1
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Becker M, Dirschl SM, Scherm MG, Serr I, Daniel C. Niche-specific control of tissue function by regulatory T cells-Current challenges and perspectives for targeting metabolic disease. Cell Metab 2024; 36:229-239. [PMID: 38218187 DOI: 10.1016/j.cmet.2023.12.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/30/2023] [Accepted: 12/15/2023] [Indexed: 01/15/2024]
Abstract
Tissue regulatory T cells (Tregs) exert pivotal functions in both immune and metabolic regulation, maintaining local tissue homeostasis, integrity, and function. Accordingly, Tregs play a crucial role in controlling obesity-induced inflammation and supporting efficient muscle function and repair. Depending on the tissue context, Tregs are characterized by unique transcriptomes, growth, and survival factors and T cell receptor (TCR) repertoires. This functional specialization offers the potential to selectively target context-specific Treg populations, tailoring therapeutic strategies to specific niches, thereby minimizing potential side effects. Here, we discuss challenges and perspectives for niche-specific Treg targeting, which holds promise for highly efficient and precise medical interventions to combat metabolic disease.
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Affiliation(s)
- Maike Becker
- Research Division Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, 80939 Munich, Germany; Deutsches Zentrum für Diabetesforschung (DZD), 85764 Munich, Germany
| | - Sandra M Dirschl
- Research Division Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, 80939 Munich, Germany; Deutsches Zentrum für Diabetesforschung (DZD), 85764 Munich, Germany
| | - Martin G Scherm
- Research Division Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, 80939 Munich, Germany; Deutsches Zentrum für Diabetesforschung (DZD), 85764 Munich, Germany
| | - Isabelle Serr
- Research Division Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, 80939 Munich, Germany; Deutsches Zentrum für Diabetesforschung (DZD), 85764 Munich, Germany
| | - Carolin Daniel
- Research Division Type 1 Diabetes Immunology, Helmholtz Diabetes Center at Helmholtz Zentrum München, 80939 Munich, Germany; Deutsches Zentrum für Diabetesforschung (DZD), 85764 Munich, Germany; Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, 80336 Munich, Germany.
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2
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Flynn AL, Gans J, Escobedo J, Zhu C, Florescu AM, Shankara S, Madden SL, Kim PS, Pao LI. RGS1 Modulates Autophagic and Metabolic Programs and Is a Critical Mediator of Human Regulatory T Cell Function. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 211:1656-1668. [PMID: 37850953 DOI: 10.4049/jimmunol.2200402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/27/2023] [Indexed: 10/19/2023]
Abstract
Regulatory T cells (Tregs) are critical mediators of immune tolerance and play a diametric role in cancer and autoimmunity. Tumor-infiltrating Tregs are often associated with poor prognosis in solid tumors because their enrichment in the tumor microenvironment contributes to immunosuppression. Conversely, dysregulation in the Treg compartment can disrupt self-tolerance, leading to autoimmunity. In the present study, we describe what is, to our knowledge, a novel regulator of Tregs, the GTPase activator regulator of G protein 1 (RGS1), demonstrating that RGS1-deficient human Tregs show downregulation of Treg-associated genes and are less immunosuppressive. These RGS1-deficient Tregs exhibit perturbations to the FOXP3-c-MYC transcriptional axis and downstream metabolic and autophagy programs by shifting their energy demands toward glycolysis and rendering them less autophagic. Taken together, RGS1 may serve as an apical node of Treg function by regulating the FOXP3-c-MYC transcriptional axis, thereby providing a therapeutic rationale for targeting RGS1 for treatment of cancer and autoimmune diseases.
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Affiliation(s)
| | - Joseph Gans
- Department of Translational Sciences, Sanofi, Cambridge, MA
| | | | - Cheng Zhu
- Department of Translational Sciences, Sanofi, Cambridge, MA
| | | | | | | | - Peter S Kim
- Department of Oncology, Sanofi, Cambridge, MA
| | - Lily I Pao
- Department of Oncology, Sanofi, Cambridge, MA
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3
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Zhou J, Li QQ. Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation. MOLECULAR HORTICULTURE 2023; 3:19. [PMID: 37789388 PMCID: PMC10536700 DOI: 10.1186/s43897-023-00066-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/07/2023] [Indexed: 10/05/2023]
Abstract
The sessile nature of plants confines their responsiveness to changing environmental conditions. Gene expression regulation becomes a paramount mechanism for plants to adjust their physiological and morphological behaviors. Alternative polyadenylation (APA) is known for its capacity to augment transcriptome diversity and plasticity, thereby furnishing an additional set of tools for modulating gene expression. APA has also been demonstrated to exhibit intimate associations with plant stress responses. In this study, we review APA dynamic features and consequences in plants subjected to both biotic and abiotic stresses. These stresses include adverse environmental stresses, and pathogenic attacks, such as cadmium toxicity, high salt, hypoxia, oxidative stress, cold, heat shock, along with bacterial, fungal, and viral infections. We analyzed the overarching research framework employed to elucidate plant APA response and the alignment of polyadenylation site transitions with the modulation of gene expression levels within the ambit of each stress condition. We also proposed a general APA model where transacting factors, including poly(A) factors, epigenetic regulators, RNA m6A modification factors, and phase separation proteins, assume pivotal roles in APA related transcriptome plasticity during stress response in plants.
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Affiliation(s)
- Jiawen Zhou
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China
| | - Qingshun Quinn Li
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystem, College of the Environment and Ecology, Xiamen University, Xiamen, 361102, Fujian, China.
- Biomedical Sciences, College of Dental Medicine, Western University of Health Sciences, Pomona, CA, 91766, USA.
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4
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Liu Y, Armbrister SA, Okeugo B, Mills TW, Daniel RC, Oh JH, van Pijkeren JP, Park ES, Saleh ZM, Lahiri S, Roos S, Rhoads JM. Probiotic-Derived Ecto-5'-Nucleotidase Produces Anti-Inflammatory Adenosine Metabolites in Treg-Deficient Scurfy Mice. Probiotics Antimicrob Proteins 2023; 15:1001-1013. [PMID: 37178405 PMCID: PMC10926147 DOI: 10.1007/s12602-023-10089-z] [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] [Accepted: 05/04/2023] [Indexed: 05/15/2023]
Abstract
Probiotic Limosilactobacillus reuteri DSM 17938 (DSM 17938) prolongs the survival of Treg-deficient scurfy (SF) mice and reduces multiorgan inflammation by a process requiring adenosine receptor 2A (A2A) on T cells. We hypothesized that L. reuteri-derived ecto-5'-nucleotidase (ecto-5'NT) activity acts to generate adenosine, which may be a central mediator for L. reuteri protection in SF mice. We evaluated DSM 17938-5'NT activity and the associated adenosine and inosine levels in plasma, gut, and liver of SF mice. We examined orally fed DSM 17938, DSM 17938Δ5NT (with a deleted 5'NT gene), and DSM 32846 (BG-R46) (a naturally selected strain derived from DSM 17938). Results showed that DSM 17938 and BG-R46 produced adenosine while "exhausting" AMP, whereas DSM 17938∆5NT did not generate adenosine in culture. Plasma 5'NT activity was increased by DSM 17938 or BG-R46, but not by DSM 17938Δ5NT in SF mice. BG-R46 increased both adenosine and inosine levels in the cecum of SF mice. DSM 17938 increased adenosine levels, whereas BG-R46 increased inosine levels in the liver. DSM 17938Δ5NT did not significantly change the levels of adenosine or inosine in the GI tract or the liver of SF mice. Although regulatory CD73+CD8+ T cells were decreased in spleen and blood of SF mice, these regulatory T cells could be increased by orally feeding DSM 17938 or BG-R46, but not DSM 17938Δ5NT. In conclusion, probiotic-5'NT may be a central mediator of DSM 17938 protection against autoimmunity. Optimal 5'NT activity from various probiotic strains could be beneficial in treating Treg-associated immune disorders in humans.
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Affiliation(s)
- Yuying Liu
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
| | - Shabba A Armbrister
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Beanna Okeugo
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Tingting W Mills
- Department of Biochemistry & Molecular Biology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Rhea C Daniel
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Jee-Hwan Oh
- Department of Food Science, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Evelyn S Park
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Zeina M Saleh
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Sharmistha Lahiri
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- BioGaia AB, Stockholm, Sweden
| | - JMarc Rhoads
- Department of Pediatrics, Division of Gastroenterology, McGovern Medical School, the University of Texas Health Science Center at Houston, Houston, TX, 77030, USA
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5
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Liu Y, Armbrister SA, Okeugo B, Mills TW, Daniel RC, Oh JH, Pijkeren JP, Park ES, Saleh ZM, Lahiri S, Roos S, Rhoads JM. Probiotic-derived ecto-5'-nucleotidase produces anti-inflammatory adenosine metabolites in Treg-deficient scurfy mice. RESEARCH SQUARE 2023:rs.3.rs-2781715. [PMID: 37066419 PMCID: PMC10104250 DOI: 10.21203/rs.3.rs-2781715/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
Probiotic Limosilactobacillus reuteri DSM 17938 (DSM 17938) prolonges the survival of Treg-deficient scurfy (SF) mice and reduces multiorgan inflammation by a process requiring adenosine receptor 2A (A 2A ) on T cells. We hypothesized that L. reuteri -derived ecto-5'-nucleotidase (ecto-5'NT) activity acts to generate adenosine, which may be a central mediator for L. reuteri protection in SF mice. We evaluated DSM 17938-5'NT activity and the associated adenosine and inosine levels in plasma, gut and liver of SF mice. We examined orally fed DSM 17938, DSM 17938Δ5NT (with a deleted 5'NT gene), and DSM 32846 (BG-R46) (a naturally selected strain derived from DSM 17938). Results showed that DSM 17938 and BG-R46 produced adenosine while "exhausting" AMP, whereas DSM 17938∆5NT did not generate adenosine in culture. Plasma 5'NT activity was increased by DSM 17938 or BG-R46, but not by DSM 17938Δ5NT in SF mice. BG-R46 increased both adenosine and inosine levels in the cecum of SF mice. DSM 17938 increased adenosine levels, whereas BG-R46 increased inosine levels in the liver. DSM 17938Δ5NT did not significantly change the levels of adenosine or inosine in the GI tract or the liver of SF mice. Although regulatory CD73 + CD8 + T cells were decreased in spleen and blood of SF mice, these regulatory T cells could be increased by orally feeding DSM 17938 or BG-R46, but not DSM 17938Δ5NT. In conclusion, probiotic-5'NT may be a central mediator of DSM 17938 protection against autoimmunity. Optimal 5'NT activity from various probiotic strains could be beneficial in treating Treg-associated immune disorders in humans.
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6
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Klaus T, Wilson A, Fichter M, Bros M, Bopp T, Grabbe S. The Role of LFA-1 for the Differentiation and Function of Regulatory T Cells—Lessons Learned from Different Transgenic Mouse Models. Int J Mol Sci 2023; 24:ijms24076331. [PMID: 37047302 PMCID: PMC10094578 DOI: 10.3390/ijms24076331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 03/30/2023] Open
Abstract
Regulatory T cells (Treg) are essential for the maintenance of peripheral tolerance. Treg dysfunction results in diverse inflammatory and autoimmune diseases with life-threatening consequences. β2-integrins (CD11a-d/CD18) play important roles in the migration of leukocytes into inflamed tissues and cell signaling. Of all β2-integrins, T cells, including Treg, only express CD11a/CD18, termed lymphocyte function-associated antigen 1 (LFA-1), on their surface. In humans, loss-of-function mutations in the common subunit CD18 result in leukocyte adhesion deficiency type-1 (LAD-1). Clinical symptoms vary depending on the extent of residual β2-integrin function, and patients may experience leukocytosis and recurrent infections. Some patients can develop autoimmune diseases, but the immune processes underlying the paradoxical situation of immune deficiency and autoimmunity have been scarcely investigated. To understand this complex phenotype, different transgenic mouse strains with a constitutive knockout of β2-integrins have been established. However, since a constitutive knockout affects all leukocytes and may limit the validity of studies focusing on their cell type-specific role, we established a Treg-specific CD18-floxed mouse strain. This mini-review aims to delineate the role of LFA-1 for the induction, maintenance, and regulatory function of Treg in vitro and in vivo as deduced from observations using the various β2-integrin-deficient mouse models.
