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Subramani PG, Fraszczak J, Helness A, Estall JL, Möröy T, Di Noia JM. Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation. EMBO Rep 2024; 25:2662-2697. [PMID: 38744970 PMCID: PMC11169469 DOI: 10.1038/s44319-024-00152-3] [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: 10/05/2023] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
The multifunctional RNA-binding protein hnRNPL is implicated in antibody class switching but its broader function in B cells is unknown. Here, we show that hnRNPL is essential for B cell activation, germinal center formation, and antibody responses. Upon activation, hnRNPL-deficient B cells show proliferation defects and increased apoptosis. Comparative analysis of RNA-seq data from activated B cells and another eight hnRNPL-depleted cell types reveals common effects on MYC and E2F transcriptional programs required for proliferation. Notably, while individual gene expression changes are cell type specific, several alternative splicing events affecting histone modifiers like KDM6A and SIRT1, are conserved across cell types. Moreover, hnRNPL-deficient B cells show global changes in H3K27me3 and H3K9ac. Epigenetic dysregulation after hnRNPL loss could underlie differential gene expression and upregulation of lncRNAs, and explain common and cell type-specific phenotypes, such as dysfunctional mitochondria and ROS overproduction in mouse B cells. Thus, hnRNPL is essential for the resting-to-activated B cell transition by regulating transcriptional programs and metabolism, at least in part through the alternative splicing of several histone modifiers.
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Affiliation(s)
- Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
| | - Jennifer Fraszczak
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Anne Helness
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Jennifer L Estall
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada.
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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2
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Lee FFY, Harris C, Alper S. RNA Binding Proteins that Mediate LPS-induced Alternative Splicing of the MyD88 Innate Immune Regulator. J Mol Biol 2024; 436:168497. [PMID: 38369277 PMCID: PMC11001520 DOI: 10.1016/j.jmb.2024.168497] [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: 12/10/2023] [Revised: 02/08/2024] [Accepted: 02/14/2024] [Indexed: 02/20/2024]
Abstract
Inflammation driven by Toll-like receptor (TLR) signaling pathways is required to combat infection. However, inflammation can damage host tissues; thus it is essential that TLR signaling ultimately is terminated to prevent chronic inflammatory disorders. One mechanism that terminates persistent TLR signaling is alternative splicing of the MyD88 signaling adaptor, which functions in multiple TLR signaling pathways. While the canonical long isoform of MyD88 (MyD88-L) mediates TLR signaling and promotes inflammation, an alternatively-spliced shorter isoform of MyD88 (MyD88-S) produces a dominant negative inhibitor of TLR signaling. MyD88-S production is induced by inflammatory agonists including lipopolysaccharide (LPS), and thus MyD88-S induction is thought to act as a negative feedback loop that prevents chronic inflammation. Despite the potential role that MyD88-S production plays in inflammatory disorders, the mechanisms controlling MyD88 alternative splicing remain unclear. Here, we identify two RNA binding proteins, SRSF1 and HNRNPU, that regulate LPS-induced alternative splicing of MyD88.
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Affiliation(s)
- Frank Fang Yao Lee
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Chelsea Harris
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA
| | - Scott Alper
- Department of Immunology and Genomic Medicine, National Jewish Health, Denver, CO 80206, USA; Center for Genes, Environment and Health, National Jewish Health, Denver, CO 80206, USA; Department of Immunology and Microbiology, University of Colorado School of Medicine, Anschutz, CO 80045, USA.
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3
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Rathore D, Marino MJ, Issara-Amphorn J, Hwan Yoon S, Manes NP, Nita-Lazar A. Lipopolysaccharide Regulates the Macrophage RNA-Binding Proteome. J Proteome Res 2024. [PMID: 38527097 DOI: 10.1021/acs.jproteome.3c00838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
RNA-protein interactions within cellular signaling pathways have significant modulatory effects on RNA binding proteins' (RBPs') effector functions. During the innate immune response, specific RNA-protein interactions have been reported as a regulatory layer of post-transcriptional control. We investigated changes in the RNA-bound proteome of immortalized mouse macrophages (IMM) following treatment with lipopolysaccharide (LPS). Stable isotope labeling by amino acids in cell culture (SILAC) of cells followed by unbiased purification of RNP complexes at two time points after LPS stimulation and bottom-up proteomic analysis by LC-MS/MS resulted in a set of significantly affected RBPs. Global RNA sequencing and LFQ proteomics were used to characterize the correlation of transcript and protein abundance changes in response to LPS at different time points with changes in protein-RNA binding. Il1α, MARCKS, and ACOD1 were noted as RBP candidates involved in innate immune signaling. The binding sites of the RBP and RNA conjugates at amino acid resolution were investigated by digesting the cross-linked oligonucleotide from peptides remaining after elution using Nuclease P1. The combined data sets provide directions for further studies of innate immune signaling regulation by RBP interactions with different classes of RNA.
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Affiliation(s)
- Deepali Rathore
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Matthew J Marino
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Jiraphorn Issara-Amphorn
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Sung Hwan Yoon
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Nathan P Manes
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Aleksandra Nita-Lazar
- Functional Cellular Networks Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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4
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Saha B, McNinch CM, Lu S, Ho MCW, De Carvalho SS, Barillas-Mury C. In-depth transcriptomic analysis of Anopheles gambiae hemocytes uncovers novel genes and the oenocytoid developmental lineage. BMC Genomics 2024; 25:80. [PMID: 38243165 PMCID: PMC10799387 DOI: 10.1186/s12864-024-09986-6] [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: 09/28/2023] [Accepted: 01/07/2024] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND Hemocytes are immune cells that patrol the mosquito hemocoel and mediate critical cellular defense responses against pathogens. However, despite their importance, a comprehensive transcriptome of these cells was lacking because they constitute a very small fraction of the total cells in the insect, limiting the study of hemocyte differentiation and immune function. RESULTS In this study, an in-depth hemocyte transcriptome was built by extensive bulk RNA sequencing and assembly of hemocyte RNAs from adult A. gambiae female mosquitoes, based on approximately 2.4 billion short Illumina and about 9.4 million long PacBio high-quality reads that mapped to the A. gambiae PEST genome (P4.14 version). A total of 34,939 transcripts were annotated including 4,020 transcripts from novel genes and 20,008 novel isoforms that result from extensive differential splicing of transcripts from previously annotated genes. Most hemocyte transcripts identified (89.8%) are protein-coding while 10.2% are non-coding RNAs. The number of transcripts identified in the novel hemocyte transcriptome is twice the number in the current annotation of the A. gambiae genome (P4.14 version). Furthermore, we were able to refine the analysis of a previously published single-cell transcriptome (scRNAseq) data set by using the novel hemocyte transcriptome as a reference to re-define the hemocyte clusters and determine the path of hemocyte differentiation. Unsupervised pseudo-temporal ordering using the Tools for Single Cell Analysis software uncovered a novel putative prohemocyte precursor cell type that gives rise to prohemocytes. Pseudo-temporal ordering with the Monocle 3 software, which analyses changes in gene expression during dynamic biological processes, determined that oenocytoids derive from prohemocytes, a cell population that also gives rise to the granulocyte lineage. CONCLUSION A high number of mRNA splice variants are expressed in hemocytes, and they may account for the plasticity required to mount efficient responses to many different pathogens. This study highlights the importance of a comprehensive set of reference transcripts to perform robust single-cell transcriptomic data analysis of cells present in low abundance. The detailed annotation of the hemocyte transcriptome will uncover new facets of hemocyte development and function in adult dipterans and is a valuable community resource for future studies on mosquito cellular immunity.
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Affiliation(s)
- Banhisikha Saha
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Colton M McNinch
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, 20892, Bethesda, MD, USA
| | - Stephen Lu
- Vector Biology Section, Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA
| | - Margaret C W Ho
- Bioinformatics and Computational Biosciences Branch, Office of Cyber Infrastructure and Computational Biology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health, 20892, Bethesda, MD, USA
| | - Stephanie Serafim De Carvalho
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA
| | - Carolina Barillas-Mury
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, USA.
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Sumitha MK, Kalimuthu M, Aarthy M, Paramasivan R, Kumar A, Gupta B. In silico identification, characterization, and expression analysis of RNA recognition motif (RRM) containing RNA-binding proteins in Aedes aegypti. Parasitol Res 2023; 122:2847-2857. [PMID: 37735272 DOI: 10.1007/s00436-023-07969-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 09/04/2023] [Indexed: 09/23/2023]
Abstract
RNA-binding proteins (RBPs) are the proteins that bind RNAs and regulate their functioning. RBPs in mosquitoes are gaining attention due to their ability to bind flaviviruses and regulate their replication and transmission. Despite their relevance, RBPs in mosquitoes are not explored much. In this study, we screened the whole genome of Aedes aegypti, the primary vector of several pathogenic viruses, and identified the proteins containing RNA recognition motif (RRM), the most abundant protein domain in eukaryotes. Using several in silico strategies, a total of 135 RRM-containing RBPs were identified in Ae. aegypti. The proteins were characterized based on their available annotations and the sequence similarity with Drosophila melanogaster. Ae. aegypti RRM-containing RBPs included serine/arginine-rich (SR) proteins, polyadenylate-binding proteins (PABP), heteronuclear ribonucleoproteins (hnRNP), small nuclear ribonucleoproteins (snRNP), splicing factors, eukaryotic initiation factors, transformers, and nucleolysins. Phylogenetic analysis revealed that the proteins and the domain organization are conserved among Ae. aegypti, Bombyx mori, and Drosophila melanogaster. However, the gene length and the intron-exon organization varied across the insect species. Expression analysis of the genes encoding RBPs using publicly available RNA sequencing data for different developmental time points of the mosquito life cycle starting from the ovary and eggs up to the adults revealed stage-specific expression with several genes preferentially expressed in early embryonic stages and blood-fed female ovaries. This is the first database for the Ae. aegypti RBPs that can serve as the reference base for future investigations. Stage-specific genes can be further explored to determine their role in mosquito growth and development with a focus on developing novel mosquito control strategies.
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Affiliation(s)
- Melveettil Kishor Sumitha
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Mariapillai Kalimuthu
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Murali Aarthy
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Rajaiah Paramasivan
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India
| | - Ashwani Kumar
- ICMR-Vector Control Research Centre (VCRC), Puducherry, India
| | - Bhavna Gupta
- ICMR-Vector Control Research Centre (VCRC), Field Station, 4, Sarojini Street Chinna Chokkikulam, Madurai, 625002, India.
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6
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Di Matteo G, Cimbalo A, Manyes L, Mannina L. Beauvericin Immunotoxicity Prevention by Gentiana lutea L. Flower In Vitro. Toxins (Basel) 2023; 15:538. [PMID: 37755964 PMCID: PMC10535299 DOI: 10.3390/toxins15090538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/22/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023] Open
Abstract
Beauvericin (BEA) is an emerging mycotoxin produced by some species of Fusarium genera that widely contaminates food and feed. Gentiana lutea is a protected medicinal plant known for its antioxidant and anti-inflammatory properties, which are attributed to its rich content of bioactive compounds. In order to evaluate the beneficial effects of G. lutea flower against BEA cytotoxicity, the aim of this study is to evaluate changes in protein expression after Jurkat cell exposure through a proteomics approach. To carry out the experiment, cells were exposed to intestinally digested G. lutea flower alone or in combination with the BEA standard (100 nM) over 7 days. Differentially expressed proteins were statistically evaluated (p < 0.05), revealing a total of 172 proteins with respect to the control in cells exposed to the BEA standard, 145 proteins for G. lutea alone, and 139 proteins when exposing the cells to the combined exposure. Bioinformatic analysis revealed processes implicated in mitochondria, ATP-related activity, and RNA binding. After careful analysis of differentially expressed proteins, it was evident that G. lutea attenuated, in most cases, the negative effects of BEA. Furthermore, it decreased the presence of major oncoproteins involved in the modulation of immune function.
