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Singh I, Kanichery A, Kotimoole CN, Modi PK, Prasad TSK, Hoti SL. Unpacking Immune Modulation as a Site of Therapeutics Innovation for Nematode Parasite Wuchereria bancrofti: A Temporal Quantitative Phosphoproteomics Profiling of Macrophage Migration Inhibitory Factor 2. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2024; 28:125-137. [PMID: 38527276 DOI: 10.1089/omi.2024.0002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Nematode infections are common in both humans and livestock, with major adverse planetary health and economic impacts. Wuchereria bancrofti is a parasitic nematode that causes lymphatic filariasis, a neglected tropical disease that can lead to severe disability and deformity worldwide. For the long-term survival of the bancroftian parasites in the host, a complex immune invasion strategy is involved through immunomodulation. Therefore, immunomodulation can serve as a site of research and innovation for molecular targets. Macrophage migration inhibitory factor (MIF) is a pleiotropic cytokine crucial to the host antimicrobial alarm system and stress response. Interestingly, the nematode parasite W. bancrofti also produces two homologs of MIF (Wba-MIF1 and 2). Using a mass spectrometry-based phosphoproteomics approach, we report new findings on the immunomodulatory effect and signaling mechanism of Wba-MIF2 in macrophage cells. Accordingly, we observed 1201 phosphorylated sites on 467 proteins. Out of the 1201 phosphorylated sites, 1075, 117, and 9 were found on serine (S), threonine (T), and tyrosine (Y) residues, respectively. Our bioinformatics analysis led to identification of major pathways, including spliceosomes, T cell receptor signaling pathway, Th17 differentiation pathway, interleukin-17 signaling pathway, and insulin signaling pathway upon Wba-MIF2 treatment. Wba-MIF2 treatment also enriched CDK4, CDK1, and DNAPK kinases. The comparison of the signaling pathway of Wba-MIF2 with that of human-MIF suggests both share similar signaling pathways. These findings collectively offer new insights into the role and mechanism of Wba-MIF2 as an immunomodulator and inform future diagnostics and drug discovery research for W. bancrofti.
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Affiliation(s)
- Ishwar Singh
- Department of Neglected Tropical Diseases and Translational Research, ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
- Department of the Interdisciplinary Science, KLE Academy of Higher Education and Research, (Deemed to be University), Belagavi, Karnataka, India
| | - Anagha Kanichery
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Chinmaya Narayana Kotimoole
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | - Prashant Kumar Modi
- Center for Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore, India
| | | | - Sugeerappa Laxamannappa Hoti
- Department of Neglected Tropical Diseases and Translational Research, ICMR-National Institute of Traditional Medicine, Belagavi, Karnataka, India
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2
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Pirmoradi S, Hosseiniyan Khatibi SM, Zununi Vahed S, Homaei Rad H, Khamaneh AM, Akbarpour Z, Seyedrezazadeh E, Teshnehlab M, Chapman KR, Ansarin K. Unraveling the link between PTBP1 and severe asthma through machine learning and association rule mining method. Sci Rep 2023; 13:15399. [PMID: 37717070 PMCID: PMC10505163 DOI: 10.1038/s41598-023-42581-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 09/12/2023] [Indexed: 09/18/2023] Open
Abstract
Severe asthma is a chronic inflammatory airway disease with great therapeutic challenges. Understanding the genetic and molecular mechanisms of severe asthma may help identify therapeutic strategies for this complex condition. RNA expression data were analyzed using a combination of artificial intelligence methods to identify novel genes related to severe asthma. Through the ANOVA feature selection approach, 100 candidate genes were selected among 54,715 mRNAs in blood samples of patients with severe asthmatic and healthy groups. A deep learning model was used to validate the significance of the candidate genes. The accuracy, F1-score, AUC-ROC, and precision of the 100 genes were 83%, 0.86, 0.89, and 0.9, respectively. To discover hidden associations among selected genes, association rule mining was applied. The top 20 genes including the PTBP1, RAB11FIP3, APH1A, and MYD88 were recognized as the most frequent items among severe asthma association rules. The PTBP1 was found to be the most frequent gene associated with severe asthma among those 20 genes. PTBP1 was the gene most frequently associated with severe asthma among candidate genes. Identification of master genes involved in the initiation and development of asthma can offer novel targets for its diagnosis, prognosis, and targeted-signaling therapy.
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Affiliation(s)
- Saeed Pirmoradi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Mahdi Hosseiniyan Khatibi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | | | - Hamed Homaei Rad
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Amir Mahdi Khamaneh
- Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Zahra Akbarpour
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran
| | - Ensiyeh Seyedrezazadeh
- Tuberculosis and Lung Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Teshnehlab
- Department of Electric and Computer Engineering, K.N. Toosi University of Technology, Tehran, Iran
| | - Kenneth R Chapman
- Division of Respiratory Medicine, Department of Medicine, University of Toronto, Toronto, ON, Canada.
| | - Khalil Ansarin
- Rahat Breath and Sleep Research Center, Tabriz University of Medical Science, Tabriz, Iran.