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7
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Šimon M, Mikec Š, Morton NM, Atanur SS, Konc J, Horvat S, Kunej T. Genome-wide screening for genetic variants in polyadenylation signal (PAS) sites in mouse selection lines for fatness and leanness. Mamm Genome 2023; 34:12-31. [PMID: 36414820 PMCID: PMC9684942 DOI: 10.1007/s00335-022-09967-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 10/31/2022] [Indexed: 11/23/2022]
Abstract
Alternative polyadenylation (APA) determines mRNA stability, localisation, translation and protein function. Several diseases, including obesity, have been linked to APA. Studies have shown that single nucleotide polymorphisms in polyadenylation signals (PAS-SNPs) can influence APA and affect phenotype and disease susceptibility. However, these studies focussed on associations between single PAS-SNP alleles with very large effects and phenotype. Therefore, we performed a genome-wide screening for PAS-SNPs in the polygenic mouse selection lines for fatness and leanness by whole-genome sequencing. The genetic variants identified in the two lines were overlapped with locations of PAS sites obtained from the PolyASite 2.0 database. Expression data for selected genes were extracted from the microarray expression experiment performed on multiple tissue samples. In total, 682 PAS-SNPs were identified within 583 genes involved in various biological processes, including transport, protein modifications and degradation, cell adhesion and immune response. Moreover, 63 of the 583 orthologous genes in human have been previously associated with human diseases, such as nervous system and physical disorders, and immune, endocrine, and metabolic diseases. In both lines, PAS-SNPs have also been identified in genes broadly involved in APA, such as Polr2c, Eif3e and Ints11. Five PAS-SNPs within 5 genes (Car, Col4a1, Itga7, Lat, Nmnat1) were prioritised as potential functional variants and could contribute to the phenotypic disparity between the two selection lines. The developed PAS-SNPs catalogue presents a key resource for planning functional studies to uncover the role of PAS-SNPs in APA, disease susceptibility and fat deposition.
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Affiliation(s)
- Martin Šimon
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Špela Mikec
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Nicholas M. Morton
- grid.511172.10000 0004 0613 128XUniversity of Edinburgh, The Queen’s Medical Research Institute, Centre for Cardiovascular Science, Edinburgh, UK
| | - Santosh S. Atanur
- grid.7445.20000 0001 2113 8111Faculty of Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- grid.4305.20000 0004 1936 7988Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Janez Konc
- grid.454324.00000 0001 0661 0844Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia
| | - Simon Horvat
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
| | - Tanja Kunej
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Domžale, Slovenia
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8
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Linder J, Koplik SE, Kundaje A, Seelig G. Deciphering the impact of genetic variation on human polyadenylation using APARENT2. Genome Biol 2022; 23:232. [PMID: 36335397 PMCID: PMC9636789 DOI: 10.1186/s13059-022-02799-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 10/19/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND 3'-end processing by cleavage and polyadenylation is an important and finely tuned regulatory process during mRNA maturation. Numerous genetic variants are known to cause or contribute to human disorders by disrupting the cis-regulatory code of polyadenylation signals. Yet, due to the complexity of this code, variant interpretation remains challenging. RESULTS We introduce a residual neural network model, APARENT2, that can infer 3'-cleavage and polyadenylation from DNA sequence more accurately than any previous model. This model generalizes to the case of alternative polyadenylation (APA) for a variable number of polyadenylation signals. We demonstrate APARENT2's performance on several variant datasets, including functional reporter data and human 3' aQTLs from GTEx. We apply neural network interpretation methods to gain insights into disrupted or protective higher-order features of polyadenylation. We fine-tune APARENT2 on human tissue-resolved transcriptomic data to elucidate tissue-specific variant effects. By combining APARENT2 with models of mRNA stability, we extend aQTL effect size predictions to the entire 3' untranslated region. Finally, we perform in silico saturation mutagenesis of all human polyadenylation signals and compare the predicted effects of [Formula: see text] million variants against gnomAD. While loss-of-function variants were generally selected against, we also find specific clinical conditions linked to gain-of-function mutations. For example, we detect an association between gain-of-function mutations in the 3'-end and autism spectrum disorder. To experimentally validate APARENT2's predictions, we assayed clinically relevant variants in multiple cell lines, including microglia-derived cells. CONCLUSIONS A sequence-to-function model based on deep residual learning enables accurate functional interpretation of genetic variants in polyadenylation signals and, when coupled with large human variation databases, elucidates the link between functional 3'-end mutations and human health.
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Affiliation(s)
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, USA
- Department of Computer Science, Stanford University, Stanford, USA
| | - Georg Seelig
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, USA
- Department of Electrical and Computer Engineering, University of Washington, Seattle, USA
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9
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Nguyen TTL, Liu D, Gao H, Ye Z, Lee J, Wei L, Yu J, Zhang L, Wang L, Ordog T, Weinshilboum RM. Glucocorticoids mediate transcriptome-wide alternative polyadenylation: Potential mechanistic and clinical implications. Clin Transl Sci 2022; 15:2758-2771. [PMID: 36128656 PMCID: PMC9652440 DOI: 10.1111/cts.13402] [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: 05/10/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 01/26/2023] Open
Abstract
Alternative polyadenylation (APA) is a common genetic regulatory mechanism that generates distinct 3' ends for RNA transcripts. Changes in APA have been associated with multiple biological processes and disease phenotypes. However, the role of hormones and their drug analogs in APA remains largely unknown. In this study, we investigated transcriptome-wide the impact of glucocorticoids on APA in 30 human B-lymphoblastoid cell lines. We found that glucocorticoids could regulate APA for a subset of genes, possibly by changing the expression of 142 RNA-binding proteins, some with known APA-regulating properties. Interestingly, genes with glucocorticoid-mediated APA were enriched in viral translation-related pathways, while genes with glucocorticoid-mediated expression were enriched in interferon and interleukin pathways, suggesting that glucocorticoid-mediated APA might result in functional consequences distinct from gene expression. For example, glucocorticoids, a pharmacotherapy for severe COVID-19, were found to change the APA but not the expression of LY6E, an important antiviral inhibitor in coronavirus diseases. Glucocorticoid-mediated APA was also cell-type-specific, suggesting an action of glucocorticoids that may be unique to immune regulation. We also observed evidence for genotype-dependent glucocorticoid-mediated APA (referred to as pharmacogenomic-alterative polyadenylation quantitative trait loci), providing potential functional mechanisms for a series of common genetic variants that had previously been associated with immune disorders, but without a clear mechanism. In summary, this study reports a series of observations regarding the impact of glucocorticoids on APA, raising the possibility that this mechanism might have implications for both disease pathophysiology and drug therapy.
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Affiliation(s)
- Thanh Thanh L. Nguyen
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA,Mayo Clinic Graduate School of Biomedical SciencesMayo ClinicRochesterMinnesotaUSA,Division of Biomedical Statistics and Informatics, Department of Health Sciences ResearchMayo ClinicRochesterMinnesotaUSA
| | - Duan Liu
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Zhenqing Ye
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA,Present address:
Greehey Children's Cancer Research InstituteUniversity of Texas Health San AntonioSan AntonioTexasUSA
| | - Jeong‐Heon Lee
- Department of Laboratory Medicine and PathologyMayo ClinicRochesterMinnesotaUSA
| | - Lixuan Wei
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Jia Yu
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Lingxin Zhang
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Liewei Wang
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
| | - Tamas Ordog
- Department of Physiology and Biomedical EngineeringMayo ClinicRochesterMinnesotaUSA,Division of Gastroenterology and Hepatology, Department of Internal MedicineMayo ClinicRochesterMinnesotaUSA
| | - Richard M. Weinshilboum
- Department of Molecular Pharmacology and Experimental TherapeuticsMayo ClinicRochesterMinnesotaUSA
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10
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Li Z, Li Y, Zhang B, Li Y, Long Y, Zhou J, Zou X, Zhang M, Hu Y, Chen W, Gao X. DeeReCT-APA: Prediction of Alternative Polyadenylation Site Usage Through Deep Learning. GENOMICS, PROTEOMICS & BIOINFORMATICS 2022; 20:483-495. [PMID: 33662629 PMCID: PMC9801043 DOI: 10.1016/j.gpb.2020.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/28/2020] [Accepted: 06/12/2020] [Indexed: 01/26/2023]
Abstract
Alternative polyadenylation (APA) is a crucial step in post-transcriptional regulation. Previous bioinformatic studies have mainly focused on the recognition of polyadenylation sites (PASs) in a given genomic sequence, which is a binary classification problem. Recently, computational methods for predicting the usage level of alternative PASs in the same gene have been proposed. However, all of them cast the problem as a non-quantitative pairwise comparison task and do not take the competition among multiple PASs into account. To address this, here we propose a deep learning architecture, Deep Regulatory Code and Tools for Alternative Polyadenylation (DeeReCT-APA), to quantitatively predict the usage of all alternative PASs of a given gene. To accommodate different genes with potentially different numbers of PASs, DeeReCT-APA treats the problem as a regression task with a variable-length target. Based on a convolutional neural network-long short-term memory (CNN-LSTM) architecture, DeeReCT-APA extracts sequence features with CNN layers, uses bidirectional LSTM to explicitly model the interactions among competing PASs, and outputs percentage scores representing the usage levels of all PASs of a gene. In addition to the fact that only our method can quantitatively predict the usage of all the PASs within a gene, we show that our method consistently outperforms other existing methods on three different tasks for which they are trained: pairwise comparison task, highest usage prediction task, and ranking task. Finally, we demonstrate that our method can be used to predict the effect of genetic variations on APA patterns and sheds light on future mechanistic understanding in APA regulation. Our code and data are available at https://github.com/lzx325/DeeReCT-APA-repo.
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Affiliation(s)
- Zhongxiao Li
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
| | - Yisheng Li
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Bin Zhang
- Cancer Science Institute of Singapore, Singapore 117599, Singapore
| | - Yu Li
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia
| | - Yongkang Long
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia,Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Juexiao Zhou
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Xudong Zou
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Min Zhang
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China
| | - Yuhui Hu
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China,Corresponding authors.
| | - Wei Chen
- Department of Biology, Southern University of Science and Technology (SUSTech), Shenzhen 518055, China,Corresponding authors.
| | - Xin Gao
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division, Thuwal 23955-6900, Saudi Arabia,Corresponding authors.
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11
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Vijayakumar A, Park A, Steitz JA. Modulation of mRNA 3'-End Processing and Transcription Termination in Virus-Infected Cells. Front Immunol 2022; 13:828665. [PMID: 35222412 PMCID: PMC8866245 DOI: 10.3389/fimmu.2022.828665] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/24/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic mRNA 3´-end processing is a multi-step process beginning with pre-mRNA transcript cleavage followed by poly(A) tail addition. Closely coupled to transcription termination, 3´-end processing is a critical step in the regulation of gene expression, and disruption of 3´-end processing is known to affect mature mRNA levels. Various viral proteins interfere with the 3´-end processing machinery, causing read-through transcription and altered levels of mature transcripts through inhibition of cleavage and polyadenylation. Thus, disruption of 3´-end processing contributes to widespread host shutoff, including suppression of the antiviral response. Additionally, observed features of read-through transcripts such as decreased polyadenylation, nuclear retention, and decreased translation suggest that viruses may utilize these mechanisms to modulate host protein production and dominate cellular machinery. The degree to which the effects of read-through transcript production are harnessed by viruses and host cells remains unclear, but existing research highlights the importance of host 3´-end processing modulation during viral infection.
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Affiliation(s)
- Aarthi Vijayakumar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
| | - Annsea Park
- Department of Immunobiology, Yale University, New Haven, CT, United States
| | - Joan A Steitz
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, United States
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12
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Fe-S clusters masquerading as zinc finger proteins. J Inorg Biochem 2022; 230:111756. [DOI: 10.1016/j.jinorgbio.2022.111756] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 02/01/2022] [Accepted: 02/06/2022] [Indexed: 02/06/2023]
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13
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Zhang Y, Song J, Zhang M, Deng Z. Analysis Polyadenylation Signal Usage in Sus scrofa. Animals (Basel) 2022; 12:ani12020194. [PMID: 35049816 PMCID: PMC8773104 DOI: 10.3390/ani12020194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 01/01/2022] [Accepted: 01/10/2022] [Indexed: 12/12/2022] Open
Abstract
RNA polyadenylation is an important step in the messenger RNA (mRNA) maturation process, and the first step is recognizing the polyadenylation signal (PAS). The PAS type and distribution is a key determinant of post-transcriptional mRNA modification and gene expression. However, little is known about PAS usage and alternative polyadenylation (APA) regulation in livestock species. Recently, sequencing technology has enabled the generation of a large amount of sequencing data revealing variation in poly(A) signals and APA regulation in Sus scrofa. We identified 62,491 polyadenylation signals in Sus scrofa using expressed sequence tag (EST) sequences combined with RNA-seq analysis. The composition and usage frequency of polyadenylation signal in Sus scrofa is similar with that of human and mouse. The most highly conserved polyadenylation signals are AAUAAA and AUUAAA, used for over 63.35% of genes. In addition, we also analyzed the U/GU-rich downstream sequence (DSE) element, located downstream of the cleavage site. Our results indicate that APA regulation was widely occurred in Sus scrofa, as in other organisms. Our result was useful for the accurate annotation of RNA 3' ends in Sus scrofa and the analysis of polyadenylation signal usage in Sus scrofa would give the new insights into the mechanisms of transcriptional regulation.
