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Wang J, Guo T, Zhang X, Guo J, Meng X, Yan S, Wang Y, Xiao Y, Xu W, Wei X, Ding K, Zhang J, Mi Y, Wu S, Chen J, Huang Y, Ren S, Hou J. Comprehensive investigation in oncogenic functions and immunological roles of NCBP2 and its validation in prostate cancer. Transl Oncol 2024; 47:102049. [PMID: 38964031 PMCID: PMC11283080 DOI: 10.1016/j.tranon.2024.102049] [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: 10/13/2023] [Revised: 06/06/2024] [Accepted: 07/01/2024] [Indexed: 07/06/2024] Open
Abstract
BACKGROUND Nuclear cap-binding protein 2 (NCBP2), as the component of the cap-binding complex, participates in a number of biological processes, including pre-mRNA splicing, transcript export, translation regulation and other gene expression steps. However, the role of NCBP2 on the tumor cells and immune microenvironment remains unclear. To systematically analyze and validate functions of NCBP2, we performed a pan-cancer analysis using multiple approaches. METHODS The data in this study were derived from sequencing, mutation, and methylation data in the TCGA cohort, normal sample sequencing data in the GTEx project, and cell line expression profile data in the CCLE database. RESULTS Survival analyses including the Cox proportional-hazards model and log-rank test revealed the poor prognostic role of NCBP2 in multiple tumors. We further validated the oncogenic ability of NCBP2 in prostate cancer cell lines, organoids and tumor-bearing mice. A negative correlation was observed between NCBP2 expression and immune score by the ESTIMATE algorithm. Simultaneously, the NCBP2-induced immunosuppressive microenvironment might be related to the decline in CD8+T cells and the increase in regulatory T cells and neutrophils, examined by flow cytometry experiments for NCBP2 overexpressed tumor-bearing mice. CONCLUSION This research offered strong proof supporting NCBP2 as the prognostic marker and the therapeutic target in the future.
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Affiliation(s)
- Jian Wang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China; Department of Urology, Shanghai Changzheng Hospital, Shanghai, China; Department of Urology, Shanghai Changhai Hospital, Shanghai, China; Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Tao Guo
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaomin Zhang
- Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Jiacheng Guo
- CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Xiangyu Meng
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing China
| | - Shi Yan
- Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Ye Wang
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China
| | - Yutian Xiao
- Department of Urology, Shanghai Changhai Hospital, Shanghai, China
| | - Weidong Xu
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China
| | - Xuedong Wei
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Keke Ding
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Jun Zhang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuanyuan Mi
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Sheng Wu
- Department of Urology, Affiliated Hospital of Jiangnan University, Wuxi, China
| | - Jie Chen
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China.
| | - Yuhua Huang
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China.
| | - Shancheng Ren
- Department of Urology, Shanghai Changzheng Hospital, Shanghai, China.
| | - Jianquan Hou
- Department of Urology, The First Affiliated Hospital of Soochow University, Suzhou, China.
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Kowalski MH, Wessels HH, Linder J, Dalgarno C, Mascio I, Choudhary S, Hartman A, Hao Y, Kundaje A, Satija R. Multiplexed single-cell characterization of alternative polyadenylation regulators. Cell 2024; 187:4408-4425.e23. [PMID: 38925112 DOI: 10.1016/j.cell.2024.06.005] [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: 02/09/2023] [Revised: 03/12/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024]
Abstract
Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity regulated by the cleavage and polyadenylation (CPA) machinery. To better understand how these proteins govern polyA site choice, we introduce CPA-Perturb-seq, a multiplexed perturbation screen dataset of 42 CPA regulators with a 3' scRNA-seq readout that enables transcriptome-wide inference of polyA site usage. We develop a framework to detect perturbation-dependent changes in polyadenylation and characterize modules of co-regulated polyA sites. We find groups of intronic polyA sites regulated by distinct components of the nuclear RNA life cycle, including elongation, splicing, termination, and surveillance. We train and validate a deep neural network (APARENT-Perturb) for tandem polyA site usage, delineating a cis-regulatory code that predicts perturbation response and reveals interactions between regulatory complexes. Our work highlights the potential for multiplexed single-cell perturbation screens to further our understanding of post-transcriptional regulation.
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Affiliation(s)
- Madeline H Kowalski
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York University Grossman School of Medicine, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA.
| | - Johannes Linder
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | | | - Isabella Mascio
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Saket Choudhary
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Yuhan Hao
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford, CA, USA; Department of Computer Science, Stanford University, Stanford, CA, USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA; New York University Grossman School of Medicine, New York, NY, USA.
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Mohammad T, Zolotovskaia MA, Suntsova MV, Buzdin AA. Cancer fusion transcripts with human non-coding RNAs. Front Oncol 2024; 14:1415801. [PMID: 38919532 PMCID: PMC11196610 DOI: 10.3389/fonc.2024.1415801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Cancer chimeric, or fusion, transcripts are thought to most frequently appear due to chromosomal aberrations that combine moieties of unrelated normal genes. When being expressed, this results in chimeric RNAs having upstream and downstream parts relatively to the breakpoint position for the 5'- and 3'-fusion components, respectively. As many other types of cancer mutations, fusion genes can be of either driver or passenger type. The driver fusions may have pivotal roles in malignisation by regulating survival, growth, and proliferation of tumor cells, whereas the passenger fusions most likely have no specific function in cancer. The majority of research on fusion gene formation events is concentrated on identifying fusion proteins through chimeric transcripts. However, contemporary studies evidence that fusion events involving non-coding RNA (ncRNA) genes may also have strong oncogenic potential. In this review we highlight most frequent classes of ncRNAs fusions and summarize current understanding of their functional roles. In many cases, cancer ncRNA fusion can result in altered concentration of the non-coding RNA itself, or it can promote protein expression from the protein-coding fusion moiety. Differential splicing, in turn, can enrich the repertoire of cancer chimeric transcripts, e.g. as observed for the fusions of circular RNAs and long non-coding RNAs. These and other ncRNA fusions are being increasingly recognized as cancer biomarkers and even potential therapeutic targets. Finally, we discuss the use of ncRNA fusion genes in the context of cancer detection and therapy.
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Affiliation(s)
- Tharaa Mohammad
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
| | - Marianna A. Zolotovskaia
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
| | | | - Anton A. Buzdin
- Laboratory for Translational and Genomic Bioinformatics, Moscow Center for Advanced Studies, Moscow, Russia
- Department of Molecular Genetic Technologies, Laboratory of Bioinformatics, Endocrinology Research Center, Moscow, Russia
- I.M. Sechenov First Moscow State Medical University, Moscow, Russia
- PathoBiology Group, European Organization for Research and Treatment of Cancer (EORTC), Brussels, Belgium
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russia
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Lin P, Cao W, Chen X, Zhang N, Xing Y, Yang N. Role of mRNA-binding proteins in retinal neovascularization. Exp Eye Res 2024; 242:109870. [PMID: 38514023 DOI: 10.1016/j.exer.2024.109870] [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: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Retinal neovascularization (RNV) is a pathological process that primarily occurs in diabetic retinopathy, retinopathy of prematurity, and retinal vein occlusion. It is a common yet debilitating clinical condition that culminates in blindness. Urgent efforts are required to explore more efficient and less limiting therapeutic strategies. Key RNA-binding proteins (RBPs), crucial for post-transcriptional regulation of gene expression by binding to RNAs, are closely correlated with RNV development. RBP-RNA interactions are altered during RNV. Here, we briefly review the characteristics and functions of RBPs, and the mechanism of RNV. Then, we present insights into the role of the regulatory network of RBPs in RNV. HuR, eIF4E, LIN28B, SRSF1, METTL3, YTHDF1, Gal-1, HIWI1, and ZFR accelerate RNV progression, whereas YTHDF2 and hnRNPA2B1 hinder it. The mechanisms elucidated in this review provide a reference to guide the design of therapeutic strategies to reverse abnormal processes.
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Affiliation(s)
- Pei Lin
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Wenye Cao
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Xuemei Chen
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China; Department of Ophthalmology, Aier Eye Hospital of Wuhan University, Hubei, China.
| | - Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
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Michaelsen GL, da Silva LDRE, de Lima DS, Jaeger MDC, Brunetto AT, Dalmolin RJS, Sinigaglia M. A Prognostic Methylation-Driven Two-Gene Signature in Medulloblastoma. J Mol Neurosci 2024; 74:47. [PMID: 38662144 DOI: 10.1007/s12031-024-02203-9] [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: 09/29/2023] [Accepted: 02/21/2024] [Indexed: 04/26/2024]
Abstract
Medulloblastoma (MB) is one of the most common pediatric brain tumors and it is estimated that one-third of patients will not achieve long-term survival. Conventional prognostic parameters have limited and unreliable correlations with MB outcome, presenting a major challenge for patients' clinical improvement. Acknowledging this issue, our aim was to build a gene signature and evaluate its potential as a new prognostic model for patients with the disease. In this study, we used six datasets totaling 1679 samples including RNA gene expression and DNA methylation data from primary MB as well as control samples from healthy cerebellum. We identified methylation-driven genes (MDGs) in MB, genes whose expression is correlated with their methylation. We employed LASSO regression, incorporating the MDGs as a parameter to develop the prognostic model. Through this approach, we derived a two-gene signature (GS-2) of candidate prognostic biomarkers for MB (CEMIP and NCBP3). Using a risk score model, we confirmed the GS-2 impact on overall survival (OS) with Kaplan-Meier analysis. We evaluated its robustness and accuracy with receiver operating characteristic curves predicting OS at 1, 3, and 5 years in multiple independent datasets. The GS-2 showed highly significant results as an independent prognostic biomarker compared to traditional MB markers. The methylation-regulated GS-2 risk score model can effectively classify patients with MB into high and low-risk, reinforcing the importance of this epigenetic modification in the disease. Such genes stand out as promising prognostic biomarkers with potential application for MB treatment.
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Affiliation(s)
- Gustavo Lovatto Michaelsen
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- Bioinformatics Multidisciplinary Environment-BioME, Digital Metropole Institute, Federal University of Rio Grande do Norte, Natal, 59076-550, RN, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil
| | - Lívia Dos Reis Edinger da Silva
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- Federal University of Health Sciences of Porto Alegre, Porto Alegre, 90050-170, RS, Brazil
| | - Douglas Silva de Lima
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- Institute of Basic Health Sciences, Federal University of Rio Grande do Sul, Porto Alegre, 90035-003, RS, Brazil
| | - Mariane da Cunha Jaeger
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil
| | - André Tesainer Brunetto
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil
| | - Rodrigo Juliani Siqueira Dalmolin
- Bioinformatics Multidisciplinary Environment-BioME, Digital Metropole Institute, Federal University of Rio Grande do Norte, Natal, 59076-550, RN, Brazil
- Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, 59064-741, RN, Brazil
| | - Marialva Sinigaglia
- Children's Cancer Institute, Porto Alegre, 90620-110, RS, Brazil.
- Bioinformatics Multidisciplinary Environment-BioME, Digital Metropole Institute, Federal University of Rio Grande do Norte, Natal, 59076-550, RN, Brazil.
- National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, 90035-003, RS, Brazil.
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Yang J, Ouedraogo SY, Wang J, Li Z, Feng X, Ye Z, Zheng S, Li N, Zhan X. Clinically relevant stratification of lung squamous carcinoma patients based on ubiquitinated proteasome genes for 3P medical approach. EPMA J 2024; 15:67-97. [PMID: 38463626 PMCID: PMC10923771 DOI: 10.1007/s13167-024-00352-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Relevance The proteasome is a crucial mechanism that regulates protein fate and eliminates misfolded proteins, playing a significant role in cellular processes. In the context of lung cancer, the proteasome's regulatory function is closely associated with the disease's pathophysiology, revealing multiple connections within the cell. Therefore, studying proteasome inhibitors as a means to identify potential pathways in carcinogenesis and metastatic progression is crucial in in-depth insight into its molecular mechanism and discovery of new therapeutic target to improve its therapy, and establishing effective biomarkers for patient stratification, predictive diagnosis, prognostic assessment, and personalized treatment for lung squamous carcinoma in the framework of predictive, preventive, and personalized medicine (PPPM; 3P medicine). Methods This study identified differentially expressed proteasome genes (DEPGs) in lung squamous carcinoma (LUSC) and developed a gene signature validated through Kaplan-Meier analysis and ROC curves. The study used WGCNA analysis to identify proteasome co-expression gene modules and their interactions with the immune system. NMF analysis delineated distinct LUSC subtypes based on proteasome gene expression patterns, while ssGSEA analysis quantified immune gene-set abundance and classified immune subtypes within LUSC samples. Furthermore, the study examined correlations between clinicopathological attributes, immune checkpoints, immune scores, immune cell composition, and mutation status across different risk score groups, NMF clusters, and immunity clusters. Results This study utilized DEPGs to develop an eleven-proteasome gene-signature prognostic model for LUSC, which divided samples into high-risk and low-risk groups with significant overall survival differences. NMF analysis identified six distinct LUSC clusters associated with overall survival. Additionally, ssGSEA analysis classified LUSC samples into four immune subtypes based on the abundance of immune cell infiltration with clinical relevance. A total of 145 DEGs were identified between high-risk and low-risk score groups, which had significant biological effects. Moreover, PSMD11 was found to promote LUSC progression by depending on the ubiquitin-proteasome system for degradation. Conclusions Ubiquitinated proteasome genes were effective in developing a prognostic model for LUSC patients. The study emphasized the critical role of proteasomes in LUSC processes, such as drug sensitivity, immune microenvironment, and mutation status. These data will contribute to the clinically relevant stratification of LUSC patients for personalized 3P medical approach. Further, we also recommend the application of the ubiquitinated proteasome system in multi-level diagnostics including multi-omics, liquid biopsy, prediction and targeted prevention of chronic inflammation and metastatic disease, and mitochondrial health-related biomarkers, for LUSC 3PM practice. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00352-w.
