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Xiang JS, Schafer DM, Rothamel KL, Yeo GW. Decoding protein-RNA interactions using CLIP-based methodologies. Nat Rev Genet 2024; 25:879-895. [PMID: 38982239 DOI: 10.1038/s41576-024-00749-3] [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: 05/21/2024] [Indexed: 07/11/2024]
Abstract
Protein-RNA interactions are central to all RNA processing events, with pivotal roles in the regulation of gene expression and cellular functions. Dysregulation of these interactions has been increasingly linked to the pathogenesis of human diseases. High-throughput approaches to identify RNA-binding proteins and their binding sites on RNA - in particular, ultraviolet crosslinking followed by immunoprecipitation (CLIP) - have helped to map the RNA interactome, yielding transcriptome-wide protein-RNA atlases that have contributed to key mechanistic insights into gene expression and gene-regulatory networks. Here, we review these recent advances, explore the effects of cellular context on RNA binding, and discuss how these insights are shaping our understanding of cellular biology. We also review the potential therapeutic applications arising from new knowledge of protein-RNA interactions.
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Affiliation(s)
- Joy S Xiang
- Division of Biomedical Sciences, UC Riverside, Riverside, CA, USA
| | - Danielle M Schafer
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Katherine L Rothamel
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Stem Cell Institute and Stem Cell Program, UC San Diego, La Jolla, CA, USA.
- Institute for Genomic Medicine, UC San Diego, La Jolla, CA, USA.
- Sanford Laboratories for Innovative Medicines, La Jolla, CA, USA.
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Aghighi A, Nakhaee A, Taheri M, Hashemi SM, Bahari G. Association of LIN28B Gene Polymorphisms (rs221634, rs221635, rs314276, rs9404590, and rs12194974) with Non-Hodgkin Lymphoma Susceptibility and Clinical/Pathological Features. Asian Pac J Cancer Prev 2023; 24:3867-3874. [PMID: 38019245 PMCID: PMC10772767 DOI: 10.31557/apjcp.2023.24.11.3867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 11/15/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND AND AIM Lymphoma is a common hematopoietic cancer. It has been proposed that LIN28B gene and its variations may have function in cancer progression and metastasis. Therefore, the purpose of this investigation has been to examine the correlation among LIN28B gene polymorphisms (such as rs221634 A>T, rs221635 T> C, rs314276 C>A, rs9404590 T>G, and rs12194974 G>A) as well as the risk of NHL in an Iranian sample. MATERIALS AND METHODS In the current case-control research, 175 individuals with Non-Hodgkin Lymphoma along with 175 normal controls participated; polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methodology has been utilized to the genotype samples. RESULTS Our data demonstrated that rs12194974 and the rs221635 variants have been correlated with higher NHL risk, while rs221634 and rs314276 variants were correlated with lower risk of NHL (P≤0.05). In addition, we detected an association between rs221634 and treatment with R-CHOP. No substantial correlation has discovered among rs9404590 polymorphism and NHL in any inheritance models (P≥0.05). CONCLUSION This was the first investigation evaluating the correlation among LIN28B gene polymorphisms as well as the occurrence of NLH. Further studies in different ethnic populations and large-scale sample size are needed to support results.
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Affiliation(s)
- Ali Aghighi
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Alireza Nakhaee
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Mohsen Taheri
- Genetics of Non- Communicable Disease Research Center, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Seyed-Mehdi Hashemi
- Clinical Immunology Research Center, Department of Internal Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Gholamreza Bahari
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran.
- Children and Adolescent Health Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan, Iran.