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Affiliation(s)
- Yuting Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.Z.); (M.Z.)
| | - Jingwen Song
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Min Zhang
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.Z.); (M.Z.)
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
| | - Zhongyuan Deng
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou 450001, China; (Y.Z.); (M.Z.)
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, China;
- Correspondence:
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14
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Mohanan NK, Shaji F, Koshre GR, Laishram RS. Alternative polyadenylation: An enigma of transcript length variation in health and disease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1692. [PMID: 34581021 DOI: 10.1002/wrna.1692] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/16/2021] [Accepted: 08/24/2021] [Indexed: 12/19/2022]
Abstract
Alternative polyadenylation (APA) is a molecular mechanism during a pre-mRNA processing that involves usage of more than one polyadenylation site (PA-site) generating transcripts of varying length from a single gene. The location of a PA-site affects transcript length and coding potential of an mRNA contributing to both mRNA and protein diversification. This variation in the transcript length affects mRNA stability and translation, mRNA subcellular and tissue localization, and protein function. APA is now considered as an important regulatory mechanism in the pathophysiology of human diseases. An important consequence of the changes in the length of 3'-untranslated region (UTR) from disease-induced APA is altered protein expression. Yet, the relationship between 3'-UTR length and protein expression remains a paradox in a majority of diseases. Here, we review occurrence of APA, mechanism of PA-site selection, and consequences of transcript length variation in different diseases. Emerging evidence reveals coordinated involvement of core RNA processing factors including poly(A) polymerases in the PA-site selection in diseases-associated APAs. Targeting such APA regulators will be therapeutically significant in combating drug resistance in cancer and other complex diseases. This article is categorized under: RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease Translation > Regulation.
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Affiliation(s)
- Neeraja K Mohanan
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Feba Shaji
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Regional Centre for Biotechnology, Faridabad, India
| | - Ganesh R Koshre
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
- Manipal Academy of Higher Education, Manipal, India
| | - Rakesh S Laishram
- Cardiovascular and Diabetes Biology Group, Rajiv Gandhi Centre for Biotechnology, Trivandrum, India
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15
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Piotrowska M, Gliwiński M, Trzonkowski P, Iwaszkiewicz-Grzes D. Regulatory T Cells-Related Genes Are under DNA Methylation Influence. Int J Mol Sci 2021; 22:7144. [PMID: 34281195 PMCID: PMC8267835 DOI: 10.3390/ijms22137144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 12/12/2022] Open
Abstract
Regulatory T cells (Tregs) exert a highly suppressive function in the immune system. Disturbances in their function predispose an individual to autoimmune dysregulation, with a predominance of the pro-inflammatory environment. Besides Foxp3, which is a master regulator of these cells, other genes (e.g., Il2ra, Ctla4, Tnfrsf18, Ikzf2, and Ikzf4) are also involved in Tregs development and function. Multidimensional Tregs suppression is determined by factors that are believed to be crucial in the action of Tregs-related genes. Among them, epigenetic changes, such as DNA methylation, tend to be widely studied over the past few years. DNA methylation acts as a repressive mark, leading to diminished gene expression. Given the role of increased CpG methylation upon Tregs imprinting and functional stability, alterations in the methylation pattern can cause an imbalance in the immune response. Due to the fact that epigenetic changes can be reversible, so-called epigenetic modifiers are broadly used in order to improve Tregs performance. In this review, we place emphasis on the role of DNA methylation of the genes that are key regulators of Tregs function. We also discuss disease settings that have an impact on the methylation status of Tregs and systematize the usefulness of epigenetic drugs as factors able to influence Tregs functions.
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Affiliation(s)
| | | | | | - Dorota Iwaszkiewicz-Grzes
- Department of Medical Immunology, Medical University of Gdansk, 80-210 Gdańsk, Poland; (M.P.); (M.G.); (P.T.)
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16
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Wright CF, Quaife NM, Ramos-Hernández L, Danecek P, Ferla MP, Samocha KE, Kaplanis J, Gardner EJ, Eberhardt RY, Chao KR, Karczewski KJ, Morales J, Gallone G, Balasubramanian M, Banka S, Gompertz L, Kerr B, Kirby A, Lynch SA, Morton JEV, Pinz H, Sansbury FH, Stewart H, Zuccarelli BD, Cook SA, Taylor JC, Juusola J, Retterer K, Firth HV, Hurles ME, Lara-Pezzi E, Barton PJR, Whiffin N. Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms. Am J Hum Genet 2021; 108:1083-1094. [PMID: 34022131 PMCID: PMC8206381 DOI: 10.1016/j.ajhg.2021.04.025] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 04/29/2021] [Indexed: 02/08/2023] Open
Abstract
Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The contribution of regulatory variation in non-coding regions to rare disease, including DD, remains very poorly understood. We screened 9,858 probands from the Deciphering Developmental Disorders (DDD) study for de novo mutations in the 5' untranslated regions (5' UTRs) of genes within which variants have previously been shown to cause DD through a dominant haploinsufficient mechanism. We identified four single-nucleotide variants and two copy-number variants upstream of MEF2C in a total of ten individual probands. We developed multiple bespoke and orthogonal experimental approaches to demonstrate that these variants cause DD through three distinct loss-of-function mechanisms, disrupting transcription, translation, and/or protein function. These non-coding region variants represent 23% of likely diagnoses identified in MEF2C in the DDD cohort, but these would all be missed in standard clinical genetics approaches. Nonetheless, these variants are readily detectable in exome sequence data, with 30.7% of 5' UTR bases across all genes well covered in the DDD dataset. Our analyses show that non-coding variants upstream of genes within which coding variants are known to cause DD are an important cause of severe disease and demonstrate that analyzing 5' UTRs can increase diagnostic yield. We also show how non-coding variants can help inform both the disease-causing mechanism underlying protein-coding variants and dosage tolerance of the gene.
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Affiliation(s)
- Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, Royal Devon & Exeter Hospital, Exeter EX2 5DW, UK
| | - Nicholas M Quaife
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Laura Ramos-Hernández
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain
| | - Petr Danecek
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Matteo P Ferla
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kaitlin E Samocha
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Joanna Kaplanis
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Eugene J Gardner
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Ruth Y Eberhardt
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Katherine R Chao
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Konrad J Karczewski
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Joannella Morales
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Cambridge CB10 1SD, UK
| | - Giuseppe Gallone
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Meena Balasubramanian
- Sheffield Clinical Genetics Service, Sheffield Children's NHS Foundation Trust, Sheffield S10 2TH, UK; Academic Unit of Child Health, Department of Oncology & Metabolism, University of Sheffield, Sheffield S10 2TH, UK
| | - Siddharth Banka
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK; Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Lianne Gompertz
- Manchester Centre for Genomic Medicine, St Mary's Hospital, Manchester University Hospitals NHS Foundation Trust, Health Innovation Manchester, Manchester M13 9WL, UK
| | - Bronwyn Kerr
- Division of Evolution and Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Amelia Kirby
- Department of Pediatrics, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Sally A Lynch
- UCD Academic Centre on Rare Diseases, School of Medicine and Medical Sciences, University College Dublin, and Clinical Genetics, Temple Street Children's University Hospital, Dublin D01 XD99, Ireland
| | - Jenny E V Morton
- West Midlands Regional Clinical Genetics Service and Birmingham Health Partners, Birmingham Women's and Children's Hospitals NHS Foundation Trust, Birmingham B4 6NH, UK
| | - Hailey Pinz
- Department of Pediatrics, Saint Louis University School of Medicine, Saint Louis, MO 63104, USA
| | - Francis H Sansbury
- All Wales Medical Genomics Service, NHS Wales Cardiff and Vale University Health Board, Institute of Medical Genetics, University Hospital of Wales, Cardiff CF14 4AY, UK
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LE, UK
| | - Britton D Zuccarelli
- Department of Neurology, University of Kansas School of Medicine-Salina Campus, Salina, KS 67401, USA
| | - Stuart A Cook
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK
| | - Jenny C Taylor
- National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | | | | | - Helen V Firth
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 0QQ, UK
| | - Matthew E Hurles
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK
| | - Enrique Lara-Pezzi
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), 28029 Madrid, Spain; CIBER de enfermedades CardioVasculares (CIBERCV), 28029 Madrid, Spain
| | - Paul J R Barton
- National Heart & Lung Institute and MRC London Institute of Medical Sciences, Imperial College London, London W12 0NN, UK; Cardiovascular Research Centre, Royal Brompton & Harefield Hospitals NHS Trust, London SW3 6NP, UK
| | - Nicola Whiffin
- Human Genetics Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1RQ, UK; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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17
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Liu Y, Hoang TK, Taylor CM, Park ES, Freeborn J, Luo M, Roos S, Rhoads JM. Limosilactobacillus reuteri and Lacticaseibacillus rhamnosus GG differentially affect gut microbes and metabolites in mice with Treg deficiency. Am J Physiol Gastrointest Liver Physiol 2021; 320:G969-G981. [PMID: 33787352 PMCID: PMC8285589 DOI: 10.1152/ajpgi.00072.2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/23/2021] [Accepted: 03/24/2021] [Indexed: 01/31/2023]
Abstract
Treg deficiency causes a lethal, CD4+ T cell-driven autoimmune disease called IPEX syndrome (immunodysregulation, polyendocrinopathy, and enteropathy, with X-linked inheritance) in humans and in the scurfy (SF) mouse, a mouse model of the disease. Feeding Limosilactobacillus reuteri DSM 17938 (LR 17938, LR) to SF mice reprograms the gut microbiota, reduces disease progression, and prolongs lifespan. However, the efficacy and mechanism of LR, compared with other probiotics, in producing these effects is unknown. We compared LR with Lacticaseibacillus rhamnosus GG (LGG), an extensively investigated probiotic. LR was more effective than LGG in prolonging survival. Both probiotics restored the fecal microbial alpha diversity, but they produced distinct fecal bacterial clusters and differentially modulated microbial relative abundance (RA). LR increased the RA of phylum_Firmicutes, genus_Oscillospira whereas LR reduced phylum_Bacteroidetes, genus_Bacteroides and genus_Parabacteroides, reversing changes attributed to the SF phenotype. LGG primarily reduced the RA of genus_Bacteroides. Both LR and LGG reduced the potentially pathogenic taxon class_γ-proteobacteria. Plasma metabolomics revealed substantial differences among 696 metabolites. We observed similar changes of many clusters of metabolites in SF mice associated with treatment with either LR or LGG. However, a unique effect of LR was to increase the abundance of plasma adenosine metabolites such as inosine, which we previously showed had immune modulatory effects. In conclusion: 1) different probiotics produce distinct signatures in the fecal microbial community in mice with Treg deficiency; and 2) when comparing different probiotics, there are strain-specific microbial products with different anti-inflammatory properties, reinforcing the concept that "one size does not fit all" in the treatment of autoimmune disease.NEW & NOTEWORTHY In the treatment of Treg-deficiency-induced autoimmunity, Limosilactobacillus reuteri DSM 17938 (LR) showed greater efficacy than Lacticaseibacillus rhamnosus GG (LGG). The study demonstrated that two different probiotics produce distinct signatures in the fecal microbial community in mice with Treg deficiency, but with many similarities in global plasma metabolites in general. However, there are strain-specific microbial products with different anti-inflammatory properties, reinforcing the concept that "one size does not fit all" in the treatment of autoimmune disease.
