1
|
PerezGrovas-Saltijeral A, Stones J, Orji OC, Shaker H, Knight HM. Modification of the RNA methylome in neurodevelopmental disorders. Curr Opin Genet Dev 2025; 92:102330. [PMID: 40080918 DOI: 10.1016/j.gde.2025.102330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 02/05/2025] [Accepted: 02/19/2025] [Indexed: 03/15/2025]
Abstract
RNA metabolism is fundamental to protein synthesis, degradation and transport of molecules. Methylation of RNA influences the processing of mRNA, noncoding RNA, tRNA and rRNA. Here, we review accumulating evidence that disruption to the RNA methylome impairs developmental processes and causes neurodevelopmental conditions. We first describe mutated RNA methylation effector protein genes that give rise to neurodevelopmental syndromes. We consider the biological processes thereby disrupted, including translational dynamics at cytoplasmic and mt-ribosomes, synaptic function, energy production and cellular stress. Finally, we discuss novel forms of methylated RNA, such as R-loops and circular RNAs, which may contribute to disease processes. These findings herald an exciting new era to brain research and highlight the significant potential of manipulating the RNA methylome as a therapeutic target in the treatment of neurodevelopmental disorders.
Collapse
Affiliation(s)
| | - Joseph Stones
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Oliver C Orji
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Hala Shaker
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Helen M Knight
- Division of Cells, Organisms and Molecular Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK.
| |
Collapse
|
2
|
Chen S, Wen JT, Zhang S, Wang JL, Yuan J, Bao HJ, Chen X, Zhao Y. SNORD9 promotes ovarian cancer tumorigenesis via METTL3/IGF2BP2-mediated NFYA m6A modification and is a potential target for antisense oligonucleotide therapy. Life Sci 2025; 368:123527. [PMID: 40044032 DOI: 10.1016/j.lfs.2025.123527] [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: 11/25/2024] [Revised: 02/17/2025] [Accepted: 03/01/2025] [Indexed: 03/15/2025]
Abstract
C/D box small nucleolar noncoding RNAs (snoRNAs) are known to bind and induce 2'-O-ribose methylation of RNAs, participate in cancer tumorigenesis and development. However, their involvement in regulating m6A modification remains unreported. Analysis of the TCGA database revealed that SNORD9 was an unfavorable prognostic factor for ovarian cancer. Besides, SNORD9 was elevated in ovarian cancer. The overexpression of SNORD9 induced ovarian cancer cell proliferation and migration in vitro and induce tumorigenicity in vivo, increased the m6A modification level by binding to m6A-methyltransferase METTL3 to affect NFYA m6A modification; besides, m6A-reader IGF2BP2 was 2'-O-methylated by SNORD9, thereby affect NFYA mRNA stability, upregulate NFYA and its downstream proteins CCND1, CDK4 and VEGFA, promote ovarian cancer tumorigenesis. ASO-mediated silencing of SNORD9 suppressed tumorigenicity both in vitro and in vivo, and effectively inhibited the growth of patient-derived organoids of ovarian cancer (OC-PDO). In conclusions, we demonstrated for the first time that SNORD9 induces NFYA m6A methylation by binding to m6A methylase METTL3; modifying IGF2BP2 mRNA by 2'-O-methylation and improve NFYA mRNA stability, thus promote the tumorigenesis of ovarian cancer. Targeting ASO to SNORD9 may have efficacy in the treatment of ovarian cancer.
Collapse
Affiliation(s)
- Shuo Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China
| | - Jing-Tao Wen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China
| | - Song Zhang
- Department of Thoracic Surgery, The First Hospital of China Medical University, Shenyang 110001, China
| | - Jie-Lin Wang
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China
| | - Jing Yuan
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China
| | - Hai-Juan Bao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China
| | - Xi Chen
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China
| | - Yang Zhao
- Department of Obstetrics and Gynecology, Department of Gynecologic Oncology Research Office; Guangzhou Key Laboratory of Targeted Therapy for Gynecologic Oncology; Guangdong Provincial Key Laboratory of Major Obstetric Diseases; Guangdong Provincial Clinical Research Center for Obstetrics and Gynecology; Guangdong-Hong Kong-Macao Greater Bay Area Higher Education Joint Laboratory of Maternal-Fetal Medicine; The Third Affiliated Hospital, Guangzhou Medical University, Guangzhou 510150, China; Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang 110042, China.
| |
Collapse
|
3
|
Li X, Guo W, Wen Y, Meng C, Zhang Q, Chen H, Zhao X, Wu B. Structural basis for the RNA binding properties of mouse IGF2BP3. Structure 2025; 33:771-785.e3. [PMID: 39986276 DOI: 10.1016/j.str.2025.01.022] [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: 07/19/2024] [Revised: 01/11/2025] [Accepted: 01/28/2025] [Indexed: 02/24/2025]
Abstract
IGF2BP family proteins (IGF2BPs) contain six tandem RNA-binding domains (RBDs), resulting in highly complex RNA binding properties. Dissecting how IGF2BPs recognize their RNA targets is essential for understanding their regulatory roles in gene expression. Here, we have determined the crystal structures of mouse IGF2BP3 constructs complexed with different RNA substrates. Our structures reveal that the IGF2BP3-RRM12 domains can recognize CA-rich elements up to 5-nt in length, mainly through RRM1. We also captured the antiparallel RNA-binding mode of the IGF2BP3-KH12 domains, with five nucleotides bound by KH1 and two nucleotides bound by KH2. Furthermore, our structural and biochemical studies suggest that the IGF2BP3-KH12 domains could recognize the "zipcode" RNA element within the β-actin mRNA. Finally, we analyzed the similarities and differences of the RNA-binding properties between the KH12 and KH34. Our studies provide structural insights into RNA target recognition by mouse IGF2BP3.
Collapse
Affiliation(s)
- Xiaojia Li
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; Department of Obstetrics and Gynecology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Wenting Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Yan Wen
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China; Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Chunyan Meng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China
| | - Qingrong Zhang
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Haitao Chen
- School of Public Health (Shenzhen), Sun Yat-Sen University, Shenzhen 518107, China
| | - Xiaomiao Zhao
- Department of Reproductive Medicine, Department of Obstetrics and Gynecology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
| | - Baixing Wu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou 510120, China.
| |
Collapse
|
4
|
Chen P, Lin L, Lin X, Liao K, Qiang J, Wang Z, Wu J, Li Y, Yang L, Yao N, Song H, Hong Y, Liu WH, Zhang Y, Chang X, Du D, Xiao C. A Csde1-Strap complex regulates plasma cell differentiation by coupling mRNA translation and decay. Nat Commun 2025; 16:2906. [PMID: 40133358 PMCID: PMC11937441 DOI: 10.1038/s41467-025-58212-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 03/13/2025] [Indexed: 03/27/2025] Open
Abstract
Upon encountering antigens, B cells may undergo multiple differentiation paths, including becoming plasma cells and memory B cells. Although it is well-known that transcription factors govern gene expression programs underpinning these fate decisions in transcriptional level, the role of post-transcriptional regulators, with a focus on RNA-binding proteins, in the fate determination are lesser known. Here we find by RNA interactome capture-coupled CRISPR/Cas9 functional screening that the Csde1-Strap complex plays an important role in plasma cell differentiation. Mechanistically, the Csde1-Strap complex establishes the expression kinetics of Bach2, a key regulator of plasma cell differentiation. Bach2 expression is rapidly induced to promote B cell expansion and then decreased to initiate plasma cell differentiation. The Csde1-Strap interaction is critical for their binding to Bach2 mRNA to couple its decay with translation to restrain the magnitude and duration of Bach2 protein expression. In the absence of Csde1 or Strap, Bach2 translation is de-coupled from mRNA decay, leading to elevated and prolonged expression of Bach2 protein and impaired plasma cell differentiation. This study thus establishes the functional RBP landscape in B cells and illustrates the fundamental importance of controlling protein expression kinetics in cell fate determination.
Collapse
Affiliation(s)
- Pengda Chen
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Lianghua Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Xinyong Lin
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Kunyu Liao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Jiali Qiang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Zhizhang Wang
- Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, China
| | - Jianfeng Wu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yang Li
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Liang Yang
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Nan Yao
- Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China
| | - Huilin Song
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Yazhen Hong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China
| | - Wen-Hsien Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Yaoyang Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China.
| | - Xing Chang
- Hangzhou First People's Hospital, School of Medicine, Westlake University, Hangzhou, China.
| | - Dan Du
- State Key Laboratory of Cellular Stress Biology, Department of Gastroenterology, Zhongshan Hospital of Xiamen University, School of Medicine, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China.
| | - Changchun Xiao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, China.
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
| |
Collapse
|
5
|
Aljouda NA, Shrestha D, DeVaux C, Olsen RR, Alleboina S, Walker M, Cheng Y, Freeman KW. Transcription factor 4 is a key mediator of oncogenesis in neuroblastoma by promoting MYC activity. Mol Oncol 2025; 19:808-824. [PMID: 39119816 PMCID: PMC11887674 DOI: 10.1002/1878-0261.13714] [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: 06/25/2024] [Accepted: 07/26/2024] [Indexed: 08/10/2024] Open
Abstract
Super-enhancer-associated transcription factor networks define cell identity in neuroblastoma (NB). Dysregulation of these transcription factors contributes to the initiation and maintenance of NB by enforcing early developmental identity states. We report that the class I basic helix-loop-helix (bHLH) transcription factor 4 (TCF4; also known as E2-2) is a critical NB dependency gene that significantly contributes to these identity states through heterodimerization with cell-identity-specific bHLH transcription factors. Knockdown of TCF4 significantly induces apoptosis in vitro and inhibits tumorigenicity in vivo. We used genome-wide expression profiling, TCF4 chromatin immunoprecipitation sequencing (ChIP-seq) and TCF4 immunoprecipitation-mass spectrometry to determine the role of TCF4 in NB cells. Our results, along with recent findings in NB for the transcription factors T-box transcription factor TBX2, heart- and neural crest derivatives-expressed protein 2 (HAND2) and twist-related protein 1 (TWIST1), propose a role for TCF4 in regulating forkhead box protein M1 (FOXM1)/transcription factor E2F-driven gene regulatory networks that control cell cycle progression in cooperation with N-myc proto-oncogene protein (MYCN), TBX2, and the TCF4 dimerization partners HAND2 and TWIST1. Collectively, we showed that TCF4 promotes cell proliferation through direct transcriptional regulation of the c-MYC/MYCN oncogenic program that drives high-risk NB. Mechanistically, our data suggest the novel finding that TCF4 acts to support MYC activity by recruiting multiple factors known to regulate MYC function to sites of colocalization between critical NB transcription factors, TCF4 and MYC oncoproteins. Many of the TCF4-recruited factors are druggable, giving insight into potential therapies for high-risk NB. This study identifies a new function for class I bHLH transcription factors (e.g., TCF3, TCF4, and TCF12) that are important in cancer and development.
Collapse
Affiliation(s)
- Nour A. Aljouda
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTNUSA
| | - Dewan Shrestha
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTNUSA
- Department of HematologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Chelsea DeVaux
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTNUSA
| | - Rachelle R. Olsen
- Department of Oncological SciencesHuntsman Cancer InstituteSalt Lake CityUTUSA
| | - Satyanarayana Alleboina
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTNUSA
| | - Megan Walker
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTNUSA
| | - Yong Cheng
- Department of HematologySt. Jude Children's Research HospitalMemphisTNUSA
| | - Kevin W. Freeman
- Department of Genetics, Genomics and InformaticsUniversity of Tennessee Health Science CenterMemphisTNUSA
| |
Collapse
|
6
|
Schott A, Simon T, Müller S, Rausch A, Busch B, Glaß M, Misiak D, Dipto M, Elrewany H, Peters L, Tripathee S, Ghazy E, Müller F, Rolnik R, Lederer M, Hmedat A, Vetter M, Wallwiener M, Sippl W, Hüttelmaier S, Bley N. The IGF2BP1 oncogene is a druggable m 6A-dependent enhancer of YAP1-driven gene expression in ovarian cancer. NAR Cancer 2025; 7:zcaf006. [PMID: 40008228 PMCID: PMC11850222 DOI: 10.1093/narcan/zcaf006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2024] [Revised: 02/02/2025] [Accepted: 02/13/2025] [Indexed: 02/27/2025] Open
Abstract
The Hippo/YAP1 signaling pathway regulates normal development by controlling contact inhibition of growth. In cancer, YAP1 activation is often dysregulated, leading to excessive tumor growth and metastasis. SRC kinase can cross talk to Hippo signaling by disrupting adherens junctions, repressing the Hippo cascade, or activating YAP1 to promote proliferation. Here, we demonstrate that the IGF2 messenger RNA-binding protein 1 (IGF2BP1) impedes the repression of YAP1 by Hippo signaling in carcinomas. IGF2BP1 stabilizes the YAP1 messenger RNA (mRNA) and enhances YAP1 protein synthesis through an m6A-dependent interaction with the 3' untranslated region of the YAP1 mRNA, thereby increasing YAP1/TAZ-driven transcription to bypass contact inhibition of tumor cell growth. Inhibiting IGF2BP1-mRNA binding using BTYNB reduces YAP1 levels and transcriptional activity, leading to significant growth inhibition in carcinoma cells and ovarian cancer organoids. In contrast, SRC inhibition with Saracatinib fails to inhibit YAP1/TAZ-driven transcription and cell growth in general. This is particularly significant in de-differentiated, rather mesenchymal carcinoma-derived cells, which exhibit high IGF2BP1 and YAP1 expression, rendering them less reliant on SRC-directed growth stimulation. In such invasive carcinoma models, the combined inhibition of SRC, IGF2BP1, and YAP1/TAZ proved superior over monotherapies. These findings highlight the therapeutic potential of targeting IGF2BP1, a key regulator of oncogenic transcription networks.
