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Huang Y, Yang F, Zhang W, Zhou Y, Duan D, Liu S, Li J, Zhao Y. A novel lysosome-related gene signature coupled with gleason score for prognosis prediction in prostate cancer. Front Genet 2023; 14:1135365. [PMID: 37065491 PMCID: PMC10098196 DOI: 10.3389/fgene.2023.1135365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/23/2023] [Indexed: 04/03/2023] Open
Abstract
Background: Prostate cancer (PCa) is highly heterogeneous, which makes it difficult to precisely distinguish the clinical stages and histological grades of tumor lesions, thereby leading to large amounts of under- and over-treatment. Thus, we expect the development of novel prediction approaches for the prevention of inadequate therapies. The emerging evidence demonstrates the pivotal role of lysosome-related mechanisms in the prognosis of PCa. In this study, we aimed to identify a lysosome-related prognostic predictor in PCa for future therapies.Methods: The PCa samples involved in this study were gathered from The Cancer Genome Atlas database (TCGA) (n = 552) and cBioPortal database (n = 82). During screening, we categorized PCa patients into two immune groups based on median ssGSEA scores. Then, the Gleason score and lysosome-related genes were included and screened out by using a univariate Cox regression analysis and the least absolute shrinkage and selection operation (LASSO) analysis. Following further analysis, the probability of progression free interval (PFI) was modeled by using unadjusted Kaplan–Meier estimation curves and a multivariable Cox regression analysis. A receiver operating characteristic (ROC) curve, nomogram and calibration curve were used to examine the predictive value of this model in discriminating progression events from non-events. The model was trained and repeatedly validated by creating a training set (n = 400), an internal validation set (n = 100) and an external validation (n = 82) from the cohort.Results: Following grouping by ssGSEA score, the Gleason score and two LRGs—neutrophil cytosolic factor 1 (NCF1) and gamma-interferon-inducible lysosomal thiol reductase (IFI30)—were screened out to differentiate patients with or without progression (1-year AUC = 0.787; 3-year AUC = 0.798; 5-year AUC = 0.772; 10-year AUC = 0.832). Patients with a higher risk showed poorer outcomes (p < 0.0001) and a higher cumulative hazard (p < 0.0001). Besides this, our risk model combined LRGs with the Gleason score and presented a more accurate prediction of PCa prognosis than the Gleason score alone. In three validation sets, our model still achieved high prediction rates.Conclusion: In conclusion, this novel lysosome-related gene signature, coupled with the Gleason score, works well in PCa for prognosis prediction.
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Affiliation(s)
- Ying Huang
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Fan Yang
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Wenyi Zhang
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Yupeng Zhou
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Dengyi Duan
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Shuang Liu
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
| | - Jianmin Li
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Jianmin Li, ; Yang Zhao,
| | - Yang Zhao
- Department of Radiology, The Second Hospital of Tianjin Medical University, Tianjin, China
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin, China
- *Correspondence: Jianmin Li, ; Yang Zhao,
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Nan X, Zhao K, Qin Y, Song Y, Guo Y, Luo Z, Li W, Wang Q. Antibacterial responses and functional characterization of the interferon gamma inducible lysosomal thiol reductase (GILT) protein in Chinese mitten crab (Eriocheir sinensis). DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2022; 136:104514. [PMID: 35977559 DOI: 10.1016/j.dci.2022.104514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
The inducible reductase of interferon gamma (IFN- γ), IFN-γ-induced lysosomal thiol reductase (GILT) is important in antiviral immunity, but its mechanism in invertebrate antimicrobial immunity is unclear. We determined that GILT protein was involved in the antibacterial immunity of Chinese mitten crab (Eriocheir sinensis). GILT protein was highly expressed in crab hemocytes and was significantly upregulated 6 h after bacterial stimulation. Recombinant E. sinensis GILT (rEsGILT) contained a CXXS active site that catalyzed disulfide bond reduction. Vibrio parahaemolyticus and Staphylococcus aureus were bound through interaction with peptidoglycan and lipopolysaccharide, respectively, and bacterial agglutination and clearance in the crabs was markedly promoted. Nevertheless, EsGILT exhibited no direct antibacterial or bactericidal activity. EsGILT also promoted crab hemocyte phagocytosis and played an anti-bacterial role, and inhibited hemocyte apoptosis. In summary, EsGILT promoted bacterial agglutination, clearance, and phagocytosis by recognizing and agglutinating pathogenic microorganisms and reduced the apoptosis level, indirectly participating in antibacterial reactions.
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Affiliation(s)
- Xingyu Nan
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Ke Zhao
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yukai Qin
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yu Song
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Yanan Guo
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Zhi Luo
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China
| | - Weiwei Li
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China.
| | - Qun Wang
- Laboratory of Invertebrate Immunological Defense and Reproductive Biology, School of Life Sciences, East China Normal University, Shanghai, China.