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Affiliation(s)
- Giacomo Di Matteo
- Food Chemistry Lab, Department of Chemistry and Technology of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy; (G.D.M.); (L.M.)
| | - Alessandra Cimbalo
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, Universitat de València, Avda Vicent Andrés Estellés s/n, 46100 Burjassot, Spain;
| | - Lara Manyes
- Laboratory of Food Chemistry and Toxicology, Faculty of Pharmacy, Universitat de València, Avda Vicent Andrés Estellés s/n, 46100 Burjassot, Spain;
| | - Luisa Mannina
- Food Chemistry Lab, Department of Chemistry and Technology of Drugs, Sapienza University of Rome, P. le Aldo Moro 5, 00185 Rome, Italy; (G.D.M.); (L.M.)
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7
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Kasamoto M, Funakoshi S, Hatani T, Okubo C, Nishi Y, Tsujisaka Y, Nishikawa M, Narita M, Ohta A, Kimura T, Yoshida Y. Am80, a retinoic acid receptor agonist, activates the cardiomyocyte cell cycle and enhances engraftment in the heart. Stem Cell Reports 2023; 18:1672-1685. [PMID: 37451261 PMCID: PMC10444569 DOI: 10.1016/j.stemcr.2023.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Human induced pluripotent stem cell-derived (hiPSC) cardiomyocytes are a promising source for regenerative therapy. To realize this therapy, however, their engraftment potential after their injection into the host heart should be improved. Here, we established an efficient method to analyze the cell cycle activity of hiPSC cardiomyocytes using a fluorescence ubiquitination-based cell cycle indicator (FUCCI) system. In vitro high-throughput screening using FUCCI identified a retinoic acid receptor (RAR) agonist, Am80, as an effective cell cycle activator in hiPSC cardiomyocytes. The transplantation of hiPSC cardiomyocytes treated with Am80 before the injection significantly enhanced the engraftment in damaged mouse heart for 6 months. Finally, we revealed that the activation of endogenous Wnt pathways through both RARA and RARB underlies the Am80-mediated cell cycle activation. Collectively, this study highlights an efficient method to activate cell cycle in hiPSC cardiomyocytes by Am80 as a means to increase the graft size after cell transplantation into a damaged heart.
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Affiliation(s)
- Manabu Kasamoto
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; Department of Cardiovascular Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Shunsuke Funakoshi
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; Takeda-CiRA Joint program (T-CiRA), Fujisawa, Japan.
| | - Takeshi Hatani
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Chikako Okubo
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yohei Nishi
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Yuta Tsujisaka
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; Department of Cardiovascular Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Misato Nishikawa
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Megumi Narita
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Akira Ohta
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan
| | - Takeshi Kimura
- Department of Cardiovascular Medicine, Kyoto University Hospital, Kyoto, Japan
| | - Yoshinori Yoshida
- Centre for iPS Cell Research and Application, Kyoto University, Kyoto, Japan; Takeda-CiRA Joint program (T-CiRA), Fujisawa, Japan.
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8
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Li Q, Kang C. Targeting RNA-binding proteins with small molecules: Perspectives, pitfalls and bifunctional molecules. FEBS Lett 2023; 597:2031-2047. [PMID: 37519019 DOI: 10.1002/1873-3468.14710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/26/2023] [Accepted: 06/28/2023] [Indexed: 08/01/2023]
Abstract
RNA-binding proteins (RBPs) play vital roles in organisms through binding with RNAs to regulate their functions. Small molecules affecting the function of RBPs have been developed, providing new avenues for drug discovery. Herein, we describe the perspectives on developing small molecule regulators of RBPs. The following types of small molecule modulators are of great interest in drug discovery: small molecules binding to RBPs to affect interactions with RNA molecules, bifunctional molecules binding to RNA or RBP to influence their interactions, and other types of molecules that affect the stability of RNA or RBPs. Moreover, we emphasize that the bifunctional molecules may play important roles in small molecule development to overcome the challenges encountered in the process of drug discovery.
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Affiliation(s)
- Qingxin Li
- Guangdong Provincial Engineering Laboratory of Biomass High Value Utilization, Institute of Biological and Medical Engineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Congbao Kang
- Experimental Drug Development Centre, Agency for Science, Technology and Research, Singapore, Singapore
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9
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Basu J, Olsson A, Ferchen K, Titerina EK, Chetal K, Nicolas E, Czyzewicz P, Levchenko D, Ge L, Hua X, Grimes HL, Salomonis N, Kappes DJ. ThPOK is a critical multifaceted regulator of myeloid lineage development. Nat Immunol 2023; 24:1295-1307. [PMID: 37474652 PMCID: PMC10792516 DOI: 10.1038/s41590-023-01549-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 06/06/2023] [Indexed: 07/22/2023]
Abstract
The transcription factor ThPOK (encoded by Zbtb7b) is well known for its role as a master regulator of CD4 lineage commitment in the thymus. Here, we report an unexpected and critical role of ThPOK as a multifaceted regulator of myeloid lineage commitment, differentiation and maturation. Using reporter and knockout mouse models combined with single-cell RNA-sequencing, progenitor transfer and colony assays, we show that ThPOK controls monocyte-dendritic cell versus granulocyte lineage production during homeostatic differentiation, and serves as a brake for neutrophil maturation in granulocyte lineage-specified cells through transcriptional regulation of lineage-specific transcription factors and RNA via altered messenger RNA splicing to reprogram intron retention.
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Affiliation(s)
- Jayati Basu
- Fox Chase Cancer Center, Philadelphia, PA, USA.
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Andre Olsson
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Kyle Ferchen
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Elizaveta K Titerina
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Kashish Chetal
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | | | | | | | - Lu Ge
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Xiang Hua
- Fox Chase Cancer Center, Philadelphia, PA, USA
| | - H Leighton Grimes
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA
| | - Nathan Salomonis
- Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Division of Biomedical Informatics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
- Department of Pediatrics, University of Cincinnati, Cincinnati, OH, USA.
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10
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Nguyen TTT, Lu W, Zhu WS, Ansel KM, Liang HE, Weiss A. Stimulation of ectopically expressed muscarinic receptors induces IFN-γ but suppresses IL-2 production by inhibiting activation of pAKT pathways in primary T cells. Proc Natl Acad Sci U S A 2023; 120:e2300987120. [PMID: 37307442 PMCID: PMC10288620 DOI: 10.1073/pnas.2300987120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/15/2023] [Indexed: 06/14/2023] Open
Abstract
T cell antigen receptor stimulation induces tyrosine phosphorylation of downstream signaling molecules and the phosphatidylinositol, Ras, MAPK, and PI3 kinase pathways, leading to T cell activation. Previously, we reported that the G-protein-coupled human muscarinic receptor could bypass tyrosine kinases to activate the phosphatidylinositol pathway and induce interleukin-2 production in Jurkat leukemic T cells. Here, we demonstrate that stimulating G-protein-coupled muscarinic receptors (M1 and synthetic hM3Dq) can activate primary mouse T cells if PLCβ1 is coexpressed. Resting peripheral hM3Dq+PLCβ1 (hM3Dq/β1) T cells did not respond to clozapine, an hM3Dq agonist, unless they were preactivated by TCR and CD28 stimulation which increased hM3Dq and PLCβ1 expression. This permitted large calcium and phosphorylated ERK responses to clozapine. Clozapine treatment induced high IFN-γ, CD69, and CD25 expression, but surprisingly did not induce substantial IL-2 in hM3Dq/β1 T cells. Importantly, costimulation of both muscarinic receptors plus the TCR even led to reduced IL-2 expression, suggesting a selective inhibitory effect of muscarinic receptor costimulation. Stimulation of muscarinic receptors induced strong nuclear translocation of NFAT and NFκB and activated AP-1. However, stimulation of hM3Dq led to reduced IL-2 mRNA stability which correlated with an effect on the IL-2 3'UTR activity. Interestingly, stimulation of hM3Dq resulted in reduced pAKT and its downstream pathway. This may explain the inhibitory impact on IL-2 production in hM3Dq/β1T cells. Moreover, an inhibitor of PI3K reduced IL-2 production in TCR-stimulated hM3Dq/β1 CD4 T cells, suggesting that activating the pAKT pathway is critical for IL-2 production in T cells.
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Affiliation(s)
- Trang T. T. Nguyen
- Rosalind Russell-Ephraim Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
| | - Wen Lu
- Rosalind Russell-Ephraim Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
| | - Wandi S. Zhu
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA94143
| | - K. Mark Ansel
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA94143
| | - Hong-Erh Liang
- Rosalind Russell-Ephraim Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
- Department of Medicine, University of California San Francisco, San Francisco, 94143
| | - Arthur Weiss
- Rosalind Russell-Ephraim Engleman Rheumatology Research Center, Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA 94143
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11
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de Morree A, Rando TA. Regulation of adult stem cell quiescence and its functions in the maintenance of tissue integrity. Nat Rev Mol Cell Biol 2023; 24:334-354. [PMID: 36922629 PMCID: PMC10725182 DOI: 10.1038/s41580-022-00568-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 03/18/2023]
Abstract
Adult stem cells are important for mammalian tissues, where they act as a cell reserve that supports normal tissue turnover and can mount a regenerative response following acute injuries. Quiescent stem cells are well established in certain tissues, such as skeletal muscle, brain, and bone marrow. The quiescent state is actively controlled and is essential for long-term maintenance of stem cell pools. In this Review, we discuss the importance of maintaining a functional pool of quiescent adult stem cells, including haematopoietic stem cells, skeletal muscle stem cells, neural stem cells, hair follicle stem cells, and mesenchymal stem cells such as fibro-adipogenic progenitors, to ensure tissue maintenance and repair. We discuss the molecular mechanisms that regulate the entry into, maintenance of, and exit from the quiescent state in mice. Recent studies revealed that quiescent stem cells have a discordance between RNA and protein levels, indicating the importance of post-transcriptional mechanisms, such as alternative polyadenylation, alternative splicing, and translation repression, in the control of stem cell quiescence. Understanding how these mechanisms guide stem cell function during homeostasis and regeneration has important implications for regenerative medicine.
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Affiliation(s)
- Antoine de Morree
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Thomas A Rando
- Department of Neurology and Neurological Science, Stanford University School of Medicine, Stanford, CA, USA.
- Paul F. Glenn Center for the Biology of Aging, Stanford University School of Medicine, Stanford, CA, USA.
- Center for Tissue Regeneration, Repair, and Restoration, Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, USA.
- Broad Stem Cell Research Center, University of California, Los Angeles, Los Angeles, CA, USA.
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12
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Bravo S, Leiva F, Moya J, Guzman O, Vidal R. Unveiling the Role of Dynamic Alternative Splicing Modulation After Infestation with Sea Lice (Caligus rogercresseyi) in Atlantic Salmon. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:223-234. [PMID: 36629943 DOI: 10.1007/s10126-023-10196-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/04/2023] [Indexed: 05/06/2023]
Abstract
Sea lice are pathogenic marine ectoparasite copepods that represent a severe risk to the worldwide salmon industry. Several transcriptomic investigations have characterized the regulation of gene expression response of Atlantic salmon to sea lice infestation. These studies have focused on the levels of transcript, overlooking the potentially relevant role of alternative splicing (AS), which corresponds to an essential control mechanism of gene expression through RNA processing. In the present study, we performed a genome-wide bioinformatics characterization of differential AS event dynamics in control and infested C. rogercresseyi Atlantic salmon and in resistant and susceptible phenotypes. We identified a significant rise of alternative splicing events and AS genes after infestation and 176 differential alternative splicing events (DASE) from 133 genes. In addition, a higher number of DASE and AS genes were observed among resistant and susceptible phenotypes. Functional annotation of AS genes shows several terms and pathways associated with behavior, RNA splicing, immune response, and RNA binding. Furthermore, three protein-coding genes were identified undergoing differential transcript usage events, among resistant and susceptible phenotypes. Our findings support AS performing a relevant regulatory role in the response of salmonids to sea lice infestation.
