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Park J, Wu J, Szkop KJ, Jeong J, Jovanovic P, Husmann D, Flores NM, Francis JW, Chen YJC, Benitez AM, Zahn E, Song S, Ajani JA, Wang L, Singh K, Larsson O, Garcia BA, Topisirovic I, Gozani O, Mazur PK. SMYD5 methylation of rpL40 links ribosomal output to gastric cancer. Nature 2024:10.1038/s41586-024-07718-0. [PMID: 39048817 DOI: 10.1038/s41586-024-07718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 06/14/2024] [Indexed: 07/27/2024]
Abstract
Dysregulated transcription due to disruption in histone lysine methylation dynamics is an established contributor to tumorigenesis1,2. However, whether analogous pathologic epigenetic mechanisms act directly on the ribosome to advance oncogenesis is unclear. Here we find that trimethylation of the core ribosomal protein L40 (rpL40) at lysine 22 (rpL40K22me3) by the lysine methyltransferase SMYD5 regulates mRNA translation output to promote malignant progression of gastric adenocarcinoma (GAC) with lethal peritoneal ascites. A biochemical-proteomics strategy identifies the monoubiquitin fusion protein partner rpL40 (ref. 3) as the principal physiological substrate of SMYD5 across diverse samples. Inhibiting the SMYD5-rpL40K22me3 axis in GAC cell lines reprogrammes protein synthesis to attenuate oncogenic gene expression signatures. SMYD5 and rpL40K22me3 are upregulated in samples from patients with GAC and negatively correlate with clinical outcomes. SMYD5 ablation in vivo in familial and sporadic mouse models of malignant GAC blocks metastatic disease, including peritoneal carcinomatosis. Suppressing SMYD5 methylation of rpL40 inhibits human cancer cell and patient-derived GAC xenograft growth and renders them hypersensitive to inhibitors of PI3K and mTOR. Finally, combining SMYD5 depletion with PI3K-mTOR inhibition and chimeric antigen receptor T cell administration cures an otherwise lethal in vivo mouse model of aggressive GAC-derived peritoneal carcinomatosis. Together, our work uncovers a ribosome-based epigenetic mechanism that facilitates the evolution of malignant GAC and proposes SMYD5 targeting as part of a potential combination therapy to treat this cancer.
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Affiliation(s)
- Juhyung Park
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Jibo Wu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Krzysztof J Szkop
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Jinho Jeong
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Predrag Jovanovic
- Lady Davis Institute and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Dylan Husmann
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Natasha M Flores
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joel W Francis
- Department of Biology, Stanford University, Stanford, CA, USA
| | - Ying-Jiun C Chen
- Department of Biology, Stanford University, Stanford, CA, USA
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Ana Morales Benitez
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Emily Zahn
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Shumei Song
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jaffer A Ajani
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Linghua Wang
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Kamini Singh
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Montefiore Einstein Cancer Center, Bronx, NY, USA
| | - Ola Larsson
- Department of Oncology-Pathology, Science for Life Laboratories, Karolinska Institute, Stockholm, Sweden
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, USA
| | - Ivan Topisirovic
- Lady Davis Institute and Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada
| | - Or Gozani
- Department of Biology, Stanford University, Stanford, CA, USA.
| | - Pawel K Mazur
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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2
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Luo J, Zhao H, Chen L, Liu M. Multifaceted functions of RPS27a: An unconventional ribosomal protein. J Cell Physiol 2023; 238:485-497. [PMID: 36580426 DOI: 10.1002/jcp.30941] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/28/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022]
Abstract
The ribosomal protein S27a (RPS27a) is cleaved from the fusion protein ubiquitin-RPS27a (Ub-RPS27a). Generally, Ub and RPS27a are coexpressed as a fusion protein but function independently after Ub is cleaved from RPS27a by a deubiquitinating enzyme. As an RP, RPS27a assembles into ribosomes, but it also functions independently of ribosomes. RPS27a is involved in the development and poor prognosis of various cancers, such as colorectal cancer, liver cancer, chronic myeloid leukemia, and renal carcinoma, and is associated with poor prognosis. Notably, the murine double minute 2/P53 axis is a major pathway through which RPS27a regulates cancer development. Moreover, RPS27a maintains sperm motility, regulates winged aphid indirect flight muscle degeneration, and facilitates plant growth. Additionally, RPS27a is a metalloprotein and mercury (Hg) biomarker. In the present review, we described the origin, structure, and biological functions of RPS27a.