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3
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Yang H, Sun W, Bi T, Wang Q, Wang W, Xu Y, Liu Z, Li J. The PTBP1‑NCOA4 axis promotes ferroptosis in liver cancer cells. Oncol Rep 2023; 49:45. [PMID: 36660932 PMCID: PMC9868890 DOI: 10.3892/or.2023.8482] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/10/2022] [Indexed: 01/15/2023] Open
Abstract
Polypyrimidine tract‑binding protein 1 (PTBP1) plays an important role in tumor immunity, cell proliferation, apoptosis, and autophagy by regulating RNA metabolism. However, the specific function and mechanism of PTBP1 in ferroptosis remain unclear. In the present study, it was investigated whether PTBP1 regulates ferroptosis and the exact mechanism. The iron, malondialdehyde (MDA), and GSH levels were detected in sorafenib (SF)‑treated liver cancer cells. si‑PTBP1 introduction into SF‑treated liver cancer cells resulted in a significant reduction in the levels of MDA and iron. Additionally, a significant recovery of GSH levels was observed after silencing PTBP1. StarBase v2.0 database was used to predict potential transcripts that can physically interact with PTBP1 and nuclear receptor coactivator 4 (NCOA4) mRNA was identified as the most enriched binding partner in the PTBP1‑RNA complex. A dual‑luciferase assay then demonstrated that PTBP1 directly interacted with NCOA4. PTBP1 silencing did not affect NCOA4 stability following treatment with cycloheximide. A pull‑down assay revealed that the PTBP1‑binding region was in the 5'‑UTR of the NCOA4 mRNA sequence. These results suggest that PTBP1 mediates ferroptosis in liver cancer cells by regulating NCOA4 translation. In vivo experiments reconfirmed the role of the PTBP1‑NCOA4 axis in a xenograft transplantation model. It was observed that the mean tumor weight increased after PTBP1 knockout. In conclusion, silencing of PTBP1 decreased the sensitivity of liver cancer cells to ferroptosis after SF treatment and regulated ferritinophagy by mediating NCOA4 translation.
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Affiliation(s)
- Hao Yang
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China
| | - Wensheng Sun
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Tao Bi
- Department of Gastrointestinal Surgery, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong 264100, P.R. China
| | - Qi Wang
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Wentao Wang
- Department of Hepatobiliary Surgery, Shandong Provincial Qianfoshan Hospital, Shandong University, Jinan, Shandong 250014, P.R. China
| | - Youxin Xu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China
| | - Zhiqian Liu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China,Correspondence to: Professor Jie Li or Dr Zhiqian Liu, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, 16766 Jingshi Road, Jinan, Shandong 250014, P.R. China, E-mail:
| | - Jie Li
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, Shandong 250014, P.R. China,Correspondence to: Professor Jie Li or Dr Zhiqian Liu, Department of Hepatobiliary Surgery, The First Affiliated Hospital of Shandong First Medical University, 16766 Jingshi Road, Jinan, Shandong 250014, P.R. China, E-mail:
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4
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Choi JO, Ham JH, Hwang SS. RNA Metabolism in T Lymphocytes. Immune Netw 2022; 22:e39. [PMID: 36381959 PMCID: PMC9634142 DOI: 10.4110/in.2022.22.e39] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 08/18/2022] [Accepted: 08/30/2022] [Indexed: 01/25/2023] Open
Abstract
RNA metabolism plays a central role in regulating of T cell-mediated immunity. RNA processing, modifications, and regulations of RNA decay influence the tight and rapid regulation of gene expression during T cell phase transition. Thymic selection, quiescence maintenance, activation, differentiation, and effector functions of T cells are dependent on selective RNA modulations. Recent technical improvements have unveiled the complex crosstalk between RNAs and T cells. Moreover, resting T cells contain large amounts of untranslated mRNAs, implying that the regulation of RNA metabolism might be a key step in controlling gene expression. Considering the immunological significance of T cells for disease treatment, an understanding of RNA metabolism in T cells could provide new directions in harnessing T cells for therapeutic implications.