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Affiliation(s)
- Jingru Yang
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Serge Yannick Ouedraogo
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Jingjing Wang
- Department of Pathology, Shandong Cancer Hospital and Institute, Shandong First Medical University, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Zhijun Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Xiaoxia Feng
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Zhen Ye
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
- School of Basic Medicine, Shandong First Medical University, 6699 Qingdao Road, Jinan, Shandong 250117 People's Republic of China
| | - Shu Zheng
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Na Li
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
| | - Xianquan Zhan
- Medical Science and Technology Innovation Center, Shandong Key Laboratory of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 People's Republic of China
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Wang J, Horlacher M, Cheng L, Winther O. DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning. Bioinformatics 2024; 40:btae065. [PMID: 38317052 PMCID: PMC10879750 DOI: 10.1093/bioinformatics/btae065] [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: 12/21/2023] [Revised: 01/22/2024] [Accepted: 02/01/2024] [Indexed: 02/07/2024] Open
Abstract
MOTIVATION Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through interaction with cis-regulatory RNA motifs, current methods do not incorporate RBP-binding information. RESULTS In this article, we propose DeepLocRNA, an interpretable deep-learning model that leverages a pre-trained multi-task RBP-binding prediction model to predict the subcellular localization of RNA molecules via fine-tuning. We constructed DeepLocRNA using a comprehensive dataset with variant RNA types and evaluated it on the held-out dataset. Our model achieved state-of-the-art performance in predicting RNA subcellular localization in mRNA and miRNA. It has also demonstrated great generalization capabilities, performing well on both human and mouse RNA. Additionally, a motif analysis was performed to enhance the interpretability of the model, highlighting signal factors that contributed to the predictions. The proposed model provides general and powerful prediction abilities for different RNA types and species, offering valuable insights into the localization patterns of RNA molecules and contributing to our understanding of cellular processes at the molecular level. A user-friendly web server is available at: https://biolib.com/KU/DeepLocRNA/.
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Affiliation(s)
- Jun Wang
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
| | - Marc Horlacher
- Computational Health Center, Helmholtz Center Munich, Neuherberg 85764, Germany
| | - Lixin Cheng
- Shenzhen People’s Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medicine College of Jinan University, Shenzhen 518020, China
| | - Ole Winther
- Bioinformatics Centre, Department of Biology, University of Copenhagen, København Ø 2100, Denmark
- Center for Genomic Medicine, Rigshospitalet (Copenhagen University Hospital), Copenhagen 2100, Denmark
- Section for Cognitive Systems, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby 2800, Denmark
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Dubiez E, Pellegrini E, Finderup Brask M, Garland W, Foucher AE, Huard K, Heick Jensen T, Cusack S, Kadlec J. Structural basis for competitive binding of productive and degradative co-transcriptional effectors to the nuclear cap-binding complex. Cell Rep 2024; 43:113639. [PMID: 38175753 DOI: 10.1016/j.celrep.2023.113639] [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: 07/17/2023] [Revised: 11/07/2023] [Accepted: 12/15/2023] [Indexed: 01/06/2024] Open
Abstract
The nuclear cap-binding complex (CBC) coordinates co-transcriptional maturation, transport, or degradation of nascent RNA polymerase II (Pol II) transcripts. CBC with its partner ARS2 forms mutually exclusive complexes with diverse "effectors" that promote either productive or destructive outcomes. Combining AlphaFold predictions with structural and biochemical validation, we show how effectors NCBP3, NELF-E, ARS2, PHAX, and ZC3H18 form competing binary complexes with CBC and how PHAX, NCBP3, ZC3H18, and other effectors compete for binding to ARS2. In ternary CBC-ARS2 complexes with PHAX, NCBP3, or ZC3H18, ARS2 is responsible for the initial effector recruitment but inhibits their direct binding to the CBC. We show that in vivo ZC3H18 binding to both CBC and ARS2 is required for nuclear RNA degradation. We propose that recruitment of PHAX to CBC-ARS2 can lead, with appropriate cues, to competitive displacement of ARS2 and ZC3H18 from the CBC, thus promoting a productive rather than a degradative RNA fate.
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Affiliation(s)
- Etienne Dubiez
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France; Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France
| | - Erika Pellegrini
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Maja Finderup Brask
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | | | - Karine Huard
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, CS 90181, 38042 Grenoble Cedex 9, France.
| | - Jan Kadlec
- Univ. Grenoble Alpes, CNRS, CEA, IBS, 38000 Grenoble, France.
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Li J, Zheng L, Song L, Dong Z, Bai W, Qi L. Identification and validation of N 7 -methylguanosine-associated gene NCBP1 as prognostic and immune-associated biomarkers in breast cancer patients. J Cell Mol Med 2024; 28:e18067. [PMID: 38071502 PMCID: PMC10826432 DOI: 10.1111/jcmm.18067] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 11/14/2023] [Accepted: 11/22/2023] [Indexed: 02/01/2024] Open
Abstract
We intend to evaluate the importance of N7 -methylguanosine (m7G) for the prognosis of breast cancer (BC). We gained 29 m7G-related genes from the published literature and among them, 16 m7G-related genes were found to have differential expression. Five differentially expressed genes (CYFIP1, EIF4E, EIF4E3, NCBP1 and WDR4) were linked to overall survival. This suggests that m7G-related genes might be prognostic or therapeutic targets for BC patients. We put the five genes to LASSO regression analysis to create a four-gene signature, including EIF4E, EIF4E3, WDR4 and NCBP1, that divides samples into two risky groups. Survival was drastically worsened in a high-risk group (p < 0.001). The signature's predictive capacity was demonstrated using ROC (10-year AUC 0.689; 10-year AUC 0.615; 3-year AUC 0.602). We found that immune status was significantly different between the two risk groups. In particular, NCBP1 also has a poor prognosis, with higher diagnostic value in ROC. NCBP1 also has different immune states according to its high or low expression. Meanwhile, knockdown of NCBP1 suppresses BC malignancy in vitro. Therefore, m7G RNA regulators are crucial participants in BC and four-gene mRNA levels are important predictors of prognosis. NCBP1 plays a critical target of m7G mechanism in BC.
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Affiliation(s)
- Jianrong Li
- Department of General Surgery SciencesShanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/ Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Lin Zheng
- Department of Vascular SurgeryThe Second Hospital of Shanxi Medical UniversityTaiyuanChina
| | - Liying Song
- Thyroid Surgery DepartmentFirst Hospital of Shanxi Medical UniversityTaiyuanChina
| | - Zhuanxia Dong
- GastroenterologyShanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Wenqi Bai
- Department of General Surgery SciencesShanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/ Cancer Hospital Affiliated to Shanxi Medical UniversityTaiyuanChina
| | - Liqiang Qi
- Department of Breast Surgery, National Cancer Center/National Cancer Clinical Medical Research Center/Cancer HospitalChinese Academy of Medical SciencesBeijingChina
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10
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Wang QH, Yan PC, Shi LZ, Teng YJ, Gao XJ, Yao LQ, Liang ZW, Zhou MH, Han W, Li R. PABPN1 functions as a predictive biomarker in colorectal carcinoma. Mol Biol Rep 2023; 51:40. [PMID: 38158471 DOI: 10.1007/s11033-023-08936-x] [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: 08/28/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
PURPOSE PABPN1 acts as a modulator of poly(A) tail length and alternative polyadenylation. This research was aimed to explore the role of PABPN1 in colorectal cancer (CRC). METHODS Public databases were performed to analyze expression, location, roles of prognosis and tumor immunity and interaction with RNAs and proteins of PABPN1. To investigate PABPN1 expression in tissues, 78 CRC specimens were collected to conduct IHC, and 30 pairs of frozen CRC and corresponding adjacent normal tissues were used to conduct qRT-PCR and WB. In addition, in vitro experiments were then carried out to identify the role of PABPN1 in CRC. RESULTS Compared with normal tissues, PABPN1 expression was significant higher in CRC. Its high level predicted poor outcome of CRC. Th1 and Treg had significant negative relationships not only with PABPN1 expression, but also with six molecules interacting with PABPN1, including IFT172, KIAA0895L, RECQL4, WDR6, PABPC1 and NCBP1. In addition, PABPN1 had negative relationships with quite a few immune markers, such as CSF1R, IL-10, CCL2 and so on. In cellular experiments, silencing PABPN1 inhibited proliferation and promoted apoptosis in HCT-116 CRC cells. CONCLUSION In summary, PABPN1 might become a novel biomarker and correlate with tumor immunity in CRC.
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Affiliation(s)
- Qing-Hua Wang
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Pei-Ci Yan
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Zhou Shi
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Ya-Jie Teng
- Department of Gastroenterology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Xiao-Jiao Gao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Li-Qian Yao
- Department of Pathology, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Zhi-Wei Liang
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Ming-Hui Zhou
- Central Laboratory, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China
| | - Wei Han
- Department of General Surgery, Kunshan First People's Hospital Affiliated to Jiangsu University, Kunshan, 215300, Jiangsu, People's Republic of China.
| | - Rui Li
- Department of Gastroenterology, The First Affiliated Hospital of Soochow University, Suzhou, 215006, Jiangsu, People's Republic of China.
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11
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Kataoka N. The Nuclear Cap-Binding Complex, a multitasking binding partner of RNA polymerase II transcripts. J Biochem 2023; 175:9-15. [PMID: 37830942 PMCID: PMC10771035 DOI: 10.1093/jb/mvad081] [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: 07/24/2023] [Revised: 09/26/2023] [Accepted: 10/03/2023] [Indexed: 10/14/2023] Open
Abstract
In eukaryotic cells, RNAs transcribed by RNA polymerase-II receive the modification at the 5' end. This structure is called the cap structure. The cap structure has a fundamental role for translation initiation by recruiting eukaryotic translation initiation factor 4F (eIF4F). The other important mediator of the cap structure is a nuclear cap-binding protein complex (CBC). CBC consists of two proteins, which are renamed as NCBP1 and NCBP2 (previously called as CBP80/NCBP and CBP20/NIP1, respectively). This review article discusses the multiple roles CBC mediates and co-ordinates in several gene expression steps in eukaryotes.
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Affiliation(s)
- Naoyuki Kataoka
- Laboratory of Cellular Biochemistry, Department of Animal Resource Sciences, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Agriculture Bldg. 7A, Room 703, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan
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12
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Xie J, Mo T, Li R, Zhang H, Liang G, Ma T, Chen J, Xie H, Wen X, Hu T, Xian Z, Pan W. The m 7G Reader NCBP2 Promotes Pancreatic Cancer Progression by Upregulating MAPK/ERK Signaling. Cancers (Basel) 2023; 15:5454. [PMID: 38001714 PMCID: PMC10670634 DOI: 10.3390/cancers15225454] [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: 08/11/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
PDAC is one of the most common malignant tumors worldwide. The difficulty of early diagnosis and lack of effective treatment are the main reasons for its poor prognosis. Therefore, it is urgent to identify novel diagnostic and therapeutic targets for PDAC patients. The m7G methylation is a common type of RNA modification that plays a pivotal role in regulating tumor development. However, the correlation between m7G regulatory genes and PDAC progression remains unclear. By integrating gene expression and related clinical information of PDAC patients from TCGA and GEO cohorts, m7G binding protein NCBP2 was found to be highly expressed in PDAC patients. More importantly, PDAC patients with high NCBP2 expression had a worse prognosis. Stable NCBP2-knockdown and overexpression PDAC cell lines were constructed to further perform in-vitro and in-vivo experiments. NCBP2-knockdown significantly inhibited PDAC cell proliferation, while overexpression of NCBP2 dramatically promoted PDAC cell growth. Mechanistically, NCBP2 enhanced the translation of c-JUN, which in turn activated MEK/ERK signaling to promote PDAC progression. In conclusion, our study reveals that m7G reader NCBP2 promotes PDAC progression by activating MEK/ERK pathway, which could serve as a novel therapeutic target for PDAC patients.
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Affiliation(s)
- Jiancong Xie
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
| | - Taiwei Mo
- Department of General Surgery, The First Affiliated Hospital of Jinan University, Guangzhou 510630, China;
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
| | - Ruibing Li
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Hao Zhang
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
| | - Guanzhan Liang
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Tao Ma
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
| | - Jing Chen
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Hanlin Xie
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Xiaofeng Wen
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Tuo Hu
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Zhenyu Xian
- Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (R.L.); (G.L.); (J.C.); (H.X.); (X.W.); (T.H.)
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
- Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China
| | - Weidong Pan
- Department of General Surgery (Pancreatic Hepatobiliary Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou 510655, China; (J.X.); (H.Z.); (T.M.)
