1
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Peng P, Chavel C, Liu W, Carlson LM, Cao S, Utley A, Olejniczak SH, Lee KP. Pro-survival signaling regulates lipophagy essential for multiple myeloma resistance to stress-induced death. Cell Rep 2024; 43:114445. [PMID: 38968073 DOI: 10.1016/j.celrep.2024.114445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 05/27/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
Pro-survival metabolic adaptations to stress in tumorigenesis remain less well defined. We find that multiple myeloma (MM) is unexpectedly dependent on beta-oxidation of long-chain fatty acids (FAs) for survival under both basal and stress conditions. However, under stress conditions, a second pro-survival signal is required to sustain FA oxidation (FAO). We previously found that CD28 is expressed on MM cells and transduces a significant pro-survival/chemotherapy resistance signal. We now find that CD28 signaling regulates autophagy/lipophagy that involves activation of the Ca2+→AMPK→ULK1 axis and regulates the translation of ATG5 through HuR, resulting in sustained lipophagy, increased FAO, and enhanced MM survival. Conversely, blocking autophagy/lipophagy sensitizes MM to chemotherapy in vivo. Our findings link a pro-survival signal to FA availability needed to sustain the FAO required for cancer cell survival under stress conditions and identify lipophagy as a therapeutic target to overcome treatment resistance in MM.
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Affiliation(s)
- Peng Peng
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Colin Chavel
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Wensheng Liu
- Department of Pediatrics, State University of New York at Buffalo, Buffalo, NY, USA
| | - Louise M Carlson
- Indiana University Simon Comprehensive Cancer Center, and the Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Sha Cao
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Adam Utley
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Scott H Olejniczak
- Department of Immunology, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Kelvin P Lee
- Indiana University Simon Comprehensive Cancer Center, and the Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA.
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2
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Duan KL, Wang TX, You JW, Wang HN, Wang ZQ, Huang ZX, Zhang JY, Sun YP, Xiong Y, Guan KL, Ye D, Chen L, Liu R, Yuan HX. PCK2 maintains intestinal homeostasis and prevents colitis by protecting antibody-secreting cells from oxidative stress. Immunology 2024. [PMID: 38934051 DOI: 10.1111/imm.13827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Accepted: 06/03/2024] [Indexed: 06/28/2024] Open
Abstract
Maintaining intracellular redox balance is essential for the survival, antibody secretion, and mucosal immune homeostasis of immunoglobulin A (IgA) antibody-secreting cells (ASCs). However, the relationship between mitochondrial metabolic enzymes and the redox balance in ASCs has yet to be comprehensively studied. Our study unveils the pivotal role of mitochondrial enzyme PCK2 in regulating ASCs' redox balance and intestinal homeostasis. We discover that PCK2 loss, whether globally or in B cells, exacerbates dextran sodium sulphate (DSS)-induced colitis due to increased IgA ASC cell death and diminished antibody production. Mechanistically, the absence of PCK2 diverts glutamine into the TCA cycle, leading to heightened TCA flux and excessive mitochondrial reactive oxygen species (mtROS) production. In addition, PCK2 loss reduces glutamine availability for glutathione (GSH) synthesis, resulting in a decrease of total glutathione level. The elevated mtROS and reduced GSH expose ASCs to overwhelming oxidative stress, culminating in cell apoptosis. Crucially, we found that the mitochondria-targeted antioxidant Mitoquinone (Mito-Q) can mitigate the detrimental effects of PCK2 deficiency in IgA ASCs, thereby alleviating colitis in mice. Our findings highlight PCK2 as a key player in IgA ASC survival and provide a potential new target for colitis treatment.
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Affiliation(s)
- Kun-Long Duan
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Tian-Xiang Wang
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jian-Wei You
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Hai-Ning Wang
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhi-Qiang Wang
- Department of Immunology, School of Basic Medical Sciences, Shanghai Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zi-Xuan Huang
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jin-Ye Zhang
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yi-Ping Sun
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yue Xiong
- Cullgen Inc., San Diego, California, USA
| | - Kun-Liang Guan
- Department of Pharmacology and Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Dan Ye
- Shanghai Key Laboratory of Clinical Geriatric Medicine, Huadong Hospital of Fudan University, Key Laboratory of Metabolism and Molecular Medicine (Ministry of Education), Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Li Chen
- Shanghai Key Laboratory of Metabolic Remodeling and Health, Institute of Metabolism and Integrative Biology, Fudan University, Shanghai, China
| | - Ronghua Liu
- Shanghai Fifth People's Hospital, Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Hai-Xin Yuan
- Shanghai Fifth People's Hospital, Molecular and Cell Biology Research Lab of Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- Basic Medicine Research and Innovation Center for Novel Target and Therapeutic Intervention, Ministry of Education, Chongqing Medical University, Chongqing, China
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3
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Zhao J, Jin D, Huang M, Ji J, Xu X, Wang F, Zhou L, Bao B, Jiang F, Xu W, Lu X, Xiao M. Glycolysis in the tumor microenvironment: a driver of cancer progression and a promising therapeutic target. Front Cell Dev Biol 2024; 12:1416472. [PMID: 38933335 PMCID: PMC11199735 DOI: 10.3389/fcell.2024.1416472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Even with sufficient oxygen, tumor cells use glycolysis to obtain the energy and macromolecules they require to multiply, once thought to be a characteristic of tumor cells known as the "Warburg effect". In fact, throughout the process of carcinogenesis, immune cells and stromal cells, two major cellular constituents of the tumor microenvironment (TME), also undergo thorough metabolic reprogramming, which is typified by increased glycolysis. In this review, we provide a full-scale review of the glycolytic remodeling of several types of TME cells and show how these TME cells behave in the acidic milieu created by glucose shortage and lactate accumulation as a result of increased tumor glycolysis. Notably, we provide an overview of putative targets and inhibitors of glycolysis along with the viability of using glycolysis inhibitors in combination with immunotherapy and chemotherapy. Understanding the glycolytic situations in diverse cells within the tumor immunological milieu will aid in the creation of subsequent treatment plans.
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Affiliation(s)
- Junpeng Zhao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Dandan Jin
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Mengxiang Huang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Jie Ji
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Xuebing Xu
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Fei Wang
- Department of Laboratory Medicine, Affiliated Hospital and Medical School of Nantong University, Nantong, Jiangsu, China
| | - Lirong Zhou
- Department of Clinical Medicine, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Baijun Bao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Feng Jiang
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
| | - Weisong Xu
- Department of Gastroenterology, Affiliated Nantong Rehabilitation Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xiaomin Lu
- Department of Oncology Affiliated Haian Hospital of Nantong University, Nantong, Jiangsu, China
| | - Mingbing Xiao
- Department of Gastroenterology, Affiliated Hospital of Nantong University, Medical School of Nantong University, Nantong, Jiangsu, China
- Department of Laboratory Medicine, Affiliated Hospital and Medical School of Nantong University, Nantong, Jiangsu, China
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4
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Wang Y, Xu X, Zhang A, Yang S, Li H. Role of alternative splicing in fish immunity. FISH & SHELLFISH IMMUNOLOGY 2024; 149:109601. [PMID: 38701992 DOI: 10.1016/j.fsi.2024.109601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
Alternative splicing serves as a pivotal source of complexity in the transcriptome and proteome, selectively connecting various coding elements to generate a diverse array of mRNAs. This process encodes multiple proteins with either similar or distinct functions, contributing significantly to the intricacies of cellular processes. The role of alternative splicing in mammalian immunity has been well studied. Remarkably, the immune system of fish shares substantial similarities with that of humans, and alternative splicing also emerges as a key player in the immune processes of fish. In this review, we offer an overview of alternative splicing and its associated functions in the immune processes of fish, and summarize the research progress on alternative splicing in the fish immunity. Furthermore, we review the impact of alternative splicing on the fish immune system's response to external stimuli. Finally, we present our perspectives on future directions in this field. Our aim is to provide valuable insights for the future investigations into the role of alternative splicing in immunity.
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Affiliation(s)
- Yunchao Wang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Xinyi Xu
- Hunan Fisheries Science Institute, Changsha, 410153, China
| | - Ailong Zhang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China
| | - Shuaiqi Yang
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China.
| | - Hongyan Li
- College of Marine Life Sciences, and Institute of Evolution & Marine Biodiversity, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, 266003, China.
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5
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Subramani PG, Fraszczak J, Helness A, Estall JL, Möröy T, Di Noia JM. Conserved role of hnRNPL in alternative splicing of epigenetic modifiers enables B cell activation. EMBO Rep 2024; 25:2662-2697. [PMID: 38744970 PMCID: PMC11169469 DOI: 10.1038/s44319-024-00152-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 04/15/2024] [Accepted: 04/24/2024] [Indexed: 05/16/2024] Open
Abstract
The multifunctional RNA-binding protein hnRNPL is implicated in antibody class switching but its broader function in B cells is unknown. Here, we show that hnRNPL is essential for B cell activation, germinal center formation, and antibody responses. Upon activation, hnRNPL-deficient B cells show proliferation defects and increased apoptosis. Comparative analysis of RNA-seq data from activated B cells and another eight hnRNPL-depleted cell types reveals common effects on MYC and E2F transcriptional programs required for proliferation. Notably, while individual gene expression changes are cell type specific, several alternative splicing events affecting histone modifiers like KDM6A and SIRT1, are conserved across cell types. Moreover, hnRNPL-deficient B cells show global changes in H3K27me3 and H3K9ac. Epigenetic dysregulation after hnRNPL loss could underlie differential gene expression and upregulation of lncRNAs, and explain common and cell type-specific phenotypes, such as dysfunctional mitochondria and ROS overproduction in mouse B cells. Thus, hnRNPL is essential for the resting-to-activated B cell transition by regulating transcriptional programs and metabolism, at least in part through the alternative splicing of several histone modifiers.
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Affiliation(s)
- Poorani Ganesh Subramani
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
| | - Jennifer Fraszczak
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Anne Helness
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Jennifer L Estall
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
| | - Tarik Möröy
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Department of Medicine, Division of Experimental Medicine, McGill University, 1001 Boulevard Decarie, Montreal, QC, H4A 3J1, Canada.
- Molecular Biology Programs, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Department of Medicine, Université de Montréal, C.P. 6128, succ. Centre-ville, Montréal, QC, H3C 3J7, Canada.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, 2900 Boul Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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6
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Abdelsam SS, Ghanem SK, Zahid MA, Abunada HH, Bader L, Raïq H, Khan A, Parray A, Djouhri L, Agouni A. Human antigen R: Exploring its inflammatory response impact and significance in cardiometabolic disorders. J Cell Physiol 2024; 239:e31229. [PMID: 38426269 DOI: 10.1002/jcp.31229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/30/2024] [Accepted: 02/14/2024] [Indexed: 03/02/2024]
Abstract
RNA-binding proteins (RBPs) play a crucial role in the regulation of posttranscriptional RNA networks, which can undergo dysregulation in many pathological conditions. Human antigen R (HuR) is a highly researched RBP that plays a crucial role as a posttranscriptional regulator. HuR plays a crucial role in the amplification of inflammatory signals by stabilizing the messenger RNA of diverse inflammatory mediators and key molecular players. The noteworthy correlations between HuR and its target molecules, coupled with the remarkable impacts reported on the pathogenesis and advancement of multiple diseases, position HuR as a promising candidate for therapeutic intervention in diverse inflammatory conditions. This review article examines the significance of HuR as a member of the RBP family, its regulatory mechanisms, and its implications in the pathophysiology of inflammation and cardiometabolic illnesses. Our objective is to illuminate potential directions for future research and drug development by conducting a comprehensive analysis of the existing body of research on HuR.
