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Ben Mrid R, El Guendouzi S, Mineo M, El Fatimy R. The emerging roles of aberrant alternative splicing in glioma. Cell Death Discov 2025; 11:50. [PMID: 39915450 PMCID: PMC11802826 DOI: 10.1038/s41420-025-02323-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Revised: 01/14/2025] [Accepted: 01/23/2025] [Indexed: 02/09/2025] Open
Abstract
Gliomas represent a heterogeneous group of uniformly fatal brain tumors. Low and high-grade gliomas have diverse molecular signatures. Despite successful advances in understanding glioma, several genetic, epigenetic, and post-transcriptional alterations leave various targeted therapies ineffective, leading to a poor prognosis for high-grade glioma. Recent advances have revealed the implication of dysregulated alternative splicing (AS) events in glioma development. AS is a process that produces, from a single genomic sequence, several mature messenger RNAs. Splicing of pre-messenger RNAs concerns at least 95% of transcripts and constitutes an important mechanism in gene expression regulation. Dysregulation of this process, through variations in spliceosome components, aberrant splicing factors and RNA-binding protein activity, disproportionate regulation of non-coding RNAs, and abnormal mRNA methylation, can contribute to the disruption of AS. Such disruptions are usually associated with the development of several cancers, including glioma. Consequently, AS constitutes a key regulatory mechanism that could serve as a target for future therapies. In this review, we explore how AS events, spliceosome components, and their regulatory mechanisms play a critical role in glioma development, highlighting their potential as targets for innovative therapeutic strategies against this challenging cancer.
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Affiliation(s)
- Reda Ben Mrid
- Institute of Biological Sciences (ISSB), Faculty of Medical Sciences, Mohammed VI Polytechnic University (FMS-UM6P), Ben-Guerir, Morocco.
| | - Sara El Guendouzi
- Institute of Biological Sciences (ISSB), Faculty of Medical Sciences, Mohammed VI Polytechnic University (FMS-UM6P), Ben-Guerir, Morocco
| | - Marco Mineo
- Harvey W. Cushing Neuro-oncology Laboratories, Department of Neurosurgery, Harvard Medical School and Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Rachid El Fatimy
- Institute of Biological Sciences (ISSB), Faculty of Medical Sciences, Mohammed VI Polytechnic University (FMS-UM6P), Ben-Guerir, Morocco.
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Li S, Chen J, Chen X, Yu J, Guo Y, Li M, Pu X. Therapeutic and prognostic potential of GPCRs in prostate cancer from multi-omics landscape. Front Pharmacol 2022; 13:997664. [PMID: 36110544 PMCID: PMC9468875 DOI: 10.3389/fphar.2022.997664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 08/09/2022] [Indexed: 11/23/2022] Open
Abstract
Prostate cancer (PRAD) is a common and fatal malignancy. It is difficult to manage clinically due to drug resistance and poor prognosis, thus creating an urgent need for novel therapeutic targets and prognostic biomarkers. Although G protein-coupled receptors (GPCRs) have been most attractive for drug development, there have been lack of an exhaustive assessment on GPCRs in PRAD like their molecular features, prognostic and therapeutic values. To close this gap, we herein systematically investigate multi-omics profiling for GPCRs in the primary PRAD by analyzing somatic mutations, somatic copy-number alterations (SCNAs), DNA methylation and mRNA expression. GPCRs exhibit low expression levels and mutation frequencies while SCNAs are more prevalent. 46 and 255 disease-related GPCRs are identified by the mRNA expression and DNA methylation analysis, respectively, complementing information lack in the genome analysis. In addition, the genomic alterations do not exhibit an observable correlation with the GPCR expression, reflecting the complex regulatory processes from DNA to RNA. Conversely, a tight association is observed between the DNA methylation and mRNA expression. The virtual screening and molecular dynamics simulation further identify four potential drugs in repositioning to PRAD. The combination of 3 clinical characteristics and 26 GPCR molecular features revealed by the transcriptome and genome exhibit good performance in predicting progression-free survival in patients with the primary PRAD, providing candidates as new biomarkers. These observations from the multi-omics analysis on GPCRs provide new insights into the underlying mechanism of primary PRAD and potential of GPCRs in developing therapeutic strategies on PRAD.