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13
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Gao X, You Z, Huang C, Liu Z, Tan Z, Li J, Liu Y, Liu X, Wei F, Fan Z, Qi S, Sun J. NCBP1 Improves Cognitive Function in Mice by Reducing Oxidative Stress, Neuronal Loss, and Glial Activation After Status Epilepticus. Mol Neurobiol 2023; 60:6676-6688. [PMID: 37474884 DOI: 10.1007/s12035-023-03497-3] [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: 12/03/2022] [Accepted: 07/10/2023] [Indexed: 07/22/2023]
Abstract
Status epilepticus (SE) is a severe manifestation of epilepsy which can cause neurologic injury and death. This study aimed to identify key proteins involved in the pathogenesis of epilepsy and find a potential drug target for SE treatment. Tandem mass tag (TMT)-based quantitative proteomic analysis was applied to screen differentially expressed proteins (DEPs) in epilepsy. The adeno-associated virus was employed to overexpress candidate DEP in mice, and kainic acid (KA) was used to generate a mouse model of epilepsy. Then histopathological examination of the hippocampal tissue was performed, and the inflammatory factors levels in serum and hippocampus were measured. The IP-MS analysis was carried out to identify the interacting protein of nuclear cap-binding protein 1 (NCBP1). The results were that NCBP1 was downregulated in the epileptic hippocampus. NCBP1 overexpression alleviated KA-induced cognitive impairment in mice and reduced the apoptosis and damage of hippocampal neurons. Additionally, overexpressed NCBP1 increased the expression of NeuN and reduced the expression of GFAP and IBA-1 in the hippocampus of the mice. Further study indicated that NCBP1 overexpression inhibited the expression of IL-6, IL-1β, and IFN-γ in serum and hippocampus as well as MDA and LDH in the hippocampus, whereas it increased the SOD levels, suggesting that overexpression of NCBP1 could diminish KA-induced inflammatory responses and oxidative stress. The IP-MS analysis identified that ELAVL4 was the NCBP1-interacting protein. In conclusion, this finding suggests that NCBP1 may potentially serve as a drug target for the treatment of epilepsy.
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Affiliation(s)
- Xiaoying Gao
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Zhipeng You
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Cong Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Zhixiong Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Zixiao Tan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Jiran Li
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Yang Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Xingan Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Fan Wei
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Zhijie Fan
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China
| | - Sihua Qi
- Department of Anesthesiology, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China.
| | - Jiahang Sun
- Department of Neurosurgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, Heilongjiang, China.
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14
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Heinz JL, Swagemakers SMA, von Hofsten J, Helleberg M, Thomsen MM, De Keukeleere K, de Boer JH, Ilginis T, Verjans GMGM, van Hagen PM, van der Spek PJ, Mogensen TH. Whole exome sequencing of patients with varicella-zoster virus and herpes simplex virus induced acute retinal necrosis reveals rare disease-associated genetic variants. Front Mol Neurosci 2023; 16:1253040. [PMID: 38025266 PMCID: PMC10630912 DOI: 10.3389/fnmol.2023.1253040] [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: 07/04/2023] [Accepted: 10/09/2023] [Indexed: 12/01/2023] Open
Abstract
Purpose Herpes simplex virus (HSV) and varicella-zoster virus (VZV) are neurotropic human alphaherpesviruses endemic worldwide. Upon primary infection, both viruses establish lifelong latency in neurons and reactivate intermittently to cause a variety of mild to severe diseases. Acute retinal necrosis (ARN) is a rare, sight-threatening eye disease induced by ocular VZV or HSV infection. The virus and host factors involved in ARN pathogenesis remain incompletely described. We hypothesize an underlying genetic defect in at least part of ARN cases. Methods We collected blood from 17 patients with HSV-or VZV-induced ARN, isolated DNA and performed Whole Exome Sequencing by Illumina followed by analysis in Varseq with criteria of CADD score > 15 and frequency in GnomAD < 0.1% combined with biological filters. Gene modifications relative to healthy control genomes were filtered according to high quality and read-depth, low frequency, high deleteriousness predictions and biological relevance. Results We identified a total of 50 potentially disease-causing genetic variants, including missense, frameshift and splice site variants and on in-frame deletion in 16 of the 17 patients. The vast majority of these genes are involved in innate immunity, followed by adaptive immunity, autophagy, and apoptosis; in several instances variants within a given gene or pathway was identified in several patients. Discussion We propose that the identified variants may contribute to insufficient viral control and increased necrosis ocular disease presentation in the patients and serve as a knowledge base and starting point for the development of improved diagnostic, prophylactic, and therapeutic applications.
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Affiliation(s)
- Johanna L. Heinz
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Sigrid M. A. Swagemakers
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Joanna von Hofsten
- Department of Clinical Neuroscience, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Ophthalmology, Halland Hospital Halmstad, Halmstad, Sweden
| | - Marie Helleberg
- Department of Infectious Diseases, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
- Center of Excellence for Health, Immunity and Infections, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Michelle M. Thomsen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Kerstin De Keukeleere
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
| | - Joke H. de Boer
- Department of Ophthalmology, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Tomas Ilginis
- Department of Ophthalmology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Georges M. G. M. Verjans
- HerpeslabNL, Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter M. van Hagen
- Department of Internal Medicine and Immunology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Peter J. van der Spek
- Department of Pathology and Clinical Bioinformatics, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Trine H. Mogensen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Department of Infectious Diseases, Aarhus University Hospital, Aarhus, Denmark
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15
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Katahira J, Ohmae T, Yasugi M, Sasaki R, Itoh Y, Kohda T, Hieda M, Yokota Hirai M, Okamoto T, Miyamoto Y. Nsp14 of SARS-CoV-2 inhibits mRNA processing and nuclear export by targeting the nuclear cap-binding complex. Nucleic Acids Res 2023; 51:7602-7618. [PMID: 37260089 PMCID: PMC10415132 DOI: 10.1093/nar/gkad483] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/12/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023] Open
Abstract
To facilitate selfish replication, viruses halt host gene expression in various ways. The nuclear export of mRNA is one such process targeted by many viruses. SARS-CoV-2, the etiological agent of severe acute respiratory syndrome, also prevents mRNA nuclear export. In this study, Nsp14, a bifunctional viral replicase subunit, was identified as a novel inhibitor of mRNA nuclear export. Nsp14 induces poly(A)+ RNA nuclear accumulation and the dissolution/coalescence of nuclear speckles. Genome-wide gene expression analysis revealed the global dysregulation of splicing and 3'-end processing defects of replication-dependent histone mRNAs by Nsp14. These abnormalities were also observed in SARS-CoV-2-infected cells. A mutation introduced at the guanine-N7-methyltransferase active site of Nsp14 diminished these inhibitory activities. Targeted capillary electrophoresis-mass spectrometry analysis (CE-MS) unveiled the production of N7-methyl-GTP in Nsp14-expressing cells. Association of the nuclear cap-binding complex (NCBC) with the mRNA cap and subsequent recruitment of U1 snRNP and the stem-loop binding protein (SLBP) were impaired by Nsp14. These data suggest that the defects in mRNA processing and export arise from the compromise of NCBC function by N7-methyl-GTP, thus exemplifying a novel viral strategy to block host gene expression.
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Affiliation(s)
- Jun Katahira
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Tatsuya Ohmae
- Laboratory of Cellular Molecular Biology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Mayo Yasugi
- Laboratory of Veterinary Public Health, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Ryosuke Sasaki
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Yumi Itoh
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Tomoko Kohda
- Laboratory of Veterinary Epidemiology, Graduate School of Veterinary Sciences, Osaka Metropolitan University, 1-58 Rinku-Orai-kita, Izumisano, Osaka 598-8531, Japan
| | - Miki Hieda
- Department of Medical Technology, Ehime Prefectural University of Health Sciences, 543 Tobe-Cho Takaoda, Iyo, Ehime791-2102, Japan
| | - Masami Yokota Hirai
- RIKEN Center for Sustainable Resource Science, Mass Spectrometry and Microscopy Unit, 1-7-22 Suehiro. Tsurumi, Yokohama, Kanagawa 230-0045, Japan
| | - Toru Okamoto
- Institute for Advanced Co-Creation Studies, Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Yoichi Miyamoto
- Laboratory of Nuclear Transport Dynamics, National Institutes of Biomedical Innovation, Health, and Nutrition (NIBIOHN), 7-6-8 Saito Asagi, Ibaraki, Osaka 567-0085, Japan
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16
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Wang T, Zhao X, Liu T, Zhang J, Qiu J, Li M, Weng R. Transcriptional investigation of the toxic mechanisms of perfluorooctane sulfonate in rats based on an RNA-Seq approach. CHEMOSPHERE 2023; 329:138629. [PMID: 37030344 DOI: 10.1016/j.chemosphere.2023.138629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 04/01/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
Perfluorooctane sulfonate (PFOS) was widely used in industrial applications before it was listed as a persistent organic pollutant by the Conference of the Parties in the Stockholm Convention in 2009. Although the potential toxicity of PFOS has been studied, its toxic mechanisms remain largely undefined. Here, we investigated novel hub genes and pathways affected by PFOS to gain new conceptions of the toxic mechanisms of PFOS. Reduced body weight gain and abnormal ultra-structures in the liver and kidney tissues were spotted in PFOS-exposed rats, indicating successful establishment of the PFOS-exposed rat model. The transcriptomic alterations of blood samples upon PFOS exposure were analysed using RNA-Seq. GO analysis indicates that the differentially expressed gene-enriched GO terms are related to metabolism, cellular processes, and biological regulation. Kyoto encyclopaedia of gene and genomes (KEGG) and gene set enrichment analysis (GSEA) were conducted to identify six key pathways: spliceosome, B cell receptor signalling pathway, acute myeloid leukaemia, protein processing in the endoplasmic reticulum, NF-kappa B signalling pathway, and Fc gamma R-mediated phagocytosis. The top 10 hub genes were screened from a protein-protein interaction network and verified via quantitative real-time polymerase chain reaction. The overall pathway network and hub genes may provide new insights into the toxic mechanisms of PFOS exposure states.
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Affiliation(s)
- Tianrun Wang
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Xuying Zhao
- Key Laboratory of Quality and Risk Assessment for Tobacco and Aromatic Plant Products (Qingdao) of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Tianze Liu
- Key Laboratory of Quality and Risk Assessment for Tobacco and Aromatic Plant Products (Qingdao) of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Jiguang Zhang
- Key Laboratory of Quality and Risk Assessment for Tobacco and Aromatic Plant Products (Qingdao) of Ministry of Agriculture and Rural Affairs, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, Shandong, China
| | - Jing Qiu
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Mei Li
- College of Chemistry and Material Science, Hebei Normal University, Shijiazhuang, 050024, Hebei, China
| | - Rui Weng
- Key Laboratory of Agro-food Safety and Quality of Ministry of Agriculture and Rural Affairs, Institute of Quality Standard and Testing Technology for Agro-Products, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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17
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Meng S, Xia Y, Li M, Wu Y, Wang D, Zhou Y, Ma D, Ye J, Sun T, Ji C. NCBP1 enhanced proliferation of DLBCL cells via METTL3-mediated m6A modification of c-Myc. Sci Rep 2023; 13:8606. [PMID: 37244946 DOI: 10.1038/s41598-023-35777-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) is malignant hyperplasia of B lymphocytes and standard care cannot satisfactorily meet clinical needs. Potential diagnostic and prognostic DLBCL biomarkers are needed. NCBP1 could bind to the 5'-end cap of pre-mRNAs to participate in RNA processing, transcript nuclear export and translation. Aberrant NCBP1 expression is involved in the pathogenesis of cancers, but little is known about NCBP1 in DLBCL. We proved that NCBP1 is significantly elevated in DLBCL patients and is associated with their poor prognosis. Then, we found that NCBP1 is important for the proliferation of DLBCL cells. Moreover, we verified that NCBP1 enhances the proliferation of DLBCL cells in a METTL3-dependent manner and found that NCBP1 enhances the m6A catalytic function of METTL3 by maintaining METTL3 mRNA stabilization. Mechanistically, the expression of c-MYC is regulated by NCBP1-enhanced METTL3, and the NCBP1/METTL3/m6A/c-MYC axis is important for DLBCL progression. We identified a new pathway for DLBCL progression and suggest innovative ideas for molecular targeted therapy of DLBCL.