Collapse
Affiliation(s)
- Annekatrin Schott
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Theresa Simon
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Simon Müller
- New York Genome Center, 10013 New York, NY, United States; Department of Biology, New York University, 10003 New York, NY, United States
| | - Alexander Rausch
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Bianca Busch
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Markus Glaß
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Danny Misiak
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Mohammad Dipto
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Hend Elrewany
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Lara Meret Peters
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Sunita Tripathee
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Ehab Ghazy
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, 01620 Halle (Saale), Germany
| | - Florian Müller
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Robin Benedikt Rolnik
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Marcell Lederer
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Ali Hmedat
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, 21163 Irbid, Jordan
| | - Martina Vetter
- Department of Gynecology, University Hospital, Martin Luther University Halle-Wittenberg, Ernst-Grube-Straße 40, 01620 Halle (Saale), Germany
| | - Markus Wallwiener
- Department of Gynecology, University Hospital, Martin Luther University Halle-Wittenberg, Ernst-Grube-Straße 40, 01620 Halle (Saale), Germany
| | - Wolfgang Sippl
- Department of Pharmaceutical Chemistry and Bioanalytics, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Straße 3, 01620 Halle (Saale), Germany
| | - Stefan Hüttelmaier
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Nadine Bley
- Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| |
Collapse
|
7
|
Lee JY, Huang N, Samuels TJ, Davis I. Imp/IGF2BP and Syp/SYNCRIP temporal RNA interactomes uncover combinatorial networks of regulators of Drosophila brain development. SCIENCE ADVANCES 2025; 11:eadr6682. [PMID: 39919181 PMCID: PMC11804933 DOI: 10.1126/sciadv.adr6682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2024] [Accepted: 01/07/2025] [Indexed: 02/09/2025]
Abstract
Temporal patterning of neural progenitors is an evolutionarily conserved mechanism generating neural diversity. In Drosophila, postembryonic neurogenesis requires the RNA binding proteins (RBPs) Imp/IGF2BP and Syp/SYNCRIP. However, how they coachieve their function is not well understood. Here, we elucidate the in vivo temporal RNA interactome landscapes of Imp and Syp during larval brain development. Imp and Syp bind a highly overlapping set of conserved mRNAs encoding proteins involved in neurodevelopment. We identify transcripts differentially occupied by Imp/Syp over time, featuring a network of known and previously unknown candidate temporal regulators that are post-transcriptionally regulated by Imp/Syp. Furthermore, the physical and coevolutionary relationships between Imp and Syp binding sites reveal a combinatorial, rather than competitive, mode of molecular interplay. Our study establishes an in vivo framework for dissecting the temporal coregulation of RBP networks as well as providing a resource for understanding neural fate specification.
Collapse
Affiliation(s)
- Jeffrey Y. Lee
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| | - Niles Huang
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
| | - Tamsin J. Samuels
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EL, UK
| | - Ilan Davis
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
- Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
| |
Collapse
|
8
|
Jia H, Zhang L. tRNA-derived small RNAs in disease immunity. Theranostics 2025; 15:245-257. [PMID: 39744232 PMCID: PMC11667222 DOI: 10.7150/thno.102650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2024] [Accepted: 11/08/2024] [Indexed: 01/11/2025] Open
Abstract
Recently, members of a unique species of non-coding RNA, known as transfer RNA-derived small RNAs (tsRNAs) have been reported to serve multiple molecular functions, including in cells that mediate immunity. Because of their low molecular weights, tsRNAs were previously difficult to detect and were thus overlooked, until now. In this review, we delve into the biogenesis of tsRNAs and their diverse biological functions, ranging from transcriptional regulation to modulation of mRNA translation. We highlight the current evidence demonstrating their involvement in the immune response, as well as how tsRNAs modulate immunity to influence tumor growth and spread, autoimmune disease pathology and infection by pathogens. We surmise that tsRNAs are likely informative as diagnostic markers of cellular homeostasis and disease, and that therapeutic targeting of tsRNAs could be beneficial for a range of human diseases. Improved knowledge on the functions for tsRNAs in the mammalian immune system will enable us to leverage tsRNAs for their effective clinical use as treatments for human health challenges.
Collapse
Affiliation(s)
- Hongyuan Jia
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Linling Zhang
- Department of Respiratory and Critical Care, Chengdu Third People's Hospital, Chengdu, China
| |
Collapse
|
9
|
Xu J, Wang Y, Ren L, Li P, Liu P. IGF2BP1 promotes multiple myeloma with chromosome 1q gain via increasing CDC5L expression in an m 6A-dependent manner. Genes Dis 2025; 12:101214. [PMID: 39534570 PMCID: PMC11554607 DOI: 10.1016/j.gendis.2024.101214] [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: 07/09/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 11/16/2024] Open
Abstract
Multiple myeloma (MM) patients with chromosome 1q gain (1q+) are clinically and biologically heterogeneous. The underlying molecular mechanisms are still under investigation, while the identification of targets for effective therapy of this subgroup of MM patients is urgently needed. We aimed to investigate the clinical significance and the regulatory mechanisms of insulin-like growth factor 2 messenger RNA (mRNA) binding protein 1 (IGF2BP1), a N6-methyladenosine (m6A) reader, in MM patients with 1q+. We found that MM patients with 1q+ exhibit a significantly higher level of IGF2BP1 mRNA than controls, while higher IGF2BP1 expression predicted a worse prognosis in MM patients with 1q+. IGF2BP1 overexpression promoted cell proliferation and G1-to-S phase transition of the cell cycle in NCI-H929 cells. Through comprehensive in silico analyses of existing public datasets and in-house generated high-throughput sequencing datasets, along with in vitro experiments, we identified CDC5L as a target of IGFBP1, which can bind to the m6A sites of CDC5L mRNA to up-regulate its protein abundance. Higher CDC5L expression also predicted a worse prognosis of MM patients with 1q+. Moreover, both knockdown and mutation of CDC5L attenuated the pro-proliferative effect of IGF2BP1. Furthermore, IGF2BP1 inhibitor BTYNB effectively inhibited CDC5L expression in MM cells with 1q+ and suppressed the proliferation of these cells in vitro and in vivo. Therefore, IGF2BP1 acts as a post-transcriptional enhancer of CDC5L in an m6A-dependent manner to promote the proliferation of MM cells with 1q+. Our work identified a novel IGF2BP1-CDC5L axis and provided new insight into developing targeted therapeutics for MM patients with 1q+.
Collapse
Affiliation(s)
- Jiadai Xu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Yawen Wang
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Liang Ren
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Panpan Li
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| | - Peng Liu
- Department of Hematology, Zhongshan Hospital, Fudan University, Shanghai 200030, China
- Cancer Center, Zhongshan Hospital, Fudan University, Shanghai 200030, China
| |
Collapse
|
10
|
Luo C, Xu X, Zhao C, Wang Q, Wang R, Lang D, Zhang J, Hu W, Mu Y. Insight Into Body Size Evolution in Aves: Based on Some Body Size-Related Genes. Integr Zool 2024. [PMID: 39663511 DOI: 10.1111/1749-4877.12927] [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: 04/01/2024] [Revised: 09/21/2024] [Accepted: 10/31/2024] [Indexed: 12/13/2024]
Abstract
Birds exhibit remarkable variations in body size, making them an ideal group for the study of adaptive evolution. However, the genetic mechanisms underlying body size evolution in avian species remain inadequately understood. This study investigates the evolutionary patterns of avian body size by analyzing 15 body-size-related genes, including GHSR, IGF2BP1, and IGFBP7 from the growth hormone/insulin-like growth factor axis, EIF2AK3, GALNS, NCAPG, PLOD1, and PLAG1 associated with tall stature, and ACAN, OBSL1, and GRB10 associated with short stature, four genes previously reported in avian species: ATP11A, PLXDC2, TNS3, and TUBGCP3. The results indicate significant adaptive evolution of body size-related genes across different avian lineages. Notably, in the IGF2BP1 gene, a significant positive correlation was observed between the evolutionary rate and body size, suggesting that larger bird species exhibit higher evolutionary rates of the IGF2BP1 gene. Furthermore, the IGFBP7 and PLXDC2 genes demonstrated accelerated evolution in large- and medium-sized birds, respectively, indicating distinct evolutionary patterns for these genes among birds of different sizes. The branch-site model analysis identified numerous positively selected sites, primarily concentrated near functional domains, thereby reinforcing the critical role of these genes in body size evolution. Interestingly, extensive convergent evolution was detected in lineages with larger body sizes. This study elucidates the genetic basis of avian body size evolution for the first time, identifying adaptive evolutionary patterns of body size-related genes across birds of varying sizes and documenting patterns of convergent evolution. These findings provide essential genetic data and novel insights into the adaptive evolution of body size in birds.
Collapse
Affiliation(s)
- Chaoyang Luo
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Xionghui Xu
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Chengfa Zhao
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Qiuping Wang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Rongxing Wang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
| | - Datian Lang
- Department of Agronomy and Life Science, Zhaotong University, Zhaotong, Yunnan, China
| | - Juan Zhang
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Key Laboratory of Ecological Adaptive Evolution and Conservation on Animals-Plants in Southwest Mountain Ecosystem of Yunnan Province Higher Institutes College, School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, China
| | - Wenxian Hu
- Erhai Watershed Ecological Environment Quality Testing Engineering Research Center of Yunnan Provincial Universities, Erhai Research Institute, West Yunnan University of Applied Sciences, Dali, Yunnan, China
| | - Yuan Mu
- Institute of Eastern-Himalaya Biodiversity Research, Dali University, Dali, Yunnan, China
- Collaborative Innovation Center for Biodiversity and Conservation in the Three Parallel Rivers Region of China, Dali, Yunnan, China
| |
Collapse
|
11
|
Sreelekshmi PK, Pooja SK, Vidya N, Sinosh S, Thejaswini V. Integrative Investigation of Flavonoids Targeting YBX1 Protein-Protein Interaction Network in Breast Cancer: From Computational Analysis to Experimental Validation. Mol Biotechnol 2024:10.1007/s12033-024-01311-6. [PMID: 39565541 DOI: 10.1007/s12033-024-01311-6] [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: 07/15/2024] [Accepted: 10/17/2024] [Indexed: 11/21/2024]
Abstract
Y-box-binding protein 1 (YBX1) is a multifunctional oncoprotein with its nuclear localization contributing to chemo-resistance in breast cancer. Through its interactions with various proteins and lncRNAs, YBX1 promotes cancer cell migration, invasion, and metastasis. Despite its significant role in cancer progression, studies on YBX1's protein-protein interactions (PPIs) remain limited. Flavonoids are natural compounds with anticancer properties that inhibit metastasis, modulate immunity, and induce apoptosis, with minimal systemic toxicity, making them strong candidates for cancer therapy. Targeting PPIs offers a promising approach for cancer therapy and flavonoids, with their anticancer properties, may modulate these interactions. Our study focused on the YBX1 PPI network, specifically targeting HSPA1A, IGF2BP1, MECP2, G3BP1, EWSR1, PURA, and SYNCRIP. We selected four flavonoids Quercetin, Fisetin, Rutin, and Myricitrin based on literature and conducted 26 docking sessions. Further ADMET analysis indicated Quercetin and Fisetin as more favorable for drug-likeness parameters than Rutin and Myricitrin, which was underscored by MD simulation data. In vitro studies showed that Quercetin and Fisetin downregulated YBX1 expression in a dose-dependent manner (50 μM to 150 μM) in MCF-7 cells. Our study provides a preliminary understanding of YBX1 PPI and the potential of flavonoids to disrupt these interactions. This study investigates the potential of flavonoids to target YBX1 PPIs, providing insights into novel therapeutic strategies for YBX1-driven cancers.
Collapse
Affiliation(s)
- Presanna Kumar Sreelekshmi
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Periye, Kasargod, Kerala, 671320, India
| | - Suresh Kumar Pooja
- Department of Biotechnology, RV College of Engineering 560059, Affiliated to Visvesvaraya Technological University, Belagavi, 590018, Karnataka, India
| | - Niranjan Vidya
- Department of Biotechnology, RV College of Engineering 560059, Affiliated to Visvesvaraya Technological University, Belagavi, 590018, Karnataka, India
| | - Skariyachan Sinosh
- Department of Microbiology, St. Pius X College, Rajapuram, Kasargod, Kerala, India
| | - Venkatesh Thejaswini
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Periye, Kasargod, Kerala, 671320, India.
| |
Collapse
|
12
|
Ritter AJ, Draper JM, Vollmers C, Sanford JR. Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation. Genome Res 2024; 34:2000-2011. [PMID: 38839373 PMCID: PMC11610577 DOI: 10.1101/gr.279170.124] [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: 02/20/2024] [Accepted: 05/21/2024] [Indexed: 06/07/2024]
Abstract
Alternative splicing (AS) alters the cis-regulatory landscape of mRNA isoforms, leading to transcripts with distinct localization, stability, and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome association, we generated subcellular fractionation and sequencing (Frac-seq) libraries using both conventional short reads and long reads from human embryonic stem cells (ESCs) and neural progenitor cells (NPCs) derived from the same ESCs. We performed de novo transcriptome assembly from high-confidence long reads from cytosolic, monosomal, light, and heavy polyribosomal fractions and quantified their abundance using short reads from their respective subcellular fractions. Thousands of transcripts in each cell type exhibited association with particular subcellular fractions relative to the cytosol. Of the multi-isoform genes, 27% and 19% exhibited significant differential isoform sedimentation in ESCs and NPCs, respectively. Alternative promoter usage and internal exon skipping accounted for the majority of differences between isoforms from the same gene. Random forest classifiers implicated coding sequence (CDS) and untranslated region (UTR) lengths as important determinants of isoform-specific sedimentation profiles, and motif analyses reveal potential cell type-specific and subcellular fraction-associated RNA-binding protein signatures. Taken together, our data demonstrate that alternative mRNA processing within the CDS and UTRs impacts the translational control of mRNA isoforms during stem cell differentiation, and highlight the utility of using a novel long-read sequencing-based method to study translational control.