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Affiliation(s)
- Yuying Liu
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Thomas K Hoang
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Christopher M Taylor
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, Louisiana
| | - Evelyn S Park
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Jasmin Freeborn
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
| | - Meng Luo
- Department of Microbiology, Immunology and Parasitology, Louisiana State University School of Medicine, New Orleans, Louisiana
| | - Stefan Roos
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences, Uppsala, Sweden
- BioGaia AB, Stockholm, Sweden
| | - J Marc Rhoads
- Division of Gastroenterology, Department of Pediatrics, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, Texas
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18
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Roos D, de Boer M. Mutations in cis that affect mRNA synthesis, processing and translation. Biochim Biophys Acta Mol Basis Dis 2021; 1867:166166. [PMID: 33971252 DOI: 10.1016/j.bbadis.2021.166166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 12/17/2022]
Abstract
Genetic mutations that cause hereditary diseases usually affect the composition of the transcribed mRNA and its encoded protein, leading to instability of the mRNA and/or the protein. Sometimes, however, such mutations affect the synthesis, the processing or the translation of the mRNA, with similar disastrous effects. We here present an overview of mRNA synthesis, its posttranscriptional modification and its translation into protein. We then indicate which elements in these processes are known to be affected by pathogenic mutations, but we restrict our review to mutations in cis, in the DNA of the gene that encodes the affected protein. These mutations can be in enhancer or promoter regions of the gene, which act as binding sites for transcription factors involved in pre-mRNA synthesis. We also describe mutations in polyadenylation sequences and in splice site regions, exonic and intronic, involved in intron removal. Finally, we include mutations in the Kozak sequence in mRNA, which is involved in protein synthesis. We provide examples of genetic diseases caused by mutations in these DNA regions and refer to databases to help identify these regions. The over-all knowledge of mRNA synthesis, processing and translation is essential for improvement of the diagnosis of patients with genetic diseases.
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Affiliation(s)
- Dirk Roos
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands.
| | - Martin de Boer
- Sanquin Blood Supply Organization, Dept. of Blood Cell Research, Landsteiner Laboratory, Amsterdam University Medical Centre, location AMC, University of Amsterdam, Amsterdam, the Netherlands
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19
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Pritts JD, Oluyadi AA, Huang W, Shimberg GD, Kane MA, Wilks A, Michel SLJ. Understanding RNA Binding by the Nonclassical Zinc Finger Protein CPSF30, a Key Factor in Polyadenylation during Pre-mRNA Processing. Biochemistry 2021; 60:780-790. [PMID: 33615774 DOI: 10.1021/acs.biochem.0c00940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Cleavage and polyadenylation specificity factor 30 (CPSF30) is a zinc finger protein that regulates pre-mRNA processing. CPSF30 contains five CCCH domains and one CCHC domain and recognizes two conserved 3' pre-mRNA sequences: an AU hexamer and a U-rich motif. AU hexamer motifs are common in pre-mRNAs and are typically defined as AAUAAA. Variations within the AAUAAA hexamer occur in certain pre-mRNAs and can affect polyadenylation efficiency or be linked to diseases. The effects of disease-related variations on CPSF30/pre-mRNA binding were determined using a construct of CPSF30 that contains just the five CCCH domains (CPSF30-5F). Bioinformatics was utilized to identify the variability within the AU hexamer sequence in pre-mRNAs. The effects of this sequence variability on CPSF30-5F/RNA binding affinities were measured. Bases at positions 1, 2, 4, and 5 within the AU hexamer were found to be important for RNA binding. Bioinformatics revealed that the three bases flanking the AU hexamer at the 5' and 3' ends are twice as likely to be adenine or uracil as guanine and cytosine. The presence of A and U residues in these flanking regions was determined to promote higher-affinity CPSF30-5F/RNA binding than G and C residues. The addition of the zinc knuckle domain to CPSF30-5F (CPSF30-FL) restored binding to AU hexamer variants. This restoration of binding is connected to the presence of a U-rich sequence within the pre-mRNA to which the zinc knuckle binds. A mechanism of differential RNA binding by CPSF30, modulated by accessibility of the two RNA binding sites, is proposed.
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Affiliation(s)
- Jordan D Pritts
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Abdulafeez A Oluyadi
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Geoffrey D Shimberg
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Maureen A Kane
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Angela Wilks
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
| | - Sarah L J Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180, United States
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20
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Searching for Peptide Inhibitors of T Regulatory Cell Activity by Targeting Specific Domains of FOXP3 Transcription Factor. Biomedicines 2021; 9:biomedicines9020197. [PMID: 33671179 PMCID: PMC7922534 DOI: 10.3390/biomedicines9020197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 02/13/2021] [Accepted: 02/14/2021] [Indexed: 12/03/2022] Open
Abstract
(1) Background: The ability of cancer cells to evade the immune system is due in part to their capacity to induce and recruit T regulatory cells (Tregs) to the tumor microenvironment. Strategies proposed to improve antitumor immunity by depleting Tregs generally lack specificity and raise the possibility of autoimmunity. Therefore, we propose to control Tregs by their functional inactivation rather than depletion. Tregs are characterized by the expression of the Forkhead box protein 3 (FOXP3) transcription factor, which is considered their “master regulator”. Its interaction with DNA is assisted primarily by its interaction with other proteins in the so-called “Foxp3 interactome”, which elicits much of the characteristic Treg cell transcriptional signature. We speculated that the disruption of such a protein complex by using synthetic peptides able to bind Foxp3 might have an impact on the functionality of Treg cells and thus have a therapeutic potential in cancer treatment. (2) Methods: By using a phage-displayed peptide library, or short synthetic peptides encompassing Foxp3 fragments, or by studying the crystal structure of the Foxp3:NFAT complex, we have identified a series of peptides that are able to bind Foxp3 and inhibit Treg activity. (3) Results: We identified some peptides encompassing fragments of the leuzin zipper or the C terminal domain of Foxp3 with the capacity to inhibit Treg activity in vitro. The acetylation/amidation of linear peptides, head-to-tail cyclization, the incorporation of non-natural aminoacids, or the incorporation of cell-penetrating peptide motifs increased in some cases the Foxp3 binding capacity and Treg inhibitory activity of the identified peptides. Some of them have shown antitumoral activity in vivo. (4) Conclusions: Synthetic peptides constitute an alternative to inhibit Foxp3 protein–protein interactions intracellularly and impair Treg immunosuppressive activity. These peptides might be considered as potential hit compounds on the design of new immunotherapeutic approaches against cancer.
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21
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McGee MC, August A, Huang W. TCR/ITK Signaling in Type 1 Regulatory T cells. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1278:115-124. [PMID: 33523446 DOI: 10.1007/978-981-15-6407-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Type 1 regulatory T (Tr1) cells can modulate inflammation through multiple direct and indirect molecular and cellular mechanisms and have demonstrated potential for anti-inflammatory therapies. Tr1 cells do not express the master transcription factor of conventional regulatory T cells, Foxp3, but express high levels of the immunomodulatory cytokine, IL-10. IL-2-inducible T-cell kinase (ITK) is conserved between mouse and human and is highly expressed in T cells. ITK signaling downstream of the T-cell receptor (TCR) is critical for T-cell subset differentiation and function. Upon activation by TCR, ITK is critical for Ras activation, leading to downstream activation of MAPKs and upregulation of IRF4, which further enable Tr1 cell differentiation and suppressive function. We summarize here the structure, signaling pathway, and function of ITK in T-cell lineage designation, with an emphasis on Tr1 cell development and function.
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Affiliation(s)
- Michael C McGee
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA
| | - Avery August
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Weishan Huang
- Department of Pathobiological Sciences, School of Veterinary Medicine, Louisiana State University, Baton Rouge, LA, USA. .,Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
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22
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Population-scale genetic control of alternative polyadenylation and its association with human diseases. QUANTITATIVE BIOLOGY 2021. [DOI: 10.15302/j-qb-021-0252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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23
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Bertolini M, McElwee K, Gilhar A, Bulfone‐Paus S, Paus R. Hair follicle immune privilege and its collapse in alopecia areata. Exp Dermatol 2020; 29:703-725. [DOI: 10.1111/exd.14155] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/18/2020] [Accepted: 07/10/2020] [Indexed: 12/11/2022]
Affiliation(s)
| | - Kevin McElwee
- Monasterium Laboratory Münster Germany
- Centre for Skin Sciences University of Bradford Bradford UK
- Department of Dermatology and Skin Science University of British Columbia Vancouver British Columbia Canada
| | - Amos Gilhar
- Laboratory for Skin Research Rappaport Faculty of Medicine Technion‐Israel Institute of Technology Haifa Israel
| | - Silvia Bulfone‐Paus
- Monasterium Laboratory Münster Germany
- Centre for Dermatology Research University of Manchester and NIHR Manchester Biomedical Research Centre Manchester UK
| | - Ralf Paus
- Monasterium Laboratory Münster Germany
- Centre for Dermatology Research University of Manchester and NIHR Manchester Biomedical Research Centre Manchester UK
- Dr. Philip Frost Department of Dermatology & Cutaneous Surgery University of Miami Miller School of Medicine Miami FL USA
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24
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Yang J, Wei P, Barbi J, Huang Q, Yang E, Bai Y, Nie J, Gao Y, Tao J, Lu Y, Xie C, Hou X, Ren J, Wu X, Meng J, Zhang Y, Fu J, Kou W, Gao Y, Chen Z, Liang R, Tsun A, Li D, Guo W, Zhang S, Zheng S, Niu J, Galardy P, Tong X, Shi G, Li H, Pan F, Li B. The deubiquitinase USP44 promotes Treg function during inflammation by preventing FOXP3 degradation. EMBO Rep 2020; 21:e50308. [PMID: 32644293 PMCID: PMC7507386 DOI: 10.15252/embr.202050308] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 06/10/2020] [Accepted: 06/18/2020] [Indexed: 12/30/2022] Open
Abstract
The transcription factor forkhead box P3 (FOXP3) is essential for the development of regulatory T cells (Tregs) and their function in immune homeostasis. Previous studies have shown that in natural Tregs (nTregs), FOXP3 can be regulated by polyubiquitination and deubiquitination. However, the molecular players active in this pathway, especially those modulating FOXP3 by deubiquitination in the distinct induced Treg (iTreg) lineage, remain unclear. Here, we identify the ubiquitin-specific peptidase 44 (USP44) as a novel deubiquitinase for FOXP3. USP44 interacts with and stabilizes FOXP3 by removing K48-linked ubiquitin modifications. Notably, TGF-β induces USP44 expression during iTreg differentiation. USP44 co-operates with USP7 to stabilize and deubiquitinate FOXP3. Tregs genetically lacking USP44 are less effective than their wild-type counterparts, both in vitro and in multiple in vivo models of inflammatory disease and cancer. These findings suggest that USP44 plays an important role in the post-translational regulation of Treg function and is thus a potential therapeutic target for tolerance-breaking anti-cancer immunotherapy.
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25
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Shulman ED, Elkon R. Systematic identification of functional SNPs interrupting 3'UTR polyadenylation signals. PLoS Genet 2020; 16:e1008977. [PMID: 32804959 PMCID: PMC7451987 DOI: 10.1371/journal.pgen.1008977] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 08/27/2020] [Accepted: 07/01/2020] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is emerging as a widespread regulatory layer since the majority of human protein-coding genes contain several polyadenylation (p(A)) sites in their 3’UTRs. By generating isoforms with different 3’UTR length, APA potentially affects mRNA stability, translation efficiency, nuclear export, and cellular localization. Polyadenylation sites are regulated by adjacent RNA cis-regulatory elements, the principals among them are the polyadenylation signal (PAS) AAUAAA and its main variant AUUAAA, typically located ~20-nt upstream of the p(A) site. Mutations in PAS and other auxiliary poly(A) cis-elements in the 3’UTR of several genes have been shown to cause human Mendelian diseases, and to date, only a few common SNPs that regulate APA were associated with complex diseases. Here, we systematically searched for SNPs that affect gene expression and human traits by modulation of 3’UTR APA. First, focusing on the variants most likely to exert the strongest effect, we identified 2,305 SNPs that interrupt the canonical PAS or its main variant. Implementing pA-QTL tests using GTEx RNA-seq data, we identified 330 PAS SNPs (called PAS pA-QTLs) that were significantly associated with the usage of their p(A) site. As expected, PAS-interrupting alleles were mostly linked with decreased cleavage at their p(A) site and the consequential 3’UTR lengthening. However, interestingly, in ~10% of the cases, the PAS-interrupting allele was associated with increased usage of an upstream p(A) site and 3’UTR shortening. As an indication of the functional effects of these PAS pA-QTLs on gene expression and complex human traits, we observed for few dozens of them marked colocalization with eQTL and/or GWAS signals. The PAS-interrupting alleles linked with 3’UTR lengthening were also strongly associated with decreased gene expression, indicating that shorter isoforms generated by APA are generally more stable than longer ones. Last, we carried out an extended, genome-wide analysis of 3’UTR variants and detected thousands of additional pA-QTLs having weaker effects compared to the PAS pA-QTLs. mRNA molecules that encode for proteins end with a long stretch of adenosines, called poly(A) tail. The poly(A) tail contributes to the stability of the mRNA molecules, their translation to proteins and their import from the nucleus to the cytoplasm. The process of adding this tail to the mRNAs is called polyadenylation, and the termination site on the mRNAs at which the poly(A) tail is added is called the poly(A) site. In recent years it became evident that the vast majority of mRNAs of human genes contain several alternative poly(A) sites and their usage generates different mRNA isoforms that differ in their stability and translation efficiency. Therefore, alternative polyadenylation (APA) is emerging as a novel and important, yet underexplored, mechanism that regulate gene expression. The choice between alternative p(A) sites in an mRNA molecule is regulated by regulatory sequences located within a region in the mRNA called the 3’ untranslated region (3’UTR). A major challenge in present human genetics research is to understand how common genetic variants affect individuals’ health. In our study, we systematically identified dozens of genetic variants that affect the choice between alternative p(A) sites and demonstrated that by that, these variants influence the expression level of the target genes. Our results help to illuminate a novel mechanism by which genetic variants that are common in the population affect different traits including our risk for developing diseases.