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Affiliation(s)
- Sibo Meng
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
- Department of Medical Oncology, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, 758 Heifei Road, Qingdao, 266035, Shandong, People's Republic of China
| | - Yuan Xia
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Mingying Li
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yuyan Wu
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Dongmei Wang
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Ying Zhou
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Daoxin Ma
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Jingjing Ye
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Tao Sun
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
| | - Chunyan Ji
- Department of Hematology, Qilu Hospital of Shandong University, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
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18
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Selvaraju S, Ramya L, Swathi D, Archana SS, Lavanya M, Krishnappa B, Binsila BK, Mahla AS, Arangasamy A, Andonissamy J, Kumar P, Sharma RK. Cryostress induces fragmentation and alters the abundance of sperm transcripts associated with fertilizing competence and reproductive processes in buffalo. Cell Tissue Res 2023:10.1007/s00441-023-03764-8. [PMID: 37079096 DOI: 10.1007/s00441-023-03764-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 03/09/2023] [Indexed: 04/21/2023]
Abstract
The study aimed to assess the influence of cryostress on RNA integrity and functional significance in sperm fertilizing ability. The fresh and post-thawed buffalo sperm (n = 6 each) samples were evaluated for their functional attributes, and sperm total RNA was subjected to transcriptome sequencing followed by validation using real-time PCR and dot blot. Overall, 6911 genes had an expression of FPKM > 1, and among these 431 genes were abundantly expressed (FPKM > 20) in buffalo sperm. These abundantly expressed genes regulate reproductive functions such as sperm motility (TEKT2, SPEM1, and PRM3, FDR = 1.10E-08), fertilization (EQTN, PLCZ1, and SPESP1, FDR = 7.25E-06) and the developmental process involved in reproduction (SPACA1, TNP1, and YBX2, FDR = 7.21E-06). Cryopreservation significantly (p < 0.05) affected the structural and functional membrane integrities of sperm. The expression levels of transcripts that regulate the metabolic activities and fertility-related functions were compromised during cryopreservation. Interestingly, cryostress induces the expression of genes involved (p < 0.05) in chemokine signaling (CX3CL1, CCL20, and CXCR4), G-protein coupled receptor binding (ADRB1, EDN1, and BRS3), translation (RPS28, MRPL28, and RPL18A), oxidative phosphorylation (ND1, ND2, and COX2), response to reactive oxygen species (GLRX2, HYAL2, and EDN1), and immune responses (CX3CL1, CCL26, and TBXA2R). These precociously expressed genes during cryopreservation alter the signaling mechanisms that govern sperm functional competence and can impact fertilization and early embryonic development.
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Affiliation(s)
- Sellappan Selvaraju
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India.
| | - Laxman Ramya
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Divakar Swathi
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | | | - Maharajan Lavanya
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Balaganur Krishnappa
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Bala Krishnan Binsila
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Ajit Singh Mahla
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
- Physiology and Biochemistry Division, ICAR-Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, 304501, India
| | - Arunachalam Arangasamy
- Reproductive Physiology Laboratory, ICAR-National Institute of Animal Nutrition and Physiology, Adugodi, Bengaluru, 560030, India
| | - Jerome Andonissamy
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India
| | - Pradeep Kumar
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India
| | - Rakesh Kumar Sharma
- Animal Physiology and Reproduction Division, ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, 125001, India
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19
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Maimaiti A, Feng Z, Liu Y, Turhon M, Xie Z, Baihetiyaer Y, Wang X, Kasimu M, Jiang L, Wang Y, Wang Z, Pei Y. N7-methylguanosin regulators-mediated methylation modification patterns and characterization of the immune microenvironment in lower-grade glioma. Eur J Med Res 2023; 28:144. [PMID: 36998056 PMCID: PMC10061823 DOI: 10.1186/s40001-023-01108-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/23/2023] [Indexed: 03/31/2023] Open
Abstract
N7-methylguanosine (m7G) modification signature has recently emerged as a crucial regulator of tumor progression and treatment in cancer. However, there is limited information available on the genomic profile of lower-grade gliomas (LGGs) related to m7G methylation modification genes' function in tumorigenesis and progression. In this study, we employed bioinformatics methods to characterize m7G modifications in individuals with LGG from The Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA). We used gene set enrichment analysis (GSEA), single sample GSEA (ssGSEA), CIBERSORT algorithm, ESTIMATE algorithm, and TIDE to evaluate the association between m7G modification patterns, tumor microenvironment (TME) cell infiltration properties, and immune infiltration markers. The m7G scoring scheme using principal component analysis (PCA) was employed to investigate the m7G modification patterns quantitatively. We examined the m7G modification hub genes' expression levels in normal samples, refractory epilepsy samples, and LGG samples using immunohistochemistry, western-blotting, and qRT-PCR. Our findings revealed that individuals with LGG could be categorized into two groups based on m7G scores (high and low) according to the properties of m7G. Moreover, we observed that high m7G score was associated with significant clinical benefit and prolonged survival duration in the anti-PD-1 cohort, while low m7G score was associated with improved prognostic outcomes and increased likelihood of complete or partial response in the anti-PD-L1 cohort. Different m7G subtypes also showed varying Tumor Mutational Burden (TMB) and immune profiles and might have distinct responses to immunotherapy. Furthermore, we identified five potential genetic markers that were highly correlated with the m7G score signature index. These findings provide insight into the features and classification associated with m7G methylation modifications and may aid in improving the clinical outcome of LGG.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China
| | - Zhaohai Feng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China
| | - Yanwen Liu
- Department of Medical Laboratory, Xinjiang Production and Construction Corps Hospital, Urumqi, 830002, Xinjiang, China
| | - Mirzat Turhon
- Department of Neurointerventional Surgery, Beijing Neurosurgical Institute, Capital Medical University, Beijing, 100070, China
- Department of Neurointerventional Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Zhihao Xie
- The Second Hospital of Jilin University, Changchun, 130041, Jilin, China
| | - Yilimire Baihetiyaer
- Department of Neurology, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, 830054, Xinjiang, China
| | - Xixian Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China
| | - Maimaitijiang Kasimu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China
| | - Lei Jiang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China.
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China.
- People's Hospital of Mongolian Autonomous Prefecture of Bayingolin, Korla, 841000, Xinjiang, China.
| | - Yinan Pei
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, No. 137, South Liyushan Road, Xinshi District, Urumqi, 830054, Xinjiang, China.
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20
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Anreiter I, Tian YW, Soller M. The cap epitranscriptome: Early directions to a complex life as mRNA. Bioessays 2023; 45:e2200198. [PMID: 36529693 DOI: 10.1002/bies.202200198] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Animal, protist and viral messenger RNAs (mRNAs) are most prominently modified at the beginning by methylation of cap-adjacent nucleotides at the 2'-O-position of the ribose (cOMe) by dedicated cap methyltransferases (CMTrs). If the first nucleotide of an mRNA is an adenosine, PCIF1 can methylate at the N6 -position (m6 A), while internally the Mettl3/14 writer complex can methylate. These modifications are introduced co-transcriptionally to affect many aspects of gene expression including localisation to synapses and local translation. Of particular interest, transcription start sites of many genes are heterogeneous leading to sequence diversity at the beginning of mRNAs, which together with cOMe and m6 Am could constitute an extensive novel layer of gene expression control. Given the role of cOMe and m6 A in local gene expression at synapses and higher brain functions including learning and memory, such code could be implemented at the transcriptional level for lasting memories through local gene expression at synapses.
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Affiliation(s)
- Ina Anreiter
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, Canada
| | - Yuan W Tian
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
| | - Matthias Soller
- Birmingham Centre for Genome Biology, University of Birmingham, Birmingham, UK.,School of Biosciences, College of Life and Environmental Sciences, University of Birmingham, Birmingham, UK
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21
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Kowalski MH, Wessels HH, Linder J, Choudhary S, Hartman A, Hao Y, Mascio I, Dalgarno C, Kundaje A, Satija R. CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.09.527751. [PMID: 36798324 PMCID: PMC9934614 DOI: 10.1101/2023.02.09.527751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Most mammalian genes have multiple polyA sites, representing a substantial source of transcript diversity that is governed by the cleavage and polyadenylation (CPA) regulatory machinery. To better understand how these proteins govern polyA site choice we introduce CPA-Perturb-seq, a multiplexed perturbation screen dataset of 42 known CPA regulators with a 3' scRNA-seq readout that enables transcriptome-wide inference of polyA site usage. We develop a statistical framework to specifically identify perturbation-dependent changes in intronic and tandem polyadenylation, and discover modules of co-regulated polyA sites exhibiting distinct functional properties. By training a multi-task deep neural network (APARENT-Perturb) on our dataset, we delineate a cis-regulatory code that predicts responsiveness to perturbation and reveals interactions between distinct regulatory complexes. Finally, we leverage our framework to re-analyze published scRNA-seq datasets, identifying new regulators that affect the relative abundance of alternatively polyadenylated transcripts, and characterizing extensive cellular heterogeneity in 3' UTR length amongst antibody-producing cells. Our work highlights the potential for multiplexed single-cell perturbation screens to further our understanding of post-transcriptional regulation in vitro and in vivo.
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Affiliation(s)
- Madeline H. Kowalski
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York University Grossman School of Medicine, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Johannes Linder
- Department of Genetics, Stanford University, Stanford USA
- Department of Computer Science, Stanford University, Stanford USA
| | - Saket Choudhary
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Yuhan Hao
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Isabella Mascio
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | | | - Anshul Kundaje
- Department of Genetics, Stanford University, Stanford USA
- Department of Computer Science, Stanford University, Stanford USA
| | - Rahul Satija
- New York Genome Center, New York, NY, USA
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York University Grossman School of Medicine, New York, NY, USA
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22
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RNAseq Analysis of FABP4 Knockout Mouse Hippocampal Transcriptome Suggests a Role for WNT/β-Catenin in Preventing Obesity-Induced Cognitive Impairment. Int J Mol Sci 2023; 24:ijms24043381. [PMID: 36834799 PMCID: PMC9961923 DOI: 10.3390/ijms24043381] [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: 12/22/2022] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Microglial fatty-acid binding protein 4 (FABP4) is a regulator of neuroinflammation. We hypothesized that the link between lipid metabolism and inflammation indicates a role for FABP4 in regulating high fat diet (HFD)-induced cognitive decline. We have previously shown that obese FABP4 knockout mice exhibit decreased neuroinflammation and cognitive decline. FABP4 knockout and wild type mice were fed 60% HFD for 12 weeks starting at 15 weeks old. Hippocampal tissue was dissected and RNA-seq was performed to measure differentially expressed transcripts. Reactome molecular pathway analysis was utilized to examine differentially expressed pathways. Results showed that HFD-fed FABP4 knockout mice have a hippocampal transcriptome consistent with neuroprotection, including associations with decreased proinflammatory signaling, ER stress, apoptosis, and cognitive decline. This is accompanied by an increase in transcripts upregulating neurogenesis, synaptic plasticity, long-term potentiation, and spatial working memory. Pathway analysis revealed that mice lacking FABP4 had changes in metabolic function that support reduction in oxidative stress and inflammation, and improved energy homeostasis and cognitive function. Analysis suggested a role for WNT/β-Catenin signaling in the protection against insulin resistance, alleviating neuroinflammation and cognitive decline. Collectively, our work shows that FABP4 represents a potential target in alleviating HFD-induced neuroinflammation and cognitive decline and suggests a role for WNT/β-Catenin in this protection.
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23
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Qin H, Sheng W, Weng J, Li G, Chen Y, Zhu Y, Wang Q, Chen Y, Yang Q, Yu F, Zeng H, Xiong A. Identification and verification of m7G-Related genes as biomarkers for prognosis of sarcoma. Front Genet 2023; 14:1101683. [PMID: 36816047 PMCID: PMC9935680 DOI: 10.3389/fgene.2023.1101683] [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: 11/21/2022] [Accepted: 01/26/2023] [Indexed: 02/05/2023] Open
Abstract
Background: Increasing evidence indicates a crucial role for N7-methylguanosine (m7G) methylation modification in human disease development, particularly cancer, and aberrant m7G levels are closely associated with tumorigenesis and progression via regulation of the expression of multiple oncogenes and tumor suppressor genes. However, the role of m7G in sarcomas (SARC) has not been adequately evaluated. Materials and methods: Transcriptome and clinical data were gathered from the TCGA database for this study. Normal and SARC groups were compared for the expression of m7G-related genes (m7GRGs). The expression of m7GRGs was verified using real-time quantitative PCR (RT-qPCR) in SARC cell lines. Then, differentially expressed genes (DEGs) were identified between high and low m7GRGs expression groups in SARC samples, and GO enrichment and KEGG pathways were evaluated. Next, prognostic values of m7GRGs were evaluated by Cox regression analysis. Subsequently, a prognostic model was constructed using m7GRGs with good prognostic values by Lasso regression analysis. Besides, the relationships between prognostic m7GRGs and immune infiltration, clinical features, cuproptosis-related genes, and antitumor drugs were investigated in patients with SARC. Finally, a ceRNA regulatory network based on m7GRGs was constructed. Results: The expression of ten m7GRGs was higher in the SARC group than in the control group. DEGs across groups with high and low m7GRGs expression were enriched for adhesion sites and cGMP-PKG. Besides, we constructed a prognostic model that consists of EIF4A1, EIF4G3, NCBP1, and WDR4 m7GRGs for predicting the survival likelihood of sarcoma patients. And the elevated expression of these four prognostic m7GRGs was substantially associated with poor prognosis and elevated expression in SARC cell lines. Moreover, we discovered that these four m7GRGs expressions were negatively correlated with CD4+ T cell levels, dendritic cell level and tumor purity, and positively correlated with tumor mutational burden, microsatellite instability, drug sensitivity and cuproptosis-related genes in patients with sarcomas. Then, a triple regulatory network of mRNA, miRNA, and lncRNA was established. Conclusion: The current study identified EIF4A1, EIF4G3, NCBP1, and WDR4 as prognostic genes for SARC that are associated with m7G.These findings extend our knowledge of m7G methylation in SARC and may guide the development of innovative treatment options.