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Affiliation(s)
- Jin Ouk Choi
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Jeong Hyeon Ham
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea
| | - Soo Seok Hwang
- Department of Biochemistry and Molecular Biology, Graduate School of Medical Science, Severance Biomedical Science Institute and Brain Korea 21 Project, Yonsei University College of Medicine, Seoul 03722, Korea.,Chronic Intractable Disease Systems Medicine Research Center, Institute of Genetic Science, Institute for Immunology and Immunological Diseases, Yonsei University College of Medicine, Seoul 03722, Korea
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5
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D'Angeli V, Monzón‐Casanova E, Matheson LS, Gizlenci Ö, Petkau G, Gooding C, Berrens RV, Smith CWJ, Turner M. Polypyrimidine tract binding protein 1 regulates the activation of mouse CD8 T cells. Eur J Immunol 2022; 52:1058-1068. [PMID: 35460072 PMCID: PMC9546061 DOI: 10.1002/eji.202149781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/20/2022] [Accepted: 04/21/2022] [Indexed: 12/30/2022]
Abstract
The RNA-binding protein polypyrimidine tract binding protein 1 (PTBP1) has been found to have roles in CD4 T-cell activation, but its function in CD8 T cells remains untested. We show it is dispensable for the development of naïve mouse CD8 T cells, but is necessary for the optimal expansion and production of effector molecules by antigen-specific CD8 T cells in vivo. PTBP1 has an essential role in regulating the early events following activation of the naïve CD8 T cell leading to IL-2 and TNF production. It is also required to protect activated CD8 T cells from apoptosis. PTBP1 controls alternative splicing of over 400 genes in naïve CD8 T cells in addition to regulating the abundance of ∼200 mRNAs. PTBP1 is required for the nuclear accumulation of c-Fos, NFATc2, and NFATc3, but not NFATc1. This selective effect on NFAT proteins correlates with PTBP1-promoted expression of the shorter Aβ1 isoform and exon 13 skipped Aβ2 isoform of the catalytic A-subunit of calcineurin phosphatase. These findings reveal a crucial role for PTBP1 in regulating CD8 T-cell activation.
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Affiliation(s)
- Vanessa D'Angeli
- Laboratory of Lymphocyte Signalling and DevelopmentThe Babraham InstituteCambridgeUK
- IONTAS, The Works, Unity CampusCambridgeCB22 3EFUK
| | - Elisa Monzón‐Casanova
- Laboratory of Lymphocyte Signalling and DevelopmentThe Babraham InstituteCambridgeUK
- Department of BiochemistryUniversity of CambridgeCambridgeUK
- Oxford Biomedica (UK) LtdOxfordOX4 6LTUK
| | - Louise S. Matheson
- Laboratory of Lymphocyte Signalling and DevelopmentThe Babraham InstituteCambridgeUK
| | - Özge Gizlenci
- Laboratory of Lymphocyte Signalling and DevelopmentThe Babraham InstituteCambridgeUK
| | - Georg Petkau
- Laboratory of Lymphocyte Signalling and DevelopmentThe Babraham InstituteCambridgeUK
| | - Clare Gooding
- Department of BiochemistryUniversity of CambridgeCambridgeUK
| | - Rebecca V. Berrens
- Cancer Research UK Cambridge InstituteUniversity of CambridgeCambridgeUnited Kingdom
| | | | - Martin Turner
- Laboratory of Lymphocyte Signalling and DevelopmentThe Babraham InstituteCambridgeUK
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6
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Dai S, Wang C, Zhang C, Feng L, Zhang W, Zhou X, He Y, Xia X, Chen B, Song W. PTB: Not just a polypyrimidine tract-binding protein. J Cell Physiol 2022; 237:2357-2373. [PMID: 35288937 DOI: 10.1002/jcp.30716] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 01/21/2023]
Abstract
Polypyrimidine tract-binding protein (PTB), as a member of the heterogeneous nuclear ribonucleoprotein family, functions by rapidly shuttling between the nucleus and the cytoplasm. PTB is involved in the alternative splicing of pre-messenger RNA (mRNA) and almost all steps of mRNA metabolism. PTB regulation is organ-specific; brain- or muscle-specific microRNAs and long noncoding RNAs partially contribute to regulating PTB, thereby modulating many physiological and pathological processes, such as embryonic development, cell development, spermatogenesis, and neuron growth and differentiation. Previous studies have shown that PTB knockout can inhibit tumorigenesis and development. The knockout of PTB in glial cells can be reprogrammed into functional neurons, which shows great promise in the field of nerve regeneration but is controversial.