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Affiliation(s)
- Scarleth Bravo
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Francisco Leiva
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile
| | - Javier Moya
- Benchmark Animal Health Chile, Santa Rosa 560 Of.26, Puerto Varas, Chile
| | - Osiel Guzman
- IDEVAC SpA, Francisco Bilbao 1129 Of. 306, Osorno, Chile
| | - Rodrigo Vidal
- Laboratory of Molecular Ecology, Genomics and Evolutionary Studies, Department of Biology, Universidad de Santiago de Chile, Santiago, Chile.
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13
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Nishanth MJ, Jha S. Computational analysis of crosstalk between transcriptional regulators and RNA-binding proteins suggests mutual regulation of polycomb proteins and SRSF1 influencing adult hippocampal neurogenesis. DISCOVER MENTAL HEALTH 2023; 3:7. [PMID: 37861946 PMCID: PMC10501017 DOI: 10.1007/s44192-023-00034-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 02/28/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND Adult hippocampal neurogenesis (AHN) is a clinically significant neural phenomenon. Understanding its molecular regulation would be important. In this regard, most studies have focused on transcriptional regulators (TRs), epigenetic modifiers, or non-coding RNAs. RNA-binding proteins (RBPs) have emerged as dominant molecular regulators. It would be significant to understand the potential cross-talk between RBPs and TRs, which could influence AHN. METHODS The present study employed computational analyses to identify RBPs and TRs regulating AHN, followed by the analysis of their interaction networks and detection of hub proteins. Next, the potential mutual regulation of hub TRs and RBPs was analyzed. Additionally, hippocampal genes differentially expressed upon exercise were analyzed for potential regulation by the identified TRs and RBPs. RESULTS 105 TRs and 26 RBPs were found to influence AHN, which could also form interactive networks. Polycomb complex proteins were among the TR network hubs, while HNRNP and SRSF family members were among the hub RBPs. Further, the polycomb complex proteins and SRSF1 could have a mutual regulatory relationship, suggesting a cross-talk between epigenetic/transcriptional and post-transcriptional regulatory pathways. A number of exercise-induced hippocampal genes were also found to be potential targets of the identified TRs and RBPs. CONCLUSION SRSF1 may influence post-transcriptional stability, localization, and alternative splicing patterns of polycomb complex transcripts, and the polycomb proteins may in turn epigenetically influence the SRSF1. Further experimental validation of these regulatory loops/networks could provide novel insights into the molecular regulation of AHN, and unravel new targets for disease-treatment.
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Affiliation(s)
- M J Nishanth
- Department of Biotechnology, School of Lifesciences, St Joseph's University, Bengaluru, India
| | - Shanker Jha
- School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India.
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14
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Regulation of the tumor immune microenvironment by cancer-derived circular RNAs. Cell Death Dis 2023; 14:132. [PMID: 36797245 PMCID: PMC9935907 DOI: 10.1038/s41419-023-05647-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 02/18/2023]
Abstract
Circular RNA (circRNAs) is a covalently closed circular non-coding RNA formed by reverse back-splicing from precursor messenger RNA. It is found widely in eukaryotic cells and can be released to the surrounding environment and captured by other cell types. This, circRNAs serve as connections between different cell types for the mediation of multiple signaling pathways. CircRNAs reshape the tumor microenvironment (TME), a key factor involved in all stages of cancer development, by regulating epithelial-stromal transformation, tumor vascularization, immune cell function, and inflammatory responses. Immune cells are the most abundant cellular TME components, and they have profound toxicity to cancer cells. This review summarizes circRNA regulation of immune cells, including T cells, natural killer cells, and macrophages; highlights the impact of circRNAs on tumor progression, treatment, and prognosis; and indicates new targets for tumor immunotherapy.
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15
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Ziegler N, Cortés-López M, Alt F, Sprang M, Ustjanzew A, Lehmann N, El Malki K, Wingerter A, Russo A, Beck O, Attig S, Roth L, König J, Paret C, Faber J. Analysis of RBP expression and binding sites identifies PTBP1 as a regulator of CD19 expression in B-ALL. Oncoimmunology 2023; 12:2184143. [PMID: 36875548 PMCID: PMC9980455 DOI: 10.1080/2162402x.2023.2184143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023] Open
Abstract
Despite massive improvements in the treatment of B-ALL through CART-19 immunotherapy, a large number of patients suffer a relapse due to loss of the targeted epitope. Mutations in the CD19 locus and aberrant splicing events are known to account for the absence of surface antigen. However, early molecular determinants suggesting therapy resistance as well as the time point when first signs of epitope loss appear to be detectable are not enlightened so far. By deep sequencing of the CD19 locus, we identified a blast-specific 2-nucleotide deletion in intron 2 that exists in 35% of B-ALL samples at initial diagnosis. This deletion overlaps with the binding site of RNA binding proteins (RBPs) including PTBP1 and might thereby affect CD19 splicing. Moreover, we could identify a number of other RBPs that are predicted to bind to the CD19 locus being deregulated in leukemic blasts, including NONO. Their expression is highly heterogeneous across B-ALL molecular subtypes as shown by analyzing 706 B-ALL samples accessed via the St. Jude Cloud. Mechanistically, we show that downregulation of PTBP1, but not of NONO, in 697 cells reduces CD19 total protein by increasing intron 2 retention. Isoform analysis in patient samples revealed that blasts, at diagnosis, express increased amounts of CD19 intron 2 retention compared to normal B cells. Our data suggest that loss of RBP functionality by mutations altering their binding motifs or by deregulated expression might harbor the potential for the disease-associated accumulation of therapy-resistant CD19 isoforms.
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Affiliation(s)
- Nicole Ziegler
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | | | - Francesca Alt
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg University Mainz, Biozentrum I, Mainz, Germany
| | - Arsenij Ustjanzew
- Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Nadine Lehmann
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Khalifa El Malki
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Arthur Wingerter
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Alexandra Russo
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Olaf Beck
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Sebastian Attig
- Department of Translational Oncology and Immunology at the Institute of Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Lea Roth
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany
| | - Julian König
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Claudia Paret
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,German Cancer Consortium (DKTK), Site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jörg Faber
- Center for Pediatric and Adolescent Medicine, Department of Pediatric Hematology/Oncology, University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,University Cancer Center (UCT), University Medical Center of the Johannes Gutenberg University Mainz, Mainz, Germany.,German Cancer Consortium (DKTK), Site Frankfurt/Mainz, Germany, German Cancer Research Center (DKFZ), Heidelberg, Germany
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16
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Martinelli M, Aguilar G, Lee DS, Kromer A, Nguyen N, Wilkins BJ, Akimova T, Beier UH, Ghanem LR. The poly(C)-binding protein Pcbp2 is essential for CD4 + T cell activation and proliferation. iScience 2022; 26:105860. [PMID: 36632062 PMCID: PMC9826892 DOI: 10.1016/j.isci.2022.105860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 11/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
The RNA-binding protein Pcbp2 is widely expressed in the innate and adaptive immune systems and is essential for mouse development. To determine whether Pcbp2 is required for CD4+ T cell development and function, we derived mice with conditional Pcbp2 deletion in CD4+ T cells and assessed their overall phenotype and proliferative responses to activating stimuli. We found that Pcbp2 is essential for T conventional cell (Tconv) proliferation, working through regulation of co-stimulatory signaling. Pcbp2 deficiency in the CD4+ lineage did not impact Treg abundance in vivo or function in vitro. In addition, our data demonstrate a clear association between Pcbp2 control of Runx1 exon 6 splicing in CD4+ T cells and a specific role for Pcbp2 in the maintenance of peripheral CD4+ lymphocyte population size. Last, we show that Pcbp2 function is required for optimal in vivo Tconv cell activation in a T cell adoptive transfer colitis model system.
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Affiliation(s)
- Massimo Martinelli
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Translational Medical Science, Section of Pediatrics, University of Naples “Federico II”, Naples 80131, Italy
| | - Gabrielle Aguilar
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - David S.M. Lee
- Department of Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA,Institute for Biomedical Informatics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrew Kromer
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Nhu Nguyen
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Benjamin J. Wilkins
- Division of Anatomic Pathology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Tatiana Akimova
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ulf H. Beier
- Division of Nephrology, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Louis R. Ghanem
- Division of Gastroenterology, Hepatology and Nutrition Division, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA,Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA,Corresponding author
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17
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Rosendo Machado S, Qu J, Koopman WJH, Miesen P. The DEAD-box RNA helicase Dhx15 controls glycolysis and arbovirus replication in Aedes aegypti mosquito cells. PLoS Pathog 2022; 18:e1010694. [PMID: 36441781 PMCID: PMC9731432 DOI: 10.1371/journal.ppat.1010694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 12/08/2022] [Accepted: 11/11/2022] [Indexed: 11/30/2022] Open
Abstract
Aedes aegypti mosquitoes are responsible for the transmission of arthropod-borne (arbo)viruses including dengue and chikungunya virus (CHIKV) but in contrast to human hosts, arbovirus-infected mosquitoes are able to efficiently control virus replication to sub-pathological levels. Yet, our knowledge of the molecular interactions of arboviruses with their mosquito hosts is incomplete. Here, we aimed to identify and characterize novel host genes that control arbovirus replication in Aedes mosquitoes. RNA binding proteins (RBPs) are well-known to regulate immune signaling pathways in all kingdoms of life. We therefore performed a knockdown screen targeting 461 genes encoding predicted RBPs in Aedes aegypti Aag2 cells and identified 15 genes with antiviral activity against Sindbis virus. Amongst these, the three DEAD-box RNA helicases AAEL004419/Dhx15, AAEL008728, and AAEL004859 also acted as antiviral factors in dengue and CHIKV infections. Here, we explored the mechanism of Dhx15 in regulating an antiviral transcriptional response in mosquitoes by silencing Dhx15 in Aag2 cells followed by deep-sequencing of poly-A enriched RNAs. Dhx15 knockdown in uninfected and CHIKV-infected cells resulted in differential expression of 856 and 372 genes, respectively. Interestingly, amongst the consistently downregulated genes, glycolytic process was the most enriched gene ontology (GO) term as the expression of all core enzymes of the glycolytic pathway was reduced, suggesting that Dhx15 regulates glycolytic function. A decrease in lactate production indicated that Dhx15 silencing indeed functionally impaired glycolysis. Modified rates of glycolytic metabolism have been implicated in controlling the replication of several classes of viruses and strikingly, infection of Aag2 cells with CHIKV by itself also resulted in the decrease of several glycolytic genes. Our data suggests that Dhx15 regulates replication of CHIKV, and possibly other arboviruses, by controlling glycolysis in mosquito cells.