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Affiliation(s)
- Haotian Qin
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Weibei Sheng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Jian Weng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Guoqing Li
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yingqi Chen
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yuanchao Zhu
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qichang Wang
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Yixiao Chen
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Qi Yang
- Department of Medical Ultrasound, Peking University Shenzhen Hospital, Shenzhen, China
| | - Fei Yu
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China,*Correspondence: Fei Yu, ; Hui Zeng, ; Ao Xiong,
| | - Hui Zeng
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China,*Correspondence: Fei Yu, ; Hui Zeng, ; Ao Xiong,
| | - Ao Xiong
- National & Local Joint Engineering Research Center of Orthopaedic Biomaterials, Peking University Shenzhen Hospital, Shenzhen, China,Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China,*Correspondence: Fei Yu, ; Hui Zeng, ; Ao Xiong,
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24
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Zhao Q, Chen Y, Qu L. Combined Transcriptomic and Proteomic Analyses Reveal the Different Responses to UVA and UVB Radiation in Human Keratinocytes. Photochem Photobiol 2023; 99:137-152. [PMID: 35638308 DOI: 10.1111/php.13658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 05/25/2022] [Indexed: 01/25/2023]
Abstract
Ultraviolet (UV) radiation from sunlight is a major risk factor for many cutaneous pathologies including skin aging and cancers. Despite decades of research, the different responses to UVA and UVB in human keratinocytes have not been systemically investigated. Here, we performed multi-omics to characterize the common and different changes in gene transcription and protein expression after exposure to UVB and UVA, respectively. Keratinocyte cells, treated with or without UV, were analyzed by TMT-labeled MS/MS spectra and RNA-sequencing. A common set of genes/proteins was found to be impacted by both UVA and UVB and the other differential genes/proteins showed wavelength specificity. The common set of genes/proteins were mainly involved in keratinization, lipid metabolic processes and stimulus response. The UVB specifically responsive genes/proteins were mainly related to RNA processing, gene silencing regulation and cytoskeleton organization. The UVA specifically responsive genes/proteins were mainly involved in vesicle-mediated transport and oxygen-containing compound response. Meanwhile, the hub differential genes/proteins in each set were identified by protein-protein interaction networks and cluster analysis. This work provided a global view of the similar and differential molecular mechanisms of UVB- and UVA-induced cell damage in keratinocytes, which would be beneficial for further studies in the prevention or treatment of UV-related pathologies.
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Affiliation(s)
- Qinqin Zhao
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China
| | - Yueyue Chen
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China.,Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China
| | - Liping Qu
- Characteristic Plants Research and Development Center, Botanee Research Institute, Shanghai Jiyan Bio-Pharmaceutical Development Co., Ltd., Shanghai, China.,Yunnan Characteristic Plant Extraction Laboratory, Yunnan Yunke Characteristic Plant Extraction Laboratory Co., Ltd., Kunming, China.,Yunnan Botanee Bio-technology Group Co., Ltd., Kunming, China
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25
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Are Antisense Long Non-Coding RNA Related to COVID-19? Biomedicines 2022; 10:biomedicines10112770. [PMID: 36359290 PMCID: PMC9687826 DOI: 10.3390/biomedicines10112770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/10/2022] [Accepted: 10/25/2022] [Indexed: 11/06/2022] Open
Abstract
Fighting external pathogens relies on the tight regulation of the gene expression of the immune system. Ferroptosis, which is a distinct form of programmed cell death driven by iron, is involved in the enhancement of follicular helper T cell function during infection. The regulation of RNA is a key step in final gene expression. The present study aimed to identify the expression level of antisense lncRNAs (A2M-AS1, DBH-AS1, FLVCR1-DT, and NCBP2AS2-1) and FLVCR1 in COVID-19 patients and its relation to the severity of the disease. COVID-19 patients as well as age and gender-matched healthy controls were enrolled in this study. The expression level of the antisense lncRNAs was measured by RT-PCR. Results revealed the decreased expression of A2M-AS1 and FLVCR1 in COVID-19 patients. Additionally, they showed the increased expression of DBH-AS1, FLVCR1-DT, and NCBP2AS2. Both FLVCR1-DT and NCBP2AS2 showed a positive correlation with interleukin-6 (IL-6). DBH-AS1 and FLVCR1-DT had a significant association with mortality, complications, and mechanical ventilation. A significant negative correlation was found between A2M-AS1 and NCBP2AS2-1 and between FLVCR1 and FLVCR1-DT. The study confirmed that the expression level of the antisense lncRNAs was deregulated in COVID-19 patients and correlated with the severity of COVID-19, and that it may have possible roles in the pathogenesis of this disease.
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26
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Malaguarnera R, Gabriele C, Santamaria G, Giuliano M, Vella V, Massimino M, Vigneri P, Cuda G, Gaspari M, Belfiore A. Comparative proteomic analysis of insulin receptor isoform A and B signaling. Mol Cell Endocrinol 2022; 557:111739. [PMID: 35940390 DOI: 10.1016/j.mce.2022.111739] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 07/17/2022] [Accepted: 07/28/2022] [Indexed: 11/30/2022]
Abstract
The insulin receptor (IR) gene undergoes differential splicing generating two IR isoforms, IR-A and IR-B. The roles of IR-A in cancer and of IR-B in metabolic regulation are well known but the molecular mechanisms responsible for their different biological effects are poorly understood. We aimed to identify different or similar protein substrates and signaling linked to each IR isoforms. We employed mouse fibroblasts lacking IGF1R gene and expressing exclusively either IR-A or IR-B. By proteomic analysis a total of 2530 proteins were identified and quantified. Proteins and pathways mostly associated with insulin-activated IR-A were involved in cancer, stemness and interferon signaling. Instead, proteins and pathways associated with insulin-stimulated IR-B-expressing cells were mostly involved in metabolic or tumor suppressive functions. These results show that IR-A and IR-B recruit partially different multiprotein complexes in response to insulin, suggesting partially different functions of IR isoforms in physiology and in disease.
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Affiliation(s)
| | - Caterina Gabriele
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy.
| | - Gianluca Santamaria
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy; Klinikum rechts der Isar, Department of Medicine and Molecular Cardiology, Technical University of Munich, Germany.
| | - Marika Giuliano
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy.
| | - Veronica Vella
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy.
| | - Michele Massimino
- Department of Clinical and Experimental Medicine, Oncology Unit, University of Catania, 95100, Catania, Italy.
| | - Paolo Vigneri
- Department of Clinical and Experimental Medicine, Oncology Unit, University of Catania, 95100, Catania, Italy.
| | - Giovanni Cuda
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy.
| | - Marco Gaspari
- Research Centre for Advanced Biochemistry and Molecular Biology, Department of Experimental and Clinical Medicine, "Magna Græcia" University of Catanzaro, 88100, Catanzaro, Italy.
| | - Antonino Belfiore
- Unit of Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Garibaldi-Nesima Hospital, 95122, Catania, Italy.
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Tao X, Huang R, Xu R, Zheng S, Yue J. A novel m7G methylation–related signature associated with chromosome homeostasis in patients with lung adenocarcinoma. Front Genet 2022; 13:998258. [DOI: 10.3389/fgene.2022.998258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 10/05/2022] [Indexed: 12/24/2022] Open
Abstract
Lung adenocarcinoma (LUAD) is a malignant tumor of the respiratory system with poor prognosis. Recent studies have revealed that N7-methylguanosine (m7G) methylation is a widespread modification occurring in RNA. But the expression of m7G methylation–related genes in LUAD and their correlations with prognosis are still unclear. In this study, we found 12 m7G methylation–related regulators with differential expression between LUAD and normal lung tissues. According to differentially expressed genes (DEGs), all LUAD cases were separated into two subtypes. The prognostic value of each m7G methylation–related gene for survival was evaluated to construct a multigene signature using The Cancer Genome Atlas (TCGA) cohort. Finally, an m7G methylation–related prognostic signature based on three genes was built to classify LUAD patients into two risk groups. Patients in the high-risk group showed significantly reduced overall survival (OS) when compared with patients in the low-risk group (p < 0.05). The receiver operating characteristic (ROC) curve analysis confirmed the predictive capacity of the signature. The Gene Ontology (GO) functional annotation analysis disclosed that chromosome homeostasis plays an important role in this process. The gene set enrichment analysis (ssGSEA) implied that the immune status was decreased in the high-risk group. To sum up, m7G methylation–related genes play a vital role in tumor immunity and the related signature is a reliable predictor for LUAD prognosis.
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Chen J, Yao S, Sun Z, Wang Y, Yue J, Cui Y, Yu C, Xu H, Li L. The pattern of expression and prognostic value of key regulators for m7G RNA methylation in hepatocellular carcinoma. Front Genet 2022; 13:894325. [PMID: 36118897 PMCID: PMC9478798 DOI: 10.3389/fgene.2022.894325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 07/26/2022] [Indexed: 11/13/2022] Open
Abstract
N7-methylguanosine (m7G) modification on internal RNA positions plays a vital role in several biological processes. Recent research shows m7G modification is associated with multiple cancers. However, in hepatocellular carcinoma (HCC), its implications remain to be determined. In this place, we need to interrogate the mRNA patterns for 29 key regulators of m7G RNA modification and assess their prognostic value in HCC. Initial, the details from The Cancer Genome Atlas (TCGA) database concerning transcribed gene data and clinical information of HCC patients were inspected systematically. Second, according to the mRNA profiles of 29 m7G RNA methylation regulators, two clusters (named 1 and 2, respectively) were identified by consensus clustering. Furthermore, robust risk signature for seven m7G RNA modification regulators was constructed. Last, we used the Gene Expression Omnibus (GEO) dataset to validate the prognostic associations of the seven-gene risk signature. We figured out that 24/29 key regulators of m7G RNA modification varied remarkably in their grades of expression between the HCC and the adjacent tumor control tissues. Cluster one compared with cluster two had a substandard prognosis and was also positively correlated with T classification (T), pathological stage, and vital status (fustat) significantly. Consensus clustering results suggested the expression pattern of m7G RNA modification regulators was correlated with the malignancy of HCC strongly. In addition, cluster one was extensively enriched in metabolic-related pathways. Seven optimal genes (METTL1, WDR4, NSUN2, EIF4E, EIF4E2, NCBP1, and NCBP2) were selected to establish the risk model for HCC. Indicating by further analyses and validation, the prognostic model has fine anticipating command and this probability signature might be a self supporting presage factor for HCC. Finally, a new prognostic nomogram based on age, gender, pathological stage, histological grade, and prospects were established to forecast the prognosis of HCC patients accurately. In essence, we detected association of HCC severity and expression levels of m7G RNA modification regulators, and developed a risk score model for predicting prognosis of HCC patients’ progression.
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Affiliation(s)
- Jianxing Chen
- College of Chemistry and Life Science, Chifeng University, Chifeng, China
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shibin Yao
- Department of Emergency, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Zhijuan Sun
- International Education School, Chifeng University, Chifeng, China
| | - Yanjun Wang
- Department of Pediatrics, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Jili Yue
- Department of General Surgery, Affiliated Hospital of Chifeng University, Chifeng, China
| | - Yongkang Cui
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengping Yu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Haozhi Xu
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linqiang Li
- Department of General Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- Key Laboratory of Hepatosplenic Surgery, Ministry of Education, Harbin Medical University, Harbin, China
- *Correspondence: Linqiang Li,
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Krobthong S, Yingchutrakul Y, Sittisaree W, Tulyananda T, Samutrtai P, Choowongkomon K, Lao-On U. Evaluation of potential anti-metastatic and antioxidative abilities of natural peptides derived from Tecoma stans (L.) Juss. ex Kunth in A549 cells. PeerJ 2022; 10:e13693. [PMID: 35818360 PMCID: PMC9270879 DOI: 10.7717/peerj.13693] [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: 02/03/2022] [Accepted: 06/16/2022] [Indexed: 01/17/2023] Open
Abstract
Background Tecoma stans (L.) Juss. ex Kunth is a well-known medicinal plant found in tropical and subtropical regions. It contains a broad range of bioactive compounds that exhibit many biological effects, including antidiabetic, antibacterial, and antioxidative activities. However, the effect of natural peptides from T. stans against cancer progression and free radical production is unknown. This study aims to evaluate the cytotoxic, anti-metastatic, and antioxidative activities of natural peptides from T. stans on A549 cells. Methods The natural peptides were extracted from the flower of T. stans using the pressurized hot water extraction (PHWE) method, followed by size exclusion chromatography and solid-phase extraction-C18. The cytotoxic and anti-metastatic effects of natural peptides were evaluated using MTT and transwell chamber assays, respectively. The free radical scavenging activity of natural peptides was determined using ABTS, DPPH, and FRAP assays. The cells were pretreated with the IC50 dosage of natural peptides and stimulated with LPS before analyzing intracellular reactive oxygen species (ROS) and proteomics. Results Natural peptides induced cell toxicity at a concentration of less than 1 ng/ml and markedly reduced cell motility of A549 cells. The cells had a migration rate of less than 10% and lost their invasion ability in the treatment condition. In addition, natural peptides showed free radical scavenging activity similar to standard antioxidants and significantly decreased intracellular ROS in the LPS-induced cells. Proteomic analysis revealed 1,604 differentially expressed proteins. The self-organizing tree algorithm (SOTA) clustered the protein abundances into eleven groups. The volcano plot revealed that the cancer-promoting proteins (NCBP2, AMD, MER34, ENC1, and COA4) were down-regulated, while the secretory glycoprotein (A1BG) and ROS-reducing protein (ASB6) were up-regulated in the treatment group. Conclusion The anti-proliferative and anti-metastatic activities of natural peptides may be attributed to the suppression of several cancer-promoting proteins. In contrast, their antioxidative activity may result from the up-regulation of ROS-reducing protein. This finding suggests that natural peptides from T. stans are viable for being the new potential anti-cancer and antioxidative agents.