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Affiliation(s)
- Shiqi Li
- College of Chemistry, Sichuan University, Chengdu, China
| | - Jianfang Chen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Xin Chen
- College of Chemistry, Sichuan University, Chengdu, China
| | - Jin Yu
- Department of Physics and Astronomy, University of California, Irvine, Irvine, CA, United States
| | - Yanzhi Guo
- College of Chemistry, Sichuan University, Chengdu, China
| | - Menglong Li
- College of Chemistry, Sichuan University, Chengdu, China
- *Correspondence: Xuemei Pu, ; Menglong Li,
| | - Xuemei Pu
- College of Chemistry, Sichuan University, Chengdu, China
- *Correspondence: Xuemei Pu, ; Menglong Li,
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Maimaiti A, Tuersunniyazi A, Meng X, Pei Y, Ji W, Feng Z, Jiang L, Wang Z, Kasimu M, Wang Y, Shi X. N6-methyladenosine RNA methylation regulator-related alternative splicing gene signature as prognostic predictor and in immune microenvironment characterization of patients with low-grade glioma. Front Genet 2022; 13:872186. [PMID: 35937991 PMCID: PMC9355308 DOI: 10.3389/fgene.2022.872186] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 07/01/2022] [Indexed: 11/13/2022] Open
Abstract
Background: N6-methyladenosine (m6A) RNA methylation is an important epigenetic modification affecting alternative splicing (AS) patterns of genes to regulate gene expression. AS drives protein diversity and its imbalance may be an important factor in tumorigenesis. However, the clinical significance of m6A RNA methylation regulator-related AS in the tumor microenvironment has not been investigated in low-grade glioma (LGG). Methods: We used 12 m6A methylation modulatory genes (WTAP, FTO, HNRNPC, YTHDF2, YTHDF1, YTHDC2, ALKBH5, YTHDC1, ZC3H13, RBM15, METTL14, and METTL3) from The Cancer Genome Atlas (TCGA) database as well as the TCGA-LGG (n = 502) dataset of AS events and transcriptome data. These data were downloaded and subjected to machine learning, bioinformatics, and statistical analyses, including gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis. Univariate Cox, the Least Absolute Shrinkage and Selection Operator (LASSO), and multivariable Cox regression were used to develop prognostic characteristics. Prognostic values were validated using Kaplan-Maier survival analysis, proportional risk models, ROC curves, and nomograms. The ESTIMATE package, TIMER database, CIBERSORT method, and ssGSEA algorithm in the R package were utilized to explore the role of the immune microenvironment in LGG. Lastly, an AS-splicing factor (SF) regulatory network was examined in the case of considering the role of SFs in regulating AS events. Results: An aggregate of 3,272 m6A regulator-related AS events in patients with LGG were screened using six machine learning algorithms. We developed eight AS prognostic characteristics based on splice subtypes, which showed an excellent prognostic prediction performance. Furthermore, quantitative prognostic nomograms were developed and showed strong validity in prognostic prediction. In addition, prognostic signatures were substantially associated with tumor immune microenvironment diversity, ICB-related genes, and infiltration status of immune cell subtypes. Specifically, UGP2 has better promise as a prognostic factor for LGG. Finally, splicing regulatory networks revealed the potential functions of SFs. Conclusion: The present research offers a novel perspective on the role of AS in m6A methylation. We reveal that m6A methylation regulator-related AS events can mediate tumor progression through the immune-microenvironment, which could serve as a viable biological marker for clinical stratification of patients with LGG so as to optimize treatment regimens.
