1
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Fagoonee S, Weiskirchen R. MicroRNAs and RNA-Binding Protein-Based Regulation of Bone Metastasis from Hepatobiliary Cancers and Potential Therapeutic Strategies. Cells 2024; 13:1935. [PMID: 39682684 DOI: 10.3390/cells13231935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Revised: 11/15/2024] [Accepted: 11/20/2024] [Indexed: 12/18/2024] Open
Abstract
Hepatobiliary cancers, such as hepatocellular carcinoma (HCC) and cholangiocarcinoma (CCA), are among the deadliest malignancies worldwide, leading to a significant number of cancer-related deaths. While bone metastases from these cancers are rare, they are highly aggressive and linked to poor prognosis. This review focuses on RNA-based molecular mechanisms that contribute to bone metastasis from hepatobiliary cancers. Specifically, the role of two key factors, microRNAs (miRNAs) and RNA-binding proteins (RBPs), which have not been extensively studied in the context of HCC and CCA, is discussed. These molecules often exhibit abnormal expression in hepatobiliary tumors, influencing cancer cell spread and metastasis by disrupting bone homeostasis, thereby aiding tumor cell migration and survival in the bone microenvironment. This review also discusses potential therapeutic strategies targeting these RNA-based pathways to reduce bone metastasis and improve patient outcomes. Further research is crucial for developing effective miRNA- and RBP-based diagnostic and prognostic biomarkers and treatments to prevent bone metastases in hepatobiliary cancers.
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Affiliation(s)
- Sharmila Fagoonee
- Institute of Biostructure and Bioimaging (CNR), Molecular Biotechnology Center "Guido Tarone", 10126 Turin, Italy
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
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2
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Ban KY, Na YW, Song J, Kim JS, Kim J. Protein-RNA interaction dynamics reveal key regulators of oncogenic KRAS-driven cancers. Sci Rep 2024; 14:27119. [PMID: 39511334 PMCID: PMC11544019 DOI: 10.1038/s41598-024-78333-2] [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: 08/16/2024] [Accepted: 10/30/2024] [Indexed: 11/15/2024] Open
Abstract
KRAS is one of the most frequently mutated oncogenes across various cancers. Oncogenic KRAS mutations rewire cellular signaling, leading to significant alterations in gene expression. RNA-binding proteins (RBPs) play a pivotal role in gene expression regulation by post-transcriptionally controlling various aspects of RNA metabolism. It has become clear that interactions between RBPs and RNA are frequently dysregulated in numerous cancers. However, how oncogenic KRAS mutations reshape the post-transcriptional regulatory network mediated by RBPs remains poorly understood. In this study, we systematically dissected oncogenic KRAS-driven alterations of RNA-RBP networks. We identified 35 cancer-associated RBPs with either increased or decreased RNA binding upon oncogenic KRAS activation, including PDCD11, which is essential for the viability of KRAS mutant cancers, and ELAVL2, which regulates cell migration in KRAS mutant lung cancers. Our study serves as a crucial resource for elucidating RBP regulatory networks in KRAS mutant cancers and may provide new avenues for therapeutic strategies targeting KRAS mutant malignancies.
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Affiliation(s)
- Ka-Yun Ban
- Department of Health Science and Technology, Lee Gil Ya Cancer and Diabetes Institute, GAIHST, Incheon, 21999, Republic of Korea
| | - Yong-Woo Na
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Juhan Song
- Department of Health Science and Technology, Lee Gil Ya Cancer and Diabetes Institute, GAIHST, Incheon, 21999, Republic of Korea
| | - Jong-Seo Kim
- School of Biological Sciences, Seoul National University, Seoul, 08826, Korea
| | - Jimi Kim
- Department of Health Science and Technology, Lee Gil Ya Cancer and Diabetes Institute, GAIHST, Incheon, 21999, Republic of Korea.
- Department of Life Sciences, Gachon University, Seongnam, 13120, Korea.
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3
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Yang PY, Yang Z, Lv J, Jiang PY, Quan TQ, Huang ZH, Xu XD, Guo R, Wei D, Sun Y. The noncanonical RNA-binding protein RAN stabilizes the mRNA of intranuclear stress granule assembly factor G3BP1 in nasopharyngeal carcinoma. J Biol Chem 2024; 300:107964. [PMID: 39510185 PMCID: PMC11635782 DOI: 10.1016/j.jbc.2024.107964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2024] [Revised: 10/13/2024] [Accepted: 10/25/2024] [Indexed: 11/15/2024] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in tumor progression by participating in the posttranscriptional regulation of RNA. However, the levels and function of RBPs in nasopharyngeal carcinoma (NPC) remain elusive. Here we identified a noncanonical RBP RAN that has the most significant role in NPC progression by a small siRNA pool screening. Functionally, RAN facilitates NPC proliferation and metastasis in vitro and in vivo. High levels of RAN are associated with poor prognosis of NPC patients and can be performed as a prognostic biomarker. Mechanistically, RAN increases the nucleus import of TDP43 and enhances TDP43 nuclear distribution. On the other hand, RAN is directly bound to the coding sequence of G3BP1 mRNA and serves as an adapter to facilitate TDP43 interacting with G3BP1 mRNA 3' UTR. These contribute to increasing G3BP1 mRNA stability in the nucleus and lead to upregulation of G3BP1, which further enhances AKT and ERK signaling and ultimately promotes NPC proliferation and metastasis. These findings reveal that RAN stabilizes intranuclear G3BP1 mRNA by dual mechanisms: recruiting TDP43 into the nucleus and enhancing its interaction with G3BP1 mRNA, suggesting a critical role of RAN in NPC progression and providing a new regulation framework of RBP-RNA.
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Affiliation(s)
- Pan-Yang Yang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Zhenyu Yang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Jiawei Lv
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Pei-Yi Jiang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Ting-Qiu Quan
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Zhuo-Hui Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Xu-Dong Xu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China
| | - Rui Guo
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Denghui Wei
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
| | - Ying Sun
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Department of Radiation Oncology, Sun Yat-sen University Cancer Center, Guangzhou, PR China.
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4
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Wang T, Zhang H. Exploring the roles and molecular mechanisms of RNA binding proteins in the sorting of noncoding RNAs into exosomes during tumor progression. J Adv Res 2024; 65:105-123. [PMID: 38030125 PMCID: PMC11518959 DOI: 10.1016/j.jare.2023.11.029] [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: 08/19/2023] [Revised: 10/26/2023] [Accepted: 11/24/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND RNA binding proteins (RBPs) play a role in sorting non-coding RNAs (ncRNAs) into exosomes. These ncRNAs, carried by exosomes, are involved in regulating various aspects of tumor progression, including metastasis, angiogenesis, control of the tumor microenvironment, and drug resistance. Recent studies have emphasized the importance of the RBP-ncRNA-exosome mechanism in tumor regulation. AIM OF REVIEW This comprehensive review aims to explore the RBP-ncRNA-exosome mechanism and its influence on tumor development. By understanding this intricate mechanism provides novel insights into tumor regulation and may lead to innovative treatment strategies in the future. KEY SCIENTIFIC CONCEPTS OF REVIEW The review discusses the formation of exosomes and the complex relationships among RBPs, ncRNAs, and exosomes. The RBP-ncRNA-exosome mechanism is shown to affect various aspects of tumor biology, including metastasis, multidrug resistance, angiogenesis, the immunosuppressive microenvironment, and tumor progression. Tumor development relies on the transmission of information between cells, with RBPs selectively mediating sorting of ncRNAs into exosomes through various mechanisms, which in turn carry ncRNAs to regulate RBPs. The review also provides an overview of potential therapeutic strategies, such as targeted drug discovery and genetic engineering for modifying therapeutic exosomes, which hold great promise for improving cancer treatment.
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Affiliation(s)
- Ting Wang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hui Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
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5
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Fang Y, Liu X, Liu Y, Xu N. Insights into the Mode and Mechanism of Interactions Between RNA and RNA-Binding Proteins. Int J Mol Sci 2024; 25:11337. [PMID: 39518890 PMCID: PMC11545484 DOI: 10.3390/ijms252111337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2024] [Revised: 10/04/2024] [Accepted: 10/16/2024] [Indexed: 11/16/2024] Open
Abstract
Both RNA and protein play important roles in the process of gene expression and regulation, and it has been widely discussed that the interactions between RNA and protein affect gene transcription, translation efficiency, and post-translational modification. As an important class of proteins, RNA-binding proteins bind to RNA and affect gene expression in various ways. Here, we review the structural and functional properties of RNA-binding proteins and illustrate the specific modes of interactions between RNA and RNA-binding proteins and describe the involvement of some representative RNA-binding protein families in this network of action. Furthermore, we also explore the association that exists between RNA-binding proteins and the onset of diseases, as well as their potential in terms of serving as a therapeutic tool for the treatment of diseases. The in-depth exploration of the interactions between RNA and RNA-binding proteins reveals the dynamic process of gene expression and regulation, as well as offering valuable insights to advance the progress in the dissection of disease mechanisms and research and discovery of drugs, which promote the development of molecular biology.
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Affiliation(s)
| | | | | | - Naiyi Xu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (Y.F.); (X.L.); (Y.L.)
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6
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Tan Y, Zhao Z, Han Q, Xu P, Shen X, Jiang Y, Xu Q, Wu X. Identification of an RNA-binding perturbing characteristic for thiopurine drugs and their derivatives to disrupt CELF1-RNA interaction. Nucleic Acids Res 2024; 52:10810-10822. [PMID: 39268573 PMCID: PMC11472155 DOI: 10.1093/nar/gkae788] [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: 03/26/2024] [Revised: 08/26/2024] [Accepted: 08/30/2024] [Indexed: 09/17/2024] Open
Abstract
RNA-binding proteins (RBPs) are attractive targets in human pathologies. Despite a number of efforts to target RBPs with small molecules, it is still difficult to develop RBP inhibitors, asking for a deeper understanding of how to chemically perturb RNA-binding activity. In this study, we found that the thiopurine drugs (6-mercaptopurine and 6-thioguanine) effectively disrupt CELF1-RNA interaction. The disrupting activity relies on the formation of disulfide bonds between the thiopurine drugs and CELF1. Mutating the cysteine residue proximal to the RNA recognition motifs (RRMs), or adding reducing agents, abolishes the disrupting activity. Furthermore, the 1,2,4-triazole-3-thione, a thiopurine analogue, was identified with 20-fold higher disrupting activity. Based on this analogue, we found that compound 9 disrupts CELF1-RNA interaction in living cells and ameliorates CELF1-mediated myogenesis deficiency. In summary, we identified a thiol-mediated binding mechanism for thiopurine drugs and their derivatives to perturb protein-RNA interaction, which provides novel insight for developing RBP inhibitors. Additionally, this work may benefit the pharmacological and toxicity research of thiopurine drugs.
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Affiliation(s)
- Yang Tan
- State Key Laboratory of Pharmaceutical Biotechnology, Drum Tower Hospital Affiliated to Medical School, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Zhibo Zhao
- State Key Laboratory of Pharmaceutical Biotechnology, Drum Tower Hospital Affiliated to Medical School, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Qingfang Han
- State Key Laboratory of Pharmaceutical Biotechnology, Drum Tower Hospital Affiliated to Medical School, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Peipei Xu
- Department of Hematology, Drum Tower Hospital Affiliated to Medical School, Nanjing University, Nanjing 210008, China
| | - Xiaopeng Shen
- College of Life Sciences, Anhui Normal University, Wuhu, China
| | - Yajun Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Qiang Xu
- State Key Laboratory of Pharmaceutical Biotechnology, Drum Tower Hospital Affiliated to Medical School, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xingxin Wu
- State Key Laboratory of Pharmaceutical Biotechnology, Drum Tower Hospital Affiliated to Medical School, School of Life Sciences, Nanjing University, Nanjing 210023, China
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7
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Peng P, Yin Q, Sun W, Han J, Guo H, Cheng C, Liu D. Global RNA Interaction and Transcriptome Profiles Demonstrate the Potential Anti-Oncogenic Targets and Pathways of RBM6 in HeLa Cells. FRONT BIOSCI-LANDMRK 2024; 29:330. [PMID: 39344314 DOI: 10.31083/j.fbl2909330] [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: 03/22/2024] [Revised: 06/01/2024] [Accepted: 06/11/2024] [Indexed: 10/01/2024]
Abstract
BACKGROUND The fate and functions of RNAs are coordinately regulated by RNA-binding proteins (RBPs), which are often dysregulated in various cancers. Known as a splicing regulator, RNA-binding motif protein 6 (RBM6) harbors tumor-suppressor activity in many cancers; however, there is a lack of research on the molecular targets and regulatory mechanisms of RBM6. METHODS In this study, we constructed an RBM6 knock-down (shRBM6) model in the HeLa cell line to investigate its functions and molecular targets. Then we applied improved RNA immunoprecipitation coupled with sequencing (iRIP-seq) and whole transcriptome sequencing approaches to investigate the potential role and RNA targets of RBM6. RESULTS Using The Cancer Genome Atlas dataset, we found that higher expression of RBM6 is associated with a better prognosis in many cancer types. In addition, we found that RBM6 knockdown promoted cell proliferation and inhibited apoptosis, demonstrating that RBM6 may act as an anti-oncogenic protein in cancer cells. RBM6 can regulate the alternative splicing (AS) of genes involved in DNA damage response, proliferation, and apoptosis-associated pathways. Meanwhile, RBM6 knockdown activated type I interferon signaling pathways and inhibited the expression of genes involved in the cell cycle, cellular responses to DNA damage, and DNA repair pathways. The differentially expressed genes (DEGs) by shRBM6 and their involved pathways were likely regulated by the transcription factors undergoing aberrant AS by RBM6 knockdown. For iRIP-seq analysis, we found that RBM6 could interact with a large number of mRNAs, with a tendency for binding motifs GGCGAUG and CUCU. RBM6 bound to the mRNA of cell proliferation- and apoptosis-associated genes with dysregulated AS after RBM6 knockdown. CONCLUSIONS In summary, our study highlights the important role of RBM6, as well as the downstream targets and regulated pathways, suggesting the potential regulatory mechanisms of RBM6 in the development of cancer.