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Affiliation(s)
- Shahenda Salah Abdelsam
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Sarah Khalaf Ghanem
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Muhammad Ammar Zahid
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Hanan H Abunada
- Office of Vice President for Research and Graduate Studies, Qatar University, Doha, Qatar
| | - Loulia Bader
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Hicham Raïq
- Department of Social Sciences, College of Arts and Sciences, Qatar University, Doha, Qatar
| | - Abbas Khan
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
| | - Aijaz Parray
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Laiche Djouhri
- Department of Basic Medical Science, College of Medicine, QU health, Qatar University, Doha, Qatar
| | - Abdelali Agouni
- Department of Pharmaceutical Sciences, College of Pharmacy, QU Health, Qatar University, Doha, Qatar
- Office of Vice President for Medical & Health Sciences, QU Health, Qatar University, Doha, Qatar
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7
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Bhat AA, Kukreti N, Afzal M, Goyal A, Thapa R, Ali H, Shahwan M, Almalki WH, Kazmi I, Alzarea SI, Singh SK, Dua K, Gupta G. Ferroptosis and circular RNAs: new horizons in cancer therapy. EXCLI JOURNAL 2024; 23:570-599. [PMID: 38887390 PMCID: PMC11180955 DOI: 10.17179/excli2024-7005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Accepted: 04/09/2024] [Indexed: 06/20/2024]
Abstract
Cancer poses intricate challenges to treatment due to its complexity and diversity. Ferroptosis and circular RNAs (circRNAs) are emerging as innovative therapeutic avenues amid the evolving landscape of cancer therapy. Extensive investigations into circRNAs reveal their diverse roles, ranging from molecular regulators to pivotal influencers of ferroptosis in cancer cell lines. The results underscore the significance of circRNAs in modulating molecular pathways that impact crucial aspects of cancer development, including cell survival, proliferation, and metastasis. A detailed analysis delineates these pathways, shedding light on the molecular mechanisms through which circRNAs influence ferroptosis. Building upon recent experimental findings, the study evaluates the therapeutic potential of targeting circRNAs to induce ferroptosis. By identifying specific circRNAs associated with the etiology of cancer, this analysis paves the way for the development of targeted therapeutics that exploit vulnerabilities in cancer cells. This review consolidates the existing understanding of ferroptosis and circRNAs, emphasizing their role in cancer therapy and providing impetus for ongoing research in this dynamic field. See also the graphical abstract(Fig. 1).
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Affiliation(s)
- Asif Ahmad Bhat
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | - Muhammad Afzal
- Department of Pharmaceutical Sciences, Pharmacy Program, Batterjee Medical College, P.O. Box 6231, Jeddah 21442, Saudi Arabia
| | - Ahsas Goyal
- Institute of Pharmaceutical Research, GLA University, Mathura, U. P., India
| | - Riya Thapa
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
| | - Haider Ali
- Center for Global Health Research, Saveetha Medical College, Saveetha Institute of Medical and Technical Sciences, Saveetha University, India
- Department of Pharmacology, Kyrgyz State Medical College, Bishkek, Kyrgyzstan
| | - Moyad Shahwan
- Department of Clinical Sciences, College of Pharmacy and Health Sciences, Ajman University, Ajman, 346, United Arab Emirates
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, Ajman, 346, United Arab Emirates
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Al-Jouf, Saudi Arabia
| | - Sachin Kumar Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara 144411, India
- Faculty of Health, Australian Research Center in Complementary and Integrative Medicine, University of Technology, Sydney, Ultimo-NSW 2007, Australia
- School of Medical and Life Sciences, Sunway University, Sunway, Malaysia
| | - Kamal Dua
- Faculty of Health, Australian Research Center in Complementary and Integrative Medicine, University of Technology, Sydney, Ultimo-NSW 2007, Australia
- Discipline of Pharmacy, Graduate School of Health, University of Technology, Sydney, Ultimo-NSW 2007, Australia
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur, India
- Centre of Medical and Bio-allied Health Sciences Research, Ajman University, Ajman, Ajman, 346, United Arab Emirates
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8
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Zhang Y, Zhang Y, Song J, Cheng X, Zhou C, Huang S, Zhao W, Zong Z, Yang L. Targeting the "tumor microenvironment": RNA-binding proteins in the spotlight in colorectal cancer therapy. Int Immunopharmacol 2024; 131:111876. [PMID: 38493688 DOI: 10.1016/j.intimp.2024.111876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/04/2024] [Accepted: 03/13/2024] [Indexed: 03/19/2024]
Abstract
Colorectal cancer (CRC) is the third most common cancer and has the second highest mortality rate among cancers. The development of CRC involves both genetic and epigenetic abnormalities, and recent research has focused on exploring the ex-transcriptome, particularly post-transcriptional modifications. RNA-binding proteins (RBPs) are emerging epigenetic regulators that play crucial roles in post-transcriptional events. Dysregulation of RBPs can result in aberrant expression of downstream target genes, thereby affecting the progression of colorectal tumors and the prognosis of patients. Recent studies have shown that RBPs can influence CRC pathogenesis and progression by regulating various components of the tumor microenvironment (TME). Although previous research on RBPs has primarily focused on their direct regulation of colorectal tumor development, their involvement in the remodeling of the TME has not been systematically reported. This review aims to highlight the significant role of RBPs in the intricate interactions within the CRC tumor microenvironment, including tumor immune microenvironment, inflammatory microenvironment, extracellular matrix, tumor vasculature, and CRC cancer stem cells. We also highlight several compounds under investigation for RBP-TME-based treatment of CRC, including small molecule inhibitors such as antisense oligonucleotides (ASOs), siRNAs, agonists, gene manipulation, and tumor vaccines. The insights gained from this review may lead to the development of RBP-based targeted novel therapeutic strategies aimed at modulating the TME, potentially inhibiting the progression and metastasis of CRC.
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Affiliation(s)
- Yiwei Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China; Queen Mary School, Nanchang University, 330006 Nanchang, China
| | - Yujun Zhang
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China
| | - Jingjing Song
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China; Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China; School of Ophthalmology and Optometry of Nanchang University, China
| | - Xifu Cheng
- School of Ophthalmology and Optometry of Nanchang University, China
| | - Chulin Zhou
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Shuo Huang
- The Second Clinical Medical College, Nanchang University, Nanchang 330006, China
| | - Wentao Zhao
- The 3rd Clinical Department of China Medical University, 10159 Shenyang, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, the Second Affiliated Hospital of Nanchang University, No. 1 MinDe Road, 330006 Nanchang, China.
| | - Lingling Yang
- Department of Gastroenterology, The Second Affiliated Hospital of Nanchang University, No. 1 Mingde Rd., Nanchang 330006, Jiangxi, China.
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9
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Saluja S, Bansal I, Bhardwaj R, Beg MS, Palanichamy JK. Inflammation as a driver of hematological malignancies. Front Oncol 2024; 14:1347402. [PMID: 38571491 PMCID: PMC10987768 DOI: 10.3389/fonc.2024.1347402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 03/05/2024] [Indexed: 04/05/2024] Open
Abstract
Hematopoiesis is a tightly regulated process that produces all adult blood cells and immune cells from multipotent hematopoietic stem cells (HSCs). HSCs usually remain quiescent, and in the presence of external stimuli like infection or inflammation, they undergo division and differentiation as a compensatory mechanism. Normal hematopoiesis is impacted by systemic inflammation, which causes HSCs to transition from quiescence to emergency myelopoiesis. At the molecular level, inflammatory cytokine signaling molecules such as tumor necrosis factor (TNF), interferons, interleukins, and toll-like receptors can all cause HSCs to multiply directly. These cytokines actively encourage HSC activation, proliferation, and differentiation during inflammation, which results in the generation and activation of immune cells required to combat acute injury. The bone marrow niche provides numerous soluble and stromal cell signals, which are essential for maintaining normal homeostasis and output of the bone marrow cells. Inflammatory signals also impact this bone marrow microenvironment called the HSC niche to regulate the inflammatory-induced hematopoiesis. Continuous pro-inflammatory cytokine and chemokine activation can have detrimental effects on the hematopoietic system, which can lead to cancer development, HSC depletion, and bone marrow failure. Reactive oxygen species (ROS), which damage DNA and ultimately lead to the transformation of HSCs into cancerous cells, are produced due to chronic inflammation. The biological elements of the HSC niche produce pro-inflammatory cytokines that cause clonal growth and the development of leukemic stem cells (LSCs) in hematological malignancies. The processes underlying how inflammation affects hematological malignancies are still not fully understood. In this review, we emphasize the effects of inflammation on normal hematopoiesis, the part it plays in the development and progression of hematological malignancies, and potential therapeutic applications for targeting these pathways for therapy in hematological malignancies.
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10
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Yoshinaga M, Takeuchi O. Regulation of inflammatory diseases via the control of mRNA decay. Inflamm Regen 2024; 44:14. [PMID: 38491500 PMCID: PMC10941436 DOI: 10.1186/s41232-024-00326-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/02/2024] [Indexed: 03/18/2024] Open
Abstract
Inflammation orchestrates a finely balanced process crucial for microorganism elimination and tissue injury protection. A multitude of immune and non-immune cells, alongside various proinflammatory cytokines and chemokines, collectively regulate this response. Central to this regulation is post-transcriptional control, governing gene expression at the mRNA level. RNA-binding proteins such as tristetraprolin, Roquin, and the Regnase family, along with RNA modifications, intricately dictate the mRNA decay of pivotal mediators and regulators in the inflammatory response. Dysregulated activity of these factors has been implicated in numerous human inflammatory diseases, underscoring the significance of post-transcriptional regulation. The increasing focus on targeting these mechanisms presents a promising therapeutic strategy for inflammatory and autoimmune diseases. This review offers an extensive overview of post-transcriptional regulation mechanisms during inflammatory responses, delving into recent advancements, their implications in human diseases, and the strides made in therapeutic exploitation.
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Affiliation(s)
- Masanori Yoshinaga
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
| | - Osamu Takeuchi
- Department of Medical Chemistry, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan.