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Affiliation(s)
- Samara Rosendo Machado
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Jieqiong Qu
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Werner J. H. Koopman
- Department of Pediatrics, Amalia Children’s Hospital, Radboud Institute for Molecular Life Sciences, Radboud Center for Mitochondrial Medicine, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Pascal Miesen
- Department of Medical Microbiology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
- * E-mail:
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18
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Nishanth MJ, Jha S. Global Exploration of RNA-Binding Proteins in Exercise-Induced Adult Hippocampal Neurogenesis: A Transcriptome Meta-analysis and Computational Study. Biochem Genet 2022; 60:2471-2488. [PMID: 35546218 DOI: 10.1007/s10528-022-10230-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/18/2022] [Indexed: 11/02/2022]
Abstract
Voluntary physical exercise is a robust enhancer of adult hippocampal neurogenesis (AHN). A complete understanding of the molecular regulation of AHN is important in order to exploit the benefits of the process toward therapeutic approaches. Several factors such as epigenetic modifiers, non-coding RNAs, and transcription factors have been reported to regulate AHN. However, there is a limited understanding of the impact of RNA-binding proteins (RBPs) on exercise-mediated AHN, in spite of their well-documented significance in embryonic neurogenesis. The present study is the first global analysis to catalog the potential RBPs influencing exercise-mediated AHN. Here, a transcriptome meta-analysis was conducted to study exercise-mediated gene expression modulation in hippocampi of adult mice. Next, potential RBPs influencing transcriptome-wide expression changes via untranslated regions (UTRs) were identified. Among other RBPs, MATR3, Musashi, TIA1, and FXR2 (known critical modulators of neurogenesis) were found to potentially regulate gene expression patterns. Subsequently, binding sites of known neurogenesis-regulating RBPs were identified in the UTRs of AHN-associated genes modulated by exercise. Finally, a number of RBPs including RBFOX1, RBFOX3, and QKI (known regulators of neurogenesis) were found to be highly expressed in mouse hippocampal formation and also potentially interact with other RBPs, suggesting their combinatorial functioning in exercise-induced AHN. Thus, the present meta-analysis-based computational study identified several RBPs potentially important in exercise-induced AHN, which could form a foundation for further experiments to unravel RBP-mediated regulation of AHN.
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Affiliation(s)
- M J Nishanth
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India
| | - Shanker Jha
- School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, 613401, India.
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19
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Grenov A, Hezroni H, Lasman L, Hanna JH, Shulman Z. YTHDF2 suppresses the plasmablast genetic program and promotes germinal center formation. Cell Rep 2022; 39:110778. [PMID: 35508130 PMCID: PMC9108551 DOI: 10.1016/j.celrep.2022.110778] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/25/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Antibody-mediated immunity is initiated by B cell differentiation into multiple cell subsets, including plasmablast, memory, and germinal center (GC) cells. B cell differentiation trajectories are determined by transcription factors, yet very few mechanisms that specifically determine early B cell fates have been described. Here, we report a post-transcriptional mechanism that suppresses the plasmablast genetic program and promotes GC B cell fate commitment. Single-cell RNA-sequencing analysis reveals that antigen-specific B cell precursors at the pre-GC stage upregulate YTHDF2, which enhances the decay of methylated transcripts. Ythdf2-deficient B cells exhibit intact proliferation and activation, whereas differentiation into GC B cells is blocked. Mechanistically, B cells require YTHDF2 to attenuate the plasmablast genetic program during GC seeding, and transcripts of key plasmablast-regulating genes are methylated and bound by YTHDF2. Collectively, this study reveals how post-transcriptional suppression of gene expression directs appropriate B cell fate commitment during initiation of the adaptive immune response. scRNA-seq of antigen-specific B cells reveals differentiation trajectories YTHDF2 is expressed by early-responding B cells and facilitates germinal center seeding YTHDF2 binds mRNAs of plasma cell-associated genes and suppresses their expression Germinal center formation does not depend on YTHDF1 and YTHDF3
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Affiliation(s)
- Amalie Grenov
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Hezroni
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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20
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Kumar S, Abatiyow BA, Haile MT, Oualim KMZ, Leeb AS, Vaughan AM, Kappe SHI. A Putative Plasmodium RNA-Binding Protein Plays a Critical Role in Female Gamete Fertility and Parasite Transmission to the Mosquito Vector. Front Cell Dev Biol 2022; 10:825247. [PMID: 35465336 PMCID: PMC9022223 DOI: 10.3389/fcell.2022.825247] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/02/2022] [Indexed: 02/04/2023] Open
Abstract
Plasmodium falciparum sexual stage gametocytes are critical for parasite transmission from the human host to the mosquito vector. Mature gametocytes generate fertile male (micro-) or female (macro-) gametes upon activation inside the mosquito midgut. While a number of parasite genes have been described that are critical for P. falciparum gametogenesis and fertility, no parasite gene has been shown to have a unique function in macrogametes. The genome of P. falciparum encodes numerous RNA-binding proteins. We identified a novel protein containing a putative RNA-binding domain, which we named Macrogamete-Contributed Factor Essential for Transmission (MaCFET). This protein is expressed in the asexual and sexual stages. Parasites that carry a deletion of MaCFET (Pfmacfet¯), developed normally as asexual stages, indicating that its function is not essential for the asexual proliferation of the parasite in vitro. Furthermore, Pfmacfet¯ male and female gametocytes developed normally and underwent activation to form microgametes and macrogametes. However, by utilizing genetic crosses, we demonstrate that Pfmacfet¯ parasites suffer a complete female-specific defect in successful fertilization. Therefore, PfMaCFET is a critical female-contributed factor for parasite transmission to the mosquito. Based on its putative RNA-binding properties, PfMaCFET might be in involved in the regulation of mRNAs that encode female-specific functions for fertilization or female-contributed factors needed post fertilization.
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Affiliation(s)
- Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Biley A Abatiyow
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Meseret T Haile
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Kenza M Z Oualim
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Amanda S Leeb
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States
| | - Ashley M Vaughan
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States
| | - Stefan H I Kappe
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, WA, United States.,Department of Pediatrics, University of Washington, Seattle, WA, United States.,Department of Global Health, University of Washington, Seattle, WA, United States
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21
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Saha D, Iannuccelli M, Brun C, Zanzoni A, Licata L. The Intricacy of the Viral-Human Protein Interaction Networks: Resources, Data, and Analyses. Front Microbiol 2022; 13:849781. [PMID: 35531299 PMCID: PMC9069133 DOI: 10.3389/fmicb.2022.849781] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/11/2022] [Indexed: 11/18/2022] Open
Abstract
Viral infections are one of the major causes of human diseases that cause yearly millions of deaths and seriously threaten global health, as we have experienced with the COVID-19 pandemic. Numerous approaches have been adopted to understand viral diseases and develop pharmacological treatments. Among them, the study of virus-host protein-protein interactions is a powerful strategy to comprehend the molecular mechanisms employed by the virus to infect the host cells and to interact with their components. Experimental protein-protein interactions described in the scientific literature have been systematically captured into several molecular interaction databases. These data are organized in structured formats and can be easily downloaded by users to perform further bioinformatic and network studies. Network analysis of available virus-host interactomes allow us to understand how the host interactome is perturbed upon viral infection and what are the key host proteins targeted by the virus and the main cellular pathways that are subverted. In this review, we give an overview of publicly available viral-human protein-protein interactions resources and the community standards, curation rules and adopted ontologies. A description of the main virus-human interactome available is provided, together with the main network analyses that have been performed. We finally discuss the main limitations and future challenges to assess the quality and reliability of protein-protein interaction datasets and resources.
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Affiliation(s)
- Deeya Saha
- Aix-Marseille Univ., Inserm, TAGC, UMR_S1090, Marseille, France
| | | | - Christine Brun
- Aix-Marseille Univ., Inserm, TAGC, UMR_S1090, Marseille, France
- CNRS, Marseille, France
| | - Andreas Zanzoni
- Aix-Marseille Univ., Inserm, TAGC, UMR_S1090, Marseille, France
- *Correspondence: Andreas Zanzoni,
| | - Luana Licata
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
- Luana Licata,
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22
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Trino S, Laurenzana I, Lamorte D, Calice G, De Stradis A, Santodirocco M, Sgambato A, Caivano A, De Luca L. Acute Myeloid Leukemia Cells Functionally Compromise Hematopoietic Stem/Progenitor Cells Inhibiting Normal Hematopoiesis Through the Release of Extracellular Vesicles. Front Oncol 2022; 12:824562. [PMID: 35371979 PMCID: PMC8965808 DOI: 10.3389/fonc.2022.824562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/17/2022] [Indexed: 12/02/2022] Open
Abstract
Acute myeloid leukemia (AML) is an aggressive and heterogeneous clonal disorder of hematopoietic stem/progenitor cells (HSPCs). It is not well known how leukemia cells alter hematopoiesis promoting tumor growth and leukemic niche formation. In this study, we investigated how AML deregulates the hematopoietic process of HSPCs through the release of extracellular vesicles (EVs). First, we found that AML cells released a heterogeneous population of EVs containing microRNAs involved in AML pathogenesis. Notably, AML-EVs were able to influence the fate of HSPCs modifying their transcriptome. In fact, gene expression profile of AML-EV-treated HSPCs identified 923 down- and 630 up-regulated genes involved in hematopoiesis/differentiation, inflammatory cytokine production and cell movement. Indeed, most of the down-regulated genes are targeted by AML-EV-derived miRNAs. Furthermore, we demonstrated that AML-EVs were able to affect HSPC phenotype, modifying several biological functions, such as inhibiting cell differentiation and clonogenicity, activating inflammatory cytokine production and compromising cell movement. Indeed, a redistribution of HSPC populations was observed in AML-EV treated cells with a significant increase in the frequency of common myeloid progenitors and a reduction in granulocyte-macrophage progenitors and megakaryocyte-erythroid progenitors. This effect was accompanied by a reduction in HSPC colony formation. AML-EV treatment of HSPCs increased the levels of CCL3, IL-1B and CSF2 cytokines, involved in the inflammatory process and in cell movement, and decreased CXCR4 expression associated with a reduction of SDF-1 mediated-migration. In conclusion, this study demonstrates the existence of a powerful communication between AML cells and HSPCs, mediated by EVs, which suppresses normal hematopoiesis and potentially contributes to create a leukemic niche favorable to neoplastic development.
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Affiliation(s)
- Stefania Trino
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Ilaria Laurenzana
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Daniela Lamorte
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Giovanni Calice
- Laboratory of Preclinical and Translational Research, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Angelo De Stradis
- Institute for Sustainable Plant Protection, National Research Council (CNR), Bari, Italy
| | - Michele Santodirocco
- Trasfusional Medicine Department, Puglia Cord Blood Bank (CBB), Casa Sollievo Della Sofferenza Hospital, San Giovanni Rotondo, Italy
| | - Alessandro Sgambato
- Scientific Direction, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Antonella Caivano
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
| | - Luciana De Luca
- Unit of Clinical Pathology, Centro di Riferimento Oncologico della Basilicata (IRCCS-CROB), Rionero in Vulture, Italy
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23
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Naddaf E, Dasari S, Selcen D, Charlesworth MC, Johnson KL, Mauermann ML, Kourelis T. Proteomic profiling of sporadic late-onset nemaline myopathy. Ann Clin Transl Neurol 2022; 9:391-402. [PMID: 35187860 PMCID: PMC8935314 DOI: 10.1002/acn3.51527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/04/2022] [Indexed: 11/08/2022] Open
Abstract
Objective To define the proteomic profile of sporadic late‐onset nemaline myopathy (SLONM) and explore its pathogenesis. Methods We performed mass spectrometry on laser‐dissected frozen muscle samples from five patients with SLONM, three of whom with an associated monoclonal protein (MP), and four controls, to determine the proteomic profile of SLONM. Furthermore, we assessed the role of the MP by evaluating the expression of the immunoglobulin light chain variable regions (IGVL). Results There were 294 differentially expressed proteins: 272 upregulated and 22 downregulated. Among the top 100 upregulated proteins, the most common categories were: nuclear or nucleic acid metabolism (24%), extracellular matrix and basal lamina (17%), immune response (13%), and actin dynamics (8%). Downregulated proteins consisted mostly of contractile proteins. Among upregulated proteins, there were 65 with a role related to the immune system, including eight proteins involved in major histocompatibility complex 1 (MHC1) and antigen processing, 15 in MHCII complex and phagocytosis, and 23 in B and/or T‐cell function. Among nine upregulated immunoglobulin proteins, there were two IGVL genes. However, these were also detected in SLONM cases without an MP, with no evidence of clonally dominant immunoglobulin deposition. In muscle sections from SLONM patients, nemaline rods tended to accumulate in atrophic fibers with marked rarefaction of the myofibrils. Increased MHC1 reactivity was present in fibers containing nemaline rods as well as adjacent nonatrophic fibers. Conclusion Our findings suggest that aberrant immune activation is present in SLONM, but do not support a direct causal relationship between the MP and SLONM.
