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Narváez-Bandera I, Suárez-Gómez D, Castro-Rivera CDM, Camasta-Beníquez A, Durán-Quintana M, Cabrera-Ríos M, Isaza CE. Hepatitis C virus infection and Parkinson's disease: insights from a joint sex-stratified BioOptimatics meta-analysis. Sci Rep 2024; 14:22838. [PMID: 39354018 PMCID: PMC11445468 DOI: 10.1038/s41598-024-73535-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 09/18/2024] [Indexed: 10/03/2024] Open
Abstract
Hepatitis C virus (HCV) infection poses a significant public health challenge and often leads to long-term health complications and even death. Parkinson's disease (PD) is a progressive neurodegenerative disorder with a proposed viral etiology. HCV infection and PD have been previously suggested to be related. This work aimed to identify potential biomarkers and pathways that may play a role in the joint development of PD and HCV infection. Using BioOptimatics-bioinformatics driven by mathematical global optimization-, 22 publicly available microarray and RNAseq datasets for both diseases were analyzed, focusing on sex-specific differences. Our results revealed that 19 genes, including MT1H, MYOM2, and RPL18, exhibited significant changes in expression in both diseases. Pathway and network analyses stratified by sex indicated that these gene expression changes were enriched in processes related to immune response regulation in females and immune cell activation in males. These findings suggest a potential link between HCV infection and PD, highlighting the importance of further investigation into the underlying mechanisms and potential therapeutic targets involved.
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Affiliation(s)
- Isis Narváez-Bandera
- Bioengineering Graduate Program, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Mayagüez, 00681, Puerto Rico
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Deiver Suárez-Gómez
- Bioengineering Graduate Program, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Mayagüez, 00681, Puerto Rico
| | - Coral Del Mar Castro-Rivera
- Biology Department, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico
| | - Alaina Camasta-Beníquez
- Biology Department, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico
| | - Morelia Durán-Quintana
- Biology Department, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico
| | - Mauricio Cabrera-Ríos
- Bioengineering Graduate Program, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Mayagüez, 00681, Puerto Rico
- Industrial Engineering Department, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Mayagüez, 00681, Puerto Rico
| | - Clara E Isaza
- Bioengineering Graduate Program, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Mayagüez, 00681, Puerto Rico.
- Biology Department, The Applied Optimization Group, University of Puerto Rico-Mayagüez, Call Box 9000, Mayagüez, 00681, Puerto Rico.
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2
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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; 632:656-663. [PMID: 39048817 DOI: 10.1038/s41586-024-07718-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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3
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Singh A, Khiabanian H. Feature selection followed by a novel residuals-based normalization that includes variance stabilization simplifies and improves single-cell gene expression analysis. BMC Bioinformatics 2024; 25:248. [PMID: 39080559 PMCID: PMC11290295 DOI: 10.1186/s12859-024-05872-w] [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: 07/04/2024] [Accepted: 07/16/2024] [Indexed: 08/02/2024] Open
Abstract
Normalization is a crucial step in the analysis of single-cell RNA-sequencing (scRNA-seq) counts data. Its principal objectives are reduction of systematic biases primarily introduced through technical sources and transformation of counts to make them more amenable for the application of established statistical frameworks. In the standard workflows, normalization is followed by feature selection to identify highly variable genes (HVGs) that capture most of the biologically meaningful variation across the cells. Here, we make the case for a revised workflow by proposing a simple feature selection method and showing that we can perform feature selection before normalization by relying on observed counts. We highlight that the feature selection step can be used to not only select HVGs but to also identify stable genes. We further propose a novel variance stabilization transformation inclusive residuals-based normalization method that in fact relies on the stable genes to inform the reduction of systematic biases. We demonstrate significant improvements in downstream clustering analyses through the application of our proposed methods on biological truth-known as well as simulated counts datasets. We have implemented this novel workflow for analyzing high-throughput scRNA-seq data in an R package called Piccolo.