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Affiliation(s)
- Aierpati Maimaiti
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | | | - Xianghong Meng
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
| | - Yinan Pei
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Wenyu Ji
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zhaohai Feng
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Lei Jiang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Zengliang Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Maimaitijiang Kasimu
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Yongxin Wang
- Department of Neurosurgery, Neurosurgery Centre, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
- *Correspondence: Xin Shi, ; Yongxin Wang,
| | - Xin Shi
- Department of Neurosurgery, Shenzhen University General Hospital and Shenzhen University Clinical Medical Academy Centre, Shenzhen University, Shenzhen, China
- *Correspondence: Xin Shi, ; Yongxin Wang,
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Wang Z, Wu Q, Liu Y, Li Q, Li J. Identification of prognostic alternative splicing signature in gastric cancer. Arch Public Health 2022; 80:145. [PMID: 35614517 PMCID: PMC9131537 DOI: 10.1186/s13690-022-00894-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 05/02/2022] [Indexed: 11/20/2022] Open
Abstract
Background Aberrant alternative splicing (AS) events could be viewed as prognostic indicators in a large number of malignancies. This study aims to identify prognostic AS events, illuminate the function of the splicing variants biomarkers and provide reliable evidence for formulating public health strategies for gastric cancer (GC) surveillance. Methods RNA-Seq data, clinical information and percent spliced in (PSI) values were available in The cancer genome atlas (TCGA) and TCGA SpliceSeq data portal. A three-step regression method was conducted to identify prognostic AS events and construct multi-AS-based signatures. The associations between prognostic AS events and splicing factors were also investigated. Results We identified a total of 1,318 survival-related AS events in GC, parent genes of which were implicated in numerous oncogenic pathways. The final prognostic signatures stratified by seven types of AS events or not stratified performed well in risk prediction for GC patients. Moreover, five signatures based on AA, AD, AT, ES and RI events function as independent prognostic indicators after multivariate adjustment of other clinical variables. Splicing network also showed marked correlation between the expression of splicing factors and PSI value of AS events in GC patients. Conclusion Our findings provide a landscape of AS events and regulatory network in GC, indicating that AS events might serve as prognostic biomarkers and therapeutic targets for GC. Supplementary Information The online version contains supplementary material available at 10.1186/s13690-022-00894-3.
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Affiliation(s)
- Zhiwu Wang
- Department of Chemoradiotherapy, Tangshan People`S Hospital, Tangshan, China
| | - Qiong Wu
- Department of Chemoradiotherapy, Tangshan People`S Hospital, Tangshan, China
| | - Yankun Liu
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Qingke Li
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China
| | - Jingwu Li
- The Cancer Institute, Tangshan People's Hospital, Tangshan, 063001, China.
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Yang Z, He Y, Wang Y, Huang L, Tang Y, He Y, Chen Y, Han Z. Genome-Wide Analysis for the Regulation of Gene Alternative Splicing by DNA Methylation Level in Glioma and its Prognostic Implications. Front Genet 2022; 13:799913. [PMID: 35309147 PMCID: PMC8931337 DOI: 10.3389/fgene.2022.799913] [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: 10/22/2021] [Accepted: 01/20/2022] [Indexed: 11/13/2022] Open
Abstract
Glioma is a primary high malignant intracranial tumor with poorly understood molecular mechanisms. Previous studies found that both DNA methylation modification and gene alternative splicing (AS) play a key role in tumorigenesis of glioma, and there is an obvious regulatory relationship between them. However, to date, no comprehensive study has been performed to analyze the influence of DNA methylation level on gene AS in glioma on a genome-wide scale. Here, we performed this study by integrating DNA methylation, gene expression, AS, disease risk methylation at position, and clinical data from 537 low-grade glioma (LGG) and glioblastoma (GBM) individuals. We first conducted a differential analysis of AS events and DNA methylation positions between LGG and GBM subjects, respectively. Then, we evaluated the influence of differential methylation positions on differential AS events. Further, Fisher’s exact test was used to verify our findings and identify potential key genes in glioma. Finally, we performed a series of analyses to investigate influence of these genes on the clinical prognosis of glioma. In total, we identified 130 glioma-related genes whose AS significantly affected by DNA methylation level. Eleven of them play an important role in glioma prognosis. In short, these results will help to better understand the pathogenesis of glioma.