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Affiliation(s)
- Jingshun Luo
- Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Central laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Hong Zhao
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
- Nursing College, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Meiqing Liu
- Key Laboratory of Cardiovascular Diseases of Yunnan Province, Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province, Central laboratory of Yan'an Hospital Affiliated to Kunming Medical University, Kunming, Yunnan, China
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Robin V, Bodein A, Scott-Boyer MP, Leclercq M, Périn O, Droit A. Overview of methods for characterization and visualization of a protein–protein interaction network in a multi-omics integration context. Front Mol Biosci 2022; 9:962799. [PMID: 36158572 PMCID: PMC9494275 DOI: 10.3389/fmolb.2022.962799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/16/2022] [Indexed: 11/26/2022] Open
Abstract
At the heart of the cellular machinery through the regulation of cellular functions, protein–protein interactions (PPIs) have a significant role. PPIs can be analyzed with network approaches. Construction of a PPI network requires prediction of the interactions. All PPIs form a network. Different biases such as lack of data, recurrence of information, and false interactions make the network unstable. Integrated strategies allow solving these different challenges. These approaches have shown encouraging results for the understanding of molecular mechanisms, drug action mechanisms, and identification of target genes. In order to give more importance to an interaction, it is evaluated by different confidence scores. These scores allow the filtration of the network and thus facilitate the representation of the network, essential steps to the identification and understanding of molecular mechanisms. In this review, we will discuss the main computational methods for predicting PPI, including ones confirming an interaction as well as the integration of PPIs into a network, and we will discuss visualization of these complex data.
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Affiliation(s)
- Vivian Robin
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Antoine Bodein
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Marie-Pier Scott-Boyer
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Mickaël Leclercq
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
| | - Olivier Périn
- Digital Sciences Department, L'Oréal Advanced Research, Aulnay-sous-bois, France
| | - Arnaud Droit
- Molecular Medicine Department, CHU de Québec Research Center, Université Laval, Québec, QC, Canada
- *Correspondence: Arnaud Droit,
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Sun Y, Chen G, He J, Li JX, Gan XY, Ji SF, Huang Y, Chen XH, He ML, Huang ZG. Clinical Significance and Underlying Mechanisms of CELSR3 in Metastatic Prostate Cancer Based on Immunohistochemistry, Data Mining, and In Silico Analysis. Cancer Biother Radiopharm 2021; 37:466-479. [PMID: 34582697 DOI: 10.1089/cbr.2021.0178] [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: 11/13/2022] Open
Abstract
Background: The treatment and survival rate of patients with metastatic prostate cancer (MPCa) remain unsatisfactory. Herein, the authors investigated the clinical value and potential mechanisms of cadherin EGF LAG seven-pass G-type receptor 3 (CELSR3) in MPCa to identify novel targets for clinical diagnosis and treatment. Materials and Methods: mRNA microarray and RNA-Seq (n = 1246 samples) data were utilized to estimate CELSR3 expression and to assess its differentiation ability in MPCa. Similar analyses were performed with miRNA-221-3p. Immunohistochemistry performed on clinical samples were used to evaluate the protein expression level of CELSR3 in MPCa. Based on CELSR3 differentially coexpressed genes (DCEGs), enrichment analysis was performed to investigate potential mechanisms of CELSR3 in MPCa. Results: The pooled standard mean difference (SMD) for CELSR3 was 0.80, demonstrating that CELSR3 expression was higher in MPCa than in localized prostate cancer (LPCa). CELSR3 showed moderate potential to distinguish MPCa from LPCa. CELSR3 protein expression was found to be markedly upregulated in MPCa than in LPCa tissues. The authors screened 894 CELSR3 DCEGs, which were notably enriched in the focal adhesion pathway. miRNA-221-3p showed a significantly negative correlation with CELSR3 in MPCa. Besides, miRNA-221-3p expression was downregulated in MPCa than in LPCa (SMD = -1.04), and miRNA-221-3p was moderately capable of distinguishing MPCa from LPCa. Conclusions: CELSR3 seems to play a pivotal role in MPCa by affecting the focal adhesion pathway and/or being targeted by miRNA-221-3p.