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Affiliation(s)
- Amartya Singh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
- Regeneron Genetics Center, Regeneron Pharmaceuticals, Tarrytown, NY, USA
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4
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Yang Y, Xing S, Luo X, Guan L, Lu Y, Wang Y, Wang F. Unraveling the prognostic significance of RGS gene family in gastric cancer and the potential implication of RGS4 in regulating tumor-infiltrating fibroblast. Front Mol Biosci 2024; 11:1158852. [PMID: 38693916 PMCID: PMC11061405 DOI: 10.3389/fmolb.2024.1158852] [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: 02/04/2023] [Accepted: 01/09/2024] [Indexed: 05/03/2024] Open
Abstract
Regulator of G-protein signaling (RGS) proteins are regulators of signal transduction mediated by G protein-coupled receptors (GPCRs). Current studies have shown that some molecules in the RGS gene family are related to the occurrence, development and poor prognosis of malignant tumors. However, the RGS gene family has been rarely studied in gastric cancer. In this study, we explored the mutation and expression profile of RGS gene family in gastric cancer, and evaluated the prognostic value of RGS expression. Then we established a prognostic model based on RGS gene family and performed functional analysis. Further studies showed that RGS4, as an independent prognostic predictor, may play an important role in regulating fibroblasts in the immune microenvironment. In conclusion, this study explores the value of RGS gene family in gastric cancer, which is of great significance for predicting the prognosis and guiding the treatment of gastric cancer.
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Affiliation(s)
| | | | | | | | | | | | - Feng Wang
- Department of Oncology, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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5
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Wang G, Qin M, Zhang B, Yan Y, Yang F, Chen Q, Liu Y, Qiao F, Ni Y. Decreased expression of RPL15 and RPL18 exacerbated the calcification of valve interstitial cells during aortic valve calcification. Cell Biol Int 2023; 47:1749-1759. [PMID: 37431269 DOI: 10.1002/cbin.12070] [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: 09/27/2022] [Revised: 06/19/2023] [Accepted: 07/02/2023] [Indexed: 07/12/2023]
Abstract
Calcific aortic valve disease (CAVD) is the most common valvular heart disease, with an increasing prevalence due to an aging population. The pathobiology of CAVD is a multifaceted and actively regulated process, but the detailed mechanisms have not been elucidated. The present study aims to identify the differentially expressed genes (DEGs) in calcified aortic valve tissues, and to analyze the correlation between DEGs and clinical features in CAVD patients. The DEGs were screened by microarray in normal and CAVD groups (n = 2 for each group), and confirmed by quantitative real-time polymerase chain reaction in normal (n = 12) and calcified aortic valve tissues (n = 34). A total of 1048 DEGs were identified in calcified aortic valve tissues, including 227 upregulated mRNAs and 821 downregulated mRNAs. Based on multiple bioinformatic analyses, three 60S ribosomal subunit components (RPL15, RPL18, and RPL18A), and two 40S ribosomal subunit components (RPS15 and RPS21) were identified as the top 5 hub genes in the protein-protein interaction network of DEGs. The expression of RPL15 and RPL18 was also found significantly decreased in calcified aortic valve tissues (both p < .01), and negatively correlated with the osteogenic differentiation marker OPN in CAVD patients (both p < .01). Moreover, inhibition of RPL15 or RPL18 exacerbated the calcification of valve interstitial cells under osteogenic induction conditions. The present study proved that decreased expression of RPL15 and RPL18 was closely associated with aortic valve calcification, which provided valuable clues to find therapeutic targets for CAVD.