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Affiliation(s)
- Elie Naddaf
- Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Surendra Dasari
- Department of Qualitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Duygu Selcen
- Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Kenneth L Johnson
- Medical Genome Facility Proteomics Core, Mayo Clinic, Rochester, Minnesota, USA
| | - Michelle L Mauermann
- Division of Neuromuscular Medicine, Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Taxiarchis Kourelis
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
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24
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Jungers CF, Djuranovic S. Modulation of miRISC-Mediated Gene Silencing in Eukaryotes. Front Mol Biosci 2022; 9:832916. [PMID: 35237661 PMCID: PMC8882679 DOI: 10.3389/fmolb.2022.832916] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 01/18/2022] [Indexed: 11/13/2022] Open
Abstract
Gene expression is regulated at multiple levels in eukaryotic cells. Regulation at the post-transcriptional level is modulated by various trans-acting factors that bind to specific sequences in the messenger RNA (mRNA). The binding of different trans factors influences various aspects of the mRNA such as degradation rate, translation efficiency, splicing, localization, etc. MicroRNAs (miRNAs) are short endogenous ncRNAs that combine with the Argonaute to form the microRNA-induced silencing complex (miRISC), which uses base-pair complementation to silence the target transcript. RNA-binding proteins (RBPs) contribute to post-transcriptional control by influencing the mRNA stability and translation upon binding to cis-elements within the mRNA transcript. RBPs have been shown to impact gene expression through influencing the miRISC biogenesis, composition, or miRISC-mRNA target interaction. While there is clear evidence that those interactions between RBPs, miRNAs, miRISC and target mRNAs influence the efficiency of miRISC-mediated gene silencing, the exact mechanism for most of them remains unclear. This review summarizes our current knowledge on gene expression regulation through interactions of miRNAs and RBPs.
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25
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Gargani S, Lourou N, Arapatzi C, Tzanos D, Saridaki M, Dushku E, Chatzimike M, Sidiropoulos ND, Andreadou M, Ntafis V, Hatzis P, Kostourou V, Kontoyiannis DL. Inactivation of AUF1 in Myeloid Cells Protects From Allergic Airway and Tumor Infiltration and Impairs the Adenosine-Induced Polarization of Pro-Angiogenic Macrophages. Front Immunol 2022; 13:752215. [PMID: 35222366 PMCID: PMC8873154 DOI: 10.3389/fimmu.2022.752215] [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: 08/02/2021] [Accepted: 01/21/2022] [Indexed: 11/13/2022] Open
Abstract
The four isoforms of the RNA-binding protein hnRNPD/AUF1 have been proposed to limit the use of inflammatory mRNAs in innate immune cells. Mice engineered to lack AUF1s in all tissues are sensitive to acute inflammatory assaults; however, they also manifest complex degenerations obscuring assessment of AUF1s’ roles in innate immune cells. Here, we restricted a debilitating AUF1 mutation to the mouse myeloid lineage and performed disease-oriented phenotypic analyses to assess the requirement of AUF1s in variable contexts of innate immune reactivity. Contrary to the whole-body mutants, the myeloid mutants of AUF1s did not show differences in their susceptibility to cytokine storms occurring during endotoxemia; neither in type-I cell-mediated reactions driving intestinal inflammation by chemical irritants. Instead, they were resistant to allergic airway inflammation and displayed reductions in inflammatory infiltrates and an altered T-helper balance. The ex-vivo analysis of macrophages revealed that the loss of AUF1s had a minimal effect on their proinflammatory gene expression. Moreover, AUF1s were dispensable for the classical polarization of cultured macrophages by LPS & IFNγ correlating with the unchanged response of mutant mice to systemic and intestinal inflammation. Notably, AUF1s were also dispensable for the alternative polarization of macrophages by IL4, TGFβ and IL10, known to be engaged in allergic reactions. In contrast, they were required to switch proinflammatory macrophages towards a pro-angiogenic phenotype induced by adenosine receptor signals. Congruent to this, the myeloid mutants of AUF1 displayed lower levels of vascular remodeling factors in exudates from allergen exposed lungs; were unable to support the growth and inflammatory infiltration of transplanted melanoma tumors; and failed to vascularize inert grafts unless supplemented with angiogenic factors. Mechanistically, adenosine receptor signals enhanced the association of AUF1s with the Vegfa, Il12b, and Tnf mRNAs to differentially regulate and facilitate the pro-angiogenic switch. Our data collectively demonstrates that AUF1s do not act as general anti-inflammatory factors in innate immune cells but have more specialized roles in regulons allowing specific innate immune cell transitions to support tissue infiltration and remodeling processes.
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Affiliation(s)
- Sofia Gargani
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Niki Lourou
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christina Arapatzi
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Dimitris Tzanos
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Marania Saridaki
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Esmeralda Dushku
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Margarita Chatzimike
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Nikolaos D. Sidiropoulos
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Margarita Andreadou
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Vasileios Ntafis
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Pantelis Hatzis
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Vassiliki Kostourou
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
| | - Dimitris L. Kontoyiannis
- Biomedical Sciences Research Centre “Alexander Fleming”, Institute of Fundamental Biomedical Research, Vari, Greece
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
- *Correspondence: Dimitris L. Kontoyiannis, ;
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26
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Louis JM, Agarwal A, Mondal S, Talukdar I. A global analysis on the differential regulation of RNA binding proteins (RBPs) by TNF–α as potential modulators of metabolic syndromes. BBA ADVANCES 2022; 2:100037. [PMID: 37082594 PMCID: PMC10074950 DOI: 10.1016/j.bbadva.2021.100037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 12/12/2021] [Accepted: 12/15/2021] [Indexed: 11/25/2022] Open
Abstract
Metabolic syndrome (MetS) is associated with a group of conditions, which enhances the risk of diabetes, heart diseases and stroke in the affected individuals. Earlier reports from our lab have shown that Tumor necrosis factor-α (TNF-α) significantly modulates the expression of 56 genes at the alternative splicing level which are involved in various signaling and metabolic pathways (MetS genes) connected to MetS. These MetS genes were predicted to interact with various RNA-binding proteins (RBPs) when exposed to TNF-α, resulting changes in their alternative splicing patterns. Here we are presenting data of an RNA-Seq analysis, which identified 1218 unique, and significantly regulated genes by TNF-α, 15% of which are RBPs . Among the 1218 genes, 204 genes have been identified as MetS genes by the ingenuity pathway analysis, and 10% of the MetS genes are found as RBPs. Our results also show that TNF-α changes the phosphorylation status of certain RBPs such as SR proteins, crucial players in alternative splicing, possibly via changing the activation status of certain upstream signaling molecules which also act as upstream kinases for these proteins. Taken together, these findings suggest that TNF-α influences the regulation of the RBPs at the various levels for their expression, which may lead to the alteration of the splicing pattern of the MetS genes. MetS genes acting as RBPs and are modulated by TNF-α, predict the existence of highly interconnected mechanisms which require further analysis to understand their dual roles on the onset of these diseases.
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27
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Schneider-Lunitz V, Ruiz-Orera J, Hubner N, van Heesch S. Multifunctional RNA-binding proteins influence mRNA abundance and translational efficiency of distinct sets of target genes. PLoS Comput Biol 2021; 17:e1009658. [PMID: 34879078 PMCID: PMC8687540 DOI: 10.1371/journal.pcbi.1009658] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 12/20/2021] [Accepted: 11/18/2021] [Indexed: 12/12/2022] Open
Abstract
RNA-binding proteins (RBPs) can regulate more than a single aspect of RNA metabolism. We searched for such previously undiscovered multifunctionality within a set of 143 RBPs, by defining the predictive value of RBP abundance for the transcription and translation levels of known RBP target genes across 80 human hearts. This led us to newly associate 27 RBPs with cardiac translational regulation in vivo. Of these, 21 impacted both RNA expression and translation, albeit for virtually independent sets of target genes. We highlight a subset of these, including G3BP1, PUM1, UCHL5, and DDX3X, where dual regulation is achieved through differential affinity for target length, by which separate biological processes are controlled. Like the RNA helicase DDX3X, the known splicing factors EFTUD2 and PRPF8—all identified as multifunctional RBPs by our analysis—selectively influence target translation rates depending on 5’ UTR structure. Our analyses identify dozens of RBPs as being multifunctional and pinpoint potential novel regulators of translation, postulating unanticipated complexity of protein-RNA interactions at consecutive stages of gene expression. The lifecycle of an RNA molecule is controlled by hundreds of proteins that can bind RNA, also known as RNA-binding proteins (RBPs). These proteins recognize landing sites within the RNA and guide the RNA’s transcription from DNA, its processing into a mature messenger RNA, its translation into protein, or its degradation once the RNA is no longer needed. Although we now mechanistically understand how certain RBPs regulate these processes, for many RBP-target interactions the consequences imposed by RNA binding are not well understood. For 143 RBPs with known RNA binding positions, the authors of the current study investigated how RNA molecules responded to fluctuations in the expression levels of these RBPs, across each of 80 human hearts. Using statistical approaches, they could show that many RBPs influenced stages of the RNA lifecycle that they were not known to be involved in. Some RBPs turned out to be true "all-rounders" of RNA metabolism: they controlled the RNA transcript levels of some genes, whereas they influenced the translation rates of others. This unexpected multifunctionality unveiled previously hidden aspects of the everyday RNA-binding protein working life.
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Affiliation(s)
- Valentin Schneider-Lunitz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Jorge Ruiz-Orera
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
| | - Norbert Hubner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- * E-mail: (NH); (SvH)
| | - Sebastiaan van Heesch
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands
- * E-mail: (NH); (SvH)
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28
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Zandhuis ND, Nicolet BP, Wolkers MC. RNA-Binding Protein Expression Alters Upon Differentiation of Human B Cells and T Cells. Front Immunol 2021; 12:717324. [PMID: 34867946 PMCID: PMC8635512 DOI: 10.3389/fimmu.2021.717324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 10/27/2021] [Indexed: 12/25/2022] Open
Abstract
B cells and T cells are key players in the defence against infections and malignancies. To exert their function, B cells and T cells differentiate into effector and memory cells. Tight regulation of these differentiation processes is key to prevent their malfunction, which can result in life-threatening disease. Lymphocyte differentiation relies on the appropriate timing and dosage of regulatory molecules, and post-transcriptional gene regulation (PTR) is a key player herein. PTR includes the regulation through RNA-binding proteins (RBPs), which control the fate of RNA and its translation into proteins. To date, a comprehensive overview of the RBP expression throughout lymphocyte differentiation is lacking. Using transcriptome and proteome analyses, we here catalogued the RBP expression for human B cells and T cells. We observed that even though the overall RBP expression is conserved, the relative RBP expression is distinct between B cells and T cells. Differentiation into effector and memory cells alters the RBP expression, resulting into preferential expression of different classes of RBPs. For instance, whereas naive T cells express high levels of translation-regulating RBPs, effector T cells preferentially express RBPs that modulate mRNA stability. Lastly, we found that cytotoxic CD8+ and CD4+ T cells express a common RBP repertoire. Combined, our study reveals a cell type-specific and differentiation-dependent RBP expression landscape in human lymphocytes, which will help unravel the role of RBPs in lymphocyte function.