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Li J, Xiao Y, Yu H, Jin X, Fan S, Liu W. Mutual connected IL-6, EGFR and LIN28/Let7-related mechanisms modulate PD-L1 and IGF upregulation in HNSCC using immunotherapy. Front Oncol 2023; 13:1140133. [PMID: 37124491 PMCID: PMC10130400 DOI: 10.3389/fonc.2023.1140133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 03/28/2023] [Indexed: 05/02/2023] Open
Abstract
The development of techniques and immunotherapies are widely applied in cancer treatment such as checkpoint inhibitors, adoptive cell therapy, and cancer vaccines apart from radiation therapy, surgery, and chemotherapy give enduring anti-tumor effects. Minority people utilize single-agent immunotherapy, and most people adopt multiple-agent immunotherapy. The difficulties are resolved by including the biomarkers to choose the non-responders' and responders' potentials. The possibility of the potential complications and side effects are examined to improve cancer therapy effects. The Head and Neck Squamous Cell Carcinoma (HNSCC) is analyzed with the help of programmed cell death ligand 1 (PD-L1) and Insulin-like growth factor (IGF). But how IGF and PD-L1 upregulation depends on IL-6, EGFR, and LIN28/Let7-related mechanisms are poorly understood. Briefly, IL-6 stimulates gene expressions of IGF-1/2, and IL-6 cross-activates IGF-1R signaling, NF-κB, and STAT3. NF-κB, up-regulating PD-L1 expressions. IL-6/JAK1 primes PD-L1 for STT3-mediated PD-L1 glycosylation, stabilizes PD-L1 and trafficks it to the cell surface. Moreover, ΔNp63 is predominantly overexpressed over TAp63 in HNSCC, elevates circulating IGF-1 levels by repressing IGFBP3, and activates insulin receptor substrate 1 (IRS1).TP63 and SOX2 form a complex with CCAT1 to promote EGFR expression. EGFR activation through EGF binding extends STAT3 activation, and EGFR and its downstream signaling prolong PD-L1 mRNA half-life. PLC-γ1 binding to a cytoplasmic motif of elevated PD-L1 improves EGF-induced activation of inositol 1,4,5-tri-phosphate (IP3), and diacylglycerol (DAG) subsequently elevates RAC1-GTP. RAC1-GTP was convincingly demonstrated to induce the autocrine production and action of IL-6/IL-6R, forming a feedback loop for IGF and PD-L1 upregulation. Furthermore, the LIN28-Let7 axis mediates the NF-κB-IL-6-STAT3 amplification loop, activated LIN28-Let7 axis up-regulates RAS, AKT, IL-6, IGF-1/2, IGF-1R, Myc, and PD-L1, plays pivotal roles in IGF-1R activation and Myc, NF-κB, STAT3 concomitant activation. Therefore, based on a detailed mechanisms review, our article firstly reveals that IL-6, EGFR, and LIN28/Let7-related mechanisms mediate PD-L1 and IGF upregulation in HNSCC, which comprehensively influences immunity, inflammation, metabolism, and metastasis in the tumor microenvironment, and might be fundamental for overcoming therapy resistance.
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Affiliation(s)
- Junjun Li
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of The Xiangya School of Medicine, Central South University, Changsha, China
| | - Yazhou Xiao
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of The Xiangya School of Medicine, Central South University, Changsha, China
| | - Huayue Yu
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of The Xiangya School of Medicine, Central South University, Changsha, China
| | - Xia Jin
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of The Xiangya School of Medicine, Central South University, Changsha, China
| | - Songqing Fan
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of The Xiangya School of Medicine, Central South University, Changsha, China
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Wei Liu
- Department of Pathology, Hunan Cancer Hospital, The Affiliated Cancer Hospital of The Xiangya School of Medicine, Central South University, Changsha, China
- Department of Pathology, The Second Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Wei Liu,
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Åkerstrand H, Boldrin E, Montano G, Vanhee S, Olsson K, Krausse N, Vergani S, Cieśla M, Bellodi C, Yuan J. Enhanced protein synthesis is a defining requirement for neonatal B cell development. Front Immunol 2023; 14:1130930. [PMID: 37138883 PMCID: PMC10149930 DOI: 10.3389/fimmu.2023.1130930] [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: 12/23/2022] [Accepted: 03/21/2023] [Indexed: 05/05/2023] Open
Abstract