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Affiliation(s)
- Guokun Wang
- Department of Cardiovascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Ming Qin
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Boyao Zhang
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yan Yan
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Cardiothoracic Surgery, No.903 Hospital of PLA, Hangzhou, Zhejiang, China
| | - Fan Yang
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Qian Chen
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yang Liu
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
- Department of Critical Care Medicine, Naval Medical Center of PLA, Shanghai, China
| | - Fan Qiao
- Department of Cardiovascular Surgery, Changhai Hospital, Naval Medical University, Shanghai, China
| | - Yiming Ni
- Department of Cardiovascular Surgery, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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6
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Zhu X, Chen H, Li H, Ren H, Ye C, Xu K, Liu J, Du F, Zhang Z, Liu Y, Xie X, Wang M, Ma T, Chong W, Shang L, Li L. ITGB1-mediated molecular landscape and cuproptosis phenotype induced the worse prognosis in diffuse gastric cancer. Front Oncol 2023; 13:1115510. [PMID: 37007126 PMCID: PMC10063208 DOI: 10.3389/fonc.2023.1115510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Diffuse type gastric cancer was identified with relatively worse prognosis than other Lauren’s histological classification. Integrin β1 (ITGB1) was a member of integrin family which played a markedly important role in tumorigenesis and progression. However, the influence of ITGB1 in diffuse gastric cancer (DGC) remains uncertain. Here, we leveraged the transcriptomic and proteomic data to explore the association between ITGB1 expression and clinicopathologic information and biological process in DGC. Cell phenotype experiments combined with quantitative-PCR (q-PCR) and western blotting were utilized to identify the potential molecular mechanism underling ITGB1.Transcriptomics and proteomics both revealed that the higher ITGB1 expression was significantly associated with worse prognosis in DGC, but not in intestinal GC. Genomic analysis indicated that the mutation frequency of significantly mutated genes of ARID1A and COL11A1, and mutational signatures of SBS6 and SBS15 were markedly increased in the ITGB1 low expression subgroup. The enrichment analysis revealed diverse pathways related to dysregulation of ITGB1 in DGC, especially in cell adhesion, proliferation, metabolism reprogramming, and immune regulation alterations. Elevated activities of kinase-ROCK1, PKACA/PRKACA and AKT1 were observed in the ITGB1 high-expression subgroup. The ssGSEA analysis also found that ITGB1 low-expression had a higher cuproptosis score and was negatively correlated with key regulators of cuproptosis, including FDX1, DLAT, and DLST. We further observed that the upregulated expression of mitochondrial tricarboxylic acid (TCA) cycle in the ITGB1 low-expression group. Reduced expression of ITGB1 inhibited the ability of cell proliferation and motility and also potentiated the cell sensitive to copper ionophores via western blotting assay. Overall, this study revealed that ITGB1 was a protumorigenic gene and regulated tumor metabolism and cuproptosis in DGC.
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Affiliation(s)
- Xingyu Zhu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Hao Chen
- Clinical Research Center of Shandong University, Clinical Epidemiology Unit, Qilu Hospital of Shandong University, Jinan, Shandong, China
| | - Han Li
- Department of Gastroenterological Surgery, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Huicheng Ren
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Chunshui Ye
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Kang Xu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Jin Liu
- Research Center for Experimental Nuclear Medicine, School of Basic Medical Sciences, Shandong University, Jinan, Shandong, China
| | - Fengying Du
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Zihao Zhang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Yuan Liu
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Xiaozhou Xie
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Mingfei Wang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Tianrong Ma
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
| | - Wei Chong
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Wei Chong, ; ; Leping Li, ; Liang Shang,
| | - Liang Shang
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Wei Chong, ; ; Leping Li, ; Liang Shang,
| | - Leping Li
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Gastrointestinal Surgery, Shandong Provincial Hospital, Shandong University, Jinan, China
- Key Laboratory of Engineering of Shandong Province, Shandong Provincial Hospital, Jinan, China
- Medical Science and Technology Innovation Center, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, China
- *Correspondence: Wei Chong, ; ; Leping Li, ; Liang Shang,
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7
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Standing S, Tran S, Murguia-Favela L, Kovalchuk O, Bose P, Narendran A. Identification of Altered Primary Immunodeficiency-Associated Genes and Their Implications in Pediatric Cancers. Cancers (Basel) 2022; 14:5942. [PMID: 36497424 PMCID: PMC9741011 DOI: 10.3390/cancers14235942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 11/25/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Cancer is the leading cause of disease-related mortality in children and malignancies are more frequently observed in individuals with primary immunodeficiencies (PIDs). This study aimed to identify and highlight the molecular mechanisms, such as oncogenesis and immune evasion, by which PID-related genes may lead to the development of pediatric cancers. METHOD We implemented a novel bioinformatics framework using patient data from the TARGET database and performed a comparative transcriptome analysis of PID-related genes in pediatric cancers between normal and cancer tissues, gene ontology enrichment, and protein-protein interaction analyses, and determined the prognostic impacts of commonly mutated and differentially expressed PID-related genes. RESULTS From the Fulgent Genetics Comprehensive Primary Immunodeficiency panel of 472 PID-related genes, 89 genes were significantly differentially expressed between normal and cancer tissues, and 20 genes were mutated in two or more patients. Enrichment analysis highlighted many immune system processes as well as additional pathways in the mutated PID-related genes related to oncogenesis. Survival outcomes for patients with altered PID-related genes were significantly different for 75 of the 89 DEGs, often resulting in a poorer prognosis. CONCLUSIONS Overall, multiple PID-related genes demonstrated the connection between PIDs and cancer development and should be studied further, with hopes of identifying new therapeutic targets.