Collapse
Affiliation(s)
- Alexander J Ritter
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Jolene M Draper
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA
| | - Jeremy R Sanford
- Department of Molecular, Cell, and Developmental Biology and Center for Molecular Biology of RNA, University of California Santa Cruz, Santa Cruz, California 95064, USA
| |
Collapse
|
13
|
Zhang X, Yan W, Jin H, Yu B, Zhang H, Ding B, Chen X, Zhang Y, Xia Q, Meng D, Hu J, Liu H, Nie Y, Liu F, Zheng Y, Lu Y, Wang J, Du M, Wang M, Yu EYW, Li X, Wang S. Transcriptional and post-transcriptional regulation of CARMN and its anti-tumor function in cervical cancer through autophagic flux blockade and MAPK cascade inhibition. J Exp Clin Cancer Res 2024; 43:305. [PMID: 39558374 PMCID: PMC11575122 DOI: 10.1186/s13046-024-03229-y] [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: 08/13/2024] [Accepted: 11/07/2024] [Indexed: 11/20/2024] Open
Abstract
BACKGROUND LncRNAs play essential roles in multiple tumors. However, research on genome-wide lncRNA alterations and their functions in cervical cancer (CC) is limited. This study aims to explore key lncRNAs in CC progression and uncover the molecular mechanisms involved in the development of CC. METHODS In this study, we analyzed 30 tissues from CC, cervical intraepithelial neoplasia (CIN), and normal (NOR) using transcriptome sequencing and weighted gene co-expression network analysis to establish gene modules related to the NOR-CIN-CC transition. Machine learning diagnostic models were employed to investigate the role of lncRNAs in this transition. Molecular biological experiments were conducted to elucidate the potential mechanisms of CARMN in CC, with a particular focus on its transcriptional and post-transcriptional regulation of abnormal expression in CC. RESULTS CARMN was identified as a hub gene in two modules significantly associated with the NOR-CIN-CC transition. Analysis using ten machine learning models confirmed its critical role in this progression. The results of RNA-seq, qPCR and RNAScope performed in another cohort of 83 cervical tissues all showed that CARMN was significantly downregulated in CC. CARMN significantly enhanced the interaction between Keap1 and Nrf2, leading to increased ROS levels. The elevated ROS levels suppressed the Akt/mTOR signaling pathway, leading to autophagy arrest via autophagic flux blockade. Additionally, CARMN interacted with TFAP2α to repress MAPK13 transcription, further inhibiting the MAPK cascade. A promoter SNP (rs12517403) was found to increase CC risk (OR = 1.34, 95% CI = 1.11-1.61) and reduce CARMN expression by decreasing SP1 binding. Furthermore, the RNA binding proteins that could modulate CARMN RNA stability were also determined using RNA-pulldown assay. The results demonstrated that YBX1, a component of the coding region instability determinant (CRD)-mediated mRNA stabilization complex, promoted CARMN RNA stability. DHX9, another component of complex, acted as a scaffold to bridge YBX1 and CARMN. CONCLUSIONS CARMN exerts an anti-cancer effect in CC progression by inhibiting the Akt-mTOR and MAPK signaling pathways. rs12517403 and the YBX1/DHX9 complex are key mechanisms influencing its transcription and stability in CC cells. CARMN represents a promising biomarker for CC diagnosis and therapeutic target.
Collapse
Affiliation(s)
- Xing Zhang
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Wenjing Yan
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Hua Jin
- Clinical Laboratory, Affiliated Tumor Hospital of Nantong University (Nantong Tumor Hospital), Nantong, China
| | - Bingjia Yu
- School of Health Management and Basic Science, Jiangsu Health Vocational College, Nanjing, China
| | - Hao Zhang
- School of Biological Sciences & Medical Engineering, Southeast University, Nanjing, China
| | - Bo Ding
- Department of Gynecology and Obstetrics, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Xue Chen
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Yan Zhang
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
- School of Medicine, Shihezi University, Xinjiang, China
| | - Qianqian Xia
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Dan Meng
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Jing Hu
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Haohan Liu
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Yamei Nie
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Fengying Liu
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Yun Zheng
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Yiran Lu
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China
| | - Juan Wang
- Clinical Laboratory, Affiliated Tumor Hospital of Nantong University (Nantong Tumor Hospital), Nantong, China
| | - Mulong Du
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, Nanjing Medical University, Nanjing, China
| | - Evan Yi-Wen Yu
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China.
| | - Xiuting Li
- School of Health Management and Basic Science, Jiangsu Health Vocational College, Nanjing, China.
| | - Shizhi Wang
- Key Laboratory of Environmental Medicine Engineering, School of Public Health, Ministry of Education, Southeast University, No. 87 Dingjiaqiao, Gulou District, Nanjing, China.
| |
Collapse
|
14
|
Karlström V, Sagredo E, Planells J, Welinder C, Jungfleisch J, Barrera-Conde A, Engfors L, Daniel C, Gebauer F, Visa N, Öhman M. ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation. Nucleic Acids Res 2024; 52:12021-12038. [PMID: 39217468 PMCID: PMC11514483 DOI: 10.1093/nar/gkae753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
ADAR3 is a catalytically inactive member of the family of adenosine deaminases acting on RNA (ADARs). Here we have investigated its function in the context of the developing mouse brain. The expression of ADAR3 gradually increases throughout embryogenesis and drops after birth. Using primary cortical neurons, we show that ADAR3 is only expressed in a subpopulation of in vitro differentiated neurons, which suggests specific functions rather than being a general regulator of ADAR editing in the brain. The analysis of the ADAR3 interactome suggested a role in mRNA stability and translation, and we show that expression of ADAR3 in a neuronal cell line that is otherwise ADAR3-negative changes the expression and stability of a large number of mRNAs. Notably, we show that ADAR3 associates with polysomes and inhibits translation. We propose that ADAR3 binds to target mRNAs and stabilizes them in non-productive polysome complexes. Interestingly, the expression of ADAR3 downregulates genes related to neuronal differentiation and inhibits neurofilament outgrowth in vitro. In summary, we propose that ADAR3 negatively regulates neuronal differentiation, and that it does so by regulating mRNA stability and translation in an editing-independent manner.
Collapse
Affiliation(s)
- Victor Karlström
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Eduardo A Sagredo
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Jordi Planells
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Charlotte Welinder
- Mass Spectrometry, Clinical Sciences, Lund University, Lund SE-221 84, Sweden
| | - Jennifer Jungfleisch
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, ES-08003 Barcelona, Spain
| | - Andrea Barrera-Conde
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, ES-08003 Barcelona, Spain
| | - Linus Engfors
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Chammiran Daniel
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, ES-08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), ES-08003 Barcelona, Spain
| | - Neus Visa
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| | - Marie Öhman
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius väg 20C, Stockholm SE-106 91, Sweden
| |
Collapse
|
15
|
Luo J, Yang C, Xu S, Ji Z, Zhang Y, Bai H, Deng Z, Liang J, Huang Y, Zhi E, Tian R, Li P, Zhao F, Zhou Z, Li Z, Yao C. RNA-binding protein IGF2BP1 is required for spermatogenesis in an age-dependent manner. Commun Biol 2024; 7:1362. [PMID: 39433965 PMCID: PMC11493986 DOI: 10.1038/s42003-024-07055-y] [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: 02/22/2024] [Accepted: 10/11/2024] [Indexed: 10/23/2024] Open
Abstract
Post-transcriptional regulation mediated by RNA binding proteins is crucial for male germline development. Insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), an RNA binding protein, is specifically expressed in human and mouse male gonads and is involved in manifold biological processes and tumorigenesis. However, the function of IGF2BP1 in mammalian spermatogenesis remains poorly understood. Herein, we generated an Igf2bp1 conditional knockout mouse model using Nanos3-Cre. Germ cell deficiency of Igf2bp1 in mice caused spermatogenic defects in an age-dependent manner, resulting in decreased numbers of undifferentiated spermatogonia and increased germ cell apoptosis. Immunoprecipitation-mass spectrometry analysis revealed that ELAV-like RNA binding protein 1, a well-recognized mRNA stabilizer, interacted with IGF2BP1. Single cell RNA-sequencing showed distinct mRNA profiles in spermatogonia from conditional knockout versus wide type mice. Further research showed that IGF2BP1 plays a vital role in the modulation of spermatogenesis by regulating Lin28a mRNA, which is essential for clonal expansion of undifferentiated spermatogonia. Thus, our results highlight the crucial effects of IGF2BP1 on spermatogonia for the long-term maintenance of spermatogenesis.
Collapse
Affiliation(s)
- Jiaqiang Luo
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chao Yang
- Department of Urology, The First Affiliated Hospital With Nanjing Medical University, Nanjing, Jiangsu, 210029, China
| | - Shuai Xu
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zhiyong Ji
- Center for Reproductive Medicine, The First Affiliated Hospital of Xiamen University, Xiamen, Fujian, 361003, China
| | - Yuxiang Zhang
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Haowei Bai
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Zhiwen Deng
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Jiayi Liang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuhua Huang
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Erlei Zhi
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Ruhui Tian
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Peng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Fujun Zhao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China
| | - Zhi Zhou
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Zheng Li
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| | - Chencheng Yao
- Department of Andrology, The Center for Men's Health, Urologic Medical Center, Shanghai Key Laboratory of Reproductive Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200080, China.
| |
Collapse
|
16
|
Chen Y, Zhou Z, Chen Y, Chen D. Reading the m 6A-encoded epitranscriptomic information in development and diseases. Cell Biosci 2024; 14:124. [PMID: 39342406 PMCID: PMC11439334 DOI: 10.1186/s13578-024-01293-7] [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: 05/04/2024] [Accepted: 08/19/2024] [Indexed: 10/01/2024] Open
Abstract
N6-methyladenosine (m6A) represents the most prevalent internal and reversible modification on RNAs. Different cell types display their unique m6A profiles, which are determined by the functions of m6A writers and erasers. M6A modifications lead to different outcomes such as decay, stabilization, or transport of the RNAs. The m6A-encoded epigenetic information is interpreted by m6A readers and their interacting proteins. M6A readers are essential for different biological processes, and the defects in m6A readers have been discovered in diverse diseases. Here, we review the latest advances in the roles of m6A readers in development and diseases. These recent studies not only highlight the importance of m6A readers in regulating cell fate transitions, but also point to the potential application of drugs targeting m6A readers in diseases.
Collapse
Affiliation(s)
- Yunbing Chen
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Ziyu Zhou
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Yanxi Chen
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China
| | - Di Chen
- Center for Reproductive Medicine of The Second Affiliated Hospital, Center for Regeneration and Cell Therapy of Zhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, Zhejiang University, Hangzhou, Zhejiang, 310003, China.
- State Key Laboratory of Biobased Transportation Fuel Technology, Haining, Zhejiang, 314400, China.
| |
Collapse
|
17
|
Jin W, Yao Y, Fu Y, Lei X, Fu W, Lu Q, Tong X, Xu Q, Su W, Hu X. WTAP/IGF2BP3-mediated GBE1 expression accelerates the proliferation and enhances stemness in pancreatic cancer cells via upregulating c-Myc. Cell Mol Biol Lett 2024; 29:97. [PMID: 38961325 PMCID: PMC11223412 DOI: 10.1186/s11658-024-00611-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
BACKGROUND Pancreatic cancer (PC) is one of the most malignant cancers with highly aggressiveness and poor prognosis. N6-methyladenosine (m6A) have been indicated to be involved in PC development. Glucan Branching Enzyme 1 (GBE1) is mainly involved in cell glycogen metabolism. However, the function of GBE1 and Whether GBE1 occurs m6A modification in PC progression remains to be illustrated. METHODS The clinical prognosis of GBE1 was analyzed through online platform. The expression of GBE1 was obtained from online platform and then verified in normal and PC cell lines. Lentivirus was used to generated GBE1 stable-overexpression or knockdown PC cells. Cell Counting Kit (CCK-8), colony formation assay, sphere formation assay and flow cytometry assay were conducted to analyze cell proliferation and stemness ability in vitro. Subcutaneous and orthotopic mouse models were used to verify the function of GBE1 in vivo. RNA immunoprecipitation (RIP) assay, RNA stability experiment and western blots were conducted to explore the molecular regulation of GBE1 in PC. RESULTS GBE1 was significantly upregulated in PC and associated with poor prognosis of PC patients. Functionally, GBE1 overexpression facilitated PC cell proliferation and stemness-like properties, while knockdown of GBE1 attenuated the malignancy of PC cells. Importantly, we found the m6A modification of GBE1 RNA, and WTAP and IGF2BP3 was revealed as the m6A regulators to increase GBE1 mRNA stability and expression. Furthermore, c-Myc was discovered as a downstream gene of GBE1 and functional rescue experiments showed that overexpression of c-Myc could rescue GBE1 knockdown-induced PC cell growth inhibition. CONCLUSIONS Our study uncovered the oncogenic role of GBE1/c-Myc axis in PC progression and revealed WTAP/IGF2BP3-mediated m6A modification of GBE1, which highlight the potential application of GBE1 in the targeted therapy of PC.