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Affiliation(s)
- Zeyuan Yang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yijie He
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yongheng Wang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- International Research Laboratory of Reproduction and Development, Chongqing Medical University, Chongqing, China
| | - Lin Huang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yaqin Tang
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yue He
- Group of Mathematics Education Teaching and Research, Chongqing Fudan Secondary School, Chongqing, China
| | - Yihan Chen
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Zhijie Han
- Department of Bioinformatics, School of Basic Medicine, Chongqing Medical University, Chongqing, China
- *Correspondence: Zhijie Han,
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Ye P, Yang Y, Zhang L, Zheng G. Prognostic Signatures of Alternative Splicing Events in Esophageal Carcinoma Based on TCGA Splice-Seq Data. Front Oncol 2021; 11:658262. [PMID: 34676158 PMCID: PMC8524056 DOI: 10.3389/fonc.2021.658262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/14/2021] [Indexed: 12/24/2022] Open
Abstract
An alternative splicing (AS) event is a highly complex process that plays an essential role in post-transcriptional gene expression. Several studies have suggested that abnormal AS events were the primary element in the pathological process of cancer. However, few works are dedicated to the study of AS events in esophageal carcinoma (EC). In the present study, clinical information and RNA-seq data of EC patients were downloaded from The Cancer Genome Atlas (TCGA) database. The percent spliced in (PSI) values of AS events were acquired from the TCGA Splice-seq. A total of 183 EC patients were enrolled in this study, and 2,212 AS events were found significantly associated with the overall survival of these patients by univariate Cox regression analysis. The prognostic signatures based on AS events were built by multivariate Cox analysis. Receiver operating characteristic (ROC) curves displayed that the area under the curve (AUC) of the following prognostic signatures, including exon skip (ES), alternate terminator (AT), alternate acceptor site (AA), alternate promoter (AP), alternate donor site (AD), retained intron (RI), and total events, was greater than 0.8, suggesting that these seven signatures had valuable prognosis prediction capacity. Finally, the risk score of prognostic signatures was indicated as an independent risk factor of survival. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the function of splicing factors (SFs) that were associated with AS events. Also, the interactive network between AS events and SFs identified several hub genes and AS events which need further study. This was a comprehensive study that explored prognosis-related AS events and established valuable prognosis signatures in EC patients. The network of interactions between AS events and SFs might offer novel insights into the fundamental mechanisms of tumorigenesis and progression of EC.
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Affiliation(s)
- Ping Ye
- National Health Commission Key Laboratory of Otorhinolaryngology, Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
| | - Yan Yang
- National Health Commission Key Laboratory of Otorhinolaryngology, Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
| | - Liqiang Zhang
- National Health Commission Key Laboratory of Otorhinolaryngology, Department of Otorhinolaryngology, Qilu Hospital of Shandong University, Jinan, China
| | - Guixi Zheng
- Department of Clinical Laboratory, Qilu Hospital of Shandong University, Jinan, China
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Mehterov N, Kazakova M, Sbirkov Y, Vladimirov B, Belev N, Yaneva G, Todorova K, Hayrabedyan S, Sarafian V. Alternative RNA Splicing-The Trojan Horse of Cancer Cells in Chemotherapy. Genes (Basel) 2021; 12:genes12071085. [PMID: 34356101 PMCID: PMC8306420 DOI: 10.3390/genes12071085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Almost all transcribed human genes undergo alternative RNA splicing, which increases the diversity of the coding and non-coding cellular landscape. The resultant gene products might have distinctly different and, in some cases, even opposite functions. Therefore, the abnormal regulation of alternative splicing plays a crucial role in malignant transformation, development, and progression, a fact supported by the distinct splicing profiles identified in both healthy and tumor cells. Drug resistance, resulting in treatment failure, still remains a major challenge for current cancer therapy. Furthermore, tumor cells often take advantage of aberrant RNA splicing to overcome the toxicity of the administered chemotherapeutic agents. Thus, deciphering the alternative RNA splicing variants in tumor cells would provide opportunities for designing novel therapeutics combating cancer more efficiently. In the present review, we provide a comprehensive outline of the recent findings in alternative splicing in the most common neoplasms, including lung, breast, prostate, head and neck, glioma, colon, and blood malignancies. Molecular mechanisms developed by cancer cells to promote oncogenesis as well as to evade anticancer drug treatment and the subsequent chemotherapy failure are also discussed. Taken together, these findings offer novel opportunities for future studies and the development of targeted therapy for cancer-specific splicing variants.