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Affiliation(s)
- Ping Peng
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Qingqing Yin
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., 430075 Wuhan, Hubei, China
| | - Wei Sun
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Jing Han
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
| | - Hao Guo
- Center for Genome Analysis, Wuhan Ruixing Biotechnology Co., Ltd., 430075 Wuhan, Hubei, China
| | - Chao Cheng
- Center for BioBigData Analysis, ABLife BioBigData Institute, 430075 Wuhan, Hubei, China
| | - Dongbo Liu
- Cancer Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, 430030 Wuhan, Hubei, China
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8
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Zhong Y, Wilkinson-White L, Zhang E, Mohanty B, Zhang BB, McRae MS, Luo R, Allport TA, Duff AP, Zhao J, El-Kamand S, Du Plessis MD, Cubeddu L, Gamsjaeger R, Ataide SF, Kwan AH. Peptide nucleic acids can form hairpins and bind RNA-binding proteins. PLoS One 2024; 19:e0310565. [PMID: 39283902 PMCID: PMC11404819 DOI: 10.1371/journal.pone.0310565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2024] [Accepted: 08/29/2024] [Indexed: 09/22/2024] Open
Abstract
RNA-binding proteins (RBPs) are a major class of proteins that interact with RNAs to change their fate or function. RBPs and the ribonucleoprotein complexes they constitute are involved in many essential cellular processes. In many cases, the molecular details of RBP:RNA interactions differ between viruses, prokaryotes and eukaryotes, making prokaryotic and viral RBPs good potential drug targets. However, targeting RBPs with small molecules has so far been met with limited success as RNA-binding sites tend to be extended, shallow and dynamic with a mixture of charged, polar and hydrophobic interactions. Here, we show that peptide nucleic acids (PNAs) with nucleic acid-like binding properties and a highly stable peptide-like backbone can be used to target some RBPs. We have designed PNAs to mimic the short RNA stem-loop sequence required for the initiation of prokaryotic signal recognition particle (SRP) assembly, a target for antibiotics development. Using a range of biophysical and biochemical assays, the designed PNAs were demonstrated to fold into a hairpin structure, bind the targeted protein and compete with the native RNA hairpin to inhibit SRP formation. To show the applicability of PNAs against other RBPs, a PNA was also shown to bind Nsp9 from SARS-CoV-2, a protein that exhibits non-sequence-specific RNA binding but preferentially binds hairpin structures. Taken together, our results support that PNAs can be a promising class of compounds for targeting RNA-binding activities in RBPs.
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Affiliation(s)
- Yichen Zhong
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Lorna Wilkinson-White
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, NSW, Australia
| | - Esther Zhang
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Biswaranjan Mohanty
- Sydney Analytical Core Research Facility, The University of Sydney, Sydney, NSW, Australia
| | - Belinda B Zhang
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Madeline S McRae
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Rachel Luo
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Thomas A Allport
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Anthony P Duff
- National Deuteration Facility, ANSTO, Lucas Heights, NSW, Australia
| | - Jennifer Zhao
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Serene El-Kamand
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | | | - Liza Cubeddu
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Roland Gamsjaeger
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- School of Science, Western Sydney University, Penrith, NSW, Australia
| | - Sandro F Ataide
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Ann H Kwan
- Currently or formerly at School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
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9
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Zhang J, He J, Chen W, Chen G, Wang L, Liu Y, Wang Z, Yang M, Huang G, Yang Y, Ma W, Li Y. Single-cell RNA-binding protein pattern-mediated molecular subtypes depict the hallmarks of the tumor microenvironment in bladder urothelial carcinoma. ONCOLOGIE 2024; 26:657-669. [DOI: 10.1515/oncologie-2024-0071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/21/2024]
Abstract
Abstract
Objectives
Bladder carcinoma (BC) is a common malignancy of the urinary tract. As a new hallmark of cancer for drug therapy, RNA-binding proteins (RBPs) are key regulatory factors in alternative splicing events. This work is to uncover the relationship between BC and RBP in order to find drug targets in BC.
Methods
In this work, data from single-cell RNA-seq GSE1355337, PRJNA662018, and the TCGA-Bladder urothelial carcinoma (BLCA) cohorts are integrated to identify their relationships. A scoring system is constructed according to RBPs gene expression and patients’ survival. A network is constructed to analyze the alternative splicing events and RBP genes.
Results
A scoring system identified 321 RBPs significantly associated with the prognosis of patients. Subsequent typing of these RBP genes in two single-cell datasets demonstrated that most of the RBP genes had variable copy numbers. Three RBP clusters were identified. Using RBP genes as a signature in BC epithelial cells allows for differentiation between different grades of BC samples. The novel RBP genes-based subtype system reflects BC clinical staging. Notably, CellChat analysis revealed that the RBP genes-associated cell subtypes of T cells had extensive interactions with epithelial cells. Further analysis showed that the ligand-receptor pair MIF-CXCR4 mediated the communication between RBP-associated subtypes of BC epithelial cells and T cells.
Conclusions
Taken together, RBP genes are associated with BC progress and offer new indicators for precision medicine in BC.
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Affiliation(s)
- Jun Zhang
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Jiejie He
- Department of Surgical Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wen Chen
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Guojun Chen
- Department of Urology Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Liang Wang
- Department of Gastrointestinal Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yuchan Liu
- Department of Gynecology and Obstetrics , Jingmen Central Hospital , Jingmen , Hubei Province , China
| | - Zhanjin Wang
- Medical College of Qinghai University , Xining , Qinghai Province , China
| | - Ming Yang
- Department of Medical Records and Statistic, Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Guoyi Huang
- Wuhan Ruixing Biotechnology Co. Ltd. , Wuhan , Hubei Province , China
| | - Yongli Yang
- Department of Gynecology , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Wei Ma
- Department of Surgery , Affiliated Hospital of Qinghai University , Xining , Qinghai Province , China
| | - Yan Li
- Department of Gynecologic Oncology , Affiliated Hospital of Qinghai University and Affiliated Cancer Hospital of Qinghai University , Xining , Qinghai Province , China
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10
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Zuo Y, Chen H, Yang L, Chen R, Zhang X, Deng Z. Research progress on prediction of RNA-protein binding sites in the past five years. Anal Biochem 2024; 691:115535. [PMID: 38643894 DOI: 10.1016/j.ab.2024.115535] [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: 01/21/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/23/2024]
Abstract
Accurately predicting RNA-protein binding sites is essential to gain a deeper comprehension of the protein-RNA interactions and their regulatory mechanisms, which are fundamental in gene expression and regulation. However, conventional biological approaches to detect these sites are often costly and time-consuming. In contrast, computational methods for predicting RNA protein binding sites are both cost-effective and expeditious. This review synthesizes already existing computational methods, summarizing commonly used databases for predicting RNA protein binding sites. In addition, applications and innovations of computational methods using traditional machine learning and deep learning for RNA protein binding site prediction during 2018-2023 are presented. These methods cover a wide range of aspects such as effective database utilization, feature selection and encoding, innovative classification algorithms, and evaluation strategies. Exploring the limitations of existing computational methods, this paper delves into the potential directions for future development. DeepRKE, RDense, and DeepDW all employ convolutional neural networks and long and short-term memory networks to construct prediction models, yet their algorithm design and feature encoding differ, resulting in diverse prediction performances.
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Affiliation(s)
- Yun Zuo
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214000, China
| | - Huixian Chen
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214000, China
| | - Lele Yang
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214000, China
| | - Ruoyan Chen
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214000, China
| | - Xiaoyao Zhang
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214000, China
| | - Zhaohong Deng
- School of Artificial Intelligence and Computer Science, Jiangnan University, Wuxi, 214000, China.
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11
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Lu Y, Yang Z, Zhang J, Ma X, Bi X, Xu L, Feng K, Wu Z, Ma X, Zhuang L. RNA-binding protein QKI promotes the progression of HCC by interacting with long non-coding RNA EGOT. Int Immunopharmacol 2024; 136:112297. [PMID: 38810307 DOI: 10.1016/j.intimp.2024.112297] [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: 02/11/2024] [Revised: 05/10/2024] [Accepted: 05/16/2024] [Indexed: 05/31/2024]
Abstract
BACKGROUND RNA-binding proteins are revealed to play important roles during the progression of hepatocellular carcinoma (HCC). However, the regulatory mechanisms of RNA-binding protein Quaking (QKI) in the expression and role of long non-coding RNAs (lncRNAs) in HCC cells remain not well understood. METHODS Cell Counting Kit-8, wound-healing, Transwell and colony-forming assays were performed to evaluate the effects of QKI and lncRNA EGOT on proliferation and migration of HCC cells. Tumor growth of HCC was analyzed using a mouse xenograft model. Immunoprecipitation (RIP) assay was used to investigate the interaction between QKI and EGOT. RESULTS The expression of QKI was significantly upregulated in HCC tissues and the higher QKI level was significantly associated with a poorer prognosis. Overexpression of QKI promoted the proliferation, migration, and colony-forming ability of HCC cells in vitro and tumor growth of HCC in vivo. Mechanistically, QKI protein could bind to EGOT RNA and increase its expression. Inhibition of EGOT attenuated the effects of QKI on the malignant phenotypes of HCC cells. In addition, both QKI and EGOT could activate the SAPK/JNK signaling pathway in HCC cells. CONCLUSIONS Our findings indicated that QKI exerted promotive effects on the malignant phenotypes of HCC through its interaction with EGOT.
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Affiliation(s)
- Yi Lu
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Zhenpeng Yang
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China
| | - Jie Zhang
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xuefeng Ma
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xiaoye Bi
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Longhai Xu
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Keqing Feng
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Zehua Wu
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China
| | - Xiang Ma
- Department of Hepatobiliary and Pancreatic Surgery, The Affiliated Hospital of Qingdao University, Qingdao 266071, China.
| | - Likun Zhuang
- Central Laboratory, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China.
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12
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Chen X, Wei H, Yue A, Zhang H, Zheng Y, Sun W, Zhou Y, Wang Y. KPNA2 promotes the progression of gastric cancer by regulating the alternative splicing of related genes. Sci Rep 2024; 14:17140. [PMID: 39060340 PMCID: PMC11282077 DOI: 10.1038/s41598-024-66678-7] [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: 01/09/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
RNA-binding proteins (RBPs) play critical roles in genome regulation. In this study, we explored the latent function of KPNA2, which is an essential member of the RBP family, in the regulation of alternative splicing (AS) in gastric cancer (GC). We analyzed the role of KPNA2 in regulating differential expression and AS via RNA sequencing (RNA-seq) and improved RNA immunoprecipitation sequencing (iRIP-seq). Clinical specimens were used to analyze the associations between KPNA2 expression and clinicopathological characteristics. CCK8 assays, transwell assays and wound healing assays were performed to explore the effect of KPNA2/WDR62 on GC cell progression. KPNA2 was shown to be highly expressed in GC cells and tissues and associated with lymph node metastases. KPNA2 promoted the proliferation, migration and invasion of GC cells and primarily regulated exon skipping, alternative 3's splice sites (A3SSs), alternative 5' splice sites (A5SSs), and cassette exons. We further revealed that KPNA2 participated in biological processes related to cell proliferation, and the immune response in GC via the regulation of transcription. In addition, KPNA2 preferentially bound to intron regions. Notably, KPNA2 regulated the A3SS AS mode of WDR62, and upregulation of WDR62 reversed the KPNA2 downregulation-induced inhibition of GC cell proliferation, migration and invasion. Finally, we discovered that the AS of immune-related molecules could be regulated by KPNA2. Overall, our results demonstrated for the first time that KPNA2 functions as an oncogenic splicing factor in GC that regulated the AS and differential expression of GC-related genes, and KPNA2 may be a potential target for GC treatment.
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Affiliation(s)
- Xia Chen
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Hui Wei
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Ailin Yue
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Huiyun Zhang
- The First Clinical Medical College, Lanzhou University, Lanzhou, 730000, China
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Ya Zheng
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Weiming Sun
- Department of Endocrinology, The First Hospital of Lanzhou University, Lanzhou, 730000, China
| | - Yongning Zhou
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
| | - Yuping Wang
- Department of Gastroenterology, Key Laboratory for Gastrointestinal Diseases of Gansu Province, The First Hospital of Lanzhou University, Lanzhou, 730000, Gansu Province, China.
- Gansu Province Clinical Research Center for Digestive Diseases, The First Hospital of Lanzhou University, Lanzhou, 730000, China.