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11
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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12
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Podszywalow-Bartnicka P, Neugebauer KM. Multiple roles for AU-rich RNA binding proteins in the development of haematologic malignancies and their resistance to chemotherapy. RNA Biol 2024; 21:1-17. [PMID: 38798162 PMCID: PMC11135835 DOI: 10.1080/15476286.2024.2346688] [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: 04/08/2024] [Indexed: 05/29/2024] Open
Abstract
Post-transcriptional regulation by RNA binding proteins can determine gene expression levels and drive changes in cancer cell proteomes. Identifying mechanisms of protein-RNA binding, including preferred sequence motifs bound in vivo, provides insights into protein-RNA networks and how they impact mRNA structure, function, and stability. In this review, we will focus on proteins that bind to AU-rich elements (AREs) in nascent or mature mRNA where they play roles in response to stresses encountered by cancer cells. ARE-binding proteins (ARE-BPs) specifically impact alternative splicing, stability, decay and translation, and formation of RNA-rich biomolecular condensates like cytoplasmic stress granules (SGs). For example, recent findings highlight the role of ARE-BPs - like TIAR and HUR - in chemotherapy resistance and in translational regulation of mRNAs encoding pro-inflammatory cytokines. We will discuss emerging evidence that different modes of ARE-BP activity impact leukaemia and lymphoma development, progression, adaptation to microenvironment and chemotherapy resistance.
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Affiliation(s)
- Paulina Podszywalow-Bartnicka
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
- Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Karla M. Neugebauer
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, CT, USA
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13
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Guo Y, Yan S, Zhang W. Translatomics to explore dynamic differences in immunocytes in the tumor microenvironment. MOLECULAR THERAPY. NUCLEIC ACIDS 2023; 34:102037. [PMID: 37808922 PMCID: PMC10551571 DOI: 10.1016/j.omtn.2023.102037] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Protein is an essential component of all living organisms and is primarily responsible for life activities; furthermore, its synthesis depends on a highly complex and accurate translation system. For proteins, the regulation at the translation level exceeds the sum of that during transcription, mRNA degradation, and protein degradation. Therefore, it is necessary to study regulation at the translation level. Imbalance in the translation process may change the cellular landscape, which not only leads to the occurrence, maintenance, progression, invasion, and metastasis of cancer but also affects the function of immune cells and changes the tumor microenvironment. Detailed analysis of transcriptional and protein atlases is needed to better understand how gene translation occurs. However, a more rigorous direct correlation between mRNA and protein levels is needed, which somewhat limits further studies. Translatomics is a technique for capturing and sequencing ribosome-related mRNAs that can effectively identify translation changes caused by ribosome stagnation and local translation abnormalities during cancer occurrence to further understand the changes in the translation landscape of cancer cells themselves and immune cells in the tumor microenvironment, which can provide new strategies and directions for tumor treatment.
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Affiliation(s)
- Yilin Guo
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
- Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Shiqi Yan
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
- Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
| | - Wenling Zhang
- Department of Laboratory Medicine, The Third Xiangya Hospital, Central South University, Changsha, Hunan 410013, P.R. China
- Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, Hunan 410013, P.R. China
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14
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Piersma SJ, Bangru S, Yoon J, Liu TW, Yang L, Hsieh CS, Plougastel-Douglas B, Kalsotra A, Yokoyama WM. NK cell expansion requires HuR and mediates control of solid tumors and long-term virus infection. J Exp Med 2023; 220:e20231154. [PMID: 37698554 PMCID: PMC10497399 DOI: 10.1084/jem.20231154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/04/2023] [Accepted: 08/08/2023] [Indexed: 09/13/2023] Open
Abstract
Natural killer (NK) cells are lymphocytes capable of controlling tumors and virus infections through direct lysis and cytokine production. While both T and NK cells expand and accumulate in affected tissues, the role of NK cell expansion in tumor and viral control is not well understood. Here, we show that posttranscriptional regulation by the RNA-binding protein HuR is essential for NK cell expansion without negatively affecting effector functions. HuR-deficient NK cells displayed defects in the metaphase of the cell cycle, including decreased expression and alternative splicing of Ska2, a component of the spindle and kinetochore complex. HuR-dependent NK cell expansion contributed to long-term cytomegalovirus control and facilitated control of subcutaneous tumors but not tumor metastases in two independent tumor models. These results show that posttranscriptional regulation by HuR specifically affects NK cell expansion, which is required for the control of long-term virus infection and solid tumors, but not acute infection or tumor metastases, highlighting fundamental differences with antigen-specific T cell control.
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Affiliation(s)
- Sytse J. Piersma
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Sushant Bangru
- Department of Biochemistry, University of Illinois Urbana-Champaign, Champaign, IL, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Jeesang Yoon
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Tom W. Liu
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Liping Yang
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Chyi-Song Hsieh
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Beatrice Plougastel-Douglas
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Auinash Kalsotra
- Department of Biochemistry, University of Illinois Urbana-Champaign, Champaign, IL, USA
- Cancer Center at Illinois, University of Illinois Urbana-Champaign, Champaign, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Champaign, IL, USA
| | - Wayne M. Yokoyama
- Division of Rheumatology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, MO, USA
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15
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Finan JM, Sutton TL, Dixon DA, Brody JR. Targeting the RNA-Binding Protein HuR in Cancer. Cancer Res 2023; 83:3507-3516. [PMID: 37683260 DOI: 10.1158/0008-5472.can-23-0972] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/12/2023] [Accepted: 09/06/2023] [Indexed: 09/10/2023]
Abstract
The RNA-binding protein human antigen R (HuR) is a well-established regulator of gene expression at the posttranscriptional level. Its dysregulation has been implicated in various human diseases, particularly cancer. In cancer, HuR is considered "active" when it shows increased subcellular localization in the cytoplasm, in addition to its normal nuclear localization. Cytoplasmic HuR plays a crucial role in stabilizing and enhancing the translation of prosurvival mRNAs that are involved in stress responses relevant to cancer progression, such as hypoxia, radiotherapy, and chemotherapy. In general, due to HuR's abundance and function in cancer cells compared with normal cells, it is an appealing target for oncology research. Exploiting the principles underlying HuR's role in tumorigenesis and resistance to stressors, targeting HuR has the potential for synergy with existing and novel oncologic therapies. This review aims to explore HuR's role in homeostasis and cancer pathophysiology, as well as current targeting strategies, which include silencing HuR expression, preventing its translocation and dimerization from the nucleus to the cytoplasm, and inhibiting mRNA binding. Furthermore, this review will discuss recent studies investigating the potential synergy between HuR inhibition and traditional chemotherapeutics.
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Affiliation(s)
- Jennifer M Finan
- Department of Surgery, Oregon Health & Science University, Portland, Oregon
| | - Thomas L Sutton
- Department of Surgery, Oregon Health & Science University, Portland, Oregon
| | - Dan A Dixon
- Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas
| | - Jonathan R Brody
- Department of Surgery, Oregon Health & Science University, Portland, Oregon
- Brenden-Colson Center for Pancreatic Care, Oregon Health & Science University, Portland, Oregon
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16
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Hakimi P, Tabatabaei F, Rahmani V, Zakariya NA, Moslehian MS, Bedate AM, Tamadon A, Rahbarghazi R, Mahdipour M. Dysregulated miRNAs in recurrent miscarriage: A systematic review. Gene 2023; 884:147689. [PMID: 37543220 DOI: 10.1016/j.gene.2023.147689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 07/12/2023] [Accepted: 08/02/2023] [Indexed: 08/07/2023]
Abstract
Recurrent miscarriage (RM) is a complex reproductive medicine disease that affects many families. The cause of RM is unclear at this time; however, lifestyle and genetic variables may influence the process. The slight alteration in miRNA expression has enormous consequences for a variety of difficulties, one of which may be RM. The target of this systematic study was to provide a framework of the dysregulated miRNAs in RM. The Prisma guidelines were applied to perform current systematic review pertaining to articles in the seven databases. Thirty-nine papers out of 245 received fulfilled all inclusion requirements. From all the mentioned miRNAs, 40 were up-regulated (65.57 %), whereas 21 were down-regulated (34.43 %). These dysregulated miRNAs contributed to the pathophysiology of RM by influencing key pathways and processes such as apoptosis, angiogenesis, epithelial-mesenchymal transition, and the immune system. Understanding the dysregulation of miRNAs, as well as the pathways and processes that engage these miRNAs and impact disease pathogenesis, may aid in clarifying the unknown underlying mechanisms of RM and the development of novel molecular therapeutic targets and medical domains.
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Affiliation(s)
- Parvin Hakimi
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fatemeh Tabatabaei
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Obstetrics and Gynecology, Division of Gynecologic Laparoscopic, Surgeries, Al-Zahra Hospital, Tabriz University of Medical Sciences, Tabriz, Iran; Iranian Society of Minimally Invasive Gynecology, Iran University of Medical, Sciences, Tehran, Iran
| | - Vahideh Rahmani
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nahideh Afshar Zakariya
- Women's Reproductive Health Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Amin Tamadon
- PerciaVista R&D Co, Shiraz, Iran; Department for Scientific Work, West Kazakhstan Marat Ospanov Medical University, Aktobe 030012, Kazakhstan
| | - Reza Rahbarghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Applied Cell Sciences, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mahdi Mahdipour
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.
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17
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Osma-Garcia IC, Mouysset M, Capitan-Sobrino D, Aubert Y, Turner M, Diaz-Muñoz MD. The RNA binding proteins TIA1 and TIAL1 promote Mcl1 mRNA translation to protect germinal center responses from apoptosis. Cell Mol Immunol 2023; 20:1063-1076. [PMID: 37474714 PMCID: PMC10469172 DOI: 10.1038/s41423-023-01063-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 06/24/2023] [Indexed: 07/22/2023] Open
Abstract
Germinal centers (GCs) are essential for the establishment of long-lasting antibody responses. GC B cells rely on post-transcriptional RNA mechanisms to translate activation-associated transcriptional programs into functional changes in the cell proteome. However, the critical proteins driving these key mechanisms are still unknown. Here, we show that the RNA binding proteins TIA1 and TIAL1 are required for the generation of long-lasting GC responses. TIA1- and TIAL1-deficient GC B cells fail to undergo antigen-mediated positive selection, expansion and differentiation into B-cell clones producing high-affinity antibodies. Mechanistically, TIA1 and TIAL1 control the transcriptional identity of dark- and light-zone GC B cells and enable timely expression of the prosurvival molecule MCL1. Thus, we demonstrate here that TIA1 and TIAL1 are key players in the post-transcriptional program that selects high-affinity antigen-specific GC B cells.
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Affiliation(s)
- Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Cambridge, UK
| | - Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, 31024, France.
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18
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Wang Y, Liu J, Zhou F. The role of TIA1 and TIAL1 in germinal center B cell function and survival. Cell Mol Immunol 2023; 20:1090-1092. [PMID: 37626212 PMCID: PMC10468532 DOI: 10.1038/s41423-023-01067-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 07/20/2023] [Indexed: 08/27/2023] Open
Affiliation(s)
- Yongqiang Wang
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215123, China
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, China
| | - Jisheng Liu
- Department of Otolaryngology Head and Neck Surgery, The First Affiliated Hospital of Soochow University, Suzhou, 215123, China.
| | - Fangfang Zhou
- Institutes of Biology and Medical Science, Soochow University, Suzhou, 215123, China.