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Affiliation(s)
- Shirui Dai
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China.,Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Chao Wang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Cheng Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Lemeng Feng
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Wulong Zhang
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xuezhi Zhou
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Ye He
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Xiaobo Xia
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
| | - Baihua Chen
- Department of Ophthalmology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Clinical Research Center of Ophthalmic Disease, Changsha, Hunan, P. R. China
| | - Weitao Song
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China.,Eye Center of Xiangya Hospital, Central South University, Changsha, Hunan, P. R. China.,Hunan Key Laboratory of Ophthalmology, Changsha, Hunan, P. R. China
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7
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Liu X, Lin J, Wu H, Wang Y, Xie L, Wu J, Qin H, Xu J. A Novel Long Noncoding RNA lincRNA00892 Activates CD4 + T Cells in Systemic Lupus Erythematosus by Regulating CD40L. Front Pharmacol 2021; 12:733902. [PMID: 34707498 PMCID: PMC8543062 DOI: 10.3389/fphar.2021.733902] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Objective: The mechanism of CD4+ T-cell dysfunction in systemic lupus erythematosus (SLE) has not been fully understood. Increasing evidence show that long noncoding RNAs (lncRNAs) can regulate immune responses and take part in some autoimmune diseases, while little is known about the lncRNA expression and function in CD4+ T of SLE. Here, we aimed to detect the expression profile of lncRNAs in lupus CD4+ T cells and explore the mechanism that how lincRNA00892 in CD4+ T cells is involved in the pathogenesis of SLE. Methods: The expression profiles of lncRNAs and mRNAs in CD4+ T cells from SLE patients and healthy controls were detected by microarray. LincRNA00892 and CD40L were chosen for validation by quantitative real-time PCR (qRT-PCR). Coexpression network was conducted to predict the potential target genes of lincRNA00892. Then lincRNA00892 was overexpressed in normal CD4+ T cells via lentivirus transfection. The expression of lincRNA00892 was detected by qRT-PCR. The expression of CD40L was detected by qRT-PCR, western blotting, and flow cytometry, respectively. The expression of CD69 and CD23 was measured by flow cytometry. The secretion of IgG was determined by enzyme-linked immunosorbent assay (ELISA). The proteins targeted by lincRNA00892 were measured by RNA pulldown and subsequent mass spectrometry (MS). The interaction between heterogeneous nuclear ribonucleoprotein K (hnRNP K) and lincRNA00892 or CD40L was detected by RNA immunoprecipitation (RIP) assay. Results: A total of 1887 lncRNAs and 3375 mRNAs were found to be aberrantly expressed in CD4+ T cells of SLE patients compared to healthy controls. LincRNA00892 and CD40L were confirmed to be upregulated in CD4+ T cells of SLE patients by qRT-PCR. The lncRNA-mRNA coexpression network analysis indicated that CD40L was a potential target of lincRNA00892. Overexpression of lincRNA00892 enhanced CD40L protein levels while exerting little influence on CD40L mRNA levels in CD4+ T cells. In addition, lincRNA00892 could induce the activation of CD4+ T cells. Furthermore, lincRNA00892 led to the activation of B cells and subsequent secretion of IgG in a CD4+ T-cell-dependent manner. Finally, hnRNP K was found to be among the proteins pulled down by lincRNA00892, and hnRNP K could bind to lincRNA00892 or CD40L directly. Conclusion: Our results showed that the lncRNA expression profile was altered in CD4+ T cells of SLE. LincRNA00892 possibly contributed to the pathogenesis of SLE by targeting hnRNP K and subsequently upregulating CD40L expression to activate CD4+ T and B cells. These provided us a potential target for further mechanistic studies of SLE pathogenesis.
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Affiliation(s)
- Xiao Liu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinran Lin
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Hao Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yilun Wang
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Lin Xie
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinfeng Wu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Haihong Qin
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jinhua Xu
- Department of Dermatology, Huashan Hospital, Fudan University, Shanghai, China
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8
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Gong FX, Zhan G, Han R, Yang Z, Fu X, Xiao R. De-dimerization of PTB is catalyzed by PDI and is involved in the regulation of p53 translation. Nucleic Acids Res 2021; 49:9342-9352. [PMID: 34403458 PMCID: PMC8450096 DOI: 10.1093/nar/gkab708] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 12/03/2022] Open
Abstract
Polypyrimidine tract-binding protein (PTB) is an RNA binding protein existing both as dimer and monomer and shuttling between nucleus and cytoplasm. However, the regulation of PTB dimerization and the relationship between their functions and subcellular localization are unknown. Here we find that PTB presents as dimer and monomer in nucleus and cytoplasm respectively, and a disulfide bond involving Cysteine 23 is critical for the dimerization of PTB. Additionally, protein disulfide isomerase (PDI) is identified to be the enzyme that catalyzes the de-dimerization of PTB, which is dependent on the CGHC active site of the a’ domain of PDI. Furthermore, upon DNA damage induced by topoisomerase inhibitors, PTB is demonstrated to be de-dimerized with cytoplasmic accumulation. Finally, cytoplasmic PTB is found to associate with the ribosome and enhances the translation of p53. Collectively, these findings uncover a previously unrecognized mechanism of PTB dimerization, and shed light on the de-dimerization of PTB functionally linking to cytoplasmic localization and translational regulation.