Collapse
Affiliation(s)
- Weiwei Jin
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
- General Surgery, Cancer Center, Department of Gastrointestinal and Pancreatic Surgery, Zhejiang Provincial People's Hospital (Affiliated People's Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Yanru Yao
- Hangzhou Medical College, Hangzhou, China
| | - Yuhan Fu
- Hangzhou Medical College, Hangzhou, China
| | | | - Wen Fu
- The Medical College of Qingdao University, Qingdao, China
| | - Qiliang Lu
- The Medical College of Qingdao University, Qingdao, China
| | - Xiangmin Tong
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China
| | - Qiuran Xu
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| | - Wei Su
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease, Hangzhou, China.
| | - Xiaoge Hu
- Zhejiang Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, China.
| |
Collapse
|
18
|
Cai Y, Ji Y, Liu Y, Zhang D, Gong Z, Li L, Chen X, Liang C, Feng S, Lu J, Qiu Q, Lin Z, Wang Y, Cui L. Microglial circ-UBE2K exacerbates depression by regulating parental gene UBE2K via targeting HNRNPU. Theranostics 2024; 14:4058-4075. [PMID: 38994030 PMCID: PMC11234284 DOI: 10.7150/thno.96890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 06/23/2024] [Indexed: 07/13/2024] Open
Abstract
Background: Knowledge about the pathogenesis of depression and treatments for this disease are lacking. Epigenetics-related circRNAs are likely involved in the mechanism of depression and have great potential as treatment targets, but their mechanism of action is still unclear. Methods: Circular RNA UBE2K (circ-UBE2K) was screened from peripheral blood of patients with major depressive disorder (MDD) and brain of depression model mice through high-throughput sequencing. Microinjection of circ-UBE2K overexpression lentivirus and adeno-associated virus for interfering with microglial circ-UBE2K into the mouse hippocampus was used to observe the role of circ-UBE2K in MDD. Sucrose preference, forced swim, tail suspension and open filed tests were performed to evaluate the depressive-like behaviors of mice. Immunofluorescence and Western blotting analysis of the effects of circ-UBE2K on microglial activation and immune inflammation. Pull-down-mass spectrometry assay, RNA immunoprecipitation (RIP) test and fluorescence in situ hybridization (FISH) were used to identify downstream targets of circ-UBE2K/ HNRNPU (heterogeneous nuclear ribonucleoprotein U) axis. Results: In this study, through high-throughput sequencing and large-scale screening, we found that circ-UBE2K levels were significantly elevated both in the peripheral blood of patients with MDD and in the brains of depression model mice. Functionally, circ-UBE2K-overexpressing mice exhibited worsened depression-like symptoms, elevated brain inflammatory factor levels, and abnormal microglial activation. Knocking down circ-UBE2K mitigated these changes. Mechanistically, we found that circ-UBE2K binds to heterogeneous nuclear ribonucleoprotein U (HNRNPU) to form a complex that upregulates the expression of the parental gene ubiquitin conjugating enzyme E2 K (UBE2K), leading to abnormal microglial activation and neuroinflammation and promoting the occurrence and development of depression. Conclusions: The findings of the present study revealed that the expression of circUBE2K, which combines with HNRNPU to form the circUBE2K/HNRNPU complex, is increased in microglia after external stress, thus regulating the expression of the parental gene UBE2K and mediating the abnormal activation of microglia to induce neuroinflammation, promoting the development of MDD. These results indicate that circ-UBE2K plays a newly discovered role in the pathogenesis of depression.
Collapse
Affiliation(s)
- Yujie Cai
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Yao Ji
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Yingxuan Liu
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Dandan Zhang
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Zheng Gong
- Institute of Laboratory Animal Center, Guangdong Medical University, Zhanjiang, China
| | - Li Li
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Xiongjin Chen
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Chunmei Liang
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Sifan Feng
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Jiongtong Lu
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Qinjie Qiu
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Zhixiong Lin
- Department of Psychiatry, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yan Wang
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Lili Cui
- Institute of Neurology, Guangdong Key Laboratory of Age-Related Cardiac and Cerebral Diseases, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
- School of Ocean and Tropical Medicine, Guangdong Medical University, Zhanjiang, Guangdong, 524023, China
| |
Collapse
|
19
|
O'Reilly ME, Ho S, Coronel J, Zhu L, Liu W, Xue C, Kim E, Cynn E, Matias CV, Soni RK, Wang C, Ionita-Laza I, Bauer RC, Ross L, Zhang Y, Corvera S, Fried SK, Reilly MP. linc-ADAIN, a human adipose lincRNA, regulates adipogenesis by modulating KLF5 and IL-8 mRNA stability. Cell Rep 2024; 43:114240. [PMID: 38753486 PMCID: PMC11334222 DOI: 10.1016/j.celrep.2024.114240] [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: 07/07/2023] [Revised: 03/01/2024] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Adipose tissue remodeling and dysfunction, characterized by elevated inflammation and insulin resistance, play a central role in obesity-related development of type 2 diabetes (T2D) and cardiovascular diseases. Long intergenic non-coding RNAs (lincRNAs) are important regulators of cellular functions. Here, we describe the functions of linc-ADAIN (adipose anti-inflammatory), an adipose lincRNA that is downregulated in white adipose tissue of obese humans. We demonstrate that linc-ADAIN knockdown (KD) increases KLF5 and interleukin-8 (IL-8) mRNA stability and translation by interacting with IGF2BP2. Upregulation of KLF5 and IL-8, via linc-ADAIN KD, leads to an enhanced adipogenic program and adipose tissue inflammation, mirroring the obese state, in vitro and in vivo. KD of linc-ADAIN in human adipose stromal cell (ASC) hTERT adipocytes implanted into mice increases adipocyte size and macrophage infiltration compared to implanted control adipocytes, mimicking hallmark features of obesity-induced adipose tissue remodeling. linc-ADAIN is an anti-inflammatory lincRNA that limits adipose tissue expansion and lipid storage.
Collapse
Affiliation(s)
- Marcella E O'Reilly
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Sebastian Ho
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Johana Coronel
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Lucie Zhu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Wen Liu
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Chenyi Xue
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Eunyoung Kim
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Esther Cynn
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Caio V Matias
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY, USA
| | - Chen Wang
- Department of Statistics, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Iuliana Ionita-Laza
- Department of Statistics, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Robert C Bauer
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Leila Ross
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Yiying Zhang
- Division of Molecular Genetics, Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - Silvia Corvera
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Susan K Fried
- Diabetes, Obesity, and Metabolism Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Muredach P Reilly
- Cardiometabolic Genomics Program, Division of Cardiology, Department of Medicine, Columbia University Medical Center, New York, NY, USA; Irving Institute for Clinical and Translational Research, Columbia University, New York, NY 10032, USA.
| |
Collapse
|
20
|
Choi Y, Um B, Na Y, Kim J, Kim JS, Kim VN. Time-resolved profiling of RNA binding proteins throughout the mRNA life cycle. Mol Cell 2024; 84:1764-1782.e10. [PMID: 38593806 DOI: 10.1016/j.molcel.2024.03.012] [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: 01/23/2024] [Revised: 02/16/2024] [Accepted: 03/14/2024] [Indexed: 04/11/2024]
Abstract
mRNAs continually change their protein partners throughout their lifetimes, yet our understanding of mRNA-protein complex (mRNP) remodeling is limited by a lack of temporal data. Here, we present time-resolved mRNA interactome data by performing pulse metabolic labeling with photoactivatable ribonucleoside in human cells, UVA crosslinking, poly(A)+ RNA isolation, and mass spectrometry. This longitudinal approach allowed the quantification of over 700 RNA binding proteins (RBPs) across ten time points. Overall, the sequential order of mRNA binding aligns well with known functions, subcellular locations, and molecular interactions. However, we also observed RBPs with unexpected dynamics: the transcription-export (TREX) complex recruited posttranscriptionally after nuclear export factor 1 (NXF1) binding, challenging the current view of transcription-coupled mRNA export, and stress granule proteins prevalent in aged mRNPs, indicating roles in late stages of the mRNA life cycle. To systematically identify mRBPs with unknown functions, we employed machine learning to compare mRNA binding dynamics with Gene Ontology (GO) annotations. Our data can be explored at chronology.rna.snu.ac.kr.
Collapse
Affiliation(s)
- Yeon Choi
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Buyeon Um
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yongwoo Na
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jeesoo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jong-Seo Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - V Narry Kim
- Center for RNA Research, Institute for Basic Science, Seoul 08826, Republic of Korea; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| |
Collapse
|
21
|
Ascanelli C, Dahir R, Wilson CH. Manipulating Myc for reparative regeneration. Front Cell Dev Biol 2024; 12:1357589. [PMID: 38577503 PMCID: PMC10991803 DOI: 10.3389/fcell.2024.1357589] [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: 12/18/2023] [Accepted: 02/15/2024] [Indexed: 04/06/2024] Open
Abstract
The Myc family of proto-oncogenes is a key node for the signal transduction of external pro-proliferative signals to the cellular processes required for development, tissue homoeostasis maintenance, and regeneration across evolution. The tight regulation of Myc synthesis and activity is essential for restricting its oncogenic potential. In this review, we highlight the central role that Myc plays in regeneration across the animal kingdom (from Cnidaria to echinoderms to Chordata) and how Myc could be employed to unlock the regenerative potential of non-regenerative tissues in humans for therapeutic purposes. Mastering the fine balance of harnessing the ability of Myc to promote transcription without triggering oncogenesis may open the door to many exciting opportunities for therapeutic development across a wide array of diseases.
Collapse
Affiliation(s)
| | | | - Catherine H. Wilson
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| |
Collapse
|
22
|
Saidu NEB, Aarsund M, Sørensen E, Stensland M, Nyman TA, Ulvmoen A, Wu Y, Inngjerdingen M. Identifying a core protein signature of small extracellular vesicles derived from B-cell precursor acute lymphoblastic leukaemia. Scand J Immunol 2024; 99:e13341. [PMID: 38441169 DOI: 10.1111/sji.13341] [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: 08/15/2023] [Revised: 10/09/2023] [Accepted: 11/10/2023] [Indexed: 03/07/2024]
Abstract
Acute paediatric leukaemia is diagnosed and monitored via bone marrow aspirate assessment of blasts as a measure of minimal residual disease. Liquid biopsies in the form of blood samples could greatly reduce the need for invasive bone marrow aspirations, but there are currently no blood markers that match the sensitivity of bone marrow diagnostics. Circulating extracellular vesicles (EVs) represent candidate biomarkers that may reflect the blast burden in bone marrow, and several studies have reported on the utility of EVs as biomarkers for adult haematological malignancies. Increased levels of EVs have been reported for several haematological malignancies, and we similarly report here elevated EV concentrations in plasma from paediatric BCP-ALL patients. Plasma EVs are very heterogeneous in terms of their cellular origin, thus identifying a cancer selective EV-marker is challenging. Here, we undertook a reductionistic approach to identify protein markers selectively associated to plasma EVs derived from BCP-ALL patients. The EV proteome of primary BCP-ALL cell-derived EVs were compared against EVs from healthy donor B cells and the BCP-ALL cell line REH, and further against EVs isolated from plasma of healthy paediatric donors and paediatric BCP-ALL patients. With this approach, we identified a signature of 6 proteins (CD317, CD38, IGF2BP1, PCNA, CSDE1, and GPR116) that were specifically identified in BCP-ALL derived EVs only and not in healthy control EVs, and that could be exploited as diagnostic biomarkers.
Collapse
Affiliation(s)
| | - Miriam Aarsund
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Eva Sørensen
- Department of Biosciences, University of Oslo, Oslo, Norway
| | - Maria Stensland
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Tuula Anneli Nyman
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Aina Ulvmoen
- Department of Pediatrics, Oslo University Hospital, Oslo, Norway
| | - Yunjie Wu
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Marit Inngjerdingen
- Department of Pharmacology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| |
Collapse
|
23
|
Duan M, Liu H, Xu S, Yang Z, Zhang F, Wang G, Wang Y, Zhao S, Jiang X. IGF2BPs as novel m 6A readers: Diverse roles in regulating cancer cell biological functions, hypoxia adaptation, metabolism, and immunosuppressive tumor microenvironment. Genes Dis 2024; 11:890-920. [PMID: 37692485 PMCID: PMC10491980 DOI: 10.1016/j.gendis.2023.06.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/24/2023] [Accepted: 06/14/2023] [Indexed: 09/12/2023] Open
Abstract
m6A methylation is the most frequent modification of mRNA in eukaryotes and plays a crucial role in cancer progression by regulating biological functions. Insulin-like growth factor 2 mRNA-binding proteins (IGF2BP) are newly identified m6A 'readers'. They belong to a family of RNA-binding proteins, which bind to the m6A sites on different RNA sequences and stabilize them to promote cancer progression. In this review, we summarize the mechanisms by which different upstream factors regulate IGF2BP in cancer. The current literature analyzed here reveals that the IGF2BP family proteins promote cancer cell proliferation, survival, and chemoresistance, inhibit apoptosis, and are also associated with cancer glycolysis, angiogenesis, and the immune response in the tumor microenvironment. Therefore, with the discovery of their role as 'readers' of m6A and the characteristic re-expression of IGF2BPs in cancers, it is important to elucidate their mechanism of action in the immunosuppressive tumor microenvironment. We also describe in detail the regulatory and interaction network of the IGF2BP family in downstream target RNAs and discuss their potential clinical applications as diagnostic and prognostic markers, as well as recent advances in IGF2BP biology and associated therapeutic value.