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Affiliation(s)
- Eldad David Shulman
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ran Elkon
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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26
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Copsel SN, Malek TR, Levy RB. Medical Treatment Can Unintentionally Alter the Regulatory T-Cell Compartment in Patients with Widespread Pathophysiologic Conditions. THE AMERICAN JOURNAL OF PATHOLOGY 2020; 190:2000-2012. [PMID: 32745461 DOI: 10.1016/j.ajpath.2020.07.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/14/2020] [Accepted: 07/20/2020] [Indexed: 12/13/2022]
Abstract
Regulatory T cells (Tregs) are non-redundant mediators of immune tolerance that are critical to prevent autoimmune disease and promote an anti-inflammatory tissue environment. Many individuals experience chronic diseases and physiologic changes associated with aging requiring long-term medication. Unfortunately, adverse effects accompany every pharmacologic intervention and may affect overall outcomes. We focus on medications typically prescribed during the treatment of prevalent chronic diseases and disorders, including cardiovascular disease, autoimmune disease, and menopausal symptoms, that affect >200 million individuals in the United States. Increasing studies continue to report that treatment of patients with estrogen, metformin, statins, vitamin D, and tumor necrosis factor blockers are unintentionally modulating the Treg compartment. Effects of these medications likely comprise direct and/or indirect interaction with Tregs via other immune and parenchymal populations. Differing and sometimes opposing effects on the Treg compartment have been observed using the same medication. The length of treatment, dosing regimen and stage of disease, patient age, ethnicity, and sex may account for such findings and determine the specific signaling pathways affected by the medication. Enhancing the Treg compartment can skew the patient's immune system toward an anti-inflammatory phenotype and therefore could provide unanticipated benefit. Currently, multiple medicines prescribed to large numbers of patients influence the Treg compartment; however, how such effects affect their disease outcome and long-term health remains unclear.
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Affiliation(s)
- Sabrina N Copsel
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida.
| | - Thomas R Malek
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida
| | - Robert B Levy
- Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, Florida
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27
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Wachs AS, Bohne J. Two sides of the same medal: Noncoding mutations reveal new pathological mechanisms and insights into the regulation of gene expression. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 12:e1616. [PMID: 32633083 DOI: 10.1002/wrna.1616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 12/22/2022]
Abstract
Noncoding sequences constitute the major part of the human genome and also of pre-mRNAs. Single nucleotide variants in these regions are often overlooked, but may be responsible for much of the variation of phenotypes observed. Mutations in the noncoding part of pre-mRNAs often reveal new and meaningful insights into the regulation of cellular gene expression. Thus, the mechanistic analysis of the pathological mechanism of such mutations will both foster a deeper understanding of the disease and the underlying cellular pathways. Even synonymous mutations can cause diseases, since the primary mRNA sequence not only encodes amino acids, but also encrypts information on RNA-binding proteins and secondary structure. In fact, the RNA sequence directs assembly of a specific mRNP complex, which in turn dictates the fate of the mRNA or regulates its biogenesis. The accumulation of genomic sequence information is increasing at a rapid pace. However, much of the diversity uncovered may not explain the phenotype of a certain syndrome or disease. For this reason, we also emphasize the value of mechanistic studies on pathological mechanisms being complementary to genome-wide studies and bioinformatic approaches. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Processing > 3' End Processing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Amelie S Wachs
- Institute of Virology, Hannover Medical School, Hanover, Germany
| | - Jens Bohne
- Institute of Virology, Hannover Medical School, Hanover, Germany
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28
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Nourse J, Spada S, Danckwardt S. Emerging Roles of RNA 3'-end Cleavage and Polyadenylation in Pathogenesis, Diagnosis and Therapy of Human Disorders. Biomolecules 2020; 10:biom10060915. [PMID: 32560344 PMCID: PMC7356254 DOI: 10.3390/biom10060915] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/10/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022] Open
Abstract
A crucial feature of gene expression involves RNA processing to produce 3′ ends through a process termed 3′ end cleavage and polyadenylation (CPA). This ensures the nascent RNA molecule can exit the nucleus and be translated to ultimately give rise to a protein which can execute a function. Further, alternative polyadenylation (APA) can produce distinct transcript isoforms, profoundly expanding the complexity of the transcriptome. CPA is carried out by multi-component protein complexes interacting with multiple RNA motifs and is tightly coupled to transcription, other steps of RNA processing, and even epigenetic modifications. CPA and APA contribute to the maintenance of a multitude of diverse physiological processes. It is therefore not surprising that disruptions of CPA and APA can lead to devastating disorders. Here, we review potential CPA and APA mechanisms involving both loss and gain of function that can have tremendous impacts on health and disease. Ultimately we highlight the emerging diagnostic and therapeutic potential CPA and APA offer.
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Affiliation(s)
- Jamie Nourse
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Stefano Spada
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
| | - Sven Danckwardt
- Institute for Clinical Chemistry and Laboratory Medicine, University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany; (J.N.); (S.S.)
- Center for Thrombosis and Hemostasis (CTH), University Medical Center of the Johannes Gutenberg University, 55131 Mainz, Germany
- German Center for Cardiovascular Research (DZHK), Rhine-Main, Germany
- Correspondence:
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29
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Yang Y, Zhang Q, Miao YR, Yang J, Yang W, Yu F, Wang D, Guo AY, Gong J. SNP2APA: a database for evaluating effects of genetic variants on alternative polyadenylation in human cancers. Nucleic Acids Res 2020; 48:D226-D232. [PMID: 31511885 PMCID: PMC6943033 DOI: 10.1093/nar/gkz793] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 09/06/2019] [Indexed: 12/18/2022] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional regulation that recognizes different polyadenylation signals (PASs), resulting in transcripts with different 3' untranslated regions, thereby influencing a series of biological processes and functions. Recent studies have revealed that some single nucleotide polymorphisms (SNPs) could contribute to tumorigenesis and development through dysregulating APA. However, the associations between SNPs and APA in human cancers remain largely unknown. Here, using genotype and APA data of 9082 samples from The Cancer Genome Atlas (TCGA) and The Cancer 3'UTR Altas (TC3A), we systematically identified SNPs affecting APA events across 32 cancer types and defined them as APA quantitative trait loci (apaQTLs). As a result, a total of 467 942 cis-apaQTLs and 30 721 trans-apaQTLs were identified. By integrating apaQTLs with survival and genome-wide association studies (GWAS) data, we further identified 2154 apaQTLs associated with patient survival time and 151 342 apaQTLs located in GWAS loci. In addition, we designed an online tool to predict the effects of SNPs on PASs by utilizing PAS motif prediction tool. Finally, we developed SNP2APA, a user-friendly and intuitive database (http://gong_lab.hzau.edu.cn/SNP2APA/) for data browsing, searching, and downloading. SNP2APA will significantly improve our understanding of genetic variants and APA in human cancers.
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Affiliation(s)
- Yanbo Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Qiong Zhang
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Ya-Ru Miao
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Jiajun Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Wenqian Yang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Fangda Yu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Dongyang Wang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - An-Yuan Guo
- Hubei Bioinformatics and Molecular Imaging Key Laboratory, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, P. R. China
| | - Jing Gong
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, P. R. China.,College of Biomedicine and Health, Huazhong Agricultural University, Wuhan 430070, P. R. China
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30
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Jamee M, Zaki-Dizaji M, Lo B, Abolhassani H, Aghamahdi F, Mosavian M, Nademi Z, Mohammadi H, Jadidi-Niaragh F, Rojas M, Anaya JM, Azizi G. Clinical, Immunological, and Genetic Features in Patients with Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-linked (IPEX) and IPEX-like Syndrome. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2020; 8:2747-2760.e7. [PMID: 32428713 DOI: 10.1016/j.jaip.2020.04.070] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a rare inborn error of immunity caused by mutations in the forkhead box P3 (FOXP3) gene. OBJECTIVE In this study, we conducted a systematic review of patients with IPEX and IPEX-like syndrome to delineate differences in these 2 major groups. METHODS The literature search was performed in PubMed, Web of Science, and Scopus databases, and demographic, clinical, immunologic, and molecular data were compared between the IPEX and IPEX-like groups. RESULTS A total of 459 patients were reported in 148 eligible articles. Major clinical differences between patients with IPEX and IPEX-like syndrome were observed in rates of pneumonia (11% vs 31%, P < .001), bronchiectasis (0.3% vs 14%, P < .001), diarrhea (56% vs 42%, P = .020), and organomegaly (10% vs 23%, P = .001), respectively. Eosinophilia (95% vs 100%), low regulatory T-cell count (68% vs 50%), and elevated IgE (87% vs 61%) were the most prominent laboratory findings in patients with IPEX and IPEX-like syndrome, respectively. In the IPEX group, a lower mortality rate was observed among patients receiving hematopoietic stem cell transplantation (HSCT) (24%) compared with other patients (43%), P = .008; however, in the IPEX-like group, it was not significant (P = .189). CONCLUSIONS Patients with IPEX syndrome generally suffer from enteropathy, autoimmunity, dermatitis, eosinophilia, and elevated serum IgE. Despite similarities in their clinical presentations, patients with IPEX-like syndrome are more likely to present common variable immunodeficiency-like phenotype such as respiratory tract infections, bronchiectasis, and organomegaly. HSCT is currently the only curative therapy for both IPEX and IPEX-like syndrome and may result in favorable outcome.
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Affiliation(s)
- Mahnaz Jamee
- Student Research Committee, Alborz University of Medical Sciences, Karaj, Iran; Alborz Office of USERN, Universal Scientific Education and Research Network (USERN), Alborz University of Medical Sciences, Karaj, Iran
| | - Majid Zaki-Dizaji
- Legal Medicine Research Center, Legal Medicine Organization, Tehran, Iran
| | - Bernice Lo
- Sidra Medicine, Division of Translational Medicine, Research Branch, Doha, Qatar
| | - Hassan Abolhassani
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institute at Karolinska University Hospital Huddinge, Stockholm, Sweden
| | - Fatemeh Aghamahdi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mehdi Mosavian
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Zohreh Nademi
- Children's Bone Marrow Transplant Unit, Great North Children's Hospital, Newcastle, United Kingdom
| | - Hamed Mohammadi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Manuel Rojas
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan-Manuel Anaya
- Center for Autoimmune Diseases Research (CREA), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Gholamreza Azizi
- Non-communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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31
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Park JH, Lee KH, Jeon B, Ochs HD, Lee JS, Gee HY, Seo S, Geum D, Piccirillo CA, Eisenhut M, van der Vliet HJ, Lee JM, Kronbichler A, Ko Y, Shin JI. Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome: A systematic review. Autoimmun Rev 2020; 19:102526. [PMID: 32234571 DOI: 10.1016/j.autrev.2020.102526] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 12/24/2022]
Abstract
BACKGROUND Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome is a monogenic disorder characterized by early onset fatal multi-system autoimmunity due to loss-of-function mutations in the gene encoding the forkhead box P3 (FOXP3) transcription factor which is crucial for the development, maturation, and maintenance of CD4+ regulatory T (T-reg) cells. Various autoimmune phenomena such as enteropathy, endocrinopathies, cytopenias, renal disease, and skin manifestations are characteristic findings in patients affected by IPEX syndrome. OBJECTIVES In this systematic review, we focus on both clinical and demographic characteristics of IPEX patients, highlighting possible genotype-phenotype correlations and address prognostic factors for disease outcome. METHODS We performed a literature search to systematically investigate the case reports of IPEX which were published before August 7th, 2017. RESULTS A total of 75 articles (195 patients) were identified. All IPEX patients included had FOXP3 mutations which were most frequently located in the forkhead domain (n = 68, 34.9%) followed by the leucine-zipper domain (n = 30, 15.4%) and repressor domain (n = 36, 18.4%). Clinical manifestations were as follows: enteropathy (n = 191, 97.9%), skin manifestations (n = 121, 62.1%), endocrinopathy (n = 104, 53.3%), hematologic abnormalities (n = 75, 38.5%), infections (n = 78, 40.0%), other immune-related complications (n = 43, 22.1%), and renal involvement (n = 32, 16.4%). Enteropathic presentations (P = 0.017), eczema (P = 0.030), autoimmune hemolytic anemia (P = 0.022) and food allergy (P = 0.009) were associated with better survival, while thrombocytopenia (P = 0.034), septic shock (P = 0.045) and mutations affecting the repressor domain (P = 0.021), intron 7 (P = 0.033) or poly A sequence (P = 0.025) were associated with increased risk of death. Immunosuppressive therapy alone was significantly associated with increased cumulative survival compared to patients who received no treatment (P = 0.041). CONCLUSIONS We report the most comprehensive summary of demographic and clinical profiles derived from a total of 195 IPEX patients with deleterious mutations in FOXP3. Analysis of our findings provides new insights into genotype/phenotype correlations, and clinical and genetic factors associated with increased risk of death and response to treatment strategies.