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19
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Xie J, Du Y, Liu D, Wu J, Yang K, He X, Zhao J, Hong P, Liao K, Zhang H, Hong Y, Teijaro JR, Kang SG, Xiao C, Liu WH. The miR-17∼92 miRNAs promote plasma cell differentiation by suppressing SOCS3-mediated NIK degradation. Cell Rep 2023; 42:112968. [PMID: 37578862 DOI: 10.1016/j.celrep.2023.112968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 06/26/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
The miR-17∼92 family microRNAs (miRNAs) play a key role in germinal center (GC) reaction through promoting T follicular helper (TFH) cell differentiation. It remains unclear whether they also have intrinsic functions in B cell differentiation and function. Here we show that mice with B cell-specific deletion of the miR-17∼92 family exhibit impaired GC reaction, plasma cell differentiation, and antibody production in response to protein antigen immunization and chronic viral infection. Employing CRISPR-mediated functional screening, we identify Socs3 as a key functional target of miR-17∼92 in regulating plasma cell differentiation. Mechanistically, SOCS3, whose expression is elevated in miR-17∼92 family-deficient B cells, interacts with NIK and promotes its ubiquitination and degradation, thereby impairing NF-κB signaling and plasma cell differentiation. This moderate increase in SOCS3 expression has little effect on IL-21-STAT3 signaling. Our study demonstrates differential sensitivity of two key signaling pathways to alterations in the protein level of an miRNA target gene.
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Affiliation(s)
- Jun Xie
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Ying Du
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Dewang Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Kang Yang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Xiaoyu He
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Jiayi Zhao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Peicheng Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Kunyu Liao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Huanrong Zhang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - Yazhen Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Seung Goo Kang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA; Division of Biomedical Convergence/Institute of Bioscience and Biotechnology, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea.
| | - Changchun Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China; Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian 361102, China.
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20
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Amin W, Nishio S, Honjo T, Kobayashi M. Necessity of HuR/ELAVL1 for the activation-induced cytidine deaminase-dependent decrease in topoisomerase 1 in antibody diversification. Int Immunol 2023; 35:361-375. [PMID: 37086201 DOI: 10.1093/intimm/dxad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 04/17/2023] [Indexed: 04/23/2023] Open
Abstract
Activation-induced cytidine deaminase (AID)-dependent DNA cleavage is the initial event of antibody gene-diversification processes such as class switch recombination (CSR) and somatic hypermutation (SHM). We previously reported the requirement of an AID-dependent decrease of topoisomerase 1 (Top1) for efficient DNA cleavage, but the underlying molecular mechanism has remained elusive. This study focuses on HuR/ELAVL1, a protein that binds to AU-rich elements in RNA. HuR-knockout (KO) CH12 cells derived from murine B lymphoma cells were found to have lower CSR and hypermutation efficiencies due to decreased AID-dependent DNA cleavage levels. The HuR-KO CH12 cells do not show impairment in cell cycles and Myc expression, which have been reported in HuR-reduced spleen B cells. Furthermore, drugs that scavenge reactive oxygen species (ROS) do not rescue the lower CSR in HuR-KO CH12 cells, meaning that ROS or decreased c-Myc protein amount is not the reason for the deficiencies of CSR and hypermutation in HuR-KO CH12 cells. We show that HuR binds to Top1 mRNA and that complete deletion of HuR abolishes AID-dependent repression of Top1 protein synthesis in CH12 cells. Additionally, reduction of CSR to IgG3 in HuR-KO cells is rescued by knockdown of Top1, indicating that elimination of the AID-dependent Top1 decrease is the cause of the inefficiency of DNA cleavage, CSR and hypermutation in HuR-KO cells. These results show that HuR is required for initiation of antibody diversification and acquired immunity through the regulation of AID-dependent DNA cleavage by repressing Top1 protein synthesis.
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Affiliation(s)
- Wajid Amin
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
| | - Shoki Nishio
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
| | - Tasuku Honjo
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
| | - Maki Kobayashi
- Department of Immunology and Genomic Medicine, Center for Cancer Immunotherapy and Immunobiology, Graduate School of Medicine, Kyoto University, 606-8501, Kyoto, Japan
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21
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Bechara R, Vagner S, Mariette X. Post-transcriptional checkpoints in autoimmunity. Nat Rev Rheumatol 2023; 19:486-502. [PMID: 37311941 DOI: 10.1038/s41584-023-00980-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/10/2023] [Indexed: 06/15/2023]
Abstract
Post-transcriptional regulation is a fundamental process in gene expression that has a role in diverse cellular processes, including immune responses. A core concept underlying post-transcriptional regulation is that protein abundance is not solely determined by transcript abundance. Indeed, transcription and translation are not directly coupled, and intervening steps occur between these processes, including the regulation of mRNA stability, localization and alternative splicing, which can impact protein abundance. These steps are controlled by various post-transcription factors such as RNA-binding proteins and non-coding RNAs, including microRNAs, and aberrant post-transcriptional regulation has been implicated in various pathological conditions. Indeed, studies on the pathogenesis of autoimmune and inflammatory diseases have identified various post-transcription factors as important regulators of immune cell-mediated and target effector cell-mediated pathological conditions. This Review summarizes current knowledge regarding the roles of post-transcriptional checkpoints in autoimmunity, as evidenced by studies in both haematopoietic and non-haematopoietic cells, and discusses the relevance of these findings for developing new anti-inflammatory therapies.
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Affiliation(s)
- Rami Bechara
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), Le Kremlin Bicêtre, France.
| | - Stephan Vagner
- Institut Curie, CNRS UMR3348, INSERM U1278, PSL Research University, Université Paris-Saclay, Orsay, France
| | - Xavier Mariette
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), Le Kremlin Bicêtre, France
- Assistance Publique - Hôpitaux de Paris, Hôpital Bicêtre, Department of Rheumatology, Le Kremlin Bicêtre, France
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22
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Liu S, Huang B, Cao J, Wang Y, Xiao H, Zhu Y, Zhang H. ROS fine-tunes the function and fate of immune cells. Int Immunopharmacol 2023; 119:110069. [PMID: 37150014 DOI: 10.1016/j.intimp.2023.110069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023]
Abstract
The redox state is essential to the process of cell life, which determines cell fate. As an important signaling molecule of the redox state, reactive oxygen species (ROS) are crucial for the homeostasis of immune cells and participate in the pathological processes of different diseases. We discuss the underlying mechanisms and possible signaling pathways of ROS to fine-tune the proliferation, differentiation, polarization and function of immune cells, including T cells, B cells, neutrophils, macrophages, myeloid-derived inhibitory cells (MDSCs) and dendritic cells (DCs). We further emphasize how excessive ROS lead to programmed immune cell death such as apoptosis, ferroptosis, pyroptosis, NETosis and necroptosis, providing valuable insights for future therapeutic strategies in human diseases.
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Affiliation(s)
- Shiyu Liu
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, 410008 Changsha, China
| | - Benqi Huang
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, 410008 Changsha, China
| | - Jingdong Cao
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, 410008 Changsha, China
| | - Yifei Wang
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, 410008 Changsha, China
| | - Hao Xiao
- Department of Clinical Medicine, Xiangya School of Medicine, Central South University, 410008 Changsha, China
| | - Yaxi Zhu
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medical Sciences, Central South University, 410008 Changsha, China.
| | - Huali Zhang
- Sepsis Translational Medicine Key Lab of Hunan Province, Department of Pathophysiology, School of Basic Medical Sciences, Central South University, 410008 Changsha, China.
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23
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Jiang S, Feng R, Tian Z, Zhou J, Zhang W. Metabolic dialogs between B cells and the tumor microenvironment: Implications for anticancer immunity. Cancer Lett 2023; 556:216076. [PMID: 36724837 DOI: 10.1016/j.canlet.2023.216076] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
Immunometabolism, a branch of biology describing the link between immunity and metabolism, is an emerging topic in cancer immunology. It is currently well accepted that B cells and tertiary lymph structures formed by them are associated with favorable outcomes when patients undergo cancer immunotherapy. Understanding the determinants of B-cell fate and function in cancer patients is necessary for improving cancer immunotherapy. Accumulating evidence points to the tumor microenvironment being a critical metabolic hurdle to an efficient antitumor B-cell response. At the same time, several B-cell-derived metabolites have recently been reported to inhibit anticancer immunity. In this literature review, key B-cell immunometabolism studies and the metabolic life of B cells were summarized. Then, we discussed the intrinsic metabolic pathways of B cells themselves and how the tumor microenvironment and B cells in tumors metabolically influence each other. Finally, we pointed out key questions to provide some inspiration for further study of the role of B-cell immunometabolism in the antitumor immune response.
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Affiliation(s)
- Su Jiang
- Department of Medical Laboratory Science, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ranran Feng
- Department of Medical Laboratory Science, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ziying Tian
- Department of Medical Laboratory Science, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jieyu Zhou
- Department of Medical Laboratory Science, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenling Zhang
- Department of Medical Laboratory Science, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China.
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24
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Imada EL, Wilks C, Langmead B, Marchionni L. REPAC: analysis of alternative polyadenylation from RNA-sequencing data. Genome Biol 2023; 24:22. [PMID: 36759904 PMCID: PMC9912678 DOI: 10.1186/s13059-023-02865-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional mechanism that has major implications in biological processes and diseases. Although specialized sequencing methods for polyadenylation exist, availability of these data are limited compared to RNA-sequencing data. We developed REPAC, a framework for the analysis of APA from RNA-sequencing data. Using REPAC, we investigate the landscape of APA caused by activation of B cells. We also show that REPAC is faster than alternative methods by at least 7-fold and that it scales well to hundreds of samples. Overall, the REPAC method offers an accurate, easy, and convenient solution for the exploration of APA.
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Affiliation(s)
- Eddie L. Imada
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
| | - Christopher Wilks
- Department of Computer Science, Johns Hopkins University, Baltimore, USA
| | - Ben Langmead
- Department of Computer Science, Johns Hopkins University, Baltimore, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, USA
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25
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RBP-RNA interactions in the control of autoimmunity and autoinflammation. Cell Res 2023; 33:97-115. [PMID: 36599968 PMCID: PMC9892603 DOI: 10.1038/s41422-022-00752-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 11/07/2022] [Indexed: 01/06/2023] Open
Abstract
Autoimmunity and autoinflammation arise from aberrant immunological and inflammatory responses toward self-components, contributing to various autoimmune diseases and autoinflammatory diseases. RNA-binding proteins (RBPs) are essential for immune cell development and function, mainly via exerting post-transcriptional regulation of RNA metabolism and function. Functional dysregulation of RBPs and abnormities in RNA metabolism are closely associated with multiple autoimmune or autoinflammatory disorders. Distinct RBPs play critical roles in aberrant autoreactive inflammatory responses via orchestrating a complex regulatory network consisting of DNAs, RNAs and proteins within immune cells. In-depth characterizations of RBP-RNA interactomes during autoimmunity and autoinflammation will lead to a better understanding of autoimmune pathogenesis and facilitate the development of effective therapeutic strategies. In this review, we summarize and discuss the functions of RBP-RNA interactions in controlling aberrant autoimmune inflammation and their potential as biomarkers and therapeutic targets.