Collapse
Affiliation(s)
- Meiqi Duan
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Haiyang Liu
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Shasha Xu
- Department of Gastroendoscopy, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Zhi Yang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Fusheng Zhang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Guang Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Yutian Wang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| | - Shan Zhao
- Department of Rheumatology and Immunology, The First Affiliated Hospital of China Medical University, Shenyang, Liaoning 110002, China
| | - Xiaofeng Jiang
- Department of General Surgery, The Fourth Affiliated Hospital of China Medical University, Shenyang, Liaoning 110032, China
| |
Collapse
|
24
|
Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
Collapse
Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| |
Collapse
|
25
|
Liu J, Wang S, Zhang C, Wei Z, Han D, Song Y, Song X, Chao F, Wu Z, Xu G, Chen G. Anillin contributes to prostate cancer progression through the regulation of IGF2BP1 to promote c-Myc and MAPK signaling. Am J Cancer Res 2024; 14:490-506. [PMID: 38455417 PMCID: PMC10915328 DOI: 10.62347/uyqh7683] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/18/2024] [Indexed: 10/25/2024] Open
Abstract
Prostate cancer (PCa), especially castration-resistant PCa, is a common and fatal disease. Anillin (ANLN) is an actin-binding protein that is involved in various malignancies, including PCa. However, the regulatory mechanism of ANLN in PCa remains unclear. Exploring the role of ANLN in PCa development and discovering novel therapeutic targets are crucial for PCa therapy. In the current work, we discovered that ANLN expression was considerably elevated in PCa tissues and cell lines when compared to nearby noncancerous prostate tissues and normal prostate epithelial cells. ANLN was associated with more advanced T stage, N stage, higher Gleason score, and prostate-specific antigen (PSA) level. In addition, we discovered that overexpression of ANLN promoted PCa cell proliferation, migration, and invasion in vitro and in vivo. Mechanistically, we performed RNA-seq to identify the regulatory influence of ANLN on the MAPK signal pathway. Furthermore, a favorable association between ANLN expression and IGF2BP1 expression was identified. The tumor-suppressive impact of ANLN downregulation on PCa cell growth was partially reversed by overexpressing IGF2BP1. Meanwhile, we discovered that ANLN can stabilize the proto-oncogene c-Myc and activate the MAPK signaling pathway through IGF2BP1. These findings indicate that ANLN could be a potential therapeutic target in PCa.
Collapse
Affiliation(s)
- Jinke Liu
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Shiyu Wang
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Ziwei Wei
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Yufeng Song
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Xiaoming Song
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Fan Chao
- Department of Urology, Zhongshan Hospital, Fudan University (Xiamen Branch)Xiamen 361015, Fujian, China
| | - Zhiming Wu
- Department of Urology, Sun Yat-sen University Cancer CenterGuangzhou 510060, Guangdong, China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| |
Collapse
|
26
|
Liu J, Wang S, Zhang C, Wei Z, Han D, Song Y, Song X, Chao F, Wu Z, Xu G, Chen G. Anillin contributes to prostate cancer progression through the regulation of IGF2BP1 to promote c-Myc and MAPK signaling. Am J Cancer Res 2024; 14:490-506. [PMID: 38455417 PMCID: PMC10915328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 01/18/2024] [Indexed: 03/09/2024] Open
Abstract
Prostate cancer (PCa), especially castration-resistant PCa, is a common and fatal disease. Anillin (ANLN) is an actin-binding protein that is involved in various malignancies, including PCa. However, the regulatory mechanism of ANLN in PCa remains unclear. Exploring the role of ANLN in PCa development and discovering novel therapeutic targets are crucial for PCa therapy. In the current work, we discovered that ANLN expression was considerably elevated in PCa tissues and cell lines when compared to nearby noncancerous prostate tissues and normal prostate epithelial cells. ANLN was associated with more advanced T stage, N stage, higher Gleason score, and prostate-specific antigen (PSA) level. In addition, we discovered that overexpression of ANLN promoted PCa cell proliferation, migration, and invasion in vitro and in vivo. Mechanistically, we performed RNA-seq to identify the regulatory influence of ANLN on the MAPK signal pathway. Furthermore, a favorable association between ANLN expression and IGF2BP1 expression was identified. The tumor-suppressive impact of ANLN downregulation on PCa cell growth was partially reversed by overexpressing IGF2BP1. Meanwhile, we discovered that ANLN can stabilize the proto-oncogene c-Myc and activate the MAPK signaling pathway through IGF2BP1. These findings indicate that ANLN could be a potential therapeutic target in PCa.
Collapse
Affiliation(s)
- Jinke Liu
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Shiyu Wang
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Cong Zhang
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Ziwei Wei
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Dunsheng Han
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Yufeng Song
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Xiaoming Song
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Fan Chao
- Department of Urology, Zhongshan Hospital, Fudan University (Xiamen Branch)Xiamen 361015, Fujian, China
| | - Zhiming Wu
- Department of Urology, Sun Yat-sen University Cancer CenterGuangzhou 510060, Guangdong, China
| | - Guoxiong Xu
- Research Center for Clinical Medicine, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| | - Gang Chen
- Department of Urology, Jinshan Hospital, Fudan UniversityShanghai 201508, China
| |
Collapse
|
27
|
Ding N, Cao G, Wang Z, Xu S, Chen W. Tumor suppressive function of IGF2BP1 in gastric cancer through decreasing MYC. Cancer Sci 2024; 115:427-438. [PMID: 38115228 PMCID: PMC10859605 DOI: 10.1111/cas.16047] [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: 06/26/2023] [Revised: 11/29/2023] [Accepted: 12/04/2023] [Indexed: 12/21/2023] Open
Abstract
Gastric cancer is one of the most common causes of cancer-related death worldwide. The N6 -methyladenosine (m6 A) reader IGF2BP1 (insulin-like growth factor-2 mRNA binding protein 1) has been reported to promote cancer progression by stabilizing oncogenic mRNAs through its m6 A-binding activity in some tumors. However, the role of IGF2BP1 in gastric carcinogenesis remains unclear. In this study, we found that IGF2BP1 is significantly downregulated in tumor tissues from patients with gastric cancer. Lower expression of IGF2BP1 is associated with poor prognosis. Gastric cancer cell proliferation is suppressed by IGF2BP1 in an m6 A-dependent manner. Additionally, IGF2BP1 is able to significantly attenuate tumor growth of gastric cancer cells. Further m6 A sequencing and m6 A-RNA immunoprecipitation assays show that MYC (c-myc proto-oncogene) mRNA is a target transcript of IGF2BP1 in gastric cancer cells. IGF2BP1 inhibits gastric cancer cell proliferation by reducing the mRNA and protein expression of MYC. Mechanistically, IGF2BP1 promotes the degradation of MYC mRNA and inhibits its translation efficiency. Taken together, these data suggest that IGF2BP1 plays a tumor-suppressive role in gastric carcinogenesis by downregulating MYC in an m6 A-dependent manner, thereby making the IGF2BP1-MYC axis a potential target for gastric cancer treatment.
Collapse
Affiliation(s)
- Ning Ding
- Department of GastroenterologyThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Zhejiang University Cancer CenterHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| | - Guodong Cao
- Department of General SurgeryFirst Affiliated Hospital of Anhui Medical UniversityHefeiChina
| | - Zhuo Wang
- Department of GastroenterologyThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Zhejiang University Cancer CenterHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| | - Shengjun Xu
- Key Laboratory of Integrated Oncology and Intelligent Medicine of Zhejiang ProvinceHangzhouChina
- Department of Hepatobiliary and Pancreatic SurgeryHangzhou First People's HospitalHangzhouChina
| | - Wenwen Chen
- Department of GastroenterologyThe Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
- Zhejiang University Cancer CenterHangzhouChina
- Institution of GastroenterologyZhejiang UniversityHangzhouChina
| |
Collapse
|
28
|
Xu M, Qian K, Shao H, Yao Y, Nair V, Ye J, Qin A. 3'UTR of ALV-J can affect viral replication through promoting transcription and mRNA nuclear export. J Virol 2023; 97:e0115223. [PMID: 37902396 PMCID: PMC10688361 DOI: 10.1128/jvi.01152-23] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 09/29/2023] [Indexed: 10/31/2023] Open
Abstract
IMPORTANCE 3'UTRs can affect gene transcription and post-transcriptional regulation in multiple ways, further influencing the function of proteins in a unique manner. Recently, ALV-J has been mutating and evolving rapidly, especially the 3'UTR of viral genome. Meanwhile, clinical symptoms caused by ALV-J have changed significantly. In this study, we found that the ALV-J strains containing △-r-TM-type 3'UTR are the most abundant. By constructing ALV-J infectious clones and subgenomic vectors containing different 3'UTRs, we prove that 3'UTRs directly affect viral tissue preference and can promote virus replication as an enhancer. ALV-J strain containing 3'UTR of △-r-TM proliferated fastest in primary cells. All five forms of 3'UTRs can assist intron-containing viral mRNA nuclear export, with similar efficiency. ALV-J mRNA half-life is not influenced by different 3'UTRs. Our results dissect the roles of 3'UTR on regulating viral replication and pathogenicity, providing novel insights into potential anti-viral strategies.
Collapse
Affiliation(s)
- Moru Xu
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Kun Qian
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Hongxia Shao
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Yongxiu Yao
- The Pirbright Institute and UK-China Centre of Excellence on Avian Disease Research, Surrey, United Kingdom
| | - Venugopal Nair
- The Pirbright Institute and UK-China Centre of Excellence on Avian Disease Research, Surrey, United Kingdom
| | - Jianqiang Ye
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Aijian Qin
- Ministry of Education Key Lab for Avian Preventive Medicine, Yangzhou University, Yangzhou, Jiangsu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| |
Collapse
|
29
|
Tang H, Zhao J, Liu J. Comprehensive analysis of the expression of the IGF2BPs gene family in head and neck squamous cell carcinoma: Association with prognostic value and tumor immunity. Heliyon 2023; 9:e20659. [PMID: 37842569 PMCID: PMC10568114 DOI: 10.1016/j.heliyon.2023.e20659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/25/2023] [Accepted: 10/03/2023] [Indexed: 10/17/2023] Open
Abstract
Background Head and neck squamous cell carcinoma (HNSCC) represents a predominant type of cancer found in the head and neck region, characterized by a high incidence and unfavorable prognosis. The IGF2BPs gene family, which belongs to the RNA-binding protein class, has been critically implicated in several cancers, and its involvement in HNSCC necessitates further exploration. Objective To explore the clinical significance and potential biological functions of the IGF2BPs gene family in HNSCC. Methods A bioinformatic methodology was employed to examine the expression profile, diagnostic and prognostic significance, and biological mechanisms of the IGF2BPs gene family in HNSCC, with a particular emphasis on its involvement in the immune function of HNSCC. This was followed by in vitro investigations to unravel the biological roles of the IGF2BPs gene family in HNSCC. Results This investigation has demonstrated that, in contrast with normal control tissue, HNSCC has a substantial elevation in the expression level of the IGF2BPs gene family. Patients with a high level of IGF2BPs gene family expression demonstrated higher prediction accuracy for HNSCC. Furthermore, patients with HNSCC and elevated IGF2BPs gene family expression levels exhibited poor survival outcomes. The IGF2BPs gene family displayed a significant association with a variety of immune infiltrating cells and immune genes in HNSCC. Studies conducted in vitro have confirmed that IGF2BP2 silencing suppressed the migration, proliferation, and invasion of HNSCC cells. Conclusions It has been determined that the IGF2BPs gene family plays a crucial part in the onset and progression of HNSCC, and its association with tumor immunity has been established. The IGF2BPs gene family holds promising potential as a diagnostic and prognostic biomarker for HNSCC.
Collapse
Affiliation(s)
- Hai Tang
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, 518001, China
| | - Jianjiang Zhao
- Shenzhen Stomatological Hospital, Southern Medical University, Shenzhen, 518001, China
| | - Jingpeng Liu
- Stomatological Hospital, Southern Medical University, Guangzhou, 510280, China
| |
Collapse
|
30
|
Su R, Yin J, Ruan X, Chen Y, Wan P, Luo Z. Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress. Comput Struct Biotechnol J 2023; 21:4478-4487. [PMID: 37736299 PMCID: PMC10510068 DOI: 10.1016/j.csbj.2023.09.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 09/06/2023] [Accepted: 09/07/2023] [Indexed: 09/23/2023] Open
Abstract
Homocysteine-inducible endoplasmic reticulum protein (HERP) is an endoplasmic reticulum (ER)-resident protein and important for the adaptation of cellular protein homeostasis by ER-associated degradation (ERAD) system. HERP interactors are critical for cellular viability and the reaction to ER stress. To explore the exact mechanisms by which HERP performed the biological functions, we conducted an interaction analysis of HERP protein in HeLa cells by co-immunoprecipitation (Co-IP) and liquid chromatography-mass spectrometer (LC-MS)/MS coupled with label-free quantification (LFQ). Among the interactome results, 123 proteins significantly interacted with HERP, which leads to numerous biological processes including protein import into nucleus, ubiquitin-dependent ERAD pathway, negative regulation of apoptotic process, and protein transport from ER, along with multiple pathways including several diseases, protein processing in ER, fatty acid metabolism, and steroid biosynthesis. Furthermore, we selected several prey proteins from the interactome data and confirmed that HERP interacted with ancient ubiquitous protein 1 (AUP1), Fas-associated factor family member 2 (FAF2), tripartite motif containing 47 (TRIM47), acyl-CoA synthetase long-chain family member 3 (ACSL3), sequestosome 1 (SQSTM1), and poly(rC) binding protein 2 (PCBP2) by Co-IP and confocal microscopy experiments, respectively. Moreover, the expression and location of several interacted proteins were obviously altered in response to ER stress induced by Thapsigargin stimulation and Enterovirus 71 infection. In conclusion, our findings revealed that the vital proteins interacted with HERP to mediate signaling transduction, thus providing novel clues for the mechanisms of HERP associated with ERAD and metabolism in response to ER stress under physiological and pathological conditions.