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Affiliation(s)
- Jae Hyon Park
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Keum Hwa Lee
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Bokyoung Jeon
- Yonsei University Wonju College of Medicine, Wonju, Republic of Korea
| | - Hans D Ochs
- Department of Pediatrics, University of Washington and Seattle Children's Research Institute, Seattle, WA, USA
| | - Joon Suk Lee
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03772, Republic of Korea
| | - Heon Yung Gee
- Department of Pharmacology, Brain Korea 21 PLUS Project for Medical Sciences, Yonsei University College of Medicine, Seoul 03772, Republic of Korea
| | - Seeun Seo
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Dongil Geum
- Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ciriaco A Piccirillo
- Department of Microbiology and Immunology, McGill University, Montréal, QC, Canada; The Research Institute of the McGill University Health Center, Montréal, QC, Canada; FOCiS Centre of Excellence in Translational Immunology (CETI), Montréal, QC H4A 3J1, Canada
| | - Michael Eisenhut
- Luton & Dunstable University Hospital NHS Foundation Trust, Lewsey Road, Luton LU4ODZ, United Kingdom
| | - Hans J van der Vliet
- Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, the Netherlands
| | - Jiwon M Lee
- Department of Pediatrics, Chungnam National University College of Medicine, Daejeon, Republic of Korea
| | - Andreas Kronbichler
- Department of Internal Medicine IV, Medical University Innsbruck, Innsbruck, Austria
| | - Younhee Ko
- Division of Biomedical Engineering, Hankuk University of Foreign Studies, Gyeonggi-do, Republic of Korea
| | - Jae Il Shin
- Department of Pediatrics, Yonsei University College of Medicine, Seoul, Republic of Korea.
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32
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Huang Q, Liu X, Zhang Y, Huang J, Li D, Li B. Molecular feature and therapeutic perspectives of immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome. J Genet Genomics 2020; 47:17-26. [PMID: 32081609 DOI: 10.1016/j.jgg.2019.11.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 11/02/2019] [Accepted: 11/10/2019] [Indexed: 01/01/2023]
Abstract
Regulatory T (Treg) cells, a subtype of immunosuppressive CD4+ T cells, are vital for maintaining immune homeostasis in healthy people. Forkhead box protein P3 (FOXP3), a member of the forkhead-winged-helix family, is the pivotal transcriptional factor of Treg cells. The expression, post-translational modifications, and protein complex of FOXP3 present a great impact on the functional stability and immune plasticity of Treg cells in vivo. In particular, the mutation of FOXP3 can result in immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome, which is a rare genetic disease mostly diagnosed in early childhood and can soon be fatal. IPEX syndrome is related to several manifestations, including dermatitis, enteropathy, type 1 diabetes, thyroiditis, and so on. Here, we summarize some recent findings on FOXP3 regulation and Treg cell function. We also review the current knowledge about the underlying mechanism of FOXP3 mutant-induced IPEX syndrome and some latest clinical prospects. At last, this review offers a novel insight into the role played by the FOXP3 complex in potential therapeutic applications in IPEX syndrome.
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Affiliation(s)
- Qianru Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Xu Liu
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Yujia Zhang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Jingyao Huang
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China
| | - Dan Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
| | - Bin Li
- Shanghai Institute of Immunology, Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, Shanghai, 200025, China.
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Functional reprogramming of regulatory T cells in the absence of Foxp3. Nat Immunol 2019; 20:1208-1219. [PMID: 31384057 PMCID: PMC6707855 DOI: 10.1038/s41590-019-0442-x] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/06/2019] [Indexed: 01/25/2023]
Abstract
Regulatory T cells (Treg cells) deficient in the transcription factor Foxp3 lack suppressor function and manifest an effector T (Teff) cell-like phenotype. We demonstrate that Foxp3 deficiency dysregulates metabolic checkpoint kinase mammalian target of rapamycin (mTOR) complex 2 (mTORC2) signaling and gives rise to augmented aerobic glycolysis and oxidative phosphorylation. Specific deletion of the mTORC2 adaptor gene Rictor in Foxp3-deficient Treg cells ameliorated disease in a Foxo1 transcription factor-dependent manner. Rictor deficiency re-established a subset of Treg cell genetic circuits and suppressed the Teff cell-like glycolytic and respiratory programs, which contributed to immune dysregulation. Treatment of Treg cells from patients with FOXP3 deficiency with mTOR inhibitors similarly antagonized their Teff cell-like program and restored suppressive function. Thus, regulatory function can be re-established in Foxp3-deficient Treg cells by targeting their metabolic pathways, providing opportunities to restore tolerance in Treg cell disorders.
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Becker M, Serr I, Salb VK, Ott VB, Mengel L, Blüher M, Weigmann B, Hauner H, Tschöp MH, Daniel C. Short-term cold exposure supports human Treg induction in vivo. Mol Metab 2019; 28:73-82. [PMID: 31427184 PMCID: PMC6822223 DOI: 10.1016/j.molmet.2019.08.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/22/2019] [Accepted: 08/01/2019] [Indexed: 01/08/2023] Open
Abstract
Objective Obesity and type-2 diabetes (T2D) are metabolic diseases that represent a critical health problem worldwide. Metabolic disease is differentially associated with fat distribution, while visceral white adipose tissue (VAT) is particularly prone to obesity-associated inflammation. Next to their canonical function of immune suppression, regulatory T cells (Tregs) are key in controlling adipose tissue homeostasis. Towards understanding the molecular underpinnings of metabolic disease, we focus on how environmental-metabolic stimuli impinge on the functional interplay between Tregs and adipose tissue. Here, cold exposure or beta3-adrenergic signaling are a promising tool to increase energy expenditure by activating brown adipose tissue, as well as by reducing local inflammation within fat depots by supporting immunosuppressive Tregs. However, in humans, the underlying mechanisms that enable the environmental-immune crosstalk in the periphery and in the respective tissue remain currently unknown. Methods We used combinatorial approaches of next generation humanized mouse models and in vitro and in vivo experiments together with beta3-adrenergic stimulation to dissect the underlying mechanisms of human Treg induction exposed to environmental stimuli such as cold. To test the translational relevance of our findings, we analyzed samples from the FREECE study in which human subjects were exposed to individualized cooling protocols. Samples were analyzed ex vivo and after in vitro Treg induction using qRT-PCR, immunofluorescence, as well as with multicolor flow cytometry and cell sorting. Results In vivo application of the beta3-adrenergic receptor agonist mirabegron in humanized mice induced thermogenesis and improved the Treg induction capacity of naïve T cells isolated from these animals. Using samples from the human FREECE study, we demonstrate that a short-term cold stimulus supports human Treg induction in vitro and in vivo. Mechanistically, we identify BORCS6 encoding the Ragulator-interacting protein C17orf59 to be significantly induced in human CD4+ T cells upon short-term cold exposure. Strong mTOR signaling is known to limit successful Treg induction and thus likely by interfering with mTOR activation at lysosomal surfaces, C17orf59 improves the Treg induction capacity of human naïve T cells upon cold exposure. Conclusions These novel insights into the molecular underpinnings of human Treg induction suggest an important role of Tregs in linking environmental stimuli with adipose tissue function and metabolic diseases. Moreover, these discoveries shed new light on potential approaches towards tailored anti-inflammatory concepts that support human adipose tissue homeostasis by enabling Tregs. Beta3-adrenergic stimulation enhances human Tregs in humanized mice. Short-term cold stimulation increases human Treg induction in vitro and in vivo. Short-term cold exposure elevates human Treg signatures genes. Short-term cold induces BORCS6 encoding C17orf59 in human CD4+T cells. C17orf59 limits mTOR signaling and thereby supports human Treg induction.
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Affiliation(s)
- Maike Becker
- Institute for Diabetes Research, Group Immune Tolerance in Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), Munich, Germany
| | - Isabelle Serr
- Institute for Diabetes Research, Group Immune Tolerance in Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), Munich, Germany
| | - Victoria K Salb
- Institute for Diabetes Research, Group Immune Tolerance in Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), Munich, Germany
| | - Verena B Ott
- Institute for Diabetes Research, Group Immune Tolerance in Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich-Neuherberg, Germany
| | - Laura Mengel
- ZIEL-Institute for Food & Health, Else Kröner-Fresenius Zentrum für Ernährungsmedizin, Technische Universität München, Freising-Weihenstephan, Germany
| | - Matthias Blüher
- Department of Medicine, University of Leipzig, Leipzig, Germany
| | - Benno Weigmann
- Department of Medicine 1, University of Erlangen-Nuremberg, Kussmaul Campus for Medical Research, Erlangen, Germany
| | - Hans Hauner
- German Center for Diabetes Research (DZD), Munich, Germany; ZIEL-Institute for Food & Health, Else Kröner-Fresenius Zentrum für Ernährungsmedizin, Technische Universität München, Freising-Weihenstephan, Germany; Institute for Nutritional Medicine, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Matthias H Tschöp
- German Center for Diabetes Research (DZD), Munich, Germany; Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Zentrum München, Munich-Neuherberg, Germany; Division of Metabolic Diseases, Department of Medicine, Technische Universität München, Munich, Germany
| | - Carolin Daniel
- Institute for Diabetes Research, Group Immune Tolerance in Diabetes, Helmholtz Diabetes Center at Helmholtz Zentrum München, German Research Center for Environmental Health, Munich-Neuherberg, Germany; German Center for Diabetes Research (DZD), Munich, Germany; Division of Clinical Pharmacology, Department of Medicine IV, Ludwig-Maximilians-Universität München, Munich, Germany.
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Abstract
Most human genes have multiple sites at which RNA 3' end cleavage and polyadenylation can occur, enabling the expression of distinct transcript isoforms under different conditions. Novel methods to sequence RNA 3' ends have generated comprehensive catalogues of polyadenylation (poly(A)) sites; their analysis using innovative computational methods has revealed how poly(A) site choice is regulated by core RNA 3' end processing factors, such as cleavage factor I and cleavage and polyadenylation specificity factor, as well as by other RNA-binding proteins, particularly splicing factors. Here, we review the experimental and computational methods that have enabled the global mapping of mRNA and of long non-coding RNA 3' ends, quantification of the resulting isoforms and the discovery of regulators of alternative cleavage and polyadenylation (APA). We highlight the different types of APA-derived isoforms and their functional differences, and illustrate how APA contributes to human diseases, including cancer and haematological, immunological and neurological diseases.
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Bogard N, Linder J, Rosenberg AB, Seelig G. A Deep Neural Network for Predicting and Engineering Alternative Polyadenylation. Cell 2019; 178:91-106.e23. [PMID: 31178116 PMCID: PMC6599575 DOI: 10.1016/j.cell.2019.04.046] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 03/18/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
Alternative polyadenylation (APA) is a major driver of transcriptome diversity in human cells. Here, we use deep learning to predict APA from DNA sequence alone. We trained our model (APARENT, APA REgression NeT) on isoform expression data from over 3 million APA reporters. APARENT's predictions are highly accurate when tasked with inferring APA in synthetic and human 3'UTRs. Visualizing features learned across all network layers reveals that APARENT recognizes sequence motifs known to recruit APA regulators, discovers previously unknown sequence determinants of 3' end processing, and integrates these features into a comprehensive, interpretable, cis-regulatory code. We apply APARENT to forward engineer functional polyadenylation signals with precisely defined cleavage position and isoform usage and validate predictions experimentally. Finally, we use APARENT to quantify the impact of genetic variants on APA. Our approach detects pathogenic variants in a wide range of disease contexts, expanding our understanding of the genetic origins of disease.
