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Wang ZZ, Yao GT, Wang LZ, Zhu YJ, Chen JH. Increased Expression and Prognostic Significance of BYSL in Melanoma. J Immunother 2024; 47:279-302. [PMID: 38980088 DOI: 10.1097/cji.0000000000000530] [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: 08/04/2023] [Accepted: 04/19/2024] [Indexed: 07/10/2024]
Abstract
We evaluated the BYSL content and underlying mechanism in melanoma (SKCM) overall survival (OS). In this study, we used a comprehensive approach combining bioinformatics tools, including miRNA estimation, quantitative real-time polymerase chain reaction (qRT-PCR) of miRNAs, E3 ligase estimation, STRING analysis, TIMER analysis, examination of associated upstream modulators, protein-protein interaction (PPI) analysis, as well as retrospective and survival analyses, alongside clinical sample validation. These methods were used to investigate the content of BYSL, its methylation status, its relation to patient outcome, and its immunologic significance in tumors. Our findings revealed that BYSL expression is negatively regulated by BYSL methylation. Analysis of 468 cases of SKCM RNA sequencing samples demonstrated that enhanced BYSL expression was associated with higher tumor grade. We identified several miRNAs, namely hsa-miR-146b-3p, hsa-miR-342-3p, hsa-miR-511-5p, hsa-miR-3690, and hsa-miR-193a-5p, which showed a strong association with BYSL levels. Furthermore, we predicted the E3 ubiquitin ligase of BYSL and identified CBL, FBXW7, FZR1, KLHL3, and MARCH1 as potential modulators of BYSL. Through our investigation, we discovered that PNO1, RIOK2, TSR1, WDR3, and NOB1 proteins were strongly associated with BYSL expression. In addition, we found a close association between BYSL levels and certain immune cells, particularly dendritic cells (DCs). Notably, we observed a significant negative correlation between miR-146b-3p and BYSL mRNA expression in SKCM sera samples. Collectively, based on the previously shown evidences, BYSL can serve as a robust bioindicator of SKCM patient prognosis, and it potentially contributes to immune cell invasion in SKCM.
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Affiliation(s)
- Zhong-Zhi Wang
- Department of Dermatology, School of Medicine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
| | - Guo-Tai Yao
- Department of Dermatology, Changzheng Hospital, Naval Medical University, Shanghai, China
| | - Liang-Zhe Wang
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai, China
| | - Yuan-Jie Zhu
- Department of Dermatology, Naval Medical Center, Naval Medical University, Shanghai, China
| | - Jiang-Han Chen
- Department of Dermatology, School of Medicine, Shanghai Fourth People's Hospital, Tongji University, Shanghai, China
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Sharma S, Mittal M, Shukla A, Khan J, Dinand V, Saluja D. Exploring serine-arginine rich splicing factors: potential predictive markers for dysregulation in oral cancer. BMC Cancer 2024; 24:1094. [PMID: 39227899 PMCID: PMC11373262 DOI: 10.1186/s12885-024-12750-4] [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: 04/29/2024] [Accepted: 08/01/2024] [Indexed: 09/05/2024] Open
Abstract
BACKGROUND Dysregulated splicing events are a common phenomenon in cancer with the Serine-arginine-rich splicing factor (SRSF) family emerging as pivotal regulators of gene expression, exerting influence over constitutive and alternative splicing processes. Although aberrations in a few SRSF family members have been implicated in various cancers, the comprehensive roles of other family constituents remain underexplored. METHODS This study delves into the expression profile of the entire SRSF family (SRSF1-SRSF12) in 23 cancerous cell lines originating from diverse tissues using quantitative Real-Time PCR. Further, the transcript levels of the SRSF family were examined in oral cancer patient samples stratified into Pre-cancer (n = 15), Early cancer (n = 11), Late cancer (n = 14), and adjacent non-tumor tissues (n = 26) as controls. The results were corroborated by a parallel investigation utilizing the transcriptomics data of oral squamous cell carcinoma (OSCC) patients (n = 319) and controls (n = 35) available in The Cancer Genome Atlas (TCGA) database. RESULTS Our investigation reveals a notable upregulation in the expression levels of key splicing factors, namely SRSF3, SRSF9, and SRSF10 in all oral cancer cell lines (SCC-4, UM-SCC-84, CAL33, SAS-H1). Conversely, no significant associations between SRSF family members and other cancer cell lines were discerned. Further, the expression profile of the SRSF family in oral cancer patient samples revealed significant upregulation of SRSF1, SRSF3, SRSF7, SRSF9, SRSF10, and SRSF11 in patients with late-stage oral cancer compared to controls. Transcriptomics data from TCGA database demonstrated remarkable upregulation of SRSF1, SRSF4, SRSF9, SRSF10, and SRSF11 in OSCC patients. CONCLUSION Collectively our results underscore the critical involvement of SRSF family members in the context of oral cancer, highlighting their potential as key players in the altered splicing dynamics associated with cancer progression.