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13
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Yasar S, Yagin FH, Melekoglu R, Ardigò LP. Integrating proteomics and explainable artificial intelligence: a comprehensive analysis of protein biomarkers for endometrial cancer diagnosis and prognosis. Front Mol Biosci 2024; 11:1389325. [PMID: 38894711 PMCID: PMC11184912 DOI: 10.3389/fmolb.2024.1389325] [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: 02/21/2024] [Accepted: 05/16/2024] [Indexed: 06/21/2024] Open
Abstract
Endometrial cancer, which is the most common gynaecological cancer in women after breast, colorectal and lung cancer, can be diagnosed at an early stage. The first aim of this study is to classify age, tumor grade, myometrial invasion and tumor size, which play an important role in the diagnosis and prognosis of endometrial cancer, with machine learning methods combined with explainable artificial intelligence. 20 endometrial cancer patients proteomic data obtained from tumor biopsies taken from different regions of EC tissue were used. The data obtained were then classified according to age, tumor size, tumor grade and myometrial invasion. Then, by using three different machine learning methods, explainable artificial intelligence was applied to the model that best classifies these groups and possible protein biomarkers that can be used in endometrial prognosis were evaluated. The optimal model for age classification was XGBoost with AUC (98.8%), for tumor grade classification was XGBoost with AUC (98.6%), for myometrial invasion classification was LightGBM with AUC (95.1%), and finally for tumor size classification was XGBoost with AUC (94.8%). By combining the optimal models and the SHAP approach, possible protein biomarkers and their expressions were obtained for classification. Finally, EWRS1 protein was found to be common in three groups (age, myometrial invasion, tumor size). This article's findings indicate that models have been developed that can accurately classify factors including age, tumor grade, and myometrial invasion all of which are critical for determining the prognosis of endometrial cancer as well as potential protein biomarkers associated with these factors. Furthermore, we were able to provide an analysis of how the quantities of the proteins suggested as biomarkers varied throughout the classes by combining the SHAP values with these ideal models.
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Affiliation(s)
- Seyma Yasar
- Department of Biostatistics, and Medical Informatics, Medicine Faculty, Inonu University, Malatya, Türkiye
| | - Fatma Hilal Yagin
- Department of Biostatistics, and Medical Informatics, Medicine Faculty, Inonu University, Malatya, Türkiye
| | - Rauf Melekoglu
- Department of Obstetrics and Gynecology, Faculty of Medicine, Inonu University, Malatya, Türkiye
| | - Luca Paolo Ardigò
- Department of Teacher Education, NLA University College, Oslo, Norway
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14
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Völkers M, Preiss T, Hentze MW. RNA-binding proteins in cardiovascular biology and disease: the beat goes on. Nat Rev Cardiol 2024; 21:361-378. [PMID: 38163813 DOI: 10.1038/s41569-023-00958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/06/2023] [Indexed: 01/03/2024]
Abstract
Cardiac development and function are becoming increasingly well understood from different angles, including signalling, transcriptional and epigenetic mechanisms. By contrast, the importance of the post-transcriptional landscape of cardiac biology largely remains to be uncovered, building on the foundation of a few existing paradigms. The discovery during the past decade of hundreds of additional RNA-binding proteins in mammalian cells and organs, including the heart, is expected to accelerate progress and has raised intriguing possibilities for better understanding the intricacies of cardiac development, metabolism and adaptive alterations. In this Review, we discuss the progress and new concepts on RNA-binding proteins and RNA biology and appraise them in the context of common cardiovascular clinical conditions, from cell and organ-wide perspectives. We also discuss how a better understanding of cardiac RNA-binding proteins can fill crucial knowledge gaps in cardiology and might pave the way to developing better treatments to reduce cardiovascular morbidity and mortality.
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Affiliation(s)
- Mirko Völkers
- Department of Cardiology, Angiology and Pneumology, University Hospital Heidelberg, Heidelberg, Germany
- DZHK (German Centre for Cardiovascular Research), partner site Heidelberg/Mannheim, Heidelberg and Mannheim, Germany
| | - Thomas Preiss
- Shine-Dalgarno Centre for RNA Innovation, John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
- Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia
| | - Matthias W Hentze
- European Molecular Biology Laboratory, Heidelberg, Germany.
- Molecular Medicine Partnership Unit (MMPU), Heidelberg, Germany.
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15
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Wang B, Fan X, Wang L, Wei X. The RNA-binding protein sorbin and SH3 domain-containing 2 are transcriptionally regulated by specificity protein 1 and function as tumor suppressors in bladder cancer by stabilizing tissue factor pathway inhibitor. Mol Carcinog 2024; 63:1174-1187. [PMID: 38501385 DOI: 10.1002/mc.23717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/27/2024] [Accepted: 03/07/2024] [Indexed: 03/20/2024]
Abstract
Sorbin and SH3 domain-containing 2 (SORBS2) is an RNA-binding protein and has been implicated in the development of some cancers. However, its role in bladder cancer (BC) is yet to be established. The expression of SORBS2 in BC tissues was determined from the Gene Expression Omnibus and Gene Expression Profiling Interactive Analysis databases and collected paired tumor/normal samples. The effects of SORBS2 on BC cells were detected by CCK-8, colony formation, Transwell, dual-luciferase, RNA immunoprecipitation, chromatin immunoprecipitation, and DNA pull-down assays. In vivo, BC cell growth and metastasis were studied by a xenograft subcutaneous model and a tail-vein metastasis model. The results showed that SORBS2 expression was significantly decreased in BC tissues and cells. SORBS2 overexpression inhibited cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro and tumor growth and metastasis in vivo, while silencing SORBS2 produced the opposite effect. Mechanistically, we found that SORBS2 enhanced the stability of tissue factor pathway inhibitor (TFPI) mRNA via direct binding to its 3' UTR. Restoration of TFPI expression reversed SORBS2 knockdown-induced malignant phenotypes of BC cells. In addition, SORBS2 expression was negatively regulated by the transcription factor specificity protein 1 (SP1). Conversely, SORBS2 can be transcriptionally regulated by SP1 and inhibit BC cell growth and metastasis via stabilization of TFPI mRNA, indicating SORBS2 may be a promising therapeutic target for BC.
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Affiliation(s)
- Beibei Wang
- Department of Pathology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xin Fan
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Lingang Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaosong Wei
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
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16
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Ciocia A, Mestre-Farràs N, Vicent-Nacht I, Guitart T, Gebauer F. CSDE1: a versatile regulator of gene expression in cancer. NAR Cancer 2024; 6:zcae014. [PMID: 38600987 PMCID: PMC11005786 DOI: 10.1093/narcan/zcae014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/13/2024] [Accepted: 03/10/2024] [Indexed: 04/12/2024] Open
Abstract
RNA-binding proteins (RBPs) have garnered significant attention in the field of cancer due to their ability to modulate diverse tumor traits. Once considered untargetable, RBPs have sparked renewed interest in drug development, particularly in the context of RNA-binding modulators of translation. This review focuses on one such modulator, the protein CSDE1, and its pivotal role in regulating cancer hallmarks. We discuss context-specific functions of CSDE1 in tumor development, its mechanisms of action, and highlight features that support its role as a molecular adaptor. Additionally, we discuss the regulation of CSDE1 itself and its potential value as biomarker and therapeutic target.
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Affiliation(s)
- Annagiulia Ciocia
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Neus Mestre-Farràs
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Ignacio Vicent-Nacht
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, Barcelona 08003, Spain
- Universitat Pompeu Fabra (UPF), Dr Aiguader 88, Barcelona, Spain
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17
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Seo Y, Rhim J, Kim JH. RNA-binding proteins and exoribonucleases modulating miRNA in cancer: the enemy within. Exp Mol Med 2024; 56:1080-1106. [PMID: 38689093 PMCID: PMC11148060 DOI: 10.1038/s12276-024-01224-z] [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: 09/30/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 05/02/2024] Open
Abstract
Recent progress in the investigation of microRNA (miRNA) biogenesis and the miRNA processing machinery has revealed previously unknown roles of posttranscriptional regulation in gene expression. The molecular mechanistic interplay between miRNAs and their regulatory factors, RNA-binding proteins (RBPs) and exoribonucleases, has been revealed to play a critical role in tumorigenesis. Moreover, recent studies have shown that the proliferation of hepatocellular carcinoma (HCC)-causing hepatitis C virus (HCV) is also characterized by close crosstalk of a multitude of host RBPs and exoribonucleases with miR-122 and its RNA genome, suggesting the importance of the mechanistic interplay among these factors during the proliferation of HCV. This review primarily aims to comprehensively describe the well-established roles and discuss the recently discovered understanding of miRNA regulators, RBPs and exoribonucleases, in relation to various cancers and the proliferation of a representative cancer-causing RNA virus, HCV. These have also opened the door to the emerging potential for treating cancers as well as HCV infection by targeting miRNAs or their respective cellular modulators.
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Affiliation(s)
- Yoona Seo
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jiho Rhim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea
| | - Jong Heon Kim
- Cancer Molecular Biology Branch, Research Institute, National Cancer Center, Goyang, 10408, Korea.
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, 10408, Korea.
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18
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Sun X, Zhao X, Xu Y, Yan Y, Han L, Wei M, He M. Potential therapeutic strategy for cancer: Multi-dimensional cross-talk between circRNAs and parental genes. Cancer Lett 2024; 588:216794. [PMID: 38453043 DOI: 10.1016/j.canlet.2024.216794] [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: 01/09/2024] [Revised: 02/27/2024] [Accepted: 03/04/2024] [Indexed: 03/09/2024]
Abstract
In many ways, circular RNAs (circRNAs) have been demonstrated to be crucial in the onset and advancement of cancer throughout the last ten years and have become a new focus of intense research in the field of RNAs. Accumulating studies have demonstrated that circRNAs can regulate parental gene expression via a variety of biological pathways. Furthermore, research into the complex interactions between circRNAs and their parental genes will shed light on their biological roles and open up new avenues for circRNAs' potential clinical translational uses. However, to date, multi-dimensional cross-talk between circRNAs and parental genes have not been systematically elucidated. Particularly intriguing is circRNA's exploration of tumor targeting, and potential therapeutic uses based on the parental gene regulation perspective. Here, we discuss their biogenesis, take a fresh look at the molecular mechanisms through which circRNAs control the expression of their parental genes in cancer. We further highlight We further highlight the latest circRNA clinical translational applications, including prognostic diagnostic markers, cancer vaccines, gDNA, and so on. Demonstrating the potential benefits and future applications of circRNA therapy.
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Affiliation(s)
- Xiaoyu Sun
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Xinyi Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Yan Xu
- Department of Urology, The First Hospital of China Medical University, Shenyang, China.
| | - Yuanyuan Yan
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Li Han
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China; Liaoning Medical Diagnosis and Treatment Center, Liaoning Province, China.
| | - Miao He
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, Liaoning Province, China; Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Shenyang, China.
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19
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Dairo G, Ward MN, Soendergaard M, Determan JJ. Bioactive compounds from Morchella esculenta as potential inhibitors of RNA-binding protein La in ovarian cancer: a molecular modeling and quantum mechanics approach. In Silico Pharmacol 2024; 12:32. [PMID: 38650742 PMCID: PMC11032304 DOI: 10.1007/s40203-024-00202-7] [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: 02/06/2024] [Accepted: 03/10/2024] [Indexed: 04/25/2024] Open
Abstract
La protein is significantly expressed in various malignant tumors, including ovarian cancer (OC), which is related to the poor response to platinum-based chemotherapy. Thus, inhibiting La protein could control the expression of the potential downstream genes involved in promoting proliferation and chemotherapy resistance to OC, which could serve as a therapeutic intervention. Through a molecular docking approach, 12 compounds from Morchella esculenta were screened against the crystal structure of La protein and four hit compounds were identified, including beta-carotene, p-hydroxybenzoic acid, gamma-tocopherol, and alpha-tocopherol, with a binding affinity of - 10.7, - 8.1, - 7.9, and - 7.6 kcal/mol, respectively, higher than pyridine-2-carboxylate (control), with a binding affinity of - 5.2 kcal/mol. To explore the interaction of the hit compounds with the target receptor, they were selected for a molecular dynamic simulation and post-simulation analysis for 100 ns. The result showed promising reliability of the ligands due to a stable interaction with the La protein crystal structure. Furthermore, the drug-likeness and physicochemical chemical properties of the compounds were investigated using ADMET study and density functional theory analysis, respectively, and the result shows that the hit compounds could serve as a promising starting for the development of novel LA protein inhibitors for OC therapeutics. Finally, this study compared HOMO and LUMO values from global hybrids with long-range corrected DFAs, and the result from the two followed the same qualitative pattern while calculating HOMO values; however, MO62X/cc-pVTZ could better predict LUMO values when considering a global hybrid.
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Affiliation(s)
- Gbenga Dairo
- Department of Biological Sciences, Western Illinois University, Macomb, IL USA
| | - Matthew N. Ward
- Department of Chemistry, Western Illinois University, Macomb, IL USA
- Department of Chemistry, The University of Memphis, Memphis, TN USA
| | | | - John J. Determan
- Department of Chemistry, Western Illinois University, Macomb, IL USA
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20
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Das S, Russon MP, Zea MP, Xing Z, Torregrosa-Allen S, Cervantes HE, Harper HA, Elzey BD, Tran EJ. WITHDRAWN: Supinoxin blocks Small Cell Lung Cancer Progression by Inhibiting Mitochondrial Respiration through the RNA Helicase DDX5. RESEARCH SQUARE 2024:rs.3.rs-4169007. [PMID: 38699339 PMCID: PMC11065055 DOI: 10.21203/rs.3.rs-4169007/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
The authors have requested that this preprint be removed from Research Square.
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Affiliation(s)
- Subhadeep Das
- Department of Biochemistry, Purdue University, BCHM A343, 175 S.
University Street, West Lafayette, Indiana 47907-2063
- Purdue University Institute for Cancer Research, Purdue
University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West
Lafayette, Indiana 47907-2064
| | - Matthew P. Russon
- Department of Biochemistry, Purdue University, BCHM A343, 175 S.
University Street, West Lafayette, Indiana 47907-2063
| | - Maria P. Zea
- Department of Biochemistry, Purdue University, BCHM A343, 175 S.
University Street, West Lafayette, Indiana 47907-2063
| | - Zheng Xing
- Department of Biochemistry, Purdue University, BCHM A343, 175 S.