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Affiliation(s)
- Nordin D. Zandhuis
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Benoit P. Nicolet
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
| | - Monika C. Wolkers
- Department of Hematopoiesis, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center (UMC), University of Amsterdam, Amsterdam, Netherlands
- Oncode Institute, Utrecht, Netherlands
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29
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Feng Q, Xia W, Wang S, Dai G, Jiao W, Guo N, Li H, Zhang G. Etodolac improves collagen induced rheumatoid arthritis in rats by inhibiting synovial inflammation, fibrosis and hyperplasia. MOLECULAR BIOMEDICINE 2021; 2:33. [PMID: 35006449 PMCID: PMC8607370 DOI: 10.1186/s43556-021-00052-1] [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: 03/16/2021] [Accepted: 08/04/2021] [Indexed: 12/14/2022] Open
Abstract
Synovial hyperplasia is the main cause of chronic rheumatoid arthritis (RA), but the mechanism of synovial hyperplasia is still unclear. Etodolac (ETD) is a selective COX-2 inhibitor for relieving pain and stiffness in RA, but the disease modifying effect is still lack of evidence. Proteomics method was used to study the differential proteome of synovial tissue in collagen induced arthritis (CIA) in rats. With the help of STRING analysis, the upregulated proteins enriched in the cluster of complement and coagulation cascades and platelet degranulation were highlighted, these proteins with fibrogenic factors Lum, CIV, CXI and Tgfbi participated in the synovial inflammation, fibrosis and hyperplasia in CIA. Based on KOG function class analysis, the proteins involved in the events of the central dogma was explored. They might be hyperplasia related proteins for most of them are related to the proliferation of cancer. ETD significantly attenuated synovial inflammation, fibrosis and hyperplasia in CIA rats by downregulating these proteins. Several proteins have not been observed in RA so far, such as Tmsb4x, Pura, Nfic, Ruvbl1, Snrpd3, U2af2, Srrm2, Srsf7, Elavl1, Hnrnph1, Wars, Yars, Bzw2, Mcts1, Eif4b, Ctsh, Lamp1, Dpp7, Ptges3, Cdc37 and Septin9, they might be potentials targets for RA. Blood biochemistry tests showed the safety of 7 months use of ETD on rats. In conclusion, present study displayed a comprehensive mechanism of synovial hyperplasia in CIA rats, on this basis, the clinical value of ETD in the treatment of RA was well confirmed.
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Affiliation(s)
- Qin Feng
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China.,National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Wenkai Xia
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Shenglan Wang
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Guoxin Dai
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Weimei Jiao
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Na Guo
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Honghua Li
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China.,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China
| | - Guimin Zhang
- Lunan Pharmaceutical Group Co., Ltd., Linyi, China. .,Center for New Drug Safety Evaluation of Lunan Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China. .,National Engineering and Technology Research Center of Chirality Pharmaceutical, Lunan Pharmaceutical Group Co. Ltd., Linyi, China.
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30
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Trigiante G, Blanes Ruiz N, Cerase A. Emerging Roles of Repetitive and Repeat-Containing RNA in Nuclear and Chromatin Organization and Gene Expression. Front Cell Dev Biol 2021; 9:735527. [PMID: 34722514 PMCID: PMC8552494 DOI: 10.3389/fcell.2021.735527] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 09/09/2021] [Indexed: 12/14/2022] Open
Abstract
Genomic repeats have been intensely studied as regulatory elements controlling gene transcription, splicing and genome architecture. Our understanding of the role of the repetitive RNA such as the RNA coming from genomic repeats, or repetitive sequences embedded in mRNA/lncRNAs, in nuclear and cellular functions is instead still limited. In this review we discuss evidence supporting the multifaceted roles of repetitive RNA and RNA binding proteins in nuclear organization, gene regulation, and in the formation of dynamic membrane-less aggregates. We hope that our review will further stimulate research in the consolidating field of repetitive RNA biology.
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Affiliation(s)
| | | | - Andrea Cerase
- Centre for Genomics and Child Health, Barts and The London School of Medicine and Dentistry, Blizard Institute, Queen Mary University of London, London, United Kingdom
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31
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Shetty A, Bhosale SD, Tripathi SK, Buchacher T, Biradar R, Rasool O, Moulder R, Galande S, Lahesmaa R. Interactome Networks of FOSL1 and FOSL2 in Human Th17 Cells. ACS OMEGA 2021; 6:24834-24847. [PMID: 34604665 PMCID: PMC8482465 DOI: 10.1021/acsomega.1c03681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Indexed: 05/10/2023]
Abstract
Dysregulated function of Th17 cells has implications in immunodeficiencies and autoimmune disorders. Th17 cell differentiation is orchestrated by a complex network of transcription factors, including several members of the activator protein (AP-1) family. Among the latter, FOSL1 and FOSL2 modulate the effector functions of Th17 cells. However, the molecular mechanisms underlying these effects are unclear, owing to the poorly characterized protein interaction networks of FOSL factors. Here, we establish the first interactomes of FOSL1 and FOSL2 in human Th17 cells, using affinity purification-mass spectrometry analysis. In addition to the known JUN proteins, we identified several novel binding partners of FOSL1 and FOSL2. Gene ontology analysis found a significant fraction of these interactors to be associated with RNA-binding activity, which suggests new mechanistic links. Intriguingly, 29 proteins were found to share interactions with FOSL1 and FOSL2, and these included key regulators of Th17 fate. We further validated the binding partners identified in this study by using parallel reaction monitoring targeted mass spectrometry and other methods. Our study provides key insights into the interaction-based signaling mechanisms of FOSL proteins that potentially govern Th17 cell differentiation and associated pathologies.
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Affiliation(s)
- Ankitha Shetty
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Santosh D. Bhosale
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- Protein
Research Group, Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M 5230, Denmark
| | - Subhash Kumar Tripathi
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
| | - Tanja Buchacher
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Rahul Biradar
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Omid Rasool
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Robert Moulder
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
| | - Sanjeev Galande
- Centre
of Excellence in Epigenetics, Department of Biology, Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Riitta Lahesmaa
- Turku
Bioscience Centre, University of Turku and
Åbo Akademi University, Turku 20520, Finland
- InFLAMES
Research Flagship Center, University of
Turku, Turku 20520, Finland
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32
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Borgonetti V, Coppi E, Galeotti N. Targeting the RNA-Binding Protein HuR as Potential Thera-Peutic Approach for Neurological Disorders: Focus on Amyo-Trophic Lateral Sclerosis (ALS), Spinal Muscle Atrophy (SMA) and Multiple Sclerosis. Int J Mol Sci 2021; 22:ijms221910394. [PMID: 34638733 PMCID: PMC8508990 DOI: 10.3390/ijms221910394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 01/03/2023] Open
Abstract
The importance of precise co- and post-transcriptional processing of RNA in the regulation of gene expression has become increasingly clear. RNA-binding proteins (RBPs) are a class of proteins that bind single- or double-chain RNA, with different affinities and selectivity, thus regulating the various functions of RNA and the fate of the cells themselves. ELAV (embryonic lethal/abnormal visual system)/Hu proteins represent an important family of RBPs and play a key role in the fate of newly transcribed mRNA. ELAV proteins bind AU-rich element (ARE)-containing transcripts, which are usually present on the mRNA of proteins such as cytokines, growth factors, and other proteins involved in neuronal differentiation and maintenance. In this review, we focused on a member of ELAV/Hu proteins, HuR, and its role in the development of neurodegenerative disorders, with a particular focus on demyelinating diseases.
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33
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Kovarik P, Bestehorn A, Fesselet J. Conceptual Advances in Control of Inflammation by the RNA-Binding Protein Tristetraprolin. Front Immunol 2021; 12:751313. [PMID: 34603339 PMCID: PMC8484758 DOI: 10.3389/fimmu.2021.751313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Regulated changes in mRNA stability are critical drivers of gene expression adaptations to immunological cues. mRNA stability is controlled mainly by RNA-binding proteins (RBPs) which can directly cleave mRNA but more often act as adaptors for the recruitment of the RNA-degradation machinery. One of the most prominent RBPs with regulatory roles in the immune system is tristetraprolin (TTP). TTP targets mainly inflammation-associated mRNAs for degradation and is indispensable for the resolution of inflammation as well as the maintenance of immune homeostasis. Recent advances in the transcriptome-wide knowledge of mRNA expression and decay rates together with TTP binding sites in the target mRNAs revealed important limitations in our understanding of molecular mechanisms of TTP action. Such orthogonal analyses lead to the discovery that TTP binding destabilizes some bound mRNAs but not others in the same cell. Moreover, comparisons of various immune cells indicated that an mRNA can be destabilized by TTP in one cell type while it remains stable in a different cell linage despite the presence of TTP. The action of TTP extends from mRNA destabilization to inhibition of translation in a subset of targets. This article will discuss these unexpected context-dependent functions and their implications for the regulation of immune responses. Attention will be also payed to new insights into the role of TTP in physiology and tissue homeostasis.
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Affiliation(s)
- Pavel Kovarik
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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34
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In Silico Analysis to Explore Lineage-Independent and -Dependent Transcriptional Programs Associated with the Process of Endothelial and Neural Differentiation of Human Induced Pluripotent Stem Cells. J Clin Med 2021; 10:jcm10184161. [PMID: 34575270 PMCID: PMC8471316 DOI: 10.3390/jcm10184161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/11/2021] [Accepted: 09/13/2021] [Indexed: 11/17/2022] Open
Abstract
Despite a major interest in understanding how the endothelial cell phenotype is established, the underlying molecular basis of this process is not yet fully understood. We have previously reported the generation of induced pluripotent stem cells (iPS) from human umbilical vein endothelial cells and differentiation of the resulting HiPS back to endothelial cells (Ec-Diff), as well as neural (Nn-Diff) cell lineage that contained both neurons and astrocytes. Furthermore, the identities of these cell lineages were established by gene array analysis. Here, we explored the same arrays to gain insight into the gene alteration processes that accompany the establishment of endothelial vs. non-endothelial neural cell phenotypes. We compared the expression of genes that code for transcription factors and epigenetic regulators when HiPS is differentiated into these endothelial and non-endothelial lineages. Our in silico analyses have identified cohorts of genes that are similarly up- or downregulated in both lineages, as well as those that exhibit lineage-specific alterations. Based on these results, we propose that genes that are similarly altered in both lineages participate in priming the stem cell for differentiation in a lineage-independent manner, whereas those that are differentially altered in endothelial compared to neural cells participate in a lineage-specific differentiation process. Specific GATA family members and their cofactors and epigenetic regulators (DNMT3B, PRDM14, HELLS) with a major role in regulating DNA methylation were among participants in priming HiPS for lineage-independent differentiation. In addition, we identified distinct cohorts of transcription factors and epigenetic regulators whose alterations correlated specifically with the establishment of endothelial vs. non-endothelial neural lineages.