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Affiliation(s)
- Fu-Xing Gong
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Guoqin Zhan
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Rong Han
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Zhigang Yang
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Xin Fu
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
| | - Ran Xiao
- Research Center of Plastic Surgery Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, 33 Ba-Da-Chu Road, Beijing 100144, PR China
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9
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Narayanan B, Prado de Maio D, La Porta J, Voskoboynik Y, Ganapathi U, Xie P, Covey LR. A Posttranscriptional Pathway of CD40 Ligand mRNA Stability Is Required for the Development of an Optimal Humoral Immune Response. THE JOURNAL OF IMMUNOLOGY 2021; 206:2552-2565. [PMID: 34031147 DOI: 10.4049/jimmunol.2001074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 03/30/2021] [Indexed: 11/19/2022]
Abstract
CD40 ligand (CD40L) mRNA stability is dependent on an activation-induced pathway that is mediated by the binding complexes containing the multifunctional RNA-binding protein, polypyrimidine tract-binding protein 1 (PTBP1) to a 3' untranslated region of the transcript. To understand the relationship between regulated CD40L and the requirement for variegated expression during a T-dependent response, we engineered a mouse lacking the CD40L stability element (CD40LΔ5) and asked how this mutation altered multiple aspects of the humoral immunity. We found that CD40LΔ5 mice expressed CD40L at 60% wildtype levels, and lowered expression corresponded to significantly decreased levels of T-dependent Abs, loss of germinal center (GC) B cells and a disorganized GC structure. Gene expression analysis of B cells from CD40LΔ5 mice revealed that genes associated with cell cycle and DNA replication were significantly downregulated and genes linked to apoptosis upregulated. Importantly, somatic hypermutation was relatively unaffected although the number of cells expressing high-affinity Abs was greatly reduced. Additionally, a significant loss of plasmablasts and early memory B cell precursors as a percentage of total GL7+ B cells was observed, indicating that differentiation cues leading to the development of post-GC subsets was highly dependent on a threshold level of CD40L. Thus, regulated mRNA stability plays an integral role in the optimization of humoral immunity by allowing for a dynamic level of CD40L expression on CD4 T cells that results in the proliferation and differentiation of pre-GC and GC B cells into functional subsets.
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Affiliation(s)
- Bitha Narayanan
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, NJ; and
| | - Diego Prado de Maio
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, NJ; and
| | - James La Porta
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, NJ; and
| | | | - Usha Ganapathi
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, NJ; and
| | - Ping Xie
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, NJ; and.,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
| | - Lori R Covey
- Department of Cell Biology and Neuroscience, Rutgers University, New Brunswick, NJ; and .,Rutgers Cancer Institute of New Jersey, New Brunswick, NJ
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10
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Geng G, Xu C, Peng N, Li Y, Liu J, Wu J, Liang J, Zhu Y, Shi L. PTBP1 is necessary for dendritic cells to regulate T-cell homeostasis and antitumour immunity. Immunology 2021; 163:74-85. [PMID: 33421118 PMCID: PMC8044338 DOI: 10.1111/imm.13304] [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: 08/13/2020] [Revised: 12/18/2020] [Accepted: 12/19/2020] [Indexed: 01/25/2023] Open
Abstract
Dendritic cells (DCs) play an important role in linking innate and adaptive immunity. DCs can sense endogenous and exogenous antigens and present those antigens to T cells to induce an immune response or immune tolerance. During activation, alternative splicing (AS) in DCs is dramatically changed to induce cytokine secretion and upregulation of surface marker expression. PTBP1, an RNA-binding protein, is essential in alternative splicing, but the function of PTBP1 in DCs is unknown. Here, we found that a specific deficiency of Ptbp1 in DCs could increase MHC II expression and perturb T-cell homeostasis without affecting DC development. Functionally, Ptbp1 deletion in DCs could enhance antitumour immunity and asthma exacerbation. Mechanistically, we found that Pkm alternative splicing and a subset of Ifn response genes could be regulated by PTBP1. These findings revealed the function of PTBP1 in DCs and indicated that PTBP1 might be a novel therapeutic target for antitumour treatment.