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Affiliation(s)
- Yu Sun
- Division of Spinal Surgery and The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Juan He
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Jing-Xiao Li
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Xiang-Yu Gan
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Shu-Fan Ji
- Division of Spinal Surgery and The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Ying Huang
- Division of Spinal Surgery and The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Xin-Hua Chen
- Division of Spinal Surgery and The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Mao-Lin He
- Division of Spinal Surgery and The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, P.R. China
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Alternative splicing acts as an independent prognosticator in ovarian carcinoma. Sci Rep 2021; 11:10413. [PMID: 34001978 PMCID: PMC8129203 DOI: 10.1038/s41598-021-89778-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 04/29/2021] [Indexed: 02/04/2023] Open
Abstract
Alternative splicing (AS) events associated with oncogenic processes present anomalous perturbations in many cancers, including ovarian carcinoma. There are no reliable features to predict survival outcomes for ovarian cancer patients. In this study, comprehensive profiling of AS events was conducted by integrating AS data and clinical information of ovarian serous cystadenocarcinoma (OV). Survival-related AS events were identified by Univariate Cox regression analysis. Then, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analysis were used to construct the prognostic signatures within each AS type. Furthermore, we established a splicing-related network to reveal the potential regulatory mechanisms between splicing factors and candidate AS events. A total of 730 AS events were identified as survival-associated splicing events, and the final prognostic signature based on all seven types of AS events could serve as an independent prognostic indicator and had powerful efficiency in distinguishing patient outcomes. In addition, survival-related AS events might be involved in tumor-related pathways including base excision repair and pyrimidine metabolism pathways, and some splicing factors might be correlated with prognosis-related AS events, including SPEN, SF3B5, RNPC3, LUC7L3, SRSF11 and PRPF38B. Our study constructs an independent prognostic signature for predicting ovarian cancer patients’ survival outcome and contributes to elucidating the underlying mechanism of AS in tumor development.
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Zhang Y, Ma S, Niu Q, Han Y, Liu X, Jiang J, Chen S, Lin H. Features of alternative splicing in stomach adenocarcinoma and their clinical implication: a research based on massive sequencing data. BMC Genomics 2020; 21:580. [PMID: 32831016 PMCID: PMC7443856 DOI: 10.1186/s12864-020-06997-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 08/17/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Alternative splicing (AS) offers a main mechanism to form protein polymorphism. A growing body of evidence indicates the correlation between splicing disorders and carcinoma. Nevertheless, an overall analysis of AS signatures in stomach adenocarcinoma (STAD) is absent and urgently needed. RESULTS 2042 splicing events were confirmed as prognostic molecular events. Furthermore, the final prognostic signature constructed by 10 AS events gave good result with an area under the curve (AUC) of receiver operating characteristic (ROC) curve up to 0.902 for 5 years, showing high potency in predicting patient outcome. We built the splicing regulatory network to show the internal regulation mechanism of splicing events in STAD. QKI may play a significant part in the prognosis induced by splicing events. CONCLUSIONS In our study, a high-efficiency prognostic prediction model was built for STAD patients, and the results showed that AS events could become potential prognostic biomarkers for STAD. Meanwhile, QKI may become an important target for drug design in the future.
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Affiliation(s)
- Yuanyuan Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Shengling Ma
- Institute of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qian Niu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yun Han
- Department of Ophthalmology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xingyu Liu
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Jie Jiang
- Department of Anesthesiology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Simiao Chen
- Department of Neurology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Haolong Lin
- Department of Hematology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
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Scarpa ES, Tasini F, Crinelli R, Ceccarini C, Magnani M, Bianchi M. The Ubiquitin Gene Expression Pattern and Sensitivity to UBB and UBC Knockdown Differentiate Primary 23132/87 and Metastatic MKN45 Gastric Cancer Cells. Int J Mol Sci 2020; 21:E5435. [PMID: 32751694 PMCID: PMC7432825 DOI: 10.3390/ijms21155435] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 07/27/2020] [Indexed: 01/01/2023] Open
Abstract
Gastric cancer (GC) is one of the most common and lethal cancers. Alterations in the ubiquitin (Ub) system play key roles in the carcinogenetic process and in metastasis development. Overexpression of transcription factors YY1, HSF1 and SP1, known to regulate Ub gene expression, is a predictor of poor prognosis and shorter survival in several cancers. In this study, we compared a primary (23132/87) and a metastatic (MKN45) GC cell line. We found a statistically significant higher expression of three out of four Ub coding genes, UBC, UBB and RPS27A, in MKN45 compared to 23132/87. However, while the total Ub protein content and the distribution of Ub between the conjugated and free pools were similar in these two GC cell lines, the proteasome activity was higher in MKN45. Ub gene expression was not affected upon YY1, HSF1 or SP1 small interfering RNA (siRNA) transfection, in both 23132/87 and MKN45 cell lines. Interestingly, the simultaneous knockdown of UBB and UBC mRNAs reduced the Ub content in both cell lines, but was more critical in the primary GC cell line 23132/87, causing a reduction in cell viability due to apoptosis induction and a decrease in the oncoprotein and metastatization marker β-catenin levels. Our results identify UBB and UBC as pro-survival genes in primary gastric adenocarcinoma 23132/87 cells.
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Affiliation(s)
- Emanuele Salvatore Scarpa
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino (PU), Italy; (F.T.); (R.C.); (C.C.); (M.M.); (M.B.)
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