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35
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Monzón-Casanova E, Bates KJ, Smith CWJ, Turner M. Essential requirement for polypyrimidine tract binding proteins 1 and 3 in the maturation and maintenance of mature B cells in mice. Eur J Immunol 2021; 51:2266-2273. [PMID: 34214192 PMCID: PMC11146436 DOI: 10.1002/eji.202149257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/20/2021] [Accepted: 07/01/2021] [Indexed: 11/09/2022]
Abstract
The maturation of immature B cells and the survival of mature B cells is stringently controlled to maintain a diverse repertoire of antibody specificities while avoiding self-reactivity. At the molecular level this is regulated by signaling from membrane Ig and the BAFF-receptor that sustain a pro-survival program of gene expression. Whether and how posttranscriptional mechanisms contribute to B cell maturation and survival remains poorly understood. Here, we show that the polypyrimidine tract binding proteins (PTBP) PTBP1 and PTBP3 bind to a large and overlapping set of transcripts in B cells. Both PTBP1 and PTBP3 bind to introns and exons where they are predicted to regulate alternative splicing. Moreover, they also show high-density of binding to 3' untranslated regions suggesting they influence the transcriptome in diverse ways. We show that PTBP1 and PTBP3 are required in B cells beyond the immature cell stage to sustain transitional B cells and the B1, marginal zone and follicular B cell lineages. Therefore, PTBP1 and PTBP3 promote the maturation of quiescent B cells by regulating gene expression at the posttranscriptional level.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kirsty J Bates
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
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36
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Crosstalk between RNA-Binding Proteins and Immune Microenvironment Revealed Two RBP Regulatory Patterns with Distinct Immunophenotypes in Periodontitis. J Immunol Res 2021; 2021:5588429. [PMID: 34285922 PMCID: PMC8275429 DOI: 10.1155/2021/5588429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 02/05/2023] Open
Abstract
Periodontitis is an inflammatory disease whose pathogenesis is closely related with immunology. RNA-binding proteins (RBPs) were found to play crucial roles in immunity. Therefore, we aimed to investigate the potential impact of RBPs in the immune microenvironment in periodontitis. The differential expressions of RBPs in periodontitis and healthy samples were determined and were used to construct an RBP-based classifier for periodontitis using logistic regression. The correlations between RBPs and immune characteristics were investigated by the Spearman correlation. Unsupervised clustering was conducted to identify the RBP regulatory patterns. RBP-related genes were identified by WGCNA, while biological distinctions were revealed by GSVA and GO. 24 dysregulated RBPs were identified, from which a 12-RBP classifier was established to distinguish periodontitis with AUC of 0.942. Close protein-protein interactions and expression correlations were observed especially between SPATS2 and ISG20. ISG20 and ESRP1 were found to be highly correlated with immunocyte infiltration, immune signaling activation, and HLA expressions in periodontitis. Two distinct RBP regulatory patterns were identified with different immune and other biological characteristics in periodontitis. Our findings indicate a significant impact of RBPs in shaping the immune microenvironment in periodontitis, which might bring new insights into the understanding of immune mechanisms in the pathogenesis of periodontitis.
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37
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Kinoshita C, Kubota N, Aoyama K. Interplay of RNA-Binding Proteins and microRNAs in Neurodegenerative Diseases. Int J Mol Sci 2021; 22:ijms22105292. [PMID: 34069857 PMCID: PMC8157344 DOI: 10.3390/ijms22105292] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/14/2021] [Accepted: 05/15/2021] [Indexed: 02/07/2023] Open
Abstract
The number of patients with neurodegenerative diseases (NDs) is increasing, along with the growing number of older adults. This escalation threatens to create a medical and social crisis. NDs include a large spectrum of heterogeneous and multifactorial pathologies, such as amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer’s disease, Parkinson’s disease, Huntington’s disease and multiple system atrophy, and the formation of inclusion bodies resulting from protein misfolding and aggregation is a hallmark of these disorders. The proteinaceous components of the pathological inclusions include several RNA-binding proteins (RBPs), which play important roles in splicing, stability, transcription and translation. In addition, RBPs were shown to play a critical role in regulating miRNA biogenesis and metabolism. The dysfunction of both RBPs and miRNAs is often observed in several NDs. Thus, the data about the interplay among RBPs and miRNAs and their cooperation in brain functions would be important to know for better understanding NDs and the development of effective therapeutics. In this review, we focused on the connection between miRNAs, RBPs and neurodegenerative diseases.
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Affiliation(s)
- Chisato Kinoshita
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
| | - Noriko Kubota
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Teikyo University Support Center for Women Physicians and Researchers, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan
| | - Koji Aoyama
- Department of Pharmacology, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi, Tokyo 173-8605, Japan;
- Correspondence: (C.K.); (K.A.); Tel.: +81-3-3964-3794 (C.K.); +81-3-3964-3793 (K.A.)
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38
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Deficiency of Tristetraprolin Triggers Hyperthermia through Enhancing Hypothalamic Inflammation. Int J Mol Sci 2021; 22:ijms22073328. [PMID: 33805094 PMCID: PMC8037390 DOI: 10.3390/ijms22073328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/19/2021] [Accepted: 03/20/2021] [Indexed: 11/17/2022] Open
Abstract
Tristetraprolin (TTP), an RNA-binding protein, controls the stability of RNA by capturing AU-rich elements on their target genes. It has recently been identified that TTP serves as an anti-inflammatory protein by guiding the unstable mRNAs of pro-inflammatory proteins in multiple cells. However, it has not yet been investigated whether TTP affects the inflammatory responses in the hypothalamus. Since hypothalamic inflammation is tightly coupled to the disturbance of energy homeostasis, we designed the current study to investigate whether TTP regulates hypothalamic inflammation and thereby affects energy metabolism by utilizing TTP-deficient mice. We observed that deficiency of TTP led to enhanced hypothalamic inflammation via stimulation of a variety of pro-inflammatory genes. In addition, microglial activation occurred in the hypothalamus, which was accompanied by an enhanced inflammatory response. In line with these molecular and cellular observations, we finally confirmed that deficiency of TTP results in elevated core body temperature and energy expenditure. Taken together, our findings unmask novel roles of hypothalamic TTP on energy metabolism, which is linked to inflammatory responses in hypothalamic microglial cells.
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39
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Schmidt N, Lareau CA, Keshishian H, Ganskih S, Schneider C, Hennig T, Melanson R, Werner S, Wei Y, Zimmer M, Ade J, Kirschner L, Zielinski S, Dölken L, Lander ES, Caliskan N, Fischer U, Vogel J, Carr SA, Bodem J, Munschauer M. The SARS-CoV-2 RNA-protein interactome in infected human cells. Nat Microbiol 2021; 6:339-353. [PMID: 33349665 PMCID: PMC7906908 DOI: 10.1038/s41564-020-00846-z] [Citation(s) in RCA: 204] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 12/03/2020] [Indexed: 01/08/2023]
Abstract
Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.
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Affiliation(s)
- Nora Schmidt
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Caleb A Lareau
- School of Medicine, Stanford University, Palo Alto, CA, USA
| | | | - Sabina Ganskih
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Cornelius Schneider
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Thomas Hennig
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | | | - Simone Werner
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Yuanjie Wei
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Matthias Zimmer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Jens Ade
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Luisa Kirschner
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Sebastian Zielinski
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
| | - Lars Dölken
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Eric S Lander
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Neva Caliskan
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
- Faculty of Medicine, University of Würzburg, Würzburg, Germany
| | - Utz Fischer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
- Department of Biochemistry, University of Würzburg, Würzburg, Germany
| | - Jörg Vogel
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - Steven A Carr
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jochen Bodem
- Institute for Virology and Immunobiology, Julius-Maximilians-University Würzburg, Würzburg, Germany.
| | - Mathias Munschauer
- Helmholtz Institute for RNA-based Infection Research, Helmholtz-Center for Infection Research, Würzburg, Germany.
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40
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Wang Z, Zhao M, Yin J, Liu L, Hu L, Huang Y, Liu A, Ouyang J, Min X, Rao S, Zhou W, Wu H, Yoshimura A, Lu Q. E4BP4-mediated inhibition of T follicular helper cell differentiation is compromised in autoimmune diseases. J Clin Invest 2021; 130:3717-3733. [PMID: 32191636 DOI: 10.1172/jci129018] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 03/17/2020] [Indexed: 12/18/2022] Open
Abstract
T follicular helper (Tfh) cells are indispensable for the formation of germinal center (GC) reactions, whereas T follicular regulatory (Tfr) cells inhibit Tfh-mediated GC responses. Aberrant activation of Tfh cells contributes substantially to the pathogenesis of autoimmune diseases, such as systemic lupus erythematosus (SLE). Nonetheless, the molecular mechanisms mitigating excessive Tfh cell differentiation are not fully understood. Herein we demonstrate that the adenovirus E4 promoter-binding protein (E4BP4) mediates a feedback loop and acts as a transcriptional brake to inhibit Tfh cell differentiation. Furthermore, we show that such an immunological mechanism is compromised in patients with SLE. Establishing mice with either conditional knockout (cKO) or knockin (cKI) of the E4bp4 gene in T cells reveals that E4BP4 strongly inhibits Tfh cell differentiation. Mechanistically, E4BP4 regulates Bcl6 transcription by recruiting the repressive epigenetic modifiers HDAC1 and EZH2. E4BP4 phosphorylation site mutants have limited capability with regard to inhibiting Tfh cell differentiation. In SLE, we detected impaired phosphorylation of E4BP4, finding that this compromised transcription factor is positively correlated with disease activity. These findings unveiled molecular mechanisms by which E4BP4 restrains Tfh cell differentiation, whose compromised function is associated with uncontrolled autoimmune reactions in SLE.
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Affiliation(s)
- Zijun Wang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Ming Zhao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Jinghua Yin
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Limin Liu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Longyuan Hu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Yi Huang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Aiyun Liu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Jiajun Ouyang
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Xiaoli Min
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Shijia Rao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Wenhui Zhou
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Haijing Wu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
| | - Akihiko Yoshimura
- Department of Microbiology and Immunology, Keio University School of Medicine, Tokyo, Japan
| | - Qianjin Lu
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, China.,Research Unit of Key Technologies of Diagnosis and Treatment for Immune-related Skin Diseases, Chinese Academy of Medical Sciences, Changsha, China
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41
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Džafo E, Bianchi N, Monticelli S. Cell-intrinsic mechanisms to restrain inflammatory responses in T lymphocytes. Immunol Rev 2021; 300:181-193. [PMID: 33507562 DOI: 10.1111/imr.12932] [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: 10/12/2020] [Revised: 10/29/2020] [Accepted: 11/08/2020] [Indexed: 12/14/2022]
Abstract
A mechanistic understanding of the regulatory circuits that control the effector responses of memory T helper lymphocytes, and in particular their ability to produce pro-inflammatory cytokines, may lead to effective therapeutic interventions in all immune-related diseases. Activation of T lymphocytes induces robust immune responses that in most cases lead to the complete eradication of invading pathogens or tumor cells. At the same time, however, such responses must be both highly controlled in magnitude and limited in time to avoid unnecessary damage. To achieve such sophisticated level of control, T lymphocytes have at their disposal an array of transcriptional and post-transcriptional regulatory mechanisms that ensure the acquisition of a phenotype that is tailored to the incoming stimulus while restraining unwarranted activation, eventually leading to the resolution of the inflammatory response. Here, we will discuss some of these cell-intrinsic mechanisms that control T cell responses and involve transcription factors, microRNAs, and RNA-binding proteins. We will also explore how the same mechanisms can be involved both in anti-tumor responses and in autoimmunity.