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Affiliation(s)
- Nicholas Bogard
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Johannes Linder
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Alexander B Rosenberg
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA
| | - Georg Seelig
- Department of Electrical & Computer Engineering, University of Washington, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA.
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Ahmed Z, Imdad A, Connelly JA, Acra S. Autoimmune Enteropathy: An Updated Review with Special Focus on Stem Cell Transplant Therapy. Dig Dis Sci 2019; 64:643-654. [PMID: 30415406 PMCID: PMC8260026 DOI: 10.1007/s10620-018-5364-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/01/2018] [Indexed: 12/12/2022]
Abstract
Autoimmune enteropathy (AIE) is a complex disease affecting both children and adults. Although associated with significant morbidity and mortality, the pathophysiology of the disease and its treatment have not been well characterized. This study aims to review the medical literature available on this rare but clinically significant ailment, to help establish a better understanding of its pathophysiology and enumerate the available diagnostic and treatment modalities. A literature search was conducted on PubMed using key terms related to autoimmune enteropathy and intractable diarrhea, with no restrictions on the date of publication or language. We found a total of 98 reports of AIE published in the form of case reports and case series. The evidence reviewed suggests that AIE is a multifaceted disorder that requires a high index of suspicion in the appropriate clinical setting to be able to make an early diagnosis. Current evidence supports the use of supportive care to correct nutritional and metabolic deficiencies, and immunosuppressives and immunomodulators as directed therapies. Hematopoietic stem cell transplant is an aggressive, but successful curative modality for patients with AIE as part of immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) syndrome. Cumulative clinical experience with management of AIE has allowed improved outcomes in transplanted and non-transplanted AIE patients even though morbidity and mortality with are still high in patients with this condition. More research is needed to further define the role of new therapies for AIE, and a central registry with participation of multiple institutions might help share and standardize care of patients with this rare but serious condition.
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Affiliation(s)
- Zunirah Ahmed
- School of Medicine, University of Alabama, Montgomery Campus, 2055 E South Blvd Ste 202, Montgomery, AL, 36116, USA
| | - Aamer Imdad
- Division of Pediatric Gastroenterology, SUNY Upstate Medical University, 725 Irving Street, Suite 501, Syracuse, NY, 13210, USA
| | - James A Connelly
- Division of Pediatric Hematology-Oncology, Vanderbilt University Medical Center, 2100 Children's Way, Nashville, TN, 37212, USA
| | - Sari Acra
- Division of Pediatric Gastroenterology, Hepatology and Nutrition, Vanderbilt University Medical Center, 2100 Children's Way, Nashville, TN, 37212, USA.
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Morales-Alvarez MC, Ricardo-Silgado ML, Lemus HN, González-Devia D, Mendivil CO. Fructosuria and recurrent hypoglycemia in a patient with a novel c.1693T>A variant in the 3' untranslated region of the aldolase B gene. SAGE Open Med Case Rep 2019; 7:2050313X18823098. [PMID: 30675358 PMCID: PMC6330728 DOI: 10.1177/2050313x18823098] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 12/13/2018] [Indexed: 11/17/2022] Open
Abstract
Hereditary fructose intolerance, caused by mutations in the ALDOB gene, is an unusual cause of hypoglycemia. ALDOB encodes the enzyme aldolase B, responsible for the hydrolysis of fructose 1-phosphate in the liver. Here, we report the case of a 33-year-old female patient who consulted due to repetitive episodes of weakness, dizziness and headache after food ingestion. An ambulatory 72-h continuous glucose monitoring revealed multiple short hypoglycemic episodes over the day. After biochemical exclusion of other endocrine causes of hypoglycemia, hereditary fructose intolerance seemed a plausible diagnosis. Repeated measurements of urinary fructose revealed pathologic fructosuria, but genetic testing for the three most common mutations in ALDOB resulted negative. We decided to perform complete Sanger sequencing of the ALDOB gene and encountered a variant consisting of a T>A substitution in position 1963 of the ALDOB transcript (c.1693T>A). This position is located within the 3′ untranslated region of exon 9, 515 nucleotides downstream the stop codon. After complete withdrawal of dietary fructose and sucrose, the patient presented no new hypoglycemic episodes.
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Affiliation(s)
| | | | | | - Deyanira González-Devia
- School of Medicine, Universidad de los Andes, Bogotá, Colombia.,Section of Endocrinology, Department of Internal Medicine, Fundación Santa Fe de Bogotá, Bogotá, Colombia
| | - Carlos O Mendivil
- School of Medicine, Universidad de los Andes, Bogotá, Colombia.,Section of Endocrinology, Department of Internal Medicine, Fundación Santa Fe de Bogotá, Bogotá, Colombia
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Behlmann AM, Goyal NA, Yang X, Chen PH, Ankala A. A Hemizygous Deletion Within the PGK1 Gene in Males with PGK1 Deficiency. JIMD Rep 2018; 45:105-110. [PMID: 30570712 PMCID: PMC6336546 DOI: 10.1007/8904_2018_147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 08/24/2018] [Accepted: 09/25/2018] [Indexed: 02/05/2023] Open
Abstract
Phosphoglycerate kinase-1 (PGK1) deficiency is a rare X-linked disorder caused by pathogenic variants in the PGK1 gene. Complete loss-of-function variants have not been reported in this gene, indicating that residual enzyme function is critical for viability in males. Therefore, copy number variants (CNVs) that include single exon or multiple exon deletions or duplications are generally not expected in individuals with PGK1 deficiency. Here we describe a 64-year-old male presenting with a family history (three additional affected males) and a personal history of childhood-onset metabolic myopathy that involves episodes of muscle pain, stiffness after activity, exercise intolerance, and myoglobinuria after exertion. Biochemical analysis on a muscle biopsy indicated significantly reduced activity (15% compared to normal) for phosphoglycerate kinase (PGK1), a glycolytic enzyme encoded by PGK1. A diagnosis of PGK1 deficiency was established by molecular analysis which detected an approximately 886 kb deletion involving the polyadenylation site in the 3'UTR of the PGK1 gene. RNA analysis showed significantly reduced PGK1 transcript levels (30% compared to normal). This is the first deletion reported in the PGK1 gene and is the first pathogenic variant involving the 3'UTR polyadenylation site of this gene. Our report emphasizes the role of 3'UTR variants in human disorders and underscores the need for exploring noncoding regions of disease-associated genes when seeking a molecular diagnosis.
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Affiliation(s)
- Andrea Medrano Behlmann
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA
| | - Namita A. Goyal
- grid.266093.80000 0001 0668 7243Department of Neurology, University of California, Irvine, CA USA
| | - Xiaoyu Yang
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Ping H. Chen
- grid.189967.80000 0001 0941 6502Department of Cell Biology, Emory University School of Medicine, Atlanta, GA USA
| | - Arunkanth Ankala
- grid.189967.80000 0001 0941 6502Department of Human Genetics, Emory University School of Medicine, Atlanta, GA USA ,EGL Genetic Diagnostics LLC, Tucker, GA USA
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Gambineri E, Ciullini Mannurita S, Hagin D, Vignoli M, Anover-Sombke S, DeBoer S, Segundo GRS, Allenspach EJ, Favre C, Ochs HD, Torgerson TR. Clinical, Immunological, and Molecular Heterogeneity of 173 Patients With the Phenotype of Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-Linked (IPEX) Syndrome. Front Immunol 2018; 9:2411. [PMID: 30443250 PMCID: PMC6223101 DOI: 10.3389/fimmu.2018.02411] [Citation(s) in RCA: 116] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022] Open
Abstract
Background: Immune Dysregulation, Polyendocrinopathy, Enteropathy, X-linked (IPEX) Syndrome is a rare recessive disorder caused by mutations in the FOXP3 gene. In addition, there has been an increasing number of patients with wild-type FOXP3 gene and, in some cases, mutations in other immune regulatory genes. Objective: To molecularly asses a cohort of 173 patients with the IPEX phenotype and to delineate the relationship between the clinical/immunologic phenotypes and the genotypes. Methods: We reviewed the clinical presentation and laboratory characteristics of each patient and compared clinical and laboratory data of FOXP3 mutation-positive (IPEX patients) with those from FOXP3 mutation-negative patients (IPEX-like). A total of 173 affected patients underwent direct sequence analysis of the FOXP3 gene while 85 IPEX-like patients with normal FOXP3 were investigated by a multiplex panel of "Primary Immune Deficiency (PID-related) genes." Results: Forty-four distinct FOXP3 variants were identified in 88 IPEX patients, 9 of which were not previously reported. Among the 85 IPEX-like patients, 19 different disease-associated variants affecting 9 distinct genes were identified. Conclusions: We provide a comprehensive analysis of the clinical features and molecular bases of IPEX and IPEX-like patients. Although we were not able to identify major distinctive clinical features to differentiate IPEX from IPEX-like syndromes, we propose a simple flow-chart to effectively evaluate such patients and to focus on the most likely molecular diagnosis. Given the large number of potential candidate genes and overlapping phenotypes, selecting a panel of PID-related genes will facilitate a molecular diagnosis.
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Affiliation(s)
- Eleonora Gambineri
- Department of NEUROFARBA, University of Florence, Florence, Italy
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | - Sara Ciullini Mannurita
- Department of NEUROFARBA, University of Florence, Florence, Italy
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | - David Hagin
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Marina Vignoli
- Department of NEUROFARBA, University of Florence, Florence, Italy
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | | | - Stacey DeBoer
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Gesmar R. S. Segundo
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Eric J. Allenspach
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Claudio Favre
- Oncology/Hematology Department, “Anna Meyer” Children's Hospital, Florence, Italy
| | - Hans D. Ochs
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
| | - Troy R. Torgerson
- Seattle Children's Research Institute, University of Washington, Seattle, WA, United States
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Wang R, Zheng D, Yehia G, Tian B. A compendium of conserved cleavage and polyadenylation events in mammalian genes. Genome Res 2018; 28:1427-1441. [PMID: 30143597 PMCID: PMC6169888 DOI: 10.1101/gr.237826.118] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2018] [Accepted: 08/08/2018] [Indexed: 12/22/2022]
Abstract
Cleavage and polyadenylation is essential for 3' end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3' UTRs and/or coding sequences. Here, we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on approximately 1.2 billion 3' end sequencing reads from more than 360 human, mouse, and rat samples. We show that ∼80% of mammalian mRNA genes contain at least one conserved PAS, and ∼50% have conserved APA events. PAS conservation generally reduces promiscuous 3' end processing, stabilizing gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with conserved APA events. Whereas tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. In addition, we show enrichment of mRNA destabilizing motifs in alternative 3' UTR sequences, leading to substantial differences in mRNA stability between 3' UTR isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Furthermore, we show that mutations of U-rich motifs around the PAS often accompany APA profile differences between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation through evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic perspective on APA functions.
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Affiliation(s)
- Ruijia Wang
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
| | - Ghassan Yehia
- Genome Editing Core Facility, Rutgers University, New Brunswick, New Jersey 08901, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, New Jersey 07103, USA
- Rutgers Cancer Institute of New Jersey, Newark, New Jersey 07103, USA
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Bamidele AO, Svingen PA, Sagstetter MR, Sarmento OF, Gonzalez M, Braga Neto MB, Kugathasan S, Lomberk G, Urrutia RA, Faubion WA. Disruption of FOXP3-EZH2 Interaction Represents a Pathobiological Mechanism in Intestinal Inflammation. Cell Mol Gastroenterol Hepatol 2018; 7:55-71. [PMID: 30510991 PMCID: PMC6260395 DOI: 10.1016/j.jcmgh.2018.08.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/30/2018] [Indexed: 02/06/2023]
Abstract
Background & Aims Forkhead box protein 3 (FOXP3)+ regulatory T cell (Treg) dysfunction is associated with autoimmune diseases; however, the mechanisms responsible for inflammatory bowel disease pathophysiology are poorly understood. Here, we tested the hypothesis that a physical interaction between transcription factor FOXP3 and the epigenetic enzyme enhancer of zeste homolog 2 (EZH2) is essential for gene co-repressive function. Methods Human FOXP3 mutations clinically relevant to intestinal inflammation were generated by site-directed mutagenesis. T lymphocytes were isolated from mice, human blood, and lamina propria of Crohn's disease (CD) patients and non-CD controls. We performed proximity ligation or a co-immunoprecipitation assay in FOXP3-mutant+, interleukin 6 (IL6)-treated or CD-CD4+ T cells to assess FOXP3-EZH2 protein interaction. We studied IL2 promoter activity and chromatin state of the interferon γ locus via luciferase reporter and chromatin-immunoprecipitation assays, respectively, in cells expressing FOXP3 mutants. Results EZH2 binding was abrogated by inflammatory bowel disease-associated FOXP3 cysteine 232 (C232) mutation. The C232 mutant showed impaired repression of IL2 and diminished EZH2-mediated trimethylation of histone 3 at lysine 27 on interferon γ, indicative of compromised Treg physiologic function. Generalizing this mechanism, IL6 impaired FOXP3-EZH2 interaction. IL6-induced effects were reversed by Janus kinase 1/2 inhibition. In lamina propria-derived CD4+T cells from CD patients, we observed decreased FOXP3-EZH2 interaction. Conclusions FOXP3-C232 mutation disrupts EZH2 recruitment and gene co-repressive function. The proinflammatory cytokine IL6 abrogates FOXP3-EZH2 interaction. Studies in lesion-derived CD4+ T cells have shown that reduced FOXP3-EZH2 interaction is a molecular feature of CD patients. Destabilized FOXP3-EZH2 protein interaction via diverse mechanisms and consequent Treg abnormality may drive gastrointestinal inflammation.