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Affiliation(s)
- Sakshi Sharma
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Manasi Mittal
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Akanksha Shukla
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Jiyauddin Khan
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India
| | - Veronique Dinand
- Bai Jerbai Wadia Hospital for Children, Parel, Mumbai, 400014, Maharashtra, India
| | - Daman Saluja
- Dr. B. R. Ambedkar Centre for Biomedical Research (ACBR), University of Delhi, Delhi, 110007, India.
- Delhi School of Public Health, IoE, University of Delhi, Delhi, 110007, India.
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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Rausch T, Snajder R, Leger A, Simovic M, Giurgiu M, Villacorta L, Henssen AG, Fröhling S, Stegle O, Birney E, Bonder MJ, Ernst A, Korbel JO. Long-read sequencing of diagnosis and post-therapy medulloblastoma reveals complex rearrangement patterns and epigenetic signatures. CELL GENOMICS 2023; 3:100281. [PMID: 37082141 PMCID: PMC10112291 DOI: 10.1016/j.xgen.2023.100281] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 06/14/2022] [Accepted: 02/22/2023] [Indexed: 04/22/2023]
Abstract
Cancer genomes harbor a broad spectrum of structural variants (SVs) driving tumorigenesis, a relevant subset of which escape discovery using short-read sequencing. We employed Oxford Nanopore Technologies (ONT) long-read sequencing in a paired diagnostic and post-therapy medulloblastoma to unravel the haplotype-resolved somatic genetic and epigenetic landscape. We assembled complex rearrangements, including a 1.55-Mbp chromothripsis event, and we uncover a complex SV pattern termed templated insertion (TI) thread, characterized by short (mostly <1 kb) insertions showing prevalent self-concatenation into highly amplified structures of up to 50 kbp in size. TI threads occur in 3% of cancers, with a prevalence up to 74% in liposarcoma, and frequent colocalization with chromothripsis. We also perform long-read-based methylome profiling and discover allele-specific methylation (ASM) effects, complex rearrangements exhibiting differential methylation, and differential promoter methylation in cancer-driver genes. Our study shows the advantage of long-read sequencing in the discovery and characterization of complex somatic rearrangements.
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Affiliation(s)
- Tobias Rausch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany
| | - Rene Snajder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Faculty for Biosciences, Heidelberg University, Heidelberg, Germany
- HIDSS4Health, Helmholtz Information and Data Science School for Health, Heidelberg, Germany
| | - Adrien Leger
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Milena Simovic
- Group “Genome Instability in Tumors,” German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Mădălina Giurgiu
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany
- Freie Universität Berlin, Berlin, Germany
| | - Laura Villacorta
- European Molecular Biology Laboratory (EMBL), GeneCore, Heidelberg, Germany
| | - Anton G. Henssen
- Department of Pediatric Oncology/Hematology, Charité-Universitätsmedizin, Berlin, Germany
- Experimental and Clinical Research Center (ECRC) of the Max Delbrück Center (MDC) and Charité-Universitätsmedizin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT), Heidelberg, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Ewan Birney
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Marc Jan Bonder
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aurelie Ernst
- Group “Genome Instability in Tumors,” German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jan O. Korbel
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
- European Molecular Biology Laboratory (EMBL), European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Bridging Research Division on Mechanisms of Genomic Variation and Data Science, DKFZ, Heidelberg, Germany
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Liu B, Pang K, Feng C, Liu Z, Li C, Zhang H, Liu P, Li Z, He S, Tu C. Comprehensive analysis of a novel cuproptosis-related lncRNA signature associated with prognosis and tumor matrix features to predict immunotherapy in soft tissue carcinoma. Front Genet 2022; 13:1063057. [PMID: 36568384 PMCID: PMC9768346 DOI: 10.3389/fgene.2022.1063057] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Background: A crucial part of the malignant processes of soft tissue sarcoma (STS) is played by cuproptosis and lncRNAs. However, the connection between cuproptosis-related lncRNAs (CRLs) and STS is nevertheless unclear. As a result, our objective was to look into the immunological activity, clinical significance, and predictive accuracy of CRLs in STS. Methods: The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, respectively, provided information on the expression patterns of STS patients and the general population. Cuproptosis-related lncRNA signature (CRLncSig) construction involved the univariate, multivariate, and