Collapse
Affiliation(s)
- Rui Su
- Henan Key Laboratory of Immunology and Targeted Drug, Xinxiang Medical University, Xinxiang 453003, China
- Department of Immunology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang 453003, China
| | - Jialing Yin
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
| | - Xiaolan Ruan
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
| | - Yanxi Chen
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
| | - Pin Wan
- Wuhan Institute of Biomedical Sciences, School of Medicine, Jianghan University, Wuhan 430072, China
- Foshan Institute of Medical Microbiology, Foshan 528315, China
| | - Zhen Luo
- Institute of Medical Microbiology, Jinan University, Guangzhou 510632, China
- Foshan Institute of Medical Microbiology, Foshan 528315, China
- Key Laboratory of Viral Pathogenesis & Infection Prevention and Control (Jinan University), Ministry of Education, Guangzhou 510632, China
| |
Collapse
|
31
|
Qiu L, Jing Q, Li Y, Han J. RNA modification: mechanisms and therapeutic targets. MOLECULAR BIOMEDICINE 2023; 4:25. [PMID: 37612540 PMCID: PMC10447785 DOI: 10.1186/s43556-023-00139-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/28/2023] [Indexed: 08/25/2023] Open
Abstract
RNA modifications are dynamic and reversible chemical modifications on substrate RNA that are regulated by specific modifying enzymes. They play important roles in the regulation of many biological processes in various diseases, such as the development of cancer and other diseases. With the help of advanced sequencing technologies, the role of RNA modifications has caught increasing attention in human diseases in scientific research. In this review, we briefly summarized the basic mechanisms of several common RNA modifications, including m6A, m5C, m1A, m7G, Ψ, A-to-I editing and ac4C. Importantly, we discussed their potential functions in human diseases, including cancer, neurological disorders, cardiovascular diseases, metabolic diseases, genetic and developmental diseases, as well as immune disorders. Through the "writing-erasing-reading" mechanisms, RNA modifications regulate the stability, translation, and localization of pivotal disease-related mRNAs to manipulate disease development. Moreover, we also highlighted in this review all currently available RNA-modifier-targeting small molecular inhibitors or activators, most of which are designed against m6A-related enzymes, such as METTL3, FTO and ALKBH5. This review provides clues for potential clinical therapy as well as future study directions in the RNA modification field. More in-depth studies on RNA modifications, their roles in human diseases and further development of their inhibitors or activators are needed for a thorough understanding of epitranscriptomics as well as diagnosis, treatment, and prognosis of human diseases.
Collapse
Affiliation(s)
- Lei Qiu
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Qian Jing
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Yanbo Li
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
- Department of Neurology, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Junhong Han
- State Key Laboratory of Biotherapy and Cancer Center, Research Laboratory of Tumor Epigenetics and Genomics, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China.
| |
Collapse
|
32
|
Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| |
Collapse
|
33
|
Deng X, Qing Y, Horne D, Huang H, Chen J. The roles and implications of RNA m 6A modification in cancer. Nat Rev Clin Oncol 2023; 20:507-526. [PMID: 37221357 DOI: 10.1038/s41571-023-00774-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 80.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 05/25/2023]
Abstract
N6-Methyladenosine (m6A), the most prevalent internal modification in eukaryotic mRNA, has been extensively and increasingly studied over the past decade. Dysregulation of RNA m6A modification and its associated machinery, including writers, erasers and readers, is frequently observed in various cancer types, and the dysregulation profiles might serve as diagnostic, prognostic and/or predictive biomarkers. Dysregulated m6A modifiers have been shown to function as oncoproteins or tumour suppressors with essential roles in cancer initiation, progression, metastasis, metabolism, therapy resistance and immune evasion as well as in cancer stem cell self-renewal and the tumour microenvironment, highlighting the therapeutic potential of targeting the dysregulated m6A machinery for cancer treatment. In this Review, we discuss the mechanisms by which m6A modifiers determine the fate of target RNAs and thereby influence protein expression, molecular pathways and cell phenotypes. We also describe the state-of-the-art methodologies for mapping global m6A epitranscriptomes in cancer. We further summarize discoveries regarding the dysregulation of m6A modifiers and modifications in cancer, their pathological roles, and the underlying molecular mechanisms. Finally, we discuss m6A-related prognostic and predictive molecular biomarkers in cancer as well as the development of small-molecule inhibitors targeting oncogenic m6A modifiers and their activity in preclinical models.
Collapse
Affiliation(s)
- Xiaolan Deng
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
| | - Ying Qing
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA
| | - David Horne
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Huilin Huang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Jianjun Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Monrovia, CA, USA.
- City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
- Gehr Family Center for Leukemia Research & City of Hope Comprehensive Cancer Center, City of Hope, Duarte, CA, USA.
| |
Collapse
|
34
|
Copeland CA, Olenchock BA, Ziehr D, McGarrity S, Leahy K, Young JD, Loscalzo J, Oldham WM. MYC overrides HIF-1α to regulate proliferating primary cell metabolism in hypoxia. eLife 2023; 12:e82597. [PMID: 37428010 DOI: 10.7554/elife.82597] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 06/27/2023] [Indexed: 07/11/2023] Open
Abstract
Hypoxia requires metabolic adaptations to sustain energetically demanding cellular activities. While the metabolic consequences of hypoxia have been studied extensively in cancer cell models, comparatively little is known about how primary cell metabolism responds to hypoxia. Thus, we developed metabolic flux models for human lung fibroblast and pulmonary artery smooth muscle cells proliferating in hypoxia. Unexpectedly, we found that hypoxia decreased glycolysis despite activation of hypoxia-inducible factor 1α (HIF-1α) and increased glycolytic enzyme expression. While HIF-1α activation in normoxia by prolyl hydroxylase (PHD) inhibition did increase glycolysis, hypoxia blocked this effect. Multi-omic profiling revealed distinct molecular responses to hypoxia and PHD inhibition, and suggested a critical role for MYC in modulating HIF-1α responses to hypoxia. Consistent with this hypothesis, MYC knockdown in hypoxia increased glycolysis and MYC over-expression in normoxia decreased glycolysis stimulated by PHD inhibition. These data suggest that MYC signaling in hypoxia uncouples an increase in HIF-dependent glycolytic gene transcription from glycolytic flux.
Collapse
Affiliation(s)
- Courtney A Copeland
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Benjamin A Olenchock
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - David Ziehr
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
- Department of Medicine, Massachusetts General Hospital, Boston, United States
| | - Sarah McGarrity
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
- Center for Systems Biology, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Kevin Leahy
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - Jamey D Young
- Departments of Chemical & Biomolecular Engineering and Molecular Physiology & Biophysics, Vanderbilt University, Nashville, United States
| | - Joseph Loscalzo
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| | - William M Oldham
- Department of Medicine, Brigham and Women's Hospital, Boston, United States
- Department of Medicine, Harvard Medical School, Boston, United States
| |
Collapse
|
35
|
Titus MB, Chang AW, Popitsch N, Ebmeier CC, Bono JM, Olesnicky EC. The identification of protein and RNA interactors of the splicing factor Caper in the adult Drosophila nervous system. Front Mol Neurosci 2023; 16:1114857. [PMID: 37435576 PMCID: PMC10332324 DOI: 10.3389/fnmol.2023.1114857] [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: 12/03/2022] [Accepted: 05/19/2023] [Indexed: 07/13/2023] Open
Abstract
Post-transcriptional gene regulation is a fundamental mechanism that helps regulate the development and healthy aging of the nervous system. Mutations that disrupt the function of RNA-binding proteins (RBPs), which regulate post-transcriptional gene regulation, have increasingly been implicated in neurological disorders including amyotrophic lateral sclerosis, Fragile X Syndrome, and spinal muscular atrophy. Interestingly, although the majority of RBPs are expressed widely within diverse tissue types, the nervous system is often particularly sensitive to their dysfunction. It is therefore critical to elucidate how aberrant RNA regulation that results from the dysfunction of ubiquitously expressed RBPs leads to tissue specific pathologies that underlie neurological diseases. The highly conserved RBP and alternative splicing factor Caper is widely expressed throughout development and is required for the development of Drosophila sensory and motor neurons. Furthermore, caper dysfunction results in larval and adult locomotor deficits. Nonetheless, little is known about which proteins interact with Caper, and which RNAs are regulated by Caper. Here we identify proteins that interact with Caper in both neural and muscle tissue, along with neural specific Caper target RNAs. Furthermore, we show that a subset of these Caper-interacting proteins and RNAs genetically interact with caper to regulate Drosophila gravitaxis behavior.
Collapse
Affiliation(s)
- M. Brandon Titus
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Adeline W. Chang
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Niko Popitsch
- Department of Biochemistry and Cell Biology, Max Perutz Labs, University of Vienna, Vienna, Austria
| | | | - Jeremy M. Bono
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| | - Eugenia C. Olesnicky
- Department of Biology, University of Colorado Colorado Springs, Colorado Springs, CO, United States
| |
Collapse
|
36
|
Liu JX, Chen AN, Yu Q, Shi KT, Liu YB, Guo CL, Wang ZZ, Yao Y, Pan L, Lu X, Xu K, Wang H, Zeng M, Liu C, Schleimer RP, Wu N, Liao B, Liu Z. MEX3B inhibits collagen production in eosinophilic nasal polyps by downregulating epithelial cell TGFBR3 mRNA stability. JCI Insight 2023; 8:e159058. [PMID: 36976645 PMCID: PMC10243817 DOI: 10.1172/jci.insight.159058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Although the expression of Mex3 RNA-binding family member B (MEX3B) is upregulated in human nasal epithelial cells (HNECs) predominately in the eosinophilic chronic rhinosinusitis (CRS) with nasal polyps (CRSwNP) subtype, its functions as an RNA binding protein in airway epithelial cells remain unknown. Here, we revealed the role of MEX3B based on different subtypes of CRS and demonstrated that MEX3B decreased the TGF-β receptor III (TGFBR3) mRNA level by binding to its 3' UTR and reducing its stability in HNECs. TGF-βR3 was found to be a TGF-β2-specific coreceptor in HNECs. Knocking down or overexpressing MEX3B promoted or inhibited TGF-β2-induced phosphorylation of SMAD2 in HNECs, respectively. TGF-βR3 and phosphorylated SMAD2 levels were downregulated in CRSwNP compared with controls and CRS without nasal polyps with a more prominent downregulation in the eosinophilic CRSwNP. TGF-β2 promoted collagen production in HNECs. Collagen abundance decreased and edema scores increased in CRSwNP compared with control, again more prominently in the eosinophilic type. Collagen expression in eosinophilic CRSwNP was negatively correlated with MEX3B but positively correlated with TGF-βR3. These results suggest that MEX3B inhibits tissue fibrosis in eosinophilic CRSwNP by downregulating epithelial cell TGFBR3 expression; consequently, MEX3B might be a valuable therapeutic target against eosinophilic CRSwNP.
Collapse
Affiliation(s)
- Jin-Xin Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Ao-Nan Chen
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Qihong Yu
- Hepatic Surgery Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Clinical Medical Research Center of Hepatic Surgery at Hubei Province, Wuhan, China
| | - Ke-Tai Shi
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Yi-Bo Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Cui-Lian Guo
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Zhe-Zheng Wang
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Yin Yao
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Li Pan
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Xiang Lu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Kai Xu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Heng Wang
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Ming Zeng
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Chaohong Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Robert P. Schleimer
- Division of Allergy-Immunology, Department of Medicine; and
- Department of Otolaryngology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ning Wu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
- Department of Immunology, School of Basic Medicine, Tongji Medical College, and
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Liao
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| | - Zheng Liu
- Department of Otolaryngology-Head and Neck Surgery, Tongji Hospital; and
| |
Collapse
|
37
|
Shi Y, Niu Y, Yuan Y, Li K, Zhong C, Qiu Z, Li K, Lin Z, Yang Z, Zuo D, Qiu J, He W, Wang C, Liao Y, Wang G, Yuan Y, Li B. PRMT3-mediated arginine methylation of IGF2BP1 promotes oxaliplatin resistance in liver cancer. Nat Commun 2023; 14:1932. [PMID: 37024475 PMCID: PMC10079833 DOI: 10.1038/s41467-023-37542-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 03/22/2023] [Indexed: 04/08/2023] Open
Abstract
Although oxaliplatin-based chemotherapy has been effective in the treatment of hepatocellular carcinoma (HCC), primary or acquired resistance to oxaliplatin remains a major challenge in the clinic. Through functional screening using CRISPR/Cas9 activation library, transcriptomic profiling of clinical samples, and functional validation in vitro and in vivo, we identify PRMT3 as a key driver of oxaliplatin resistance. Mechanistically, PRMT3-mediated oxaliplatin-resistance is in part dependent on the methylation of IGF2BP1 at R452, which is critical for the function of IGF2BP1 in stabilizing the mRNA of HEG1, an effector of PRMT3-IGF2BP1 axis. Also, PRMT3 overexpression may serve as a biomarker for oxaliplatin resistance in HCC patients. Collectively, our study defines the PRTM3-IGF2BP1-HEG1 axis as important regulators and therapeutic targets in oxaliplatin-resistance and suggests the potential to use PRMT3 expression level in pretreatment biopsy as a biomarker for oxaliplatin-resistance in HCC patients.