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Affiliation(s)
- Sucheewin Krobthong
- Center for Neuroscience, Faculty of Science, Mahidol University, Bangkok, Thailand,Interdisciplinary Graduate Program in Genetic Engineering, Kasetsart University, Bangkok, Thailand
| | - Yodying Yingchutrakul
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | | | - Tatpong Tulyananda
- School of Bioinnovation and Bio-Based Product Intelligence, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pawitrabhorn Samutrtai
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai, Thailand
| | | | - Udom Lao-On
- Department of Medical Technology, School of Allied Health Sciences, Walailak University, Nakhon Si Thammarat, Thailand,Hematology and Transfusion Science Research Center (HTSRC), Walailak University, Nakhon Si Thammarat, Thailand
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30
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DNA damage promotes HLA class I presentation by stimulating a pioneer round of translation-associated antigen production. Mol Cell 2022; 82:2557-2570.e7. [PMID: 35594857 DOI: 10.1016/j.molcel.2022.04.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 12/14/2022]
Abstract
Antigen presentation by the human leukocyte antigen (HLA) on the cell surface is critical for the transduction of the immune signal toward cytotoxic T lymphocytes. DNA damage upregulates HLA class I presentation; however, the mechanism is unclear. Here, we show that DNA-damage-induced HLA (di-HLA) presentation requires an immunoproteasome, PSMB8/9/10, and antigen-transporter, TAP1/2, demonstrating that antigen production is essential. Furthermore, we show that di-HLA presentation requires ATR, AKT, mTORC1, and p70-S6K signaling. Notably, the depletion of CBP20, a factor initiating the pioneer round of translation (PRT) that precedes nonsense-mediated mRNA decay (NMD), abolishes di-HLA presentation, suggesting that di-antigen production requires PRT. RNA-seq analysis demonstrates that DNA damage reduces NMD transcripts in an ATR-dependent manner, consistent with the requirement for ATR in the initiation of PRT/NMD. Finally, bioinformatics analysis identifies that PRT-derived 9-mer peptides bind to HLA and are potentially immunogenic. Therefore, DNA damage signaling produces immunogenic antigens by utilizing the machinery of PRT/NMD.
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31
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Boris-Lawrie K, Singh G, Osmer PS, Zucko D, Staller S, Heng X. Anomalous HIV-1 RNA, How Cap-Methylation Segregates Viral Transcripts by Form and Function. Viruses 2022; 14:935. [PMID: 35632676 PMCID: PMC9145092 DOI: 10.3390/v14050935] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/25/2022] [Accepted: 04/25/2022] [Indexed: 12/11/2022] Open
Abstract
The acquisition of m7G-cap-binding proteins is now recognized as a major variable driving the form and function of host RNAs. This manuscript compares the 5'-cap-RNA binding proteins that engage HIV-1 precursor RNAs, host mRNAs, small nuclear (sn)- and small nucleolar (sno) RNAs and sort into disparate RNA-fate pathways. Before completion of the transcription cycle, the transcription start site of nascent class II RNAs is appended to a non-templated guanosine that is methylated (m7G-cap) and bound by hetero-dimeric CBP80-CBP20 cap binding complex (CBC). The CBC is a nexus for the co-transcriptional processing of precursor RNAs to mRNAs and the snRNA and snoRNA of spliceosomal and ribosomal ribonucleoproteins (RNPs). Just as sn/sno-RNAs experience hyper-methylation of m7G-cap to trimethylguanosine (TMG)-cap, so do select HIV RNAs and an emerging cohort of mRNAs. TMG-cap is blocked from Watson:Crick base pairing and disqualified from participating in secondary structure. The HIV TMG-cap has been shown to license select viral transcripts for specialized cap-dependent translation initiation without eIF4E that is dependent upon CBP80/NCBP3. The exceptional activity of HIV precursor RNAs secures their access to maturation pathways of sn/snoRNAs, canonical and non-canonical host mRNAs in proper stoichiometry to execute the retroviral replication cycle.
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Affiliation(s)
- Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN 55455, USA
| | - Patrick S. Osmer
- Department of Astronomy, The Ohio State University, Columbus, OH 43210, USA;
| | - Dora Zucko
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, MN 55108, USA; (G.S.); (D.Z.)
| | - Seth Staller
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
| | - Xiao Heng
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA;
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32
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Li JR, Tang M, Li Y, Amos CI, Cheng C. Genetic variants associated mRNA stability in lung. BMC Genomics 2022; 23:196. [PMID: 35272635 PMCID: PMC8915503 DOI: 10.1186/s12864-022-08405-y] [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: 07/31/2021] [Accepted: 02/21/2022] [Indexed: 12/04/2022] Open
Abstract
Background Expression quantitative trait loci (eQTLs) analyses have been widely used to identify genetic variants associated with gene expression levels to understand what molecular mechanisms underlie genetic traits. The resultant eQTLs might affect the expression of associated genes through transcriptional or post-transcriptional regulation. In this study, we attempt to distinguish these two types of regulation by identifying genetic variants associated with mRNA stability of genes (stQTLs). Results Here, we presented a computational framework that takes advantage of recently developed methods to infer the mRNA stability of genes based on RNA-seq data and performed association analysis to identify stQTLs. Using the Genotype-Tissue Expression (GTEx) lung RNA-Seq data, we identified a total of 142,801 stQTLs for 3942 genes and 186,132 eQTLs for 4751 genes from 15,122,700 genetic variants for 13,476 genes on the autosomes, respectively. Interestingly, our results indicated that stQTLs were enriched in the CDS and 3’UTR regions, while eQTLs are enriched in the CDS, 3’UTR, 5’UTR, and upstream regions. We also found that stQTLs are more likely than eQTLs to overlap with RNA binding protein (RBP) and microRNA (miRNA) binding sites. Our analyses demonstrate that simultaneous identification of stQTLs and eQTLs can provide more mechanistic insight on the association between genetic variants and gene expression levels. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08405-y.
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Affiliation(s)
- Jian-Rong Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA
| | - Mabel Tang
- Department of BioSciences, Biochemistry and Cell Biology, Rice University, Houston, TX, USA
| | - Yafang Li
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Christopher I Amos
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA.,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA.,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA
| | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA. .,Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, TX, USA. .,Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, USA.
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33
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Bartas M, Volná A, Beaudoin CA, Poulsen ET, Červeň J, Brázda V, Špunda V, Blundell TL, Pečinka P. Unheeded SARS-CoV-2 proteins? A deep look into negative-sense RNA. Brief Bioinform 2022; 23:6539840. [PMID: 35229157 PMCID: PMC9116216 DOI: 10.1093/bib/bbac045] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 01/13/2022] [Accepted: 01/29/2022] [Indexed: 01/27/2023] Open
Abstract
SARS-CoV-2 is a novel positive-sense single-stranded RNA virus from the Coronaviridae family (genus Betacoronavirus), which has been established as causing the COVID-19 pandemic. The genome of SARS-CoV-2 is one of the largest among known RNA viruses, comprising of at least 26 known protein-coding loci. Studies thus far have outlined the coding capacity of the positive-sense strand of the SARS-CoV-2 genome, which can be used directly for protein translation. However, it has been recently shown that transcribed negative-sense viral RNA intermediates that arise during viral genome replication from positive-sense viruses can also code for proteins. No studies have yet explored the potential for negative-sense SARS-CoV-2 RNA intermediates to contain protein-coding loci. Thus, using sequence and structure-based bioinformatics methodologies, we have investigated the presence and validity of putative negative-sense ORFs (nsORFs) in the SARS-CoV-2 genome. Nine nsORFs were discovered to contain strong eukaryotic translation initiation signals and high codon adaptability scores, and several of the nsORFs were predicted to interact with RNA-binding proteins. Evolutionary conservation analyses indicated that some of the nsORFs are deeply conserved among related coronaviruses. Three-dimensional protein modeling revealed the presence of higher order folding among all putative SARS-CoV-2 nsORFs, and subsequent structural mimicry analyses suggest similarity of the nsORFs to DNA/RNA-binding proteins and proteins involved in immune signaling pathways. Altogether, these results suggest the potential existence of still undescribed SARS-CoV-2 proteins, which may play an important role in the viral lifecycle and COVID-19 pathogenesis.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Adriana Volná
- Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Christopher A Beaudoin
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK
| | | | - Jiří Červeň
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Václav Brázda
- Institute of Biophysics, Czech Academy of Sciences, Brno, 612 65, Czech Republic
| | - Vladimír Špunda
- Department of Physics, University of Ostrava, Ostrava 710 00, Czech Republic.,Global Change Research Institute, Czech Academy of Sciences, Brno, 603 00, Czech Republic
| | - Tom L Blundell
- Department of Biochemistry, Sanger Building, University of Cambridge, Tennis Court Rd, Cambridge CB2 1GA, UK
| | - Petr Pečinka
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
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HIV-1 hypermethylated guanosine cap licenses specialized translation unaffected by mTOR. Proc Natl Acad Sci U S A 2022; 119:2105153118. [PMID: 34949712 PMCID: PMC8740576 DOI: 10.1073/pnas.2105153118] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 12/29/2022] Open
Abstract
The proliferation of viral pathogens is restricted by hosts, but resilient pathogens antagonize the restriction by hosts. Findings explain that HIV-1 blocked mono-methylated guanosine cap by hypermethylation and engaged novel cap-binding complex for virion protein translation unaffected by global translation inhibition. The hypermethylated cap activity required RNA-structure-dependent binding of RNA helicase A/DHX9. eIF4E interaction proceeded on completely spliced HIV messenger RNA templates encoding viral regulatory proteins, thus eIF4E inactivation by catalytic site mTOR inhibitor suppressed regulatory protein translation, while structural/accessory protein translation was maintained. Two mutually exclusive translation pathways antagonize hosts and facilitate HIV-1 proliferation in primary CD4+ T cells to the detriment of hosts. eIF4E inactivation imposed an operational rheostat that suppressed regulatory proteins, while maintaining virion production in immune cells. Appended to the 5′ end of nascent RNA polymerase II transcripts is 7-methyl guanosine (m7G-cap) that engages nuclear cap-binding complex (CBC) to facilitate messenger RNA (mRNA) maturation. Mature mRNAs exchange CBC for eIF4E, the rate-limiting translation factor that is controlled through mTOR. Experiments in immune cells have now documented HIV-1 incompletely processed transcripts exhibited hypermethylated m7G-cap and that the down-regulation of the trimethylguanosine synthetase-1–reduced HIV-1 infectivity and virion protein synthesis by several orders of magnitude. HIV-1 cap hypermethylation required nuclear RNA helicase A (RHA)/DHX9 interaction with the shape of the 5′ untranslated region (UTR) primer binding site (PBS) segment. Down-regulation of RHA or the anomalous shape of the PBS segment abrogated hypermethylated caps and derepressed eIF4E binding for virion protein translation during global down-regulation of host translation. mTOR inhibition was detrimental to HIV-1 proliferation and attenuated Tat, Rev, and Nef synthesis. This study identified mutually exclusive translation pathways and the calibration of virion structural/accessory protein synthesis with de novo synthesis of the viral regulatory proteins. The hypermethylation of select, viral mRNA resulted in CBC exchange to heterodimeric CBP80/NCBP3 that expanded the functional capacity of HIV-1 in immune cells.
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35
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SARS-CoV-2 Exacerbates Beta-Amyloid Neurotoxicity, Inflammation and Oxidative Stress in Alzheimer's Disease Patients. Int J Mol Sci 2021; 22:ijms222413603. [PMID: 34948400 PMCID: PMC8705864 DOI: 10.3390/ijms222413603] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 02/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggered the pandemic Coronavirus Disease 19 (COVID-19), causing millions of deaths. The elderly and those already living with comorbidity are likely to die after SARS-CoV-2 infection. People suffering from Alzheimer’s disease (AD) have a higher risk of becoming infected, because they cannot easily follow health roles. Additionally, those suffering from dementia have a 40% higher risk of dying from COVID-19. Herein, we collected from Gene Expression Omnibus repository the brain samples of AD patients who died of COVID-19 (AD+COVID-19), AD without COVID-19 (AD), COVID-19 without AD (COVID-19) and control individuals. We inspected the transcriptomic and interactomic profiles by comparing the COVID-19 cohort against the control cohort and the AD cohort against the AD+COVID-19 cohort. SARS-CoV-2 in patients without AD mainly activated processes related to immune response and cell cycle. Conversely, 21 key nodes in the interactome are deregulated in AD. Interestingly, some of them are linked to beta-amyloid production and clearance. Thus, we inspected their role, along with their interactors, using the gene ontologies of the biological process that reveals their contribution in brain organization, immune response, oxidative stress and viral replication. We conclude that SARS-CoV-2 worsens the AD condition by increasing neurotoxicity, due to higher levels of beta-amyloid, inflammation and oxidative stress.
