolutionary pressure that maintains high eIF6 levels. Here we show that, in mice and humans, high levels of eIF6 are required for proper immune functions. First, eIF6 heterozygous (het) mice show an increased mortality during viral infection and a reduction of peripheral blood CD4+ Effector Memory T cells. In human CD4+ T cells, eIF6 levels rapidly increase upon T-cell receptor activation and drive the glycolytic switch and the acquisition of effector functions. Importantly, in CD4+ T cells, eIF6 levels control interferon-γ (IFN-γ) secretion without affecting proliferation. In conclusion, the immune system has a high evolutionary pressure for the maintenance of a dynamic and powerful regulation of the translational machinery.
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Affiliation(s)
- Nicola Manfrini
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy.
| | - Sara Ricciardi
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy
| | - Annarita Miluzio
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy
| | - Maya Fedeli
- Experimental Immunology Unit, Division of Immunology, Transplantation and Infectious Diseases, DIBIT, H. San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy
| | - Alessandra Scagliola
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Simone Gallo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy
| | - Daniela Brina
- Molecular Oncology Group, Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Via Mirasole 22A, Bellinzona, Switzerland
| | - Thure Adler
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Dirk H Busch
- Institute for Medical Microbiology, Immunology and Hygiene, Technische Universität München, Trogerstrasse 30, 81675 Munich, Germany
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany
| | - Martin Hrabě de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health, 85764 Neuherberg, Germany; Center of Life and Food Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany; German Center for Diabetes Research, 85764 Neuherberg, Germany
| | - Stefano Biffo
- National Institute of Molecular Genetics "Romeo ed Enrica Invernizzi" - INGM, Via F. Sforza 35, 20122 Milan, Italy; Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milan, Italy.
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19
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Emerging roles for long noncoding RNAs in B-cell development and malignancy. Crit Rev Oncol Hematol 2017; 120:77-85. [PMID: 29198340 DOI: 10.1016/j.critrevonc.2017.08.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2017] [Revised: 08/09/2017] [Accepted: 08/09/2017] [Indexed: 12/14/2022] Open
Abstract
Long noncoding (lnc)RNAs have emerged as essential mediators of cellular biology, differentiation and malignant transformation. LncRNAs have a broad range of possible functions at the transcriptional, posttranscriptional and protein level and their aberrant expression significantly contributes to the hallmarks of cancer cell biology. In addition, their high tissue- and cell-type specificity makes lncRNAs especially interesting as biomarkers, prognostic factors or specific therapeutic targets. Here, we review current knowledge on lncRNA expression changes during normal B-cell development, indicating essential functions in the differentiation process. In addition we address lncRNA deregulation in B-cell malignancies, the putative prognostic value of this as well as the molecular functions of multiple deregulated lncRNAs. Altogether, the discussed work indicates major roles for lncRNAs in normal and malignant B cells affecting oncogenic pathways as well as the response to common therapeutics.
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20
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Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet 2017; 49:1602-1612. [PMID: 28945252 DOI: 10.1038/ng.3963] [Citation(s) in RCA: 316] [Impact Index Per Article: 45.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Evan A Boyle
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Nabeela Suliman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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21
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Flicr, a long noncoding RNA, modulates Foxp3 expression and autoimmunity. Proc Natl Acad Sci U S A 2017; 114:E3472-E3480. [PMID: 28396406 DOI: 10.1073/pnas.1700946114] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
A combination of transcription factors, enhancers, and epigenetic marks determines the expression of the key transcription factor FoxP3 in regulatory T cells (Tregs). Adding an additional layer of complexity, the long noncoding RNA (lncRNA) Flicr (Foxp3 long intergenic noncoding RNA) is a negative regulator that tunes Foxp3 expression, resulting in a subset of Tregs with twofold- to fivefold-lower levels of FoxP3 protein. The impact of Flicr is particularly marked in conditions of IL-2 deficiency, and, conversely, IL-2 represses Flicr expression. Flicr neighbors Foxp3 in mouse and human genomes, is specifically expressed in mature Tregs, and acts only in cis It does not affect DNA methylation, but modifies chromatin accessibility in the conserved noncoding sequence 3 (CNS3)/Accessible region 5 (AR5) region of Foxp3 Like many lncRNAs, Flicr's molecular effects are subtle, but by curtailing Treg activity, Flicr markedly promotes autoimmune diabetes and, conversely, restrains antiviral responses. This mechanism of FoxP3 control may allow escape from dominant Treg control during infection or cancer, at the cost of heightened autoimmunity.
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22
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Abstract
The discovery of long noncoding RNAs (lncRNA) has provided a new perspective on gene regulation in diverse biological contexts. lncRNAs are remarkably versatile molecules that interact with RNA, DNA, or proteins to promote or restrain the expression of protein-coding genes. Activation of immune cells is associated with dynamic changes in expression of genes, the products of which combat infectious microorganisms, initiate repair, and resolve inflammatory responses in cells and tissues. Recent evidence indicates that lncRNAs play important roles in directing the development of diverse immune cells and controlling the dynamic transcriptional programs that are a hallmark of immune cell activation. The importance of these molecules is underscored by their newly recognized roles in inflammatory diseases. In this review, we discuss the contribution of lncRNAs in the development and activation of immune cells and their roles in immune-related diseases. We also discuss challenges faced in identifying biological functions for this large and complex class of genes.