University Street, West Lafayette, Indiana 47907-2063
| | - Sandra Torregrosa-Allen
- Purdue University Institute for Cancer Research, Purdue
University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West
Lafayette, Indiana 47907-2064
| | - Heidi E. Cervantes
- Purdue University Institute for Cancer Research, Purdue
University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West
Lafayette, Indiana 47907-2064
| | - Haley Ann Harper
- Purdue University Institute for Cancer Research, Purdue
University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West
Lafayette, Indiana 47907-2064
| | - Bennett D. Elzey
- Purdue University Institute for Cancer Research, Purdue
University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West
Lafayette, Indiana 47907-2064
- Department of Comparative Pathobiology, Purdue University, West
Lafayette, IN, USA
| | - Elizabeth J. Tran
- Department of Biochemistry, Purdue University, BCHM A343, 175 S.
University Street, West Lafayette, Indiana 47907-2063
- Purdue University Institute for Cancer Research, Purdue
University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West
Lafayette, Indiana 47907-2064
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21
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Indacochea A, Guitart T, Boada A, Peg V, Quer A, Laayouni H, Condal L, Espinosa P, Manzano JL, Gebauer F. CSDE1 Intracellular Distribution as a Biomarker of Melanoma Prognosis. Int J Mol Sci 2024; 25:2319. [PMID: 38396995 PMCID: PMC10889260 DOI: 10.3390/ijms25042319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 02/08/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
RNA-binding proteins are emerging as critical modulators of oncogenic cell transformation, malignancy and therapy resistance. We have previously found that the RNA-binding protein Cold Shock Domain containing protein E1 (CSDE1) promotes invasion and metastasis of melanoma, the deadliest form of skin cancer and also a highly heterogeneous disease in need of predictive biomarkers and druggable targets. Here, we design a monoclonal antibody useful for IHC in the clinical setting and use it to evaluate the prognosis potential of CSDE1 in an exploratory cohort of 149 whole tissue sections including benign nevi and primary tumors and metastasis from melanoma patients. Contrary to expectations for an oncoprotein, we observed a global decrease in CSDE1 levels with increasing malignancy. However, the CSDE1 cytoplasmic/nuclear ratio exhibited a positive correlation with adverse clinical features of primary tumors and emerged as a robust indicator of progression free survival in cutaneous melanoma, highlighting the potential of CSDE1 as a biomarker of prognosis. Our findings provide a novel feature for prognosis assessment and highlight the intricacies of RNA-binding protein dynamics in cancer progression.
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Affiliation(s)
- Alberto Indacochea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
| | - Tanit Guitart
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
| | - Aram Boada
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Institut d’investigació Germans Trias I Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (A.B.); (L.C.)
| | - Vicente Peg
- Pathology Department, Vall d’Hebron University Hospital, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain;
| | - Ariadna Quer
- Pathology Department, Hospital Universitari Germans Trias I Pujol, Institut d’Investigació Germans Trias I Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain;
- Barcelona Beta Brain Research Center, Pasqual Maragall Foundation, C/Wellington 30, 08006 Barcelona, Spain
| | - Laura Condal
- Dermatology Department, Hospital Universitari Germans Trias i Pujol, Institut d’investigació Germans Trias I Pujol, Universitat Autònoma de Barcelona, 08916 Badalona, Spain; (A.B.); (L.C.)
| | - Pablo Espinosa
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
| | - Jose Luis Manzano
- Medical Oncology Department, Catalonian Institute of Oncology, (ICO), Hospital Germans Trias I Pujol, 08916 Badalona, Spain;
| | - Fátima Gebauer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr Aiguader 88, 08003 Barcelona, Spain; (A.I.); (T.G.); (P.E.)
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Dr Aiguader 88, 08003 Barcelona, Spain
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22
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Khan FA, Fang N, Zhang W, Ji S. The multifaceted role of Fragile X-Related Protein 1 (FXR1) in cellular processes: an updated review on cancer and clinical applications. Cell Death Dis 2024; 15:72. [PMID: 38238286 PMCID: PMC10796922 DOI: 10.1038/s41419-023-06413-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024]
Abstract
RNA-binding proteins (RBPs) modulate the expression level of several target RNAs (such as mRNAs) post-transcriptionally through interactions with unique binding sites in the 3'-untranslated region. There is mounting information that suggests RBP dysregulation plays a significant role in carcinogenesis. However, the function of FMR1 autosomal homolog 1(FXR1) in malignancies is just beginning to be unveiled. Due to the diversity of their RNA-binding domains and functional adaptability, FXR1 can regulate diverse transcript processing. Changes in FXR1 interaction with RNA networks have been linked to the emergence of cancer, although the theoretical framework defining these alterations in interaction is insufficient. Alteration in FXR1 expression or localization has been linked to the mRNAs of cancer suppressor genes, cancer-causing genes, and genes involved in genomic expression stability. In particular, FXR1-mediated gene regulation involves in several cellular phenomena related to cancer growth, metastasis, epithelial-mesenchymal transition, senescence, apoptosis, and angiogenesis. FXR1 dysregulation has been implicated in diverse cancer types, suggesting its diagnostic and therapeutic potential. However, the molecular mechanisms and biological effects of FXR1 regulation in cancer have yet to be understood. This review highlights the current knowledge of FXR1 expression and function in various cancer situations, emphasizing its functional variety and complexity. We further address the challenges and opportunities of targeting FXR1 for cancer diagnosis and treatment and propose future directions for FXR1 research in oncology. This work intends to provide an in-depth review of FXR1 as an emerging oncotarget with multiple roles and implications in cancer biology and therapy.
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Affiliation(s)
- Faiz Ali Khan
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China
- Department of Basic Sciences Research, Shaukat Khanum Memorial Cancer Hospital and Research Centre (SKMCH&RC), Lahore, Pakistan
| | - Na Fang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Weijuan Zhang
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
| | - Shaoping Ji
- Huaihe Hospital,Medical School, Henan University, Kaifeng, China.
- Laboratory of Cell Signal Transduction, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Henan University, Kaifeng, China.
- Zhengzhou Shuqing Medical College, Zhengzhou, China.
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23
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Yang J, Yang S, Cai J, Chen H, Sun L, Wang J, Hou G, Gu S, Ma J, Ge J. A Transcription Factor ZNF384, Regulated by LINC00265, Activates the Expression of IFI30 to Stimulate Malignant Progression in Glioma. ACS Chem Neurosci 2024; 15:290-299. [PMID: 38141017 DOI: 10.1021/acschemneuro.3c00562] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2023] Open
Abstract
Glioma remains one of the most challenging primary brain malignancies to treat. Long noncoding RNAs (lncRNAs) and mRNAs (mRNAs) are implicated in regulating the malignant phenotypes of cancers including glioma. This study aimed to elucidate the functions and mechanisms of lncRNA LINC00265 and mRNA IFI30 in the pathogenesis of glioma. Quantitative real-time polymerase chain reaction (RT-qPCR) analysis revealed the upregulated expression of LINC00265 and IFI30 in glioma cells compared to normal human astrocytes. Western blot (WB) quantified the associated proteins. Glioma stemness and epithelial-to-mesenchymal transition (EMT) were assessed by aldehyde dehydrogenase 1 (ALDH1) activity, sphere formation, and WB. Mechanistic and rescue assays evaluated the LINC00265/miR-let-7d-5p/IFI30/ZNF384/IGF2BP2 axis. The results demonstrated that LINC00265 and IFI30 were highly expressed in glioma cells, promoting stemness and EMT. ZNF384 was identified as a transcription factor that upregulates IFI30. Moreover, LINC00265 elevated ZNF384 by sponging miR-let-7d-5p and recruiting IGF2BP2. In conclusion, LINC00265 and IFI30 act as oncogenes in glioma by driving stemness and EMT, underscoring their potential as therapeutic targets.
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Affiliation(s)
- Jian Yang
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, No.160 Pujian Road, Pudong New Area, Shanghai 200127, China
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Shenghe Yang
- Yancheng Tinghu District People's Hospital, Yancheng, Jiangsu 224002, China
| | - Jinlian Cai
- 910 Hospital of the Joint Logistics Team, Quanzhou, Fujian 362000, China
| | - Hongjin Chen
- Shanghai Ninth People's Hospital, Shanghai Jiaotong University, School of Medicine, Shanghai 200240, China
| | - Lihua Sun
- Hainan Women and Children's Medical Center, Haikou, Hainan 571199, China
| | - Jiajia Wang
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Guoqiang Hou
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, No.160 Pujian Road, Pudong New Area, Shanghai 200127, China
| | - Shuo Gu
- Hainan Women and Children's Medical Center, Haikou, Hainan 571199, China
| | - Jie Ma
- Xinhua Hospital Affiliated to Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Jianwei Ge
- Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine, No.160 Pujian Road, Pudong New Area, Shanghai 200127, China
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24
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Jaiswal AK, Thaxton ML, Scherer GM, Sorrentino JP, Garg NK, Rao DS. Small molecule inhibition of RNA binding proteins in haematologic cancer. RNA Biol 2024; 21:1-14. [PMID: 38329136 PMCID: PMC10857685 DOI: 10.1080/15476286.2024.2303558] [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] [Revised: 12/18/2023] [Accepted: 01/05/2024] [Indexed: 02/09/2024] Open
Abstract
In recent years, advances in biomedicine have revealed an important role for post-transcriptional mechanisms of gene expression regulation in pathologic conditions. In cancer in general and leukaemia specifically, RNA binding proteins have emerged as important regulator of RNA homoeostasis that are often dysregulated in the disease state. Having established the importance of these pathogenetic mechanisms, there have been a number of efforts to target RNA binding proteins using oligonucleotide-based strategies, as well as with small organic molecules. The field is at an exciting inflection point with the convergence of biomedical knowledge, small molecule screening strategies and improved chemical methods for synthesis and construction of sophisticated small molecules. Here, we review the mechanisms of post-transcriptional gene regulation, specifically in leukaemia, current small-molecule based efforts to target RNA binding proteins, and future prospects.
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Affiliation(s)
- Amit K. Jaiswal
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Michelle L. Thaxton
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
| | - Georgia M. Scherer
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Jacob P. Sorrentino
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Neil K. Garg
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dinesh S. Rao
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, CA, USA
- Jonsson Comprehensive Cancer Center, University of California Los Angeles, CA, USA
- Broad Stem Cell Research Center, University of California, Los Angeles, CA, USA
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25
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Zhang X, Yang L, Liu X, Nie Z, Liu M, Wang T, Lu Y, Pan Y, Zhan Y, Wang Z, Luo J. Regulatory role of RBM39 in acute myeloid leukemia: Mediation through the PI3K/AKT pathway. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119607. [PMID: 37852323 DOI: 10.1016/j.bbamcr.2023.119607] [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: 08/20/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 10/20/2023]
Abstract
BACKGROUND Acute myeloid leukemia (AML) presents ongoing therapeutic challenges due to its intricate molecular pathogenesis. This study aimed to elucidate the role of RNA binding motif protein 39 (RBM39) in AML cell proliferation, apoptosis, and chemosensitivity, and its potential modulation of the PI3K/AKT pathway. METHODS In vitro and in vivo experiments were conducted using AML cell lines (K562 and U937) and bone marrow mononuclear cells (BM-MNCs) from AML patients and healthy donors. RBM39 mRNA and protein levels were measured using qRT-PCR and Western blotting. Cells were transfected with sh-RBM39 or sh-control, and then treated with daunorubicin (DNR) or homoharringtonine (HHT) at varied concentrations. Cell proliferation, chemosensitivity, and apoptosis were assessed through CCK-8 assay and Annexin V-APC/PI staining. RNA sequencing identified differentially expressed genes (DEGs) post RBM39 knockdown. An in vivo xenograft AML model using E7070, a selective RBM39 inhibitor, was employed to evaluate RBM39 modulation effects. RESULTS Elevated RBM39 levels were found in AML patients and cell lines compared to controls. RBM39 knockdown promoted apoptosis, curtailed cell proliferation, and enhanced chemosensitivity to DNR and HHT in vitro. Drug-resistant or relapsed AML patients displayed higher RBM39 levels. RNA sequencing after RBM39 knockdown revealed downregulated PI3K/AKT signaling. The xenograft model validated in vitro results, as E7070 treatment suppressed AML xenograft growth via RBM39-mediated PI3K/AKT pathway suppression. CONCLUSION RBM39 plays a pivotal role in AML progression through the PI3K/AKT signaling pathway. Targeting RBM39, potentially with E7070, could inhibit proliferation and induce apoptosis in AML cells, offering a promising avenue for future AML research and treatment.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
| | - Lin Yang
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Xiaojun Liu
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ziyuan Nie
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Menghan Liu
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Tianyang Wang
- Department of Hepatobiliary Surgery, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Yaqiong Lu
- Department of Hematology Oncology, Hebei Children's Hospital, Shijiazhuang, China
| | - Yuxia Pan
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Ying Zhan
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Zhenzhen Wang
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Jianmin Luo
- Department of Hematology, Key Laboratory of Hematology, The Second Hospital of Hebei Medical University, Shijiazhuang, China.
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26
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Borgelt L, Hohnen L, Pallesen JS, Hommen P, Goebel GL, Bosica F, Liu Y, O’Mahony G, Wu P. N-Biphenyl Pyrrolinones and Dibenzofurans as RNA-Binding Protein LIN28 Inhibitors Disrupting the LIN28- Let-7 Interaction. ACS Med Chem Lett 2023; 14:1707-1715. [PMID: 38116413 PMCID: PMC10726440 DOI: 10.1021/acsmedchemlett.3c00341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 10/27/2023] [Accepted: 11/08/2023] [Indexed: 12/21/2023] Open
Abstract
The RNA-binding protein LIN28 is a regulator of miRNA let-7 biogenesis. Inhibitors of LIN28 are highly sought after given the central role that LIN28 plays in tumorigenesis and development of cancer stem cells as well as LIN28's association with poor clinical prognosis. Although LIN28 inhibitors of different scaffolds have been reported, the potential of most LIN28 inhibiting small molecules was not fully explored since very limited structure-activity relationship (SAR) studies have been performed. We previously identified trisubstituted pyrrolinones as a new class of LIN28 inhibitors disrupting the LIN28-let-7 interaction. Here, we performed extensive SAR by evaluating 95 small molecules and identified new trisubstituted pyrrolinones featuring either an N-biphenyl or N-dibenzofuran substituent, overthrowing the existing conclusion that a salicylic acid moiety is indispensable for activity. Exchange of the negatively charged salicylic acid moiety in LIN28 inhibitors with a heterocyclic substituent is beneficial for membrane permeability, leading to increased activity in a cellular assay, and will potentially reduce toxicity.