least absolute shrinkage and selection operator Cox regression analysis. The predictive performance of the CRLncSig was evaluated using a serial analysis. Further research was done on the connections between the CRLncSig and the tumor immune milieu, somatic mutation, immunotherapy response, and chemotherapeutic drug susceptibility. Notably, an in vitro investigation served to finally validate the expression of the hallmark CRLs. Results: A novel efficient CRLncSig composed of seven CRLs was successfully constructed. Additionally, the low-CRLncSig group's prognosis was better than that of the high-CRLncSig group's based on the new CRLncSig. The innovative CRLncSig then demonstrated outstanding, consistent, and independent prognostic and predictive usefulness for patients with STS, according to the evaluation and validation data. The low-CRLncSig group's patients also displayed improved immunoreactivity phenotype, increased immune infiltration abundance and checkpoint expression, and superior immunotherapy response, whereas those in the high-CRLncSig group with worse immune status, increased tumor stemness, and higher collagen levels in the extracellular matrix. Additionally, there is a noticeable disparity in the sensitivity of widely used anti-cancer drugs amongst various populations. What's more, the nomogram constructed based on CRLncSig and clinical characteristics of patients also showed good predictive ability. Importantly, Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR) demonstrated that the signature CRLs exhibited a significantly differential expression level in STS cell lines. Conclusion: In summary, this study revealed the novel CRLncSig could be used as a promising predictor for prognosis prediction, immune activity, tumor immune microenvironment, immune response, and chemotherapeutic drug susceptibility in patients with STS. This may provide an important direction for the clinical decision-making and personalized therapy of STS.
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Affiliation(s)
- Binfeng Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ke Pang
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chengyao Feng
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhongyue Liu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Chenbei Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haixia Zhang
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Ping Liu
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Zhihong Li
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Shasha He
- Department of Oncology, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
| | - Chao Tu
- Department of Orthopaedics, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,Hunan Key Laboratory of Tumor Models and Individualized Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China,*Correspondence: Shasha He, ; Chao Tu,
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Chen X, Cao M, Wang P, Chu S, Li M, Hou P, Zheng J, Li Z, Bai J. The emerging roles of TRIM21 in coordinating cancer metabolism, immunity and cancer treatment. Front Immunol 2022; 13:968755. [PMID: 36159815 PMCID: PMC9506679 DOI: 10.3389/fimmu.2022.968755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/24/2022] [Indexed: 11/13/2022] Open
Abstract
Tripartite motif containing-21 (TRIM21), an E3 ubiquitin ligase, was initially found to be involved in antiviral responses and autoimmune diseases. Recently studies have reported that TRIM21 plays a dual role in cancer promoting and suppressing in the occurrence and development of various cancers. Despite the fact that TRIM21 has effects on multiple metabolic processes, inflammatory responses and the efficacy of tumor therapy, there has been no systematic review of these topics. Herein, we discuss the emerging role and function of TRIM21 in cancer metabolism, immunity, especially the immune response to inflammation associated with tumorigenesis, and also the cancer treatment, hoping to shine a light on the great potential of targeting TRIM21 as a therapeutic target.
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Affiliation(s)
- Xintian Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Menghan Cao
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Pengfei Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Sufang Chu
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Minle Li
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Pingfu Hou
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Junnian Zheng
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Jin Bai, ; Zhongwei Li, ; Junnian Zheng,
| | - Zhongwei Li
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Jin Bai, ; Zhongwei Li, ; Junnian Zheng,
| | - Jin Bai
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
- Center of Clinical Oncology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
- Jiangsu Center for the Collaboration and Innovation of Cancer Biotherapy, Cancer Institute, Xuzhou Medical University, Xuzhou, China
- *Correspondence: Jin Bai, ; Zhongwei Li, ; Junnian Zheng,
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