Collapse
Affiliation(s)
- Yunxing Shi
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yi Niu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yichuan Yuan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Kai Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Chengrui Zhong
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhiyu Qiu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Keren Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhu Lin
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Zhiwen Yang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Dinglan Zuo
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jiliang Qiu
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Wei He
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Chenwei Wang
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Yadi Liao
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Guocan Wang
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Yunfei Yuan
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Binkui Li
- State Key Laboratory of Oncology in South China and Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
- Department of Liver Surgery, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| |
Collapse
|
38
|
Lin C, Li T, Wang Y, Lai S, Huang Y, Guo Z, Zhang X, Weng S. METTL3 enhances pancreatic ductal adenocarcinoma progression and gemcitabine resistance through modifying DDX23 mRNA N6 adenosine methylation. Cell Death Dis 2023; 14:221. [PMID: 36977668 PMCID: PMC10050319 DOI: 10.1038/s41419-023-05715-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 02/24/2023] [Accepted: 02/27/2023] [Indexed: 03/30/2023]
Abstract
The aim of the present study was to clarify the mechanism of how METTL3 regulated pancreatic ductal adenocarcinoma (PDAC) progression by m6A modification of its downstream target mRNA and signaling pathway. Immunoblotting and qRT-PCR assays was employed to determine the expression levels of METTL3. In situ fluorescence hybridization was conducted to localize the cellular distribution of METTL3 and DEAD-box helicase 23 (DDX23). CCK8, colony formation, EDU incorporation, TUNEL, wound healing and Transwell assays were carried out accordingly to study the viability, proliferation, apoptosis, and mobility of cells under different treatments in vitro. Xenograft and animal lung metastasis experiments were also conducted to study the functional role of METTL3 or DDX23 on tumor growth and lung metastasis in vivo. MeRIP-qPCR and bioinformatical analyses were used to obtain the potential direct targets of METTL3. It was shown that m6A methyltransferase METTL3 was upregulated in PDAC tissues with gemcitabine resistance, and its knockdown sensitized pancreatic cancer cells to chemotherapy. Furthermore, silencing METTL3 remarkably reduced pancreatic cancer cell proliferation, migration, and invasion both in vitro and in vivo. Mechanistically, validation experiments confirmed that DDX23 mRNA was a direct target of METTL3 in YTHDF1-dependent manner. Additionally, DDX23 silence resulted in the suppression of pancreatic cancer cell malignancy and PIAK/Akt signaling inactivation. Strikingly, rescuse experiments demonstrated the inhibitive effects of METTL3 silence on cell phenotypes and gemcitabine resistance were partially reversed by forcibly expressed DDX23. In summary, METTL3 promotes PDAC progression and gemcitabine resistance by modifying DDX23 mRNA m6A methylation and enhancing PI3K/Akt signaling activation. Our findings establish a potential tumor promotive and chemo-resistant role for METTL3/DDX23 axis in PDAC.
Collapse
Affiliation(s)
- Chengjie Lin
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Ting Li
- Department of Oncology, Fujian Provincial Hospital, Provincial Clinical College of Fujian Medical University, Fuzhou, Fujian, 350001, China
| | - Yan Wang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Shihui Lai
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Yue Huang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Zhenyun Guo
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China
| | - Xiang Zhang
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China.
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China.
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China.
| | - Shangeng Weng
- Department of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, Fujian, 350001, China.
- Fujian Abdominal Surgery Research Institute, The First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350001, China.
- National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, Fujian, 350212, China.
| |
Collapse
|
39
|
LOC101929709 promotes gastric cancer progression by aiding LIN28B to stabilize c-MYC mRNA. Gastric Cancer 2023; 26:169-186. [PMID: 36284068 DOI: 10.1007/s10120-022-01348-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/15/2022] [Indexed: 02/07/2023]
Abstract
BACKGROUND LIN28B plays a critical role in the Warburg effect. However, its underlying mechanism remains elusive. Recently, it has been reported that LIN28B could collaborate with IGF2BP3, which can bind to m6A-modified c-MYC transcripts. Therefore, this study investigated if LIN28B recognises methylated c-MYC mRNA to promote the Warburg effect in gastric cancer. METHODS Effects of LIN28B on gastric cancer were confirmed in vitro and in vivo. On the basis of bioinformatics analysis, the association between LIN28B and c-MYC mRNA was shown using RNA immunoprecipitation (RIP) and luciferase reporter assays. The role of m6A was identified by RNA pull-down assays. We further performed RIP-seq to search for long non-coding RNAs (lncRNAs) participating in the LIN28B binding process. Chromatin immunoprecipitation was used to show the impact of c-MYC on transcription of LIN28B and lncRNAs. RESULTS LIN28B was identified to stabilize c-MYC mRNA by recognizing m6A. Furthermore, the interaction between c-MYC mRNA and LIN28B is speculated to be supported by LOC101929709, which binds to both LIN28B and IGF2BP3. Functional experiments revealed that LOC101929709 promotes the proliferation, migration and glycolysis of gastric cancer. Mechanistically, LOC101929709 enriched in the cytoplasm helps LIN28B stabilize c-MYC mRNA. Moreover, c-MYC promoted the transcription of both LOC101929709 and LIN28B. Additionally, LOC101929709 also activated the PI3K/AKT pathway. CONCLUSIONS The c-MYC/LOC101929709/LIN28B axis promotes aerobic glycolysis and tumour progression. Thus, LOC101929709 can be a novel potential target for gastric cancer treatment.
Collapse
|
40
|
Xu C, Li B, Yu N, Yao B, Wang F, Mei Y. The c-Myc targeting hnRNPAB promotes lung adenocarcinoma cell proliferation via stabilization of CDK4 mRNA. Int J Biochem Cell Biol 2023; 156:106372. [PMID: 36657708 DOI: 10.1016/j.biocel.2023.106372] [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: 11/25/2022] [Revised: 01/12/2023] [Accepted: 01/16/2023] [Indexed: 01/19/2023]
Abstract
The c-Myc oncoprotein plays a pivotal role in tumorigenesis. The deregulated expression of c-Myc has been linked to a variety of human cancers including lung adenocarcinoma. The oncogenic function of c-Myc has been largely attributed to its intrinsic nature as a transcription factor. Here we reported the RNA binding protein hnRNPAB as a direct transcriptional target of c-Myc by performing quantitative real-time polymerase chain reaction (qRT-PCR), western blot, chromatin immunoprecipitation (ChIP), and luciferase reporter analyses. Flow cytometry, colony formation, and RNA immunoprecipitation (RIP) assays were used to investigate the role of hnRNPAB in lung adenocarcinoma cell proliferation, as well as the underlying mechanism. HnRNPAB was functionally shown to promote lung adenocarcinoma cell proliferation by accelerating G1/S cell cycle progression. Mechanistically, hnRNPAB interacted with and stabilized CDK4 mRNA, thereby increasing CDK4 expression. Moreover, hnRNPAB was able to promote G1/S cell cycle progression and cell proliferation via the regulation of CDK4. HnRNPAB was also revealed as a mediator of the promoting effect of c-Myc on cell proliferation. Together, these findings demonstrate that hnRNPAB is an important regulator of lung adenocarcinoma cell proliferation. They also add new insights into the mechanisms of how c-Myc promotes tumorigenesis.
Collapse
Affiliation(s)
- Chen Xu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bingyan Li
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Ning Yu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Bo Yao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fang Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Yide Mei
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China; The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| |
Collapse
|
41
|
Ivanova OM, Anufrieva KS, Kazakova AN, Malyants IK, Shnaider PV, Lukina MM, Shender VO. Non-canonical functions of spliceosome components in cancer progression. Cell Death Dis 2023; 14:77. [PMID: 36732501 PMCID: PMC9895063 DOI: 10.1038/s41419-022-05470-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 02/04/2023]
Abstract
Dysregulation of pre-mRNA splicing is a common hallmark of cancer cells and it is associated with altered expression, localization, and mutations of the components of the splicing machinery. In the last few years, it has been elucidated that spliceosome components can also influence cellular processes in a splicing-independent manner. Here, we analyze open source data to understand the effect of the knockdown of splicing factors in human cells on the expression and splicing of genes relevant to cell proliferation, migration, cell cycle regulation, DNA repair, and cell death. We supplement this information with a comprehensive literature review of non-canonical functions of splicing factors linked to cancer progression. We also specifically discuss the involvement of splicing factors in intercellular communication and known autoregulatory mechanisms in restoring their levels in cells. Finally, we discuss strategies to target components of the spliceosome machinery that are promising for anticancer therapy. Altogether, this review greatly expands understanding of the role of spliceosome proteins in cancer progression.
Collapse
Affiliation(s)
- Olga M Ivanova
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Institute for Regenerative Medicine, Sechenov University, Moscow, 119991, Russian Federation.
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, 141701, Russian Federation
| | - Irina K Malyants
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Chemical-Pharmaceutical Technologies and Biomedical Drugs, Mendeleev University of Chemical Technology of Russia, Moscow, 125047, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119991, Russian Federation
| | - Maria M Lukina
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation
| | - Victoria O Shender
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow, 119435, Russian Federation.
- Federal Research and Clinical Center of Physical-Chemical Medicine of the Federal Medical and Biological Agency, Moscow, 119435, Russian Federation.
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, 117997, Russian Federation.
| |
Collapse
|
42
|
Habashy DA, Hamad MHM, Ragheb M, Khalil ZA, El Sobky SA, Hosny KA, Esmat G, El-Ekiaby N, Fawzy IO, Abdelaziz AI. Regulation of IGF2BP1 by miR-186 and its impact on downstream lncRNAs H19, FOXD2-AS1, and SNHG3 in HCC. Life Sci 2022; 310:121075. [PMID: 36243115 DOI: 10.1016/j.lfs.2022.121075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 10/02/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
|
43
|
Ramesh-Kumar D, Guil S. The IGF2BP family of RNA binding proteins links epitranscriptomics to cancer. Semin Cancer Biol 2022; 86:18-31. [PMID: 35643219 DOI: 10.1016/j.semcancer.2022.05.009] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/10/2022] [Accepted: 05/17/2022] [Indexed: 02/06/2023]
Abstract
RNA binding proteins that act at the post-transcriptional level display a richness of mechanisms to modulate the transcriptional output and respond to changing cellular conditions. The family of IGF2BP proteins recognize mRNAs modified by methylation and lengthen their lifecycle in the context of stable ribonucleoprotein particles to promote cancer progression. They are emerging as key 'reader' proteins in the epitranscriptomic field, driving the fate of bound substrates under physiological and disease conditions. Recent developments in the field include the recognition that noncoding substrates play crucial roles in mediating the pro-growth features of IGF2BP family, not only as regulated targets, but also as modulators of IGF2BP function themselves. In this review, we summarize the regulatory roles of IGF2BP proteins and link their molecular role as m6A modification readers to the cellular phenotype, thus providing a comprehensive insight into IGF2BP function.
Collapse
Affiliation(s)
- Deepthi Ramesh-Kumar
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia 08916, Spain
| | - Sonia Guil
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia 08916, Spain.
| |
Collapse
|
44
|
Nag S, Goswami B, Das Mandal S, Ray PS. Cooperation and competition by RNA-binding proteins in cancer. Semin Cancer Biol 2022; 86:286-297. [PMID: 35248729 DOI: 10.1016/j.semcancer.2022.02.023] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/24/2022] [Accepted: 02/25/2022] [Indexed: 02/07/2023]
Abstract
Post-transcriptional regulation of gene expression plays a major role in determining the cellular proteome in health and disease. Post-transcriptional control mechanisms are disrupted in many cancers, contributing to multiple processes of tumorigenesis. RNA-binding proteins (RBPs), the main post-transcriptional regulators, often show altered expression and activity in cancer cells. Dysregulation of RBPs contributes to many cancer phenotypes, functioning in complex regulatory networks with other cellular players such as non-coding RNAs, signaling mediators and transcription factors to alter the expression of oncogenes and tumor suppressor genes. RBPs often function combinatorially, based on their binding to target sequences/structures on shared mRNA targets, to regulate the expression of cancer-related genes. This gives rise to cooperativity and competition between RBPs in mRNA binding and resultant functional outcomes in post-transcriptional processes such as mRNA splicing, stability, export and translation. Cooperation and competition is also observed in the case of interaction of RBPs and microRNAs with mRNA targets. RNA structural change is a common mechanism mediating the cooperative/competitive interplay between RBPs and between RBPs and microRNAs. RNA modifications, leading to changes in RNA structure, add a new dimension to cooperative/competitive binding of RBPs to mRNAs, further expanding the RBP regulatory landscape. Therefore, cooperative/competitive interplay between RBPs is a major determinant of the RBP interactome and post-transcriptional regulation of gene expression in cancer cells.
Collapse
Affiliation(s)
- Sharanya Nag
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Binita Goswami
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Sukhen Das Mandal
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India
| | - Partho Sarothi Ray
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India.
| |
Collapse
|
45
|
Qi X, Yan Q, Shang Y, Zhao R, Ding X, Gao SJ, Li W, Lu C. A viral interferon regulatory factor degrades RNA-binding protein hnRNP Q1 to enhance aerobic glycolysis via recruiting E3 ubiquitin ligase KLHL3 and decaying GDPD1 mRNA. Cell Death Differ 2022; 29:2233-2246. [PMID: 35538151 PMCID: PMC9613757 DOI: 10.1038/s41418-022-01011-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/09/2022] Open
Abstract
Reprogramming of host metabolism is a common strategy of viral evasion of host cells, and is essential for successful viral infection and induction of cancer in the context cancer viruses. Kaposi's sarcoma (KS) is the most common AIDS-associated cancer caused by KS-associated herpesvirus (KSHV) infection. KSHV-encoded viral interferon regulatory factor 1 (vIRF1) regulates multiple signaling pathways and plays an important role in KSHV infection and oncogenesis. However, the role of vIRF1 in KSHV-induced metabolic reprogramming remains elusive. Here we show that vIRF1 increases glucose uptake, ATP production and lactate secretion by downregulating heterogeneous nuclear ribonuclear protein Q1 (hnRNP Q1). Mechanistically, vIRF1 upregulates and recruits E3 ubiquitin ligase Kelch-like 3 (KLHL3) to degrade hnRNP Q1 through a ubiquitin-proteasome pathway. Furthermore, hnRNP Q1 binds to and stabilizes the mRNA of glycerophosphodiester phosphodiesterase domain containing 1 (GDPD1). However, vIRF1 targets hnRNP Q1 for degradation, which destabilizes GDPD1 mRNA, resulting in induction of aerobic glycolysis. These results reveal a novel role of vIRF1 in KSHV metabolic reprogramming, and identifying a potential therapeutic target for KSHV infection and KSHV-induced cancers.