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Affiliation(s)
- Lydia Borgelt
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Lisa Hohnen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Biochemistry, Ruhr-University
Bochum, Universitätsstr.
150, Bochum 44801, Germany
| | - Jakob S. Pallesen
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Pascal Hommen
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Georg L. Goebel
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Francesco Bosica
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Yang Liu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
- Faculty
of Chemistry and Chemical Biology, TU Dortmund
University, Otto-Hahn
Str. 6, Dortmund 44227, Germany
| | - Gavin O’Mahony
- Medicinal
Chemistry, Research and Early Development, Cardiovascular, Renal and
Metabolism, BioPharmaceuticals R&D, AstraZeneca, SE-431 83 Mölndal, Sweden
| | - Peng Wu
- Chemical
Genomics Centre, Max Planck Institute of
Molecular Physiology, Otto-Hahn Str. 15, Dortmund 44227, Germany
- Department
of Chemical Biology, Max Planck Institute
of Molecular Physiology, Otto-Hahn Str. 11, Dortmund 44227, Germany
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27
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Salvato I, Ricciardi L, Nucera F, Nigro A, Dal Col J, Monaco F, Caramori G, Stellato C. RNA-Binding Proteins as a Molecular Link between COPD and Lung Cancer. COPD 2023; 20:18-30. [PMID: 36655862 DOI: 10.1080/15412555.2022.2107500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chronic obstructive pulmonary disease (COPD) represents an independent risk factor for lung cancer development. Accelerated cell senescence, induced by oxidative stress and inflammation, is a common pathogenic determinant of both COPD and lung cancer. The post transcriptional regulation of genes involved in these processes is finely regulated by RNA-binding proteins (RBPs), which regulate mRNA turnover, subcellular localization, splicing and translation. Multiple pro-inflammatory mediators (including cytokines, chemokines, proteins, growth factors and others), responsible of lung microenvironment alteration, are regulated by RBPs. Several mouse models have shown the implication of RBPs in multiple mechanisms that sustain chronic inflammation and neoplastic transformation. However, further studies are required to clarify the role of RBPs in the pathogenic mechanisms shared by lung cancer and COPD, in order to identify novel biomarkers and therapeutic targets. This review will therefore focus on the studies collectively indicating the role of RBPs in oxidative stress and chronic inflammation as common pathogenic mechanisms shared by lung cancer and COPD.
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Affiliation(s)
- Ilaria Salvato
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Luca Ricciardi
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Francesco Nucera
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
| | - Francesco Monaco
- Chirurgia Toracica, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Gaetano Caramori
- Pneumologia, Dipartimento di Scienze Biomediche, Odontoiatriche e delle Immagini Morfologiche e Funzionali (BIOMORF), Università degli Studi di Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry "Scuola Medica Salernitana", University of Salerno, Salerno, Italy
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28
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Li M, Li D, Lin L, Wang P, Zhao W. Precise Interference of RNA-Protein Interaction by CRISPR-Cas13-Mediated Peptide Competition. ACS Synth Biol 2023; 12:2827-2833. [PMID: 37708031 DOI: 10.1021/acssynbio.3c00287] [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] [Indexed: 09/16/2023]
Abstract
RNA-protein interactions are essential nodes of cellular regulatory circuits and play critical roles in normal physiology and disease. However, the precise roles of individual RNA-protein interactions remain elusive. Here we report a method for precise interference of endogenous RNA interacting with the RNA binding protein (RBP). TTP is an RBP that recognizes the AU-rich element (ARE) of mRNA via the binding domain TZF and represses gene expression. We engineer Cas13b, a class 2 type VI CRISPR-Cas endonuclease that exclusively targets RNA, to direct the peptide of TZF to the binding site and compete with endogenous TTP. We show that this tool specifically interferes with TTP interacting with the PIM1 and IL-2 3' UTR under the guidance of the gRNA specific for the AREs. Further, precise interference with the TTP-PIM1 interaction exerts a distinct effect on cell proliferation compared to transcriptome-wide interference. Thus, our work establishes a tool for deep understanding of RNA-RBP interactions.
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Affiliation(s)
- Meng Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Dan Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Leiruo Lin
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Panpan Wang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
| | - Wenxue Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen 518107, China
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29
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Noblejas-López MDM, Tébar-García D, López-Rosa R, Alcaraz-Sanabria A, Cristóbal-Cueto P, Pinedo-Serrano A, Rivas-García L, Galán-Moya EM. TACkling Cancer by Targeting Selective Protein Degradation. Pharmaceutics 2023; 15:2442. [PMID: 37896202 PMCID: PMC10610449 DOI: 10.3390/pharmaceutics15102442] [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: 09/04/2023] [Revised: 10/04/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Targeted protein degradation has emerged as an alternative therapy against cancer, offering several advantages over traditional inhibitors. The new degrader drugs provide different therapeutic strategies: they could cross the phospholipid bilayer membrane by the addition of specific moieties to extracellular proteins. On the other hand, they could efficiently improve the degradation process by the generation of a ternary complex structure of an E3 ligase. Herein, we review the current trends in the use of TAC-based technologies (TACnologies), such as PROteolysis TArgeting Chimeras (PROTAC), PHOtochemically TArgeting Chimeras (PHOTAC), CLIck-formed Proteolysis TArgeting Chimeras (CLIPTAC), AUtophagy TArgeting Chimeras (AUTAC), AuTophagosome TEthering Compounds (ATTEC), LYsosome-TArgeting Chimeras (LYTAC), and DeUBiquitinase TArgeting Chimeras (DUBTAC), in experimental development and their progress towards clinical applications.
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Affiliation(s)
- María del Mar Noblejas-López
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
- Unidad de Investigación, Complejo Hospitalario Universitario de Albacete, 02008 Albacete, Spain
| | - David Tébar-García
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
- Unidad de Investigación, Complejo Hospitalario Universitario de Albacete, 02008 Albacete, Spain
| | - Raquel López-Rosa
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
- Unidad de Investigación, Complejo Hospitalario Universitario de Albacete, 02008 Albacete, Spain
| | - Ana Alcaraz-Sanabria
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
- Unidad de Investigación, Complejo Hospitalario Universitario de Albacete, 02008 Albacete, Spain
| | - Pablo Cristóbal-Cueto
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
| | - Alejandro Pinedo-Serrano
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
| | - Lorenzo Rivas-García
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
| | - Eva M. Galán-Moya
- Centro Regional de Investigaciones Biomédicas (CRIB), Campus de Albacete, Universidad de Castilla-La Mancha, 02008 Albacete, Spain; (M.d.M.N.-L.); (D.T.-G.); (R.L.-R.); (A.A.-S.); (P.C.-C.); (A.P.-S.)
- Unidad de Investigación, Complejo Hospitalario Universitario de Albacete, 02008 Albacete, Spain
- Facultad de Enfermería, Campus de Albacete, Universidad de Castilla-La Mancha, 02006 Albacete, Spain
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30
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Hao L, Zhang J, Liu Z, Zhang Z, Mao T, Guo J. Role of the RNA-binding protein family in gynecologic cancers. Am J Cancer Res 2023; 13:3799-3821. [PMID: 37693158 PMCID: PMC10492115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 08/15/2023] [Indexed: 09/12/2023] Open
Abstract
Gynecological cancers pose a threat to women's health. Although early-stage gynecological cancers show good outcomes after standardized treatment, the prognosis of patients with advanced, met-astatic, and recurrent cancers is poor. RNA-binding proteins (RBPs) are important cellular proteins that interact with RNA through RNA-binding domains and participate extensively in post-transcriptional regulatory processes, such as mRNA alternative splicing, polyadenylation, intracellular localization and stability, and translation. Abnormal RBP expression affects the normal function of oncogenes and tumor suppressor genes in many malignancies, thus leading to the occurrence or progression of cancers. Similarly, RBPs play crucial roles in gynecological carcinogenesis. We summarize the role of RBPs in gynecological malignancies and explore their potential in the diagnosis and treatment of cancers. The findings summarized in this review may provide a guide for future research on the functions of RBPs.
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Affiliation(s)
- Linlin Hao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Jian Zhang
- School of Life Sciences, Department of Biology, Southern University of Science and TechnologyShenzhen 518055, Guangdong, China
| | - Zhongshan Liu
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Zhiliang Zhang
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Tiezhu Mao
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
| | - Jie Guo
- Department of Tumor Radiotherapy, The Second Hospital of Jilin UniversityChangchun 130041, Jilin, China
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Schmeing S, Amrahova G, Bigler K, Chang JY, Openy J, Pal S, Posada L, Gasper R, 't Hart P. Rationally designed stapled peptides allosterically inhibit PTBP1-RNA-binding. Chem Sci 2023; 14:8269-8278. [PMID: 37564416 PMCID: PMC10411625 DOI: 10.1039/d3sc00985h] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 06/28/2023] [Indexed: 08/12/2023] Open
Abstract
The diverse role of the splicing factor PTBP1 in human cells has been widely studied and was found to be a driver for several diseases. PTBP1 binds RNA through its RNA-recognition motifs which lack obvious pockets for inhibition. A unique transient helix has been described to be part of its first RNA-recognition motif and to be important for RNA binding. In this study, we further confirmed the role of this helix and envisioned its dynamic nature as a unique opportunity to develop stapled peptide inhibitors of PTBP1. The peptides were found to be able to inhibit RNA binding via fluorescence polarization assays and directly occupy the helix binding site as observed by protein crystallography. These cell-permeable inhibitors were validated in cellulo to alter the regulation of alternative splicing events regulated by PTBP1. Our study demonstrates transient secondary structures of a protein can be mimicked by stapled peptides to inhibit allosteric mechanisms.
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Affiliation(s)
- Stefan Schmeing
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Gulshan Amrahova
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Katrin Bigler
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Jen-Yao Chang
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Joseph Openy
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Sunit Pal
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Laura Posada
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Raphael Gasper
- Crystallography and Biophysics Unit, Max-Planck-Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
| | - Peter 't Hart
- Chemical Genomics Centre of the Max Planck Society, Max Planck Institute of Molecular Physiology Otto-Hahn-Strasse 11 44227 Dortmund Germany
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Feng Y, Zhu S, Liu T, Zhi G, Shao B, Liu J, Li B, Jiang C, Feng Q, Wu P, Wang D. Surmounting Cancer Drug Resistance: New Perspective on RNA-Binding Proteins. Pharmaceuticals (Basel) 2023; 16:1114. [PMID: 37631029 PMCID: PMC10458901 DOI: 10.3390/ph16081114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/20/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
RNA-binding proteins (RBPs), being pivotal elements in both physiological and pathological processes, possess the ability to directly impact RNA, thereby exerting a profound influence on cellular life. Furthermore, the dysregulation of RBPs not only induces alterations in the expression levels of genes associated with cancer but also impairs the occurrence of post-transcriptional regulatory mechanisms. Consequently, these circumstances can give rise to aberrations in cellular processes, ultimately resulting in alterations within the proteome. An aberrant proteome can disrupt the equilibrium between oncogenes and tumor suppressor genes, promoting cancer progression. Given their significant role in modulating gene expression and post-transcriptional regulation, directing therapeutic interventions towards RBPs represents a viable strategy for combating drug resistance in cancer treatment. RBPs possess significant potential as diagnostic and prognostic markers for diverse cancer types. Gaining comprehensive insights into the structure and functionality of RBPs, along with delving deeper into the molecular mechanisms underlying RBPs in tumor drug resistance, can enhance cancer treatment strategies and augment the prognostic outcomes for individuals afflicted with cancer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Peijie Wu
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
| | - Dong Wang
- School of Basic Medical Sciences and State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; (Y.F.); (S.Z.); (T.L.); (G.Z.); (B.S.); (J.L.); (B.L.); (C.J.); (Q.F.)
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Yang JJ, Yang YJ, Gu YL, Tong L, Liu YF, Zhang JG. High SNRPA1 expression leads to poor prognosis in patients with lung adenocarcinoma. THE CLINICAL RESPIRATORY JOURNAL 2023; 17:719-732. [PMID: 37277111 PMCID: PMC10435942 DOI: 10.1111/crj.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/22/2023] [Indexed: 06/07/2023]
Abstract
OBJECTIVE SNRPA1, a subunit of spliceosome complex, has been implicated in diverse cancers, while its biological effect in LUAD remains elusive. Therefore, we sought to decipher the relationship between SNRPA1 expression and the prognosis of patients with LUAD and reveal the underlying molecular mechanism. MATERIALS AND METHODS Based on the clinical data from TCGA databases, the multivariate Cox model was constructed to screen the prognostic value of SNRPA1. qRT-PCR and immunohistochemical staining were used to examine SNRPA1 mRNA and protein expression in LUAD. The effect of SNRPA1 on LUAD cell proliferation, migration, and epithelial mesenchymal transformation were examined using colony formation assays, wound healing, and western blot assays, respectively. Finally, the influence of SNRPA1 on LUAD immune microenvironment were validated from the Tumor Immune Estimation Resource database. RESULTS SNRPA1 was significantly upregulated in both LUAD tissues and cell lines, and highly expressed SNRPA1 contributed to poor prognosis of LUAD patients. In vitro, SNRPA1 knockdown inhibited the proliferation and migration, as well as delayed the EMT differentiation of LUAD cells. Lastly, SNRPA1 was found to be positively associated with immune infiltration and some immune-check-point markers. CONCLUSIONS Our findings indicate that SNRPA1 may be a new biomarker for prognostic prediction and a potential therapeutic target in the treatment of LUAD.