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Affiliation(s)
- Guangfeng Geng
- State Key Laboratory of Experimental HematologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Changlu Xu
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Nan Peng
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Yue Li
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jinhua Liu
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jing Wu
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Jing Liang
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
| | - Yushan Zhu
- State Key Laboratory of Experimental HematologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjinChina
| | - Lihong Shi
- State Key Laboratory of Experimental HematologyState Key Laboratory of Medicinal Chemical BiologyCollege of Life SciencesNankai UniversityTianjinChina
- State Key Laboratory of Experimental HematologyNational Clinical Research Center for Blood DiseasesInstitute of Hematology & Blood Diseases HospitalChinese Academy of Medical Sciences & Peking Union Medical CollegeTianjinChina
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11
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Su Z, Huang D. Alternative Splicing of Pre-mRNA in the Control of Immune Activity. Genes (Basel) 2021; 12:genes12040574. [PMID: 33921058 PMCID: PMC8071365 DOI: 10.3390/genes12040574] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 02/07/2023] Open
Abstract
The human immune response is a complex process that responds to numerous exogenous antigens in preventing infection by microorganisms, as well as to endogenous components in the surveillance of tumors and autoimmune diseases, and a great number of molecules are necessary to carry the functional complexity of immune activity. Alternative splicing of pre-mRNA plays an important role in immune cell development and regulation of immune activity through yielding diverse transcriptional isoforms to supplement the function of limited genes associated with the immune reaction. In addition, multiple factors have been identified as being involved in the control of alternative splicing at the cis, trans, or co-transcriptional level, and the aberrant splicing of RNA leads to the abnormal modulation of immune activity in infections, immune diseases, and tumors. In this review, we summarize the recent discoveries on the generation of immune-associated alternative splice variants, clinical disorders, and possible regulatory mechanisms. We also discuss the immune responses to the neoantigens produced by alternative splicing, and finally, we issue some alternative splicing and immunity correlated questions based on our knowledge.
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Affiliation(s)
- Zhongjing Su
- Department of Histology and Embryology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China
- Correspondence: (Z.S.); (D.H.)
| | - Dongyang Huang
- Department of Cell Biology, Shantou University Medical College, No. 22, Xinling Road, Shantou 515041, China
- Correspondence: (Z.S.); (D.H.)
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12
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A Single Nucleotide ADA Genetic Variant Is Associated to Central Inflammation and Clinical Presentation in MS: Implications for Cladribine Treatment. Genes (Basel) 2020; 11:genes11101152. [PMID: 33007809 PMCID: PMC7601054 DOI: 10.3390/genes11101152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 09/22/2020] [Accepted: 09/23/2020] [Indexed: 12/22/2022] Open
Abstract
In multiple sclerosis (MS), activated T and B lymphocytes and microglial cells release various proinflammatory cytokines, promoting neuroinflammation and negatively affecting the course of the disease. The immune response homeostasis is crucially regulated by the activity of the enzyme adenosine deaminase (ADA), as evidenced in patients with genetic ADA deficiency and in those treated with cladribine tablets. We investigated in a group of patients with MS the associations of a single nucleotide polymorphism (SNP) of ADA gene with disease characteristics and cerebrospinal fluid (CSF) inflammation. The SNP rs244072 of the ADA gene was determined in 561 patients with MS. Disease characteristics were assessed at the time of diagnosis; furthermore, in 258 patients, proinflammatory and anti-inflammatory molecules were measured in the CSF. We found a significant association between rs244072 and both clinical characteristics and central inflammation. In C-carriers, significantly enhanced disability and increased CSF levels of TNF, IL-5 and RANTES was observed. In addition, lower CSF levels of the anti-inflammatory cytokine IL-10 were found. Finally, the presence of the C allele was associated with a tendency of increased lymphocyte count. In MS patients, ADA SNP rs244072 is associated with CSF inflammation and disability. The selective targeting of the ADA pathway through cladribine tablet therapy could be effective in MS by acting on a pathogenically relevant biological mechanism.
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13
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Monzón-Casanova E, Matheson LS, Tabbada K, Zarnack K, Smith CWJ, Turner M. Polypyrimidine tract-binding proteins are essential for B cell development. eLife 2020; 9:e53557. [PMID: 32081131 PMCID: PMC7058386 DOI: 10.7554/elife.53557] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 02/20/2020] [Indexed: 12/17/2022] Open
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) is a RNA-binding protein (RBP) expressed throughout B cell development. Deletion of Ptbp1 in mouse pro-B cells results in upregulation of PTBP2 and normal B cell development. We show that PTBP2 compensates for PTBP1 in B cell ontogeny as deletion of both Ptbp1 and Ptbp2 results in a complete block at the pro-B cell stage and a lack of mature B cells. In pro-B cells PTBP1 ensures precise synchronisation of the activity of cyclin dependent kinases at distinct stages of the cell cycle, suppresses S-phase entry and promotes progression into mitosis. PTBP1 controls mRNA abundance and alternative splicing of important cell cycle regulators including CYCLIN-D2, c-MYC, p107 and CDC25B. Our results reveal a previously unrecognised mechanism mediated by a RBP that is essential for B cell ontogeny and integrates transcriptional and post-translational determinants of progression through the cell cycle.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
- Department of Biochemistry, University of CambridgeCambridgeUnited Kingdom
| | - Louise S Matheson
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
| | - Kristina Tabbada
- Next Generation Sequencing Facility, The Babraham InstituteCambridgeUnited Kingdom
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences, Goethe University FrankfurtFrankfurt am MainGermany
| | | | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham InstituteCambridgeUnited Kingdom
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14
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Zhu W, Zhou BL, Rong LJ, Ye L, Xu HJ, Zhou Y, Yan XJ, Liu WD, Zhu B, Wang L, Jiang XJ, Ren CP. Roles of PTBP1 in alternative splicing, glycolysis, and oncogensis. J Zhejiang Univ Sci B 2020; 21:122-136. [PMID: 32115910 DOI: 10.1631/jzus.b1900422] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Polypyrimidine tract-binding protein 1 (PTBP1) plays an essential role in splicing and is expressed in almost all cell types in humans, unlike the other proteins of the PTBP family. PTBP1 mediates several cellular processes in certain types of cells, including the growth and differentiation of neuronal cells and activation of immune cells. Its function is regulated by various molecules, including microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and RNA-binding proteins. PTBP1 plays roles in various diseases, particularly in some cancers, including colorectal cancer, renal cell cancer, breast cancer, and glioma. In cancers, it acts mainly as a regulator of glycolysis, apoptosis, proliferation, tumorigenesis, invasion, and migration. The role of PTBP1 in cancer has become a popular research topic in recent years, and this research has contributed greatly to the formulation of a useful therapeutic strategy for cancer. In this review, we summarize recent findings related to PTBP1 and discuss how it regulates the development of cancer cells.