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36
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Mars JC, Ghram M, Culjkovic-Kraljacic B, Borden KLB. The Cap-Binding Complex CBC and the Eukaryotic Translation Factor eIF4E: Co-Conspirators in Cap-Dependent RNA Maturation and Translation. Cancers (Basel) 2021; 13:6185. [PMID: 34944805 PMCID: PMC8699206 DOI: 10.3390/cancers13246185] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/26/2022] Open
Abstract
The translation of RNA into protein is a dynamic process which is heavily regulated during normal cell physiology and can be dysregulated in human malignancies. Its dysregulation can impact selected groups of RNAs, modifying protein levels independently of transcription. Integral to their suitability for translation, RNAs undergo a series of maturation steps including the addition of the m7G cap on the 5' end of RNAs, splicing, as well as cleavage and polyadenylation (CPA). Importantly, each of these steps can be coopted to modify the transcript signal. Factors that bind the m7G cap escort these RNAs through different steps of maturation and thus govern the physical nature of the final transcript product presented to the translation machinery. Here, we describe these steps and how the major m7G cap-binding factors in mammalian cells, the cap binding complex (CBC) and the eukaryotic translation initiation factor eIF4E, are positioned to chaperone transcripts through RNA maturation, nuclear export, and translation in a transcript-specific manner. To conceptualize a framework for the flow and integration of this genetic information, we discuss RNA maturation models and how these integrate with translation. Finally, we discuss how these processes can be coopted by cancer cells and means to target these in malignancy.
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Affiliation(s)
- Jean-Clement Mars
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Mehdi Ghram
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Biljana Culjkovic-Kraljacic
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
| | - Katherine L B Borden
- Institute for Research in Immunology and Cancer (IRIC), Université de Montréal, Pavillion Marcelle-Coutu, Chemin Polytechnique, Montreal, QC H3T 1J4, Canada
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Ye F, Wang X, Tu S, Zeng L, Deng X, Luo W, Zhang Z. The effects of NCBP3 on METTL3-mediated m6A RNA methylation to enhance translation process in hypoxic cardiomyocytes. J Cell Mol Med 2021; 25:8920-8928. [PMID: 34382339 PMCID: PMC8435433 DOI: 10.1111/jcmm.16852] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/22/2021] [Accepted: 07/31/2021] [Indexed: 12/02/2022] Open
Abstract
Hypoxia as a crucial pathogenesis factor usually results in huge harmful effects on cardiac injury and dysfunction. Our previous study has uncovered the global transcriptome and translatome profiles of cardiomyocytes in vitro and in vivo to response to hypoxia by RNA sequencing and ribosome profiling sequencing. We observe a series of differential expressed genes between transcription and translation, which may be attributed to the hypoxia‐specific binding affinity of nuclear cap‐binding subunit 3 (NCBP3) at 5' untranslation region of target genes. Although we observe that NCBP3 can facilitate translational process in myocardium under hypoxia stress, the underlying molecular mechanism of NCBP3 for gene translation modulation remains unclear. In this study, we performed NCBP3 immunoprecipitation for mass spectrum and found that METTL3 and eIF4A2 particularly interacted with NCBP3 in hypoxic rat H9C2 cardiomyocytes. Furthermore, we observed that METTL3‐mediated N6‐methyladenosine (m6A) methylation was elevated in hypoxia, but compromised by NCBP3 or METTL3 knockdown. Finally, we also demonstrated that NCBP3/METTL3/eIF4A2 regulatory axis plays a specific role in cardiomyocytes undergoing hypoxic stress. Taken together, we unmasked NCBP3, a novel hypoxia‐specific response protein functions as a scaffold to coordinate METTL3 and eIF4A2 for enhancing gene translation by m6A RNA methylation in cardiomyocytes upon hypoxic stress.
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Affiliation(s)
- Fei Ye
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xiaoyan Wang
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - San Tu
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Lixiong Zeng
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Xu Deng
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Wenzhi Luo
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
| | - Zhihui Zhang
- Department of Cardiology, The Third Xiangya Hospital of Central South University, Changsha, China
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ARS2/SRRT: at the nexus of RNA polymerase II transcription, transcript maturation and quality control. Biochem Soc Trans 2021; 49:1325-1336. [PMID: 34060620 DOI: 10.1042/bst20201008] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/26/2023]
Abstract
ARS2/SRRT is an essential eukaryotic protein that has emerged as a critical factor in the sorting of functional from non-functional RNA polymerase II (Pol II) transcripts. Through its interaction with the Cap Binding Complex (CBC), it associates with the cap of newly made RNAs and acts as a hub for competitive exchanges of protein factors that ultimately determine the fate of the associated RNA. The central position of the protein within the nuclear gene expression machinery likely explains why its depletion causes a broad range of phenotypes, yet an exact function of the protein remains elusive. Here, we consider the literature on ARS2/SRRT with the attempt to garner the threads into a unifying working model for ARS2/SRRT function at the nexus of Pol II transcription, transcript maturation and quality control.
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García-de-Gracia F, Gaete-Argel A, Riquelme-Barrios S, Pereira-Montecinos C, Rojas-Araya B, Aguilera P, Oyarzún-Arrau A, Rojas-Fuentes C, Acevedo ML, Chnaiderman J, Valiente-Echeverría F, Toro-Ascuy D, Soto-Rifo R. CBP80/20-dependent translation initiation factor (CTIF) inhibits HIV-1 Gag synthesis by targeting the function of the viral protein Rev. RNA Biol 2021; 18:745-758. [PMID: 33103564 PMCID: PMC8078705 DOI: 10.1080/15476286.2020.1832375] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 09/25/2020] [Accepted: 09/30/2020] [Indexed: 02/07/2023] Open
Abstract
Translation initiation of the human immunodeficiency virus type-1 (HIV-1) full-length RNA has been shown to occur through cap-dependent and IRES-driven mechanisms. Previous studies suggested that the nuclear cap-binding complex (CBC) rather than eIF4E drives cap-dependent translation of the full-length RNA and we have recently reported that the CBC subunit CBP80 supports the function of the viral protein Rev during nuclear export and translation of this viral transcript. Ribosome recruitment during CBC-dependent translation of cellular mRNAs relies on the activity CBP80/20 translation initiation factor (CTIF), which bridges CBP80 and the 40S ribosomal subunit through interactions with eIF3g. Here, we report that CTIF inhibits HIV-1 and HIV-2 Gag synthesis from the full-length RNA. Our results indicate that CTIF associates with HIV-1 Rev through its N-terminal domain and is recruited onto the full-length RNA ribonucleoprotein complex in order to interfere with Gag synthesis. We also demonstrate that CTIF induces the cytoplasmic accumulation of Rev impeding the association of the viral protein with CBP80. We finally show that Rev interferes with the association of CTIF with CBP80 indicating that CTIF and Rev compete for the CBC subunit.
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Affiliation(s)
- Francisco García-de-Gracia
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aracelly Gaete-Argel
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Sebastián Riquelme-Barrios
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Camila Pereira-Montecinos
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Bárbara Rojas-Araya
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Paulina Aguilera
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Aarón Oyarzún-Arrau
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Cecilia Rojas-Fuentes
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Mónica L. Acevedo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Jonás Chnaiderman
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Fernando Valiente-Echeverría
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Daniela Toro-Ascuy
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
| | - Ricardo Soto-Rifo
- Laboratory of Molecular and Cellular Virology, Virology Program, Institute of Biomedical Sciences, Faculty of Medicine, Universidad de Chile, Santiago, Chile
- HIV/AIDS Workgroup, Faculty of Medicine, Universidad de Chile, Santiago, Chile
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Rambout X, Maquat LE. The nuclear cap-binding complex as choreographer of gene transcription and pre-mRNA processing. Genes Dev 2021; 34:1113-1127. [PMID: 32873578 PMCID: PMC7462061 DOI: 10.1101/gad.339986.120] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this review, Rambout and Maquat discuss known roles of the nuclear cap-binding complex (CBC) during the transcription of genes that encode proteins, stitching together past studies from diverse groups to describe the continuum of CBC-mediated checks and balances in eukaryotic cells. The largely nuclear cap-binding complex (CBC) binds to the 5′ caps of RNA polymerase II (RNAPII)-synthesized transcripts and serves as a dynamic interaction platform for a myriad of RNA processing factors that regulate gene expression. While influence of the CBC can extend into the cytoplasm, here we review the roles of the CBC in the nucleus, with a focus on protein-coding genes. We discuss differences between CBC function in yeast and mammals, covering the steps of transcription initiation, release of RNAPII from pausing, transcription elongation, cotranscriptional pre-mRNA splicing, transcription termination, and consequences of spurious transcription. We describe parameters known to control the binding of generic or gene-specific cofactors that regulate CBC activities depending on the process(es) targeted, illustrating how the CBC is an ever-changing choreographer of gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, New York 14642, USA.,Center for RNA Biology, University of Rochester, Rochester, New York 14642, USA
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Selective Interaction of Sugarcane eIF4E with VPgs from Sugarcane Mosaic Pathogens. Viruses 2021; 13:v13030518. [PMID: 33809985 PMCID: PMC8005120 DOI: 10.3390/v13030518] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 03/18/2021] [Accepted: 03/20/2021] [Indexed: 12/25/2022] Open
Abstract
Eukaryotic translation initiation factor 4E (eIF4E) plays a key role in the infection of potyviruses in susceptible plants by interacting with viral genome-linked protein (VPg). Sugarcane (Saccharum spp.) production is threatened by mosaic disease caused by Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), and Sugarcane streak mosaic virus (SCSMV). In this study, two eIF4Es and their isoform eIF(iso)4E and 4E-binding protein coding genes were cloned from sugarcane cultivar ROC22 and designated SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP, respectively. Real-time quantitative PCR analysis showed different expression profiles of these four genes upon SCMV challenge. A subcellular localization assay showed that SceIF4Ea, SceIF4Eb, SceIF(iso)4E, and ScnCBP were distributed in the nucleus and cytoplasm. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that SceIF4Ea/b and SceIF(iso)4E were selectively employed by different sugarcane mosaic pathogens, i.e., SCMV-VPg interacted with SceIF4Ea/b and SceIF(iso)4E, SrMV-VPg interacted with both SceIF4Eb and SceIF(iso)4E, and SCSMV-VPg interacted only with SceIF(iso)4E. Intriguingly, the BiFC assays, but not the Y2H assays, showed that ScnCBP interacted with the VPgs of SCMV, SrMV, and SCSMV. Competitive interaction assays showed that SCMV-VPg, SrMV-VPg, and SCMV-VPg did not compete with each other to interact with SceIF(iso)4E, and SceIF(iso)4E competed with SceIF4Eb to interact with SrMV-VPg but not SCMV-VPg. This study sheds light on the molecular mechanism of sugarcane mosaic pathogen infection of sugarcane plants and benefits sugarcane breeding against the sugarcane mosaic disease.
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42
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Dou Y, Barbosa I, Jiang H, Iasillo C, Molloy KR, Schulze WM, Cusack S, Schmid M, Le Hir H, LaCava J, Jensen TH. NCBP3 positively impacts mRNA biogenesis. Nucleic Acids Res 2020; 48:10413-10427. [PMID: 32960271 PMCID: PMC7544205 DOI: 10.1093/nar/gkaa744] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/19/2020] [Accepted: 08/26/2020] [Indexed: 12/26/2022] Open
Abstract
The nuclear Cap-Binding Complex (CBC), consisting of Nuclear Cap-Binding Protein 1 (NCBP1) and 2 (NCBP2), associates with the nascent 5′cap of RNA polymerase II transcripts and impacts RNA fate decisions. Recently, the C17orf85 protein, also called NCBP3, was suggested to form an alternative CBC by replacing NCBP2. However, applying protein–protein interaction screening of NCBP1, 2 and 3, we find that the interaction profile of NCBP3 is distinct. Whereas NCBP1 and 2 identify known CBC interactors, NCBP3 primarily interacts with components of the Exon Junction Complex (EJC) and the TRanscription and EXport (TREX) complex. NCBP3-EJC association in vitro and in vivo requires EJC core integrity and the in vivo RNA binding profiles of EJC and NCBP3 overlap. We further show that NCBP3 competes with the RNA degradation factor ZC3H18 for binding CBC-bound transcripts, and that NCBP3 positively impacts the nuclear export of polyadenylated RNAs and the expression of large multi-exonic transcripts. Collectively, our results place NCBP3 with the EJC and TREX complexes in supporting mRNA expression.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Isabelle Barbosa
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Claudia Iasillo
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Wiebke Manuela Schulze
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, CS 90181, Grenoble Cedex 9 38042, France
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
| | - Hervé Le Hir
- Institut de Biologie de l'ENS (IBENS), Département de biologie, École normale supérieure, CNRS, INSERM, Université PSL, 75005 Paris, France
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, Groningen 9713 AV, Netherlands
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, C.F. Møllers Allé 3, Aarhus 8000, Denmark
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43
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Dou Y, Kalmykova S, Pashkova M, Oghbaie M, Jiang H, Molloy KR, Chait BT, Rout MP, Fenyö D, Jensen TH, Altukhov I, LaCava J. Affinity proteomic dissection of the human nuclear cap-binding complex interactome. Nucleic Acids Res 2020; 48:10456-10469. [PMID: 32960270 PMCID: PMC7544204 DOI: 10.1093/nar/gkaa743] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/22/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022] Open
Abstract
A 5′,7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and a textbook aspect of co-transcriptional RNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Interest in the CBC has recently renewed due to its participation in RNA-fate decisions via interactions with RNA productive factors as well as with adapters of the degradative RNA exosome. A novel cap-binding protein, NCBP3, was recently proposed to form an alternative CBC together with NCBP1, and to interact with the canonical CBC along with the protein SRRT. The theme of post-transcriptional RNA fate, and how it relates to co-transcriptional ribonucleoprotein assembly, is abundant with complicated, ambiguous, and likely incomplete models. In an effort to clarify the compositions of NCBP1-, 2- and 3-related macromolecular assemblies, we have applied an affinity capture-based interactome screen where the experimental design and data processing have been modified to quantitatively identify interactome differences between targets under a range of experimental conditions. This study generated a comprehensive view of NCBP-protein interactions in the ribonucleoprotein context and demonstrates the potential of our approach to benefit the interpretation of complex biological pathways.