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Affiliation(s)
- Juan Juan Yang
- Research Center of Clinical MedicineAffiliated Hospital of Nantong UniversityNantongJiangsuChina
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Yu Jia Yang
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Yi Lu Gu
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Li Tong
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Yi Fei Liu
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
| | - Jian Guo Zhang
- Department of PathologyAffiliated Hospital and Medical School of Nantong UniversityNantongJiangsuChina
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Salvato I, Ricciardi L, Dal Col J, Nigro A, Giurato G, Memoli D, Sellitto A, Lamparelli EP, Crescenzi MA, Vitale M, Vatrella A, Nucera F, Brun P, Caicci F, Dama P, Stiff T, Castellano L, Idrees S, Johansen MD, Faiz A, Wark PA, Hansbro PM, Adcock IM, Caramori G, Stellato C. Expression of targets of the RNA-binding protein AUF-1 in human airway epithelium indicates its role in cellular senescence and inflammation. Front Immunol 2023; 14:1192028. [PMID: 37483631 PMCID: PMC10360199 DOI: 10.3389/fimmu.2023.1192028] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Introduction The RNA-binding protein AU-rich-element factor-1 (AUF-1) participates to posttranscriptional regulation of genes involved in inflammation and cellular senescence, two pathogenic mechanisms of chronic obstructive pulmonary disease (COPD). Decreased AUF-1 expression was described in bronchiolar epithelium of COPD patients versus controls and in vitro cytokine- and cigarette smoke-challenged human airway epithelial cells, prompting the identification of epithelial AUF-1-targeted transcripts and function, and investigation on the mechanism of its loss. Results RNA immunoprecipitation-sequencing (RIP-Seq) identified, in the human airway epithelial cell line BEAS-2B, 494 AUF-1-bound mRNAs enriched in their 3'-untranslated regions for a Guanine-Cytosine (GC)-rich binding motif. AUF-1 association with selected transcripts and with a synthetic GC-rich motif were validated by biotin pulldown. AUF-1-targets' steady-state levels were equally affected by partial or near-total AUF-1 loss induced by cytomix (TNFα/IL1β/IFNγ/10 nM each) and siRNA, respectively, with differential transcript decay rates. Cytomix-mediated decrease in AUF-1 levels in BEAS-2B and primary human small-airways epithelium (HSAEC) was replicated by treatment with the senescence- inducer compound etoposide and associated with readouts of cell-cycle arrest, increase in lysosomal damage and senescence-associated secretory phenotype (SASP) factors, and with AUF-1 transfer in extracellular vesicles, detected by transmission electron microscopy and immunoblotting. Extensive in-silico and genome ontology analysis found, consistent with AUF-1 functions, enriched RIP-Seq-derived AUF-1-targets in COPD-related pathways involved in inflammation, senescence, gene regulation and also in the public SASP proteome atlas; AUF-1 target signature was also significantly represented in multiple transcriptomic COPD databases generated from primary HSAEC, from lung tissue and from single-cell RNA-sequencing, displaying a predominant downregulation of expression. Discussion Loss of intracellular AUF-1 may alter posttranscriptional regulation of targets particularly relevant for protection of genomic integrity and gene regulation, thus concurring to airway epithelial inflammatory responses related to oxidative stress and accelerated aging. Exosomal-associated AUF-1 may in turn preserve bound RNA targets and sustain their function, participating to spreading of inflammation and senescence to neighbouring cells.
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Affiliation(s)
- Ilaria Salvato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Luca Ricciardi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Jessica Dal Col
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Annunziata Nigro
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Giorgio Giurato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Domenico Memoli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Assunta Sellitto
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Erwin Pavel Lamparelli
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Maria Assunta Crescenzi
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Monica Vitale
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Alessandro Vatrella
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Paola Brun
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | | | - Paola Dama
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Thomas Stiff
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Leandro Castellano
- Department of Biochemistry and Biomedicine, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Sobia Idrees
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Matt D. Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Alen Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
| | - Peter A. Wark
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Philip M. Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, School of Life Sciences, Sydney, NSW, Australia
- Immune Health, Hunter Medical Research Institute and The University of Newcastle, Newcastle, NSW, Australia
| | - Ian M. Adcock
- National Heart and Lung Institute, Imperial College London and the National Institute for Health and Care Research (NIHR) Imperial Biomedical Research Centre, London, United Kingdom
| | - Gaetano Caramori
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry ‘Scuola Medica Salernitana’, University of Salerno, Salerno, Italy
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Danckwardt S, Trégouët DA, Castoldi E. Post-transcriptional control of haemostatic genes: mechanisms and emerging therapeutic concepts in thrombo-inflammatory disorders. Cardiovasc Res 2023; 119:1624-1640. [PMID: 36943786 PMCID: PMC10325701 DOI: 10.1093/cvr/cvad046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 03/23/2023] Open
Abstract
The haemostatic system is pivotal to maintaining vascular integrity. Multiple components involved in blood coagulation have central functions in inflammation and immunity. A derailed haemostasis is common in prevalent pathologies such as sepsis, cardiovascular disorders, and lately, COVID-19. Physiological mechanisms limit the deleterious consequences of a hyperactivated haemostatic system through adaptive changes in gene expression. While this is mainly regulated at the level of transcription, co- and posttranscriptional mechanisms are increasingly perceived as central hubs governing multiple facets of the haemostatic system. This layer of regulation modulates the biogenesis of haemostatic components, for example in situations of increased turnover and demand. However, they can also be 'hijacked' in disease processes, thereby perpetuating and even causally entertaining associated pathologies. This review summarizes examples and emerging concepts that illustrate the importance of posttranscriptional mechanisms in haemostatic control and crosstalk with the immune system. It also discusses how such regulatory principles can be used to usher in new therapeutic concepts to combat global medical threats such as sepsis or cardiovascular disorders.
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Affiliation(s)
- Sven Danckwardt
- Centre for Thrombosis and Hemostasis (CTH), University Medical Centre
Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- German Centre for Cardiovascular Research (DZHK),
Berlin, Germany
- Posttranscriptional Gene Regulation, University Medical Centre
Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
- Institute for Clinical Chemistry and Laboratory Medicine, University
Medical Centre Mainz, Langenbeckstr. 1, 55131
Mainz, Germany
- Center for Healthy Aging (CHA), Mainz,
Germany
| | - David-Alexandre Trégouët
- INSERM, Bordeaux Population Health Research Center, UMR 1219, Department of
Molecular Epidemiology of Vascular and Brain Disorders (ELEANOR), University of
Bordeaux, Bordeaux, France
| | - Elisabetta Castoldi
- Department of Biochemistry, Cardiovascular Research Institute Maastricht
(CARIM), Maastricht University, Universiteitsingel 50, 6229
ER Maastricht, The Netherlands
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Ning ZK, Tian HK, Liu J, Hu CG, Liu ZT, Li H, Zong Z. Analysis and application of RNA binding protein gene pairs to predict the prognosis of gastric cancer. Heliyon 2023; 9:e18242. [PMID: 37539127 PMCID: PMC10393628 DOI: 10.1016/j.heliyon.2023.e18242] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 06/28/2023] [Accepted: 07/12/2023] [Indexed: 08/05/2023] Open
Abstract
Background RNA-binding proteins (RBPs) are closely related to tumors, but little is known about the mechanism of RBPs in tumorigenesis and progression of gastric cancer (GC). As genes do not usually act alone in the pathway deregulation, gene pair combinations are more likely to become stable and accurate biomarkers. The purpose of our research is to establish a novel signature based on RBP gene pairs to predict the prognosis of gastric cancer patients. Methods We downloaded genetic and clinical information from the TCGA and GEO database. TCGA and GSE13911 were used for screening differentially expressed genes (DEGs). The RBP genes were gathered from previous studies and employed to screen out DE-RBP genes after intersecting with DEGs. Samples were classified according to the relative expression of each pair of DE-RBP genes. The univariate Cox regression analysis and random forest were used to identify hub gene pairs to construct signature for predicting the prognosis of gastric cancer. Time-dependent ROC curves and KM survival curves were performed to evaluate the signature. GSEA was performed in TCGA training cohort and GSE62254 testing cohort to analyze enrichment pathways. Finally, the influence of these gene pairs on the prognosis of GC patients was further elucidated respectively through the combination of high and low expression of the two genes in each hub gene pair. Results We screened out 6 hub RBP gene pairs (COL5A2/FEN1, POP1/GFRA1, EXO1/PLEKHS1, SLC39A10/CHI3L1, MMP7/PPP1R1 B and SLC5A6/BYSL) to predict the prognosis of patients with gastric cancer. Using the optimal cut-off value to divide patients into high-risk and low-risk groups in the training and testing cohort, we found that the overall survival (OS) of the low-risk group was higher than that of the high-risk group (P < 0.05). The area under the ROC curves for 1, 3, and 5 years were (0.659, 0.744, 0.758) and (0.624, 0.650, 0.653) in two cohorts. Univariate and multivariate Cox regression analysis showed that 6 RBP gene pairs signature were independent prognostic factors for gastric cancer (P < 0.05). In addition, the prognostic survival analysis showed that COL5A2-high/FEN1-low, POP1-low/GFRA1-high, EXO1-low/PLEKHS1-low,SLC39A10-high/CHI3L1-low, MMP7-high/PPP1R1 B-low, SLC5A6-low/BYSL-low had worse OS (P < 0.05). And the gene correlation analysis showed that there was no obvious correlation between the genes in each gene pairs except SLC5A6/BYSL and POP1/GFRA1. Finally, GSEA analysis showed that the high-risk group was enriched in tumor migration, invasion and growth-related pathways. Conclusion Our study identified a novel 6 RBP gene pairs signature to predict the prognosis of gastric cancer patients and provide potential targets for clinical gene therapy.
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Affiliation(s)
- Zhi-kun Ning
- Department of Day Ward, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hua-kai Tian
- Department of General Surgery, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jiang Liu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Ce-gui Hu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zi-tao Liu
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hui Li
- Department of Rheumatology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhen Zong
- Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Swahn H, Olmer M, Lotz MK. RNA-binding proteins that are highly expressed and enriched in healthy cartilage but suppressed in osteoarthritis. Front Cell Dev Biol 2023; 11:1208315. [PMID: 37457300 PMCID: PMC10349536 DOI: 10.3389/fcell.2023.1208315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/13/2023] [Indexed: 07/18/2023] Open
Abstract
Objectives: RNA-binding proteins (RBPs) have diverse and essential biological functions, but their role in cartilage health and disease is largely unknown. The objectives of this study were (i) map the global landscape of RBPs expressed and enriched in healthy cartilage and dysregulated in osteoarthritis (OA); (ii) prioritize RBPs for their potential role in cartilage and in OA pathogenesis and as therapeutic targets. Methods: Our published bulk RNA-sequencing (RNA-seq) data of healthy and OA human cartilage, and a census of 1,542 RBPs were utilized to identify RBPs that are expressed in healthy cartilage and differentially expressed (DE) in OA. Next, our comparison of healthy cartilage RNA-seq data to 37 transcriptomes in the Genotype-Tissue Expression (GTEx) database was used to determine RBPs that are enriched in cartilage. Finally, expression of RBPs was analyzed in our single cell RNA-sequencing (scRNA-seq) data from healthy and OA human cartilage. Results: Expression of RBPs was higher than nonRBPs in healthy cartilage. In OA cartilage, 188 RBPs were differentially expressed, with a greater proportion downregulated. Ribosome biogenesis was enriched in the upregulated RBPs, while splicing and transport were enriched in the downregulated. To further prioritize RBPs, we selected the top 10% expressed RBPs in healthy cartilage and those that were cartilage-enriched according to GTEx. Intersecting these criteria, we identified Tetrachlorodibenzodioxin (TCDD) Inducible Poly (ADP-Ribose) Polymerase (TIPARP) as a candidate RBP. TIPARP was downregulated in OA. scRNA-seq data revealed TIPARP was most significantly downregulated in the "pathogenic cluster". Conclusion: Our global analyses reveal expression patterns of RBPs in healthy and OA cartilage. We also identified TIPARP and other RBPs as novel mediators in OA pathogenesis and as potential therapeutic targets.
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Affiliation(s)
| | | | - Martin K. Lotz
- Department of Molecular Medicine, Scripps Research, La Jolla, CA, United States
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38
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Que Z, Yang K, Wang N, Li S, Li T. Functional Role of RBP in Osteosarcoma: Regulatory Mechanism and Clinical Therapy. Anal Cell Pathol (Amst) 2023; 2023:9849719. [PMID: 37426488 PMCID: PMC10328736 DOI: 10.1155/2023/9849719] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 05/06/2023] [Accepted: 06/11/2023] [Indexed: 07/11/2023] Open
Abstract
Malignant bone neoplasms can be represented by osteosarcoma (OS), which accounts for 36% of all sarcomas. To reduce tumor malignancy, extensive efforts have been devoted to find an ideal target from numerous candidates, among which RNA-binding proteins (RBPs) have shown their unparalleled competitiveness. With the special structure of RNA-binding domains, RBPs have the potential to establish relationships with RNAs or small molecules and are considered regulators of different sections of RNA processes, including splicing, transport, translation, and degradation of RNAs. RBPs have considerable significant roles in various cancers, and experiments revealed that there was a strong association of RBPs with tumorigenesis and tumor cell progression. Regarding OS, RBPs are a new orientation, but achievements in hand are noteworthy. Higher or lower expression of RBPs was first found in tumor cells compared to normal tissue. By binding to different molecules, RBPs are capable of influencing tumor cell phenotypes through different signaling pathways or other axes, and researches on medical treatment have been largely inspired. Exploring the prognostic and therapeutic values of RBPs in OS is a hotspot where diverse avenues on regulating RBPs have achieved dramatical effects. In this review, we briefly summarize the contribution of RBPs and their binding molecules to OS oncogenicity and generally introduce distinctive RBPs as samples. Moreover, we focus on the attempts to differentiate RBP's opposite functions in predicting prognosis and collect possible strategies for treatment. Our review provides forwards insight into improving the understanding of OS and suggests RBPs as potential biomarkers for therapies.