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26
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Osma-Garcia IC, Capitan-Sobrino D, Mouysset M, Aubert Y, Maloudi O, Turner M, Diaz-Muñoz MD. The splicing regulators TIA1 and TIAL1 are required for the expression of the DNA damage repair machinery during B cell lymphopoiesis. Cell Rep 2022; 41:111869. [PMID: 36543128 PMCID: PMC9794549 DOI: 10.1016/j.celrep.2022.111869] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 10/01/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
B cell lymphopoiesis requires dynamic modulation of the B cell transcriptome for timely coordination of somatic mutagenesis and DNA repair in progenitor B (pro-B) cells. Here, we show that, in pro-B cells, the RNA-binding proteins T cell intracellular antigen 1 (TIA1) and TIA1-like protein (TIAL1) act redundantly to enable developmental progression. They are global splicing regulators that control the expression of hundreds of mRNAs, including those involved in DNA damage repair. Mechanistically, TIA1 and TIAL1 bind to 5' splice sites for exon definition, splicing, and expression of DNA damage sensors, such as Chek2 and Rif1. In their absence, pro-B cells show exacerbated DNA damage, altered P53 expression, and increased cell death. Our study uncovers the importance of tight regulation of RNA splicing by TIA1 and TIAL1 for the expression of integrative transcriptional programs that control DNA damage sensing and repair during B cell development.
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Affiliation(s)
- Ines C. Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Yann Aubert
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Orlane Maloudi
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Manuel D. Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITy), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse 31024, France,Corresponding author
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27
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Kunder N, de la Peña JB, Lou TF, Chase R, Suresh P, Lawson J, Shukla T, Black B, Campbell ZT. The RNA-Binding Protein HuR Is Integral to the Function of Nociceptors in Mice and Humans. J Neurosci 2022; 42:9129-9141. [PMID: 36270801 PMCID: PMC9761683 DOI: 10.1523/jneurosci.1630-22.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/04/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
HuR is an RNA-binding protein implicated in RNA processing, stability, and translation. Previously, we examined protein synthesis in dorsal root ganglion (DRG) neurons treated with inflammatory mediators using ribosome profiling. We found that the HuR consensus binding element was enriched in transcripts with elevated translation. HuR is expressed in the soma of nociceptors and their axons. Pharmacologic inhibition of HuR with the small molecule CMLD-2 reduced the activity of mouse and human sensory neurons. Peripheral administration of CMLD-2 in the paw or genetic elimination of HuR from sensory neurons diminished behavioral responses associated with NGF- and IL-6-induced allodynia in male and female mice. Genetic disruption of HuR altered the proximity of mRNA decay factors near a key neurotrophic factor (TrkA). Collectively, the data suggest that HuR is required for local control of mRNA stability and reveals a new biological function for a broadly conserved post-transcriptional regulatory factor.SIGNIFICANCE STATEMENT Nociceptors undergo long-lived changes in excitability, which may contribute to chronic pain. Noxious cues that promote pain lead to rapid induction of protein synthesis. The underlying mechanisms that confer specificity to mRNA control in nociceptors are unclear. Here, we identify a conserved RNA-binding protein called HuR as a key regulatory factor in sensory neurons. Using a combination of genetics and pharmacology, we demonstrate that HuR is required for signaling in nociceptors. In doing so, we report an important mechanism of mRNA control in sensory neurons that ensures appropriate nociceptive responses to inflammatory mediators.
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Affiliation(s)
- Nikesh Kunder
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - June Bryan de la Peña
- Department of Anesthesiology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Tzu-Fang Lou
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Rebecca Chase
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Prarthana Suresh
- Department of Biological Sciences, University of Texas at Dallas, Richardson, Texas 75080
| | - Jennifer Lawson
- Department of Biomedical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts 01854
| | - Tarjani Shukla
- Department of Anesthesiology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53792
| | - Bryan Black
- Department of Biomedical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts 01854
| | - Zachary T Campbell
- Department of Anesthesiology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53792
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53792
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28
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Tran TM, Rao DS. RNA binding proteins in MLL-rearranged leukemia. Exp Hematol Oncol 2022; 11:80. [PMID: 36307883 PMCID: PMC9615162 DOI: 10.1186/s40164-022-00343-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 10/18/2022] [Indexed: 11/10/2022] Open
Abstract
AbstractRNA binding proteins (RBPs) have recently emerged as important post-transcriptional gene expression regulators in both normal development and disease. RBPs influence the fate of mRNAs through multiple mechanisms of action such as RNA modifications, alternative splicing, and miR-mediated regulation. This complex and, often, combinatorial regulation by RBPs critically impacts the expression of oncogenic transcripts and, thus, the activation of pathways that drive oncogenesis. Here, we focus on the major features of RBPs, their mechanisms of action, and discuss the current progress in investigating the function of important RBPs in MLL-rearranged leukemia.
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29
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Hansen GE, Gibson GE. The α-Ketoglutarate Dehydrogenase Complex as a Hub of Plasticity in Neurodegeneration and Regeneration. Int J Mol Sci 2022; 23:12403. [PMID: 36293260 PMCID: PMC9603878 DOI: 10.3390/ijms232012403] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 07/30/2023] Open
Abstract
Abnormal glucose metabolism is central to neurodegeneration, and considerable evidence suggests that abnormalities in key enzymes of the tricarboxylic acid (TCA) cycle underlie the metabolic deficits. Significant recent advances in the role of metabolism in cancer provide new insight that facilitates our understanding of the role of metabolism in neurodegeneration. Research indicates that the rate-limiting step of the TCA cycle, the α-ketoglutarate dehydrogenase complex (KGDHC) and its substrate alpha ketoglutarate (KG), serve as a signaling hub that regulates multiple cellular processes: (1) is the rate-limiting step of the TCA cycle, (2) is sensitive to reactive oxygen species (ROS) and produces ROS, (3) determines whether KG is used for energy or synthesis of compounds to support growth, (4) regulates the cellular responses to hypoxia, (5) controls the post-translational modification of hundreds of cell proteins in the mitochondria, cytosol, and nucleus through succinylation, (6) controls critical aspects of transcription, (7) modulates protein signaling within cells, and (8) modulates cellular calcium. The primary focus of this review is to understand how reductions in KGDHC are translated to pathologically important changes that underlie both neurodegeneration and cancer. An understanding of each role is necessary to develop new therapeutic strategies to treat neurodegenerative disease.
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Affiliation(s)
- Grace E. Hansen
- Department of Biology, University of Massachusetts, Lowell, MA 01852, USA
| | - Gary E. Gibson
- Weill Cornell Medicine, Brain and Mind Research Institute, Burke Neurological Institute, White Plains, NY 10605, USA
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30
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Majumder M, Chakraborty P, Mohan S, Mehrotra S, Palanisamy V. HuR as a molecular target for cancer therapeutics and immune-related disorders. Adv Drug Deliv Rev 2022; 188:114442. [PMID: 35817212 DOI: 10.1016/j.addr.2022.114442] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 04/12/2022] [Accepted: 07/05/2022] [Indexed: 11/19/2022]
Abstract
The control of eukaryotic gene expression occurs at multiple levels, from transcription to messenger RNA processing, transport, localization, turnover, and translation. RNA-binding proteins control gene expression and are involved in different stages of mRNA processing, including splicing, maturation, turnover, and translation. A ubiquitously expressed RBP Human antigen R is engaged in the RNA processes mentioned above but, most importantly, controls mRNA stability and turnover. Dysregulation of HuR is linked to many diseases, including cancer and other immune-related disorders. HuR targets mRNAs containing AU-rich elements at their 3'untranslated region, which encodes proteins involved in cell growth, proliferation, tumor formation, angiogenesis, immune evasion, inflammation, invasion, and metastasis. HuR overexpression has been reported in many tumor types, which led to a poor prognosis for patients. Hence, HuR is considered an appealing drug target for cancer treatment. Therefore, multiple attempts have been made to identify small molecule inhibitors for blocking HuR functions. This article reviews the current prospects of drugs that target HuR in numerous cancer types, their mode of action, and off-target effects. Furthermore, we will summarize drugs that interfered with HuR-RNA interactions and established themselves as novel therapeutics. We will also highlight the significance of HuR overexpression in multiple cancers and discuss its role in immune functions. This review provides evidence of a new era of HuR-targeted small molecules that can be used for cancer therapeutics either as a monotherapy or in combination with other cancer treatment modalities.
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Affiliation(s)
- Mrinmoyee Majumder
- Department of Biochemistry and Molecular Biology, Charleston, SC 29425, USA
| | - Paramita Chakraborty
- Department of Surgery, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Sarumathi Mohan
- Department of Biochemistry and Molecular Biology, Charleston, SC 29425, USA
| | - Shikhar Mehrotra
- Department of Surgery, College of Medicine, Medical University of South Carolina, Charleston, SC 29425, USA
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31
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Grenov A, Hezroni H, Lasman L, Hanna JH, Shulman Z. YTHDF2 suppresses the plasmablast genetic program and promotes germinal center formation. Cell Rep 2022; 39:110778. [PMID: 35508130 PMCID: PMC9108551 DOI: 10.1016/j.celrep.2022.110778] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 02/25/2022] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Antibody-mediated immunity is initiated by B cell differentiation into multiple cell subsets, including plasmablast, memory, and germinal center (GC) cells. B cell differentiation trajectories are determined by transcription factors, yet very few mechanisms that specifically determine early B cell fates have been described. Here, we report a post-transcriptional mechanism that suppresses the plasmablast genetic program and promotes GC B cell fate commitment. Single-cell RNA-sequencing analysis reveals that antigen-specific B cell precursors at the pre-GC stage upregulate YTHDF2, which enhances the decay of methylated transcripts. Ythdf2-deficient B cells exhibit intact proliferation and activation, whereas differentiation into GC B cells is blocked. Mechanistically, B cells require YTHDF2 to attenuate the plasmablast genetic program during GC seeding, and transcripts of key plasmablast-regulating genes are methylated and bound by YTHDF2. Collectively, this study reveals how post-transcriptional suppression of gene expression directs appropriate B cell fate commitment during initiation of the adaptive immune response. scRNA-seq of antigen-specific B cells reveals differentiation trajectories YTHDF2 is expressed by early-responding B cells and facilitates germinal center seeding YTHDF2 binds mRNAs of plasma cell-associated genes and suppresses their expression Germinal center formation does not depend on YTHDF1 and YTHDF3
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Affiliation(s)
- Amalie Grenov
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Hadas Hezroni
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lior Lasman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Shulman
- Department of Systems Immunology, Weizmann Institute of Science, Rehovot, Israel.