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Affiliation(s)
- Shaelene Standing
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Son Tran
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Luis Murguia-Favela
- Section of Pediatric Hematology and Immunology, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
| | - Olga Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Pinaki Bose
- Departments of Oncology, Biochemistry and Molecular Biology, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Aru Narendran
- Section of Pediatric Oncology and Blood and Marrow Transplantation, Division of Pediatrics, Alberta Children’s Hospital and University of Calgary, Calgary, AB T3B 6A8, Canada
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8
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Buchanan IM, Smith TM, Gerber AP, Seibt J. Are there roles for heterogeneous ribosomes during sleep in the rodent brain? Front Mol Biosci 2022; 9:1008921. [PMID: 36275625 PMCID: PMC9582285 DOI: 10.3389/fmolb.2022.1008921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/20/2022] [Indexed: 11/16/2022] Open
Abstract
The regulation of mRNA translation plays an essential role in neurons, contributing to important brain functions, such as brain plasticity and memory formation. Translation is conducted by ribosomes, which at their core consist of ribosomal proteins (RPs) and ribosomal RNAs. While translation can be regulated at diverse levels through global or mRNA-specific means, recent evidence suggests that ribosomes with distinct configurations are involved in the translation of different subsets of mRNAs. However, whether and how such proclaimed ribosome heterogeneity could be connected to neuronal functions remains largely unresolved. Here, we postulate that the existence of heterologous ribosomes within neurons, especially at discrete synapses, subserve brain plasticity. This hypothesis is supported by recent studies in rodents showing that heterogeneous RP expression occurs in dendrites, the compartment of neurons where synapses are made. We further propose that sleep, which is fundamental for brain plasticity and memory formation, has a particular role in the formation of heterologous ribosomes, specialised in the translation of mRNAs specific for synaptic plasticity. This aspect of our hypothesis is supported by recent studies showing increased translation and changes in RP expression during sleep after learning. Thus, certain RPs are regulated by sleep, and could support different sleep functions, in particular brain plasticity. Future experiments investigating cell-specific heterogeneity in RPs across the sleep-wake cycle and in response to different behaviour would help address this question.
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Affiliation(s)
- Isla M. Buchanan
- Integrated Master Programme in Biochemistry, University of Surrey, Guildford, United Kingdom
| | - Trevor M. Smith
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
| | - André P. Gerber
- Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
- *Correspondence: André P. Gerber, ; Julie Seibt,
| | - Julie Seibt
- Surrey Sleep Research Centre, University of Surrey, Guildford, United Kingdom
- *Correspondence: André P. Gerber, ; Julie Seibt,
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9
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Larionova TD, Bastola S, Aksinina TE, Anufrieva KS, Wang J, Shender VO, Andreev DE, Kovalenko TF, Arapidi GP, Shnaider PV, Kazakova AN, Latyshev YA, Tatarskiy VV, Shtil AA, Moreau P, Giraud F, Li C, Wang Y, Rubtsova MP, Dontsova OA, Condro M, Ellingson BM, Shakhparonov MI, Kornblum HI, Nakano I, Pavlyukov MS. Alternative RNA splicing modulates ribosomal composition and determines the spatial phenotype of glioblastoma cells. Nat Cell Biol 2022; 24:1541-1557. [PMID: 36192632 PMCID: PMC10026424 DOI: 10.1038/s41556-022-00994-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/15/2022] [Indexed: 02/08/2023]
Abstract
Glioblastoma (GBM) is characterized by exceptionally high intratumoral heterogeneity. However, the molecular mechanisms underlying the origin of different GBM cell populations remain unclear. Here, we found that the compositions of ribosomes of GBM cells in the tumour core and edge differ due to alternative RNA splicing. The acidic pH in the core switches before messenger RNA splicing of the ribosomal gene RPL22L1 towards the RPL22L1b isoform. This allows cells to survive acidosis, increases stemness and correlates with worse patient outcome. Mechanistically, RPL22L1b promotes RNA splicing by interacting with lncMALAT1 in the nucleus and inducing its degradation. Contrarily, in the tumour edge region, RPL22L1a interacts with ribosomes in the cytoplasm and upregulates the translation of multiple messenger RNAs including TP53. We found that the RPL22L1 isoform switch is regulated by SRSF4 and identified a compound that inhibits this process and decreases tumour growth. These findings demonstrate how distinct GBM cell populations arise during tumour growth. Targeting this mechanism may decrease GBM heterogeneity and facilitate therapy.