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Key Words
- C232, cysteine 232
- CD, Crohn’s disease
- ChIP, chromatin-immunoprecipitation
- Crohn’s Disease
- EED, embryonic ectoderm development
- EZH2, enhancer of zeste homolog 2
- Epigenetics
- FCS, fetal calf serum
- FOXP3, forkhead domain-containing X-chromosome–encoded protein
- H3K27me3, trimethylated histone H3 at lysine 27
- IBD, inflammatory bowel disease
- IL, interleukin
- IPEX, immune dysregulation, polyendocrinopathy, enteropathy, X-linked
- JAK, Janus kinase
- LZ, leucine zipper
- PBMC, peripheral blood mononuclear cell
- PBS, phosphate-buffered saline
- PLA, proximity ligation assay
- PMA, phorbol 12-myristate 13-acetate
- PRC2, polycomb repressive complex 2
- Proinflammatory Cytokine
- Regulatory T Cells
- STAT, signal transducer and activator of transcription
- SUZ12, suppressor of zeste
- Th, T helper
- Treg, regulatory T cell
- WT, wild-type
- co-IP, co-immunoprecipitation
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Affiliation(s)
- Adebowale O Bamidele
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Phyllis A Svingen
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Mary R Sagstetter
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Olga F Sarmento
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Michelle Gonzalez
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Manuel B Braga Neto
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota
| | - Subra Kugathasan
- Department of Pediatrics, Emory University, School of Medicine, Atlanta, Georgia
| | - Gwen Lomberk
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Raul A Urrutia
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - William A Faubion
- Epigenetics and Chromatin Dynamics Laboratory, Division of Gastroenterology and Hepatology and Translational Epigenomic Program, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota.
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Genome-wide atlas of alternative polyadenylation in the forage legume red clover. Sci Rep 2018; 8:11379. [PMID: 30054540 PMCID: PMC6063945 DOI: 10.1038/s41598-018-29699-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 07/05/2018] [Indexed: 12/13/2022] Open
Abstract
Studies on prevalence and significance of alternative polyadenylation (APA) in plants have been so far limited mostly to the model plants. Here, a genome-wide analysis of APA was carried out in different tissue types in the non-model forage legume red clover (Trifolium pratense L). A profile of poly(A) sites in different tissue types was generated using so-called 'poly(A)-tag sequencing' (PATseq) approach. Our analysis revealed tissue-wise dynamics of usage of poly(A) sites located at different genomic locations. We also identified poly(A) sites and underlying genes displaying APA in different tissues. Functional categories enriched in groups of genes manifesting APA between tissue types were determined. Analysis of spatial expression of genes encoding different poly(A) factors showed significant differential expression of genes encoding orthologs of FIP1(V) and PCFS4, suggesting that these two factors may play a role in regulating spatial APA in red clover. Our analysis also revealed a high degree of conservation in diverse plant species of APA events in mRNAs encoding two key polyadenylation factors, CPSF30 and FIP1(V). Together with our previously reported study of spatial gene expression in red clover, this study will provide a comprehensive account of transcriptome dynamics in this non-model forage legume.
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Profile of Alexander Y. Rudensky, winner of the 2018 Vilcek Prize in Biomedical Science. Proc Natl Acad Sci U S A 2018; 115:4301-4304. [PMID: 29632182 DOI: 10.1073/pnas.1804659115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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Steri M, Idda ML, Whalen MB, Orrù V. Genetic variants in mRNA untranslated regions. WILEY INTERDISCIPLINARY REVIEWS-RNA 2018; 9:e1474. [PMID: 29582564 DOI: 10.1002/wrna.1474] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/05/2018] [Accepted: 02/11/2018] [Indexed: 12/24/2022]
Abstract
Genome Wide Association Studies (GWAS) have mapped thousands of genetic variants associated with complex disease risk and regulating quantitative traits, thus exploiting an unprecedented high-resolution genetic characterization of the human genome. A small fraction (3.7%) of the identified associations is located in untranslated regions (UTRs), and the molecular mechanism has been elucidated for few of them. Genetic variations at UTRs may modify regulatory elements affecting the interaction of the UTRs with proteins and microRNAs. The overall functional consequences include modulation of messenger RNA (mRNA) transcription, secondary structure, stability, localization, translation, and access to regulators like microRNAs (miRNAs) and RNA-binding proteins (RBPs). Alterations of these regulatory mechanisms are known to modify molecular pathways and cellular processes, potentially leading to disease processes. Here, we analyze some examples of genetic risk variants mapping in the UTR regulatory elements. We describe a recently identified genetic variant localized in the 3'UTR of the TNFSF13B gene, associated with autoimmunity risk and responsible of an increased stability and translation of TNFSF13B mRNA. We discuss how the correct use and interpretation of public GWAS repositories could lead to a better understanding of etiopathogenetic mechanisms and the generation of robust biological hypothesis as starting point for further functional studies. This article is categorized under: RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Evolution and Genomics > Computational Analyses of RNA RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - M Laura Idda
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institute of Health, Baltimore, Maryland
| | - Michael B Whalen
- Istituto di Biofisica, Consiglio Nazionale delle Ricerche (CNR), Trento, Italy
| | - Valeria Orrù
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
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Chang JW, Yeh HS, Yong J. Alternative Polyadenylation in Human Diseases. Endocrinol Metab (Seoul) 2017; 32:413-421. [PMID: 29271615 PMCID: PMC5744726 DOI: 10.3803/enm.2017.32.4.413] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 11/23/2017] [Accepted: 11/27/2017] [Indexed: 12/02/2022] Open
Abstract
Varying length of messenger RNA (mRNA) 3'-untranslated region is generated by alternating the usage of polyadenylation sites during pre-mRNA processing. It is prevalent through all eukaryotes and has emerged as a key mechanism for controlling gene expression. Alternative polyadenylation (APA) plays an important role for cell growth, proliferation, and differentiation. In this review, we discuss the functions of APA related with various physiological conditions including cellular metabolism, mRNA processing, and protein diversity in a variety of disease models. We also discuss the molecular mechanisms underlying APA regulation, such as variations in the concentration of mRNA processing factors and RNA-binding proteins, as well as global transcriptome changes under cellular signaling pathway.
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Affiliation(s)
- Jae Woong Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, MN, USA
| | - Hsin Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, MN, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities College of Biological Sciences, Minneapolis, MN, USA.
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Delalat B, Harding F, Gundsambuu B, De-Juan-Pardo EM, Wunner FM, Wille ML, Jasieniak M, Malatesta KA, Griesser HJ, Simula A, Hutmacher DW, Voelcker NH, Barry SC. 3D printed lattices as an activation and expansion platform for T cell therapy. Biomaterials 2017. [DOI: 10.1016/j.biomaterials.2017.05.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Neve J, Patel R, Wang Z, Louey A, Furger AM. Cleavage and polyadenylation: Ending the message expands gene regulation. RNA Biol 2017; 14:865-890. [PMID: 28453393 PMCID: PMC5546720 DOI: 10.1080/15476286.2017.1306171] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/02/2017] [Accepted: 03/09/2017] [Indexed: 12/13/2022] Open
Abstract
Cleavage and polyadenylation (pA) is a fundamental step that is required for the maturation of primary protein encoding transcripts into functional mRNAs that can be exported from the nucleus and translated in the cytoplasm. 3'end processing is dependent on the assembly of a multiprotein processing complex on the pA signals that reside in the pre-mRNAs. Most eukaryotic genes have multiple pA signals, resulting in alternative cleavage and polyadenylation (APA), a widespread phenomenon that is important to establish cell state and cell type specific transcriptomes. Here, we review how pA sites are recognized and comprehensively summarize how APA is regulated and creates mRNA isoform profiles that are characteristic for cell types, tissues, cellular states and disease.
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Affiliation(s)
- Jonathan Neve
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Radhika Patel
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Zhiqiao Wang
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
| | - Alastair Louey
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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Schuster M, Plaza-Sirvent C, Matthies AM, Heise U, Jeron A, Bruder D, Visekruna A, Huehn J, Schmitz I. c-REL and IκB NS Govern Common and Independent Steps of Regulatory T Cell Development from Novel CD122-Expressing Pre-Precursors. THE JOURNAL OF IMMUNOLOGY 2017; 199:920-930. [PMID: 28652399 DOI: 10.4049/jimmunol.1600877] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 05/31/2017] [Indexed: 01/13/2023]
Abstract
Foxp3-expressing regulatory T cells (Tregs) are essential regulators of immune homeostasis and, thus, are prime targets for therapeutic interventions of diseases such as cancer and autoimmunity. c-REL and IκBNS are important regulators of Foxp3 induction in Treg precursors upon γ-chain cytokine stimulation. In c-REL/IκBNS double-deficient mice, Treg numbers were dramatically reduced, indicating that together, c-REL and IκBNS are pivotal for Treg development. However, despite the highly reduced Treg compartment, double-deficient mice did not develop autoimmunity even when aged to more than 1 y, suggesting that c-REL and IκBNS are required for T cell effector function as well. Analyzing Treg development in more detail, we identified a CD122+ subset within the CD25-Foxp3- precursor population, which gave rise to classical CD25+Foxp3- Treg precursors. Importantly, c-REL, but not IκBNS, controlled the generation of classical CD25+Foxp3- precursors via direct binding to the Cd25 locus. Thus, we propose that CD4+GITR+CD122+CD25-Foxp3- cells represent a Treg pre-precursor population, whose transition into Treg precursors is mediated via c-REL.
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Affiliation(s)
- Marc Schuster
- Systems-Oriented Immunology and Inflammation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Carlos Plaza-Sirvent
- Systems-Oriented Immunology and Inflammation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Anne-Marie Matthies
- Systems-Oriented Immunology and Inflammation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany.,Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120 Magdeburg, Germany
| | - Ulrike Heise
- Mouse Pathology Platform, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Andreas Jeron
- Institute of Medical Microbiology, Otto-von-Guericke University, 39120 Magdeburg, Germany.,Immune Regulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Dunja Bruder
- Institute of Medical Microbiology, Otto-von-Guericke University, 39120 Magdeburg, Germany.,Immune Regulation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Alexander Visekruna
- Institute of Medical Microbiology and Hospital Hygiene, Phillips-University Marburg, 35043 Marburg, Germany; and
| | - Jochen Huehn
- Department of Experimental Immunology, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Ingo Schmitz
- Systems-Oriented Immunology and Inflammation Research Group, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany; .,Institute of Molecular and Clinical Immunology, Otto-von-Guericke University, 39120 Magdeburg, Germany
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Pereira LMS, Gomes STM, Ishak R, Vallinoto ACR. Regulatory T Cell and Forkhead Box Protein 3 as Modulators of Immune Homeostasis. Front Immunol 2017; 8:605. [PMID: 28603524 PMCID: PMC5445144 DOI: 10.3389/fimmu.2017.00605] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 05/08/2017] [Indexed: 12/15/2022] Open
Abstract
The transcription factor forkhead box protein 3 (FOXP3) is an essential molecular marker of regulatory T cell (Treg) development in different microenvironments. Tregs are cells specialized in the suppression of inadequate immune responses and the maintenance of homeostatic tolerance. Studies have addressed and elucidated the role played by FOXP3 and Treg in countless autoimmune and infectious diseases as well as in more specific cases, such as cancer. Within this context, the present article reviews aspects of the immunoregulatory profile of FOXP3 and Treg in the management of immune homeostasis, including issues relating to pathology as well as immune tolerance.
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Affiliation(s)
- Leonn Mendes Soares Pereira
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.,Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Samara Tatielle Monteiro Gomes
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil.,Programa de Pós-Graduação em Biologia de Agentes Infecciosos e Parasitários, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Ricardo Ishak
- Laboratório de Virologia, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Pará, Brazil
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