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32
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Tang H, Li Y, Wang S, Ji J, Zhu X, Bao Y, Huang C, Luo Y, Huang L, Gao Y, Wei C, Liu J, Fang X, Sun L, Ouyang K. IPR-mediated Ca signaling controls B cell proliferation through metabolic reprogramming. iScience 2022; 25:104209. [PMID: 35494252 PMCID: PMC9046235 DOI: 10.1016/j.isci.2022.104209] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 03/05/2022] [Accepted: 04/04/2022] [Indexed: 11/29/2022] Open
Affiliation(s)
- Huayuan Tang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China
- Corresponding author
| | - Yali Li
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Institute of Neurological and Psychiatric Disorders, Shenzhen Bay Laboratory, Shenzhen 518132, China
| | - Shijia Wang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Jing Ji
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Xiangbin Zhu
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yutong Bao
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Can Huang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Ye Luo
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Lei Huang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yan Gao
- Department of Cardiovascular Medicine, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen Shekou People’s Hospital, Shenzhen, China
| | - Chaoliang Wei
- Department of Pathophysiology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Jie Liu
- Department of Pathophysiology, School of Medicine, Shenzhen University, Shenzhen, China
| | - Xi Fang
- Department of Medicine, School of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Lu Sun
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Corresponding author
| | - Kunfu Ouyang
- Department of Cardiovascular Surgery, Peking University Shenzhen Hospital, State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
- Corresponding author
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33
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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Assoni G, La Pietra V, Digilio R, Ciani C, Licata NV, Micaelli M, Facen E, Tomaszewska W, Cerofolini L, Pérez-Ràfols A, Varela Rey M, Fragai M, Woodhoo A, Marinelli L, Arosio D, Bonomo I, Provenzani A, Seneci P. HuR-targeted agents: An insight into medicinal chemistry, biophysical, computational studies and pharmacological effects on cancer models. Adv Drug Deliv Rev 2022; 181:114088. [PMID: 34942276 DOI: 10.1016/j.addr.2021.114088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 10/07/2021] [Accepted: 12/16/2021] [Indexed: 12/13/2022]
Abstract
The Human antigen R (HuR) protein is an RNA-binding protein, ubiquitously expressed in human tissues, that orchestrates target RNA maturation and processing both in the nucleus and in the cytoplasm. A survey of known modulators of the RNA-HuR interactions is followed by a description of its structure and molecular mechanism of action - RRM domains, interactions with RNA, dimerization, binding modes with naturally occurring and synthetic HuR inhibitors. Then, the review focuses on HuR as a validated molecular target in oncology and briefly describes its role in inflammation. Namely, we show ample evidence for the involvement of HuR in the hallmarks and enabling characteristics of cancer, reporting findings from in vitro and in vivo studies; and we provide abundant experimental proofs of a beneficial role for the inhibition of HuR-mRNA interactions through silencing (CRISPR, siRNA) or pharmacological inhibition (small molecule HuR inhibitors).
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Affiliation(s)
- Giulia Assoni
- Chemistry Department, University of Milan, Via Golgi 19, I-20133 Milan, Italy; Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Valeria La Pietra
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Rosangela Digilio
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Caterina Ciani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Nausicaa Valentina Licata
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Mariachiara Micaelli
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Elisa Facen
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Weronika Tomaszewska
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Linda Cerofolini
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Anna Pérez-Ràfols
- Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino (FI), Italy
| | - Marta Varela Rey
- Gene Regulatory Control in Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, Spain
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence and Interuniversity Consortium for Magnetic Resonance of Metalloproteins (CIRMMP), Via L. Sacconi 6, 50019 Sesto Fiorentino (FI), Italy
| | - Ashwin Woodhoo
- Gene Regulatory Control in Disease Group, Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, 15706 Santiago de Compostela, Spain; Department of Functional Biology, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain; Galician Agency of Innovation (GAIN), Xunta de Galicia, Santiago de Compostela, Spain; Center for Cooperative Research in Biosciences (CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao 48013, Spain
| | - Luciana Marinelli
- Department of Pharmacy, University of Napoli Federico II, Via D. Montesano 49, 80131 Napoli, Italy
| | - Daniela Arosio
- Istituto di Scienze e Tecnologie Chimiche "G. Natta" (SCITEC), National Research Council (CNR), Via C. Golgi 19, I-20133 Milan, Italy
| | - Isabelle Bonomo
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy
| | - Alessandro Provenzani
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, via Sommarive 9, 38123 Trento, Italy.
| | - Pierfausto Seneci
- Chemistry Department, University of Milan, Via Golgi 19, I-20133 Milan, Italy.
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Increasing Inhibition of the Rat Brain 2-Oxoglutarate Dehydrogenase Decreases Glutathione Redox State, Elevating Anxiety and Perturbing Stress Adaptation. Pharmaceuticals (Basel) 2022; 15:ph15020182. [PMID: 35215295 PMCID: PMC8875720 DOI: 10.3390/ph15020182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/28/2022] [Accepted: 01/28/2022] [Indexed: 12/10/2022] Open
Abstract
Specific inhibitors of mitochondrial 2-oxoglutarate dehydrogenase (OGDH) are administered to animals to model the downregulation of the enzyme as observed in neurodegenerative diseases. Comparison of the effects of succinyl phosphonate (SP, 0.02 mmol/kg) and its uncharged precursor, triethyl succinyl phosphonate (TESP, 0.02 and 0.1 mmol/kg) reveals a biphasic response of the rat brain metabolism and physiology to increasing perturbation of OGDH function. At the low (TE)SP dose, glutamate, NAD+, and the activities of dehydrogenases of 2-oxoglutarate and malate increase, followed by their decreases at the high TESP dose. The complementary changes, i.e., an initial decrease followed by growth, are demonstrated by activities of pyruvate dehydrogenase and glutamine synthetase, and levels of oxidized glutathione and citrulline. While most of these indicators return to control levels at the high TESP dose, OGDH activity decreases and oxidized glutathione increases, compared to their control values. The first phase of metabolic perturbations does not cause significant physiological changes, but in the second phase, the ECG parameters and behavior reveal decreased adaptability and increased anxiety. Thus, lower levels of OGDH inhibition are compensated by the rearranged metabolic network, while the increased levels induce a metabolic switch to a lower redox state of the brain, associated with elevated stress of the animals.
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Shah JS, Milevskiy MJG, Petrova V, Au AYM, Wong JJL, Visvader JE, Schmitz U, Rasko JEJ. Towards resolution of the intron retention paradox in breast cancer. Breast Cancer Res 2022; 24:100. [PMID: 36581993 PMCID: PMC9798573 DOI: 10.1186/s13058-022-01593-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 12/12/2022] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND After many years of neglect in the field of alternative splicing, the importance of intron retention (IR) in cancer has come into focus following landmark discoveries of aberrant IR patterns in cancer. Many solid and liquid tumours are associated with drastic increases in IR, and such patterns have been pursued as both biomarkers and therapeutic targets. Paradoxically, breast cancer (BrCa) is the only tumour type in which IR is reduced compared to adjacent normal breast tissue. METHODS In this study, we have conducted a pan-cancer analysis of IR with emphasis on BrCa and its subtypes. We explored mechanisms that could cause aberrant and pathological IR and clarified why normal breast tissue has unusually high IR. RESULTS Strikingly, we found that aberrantly decreasing IR in BrCa can be largely attributed to normal breast tissue having the highest occurrence of IR events compared to other healthy tissues. Our analyses suggest that low numbers of IR events in breast tumours are associated with poor prognosis, particularly in the luminal B subtype. Interestingly, we found that IR frequencies negatively correlate with cell proliferation in BrCa cells, i.e. rapidly dividing tumour cells have the lowest number of IR events. Aberrant RNA-binding protein expression and changes in tissue composition are among the causes of aberrantly decreasing IR in BrCa. CONCLUSIONS Our results suggest that IR should be considered for therapeutic manipulation in BrCa patients with aberrantly low IR levels and that further work is needed to understand the cause and impact of high IR in other tumour types.
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Affiliation(s)
- Jaynish S. Shah
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1002.30000 0004 1936 7857Australian Centre for Blood Diseases, Central Clinical School, Monash University and Alfred Health, Melbourne, VIC Australia
| | - Michael J. G. Milevskiy
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Veronika Petrova
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Amy Y. M. Au
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia
| | - Justin J. L. Wong
- grid.1013.30000 0004 1936 834XEpigenetics and RNA Biology Program Centenary Institute, The University of Sydney, Camperdown, 2050 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia
| | - Jane E. Visvader
- grid.1042.70000 0004 0432 4889ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052 Australia ,grid.1008.90000 0001 2179 088XDepartment of Medical Biology, The University of Melbourne, Parkville, VIC 3010 Australia
| | - Ulf Schmitz
- grid.1013.30000 0004 1936 834XComputational BioMedicine Laboratory Centenary Institute, The University of Sydney, Camperdown, Australia ,grid.1011.10000 0004 0474 1797Department of Molecular and Cell Biology, College of Public Health, Medical and Veterinary Sciences, James Cook University, 1 James Cook Drive, Townsville, QLD 4811 Australia ,grid.1011.10000 0004 0474 1797Centre for Tropical Bioinformatics and Molecular Biology, Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, 4878 Australia
| | - John E. J. Rasko
- grid.1013.30000 0004 1936 834XGene and Stem Cell Therapy Program Centenary Institute, The University of Sydney, Locked Bag No. 6, Newtown, NSW 2042 Australia ,grid.1013.30000 0004 1936 834XFaculty of Medicine and Health, The University of Sydney, Camperdown, Australia ,grid.413249.90000 0004 0385 0051Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, Australia
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Raguraman R, Shanmugarama S, Mehta M, Elle Peterson J, Zhao YD, Munshi A, Ramesh R. Drug delivery approaches for HuR-targeted therapy for lung cancer. Adv Drug Deliv Rev 2022; 180:114068. [PMID: 34822926 PMCID: PMC8724414 DOI: 10.1016/j.addr.2021.114068] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/18/2021] [Indexed: 01/03/2023]
Abstract
Lung cancer (LC) is often diagnosed at an advanced stage and conventional treatments for disease management have limitations associated with them. Novel therapeutic targets are thus avidly sought for the effective management of LC. RNA binding proteins (RBPs) have been convincingly established as key players in tumorigenesis, and their dysregulation is linked to multiple cancers, including LC. In this context, we review the role of Human antigen R (HuR), an RBP that is overexpressed in LC, and further associated with various aspects of LC tumor growth and response to therapy. Herein, we describe the role of HuR in LC progression and outline the evidences supporting various pharmacologic and biologic approaches for inhibiting HuR expression and function. These approaches, including use of small molecule inhibitors, siRNAs and shRNAs, have demonstrated favorable results in reducing tumor cell growth, invasion and migration, angiogenesis and metastasis. Hence, HuR has significant potential as a key therapeutic target in LC. Use of siRNA-based approaches, however, have certain limitations that prevent their maximal exploitation as cancer therapies. To address this, in the conclusion of this review, we provide a list of nanomedicine-based HuR targeting approaches currently being employed for siRNA and shRNA delivery, and provide a rationale for the immense potential therapeutic benefits offered by nanocarrier-based HuR targeting and its promise for treating patients with LC.