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Affiliation(s)
- Emina Džafo
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Niccolò Bianchi
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Silvia Monticelli
- Institute for Research in Biomedicine (IRB), Università della Svizzera italiana (USI), Bellinzona, Switzerland
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42
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Zhang Y, Wei Z, Dong H, Zhou J, Yuan J, Ni B, Wu Y, Han C, Tian Y. Regulation of mRNA stability by RBPs and noncoding RNAs contributing to the pathogenicity of Th17 cells. RNA Biol 2020; 18:647-656. [PMID: 33302787 DOI: 10.1080/15476286.2020.1862567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Th17 cells remain one of the most important subsets of T cells in numerous autoimmune and chronic inflammatory diseases. Posttranscriptional regulation (PTR), especially mRNA stability, has recently emerged as an important mechanism that controls the fate of Th17 cells. This review summarizes the current knowledge on RNA-binding proteins (RBPs), microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) that induce mRNA stability changes and their roles in mediating the differentiation, proliferation, function, and migration of Th17 cells. In addition, we summarize the role of RNA modifications and nonsense-mediated mRNA decay (NMD) in Th17 cells. Ongoing research will help to identify practical applications for the regulation of mRNA stability and provide potential targets to prevent and treat Th17-related autoimmune diseases.
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Affiliation(s)
- Yiwei Zhang
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China.,Department of Orthopedics, The First Affiliated Hospital of Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Zhiyuan Wei
- Department of Orthopedics, The First Affiliated Hospital of Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Hui Dong
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Jian Zhou
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Jizhao Yuan
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Bing Ni
- Department of Pathophysiology, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Yuzhang Wu
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Chao Han
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
| | - Yi Tian
- Institute of Immunology, PLA, Third Military Medical University (Army Medical University), Chongqing, PR China
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43
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Development and validation of a six-RNA binding proteins prognostic signature and candidate drugs for prostate cancer. Genomics 2020; 112:4980-4992. [PMID: 32882325 DOI: 10.1016/j.ygeno.2020.08.034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/09/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023]
Abstract
The dysregulation of RNA binding proteins (RBPs) regulates the progression of several cancers. However, information on the overall functions of RBPs in prostate cancer (PCa) remains largely understudied. Therefore, based on the TCGA dataset, this study identified 144 differentially expressed RBPs in tumors compared to normal tissues. Subsequently, through univariate, LASSO and multivariate Cox regression analysis, 6 RBP genes among them, MSI1, MBNL2, LENG9, REXO2, RNASE1, and PABPC1L were screened as prognostic hub genes and prognostic signature was further identified. Further analysis indicated that the high-risk group was significantly associated with poor RFS, which was validated in the MSKCC cohort. Besides, patients in the high-risk group were closely associated with dysregulation of DNA damage repair pathway, copy number alteration, tumor burden mutation, and low-response to cisplatin (P < 0.001), and bicalutamide (P < 0.001). Using the Connectivity Map, we finally predicted 3 drugs including, ribavirin, carmustine, and carbenoxolone. In summary, we identified six-RBP gene signature and 3 potential drugs against PCa, which might promote the individualized treatment strategies and further improve the quality of life among PCa patients.
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Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood 2020; 136:572-584. [PMID: 32160292 PMCID: PMC7440974 DOI: 10.1182/blood.2019002385] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established, and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we resequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent noncoding mutations surrounding a single exon of the HNRNPH1gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent noncoding mutations in disrupting an autoregulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly imply a role for aberrant regulation of messenger RNA processing in MCL pathobiology.
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Affiliation(s)
- Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Barbara Meissner
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Merrill Boyle
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Quratulain Qureshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - Constantine S Tam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Rishu Agarwal
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Randy D Gascoyne
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Christian Steidl
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Joseph Connors
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Diego Villa
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Marra
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - David W Scott
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
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45
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Sneezum L, Eislmayr K, Dworak H, Sedlyarov V, Le Heron A, Ebner F, Fischer I, Iwakura Y, Kovarik P. Context-Dependent IL-1 mRNA-Destabilization by TTP Prevents Dysregulation of Immune Homeostasis Under Steady State Conditions. Front Immunol 2020; 11:1398. [PMID: 32733464 PMCID: PMC7358311 DOI: 10.3389/fimmu.2020.01398] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/01/2020] [Indexed: 12/24/2022] Open
Abstract
The bioavailability of the major pro-inflammatory cytokines IL-1α and IL-1β is tightly controlled by transcription and post-translational processing to prevent hyperinflammation. The role of mRNA decay in maintenance of physiological IL-1 amounts remained unknown. Here we show that the down-regulation of Il1a and Il1b mRNA by the mRNA-destabilizing protein TTP (gene Zfp36) is required for immune homeostasis. The TTP deficiency syndrome, a multi organ inflammation in TTP-/- mice, was significantly ameliorated upon deletion of the IL-1 receptor. Il1a and Il1b played non-redundant roles in triggering the pathological IL-1 signaling in TTP-/- mice. Accordingly, tissues from TTP-/- animals contained increased amounts of Il1b mRNA. Unexpectedly, TTP destabilized Il1b mRNA in cell type-specific ways as evident from RNA-Seq and mRNA stability assays. These results demonstrate that TTP-driven mRNA destabilization depends on the cellular context. Moreover, such context-defined mRNA decay is essential for keeping steady state IL-1 levels in the physiological range.
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Affiliation(s)
- Lucy Sneezum
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Kevin Eislmayr
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Helene Dworak
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Vitaly Sedlyarov
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Anita Le Heron
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Florian Ebner
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Irmgard Fischer
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Yoichiro Iwakura
- Research Institute for Biomedical Sciences, Tokyo University of Science, Tokyo, Japan
| | - Pavel Kovarik
- Max Perutz Labs, Vienna Biocenter, University of Vienna, Vienna, Austria
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Zhang H, Brown RD, Stenmark KR, Hu CJ. RNA-Binding Proteins in Pulmonary Hypertension. Int J Mol Sci 2020; 21:ijms21113757. [PMID: 32466553 PMCID: PMC7312837 DOI: 10.3390/ijms21113757] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 12/21/2022] Open
Abstract
Pulmonary hypertension (PH) is a life-threatening disease characterized by significant vascular remodeling and aberrant expression of genes involved in inflammation, apoptosis resistance, proliferation, and metabolism. Effective therapeutic strategies are limited, as mechanisms underlying PH pathophysiology, especially abnormal expression of genes, remain unclear. Most PH studies on gene expression have focused on gene transcription. However, post-transcriptional alterations have been shown to play a critical role in inflammation and metabolic changes in diseases such as cancer and systemic cardiovascular diseases. In these diseases, RNA-binding proteins (RBPs) have been recognized as important regulators of aberrant gene expression via post-transcriptional regulation; however, their role in PH is less clear. Identifying RBPs in PH is of great importance to better understand PH pathophysiology and to identify new targets for PH treatment. In this manuscript, we review the current knowledge on the role of dysregulated RBPs in abnormal mRNA gene expression as well as aberrant non-coding RNA processing and expression (e.g., miRNAs) in PH.
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Affiliation(s)
- Hui Zhang
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - R. Dale Brown
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - Kurt R. Stenmark
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
| | - Cheng-Jun Hu
- Cardiovascular Pulmonary Research Laboratories, Departments of Pediatrics and Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; (H.Z.); (R.D.B.); (K.R.S.)
- Department of Craniofacial Biology School of Dental Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Correspondence: ; Tel.: +1-303-724-4576; Fax: +1-303-724-4580
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Tu Y, Wu X, Yu F, Dang J, Wei Y, Yu H, Liao W, Zhang Y, Wang J. Tristetraprolin-RNA interaction map reveals a novel TTP-RelB regulatory network for innate immunity gene expression. Mol Immunol 2020; 121:59-71. [DOI: 10.1016/j.molimm.2020.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 01/03/2020] [Accepted: 02/07/2020] [Indexed: 02/03/2023]
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48
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Chagas PF, Baroni M, Brassesco MS, Tone LG. Interplay between the RNA binding‐protein Musashi and developmental signaling pathways. J Gene Med 2020; 22:e3136. [DOI: 10.1002/jgm.3136] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/19/2019] [Accepted: 10/20/2019] [Indexed: 12/17/2022] Open
Affiliation(s)
- Pablo Ferreira Chagas
- Department of GeneticsRibeirão Preto Medical School, University of São Paulo Ribeirão Preto São Paulo Brazil
| | - Mirella Baroni
- Department of GeneticsRibeirão Preto Medical School, University of São Paulo Ribeirão Preto São Paulo Brazil
| | - María Sol Brassesco
- Department of Biology, Faculty of Philosophy, Sciences and Letters at Ribeirão PretoUniversity of São Paulo Brazil
| | - Luiz Gonzaga Tone
- Department of GeneticsRibeirão Preto Medical School, University of São Paulo Ribeirão Preto São Paulo Brazil
- Department of PediatricsRibeirão Preto Medical School São Paulo
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49
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Govindappa PK, Patil M, Garikipati VNS, Verma SK, Saheera S, Narasimhan G, Zhu W, Kishore R, Zhang J, Krishnamurthy P. Targeting exosome-associated human antigen R attenuates fibrosis and inflammation in diabetic heart. FASEB J 2019; 34:2238-2251. [PMID: 31907992 DOI: 10.1096/fj.201901995r] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 11/14/2019] [Accepted: 11/21/2019] [Indexed: 12/16/2022]
Abstract
RNA-binding proteins like human antigen R (HuR) are key regulators in post-transcriptional control of gene expression in several pathophysiological conditions. Diabetes adversely affects monocyte/macrophage biology and function. It is not known whether diabetic milieu affects cellular/exosome-HuR and its implications on cardiac inflammation and fibrosis. Here, we evaluate in vitro and in vivo effects of diabetic milieu on macrophage cellular/exosome-HuR, alterations in intercellular cross talk with fibroblasts, and its impact on cardiac remodeling. Human failing hearts show higher HuR levels. Diabetic milieu activates HuR expression in cardiac- and cultured bone marrow-derived macrophages (BMMØ) and stimulates HuR nuclear-to-cytoplasmic translocation and exosome transfer. Exosomes from macrophages exposed to diabetic milieu (high glucose or db/db mice) significantly increase inflammatory and profibrogenic responses in fibroblast (in vitro) and cardiac fibrosis in mice. Intriguingly, Exo-HuR deficiency (HuR knockdown in macrophage) abrogates the above effects. In diabetic mice, macrophage depletion followed by reconstitution with BMMØ-derived HuR-deficient exosomes inhibits angiotensin II-induced cardiac fibrosis response and preserves left ventricle function as compared to control-exosome administration. To the best of our knowledge, this is the first study to demonstrate that diabetes activates BMMØ HuR expression and its transfer into exosome. The data suggest that HuR might be targeted to alleviate macrophage dysfunction and pathological fibrosis in diabetes.
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Affiliation(s)
- Prem Kumar Govindappa
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
| | - Mallikarjun Patil
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
| | | | - Suresh K Verma
- Division of Cardiovascular Disease, School of Medicine, University of Alabama at Birmingham, AL, USA
| | - Sherin Saheera
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
| | - Gayathri Narasimhan
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
| | - Wuqiang Zhu
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
| | - Raj Kishore
- Center for Translational Medicine, Temple University School of Medicine, Philadelphia, PA, USA
| | - Jianyi Zhang
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
| | - Prasanna Krishnamurthy
- Department of Biomedical Engineering, Schools of Medicine and Engineering, The University of Alabama at Birmingham, AL, USA
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50
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Horwitz V, Cohen-Gihon I, Egoz I, Dachir S, Cohen M, Cohen L, Gutman H, Gez R, Kadar T, Gore A, Beth-Din A, Zvi A, Zaide G, Israeli O. A comprehensive analysis of corneal mRNA levels during sulfur mustard induced ocular late pathology in the rabbit model using RNA sequencing. Exp Eye Res 2019; 184:201-212. [DOI: 10.1016/j.exer.2019.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 04/12/2019] [Indexed: 01/21/2023]
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