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Affiliation(s)
- Yuhui Dou
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Maria Pashkova
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Mehrnoosh Oghbaie
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Hua Jiang
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, USA
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA
| | - David Fenyö
- Department of Biochemistry and Molecular Pharmacology, Institute for Systems Genetics, NYU Langone Health, New York, USA
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Ilya Altukhov
- Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - John LaCava
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, USA.,European Research Institute for the Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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44
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Translatome and Transcriptome Profiling of Hypoxic-Induced Rat Cardiomyocytes. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:1016-1024. [PMID: 33294289 PMCID: PMC7689039 DOI: 10.1016/j.omtn.2020.10.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/18/2020] [Indexed: 01/09/2023]
Abstract
Adult cardiac hypoxia as a crucial pathogenesis factor can induce detrimental effects on cardiac injury and dysfunction. The global transcriptome and translatome reflecting the cellular response to hypoxia have not yet been extensively studied in myocardium. In this study, we conducted RNA sequencing (RNA-seq) and ribosome profiling technique (polyribo-seq) in rat heart tissues and H9C2 cells exposed to different periods of hypoxia stress in vivo and in vitro. The temporal gene-expression profiling displayed the distinction of transcriptome and translatome, which were mainly concentrated in cell apoptosis, autophagy, DNA repair, angiogenesis, vascular process, and cardiac cell proliferation and differentiation. A large number of genes such as GNAI3, SEPT4, FANCL, BNIP3, TBX3, ESR2, PTGS2, KLF4, and ADRB2, whose transcript and translation levels are closely correlated, were identified to own a common RNA motif “5′-GAAGCUGCC-3′” in 5′ UTR. NCBP3 was further determined to recognize this RNA motif and facilitate translational process in myocardium under hypoxia stress. Taken together, our data show the close connection between alterations of transcriptome and translatome after hypoxia exposure, emphasizing the significance of translational regulation in related studies. The profiled molecular responses in current study may be valuable resources for advanced understanding of the mechanisms underlying hypoxia-induced effect on heart diseases.
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45
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Wang H, Liu L, Rao X, Zeng B, Yu Y, Zhou C, Zeng L, Zheng P, Pu J, Xu S, Cheng K, Zhang H, Ji P, Wei H, Xie P. Integrated phosphoproteomic and metabolomic profiling reveals perturbed pathways in the hippocampus of gut microbiota dysbiosis mice. Transl Psychiatry 2020; 10:346. [PMID: 33051451 PMCID: PMC7553953 DOI: 10.1038/s41398-020-01024-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 08/27/2020] [Accepted: 09/22/2020] [Indexed: 12/12/2022] Open
Abstract
The dysbiosis of gut microbiota is an important environmental factor that can induce mental disorders, such as depression, through the microbiota-gut-brain axis. However, the underlying pathogenic mechanisms are complex and not completely understood. Here we utilized mass spectrometry to identify the global phosphorylation dynamics in hippocampus tissue in germ-free mice and specific pathogen-free mice (GF vs SPF), fecal microbiota transplantation (FMT) model ("depression microbiota" and the "healthy microbiota" recipient mice). As a result, 327 phosphosites of 237 proteins in GF vs SPF, and 478 phosphosites of 334 proteins in "depression microbiota" vs "healthy microbiota" recipient mice were identified as significant. These phosphorylation dysregulations were consistently associated with glutamatergic neurotransmitter system disturbances. The FMT mice exhibited disturbances in lipid metabolism and amino acid metabolism in both the periphery and brain through integrating phosphoproteomic and metabolomic analysis. Moreover, CAMKII-CREB signaling pathway, in response to these disturbances, was the primary common perturbed cellular process. In addition, we demonstrated that the spliceosome, never directly implicated in mental disorders previously, was a substantially neuronal function disrupted by gut microbiota dysbiosis, and the NCBP1 phosphorylation was identified as a novel pathogenic target. These results present a new perspective to study the pathologic mechanisms of gut microbiota dysbiosis related depression and highlight potential gut-mediated therapies for depression.
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Affiliation(s)
- Haiyang Wang
- grid.459985.cChongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, 401147 Chongqing, China ,grid.203458.80000 0000 8653 0555College of Biomedical Engineering, Chongqing Medical University, 400016 Chongqing, China ,grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Lanxiang Liu
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China ,grid.203458.80000 0000 8653 0555Department of Neurology, Yongchuan Hospital of Chongqing Medical University, 402460 Chongqing, China
| | - Xuechen Rao
- grid.203458.80000 0000 8653 0555College of Biomedical Engineering, Chongqing Medical University, 400016 Chongqing, China ,grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Benhua Zeng
- grid.410570.70000 0004 1760 6682Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, 400038 Chongqing, China
| | - Ying Yu
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Chanjuan Zhou
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Li Zeng
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China ,grid.412461.4Department of Nephrology, The Second Affiliated Hospital of Chongqing Medical University, 400010 Chongqing, China
| | - Peng Zheng
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China ,grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Juncai Pu
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China ,grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Shaohua Xu
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Ke Cheng
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China ,grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Hanping Zhang
- grid.452206.7NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China ,grid.452206.7Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016 Chongqing, China
| | - Ping Ji
- grid.459985.cChongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, 401147 Chongqing, China
| | - Hong Wei
- Department of Laboratory Animal Science, College of Basic Medical Sciences, Third Military Medical University, 400038, Chongqing, China.
| | - Peng Xie
- Chongqing Key Laboratory of Oral Diseases and Biomedical Sciences, Stomatological Hospital of Chongqing Medical University, 401147, Chongqing, China. .,NHC Key Laboratory of Diagnosis and Treatment on Brain Functional Diseases, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China. .,Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, 400016, Chongqing, China.
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Rambout X, Maquat LE. NCBP3: A Multifaceted Adaptive Regulator of Gene Expression. Trends Biochem Sci 2020; 46:87-96. [PMID: 33032857 DOI: 10.1016/j.tibs.2020.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/31/2020] [Accepted: 09/08/2020] [Indexed: 12/29/2022]
Abstract
Eukaryotic cells have divided the steps of gene expression between their nucleus and cytoplasm. Protein-encoding genes generate mRNAs in the nucleus and mRNAs undergo transport to the cytoplasm for the purpose of producing proteins. Cap-binding protein (CBP)20 and its binding partner CBP80 have been thought to constitute the cap-binding complex (CBC) that is acquired co-transcriptionally by the precursors of all mRNAs. However, this principle has recently been challenged by studies of nuclear cap-binding protein 3 (NCBP3). Here we submit how NCBP3, as an alternative to CBP20, an accessory to the canonical CBP20-CBP80 CBC, and/or an RNA-binding protein - possibly in association with the exon-junction complex (EJC) - expands the capacity of cells to regulate gene expression.
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Affiliation(s)
- Xavier Rambout
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA
| | - Lynne E Maquat
- Department of Biochemistry and Biophysics, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA; Center for RNA Biology, University of Rochester, Rochester, NY 14642, USA.
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47
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Li X, Zhang F, Ma J, Ruan X, Liu X, Zheng J, Liu Y, Cao S, Shen S, Shao L, Cai H, Li Z, Xue Y. NCBP3/SNHG6 inhibits GBX2 transcription in a histone modification manner to facilitate the malignant biological behaviour of glioma cells. RNA Biol 2020; 18:47-63. [PMID: 32618493 DOI: 10.1080/15476286.2020.1790140] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
RNA-binding proteins (RBPs) are significantly dysregulated in glioma. In this study, we demonstrated the upregulation of Nuclear cap-binding subunit 3 (NCBP3) in glioma tissues and cells. Further, knockdown of NCBP3 inhibited the malignant progression of glioma. NCBP3 directly bound to small nucleolar RNA host gene 6 (SNHG6) and stabilized SNHG6 expression. In contrast, the gastrulation brain homeobox 2 (GBX2) transcription factor was downregulated in glioma tissues and cells. SNHG6 inhibited GBX2 transcription by mediating the H3K27me3 modification induced by polycomb repressive complex 2 (PRC2). Moreover, GBX2 decreased the promoter activities and downregulated the expression of the flotillin protein family 1 (FLOT1) oncogene. In conclusion, NCBP3/SNHG6 inhibits GBX2 transcription in a PRC2-dependent manner to facilitate the malignant progression of gliomas.
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Affiliation(s)
- Xiwen Li
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Fangfang Zhang
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Jun Ma
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Xuelei Ruan
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Xiaobai Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Jian Zheng
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Yunhui Liu
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Shuo Cao
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Shuyuan Shen
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Lianqi Shao
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
| | - Heng Cai
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Zhen Li
- Department of Neurosurgery, Shengjing Hospital of China Medical University , Shenyang, China.,Liaoning Clinical Medical Research Center in Nervous System Disease , Shenyang, China.,Key Laboratory of Neuro-oncology in Liaoning Province , Shenyang, China
| | - Yixue Xue
- Department of Neurobiology, School of Life Sciences, China Medical University , Shenyang, China.,Key Laboratory of Cell Biology, Ministry of Public Health of China, China Medical University , Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education of China, China Medical University , Shenyang, China
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48
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Abstract
In the filamentous fungus Neurospora crassa, genes unpaired during meiosis are silenced by a process known as meiotic silencing by unpaired DNA (MSUD). MSUD utilizes common RNA interference (RNAi) proteins, such as Dicer and Argonaute, to target homologous mRNAs for silencing. Previously, we demonstrated that nuclear cap-binding proteins NCBP1 and NCBP2 are involved in MSUD. We report here that SAD-8, a protein similar to human NCBP3, also mediates silencing. Although SAD-8 is not essential for either vegetative or sexual development, it is required for MSUD. SAD-8 localizes predominantly in the nucleus and interacts with both NCBP1 and NCBP2. Similar to NCBP1 and NCBP2, SAD-8 interacts with a component (Argonaute) of the perinuclear meiotic silencing complex (MSC), further implicating the involvement of cap-binding proteins in silencing.
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49
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Singh G, Fritz SE, Seufzer B, Boris-Lawrie K. The mRNA encoding the JUND tumor suppressor detains nuclear RNA-binding proteins to assemble polysomes that are unaffected by mTOR. J Biol Chem 2020; 295:7763-7773. [PMID: 32312751 DOI: 10.1074/jbc.ra119.012005] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 04/14/2020] [Indexed: 12/16/2022] Open
Abstract
One long-standing knowledge gap is the role of nuclear proteins in mRNA translation. Nuclear RNA helicase A (DHX9/RHA) is necessary for the translation of the mRNAs of JUND (JunD proto-oncogene AP-1 transcription factor subunit) and HIV-1 genes, and nuclear cap-binding protein 1 (NCBP1)/CBP80 is a component of HIV-1 polysomes. The protein kinase mTOR activates canonical messenger ribonucleoproteins by post-translationally down-regulating the eIF4E inhibitory protein 4E-BP1. We posited here that NCBP1 and DHX9/RHA (RHA) support a translation pathway of JUND RNA that is independent of mTOR. We present evidence from reciprocal immunoprecipitation experiments indicating that NCBP1 and RHA both are components of messenger ribonucleoproteins in several cell types. Moreover, tandem affinity and RT-quantitative PCR results revealed that JUND mRNA is a component of a previously unknown ribonucleoprotein complex. Results from the tandem IP indicated that another component of the JUND-containing ribonucleoprotein complex is NCBP3, a recently identified ortholog of NCBP2/CBP20. We also found that NCBP1, NCBP3, and RHA, but not NCBP2, are components of JUND-containing polysomes. Mutational analysis uncovered two dsRNA-binding domains of RHA that are necessary to tether JUND-NCBP1/NCBP3 to polysomes. We also found that JUND translation is unaffected by inhibition of mTOR, unless RHA was down-regulated by siRNA. These findings uncover a noncanonical cap-binding complex consisting of NCBP1/NCBP3 and RHA substitutes for the eukaryotic translation initiation factors 4E and 4G and activates mTOR-independent translation of the mRNA encoding the tumor suppressor JUND.
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Affiliation(s)
- Gatikrushna Singh
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Sarah E Fritz
- Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
| | - Bradley Seufzer
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108
| | - Kathleen Boris-Lawrie
- Department of Veterinary and Biomedical Sciences, University of Minnesota, Saint Paul, Minnesota 55108 .,Integrated Biomedical Science Graduate Program, Ohio State University, Columbus, Ohio 43210
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50
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Zhao L, Cong X, Zhai L, Hu H, Xu JY, Zhao W, Zhu M, Tan M, Ye BC. Comparative evaluation of label-free quantification strategies. J Proteomics 2020; 215:103669. [DOI: 10.1016/j.jprot.2020.103669] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 12/28/2019] [Accepted: 01/22/2020] [Indexed: 12/17/2022]
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