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Affiliation(s)
- Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Santny Shanmugarama
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA
| | - Meghna Mehta
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Jo Elle Peterson
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Yan D Zhao
- Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Anupama Munshi
- Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA; Graduate Program in Biomedical Sciences, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA.
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38
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Osma-Garcia IC, Capitan-Sobrino D, Mouysset M, Bell SE, Lebeurrier M, Turner M, Diaz-Muñoz MD. The RNA-binding protein HuR is required for maintenance of the germinal centre response. Nat Commun 2021; 12:6556. [PMID: 34772950 PMCID: PMC8590059 DOI: 10.1038/s41467-021-26908-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/22/2021] [Indexed: 11/09/2022] Open
Abstract
The germinal centre (GC) is required for the generation of high affinity antibodies and immunological memory. Here we show that the RNA binding protein HuR has an essential function in GC B cells to sustain the GC response. In its absence, the GC reaction and production of high-affinity antibody is severely impaired. Mechanistically, HuR affects the transcriptome qualitatively and quantitatively. The expression and splicing patterns of hundreds of genes are altered in the absence of HuR. Among these genes, HuR is required for the expression of Myc and a Myc-dependent transcriptional program that controls GC B cell proliferation and Ig somatic hypermutation. Additionally, HuR regulates the splicing and abundance of mRNAs required for entry into and transition through the S phase of the cell cycle, and it modulates a gene signature associated with DNA deamination protecting GC B cells from DNA damage and cell death.
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Affiliation(s)
- Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, France
| | - Dunja Capitan-Sobrino
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, France
| | - Mailys Mouysset
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, France
| | - Sarah E Bell
- Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Manuel Lebeurrier
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, France
| | - Martin Turner
- Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
| | - Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases (Infinity), Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, CHU Purpan, Toulouse, France. .,Immunology Program, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, UK.
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Si R, Cabrera JTO, Tsuji-Hosokawa A, Guo R, Watanabe M, Gao L, Lee YS, Moon JS, Scott BT, Wang J, Ashton AW, Rao JN, Wang JY, Yuan JXJ, Makino A. HuR/Cx40 downregulation causes coronary microvascular dysfunction in type 2 diabetes. JCI Insight 2021; 6:147982. [PMID: 34747371 PMCID: PMC8663561 DOI: 10.1172/jci.insight.147982] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 09/29/2021] [Indexed: 11/30/2022] Open
Abstract
Patients with diabetes with coronary microvascular disease (CMD) exhibit higher cardiac mortality than patients without CMD. However, the molecular mechanism by which diabetes promotes CMD is poorly understood. RNA-binding protein human antigen R (HuR) is a key regulator of mRNA stability and translation; therefore, we investigated the role of HuR in the development of CMD in mice with type 2 diabetes. Diabetic mice exhibited decreases in coronary flow velocity reserve (CFVR; a determinant of coronary microvascular function) and capillary density in the left ventricle. HuR levels in cardiac endothelial cells (CECs) were significantly lower in diabetic mice and patients with diabetes than the controls. Endothelial-specific HuR-KO mice also displayed significant reductions in CFVR and capillary density. By examining mRNA levels of 92 genes associated with endothelial function, we found that HuR, Cx40, and Nox4 levels were decreased in CECs from diabetic and HuR-KO mice compared with control mice. Cx40 expression and HuR binding to Cx40 mRNA were downregulated in CECs from diabetic mice. Cx40-KO mice exhibited decreased CFVR and capillary density, whereas endothelium-specific Cx40 overexpression increased capillary density and improved CFVR in diabetic mice. These data suggest that decreased HuR contributes to the development of CMD in diabetes through downregulation of gap junction protein Cx40 in CECs.
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Affiliation(s)
- Rui Si
- Department of Physiology, The University of Arizona (UA), Tucson, Arizona, USA.,Department of Cardiology, Xijing Hospital, Fourth Military Medical University, Shaanxi, China
| | | | | | - Rui Guo
- Department of Physiology, The University of Arizona (UA), Tucson, Arizona, USA
| | - Makiko Watanabe
- Department of Physiology, The University of Arizona (UA), Tucson, Arizona, USA
| | - Lei Gao
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Yun Sok Lee
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Jae-Su Moon
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Brian T Scott
- Department of Medicine, UCSD, La Jolla, California, USA
| | - Jian Wang
- Department of Physiology, The University of Arizona (UA), Tucson, Arizona, USA.,State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Anthony W Ashton
- Division of Perinatal Research, Kolling Institute of Medical Research, University of Sydney, New South Wales, Australia
| | - Jaladanki N Rao
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jian-Ying Wang
- Department of Surgery, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | | | - Ayako Makino
- Department of Physiology, The University of Arizona (UA), Tucson, Arizona, USA.,Department of Medicine, UCSD, La Jolla, California, USA
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40
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Grenov AC, Moss L, Edelheit S, Cordiner R, Schmiedel D, Biram A, Hanna JH, Jensen TH, Schwartz S, Shulman Z. The germinal center reaction depends on RNA methylation and divergent functions of specific methyl readers. J Exp Med 2021; 218:e20210360. [PMID: 34402854 PMCID: PMC8374864 DOI: 10.1084/jem.20210360] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 06/02/2021] [Accepted: 07/22/2021] [Indexed: 12/19/2022] Open
Abstract
Long-lasting immunity depends on the generation of protective antibodies through the germinal center (GC) reaction. N6-methyladenosine (m6A) modification of mRNAs by METTL3 activity modulates transcript lifetime primarily through the function of m6A readers; however, the physiological role of this molecular machinery in the GC remains unknown. Here, we show that m6A modifications by METTL3 are required for GC maintenance through the differential functions of m6A readers. Mettl3-deficient GC B cells exhibited reduced cell-cycle progression and decreased expression of proliferation- and oxidative phosphorylation-related genes. The m6A binder, IGF2BP3, was required for stabilization of Myc mRNA and expression of its target genes, whereas the m6A reader, YTHDF2, indirectly regulated the expression of the oxidative phosphorylation gene program. Our findings demonstrate how two independent gene networks that support critical GC functions are modulated by m6A through distinct mRNA binders.
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Affiliation(s)
- Amalie C. Grenov
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Lihee Moss
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Sarit Edelheit
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ross Cordiner
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Dominik Schmiedel
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Adi Biram
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Jacob H. Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Schraga Schwartz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ziv Shulman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
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Kovarik P, Bestehorn A, Fesselet J. Conceptual Advances in Control of Inflammation by the RNA-Binding Protein Tristetraprolin. Front Immunol 2021; 12:751313. [PMID: 34603339 PMCID: PMC8484758 DOI: 10.3389/fimmu.2021.751313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/01/2021] [Indexed: 11/16/2022] Open
Abstract
Regulated changes in mRNA stability are critical drivers of gene expression adaptations to immunological cues. mRNA stability is controlled mainly by RNA-binding proteins (RBPs) which can directly cleave mRNA but more often act as adaptors for the recruitment of the RNA-degradation machinery. One of the most prominent RBPs with regulatory roles in the immune system is tristetraprolin (TTP). TTP targets mainly inflammation-associated mRNAs for degradation and is indispensable for the resolution of inflammation as well as the maintenance of immune homeostasis. Recent advances in the transcriptome-wide knowledge of mRNA expression and decay rates together with TTP binding sites in the target mRNAs revealed important limitations in our understanding of molecular mechanisms of TTP action. Such orthogonal analyses lead to the discovery that TTP binding destabilizes some bound mRNAs but not others in the same cell. Moreover, comparisons of various immune cells indicated that an mRNA can be destabilized by TTP in one cell type while it remains stable in a different cell linage despite the presence of TTP. The action of TTP extends from mRNA destabilization to inhibition of translation in a subset of targets. This article will discuss these unexpected context-dependent functions and their implications for the regulation of immune responses. Attention will be also payed to new insights into the role of TTP in physiology and tissue homeostasis.
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Affiliation(s)
- Pavel Kovarik
- Max Perutz Labs, University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
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42
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Monzón-Casanova E, Bates KJ, Smith CWJ, Turner M. Essential requirement for polypyrimidine tract binding proteins 1 and 3 in the maturation and maintenance of mature B cells in mice. Eur J Immunol 2021; 51:2266-2273. [PMID: 34214192 PMCID: PMC11146436 DOI: 10.1002/eji.202149257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/20/2021] [Accepted: 07/01/2021] [Indexed: 11/09/2022]
Abstract
The maturation of immature B cells and the survival of mature B cells is stringently controlled to maintain a diverse repertoire of antibody specificities while avoiding self-reactivity. At the molecular level this is regulated by signaling from membrane Ig and the BAFF-receptor that sustain a pro-survival program of gene expression. Whether and how posttranscriptional mechanisms contribute to B cell maturation and survival remains poorly understood. Here, we show that the polypyrimidine tract binding proteins (PTBP) PTBP1 and PTBP3 bind to a large and overlapping set of transcripts in B cells. Both PTBP1 and PTBP3 bind to introns and exons where they are predicted to regulate alternative splicing. Moreover, they also show high-density of binding to 3' untranslated regions suggesting they influence the transcriptome in diverse ways. We show that PTBP1 and PTBP3 are required in B cells beyond the immature cell stage to sustain transitional B cells and the B1, marginal zone and follicular B cell lineages. Therefore, PTBP1 and PTBP3 promote the maturation of quiescent B cells by regulating gene expression at the posttranscriptional level.