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Affiliation(s)
- Ziyuan Que
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Kang Yang
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
| | - Nan Wang
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Shuying Li
- Yangzhou University Medical College, Yangzhou University, Yangzhou 225009, Jiangsu Province, China
| | - Tao Li
- Department of Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, Zhejiang, China
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Coleman JC, Hallett SR, Grigoriadis AE, Conte MR. LARP4A and LARP4B in cancer: The new kids on the block. Int J Biochem Cell Biol 2023; 161:106441. [PMID: 37356415 DOI: 10.1016/j.biocel.2023.106441] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/09/2023] [Accepted: 06/17/2023] [Indexed: 06/27/2023]
Abstract
Recent developments have mounted a stunning body of evidence underlying the importance of RNA binding proteins (RBPs) in cancer research. In this minireview we focus on LARP4A and LARP4B, two paralogs belonging to the superfamily of La-related proteins, and provide a critical overview of current research, including their roles in cancer pathogenesis and cell proliferation, migration, cell cycle and apoptosis. We highlight current controversies surrounding LARP4A and LARP4B and conclude that their complex roles in tumorigenesis are cell-, tissue- and context-dependent, warning that caution must be exercised before categorising either protein as an oncoprotein or tumour-suppressor. We also reveal that LARP4A and LARP4B have often been confused with one another, adding uncertainty in delineating their functions. We suggest that further functional and mechanistic studies of LARP4 proteins present significant challenges for future investigations to recognise the vital contributions of these RBPs in cancer research.
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Affiliation(s)
- Jennifer C Coleman
- Centre for Craniofacial & Regenerative Biology, King's College London, London SE1 9RT, UK
| | - Sadie R Hallett
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK
| | | | - Maria R Conte
- Randall Centre for Cell and Molecular Biophysics, King's College London, London SE1 1UL, UK.
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40
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Sachse M, Tual-Chalot S, Ciliberti G, Amponsah-Offeh M, Stamatelopoulos K, Gatsiou A, Stellos K. RNA-binding proteins in vascular inflammation and atherosclerosis. Atherosclerosis 2023; 374:55-73. [PMID: 36759270 DOI: 10.1016/j.atherosclerosis.2023.01.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/01/2022] [Accepted: 01/12/2023] [Indexed: 01/19/2023]
Abstract
Atherosclerotic cardiovascular disease (ASCVD) remains the major cause of premature death and disability worldwide, even when patients with an established manifestation of atherosclerotic heart disease are optimally treated according to the clinical guidelines. Apart from the epigenetic control of transcription of the genetic information to messenger RNAs (mRNAs), gene expression is tightly controlled at the post-transcriptional level before the initiation of translation. Although mRNAs are traditionally perceived as the messenger molecules that bring genetic information from the nuclear DNA to the cytoplasmic ribosomes for protein synthesis, emerging evidence suggests that processes controlling RNA metabolism, driven by RNA-binding proteins (RBPs), affect cellular function in health and disease. Over the recent years, vascular endothelial cell, smooth muscle cell and immune cell RBPs have emerged as key co- or post-transcriptional regulators of several genes related to vascular inflammation and atherosclerosis. In this review, we provide an overview of cell-specific function of RNA-binding proteins involved in all stages of ASCVD and how this knowledge may be used for the development of novel precision medicine therapeutics.
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Affiliation(s)
- Marco Sachse
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Department of Cardiovascular Surgery, University Heart Center, University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Simon Tual-Chalot
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK.
| | - Giorgia Ciliberti
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung, DZHK), Heidelberg/Mannheim Partner Site, Mannheim, Germany
| | - Michael Amponsah-Offeh
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung, DZHK), Heidelberg/Mannheim Partner Site, Mannheim, Germany
| | - Kimon Stamatelopoulos
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Aikaterini Gatsiou
- Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Konstantinos Stellos
- Department of Cardiovascular Research, European Center for Angioscience (ECAS), Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany; Biosciences Institute, Vascular Biology and Medicine Theme, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK; German Centre for Cardiovascular Research (Deutsches Zentrum für Herz-Kreislauf-Forschung, DZHK), Heidelberg/Mannheim Partner Site, Mannheim, Germany; Department of Cardiology, University Hospital Mannheim, Heidelberg University, Manheim, Germany.
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41
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Eraso P, Mazón MJ, Jiménez V, Pizarro-García P, Cuevas EP, Majuelos-Melguizo J, Morillo-Bernal J, Cano A, Portillo F. New Functions of Intracellular LOXL2: Modulation of RNA-Binding Proteins. Molecules 2023; 28:molecules28114433. [PMID: 37298909 DOI: 10.3390/molecules28114433] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Lysyl oxidase-like 2 (LOXL2) was initially described as an extracellular enzyme involved in extracellular matrix remodeling. Nevertheless, numerous recent reports have implicated intracellular LOXL2 in a wide variety of processes that impact on gene transcription, development, differentiation, proliferation, migration, cell adhesion, and angiogenesis, suggesting multiple different functions for this protein. In addition, increasing knowledge about LOXL2 points to a role in several types of human cancer. Moreover, LOXL2 is able to induce the epithelial-to-mesenchymal transition (EMT) process-the first step in the metastatic cascade. To uncover the underlying mechanisms of the great variety of functions of intracellular LOXL2, we carried out an analysis of LOXL2's nuclear interactome. This study reveals the interaction of LOXL2 with numerous RNA-binding proteins (RBPs) involved in several aspects of RNA metabolism. Gene expression profile analysis of cells silenced for LOXL2, combined with in silico identification of RBPs' targets, points to six RBPs as candidates to be substrates of LOXL2's action, and that deserve a more mechanistic analysis in the future. The results presented here allow us to hypothesize novel LOXL2 functions that might help to comprehend its multifaceted role in the tumorigenic process.
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Affiliation(s)
- Pilar Eraso
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - María J Mazón
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Victoria Jiménez
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Patricia Pizarro-García
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Eva P Cuevas
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Jara Majuelos-Melguizo
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Jesús Morillo-Bernal
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
| | - Amparo Cano
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Francisco Portillo
- Departamento de Bioquímica UAM, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC-UAM, 28029 Madrid, Spain
- Instituto de Investigación Sanitaria del Hospital Universitario La Paz-IdiPAZ, 28029 Madrid, Spain
- Centro de Investigación Biomédica en Red, Área de Cáncer (CIBERONC), Instituto de Salud Carlos III, 28029 Madrid, Spain
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Ferrari A, Fiocca R, Bonora E, Domizio C, Fonzi E, Angeli D, Domenico Raulli G, Mattioli S, Martinelli G, Molinari C. Detection of a Novel MSI2-C17orf64 Transcript in a Patient with Aggressive Adenocarcinoma of the Gastroesophageal Junction: A Case Report. Genes (Basel) 2023; 14:genes14040918. [PMID: 37107676 PMCID: PMC10137952 DOI: 10.3390/genes14040918] [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: 03/16/2023] [Revised: 04/06/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
Adenocarcinoma of the esophagus (EAC) and gastroesophageal junction (GEJ-AC) is associated with poor prognosis, treatment resistance and limited systemic therapeutic options. To deeply understand the genomic landscape of this cancer type, and potentially identify a therapeutic target in a neoadjuvant chemotherapy non-responder 48-year-old man, we adopted a multi-omic approach. We simultaneously evaluated gene rearrangements, mutations, copy number status, microsatellite instability and tumor mutation burden. The patient displayed pathogenic mutations of the TP53 and ATM genes and variants of uncertain significance of three kinases genes (ERBB3, CSNK1A1 and RPS6KB2), along with FGFR2 and KRAS high copy number amplification. Interestingly, transcriptomic analysis revealed the Musashi-2 (MSI2)-C17orf64 fusion that has never been reported before. Rearrangements of the RNA-binding protein MSI2 with a number of partner genes have been described across solid and hematological tumors. MSI2 regulates several biological processes involved in cancer initiation, development and resistance to treatment, and deserves further investigation as a potential therapeutic target. In conclusion, our extensive genomic characterization of a gastroesophageal tumor refractory to all therapeutic approaches led to the discovery of the MSI2-C17orf64 fusion. The results underlie the importance of deep molecular analyses enabling the identification of novel patient-specific markers to be monitored during therapy or even targeted at disease evolution.
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Affiliation(s)
- Anna Ferrari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | - Roberto Fiocca
- Unit of Anatomic Pathology, Ospedale Policlinico San Martino IRCCS, 16125 Genova, Italy
- Department of Surgical and Diagnostic Sciences (DISC), University of Genova, 16125 Genova, Italy
| | - Elena Bonora
- Department of Medical and Surgical Sciences (DIMEC), Alma Mater Studiorum, University of Bologna, Via Massarenti 9, 40126 Bologna, Italy
| | - Chiara Domizio
- Department of Life Sciences and Biotechnology, Ferrara University, 44124 Ferrara, Italy
| | - Eugenio Fonzi
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | - Davide Angeli
- Unit of Biostatistics and Clinical Trials, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | | | - Sandro Mattioli
- GVM Care & Research Group, Division of Thoracic Surgery-Maria Cecilia Hospital, 48022 Cotignola, RA, Italy
- Alma Mater Studiorum-University of Bologna, 40126 Bologna, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
| | - Chiara Molinari
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) "Dino Amadori", 47014 Meldola, FC, Italy
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43
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Steinmetz B, Smok I, Bikaki M, Leitner A. Protein-RNA interactions: from mass spectrometry to drug discovery. Essays Biochem 2023; 67:175-186. [PMID: 36866608 PMCID: PMC10070478 DOI: 10.1042/ebc20220177] [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: 10/30/2022] [Revised: 01/25/2023] [Accepted: 01/26/2023] [Indexed: 03/04/2023]
Abstract
Proteins and RNAs are fundamental parts of biological systems, and their interactions affect many essential cellular processes. Therefore, it is crucial to understand at a molecular and at a systems level how proteins and RNAs form complexes and mutually affect their functions. In the present mini-review, we will first provide an overview of different mass spectrometry (MS)-based methods to study the RNA-binding proteome (RBPome), most of which are based on photochemical cross-linking. As we will show, some of these methods are also able to provide higher-resolution information about binding sites, which are important for the structural characterisation of protein-RNA interactions. In addition, classical structural biology techniques such as nuclear magnetic resonance (NMR) spectroscopy and biophysical methods such as electron paramagnetic resonance (EPR) spectroscopy and fluorescence-based methods contribute to a detailed understanding of the interactions between these two classes of biomolecules. We will discuss the relevance of such interactions in the context of the formation of membrane-less organelles (MLOs) by liquid-liquid phase separation (LLPS) processes and their emerging importance as targets for drug discovery.
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Affiliation(s)
- Benjamin Steinmetz
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
- RNA Biology PhD Program, University of Zurich and ETH Zürich, Zurich, Switzerland
| | - Izabela Smok
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
- RNA Biology PhD Program, University of Zurich and ETH Zürich, Zurich, Switzerland
| | - Maria Bikaki
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
| | - Alexander Leitner
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, 8093 Zurich, Switzerland
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Xu J, Liu X, Wu S, Zhang D, Liu X, Xia P, Ling J, Zheng K, Xu M, Shen Y, Zhang J, Yu P. RNA-binding proteins in metabolic-associated fatty liver disease (MAFLD): From mechanism to therapy. Biosci Trends 2023; 17:21-37. [PMID: 36682800 DOI: 10.5582/bst.2022.01473] [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] [Indexed: 01/22/2023]
Abstract
Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease globally and seriously increases the public health burden, affecting approximately one quarter of the world population. Recently, RNA binding proteins (RBPs)-related pathogenesis of MAFLD has received increasing attention. RBPs, vividly called the gate keepers of MAFLD, play an important role in the development of MAFLD through transcription regulation, alternative splicing, alternative polyadenylation, stability and subcellular localization. In this review, we describe the mechanisms of different RBPs in the occurrence and development of MAFLD, as well as list some drugs that can improve MAFLD by targeting RBPs. Considering the important role of RBPs in the development of MAFLD, elucidating the RNA regulatory networks involved in RBPs will facilitate the design of new drugs and biomarkers discovery.