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Affiliation(s)
- Maninjay K Atianand
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | - Daniel R Caffrey
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
| | - Katherine A Fitzgerald
- Program in Innate Immunity, Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605;
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23
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Ranzani V, Arrigoni A, Rossetti G, Panzeri I, Abrignani S, Bonnal RJP, Pagani M. Next-Generation Sequencing Analysis of Long Noncoding RNAs in CD4+ T Cell Differentiation. Methods Mol Biol 2017; 1514:173-185. [PMID: 27787801 DOI: 10.1007/978-1-4939-6548-9_14] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Next-generation sequencing approaches, in particular RNA-seq, provide a genome-wide expression profiling allowing the identification of novel and rare transcripts such as long noncoding RNAs (lncRNA). Many RNA-seq studies have now been performed aimed at the characterization of lncRNAs and their possible involvement in cell development and differentiation in different organisms, cell types, and tissues. The adaptive immune system is an extraordinary context for the study of the role of lncRNAs in differentiation. Indeed lncRNAs seem to be key drivers in governing flexibility and plasticity of both CD8+ and CD4+ T cell, together with lineage-specific transcription factors and cytokines, acting as fine-tuners of fate choices in T cell differentiation.We describe here a pipeline for the identification of lncRNAs starting from RNA-Seq raw data.
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Affiliation(s)
- Valeria Ranzani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Alberto Arrigoni
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Grazisa Rossetti
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Ilaria Panzeri
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
| | - Sergio Abrignani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy
- Department of Clinical Sciences and Community Health, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, 20122, Italy
| | - Raoul J P Bonnal
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
| | - Massimiliano Pagani
- Istituto Nazionale Genetica Molecolare "Romeo ed Enrica Invernizzi", Via F. Sforza 35, Milan, 20122, Italy.
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Festa del Perdono 7, Milan, 20122, Italy.
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24
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Tayari MM, Winkle M, Kortman G, Sietzema J, de Jong D, Terpstra M, Mestdagh P, Kroese FGM, Visser L, Diepstra A, Kok K, van den Berg A, Kluiver J. Long Noncoding RNA Expression Profiling in Normal B-Cell Subsets and Hodgkin Lymphoma Reveals Hodgkin and Reed-Sternberg Cell-Specific Long Noncoding RNAs. THE AMERICAN JOURNAL OF PATHOLOGY 2016; 186:2462-72. [PMID: 27423697 DOI: 10.1016/j.ajpath.2016.05.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 05/13/2016] [Accepted: 05/18/2016] [Indexed: 12/22/2022]
Abstract
Hodgkin lymphoma (HL) is a malignancy of germinal center (GC) B-cell origin. To explore the role of long noncoding RNAs (lncRNAs) in HL, we studied lncRNA expression patterns in normal B-cell subsets, HL cell lines, and tissues. Naive and memory B cells showed a highly similar lncRNA expression pattern, distinct from GC-B cells. Significant differential expression between HL and normal GC-B cells was observed for 475 lncRNA loci. For two validated lncRNAs, an enhanced expression was observed in HL, diffuse large B-cell lymphoma, and lymphoblastoid cell lines. For a third lncRNA, increased expression levels were observed in HL and part of Burkitt lymphoma cell lines. RNA fluorescence in situ hybridization on primary HL tissues revealed a tumor cell-specific expression pattern for all three lncRNAs. A potential cis-regulatory role was observed for 107 differentially expressed lncRNA-mRNA pairs localizing within a 60-kb region. Consistent with a cis-acting role, we showed a preferential nuclear localization for two selected candidates. Thus, we showed dynamic lncRNA expression changes during the transit of normal B cells through the GC reaction and widely deregulated lncRNA expression patterns in HL. Three lncRNAs showed a tumor cell-specific expression pattern in HL tissues and might therefore be of value as a biomarker.
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Affiliation(s)
- Mina Masoumeh Tayari
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Gertrud Kortman
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Jantine Sietzema
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Martijn Terpstra
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Pieter Mestdagh
- Center for Medical Genetics, Ghent University, Ghent, Belgium
| | - Frans G M Kroese
- Department of Rheumatology and Clinical Immunology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Lydia Visser
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands.
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25
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Long noncoding RNAs in B-cell development and activation. Blood 2016; 128:e10-9. [PMID: 27381906 DOI: 10.1182/blood-2015-11-680843] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 06/28/2016] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are potentially important regulators of cell differentiation and development, but little is known about their roles in B lymphocytes. Using RNA-seq and de novo transcript assembly, we identified 4516 lncRNAs expressed in 11 stages of B-cell development and activation. Most of these lncRNAs have not been previously detected, even in the closely related T-cell lineage. Comparison with lncRNAs previously described in human B cells identified 185 mouse lncRNAs that have human orthologs. Using chromatin immunoprecipitation-seq, we classified 20% of the lncRNAs as either enhancer-associated (eRNA) or promoter-associated RNAs. We identified 126 eRNAs whose expression closely correlated with the nearest coding gene, thereby indicating the likely location of numerous enhancers active in the B-cell lineage. Furthermore, using this catalog of newly discovered lncRNAs, we show that PAX5, a transcription factor required to specify the B-cell lineage, bound to and regulated the expression of 109 lncRNAs in pro-B and mature B cells and 184 lncRNAs in acute lymphoblastic leukemia.
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