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Affiliation(s)
- Wei Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bo-Lun Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li-Juan Rong
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Li Ye
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hong-Juan Xu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yao Zhou
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xue-Jun Yan
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei-Dong Liu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Bin Zhu
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Lei Wang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Xing-Jun Jiang
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Cai-Ping Ren
- NHC Key Laboratory of Carcinogenesis (Central South University) and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute, Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
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15
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Sasanuma H, Ozawa M, Yoshida N. RNA-binding protein Ptbp1 is essential for BCR-mediated antibody production. Int Immunol 2020; 31:157-166. [PMID: 30476084 PMCID: PMC6400050 DOI: 10.1093/intimm/dxy077] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/21/2018] [Indexed: 11/22/2022] Open
Abstract
The RNA-binding protein polypyrimidine tract-binding protein-1 (Ptbp1) binds to the pyrimidine-rich sequence of target RNA and controls gene expression via post-transcriptional regulation such as alternative splicing. Although Ptbp1 is highly expressed in B lymphocytes, its role to date is largely unknown. To clarify the role of Ptbp1 in B-cell development and function, we generated B-cell-specific Ptbp1-deficient (P1BKO) mice. B-cell development in the bone marrow, spleen and peritoneal cavity of the P1BKO mice was nearly normal. However, the P1BKO mice had significantly lower levels of natural antibodies in serum compared with those of the control mice. To investigate the effect of Ptbp1 deficiency on the immune response in vivo, we immunized the P1BKO mice with T-cell-independent type-2 (TI-2) antigen NP-Ficoll and T-cell-dependent (TD) antigen NP-CGG. We found that B-cell-specific Ptbp1 deficiency causes an immunodeficiency phenotype due to defective production of antibody against both TI-2 and TD antigen. This immunodeficiency was accompanied by impaired B-cell receptor (BCR)-mediated B-cell activation and plasmablast generation. These findings demonstrate that Ptbp1 is essential for the humoral immune response.
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Affiliation(s)
- Hiroki Sasanuma
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
| | - Manabu Ozawa
- Laboratory of Reproductive Systems Biology, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
| | - Nobuaki Yoshida
- Laboratory of Developmental Genetics, Center for Experimental Medicine and Systems Biology, The Institute of Medical Science, The University of Tokyo, Shirokanedai, Minato-ku, Tokyo, Japan
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16
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Díaz-Muñoz MD, Turner M. Uncovering the Role of RNA-Binding Proteins in Gene Expression in the Immune System. Front Immunol 2018; 9:1094. [PMID: 29875770 PMCID: PMC5974052 DOI: 10.3389/fimmu.2018.01094] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 05/02/2018] [Indexed: 12/29/2022] Open
Abstract
Fighting external pathogens requires an ever-changing immune system that relies on tight regulation of gene expression. Transcriptional control is the first step to build efficient responses while preventing immunodeficiencies and autoimmunity. Post-transcriptional regulation of RNA editing, location, stability, and translation are the other key steps for final gene expression, and they are all controlled by RNA-binding proteins (RBPs). Nowadays we have a deep understanding of how transcription factors control the immune system but recent evidences suggest that post-transcriptional regulation by RBPs is equally important for both development and activation of immune responses. Here, we review current knowledge about how post-transcriptional control by RBPs shapes our immune system and discuss the perspective of RBPs being the key players of a hidden immune cell epitranscriptome.