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Affiliation(s)
- Nikolay Mehterov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Maria Kazakova
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Yordan Sbirkov
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
| | - Boyan Vladimirov
- Department of Maxillofacial Surgery, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Nikolay Belev
- Medical Simulation and Training Center, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria;
| | - Galina Yaneva
- Department of Biology, Faculty of Pharmacy, Medical University of Varna, 9002 Varna, Bulgaria;
| | - Krassimira Todorova
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Soren Hayrabedyan
- Laboratory of Reproductive OMICs Technologies, Institute of Biology and Immunology of Reproduction, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; (K.T.); (S.H.)
| | - Victoria Sarafian
- Department of Medical Biology, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria; (N.M.); (M.K.); (Y.S.)
- Research Institute, Medical University-Plovdiv, 4002 Plovdiv, Bulgaria
- Correspondence: ; Tel.: +359-882-512-952
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Wang M, Zhou Z, Zheng J, Xiao W, Zhu J, Zhang C, Jiang X. Identification and Validation of a Prognostic Immune-Related Alternative Splicing Events Signature for Glioma. Front Oncol 2021; 11:650153. [PMID: 34055619 PMCID: PMC8155679 DOI: 10.3389/fonc.2021.650153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/22/2021] [Indexed: 01/25/2023] Open
Abstract
Background Glioma is the most common malignant brain tumor in adults, with its tumor-promoting immune microenvironment always being intricate to handle with. Amounts of evidence has accumulated to suggest that alternative splicing (AS) is related to tumor immune microenvironment. However, comprehensive analysis of immune-related AS events and their clinical significance are still lacking in glioma. Methods AS events and transcriptome data of 653 glioma patients were downloaded online. ssGSEA was performed on transcriptome data of 653 patients to divided them into low, medium and high immune cell infiltration groups. Immune-related AS events were filtrated based on this grouping. Then lasso Cox regression analysis and multivariate Cox regression analysis were done to achieve an immune-related AS events prognostic signature for glioma. Kaplan-Meier analysis, ROC analyses, univariate Cox regression and multivariate Cox regression were performed to reveal the independent prognostic role of this signature. Meanwhile, a nomogram was constructed to achieved better prognostic value for glioma patients. Besides, functional enrichment analyses and correlation analyses with immune cells infiltration were used to validated the immune-related characteristic of this signature. Results 36 immune-related AS events were achieved based on the grouping mentioned above. A nine-immune-related alternative splicing event signature was built for glioma patients. This signature showed an independent prognostic value and a nomogram containing gender, age, Karnofsky performance score, grade, IDH status, MGMT promoter status and risk score derived from the signature was constructed with a higher predictive ability for overall survival. Association with the infiltration of immune cell subtypes was validated and functional enrichment analysis found that the signature was mainly enriched in immune-related and pro-tumor functions. Conclusion Our research presented all immune-related AS events in glioma, identified an immune-related prognostic AS events risk model and a nomogram was constructed to predict the prognosis individually and more precisely. Tight connection was verified between this signature and clinical characteristics. Also, immune cells infiltration and immune checkpoints expression level were proved to link to risk scores, which enhanced the understanding of relationship between AS events and glioma immune microenvironment, firstly revealing the potential role of AS in immunotherapy of glioma.