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Yin X, Wu Q, Hao Z, Chen L. Identification of novel prognostic targets in glioblastoma using bioinformatics analysis. Biomed Eng Online 2022; 21:26. [PMID: 35436915 PMCID: PMC9014588 DOI: 10.1186/s12938-022-00995-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 04/07/2022] [Indexed: 11/17/2022] Open
Abstract
Background Glioblastoma (GBM) is the most malignant grade of glioma. Highly aggressive characteristics of GBM and poor prognosis cause GBM-related deaths. The potential prognostic biomarkers remain to be demonstrated. This research builds up predictive gene targets of expression alterations in GBM utilizing bioinformatics analysis. Methods and results The microarray datasets (GSE15824 and GSE16011) associated with GBM were obtained from Gene Expression Omnibus (GEO) database to identify the differentially expressed genes (DEGs) between GBM and non-tumor tissues. In total, 719 DEGs were obtained and subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) for function enrichment analysis. Furthermore, we constructed protein–protein Interaction (PPI) network among DEGs utilizing Search Tool for the Retrieval of Interacting Genes (STRING) online tool and Cytoscape software. The DEGs of degree > 10 was selected as hub genes, including 73 upregulated genes and 21 downregulated genes. Moreover, MCODE application in Cytoscape software was employed to identify three key modules involved in GBM development and prognosis. Additionally, we used the Gene expression profiling and interactive analyses (GEPIA) online tool to further confirm four genes involving in poor prognosis of GBM patients, including interferon-gamma-inducible protein 30 (IFI30), major histocompatibility complex class II-DM alpha (HLA-DMA), Prolyl 4-hydroxylase beta polypeptide (P4HB) and reticulocalbin-1 (RCN1). Furthermore, the correlation analysis indicated that the expression of IFI30, an acknowledged biomarker in glioma, was positively correlated with HLA-DMA, P4HB and RCN1. RCN1 expression was positively correlated with P4HB and HLA-DMA. Moreover, qRT-PCR and immunohistochemistry analysis further validated the upregulation of four prognostic markers in GBM tissues. Conclusions Analysis of multiple datasets combined with global network information and experimental verification presents a successful approach to uncover the risk hub genes and prognostic markers of GBM. Our study identified four risk- and prognostic-related gene signatures, including IFI30, HLA-DMA, P4HB and RCN1. This gene sets contribute a new perspective to improve the diagnostic, prognostic, and therapeutic outcomes of GBM.
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Affiliation(s)
- Xiaofeng Yin
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Quansheng Wu
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Zheng Hao
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China
| | - Laizhao Chen
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, No.382 Wuyi Road, Taiyuan, 030000, Shanxi, China.
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Zhang H, Zhu S, Xing Y, Liu Q, Guo Z, Cai Z, Shen Z, Xia Q, Sheng H. Effect of cryopreservation on A172 and U251 glioma cells infected with lentiviral vectors designed for CRISPR/Cas9-mediated aquaporin-8 knock-out. PLoS One 2022; 17:e0263162. [PMID: 35245307 PMCID: PMC8896708 DOI: 10.1371/journal.pone.0263162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 11/18/2022] Open
Abstract
Among the three existing targeted gene editing technologies, zinc-finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats-CRISPR-associated 9 (CRISPR-Cas9), the latter is widely used owing to its simplicity, efficiency, and low cost. Here, we routinely infected A172 and U251 cells with lentiviral vectors, in which aquaporin-8 (AQP8) was knocked out using CRISPR/Cas9. Our results indicated that cryopreservation did not significantly alter the viral infection efficiency, but influenced AQP8 expression in the infected cells at both protein and mRNA levels compared with the non-cryopreserved samples. Further, AQP8 expression at protein and mRNA levels in recovered cryopreserved infected cells did not significantly differ from those in the blank and negative controls, indicating that the lentivirus was still infectious at low temperatures. However, it failed to release the AQP8-targeting guide RNA in the infected cells, or the guide RNA was released, but underwent changes that caused it to malfunction in the cells with CRISPR/Cas9-mediated AQP8 knock-out. Our findings possibly provide some insights into the reliability of lentiviruses as CRISPR/Cas9 vectors.