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Affiliation(s)
- Elisa Monzón-Casanova
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Kirsty J Bates
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
| | | | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, UK
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43
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Diaz-Muñoz MD, Osma-Garcia IC. The RNA regulatory programs that govern lymphocyte development and function. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1683. [PMID: 34327847 DOI: 10.1002/wrna.1683] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 05/25/2021] [Accepted: 07/08/2021] [Indexed: 12/16/2022]
Abstract
Lymphocytes require of constant and dynamic changes in their transcriptome for timely activation and production of effector molecules to combat external pathogens. Synthesis and translation of messenger (m)RNAs into these effector proteins is controlled both quantitatively and qualitatively by RNA binding proteins (RBPs). RBP-dependent regulation of RNA editing, subcellular location, stability, and translation shapes immune cell development and immunity. Extensive evidences have now been gathered from few model RBPs, HuR, PTBP1, ZFP36, and Roquin. However, recently developed methodologies for global characterization of protein:RNA interactions suggest the existence of complex RNA regulatory networks in which RBPs co-ordinately regulate the fate of sets of RNAs controlling cellular pathways and functions. In turn, RNA can also act as scaffolding of functionally related proteins modulating their activation and function. Here we review current knowledge about how RBP-dependent regulation of RNA shapes our immune system and discuss about the existence of a hidden immune cell epitranscriptome. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Manuel D Diaz-Muñoz
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
| | - Ines C Osma-Garcia
- Toulouse Institute for Infectious and Inflammatory Diseases, Inserm UMR1291, CNRS UMR5051, University Paul Sabatier, Toulouse, France
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Crosstalk between RNA-Binding Proteins and Immune Microenvironment Revealed Two RBP Regulatory Patterns with Distinct Immunophenotypes in Periodontitis. J Immunol Res 2021; 2021:5588429. [PMID: 34285922 PMCID: PMC8275429 DOI: 10.1155/2021/5588429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 06/10/2021] [Accepted: 06/15/2021] [Indexed: 02/05/2023] Open
Abstract
Periodontitis is an inflammatory disease whose pathogenesis is closely related with immunology. RNA-binding proteins (RBPs) were found to play crucial roles in immunity. Therefore, we aimed to investigate the potential impact of RBPs in the immune microenvironment in periodontitis. The differential expressions of RBPs in periodontitis and healthy samples were determined and were used to construct an RBP-based classifier for periodontitis using logistic regression. The correlations between RBPs and immune characteristics were investigated by the Spearman correlation. Unsupervised clustering was conducted to identify the RBP regulatory patterns. RBP-related genes were identified by WGCNA, while biological distinctions were revealed by GSVA and GO. 24 dysregulated RBPs were identified, from which a 12-RBP classifier was established to distinguish periodontitis with AUC of 0.942. Close protein-protein interactions and expression correlations were observed especially between SPATS2 and ISG20. ISG20 and ESRP1 were found to be highly correlated with immunocyte infiltration, immune signaling activation, and HLA expressions in periodontitis. Two distinct RBP regulatory patterns were identified with different immune and other biological characteristics in periodontitis. Our findings indicate a significant impact of RBPs in shaping the immune microenvironment in periodontitis, which might bring new insights into the understanding of immune mechanisms in the pathogenesis of periodontitis.
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Hu F, Lu J, Matheson LS, Díaz-Muñoz MD, Saveliev A, Turner M. ORFLine: a bioinformatic pipeline to prioritise small open reading frames identifies candidate secreted small proteins from lymphocytes. Bioinformatics 2021; 37:3152-3159. [PMID: 33970232 PMCID: PMC8504629 DOI: 10.1093/bioinformatics/btab339] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 03/25/2021] [Accepted: 04/30/2021] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION The annotation of small open reading frames (smORFs) of less than 100 codons (<300 nucleotides) is challenging due to the large number of such sequences in the genome. RESULTS In this study, we developed a computational pipeline, which we have named ORFLine, that stringently identifies smORFs and classifies them according to their position within transcripts. We identified a total of 5744 unique smORFs in datasets from mouse B and T lymphocytes and systematically characterized them using ORFLine. We further searched smORFs for the presence of a signal peptide, which predicted known secreted chemokines as well as novel micropeptides. Four novel micropeptides show evidence of secretion and are therefore candidate mediators of immunoregulatory functions. AVAILABILITY Freely available on the web at https://github.com/boboppie/ORFLine. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Fengyuan Hu
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Jia Lu
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Louise S Matheson
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Manuel D Díaz-Muñoz
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Alexander Saveliev
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
| | - Martin Turner
- Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Babraham Research Campus, Cambridge, CB22 3AT, United Kingdom
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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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Boyko A, Tsepkova P, Aleshin V, Artiukhov A, Mkrtchyan G, Ksenofontov A, Baratova L, Ryabov S, Graf A, Bunik V. Severe Spinal Cord Injury in Rats Induces Chronic Changes in the Spinal Cord and Cerebral Cortex Metabolism, Adjusted by Thiamine That Improves Locomotor Performance. Front Mol Neurosci 2021; 14:620593. [PMID: 33867932 PMCID: PMC8044794 DOI: 10.3389/fnmol.2021.620593] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/05/2021] [Indexed: 01/23/2023] Open
Abstract
Our study aims at developing knowledge-based strategies minimizing chronic changes in the brain after severe spinal cord injury (SCI). The SCI-induced long-term metabolic alterations and their reactivity to treatments shortly after the injury are characterized in rats. Eight weeks after severe SCI, significant mitochondrial lesions outside the injured area are demonstrated in the spinal cord and cerebral cortex. Among the six tested enzymes essential for the TCA cycle and amino acid metabolism, mitochondrial 2-oxoglutarate dehydrogenase complex (OGDHC) is the most affected one. SCI downregulates this complex by 90% in the spinal cord and 30% in the cerebral cortex. This is associated with the tissue-specific changes in other enzymes of the OGDHC network. Single administrations of a pro-activator (thiamine, or vitamin B1, 1.2 mmol/kg) or a synthetic pro-inhibitor (triethyl glutaryl phosphonate, TEGP, 0.02 mmol/kg) of OGDHC within 15–20 h after SCI are tested as protective strategies. The biochemical and physiological assessments 8 weeks after SCI reveal that thiamine, but not TEGP, alleviates the SCI-induced perturbations in the rat brain metabolism, accompanied by the decreased expression of (acetyl)p53, increased expression of sirtuin 5 and an 18% improvement in the locomotor recovery. Treatment of the non-operated rats with the OGDHC pro-inhibitor TEGP increases the p53 acetylation in the brain, approaching the brain metabolic profiles to those after SCI. Our data testify to an important contribution of the OGDHC regulation to the chronic consequences of SCI and their control by p53 and sirtuin 5.
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Affiliation(s)
- Alexandra Boyko
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Polina Tsepkova
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Vasily Aleshin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Artem Artiukhov
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Garik Mkrtchyan
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Alexander Ksenofontov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Lyudmila Baratova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Sergey Ryabov
- Russian Cardiology Research-and-Production Complex, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Anastasia Graf
- Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.,Faculty of Nano-, Bio-, Informational and Cognitive Technologies, Moscow Institute of Physics and Technology, Moscow, Russia
| | - Victoria Bunik
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.,Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.,Department of Biological Chemistry, Sechenov University, Moscow, Russia
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Ge L, Zhang Y, Zhao X, Wang J, Zhang Y, Wang Q, Yu H, Zhang Y, You Y. EIF2AK2 selectively regulates the gene transcription in immune response and histones associated with systemic lupus erythematosus. Mol Immunol 2021; 132:132-141. [PMID: 33588244 DOI: 10.1016/j.molimm.2021.01.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 01/21/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022]
Abstract
PKR, also known as EIF2AK2, is an IFN-stimulated gene (ISG) and shows a higher expression in probands with systemic lupus erythematosus (SLE), which is likely responsible for the impaired translational and proliferative responses to mitogens in T cells from SLE patients. In this study, we overexpressed EIF2AK2 in HeLa cells to study EIF2AK2-regulated genes using RNA-seq technology, followed by bioinformatic analysis of target genes of EIF2AK2-regulated transcriptional factors (TFs). Overexpression of EIF2AK2 promotes HeLa cell apoptosis. EIF2AK2 selectively represses the transcription of histone protein genes associated with SLE, immune response genes and TF genes, which was validated by RT-qPCR experiments. Analysis of motifs overrepresented in the promoter regions of EIF2AK2-regulated genes revealed eighteen EIF2AK2-regulated TFs involved in establishing the EIF2AK2 network. Eight out of these predicted EIF2AK2-regulated TFs were further verified by RT-qPCR selectively in both HeLa and Jurkat cells, and most such as HEY2, TFEC, BATF2, GATA3 and ATF3 and FOXO6 are known to regulate immune response. Our results suggest that the dsRNA-dependent kinase EIF2AK2 selectively regulates the transcription of immune response and SLE-associated histone protein genes, and such a selectivity is likely to be operated by EIF2AK2-targeted TFs. The EIF2AK2-TFs axis potentially offers new therapeutic targets for counteracting immunological disease in the future.
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Affiliation(s)
- Lan Ge
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
| | - Yuhong Zhang
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, Hubei 430075, China; Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Xingwang Zhao
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
| | - Juan Wang
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
| | - Yu Zhang
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Qi Wang
- Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Han Yu
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Yi Zhang
- Laboratory of Human Health and Genome Regulation, ABLife Inc., Wuhan, Hubei 430075, China; Center for Genome Analysis, ABLife Inc., Wuhan, Hubei 430075, China.
| | - Yi You
- Department of Dermatology, Southwest Hospital, Third Military Medical University(Army Medical University), Chongqing, 400038, China.
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Abstract
Posttranscriptional control of mRNA regulates various biological processes, including inflammatory and immune responses. RNA-binding proteins (RBPs) bind cis-regulatory elements in the 3' untranslated regions (UTRs) of mRNA and regulate mRNA turnover and translation. In particular, eight RBPs (TTP, AUF1, KSRP, TIA-1/TIAR, Roquin, Regnase, HuR, and Arid5a) have been extensively studied and are key posttranscriptional regulators of inflammation and immune responses. These RBPs sometimes collaboratively or competitively bind the same target mRNA to enhance or dampen regulatory activities. These RBPs can also bind their own 3' UTRs to negatively or positively regulate their expression. Both upstream signaling pathways and microRNA regulation shape the interactions between RBPs and target RNA. Dysregulation of RBPs results in chronic inflammation and autoimmunity. Here, we summarize the functional roles of these eight RBPs in immunity and their associated diseases.
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Affiliation(s)
- Shizuo Akira
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0874, Japan.,Department of Host Defense, Division of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0874, Japan;
| | - Kazuhiko Maeda
- Laboratory of Host Defense, WPI Immunology Frontier Research Center (IFReC), Osaka University, Osaka 565-0874, Japan.,Department of Host Defense, Division of Host Defense, Research Institute for Microbial Diseases (RIMD), Osaka University, Osaka 565-0874, Japan;
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Abstract
Metabolic pathways and redox reactions are at the core of life. In the past decade(s), numerous discoveries have shed light on how metabolic pathways determine the cellular fate and function of lymphoid and myeloid cells, giving rise to an area of research referred to as immunometabolism. Upon activation, however, immune cells not only engage specific metabolic pathways but also rearrange their oxidation-reduction (redox) system, which in turn supports metabolic reprogramming. In fact, studies addressing the redox metabolism of immune cells are an emerging field in immunology. Here, we summarize recent insights revealing the role of reactive oxygen species (ROS) and the differential requirement of the main cellular antioxidant pathways, including the components of the thioredoxin (TRX) and glutathione (GSH) pathways, as well as their transcriptional regulator NF-E2-related factor 2 (NRF2), for proliferation, survival and function of T cells, B cells and macrophages.
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Affiliation(s)
- Jonathan Muri
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland.
| | - Manfred Kopf
- Institute of Molecular Health Sciences, Department of Biology, ETH Zürich, Zürich, Switzerland.
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