Collapse
Affiliation(s)
- Xiaoyu Qi
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Qin Yan
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Yuancui Shang
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Runran Zhao
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China
| | - Xiangya Ding
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China
| | - Shou-Jiang Gao
- Tumor Virology Program, UPMC Hillman Cancer Center, and Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA, 15232, USA
| | - Wan Li
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China.
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China.
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China.
| | - Chun Lu
- State Key Laboratory of Reproductive Medicine, Department of Gynecology, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing Medical University, Nanjing, 210004, P. R. China.
- Department of Microbiology, Nanjing Medical University, Nanjing, 211166, P. R. China.
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, 211166, P. R. China.
| |
Collapse
|
46
|
Bi Y, Jing Y, Guo L. Construction and validation of a prognostic marker and risk model for HCC ultrasound therapy combined with WGCNA identification. Front Genet 2022; 13:1017551. [PMID: 36263426 PMCID: PMC9573990 DOI: 10.3389/fgene.2022.1017551] [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: 08/12/2022] [Accepted: 09/12/2022] [Indexed: 11/23/2022] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a malignant tumor with a highly aggressive and metastatic nature. Ultrasound remains a routine monitoring tool for screening, treatment and post-treatment recheck of HCC. Therefore, it is of great significance to explore the role of ultrasound therapy and related genes in prognosis prediction and clinical diagnosis and treatment of HCC. Methods: Gene co-expression networks were developed utilizing the R package WGCNA as per the expression profiles and clinical features of TCGA HCC samples, key modules were identified by the correlation coefficients between clinical features and modules, and hub genes of modules were determined as per the GS and MM values. Ultrasound treatment differential expression genes were identified using R package limma, and univariate Cox analysis was conducted on the intersection genes of ultrasound differential expression genes and hub genes of key HCC modules to screen the signatures linked with HCC prognosis and construct a risk model. The median risk score was used as the threshold point to classify tumor samples into high- and low-risk groups, and the R package IOBR was used to assess the proportion of immune cells in high- and low-risk groups, R package maftools to assess the genomic mutation differences in high- and low-risk groups, R package GSVA’s ssgsea algorithm to assess the HALLMARK pathway enrichment analysis, and R package pRRophetic to analyze drug sensitivity in patients with HCC. Results: WGCNA analysis based on the expression profiles and clinical data of the TCGA LIHC cohort identified three key modules with two major clinical features associated with HCC. The intersection of ultrasound-related differential genes and module hub genes was selected for univariate Cox analysis to identify prognostic factors significantly associated with HCC, and a risk score model consisting of six signatures was finally developed to analyze the prognosis of individuals with HCC. The risk model showed strength in the training set, overall set, and external validation set. The percentage of immune cell infiltration, genomic mutations, pathway enrichment scores, and chemotherapy drug resistance were significantly different between high- and low-risk groups according to the risk scores. Expression of model genes correlated with tumor immune microenvironment and clinical tumor characteristics while generally differentially expressed in pan-cancer tumor and healthy samples. In the immunotherapy dataset, patients in the high-risk group had a worse prognosis with immunotherapy, indicating that subjects in the low-risk group are more responsive to immunotherapy. Conclusion: The 6-gene signature constructed by ultrasound treatment of HCC combined with WGCNA analysis can be used for prognosis prediction of HCC patients and may become a marker for immune response.
Collapse
Affiliation(s)
- Yunlong Bi
- Department of Orthopedics, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Yu Jing
- Department of Oncology, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
| | - Lingling Guo
- Department of Ultrasound, First Affiliated Hospital of Jinzhou Medical University, Jinzhou, China
- *Correspondence: Lingling Guo,
| |
Collapse
|
47
|
[Clinical significance and pathogenesis analysis of heterogeneous nuclear ribonucleoprotein U in acute myeloid leukemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2022; 43:745-752. [PMID: 36709168 PMCID: PMC9613492 DOI: 10.3760/cma.j.issn.0253-2727.2022.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Objective: To investigate the clinical significance and pathogenesis of heterogeneous nuclear ribonucleoprotein U (hnRNP U) in acute myeloid leukemia (AML) . Methods: The expression of hnRNP U, an RNA binding protein, in patients with AML and healthy controls was compared based on the Gene Expression Profiling Interactive Analysis database and the data of the center. The Beat AML Dataset (n=158) was downloaded from the cBioPortal database. The hnRNP U expression level was divided into the high-expression group (n=89) and low-expression group (n=69) , and patients' clinical characteristics were compared. The effect of hnRNP U on the biological behavior of human AML cell lines was studied by Cell Counting Kit-8 assay to detect cell proliferation. Annexin Ⅴ-APC/7-AAD antibodies were used to detect cell apoptosis. DNA content (PI staining) was quantitatively analyzed to detect cell cycle changes, and colony formation experiments were performed to detect cell cloning formation ability after hnRNP U knockdown in Kasumi-1 and MOLM-13 cells. To study the effect of hnRNP U knockdown on the DNA damage response (DDR) pathway proteins of cleaved-PARP, immunoblot analysis using p-H2A.X was conducted. Results: ①Pan-cancer analysis showed that hnRNP U was highly expressed in patients with AML, and the expression level of hnRNP U mRNA in peripheral blood mononuclear cells was significantly higher in patients with AML than in healthy controls (0.0315±0.0042 vs 0.0195±0.0006, respectively, P<0.01) . ②The age of onset was 56 (2-87) years in the high-expression group and 65 (8-85) years in the low-expression group (t=-2.681, P=0.007) . Moreover, the high-expression group had a higher proportion of combined FLT3 mutations than the low-expression group (χ(2)=4.069, P=0.044) . ③Compared with the negative control, hnRNP U knockdown inhibited the proliferation (P<0.001 and P<0.001) , promoted the apoptosis (P<0.01 and P<0.001) , decreased the colony formation ability (P<0.001 and P<0.001) , and arrested the cell cycles in the G(2)/M phase (P<0.05 and P<0.01) of Kasumi-1 and MOLM-13 cells, respectively. ④hnRNP U knockdown could increase the protein expression of cleaved-PARP and p-H2A.X on the DDR pathway. Conclusion: hnRNP U is highly expressed in AML, and hnRNP U knockdown can inhibit the occurrence and development of AML possibly through the activation of the DDR pathway.
Collapse
|
48
|
He Q, Hao P, He G, Mai H, Liu W, Zhang W, Zhang K, Zhong G, Guo R, Yu C, Li Y, Wong C, Chen Q, Chen Y. IGF2BP1-regulated expression of ERRα is involved in metabolic reprogramming of chemotherapy resistant osteosarcoma cells. Lab Invest 2022; 20:348. [PMID: 35918761 PMCID: PMC9344706 DOI: 10.1186/s12967-022-03549-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 07/18/2022] [Indexed: 11/15/2022]
Abstract
Doxorubicin (Dox) is the standard treatment approach for osteosarcoma (OS), while acquired drug resistance seriously attenuates its treatment efficiency. The present study aimed to investigate the potential roles of metabolic reprogramming and the related regulatory mechanism in Dox-resistant OS cells. The results showed that the ATP levels, lactate generation, glucose consumption and oxygen consumption rate were significantly increased in Dox-resistant OS cells compared with parental cells. Furthermore, the results revealed that the increased expression of estrogen-related receptor alpha (ERRα) was involved in metabolic reprogramming in chemotherapy resistant OS cells, since targeted inhibition of ERRα restored the shifting of metabolic profiles. Mechanistic analysis indicated that the mRNA stability, rather than ERRα transcription was markedly increased in chemoresistant OS cells. Therefore, it was hypothesized that the 3ʹ-untranslated region of ERRα mRNA was methylated by N6-methyladenine, which could further recruit insulin-like growth factor 2 mRNA binding protein 1 (IGF2BP1) to suppress mRNA decay and increase mRNA stability. IGF2BP1 knockdown downregulated ERRα and reversed the metabolic alteration of resistant OS cells. Additionally, the oncogenic effect of the IGF2BP1/ERRα axis on Dox-resistant OS cells was verified by in vitro and in vivo experiments. Clinical analysis also revealed that the expression levels of IGF2BP1 and ERRα were associated with the clinical progression of OS. Collectively, the current study suggested that the IGF2BP1/ERRα axis could regulate metabolic reprogramming to contribute to the chemoresistance of OS cells.
Collapse
Affiliation(s)
- Qing He
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Peng Hao
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Gang He
- Department of Orthopedics, Guangzhou Zengcheng District People's Hospital, Guangzhou, China
| | - Hantao Mai
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wenzhou Liu
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, Yanjiang West Road, Yuexiu, Guangzhou, 510120, China
| | - Weiqiong Zhang
- Department of Orthopedics, Guangzhou Zengcheng District People's Hospital, Guangzhou, China
| | - Kelin Zhang
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Guifang Zhong
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ruilian Guo
- Department of Surgical Intensive Care Unit, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Changzhi Yu
- Department of Chinese Traditional Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yang Li
- Pediatric Hematology & Oncology, Sun Yat-sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China
| | - Chipiu Wong
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, Yanjiang West Road, Yuexiu, Guangzhou, 510120, China
| | - Qian Chen
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, Yanjiang West Road, Yuexiu, Guangzhou, 510120, China
| | - Yantao Chen
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, No.107, Yanjiang West Road, Yuexiu, Guangzhou, 510120, China.
| |
Collapse
|
49
|
Triantopoulou N, Vidaki M. Local mRNA translation and cytoskeletal reorganization: Mechanisms that tune neuronal responses. Front Mol Neurosci 2022; 15:949096. [PMID: 35979146 PMCID: PMC9376447 DOI: 10.3389/fnmol.2022.949096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/07/2022] [Indexed: 12/31/2022] Open
Abstract
Neurons are highly polarized cells with significantly long axonal and dendritic extensions that can reach distances up to hundreds of centimeters away from the cell bodies in higher vertebrates. Their successful formation, maintenance, and proper function highly depend on the coordination of intricate molecular networks that allow axons and dendrites to quickly process information, and respond to a continuous and diverse cascade of environmental stimuli, often without enough time for communication with the soma. Two seemingly unrelated processes, essential for these rapid responses, and thus neuronal homeostasis and plasticity, are local mRNA translation and cytoskeletal reorganization. The axonal cytoskeleton is characterized by high stability and great plasticity; two contradictory attributes that emerge from the powerful cytoskeletal rearrangement dynamics. Cytoskeletal reorganization is crucial during nervous system development and in adulthood, ensuring the establishment of proper neuronal shape and polarity, as well as regulating intracellular transport and synaptic functions. Local mRNA translation is another mechanism with a well-established role in the developing and adult nervous system. It is pivotal for axonal guidance and arborization, synaptic formation, and function and seems to be a key player in processes activated after neuronal damage. Perturbations in the regulatory pathways of local translation and cytoskeletal reorganization contribute to various pathologies with diverse clinical manifestations, ranging from intellectual disabilities (ID) to autism spectrum disorders (ASD) and schizophrenia (SCZ). Despite the fact that both processes are essential for the orchestration of pathways critical for proper axonal and dendritic function, the interplay between them remains elusive. Here we review our current knowledge on the molecular mechanisms and specific interaction networks that regulate and potentially coordinate these interconnected processes.
Collapse
Affiliation(s)
- Nikoletta Triantopoulou
- Division of Basic Sciences, Medical School, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Greece
| | - Marina Vidaki
- Division of Basic Sciences, Medical School, University of Crete, Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas (IMBB-FORTH), Heraklion, Greece
- *Correspondence: Marina Vidaki,
| |
Collapse
|
50
|
Wu S, Yin Y, Wang X. The epigenetic regulation of the germinal center response. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194828. [PMID: 35643396 DOI: 10.1016/j.bbagrm.2022.194828] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
In response to T-cell-dependent antigens, antigen-experienced B cells migrate to the center of the B-cell follicle to seed the germinal center (GC) response after cognate interactions with CD4+ T cells. These GC B cells eventually mature into memory and long-lived antibody-secreting plasma cells, thus generating long-lived humoral immunity. Within GC, B cells undergo somatic hypermutation of their B cell receptors (BCR) and positive selection for the emergence of high-affinity antigen-specific B-cell clones. However, this process may be dangerous, as the accumulation of aberrant mutations could result in malignant transformation of GC B cells or give rise to autoreactive B cell clones that can cause autoimmunity. Because of this, better understanding of GC development provides diagnostic and therapeutic clues to the underlying pathologic process. A productive GC response is orchestrated by multiple mechanisms. An emerging important regulator of GC reaction is epigenetic modulation, which has key transcriptional regulatory properties. In this review, we summarize the current knowledge on the biology of epigenetic mechanisms in the regulation of GC reaction and outline its importance in identification of immunotherapy decision making.
Collapse
Affiliation(s)
- Shusheng Wu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuye Yin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China.
| |
Collapse
|