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Affiliation(s)
- Tatyana D Larionova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Soniya Bastola
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Tatiana E Aksinina
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Ksenia S Anufrieva
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Jia Wang
- Department of Neurosurgery, Centre of Brain Science, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Victoria O Shender
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Dmitriy E Andreev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Tatiana F Kovalenko
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
| | - Georgij P Arapidi
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Polina V Shnaider
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Moscow, Russian Federation
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Anastasia N Kazakova
- Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical and Biological Agency, Moscow, Russian Federation
| | - Yaroslav A Latyshev
- N.N. Burdenko National Medical Research Center of Neurosurgery, Ministry of Health of the Russian Federation, Moscow, Russian Federation
| | - Victor V Tatarskiy
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander A Shtil
- Blokhin National Medical Research Center of Oncology, Moscow, Russian Federation
| | - Pascale Moreau
- Institute of Chemistry of Clermont-Ferrand, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Francis Giraud
- Institute of Chemistry of Clermont-Ferrand, CNRS, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Chaoxi Li
- Department of Neurosurgery, School of Medicine and O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Yichan Wang
- Department of Neurosurgery, Centre of Brain Science, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Maria P Rubtsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Olga A Dontsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Russian Federation
| | - Michael Condro
- Department of Bioengineering, University of California Los Angeles, Los Angeles, CA, USA
| | - Benjamin M Ellingson
- Brain Tumor Imaging Laboratory, Center for Computer Vision and Imaging Biomarkers, University of California Los Angeles, Los Angeles, CA, USA
- Department of Radiological Sciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychiatry, University of California Los Angeles, Los Angeles, CA, USA
- Department of Neurosurgery, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Harley I Kornblum
- Intellectual and Developmental Disabilities Research Center, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Ichiro Nakano
- Department of Neurosurgery, Medical Institute of Hokuto, Hokkaido, Japan.
| | - Marat S Pavlyukov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, Russian Federation.
- Centre for Genomic Regulation, Barcelona Institute of Science and Technology, Barcelona, Spain.
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10
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A few good peptides: MHC class I-based cancer immunosurveillance and immunoevasion. Nat Rev Immunol 2020; 21:116-128. [PMID: 32820267 DOI: 10.1038/s41577-020-0390-6] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/30/2020] [Indexed: 12/25/2022]
Abstract
The remarkable success of immune checkpoint inhibitors demonstrates the potential of tumour-specific CD8+ T cells to prevent and treat cancer. Although the number of lives saved by immunotherapy mounts, only a relatively small fraction of patients are cured. Here, we review two of the factors that limit the application of CD8+ T cell immunotherapies: difficulties in identifying tumour-specific peptides presented by MHC class I molecules and the ability of tumour cells to impair antigen presentation as they evolve under T cell selection. We describe recent advances in understanding how peptides are generated from non-canonical translation of defective ribosomal products, relate this to the dysregulated translation that is a feature of carcinogenesis and propose dysregulated translation as an important new source of tumour-specific peptides. We discuss how the synthesis and function of components of the antigen-processing and presentation pathway, including the recently described immunoribosome, are manipulated by tumours for immunoevasion and point to common druggable targets that may enhance immunotherapy.
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