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Affiliation(s)
- Minjie Wang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zijie Zhou
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianglin Zheng
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wenxuan Xiao
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiameng Zhu
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Chaocai Zhang
- Department of Neurosurgery, Hainan General Hospital/Hainan Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Xiaobing Jiang
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Xue J, Sang W, Su LP, Gao HX, Cui WL, Abulajiang G, Wang Q, Zhang J, Zhang W. Proteomics reveals protein phosphatase 1γ as a biomarker associated with Hippo signal pathway in glioma. Pathol Res Pract 2020; 216:153187. [PMID: 32919304 DOI: 10.1016/j.prp.2020.153187] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 08/13/2020] [Accepted: 08/15/2020] [Indexed: 12/12/2022]
Abstract
Hub proteins related with Hippo signal pathway in glioma were investigated using proteomics methods (Tandem Mass Tag, TMT) to determine the differentially expressed proteins in glioblastoma (GBM). Ingenuity Pathway Analysis (IPA) was performed to complement proteomic findings by identifying the top canonical pathways as well as to suggest novel proteins for the targeted therapy of glioma. A total of 222 formalin-fixed paraffin-embedded (FFPE) glioma tissue samples were used to verify the expression of protein phosphatase 1γ (PP1γ), Yes-associated protein 1 (YAP1), and SOX2 via immunohistochemistry. Bioinformatics analysis revealed these proteins as crucial in the Hippo signaling pathway in GBM. Spearman correlation was performed to analyze the relationship of these three proteins, and survival analysis was conducted to investigate their effects on prognosis. Among the 5808 proteins identified by TMT with the standard of P-value < 0.05 and fold change (FC) of>1.2 or <0.83, 1398 upregulated and 1060 downregulated differentially expressed proteins were found. IPA revealed that the Hippo signaling was activated in the top 10 canonical pathways, and PP1γ was activated in the Hippo signaling. Immunohistochemistry analysis indicated that PP1γ, YAP1, and SOX2 were highly and positively expressed in glioma. PP1γ expression was related to WHO grade (p = 0.003) and ki-67 expression (p = 0.012). Low PP1γ expression was associated with IDH1-mut in low-grade glioma (LGG; WHO grades II and III) (p = 0.037). PP1γ was positively correlated with YAP1 (p < 0.001; r = 0.259) and SOX2 (p = 0.009; r = 0.175). In survival analysis, age, WHO grade, ki-67 expression, and PP1γ expression independently predicted a short OS in total cohort (p < 0.05). Therefore, PP1γ is a hub protein associated with Hippo signal pathway in glioma, and its expression indicates poor prognosis in patients with glioma. Therefore, PP1γ may be a promising prognostic biomarker and a therapeutic target in glioma.
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Affiliation(s)
- Jing Xue
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China; Xinjiang Medical University, No. 393 Xinyi Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830011, PR China; Department of Pathology, Affiliated Traditional Chinese Medicine Hospital of Xinjiang Medical University, No. 116 Huanghe Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830000, PR China
| | - Wei Sang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China
| | - Li-Ping Su
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China
| | - Hai-Xia Gao
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China; Xinjiang Medical University, No. 393 Xinyi Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830011, PR China
| | - Wen-Li Cui
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China
| | - Gulinaer Abulajiang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China
| | - Qian Wang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China; Xinjiang Medical University, No. 393 Xinyi Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830011, PR China
| | - Jing Zhang
- Department of Pathology, Affiliated Traditional Chinese Medicine Hospital of Xinjiang Medical University, No. 116 Huanghe Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830000, PR China
| | - Wei Zhang
- Department of Pathology, The First Affiliated Hospital of Xinjiang Medical University, No. 137 Liyushan Southern Road, Urumqi, The Xinjiang Uygur Autonomous Region of China, 830054, PR China.
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