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Affiliation(s)
- Manuel D Díaz-Muñoz
- Centre de Physiopathologie Toulouse-Purpan, INSERM UMR1043/CNRS U5282, Toulouse, France
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, United Kingdom
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17
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RNA-binding proteins control gene expression and cell fate in the immune system. Nat Immunol 2018; 19:120-129. [PMID: 29348497 DOI: 10.1038/s41590-017-0028-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 11/29/2017] [Indexed: 12/19/2022]
Abstract
RNA-binding proteins (RBPs) are essential for the development and function of the immune system. They interact dynamically with RNA to control its biogenesis and turnover by transcription-dependent and transcription-independent mechanisms. In this Review, we discuss the molecular mechanisms by which RBPs allow gene expression changes to occur at different speeds and to varying degrees, and which RBPs regulate the diversity of the transcriptome and proteome. These proteins are nodes for integration of transcriptional and signaling networks and are intimately linked to intermediary metabolism. They are essential components of regulatory feedback mechanisms that maintain immune tolerance and limit inflammation. The role of RBPs in malignancy and autoimmunity has led to their emergence as targets for the development of new therapeutic modalities.
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18
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Monzón-Casanova E, Screen M, Díaz-Muñoz MD, Coulson RMR, Bell SE, Lamers G, Solimena M, Smith CWJ, Turner M. The RNA-binding protein PTBP1 is necessary for B cell selection in germinal centers. Nat Immunol 2018; 19:267-278. [PMID: 29358707 PMCID: PMC5842895 DOI: 10.1038/s41590-017-0035-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 12/12/2017] [Indexed: 12/17/2022]
Abstract
Antibody affinity maturation occurs in germinal centres (GC) where B
cells cycle between the light zone (LZ) and the dark zone. In the LZ GC B cells
bearing immunoglobulins with the highest affinity for antigen receive positive
selection signals from T helper cells that promotes their rapid proliferation.
Here we show that the RNA binding protein PTBP1 is necessary for the progression
of GC B cells through late S-phase of the cell cycle and for affinity
maturation. PTBP1 is required for the proper expression of the c-MYC-dependent
gene program induced in GC B cells receiving T cell help and directly regulates
the alternative splicing and abundance of transcripts increased during positive
selection to promote proliferation.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK.,Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Michael Screen
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Manuel D Díaz-Muñoz
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Richard M R Coulson
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Sarah E Bell
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Greta Lamers
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK
| | - Michele Solimena
- Molecular Diabetology, University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,Paul Langerhans Institute Dresden of the Helmholtz Center Munich at University Hospital and Faculty of Medicine, Technische Universität Dresden, Dresden, Germany.,Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany.,German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | | | - Martin Turner
- Laboratory of Lymphocyte Signaling and Development, The Babraham Institute, Cambridge, UK.
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19
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Jiang J, Chen X, Liu H, Shao J, Xie R, Gu P, Duan C. Polypyrimidine Tract-Binding Protein 1 promotes proliferation, migration and invasion in clear-cell renal cell carcinoma by regulating alternative splicing of PKM. Am J Cancer Res 2017; 7:245-259. [PMID: 28337374 PMCID: PMC5336499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 01/16/2017] [Indexed: 06/06/2023] Open
Abstract
Polypyrimidine Tract-Binding Protein 1 (PTBP1) is an essential RNA-binding protein that regulates diverse biological events through regulating alternative splice of mRNA. PTBP1 induces cancer-promoting splice variants and is related to tumorigenesis in several cancers. However, both the expression patterns and biological mechanisms of PTBP1 in clear-cell renal cell carcinoma (ccRCC) are unclear. We investigated PTBP1 expression in 533 ccRCC patients from TCGA and 30 ccRCC patients by immunohistochemistry, and found that PTBP1 expression levels were significantly increased in ccRCC tissues and that high PTBP1 expression was closely correlated with advanced tumor stage, AJCC stage and poor prognosis. Cell biological assays with siRNA-mediated knockdown and lentivirus vector-mediated over-expression demonstrated that PTBP1 promoted proliferation, migration and invasion in ccRCC cells in vitro. Furthermore, PTBP1 increased the transformation from pyruvate kinase muscle 1 (PKM1) to PKM2. Knockdown of PKM2 mainly abolished PTBP1-induced proliferation, migration and invasion in ccRCC cells in vitro. In conclusion, our study indicates that PTBP1 plays a tumorigenic role in ccRCC by mediating PKM2 alternative splicing and it may be a potential prognostic marker and a promising target for treatment of ccRCC.
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Affiliation(s)
- Junyi Jiang
- Department of Laboratory Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Xu Chen
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Hao Liu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Jing Shao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Ruihui Xie
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Peng Gu
- Department of Urology, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
| | - Chaohui Duan
- Department of Laboratory Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen UniversityGuangzhou, China
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