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Affiliation(s)
- Jiawei Xu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xingyu Liu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Shuqin Wu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Deju Zhang
- Food and Nutritional Sciences, School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Xiao Liu
- Department of Cardiology, The Second Affiliated Hospital of Sun Yat-Sen University, Guangzhou, Guangdong, China
| | - Panpan Xia
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jitao Ling
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Kai Zheng
- Medical Care Strategic Customer Department, China Merchants Bank Shenzhen Branch, Shenzhen, Guangdong, Guangdong, China
| | - Minxuan Xu
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Yunfeng Shen
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Jing Zhang
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of Anesthesiology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Peng Yu
- The Second Clinical Medical College / The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
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45
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Targeting KK-LC-1 inhibits malignant biological behaviors of triple-negative breast cancer. J Transl Med 2023; 21:184. [PMID: 36895039 PMCID: PMC9996895 DOI: 10.1186/s12967-023-04030-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 03/01/2023] [Indexed: 03/11/2023] Open
Abstract
BACKGROUND Cancer/testis antigens (CTAs) participate in the regulation of malignant biological behaviors in breast cancer. However, the function and mechanism of KK-LC-1, a member of the CTA family, in breast cancer are still unclear. METHODS Bioinformatic tools, immunohistochemistry, and western blotting were utilized to detect the expression of KK-LC-1 in breast cancer and to explore the prognostic effect of KK-LC-1 expression in breast cancer patients. Cell function assays, animal assays, and next-generation sequencing were utilized to explore the function and mechanism of KK-LC-1 in the malignant biological behaviors of triple-negative breast cancer. Small molecular compounds targeting KK-LC-1 were also screened and drug susceptibility testing was performed. RESULTS KK-LC-1 was significantly highly expressed in triple-negative breast cancer tissues than in normal breast tissues. KK-LC-1 high expression was related to poor survival outcomes in patients with breast cancer. In vitro studies suggested that KK-LC-1 silencing can inhibit triple-negative breast cancer cell proliferation, invasion, migration, and scratch healing ability, increase cell apoptosis ratio, and arrest the cell cycle in the G0-G1 phase. In vivo studies have suggested that KK-LC-1 silencing decreases tumor weight and volume in nude mice. Results showed that KK-CL-1 can regulate the malignant biological behaviors of triple-negative breast cancer via the MAL2/MUC1-C/PI3K/AKT/mTOR pathway. The small-molecule compound Z839878730 had excellent KK-LC-1 targeting ability and cancer cell killing ability. The EC50 value was 9.7 μM for MDA-MB-231 cells and 13.67 µM for MDA-MB-468 cells. Besides, Z839878730 has little tumor-killing effect on human normal mammary epithelial cells MCF10A and can inhibit the malignant biological behaviors of triple-negative breast cancer cells by MAL2/MUC1-C/PI3K/AKT/mTOR pathway. CONCLUSIONS Our findings suggest that KK-LC-1 may serve as a novel therapeutic target for triple-negative breast cancer. Z839878730, which targets KK-LC-1, presents a new path for breast cancer clinical treatment.
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Zheng R, Dunlap M, Lyu J, Gonzalez-Figueroa C, Bobkov G, Harvey SE, Chan TW, Quinones-Valdez G, Choudhury M, Vuong A, Flynn RA, Chang HY, Xiao X, Cheng C. LINE-associated cryptic splicing induces dsRNA-mediated interferon response and tumor immunity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529804. [PMID: 36865202 PMCID: PMC9980139 DOI: 10.1101/2023.02.23.529804] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
RNA splicing plays a critical role in post-transcriptional gene regulation. Exponential expansion of intron length poses a challenge for accurate splicing. Little is known about how cells prevent inadvertent and often deleterious expression of intronic elements due to cryptic splicing. In this study, we identify hnRNPM as an essential RNA binding protein that suppresses cryptic splicing through binding to deep introns, preserving transcriptome integrity. Long interspersed nuclear elements (LINEs) harbor large amounts of pseudo splice sites in introns. hnRNPM preferentially binds at intronic LINEs and represses LINE-containing pseudo splice site usage for cryptic splicing. Remarkably, a subgroup of the cryptic exons can form long dsRNAs through base-pairing of inverted Alu transposable elements scattered in between LINEs and trigger interferon immune response, a well-known antiviral defense mechanism. Notably, these interferon-associated pathways are found to be upregulated in hnRNPM-deficient tumors, which also exhibit elevated immune cell infiltration. These findings unveil hnRNPM as a guardian of transcriptome integrity. Targeting hnRNPM in tumors may be used to trigger an inflammatory immune response thereby boosting cancer surveillance.
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47
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Zhang S, Lv C, Niu Y, Li C, Li X, Shang Y, Zhang Y, Zhang Y, Zhang Y, Zeng Y. RBM3 suppresses stemness remodeling of prostate cancer in bone microenvironment by modulating N6-methyladenosine on CTNNB1 mRNA. Cell Death Dis 2023; 14:91. [PMID: 36750551 PMCID: PMC9905585 DOI: 10.1038/s41419-023-05627-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 01/23/2023] [Accepted: 01/26/2023] [Indexed: 02/09/2023]
Abstract
Bone metastasis is the most happened metastatic event in prostate cancer (PCa) and needs a large effort in treatment. When PCa metastasizes to the bone, the new microenvironment can induce the epigenome reprogramming and stemness remodeling of cancer cells, thereby increasing the adaptability of cancer cells to the bone microenvironment, and this even leads to the occurrence of secondary tumor metastasis. Our group has previously found that RNA binding motif 3 (RBM3) affects the stem cell-like properties of PCa by interfering with alternative splicing of CD44. However, whether RBM3, as a stress-response protein, can resist microenvironmental remodeling of PCa particularly in bone metastasis remains unknown. By co-culturing PCa cells with osteoblasts to mimic PCa bone metastases, we found that RBM3 upregulates the N6-methyladenosine (m6A) methylation on the mRNA of catenin beta 1 (CTNNB1) in a manner dependent on methyltransferase 3 (METTL3), an N6-adenosine-methyltransferase complex catalytic subunit. Consequently, this modification results in a decreased stability of CTNNB1 mRNA and a followed inactivation of Wnt signaling, which ultimately inhibits the stemness remodeling of PCa cells by osteoblasts. Thus, the present study may extend our understanding of the inhibitory role of RBM3 on particularly bone metastasis of PCa.
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Affiliation(s)
- Shouyi Zhang
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Chengcheng Lv
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yichen Niu
- Department of Laboratory Medicine, the First Affiliated Hospital of China Medical University, Shenyang, Liaoning, 110001, China
| | - Changqi Li
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Xiuming Li
- Department of Urology, the Affiliated Hospital of Chengde Medical University, Chengde, Hebei, 067000, China
| | - Yu Shang
- Department of Oncology, the Second Hospital of Dalian Medical University, Dalian, Liaoning, 116000, China
| | - Yunchao Zhang
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yue Zhang
- Department of Pathology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yong Zhang
- Department of Pathology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China
| | - Yu Zeng
- Department of Urology, the Cancer Hospital of Dalian University of Technology & Liaoning Cancer Hospital, Shenyang, Liaoning, 110042, China.
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48
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Lv J, Zhou Y, Zhou N, Wang Z, Chen J, Chen H, Wang D, Zhou L, Wei K, Zhang H, Tang K, Ma J, Liu Y, Wan Y, Zhang Y, Zhang H, Huang B. Epigenetic modification of CSDE1 locus dictates immune recognition of nascent tumorigenic cells. Sci Transl Med 2023; 15:eabq6024. [PMID: 36724242 DOI: 10.1126/scitranslmed.abq6024] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Weak immunogenicity of tumor cells is a root cause for the ultimate failure of immunosurveillance and immunotherapy. Although tumor evolution can be shaped by immunoediting toward a less immunogenic phenotype, mechanisms governing the initial immunogenicity of primordial tumor cells or original cancer stem cells remain obscure. Here, using a single tumor-repopulating cell (TRC) to form tumors in immunodeficient or immunocompetent mice, we demonstrated that immunogenic heterogeneity is an inherent trait of tumorigenic cells defined by the activation status of signal transducer and activator of transcription 1 (STAT1) protein in the absence of immune pressure. Subsequent investigation identified that the RNA binding protein cold shock domain-containing protein E1 (CSDE1) can promote STAT1 dephosphorylation by stabilizing T cell protein tyrosine phosphatase (TCPTP). A methyltransferase SET and MYN domain-containing 3 (SMYD3) was further identified to mediate H3K4 trimethylation of CSDE1 locus, which was under the regulation of mechanotransduction by cell-matrix and cell-cell contacts. Thus, owing to the differential epigenetic modification and subsequent differential expression of CSDE1, nascent tumorigenic cells may exhibit either a high or low immunogenicity. This identified SMYD3-CSDE1 pathway represents a potential prognostic marker for cancer immunotherapy effectiveness that requires further investigation.
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Affiliation(s)
- Jiadi Lv
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Yabo Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Nannan Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Zhenfeng Wang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Jie Chen
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Haoran Chen
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Dianheng Wang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Li Zhou
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Keke Wei
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huafeng Zhang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ke Tang
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jingwei Ma
- Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yuying Liu
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China
| | - Yonghong Wan
- McMaster Immunology Research Centre and Department of Medicine, McMaster University, Hamilton, ON L8S 4K1, Canada
| | - Yi Zhang
- Biotherapy Center and Cancer Center, First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haizeng Zhang
- Department of Medical Oncology, National Cancer Center, Cancer Hospital, CAMS and Peking Union Medical College, Beijing 100021, China
| | - Bo Huang
- Department of Immunology and National Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College, Beijing 100005, China.,Department of Biochemistry and Molecular Biology, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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Three RNA-binding protein signature as a novel biomarker to predict endometrial cancer prognosis. Am J Transl Res 2023; 15:476-492. [PMID: 36777835 PMCID: PMC9908450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Accepted: 11/14/2022] [Indexed: 02/14/2023]
Abstract
The aim of this study was to build a prognostic model for endometrial cancer (EC) patients based on RNA-binding proteins (RBPs). RNA sequencing and clinical data for uterine corpus EC (UCEC) were obtained from The Cancer Genome Atlas (TCGA). Univariate and multivariate Cox regression analysis were used to obtain the following risk formula: score = sum (corresponding coefficient × expression of each gene). A nomogram was developed to accurately predict patient survival based on risk score, age, stage, and grade. Immunohistochemistry (IHC) was used to verify the expression of RBPs in EC. The mRNA expression of RBPs was measured by qRT-PCR. The effects of RBPs on the malignant biologic behavior of EC were detected using CCK-8, colony formation, and transwell invasion assays. A novel prognostic signature was constructed, comprising three RBPs (CD3EAP, SBDS, and TDRKH). The risk score was: Risk score = (0.860 × CD3EAP expression) + (0.622 × 6SBDS expression) + (0.427 × 4TDRKH expression). The area under the receiver operating characteristic curves (AUCs) of risk score for 1-, 3-, and 5-year overall survival (OS) was 0.75, 0.68, and 0.65, respectively. The AUCs of the nomogram for 1-, 3-, and 5-year OS were 0.811, 0.793, and 0.814, respectively. In our independent cohort, the IHC results revealed that CD3EAP (P < 0.001) and TDRKH (P < 0.001) were upregulated and SBDS (P < 0.001) was downregulated in EC. Immunostaining showed the expression levels of CD3EAP, SBDS and TDRKH for each patient and these were multiplied by their respective coefficients of 0.860, 0.622 and 0.427 to obtain the risk scores. The AUCs of risk score for 1-, 3-, and 5-year OS were 0.888, 0.793, and 0.780 respectively. The AUCs of the nomogram for 1-, 3-, and 5-year OS were 0.790, 0.826, and 0.906, respectively. Cell functional experiments also confirmed the influence of the key RBPs on the malignant biologic behavior of EC. In summary, a characteristic model based on our three RBPs accurately predicted the prognosis of EC. Our in-depth analysis of these RBPs may inform the development of novel strategies for the diagnosis and treatment of EC.
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Bai N, Adeshina Y, Bychkov I, Xia Y, Gowthaman R, Miller SA, Gupta AK, Johnson DK, Lan L, Golemis EA, Makhov PB, Xu L, Pillai MM, Boumber Y, Karanicolas J. Rationally designed inhibitors of the Musashi protein-RNA interaction by hotspot mimicry. RESEARCH SQUARE 2023:rs.3.rs-2395172. [PMID: 36711552 PMCID: PMC9882606 DOI: 10.21203/rs.3.rs-2395172/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
RNA-binding proteins (RBPs) are key post-transcriptional regulators of gene expression, and thus underlie many important biological processes. Here, we developed a strategy that entails extracting a "hotspot pharmacophore" from the structure of a protein-RNA complex, to create a template for designing small-molecule inhibitors and for exploring the selectivity of the resulting inhibitors. We demonstrate this approach by designing inhibitors of Musashi proteins MSI1 and MSI2, key regulators of mRNA stability and translation that are upregulated in many cancers. We report this novel series of MSI1/MSI2 inhibitors is specific and active in biochemical, biophysical, and cellular assays. This study extends the paradigm of "hotspots" from protein-protein complexes to protein-RNA complexes, supports the "druggability" of RNA-binding protein surfaces, and represents one of the first rationally-designed inhibitors of non-enzymatic RNA-binding proteins. Owing to its simplicity and generality, we anticipate that this approach may also be used to develop inhibitors of many other RNA-binding proteins; we also consider the prospects of identifying potential off-target interactions by searching for other RBPs that recognize their cognate RNAs using similar interaction geometries. Beyond inhibitors, we also expect that compounds designed using this approach can serve as warheads for new PROTACs that selectively degrade RNA-binding proteins.
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Affiliation(s)
- Nan Bai
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Yusuf Adeshina
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Igor Bychkov
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - Yan Xia
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Ragul Gowthaman
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Sven A. Miller
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Abhishek K. Gupta
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - David K. Johnson
- Center for Computational Biology, University of Kansas, Lawrence KS 66045
| | - Lan Lan
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
| | - Erica A. Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, PA 19140
| | - Petr B. Makhov
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
| | - Liang Xu
- Department of Molecular Biosciences, University of Kansas, Lawrence KS 66045
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City KS 66160
| | - Manoj M. Pillai
- Section of Hematology, Yale Cancer Center, New Haven CT 06520
- Department of Pathology, Yale University School of Medicine, New Haven CT 06520
| | - Yanis Boumber
- Division of Hematology/Oncology, Department of Medicine, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611
| | - John Karanicolas
- Program in Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia PA 19111
- Moulder Center for Drug Discovery Research, Temple University School of Pharmacy, Philadelphia, PA 19140
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