The LIN28B RNA binding protein exhibits an ontogenically restricted expression pattern and is a key molecular regulator of fetal and neonatal B lymphopoiesis. It enhances the positive selection of CD5+ immature B cells early in life through amplifying the CD19/PI3K/c-MYC pathway and is sufficient to reinitiate self-reactive B-1a cell output when ectopically expressed in the adult. In this study, interactome analysis in primary B cell precursors showed direct binding by LIN28B to numerous ribosomal protein transcripts, consistent with a regulatory role in cellular protein synthesis. Induction of LIN28B expression in the adult setting is sufficient to promote enhanced protein synthesis during the small Pre-B and immature B cell stages, but not during the Pro-B cell stage. This stage dependent effect was dictated by IL-7 mediated signaling, which masked the impact of LIN28B through an overpowering stimulation on the c-MYC/protein synthesis axis in Pro-B cells. Importantly, elevated protein synthesis was a distinguishing feature between neonatal and adult B cell development that was critically supported by endogenous Lin28b expression early in life. Finally, we used a ribosomal hypomorphic mouse model to demonstrate that subdued protein synthesis is specifically detrimental for neonatal B lymphopoiesis and the output of B-1a cells, without affecting B cell development in the adult. Taken together, we identify elevated protein synthesis as a defining requirement for early-life B cell development that critically depends on Lin28b. Our findings offer new mechanistic insights into the layered formation of the complex adult B cell repertoire.
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Affiliation(s)
- Hugo Åkerstrand
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Elena Boldrin
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Giorgia Montano
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Stijn Vanhee
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Karin Olsson
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Niklas Krausse
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Stefano Vergani
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Maciej Cieśla
- RNA and Stem Cell Biology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Cristian Bellodi
- RNA and Stem Cell Biology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
| | - Joan Yuan
- Developmental Immunology Unit, Department of Molecular Hematology, Lund Stem Cell Center, Lund University, Lund, Sweden
- *Correspondence: Joan Yuan,
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Sirt6 inhibits vascular endothelial cell pyroptosis by regulation of the Lin28b/let-7 pathway in atherosclerosis. Int Immunopharmacol 2022; 110:109056. [DOI: 10.1016/j.intimp.2022.109056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/03/2022] [Accepted: 07/11/2022] [Indexed: 11/24/2022]
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LIN28B inhibition sensitizes cells to p53-restoring PPI therapy through unleashed translational suppression. Oncogenesis 2022; 11:37. [PMID: 35780125 PMCID: PMC9250532 DOI: 10.1038/s41389-022-00412-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 06/16/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022] Open
Abstract
p53 is the most highly mutated tumor suppressor across multiple types of human cancers. The level and function of p53 are fine-tuned through multifaced mechanisms in which the protein–protein interaction between p53 and MDM2 is considered as a major circuit. Recent studies suggest therapeutic strategy attempts to restore p53 function by small molecule inhibitors targeting p53–MDM2 interaction can be a promising direction in treating cancers with wild-type or functional p53. Currently, clinical tests of the p53–MDM2 protein–protein interaction inhibitors (PPIs) are underway. However, it remains elusive about the biomarkers that may predict the therapeutic responses to those inhibitors. Here we report that RNA-binding protein LIN28B directly regulates p53 through binding to the 5′΄ untranslated region of p53 mRNA and blocks its translation by competing with a translation enhancer protein, ribosomal protein L26 (RPL26). This regulatory mechanism of LIN28B does not involve let-7 maturation or the canonical protein turnover pathway of p53. Furthermore, we show that inhibition of LIN28B unleashes the translational suppression of p53 through RPL26, and leads to enhanced sensitivities of cancer cells to inhibitors of p53–MDM2 interaction. Together, we demonstrate a competitive regulatory mechanism of p53 by LIN28B, which has important implications in developing biomarkers to the therapies aiming to reinstate p53 function.
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