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Affiliation(s)
- Hao Zhang
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Shujuan Zhu
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Yu Xing
- Department of Forensic Medicine, Chongqing Medical University, Chongqing, China
| | - Qian Liu
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Zhen Guo
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Ziling Cai
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Zihao Shen
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Qingqian Xia
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
| | - Huajun Sheng
- Department of Human Anatomy, College of Basic Medicine, Chongqing Medical University, Chongqing, China
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5
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GILT Expression in Human Melanoma Cells Enhances Generation of Antigenic Peptides for HLA Class II-Mediated Immune Recognition. Int J Mol Sci 2022; 23:ijms23031066. [PMID: 35162988 PMCID: PMC8835040 DOI: 10.3390/ijms23031066] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 01/11/2022] [Indexed: 12/27/2022] Open
Abstract
Melanoma is an aggressive skin cancer that has become increasingly prevalent in western populations. Current treatments such as surgery, chemotherapy, and high-dose radiation have had limited success, often failing to treat late stage, metastatic melanoma. Alternative strategies such as immunotherapies have been successful in treating a small percentage of patients with metastatic disease, although these treatments to date have not been proven to enhance overall survival. Several melanoma antigens (Ags) proposed as targets for immunotherapeutics include tyrosinase, NY-ESO-1, gp-100, and Mart-1, all of which contain both human leukocyte antigen (HLA) class I and class II-restricted epitopes necessary for immune recognition. We have previously shown that an enzyme, gamma-IFN-inducible lysosomal thiol-reductase (GILT), is abundantly expressed in professional Ag presenting cells (APCs), but absent or expressed at greatly reduced levels in many human melanomas. In the current study, we report that increased GILT expression generates a greater pool of antigenic peptides in melanoma cells for enhanced CD4+ T cell recognition. Our results suggest that the induction of GILT in human melanoma cells could aid in the development of a novel whole-cell vaccine for the enhancement of immune recognition of metastatic melanoma.
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Broxmeyer HE, Cooper S, Blum JS. Expression of gilt acts as a positive regulator of mouse hematopoietic progenitor cells. Blood Cells Mol Dis 2021; 90:102574. [PMID: 34015674 DOI: 10.1016/j.bcmd.2021.102574] [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: 04/23/2021] [Accepted: 04/26/2021] [Indexed: 11/16/2022]
Abstract
Gamma interferon inducible lysosomal thiol reductase (GILT), is known to be involved in immunity, but its role in hematopoiesis has not been previously reported. Herein, we demonstrate using gilt knockout (-/-) mice that loss of gilt associates with decreased numbers and cycling status of femoral hematopoietic progenitor cells (CFU-GM, BFU-E, and CFU-GEMM) with more modest effects on splenic progenitor cells. Thus, GILT is associated with positive regulation of hematopoietic progenitor cells in mice, mainly in bone marrow.
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Affiliation(s)
- Hal E Broxmeyer
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA.
| | - Scott Cooper
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Janice S Blum
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, USA
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7
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Fan Y, Wang X, Li Y. IFI30 expression predicts patient prognosis in breast cancer and dictates breast cancer cells proliferation via regulating autophagy. Int J Med Sci 2021; 18:3342-3352. [PMID: 34400904 PMCID: PMC8364447 DOI: 10.7150/ijms.62870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
Introduction: Incidence and mortality rates of breast cancer are increasing in women worldwide. Immunotherapy is a relatively popular treatment modality for all malignant tumors including breast cancer in recent years. Interferon γ-inducible protein 30 (IFI30) could catalyze the reduction of disulfide bonds and enhance major histocompatibility complex (MHC) class II-restricted antigen processing. Recent studies showed that IFI30 played an important role in the immune response of malignant tumors. Methods: The Cancer Genome Atlas (TCGA) database and clinical proteomic tumor Analysis consortium (CPTAC) database were applied to predict the role of IFI30 in breast cancer and the relationship between IFI30 and prognosis of breast cancer patients. Then we detected the expression of IFI30 in clinical samples of breast cancer patients, and analyzed the relationship between IFI30 and the prognosis of breast cancer patients. We used lentivirus infection method to construct a stable IFI30 knockdown cell line, and detected the effect of IFI30 in breast cancer cells. Nude mice tumor bearing experiment was performed to investigate the effect of IFI30 on breast cancer cells in vivo. Western blot was used to verify the regulation of autophagy related protein LC3 and p62 by IFI30. Results: We found that IFI30 was highly expressed in breast cancer tissues and was associated with poor outcome of patients. The knockdown of IFI30 could inhibit the proliferation, migration and invasion of breast cancer cells and significantly inhibit tumor growth in vivo. Increased accumulation of LC3-II and p62 suggested impaired autophagy in IFI30 knockdown cells. Discussion: As a result, we suggested that IFI30 might play a key role in the initiation and progression of human breast cancer and might be a new therapeutic target in breast cancer.
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Affiliation(s)
- Yan Fan
- Department of Pediatrics, The First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang , Liaoning, 110001 China
| | - Xu Wang
- Department of Breast Surgery, Department of Surgical Oncology, Research Unit of General Surgery, The First Affiliated Hospital of China Medical University, No. 155, North Nanjing Street, Heping District, Shenyang , Liaoning, 110001 China
| | - Yang Li
- Department of Cell Biology, Key Laboratory of Cell Biology, National Health Commission of the PRC, and Key Laboratory of Medical Cell Biology, Ministry of Education of the PRC, China Medical University, No. 77, Puhe Road, Shenyang North New Area, Shenyang, Liaoning,110122 China
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8
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Liu X, Song C, Yang S, Ji Q, Chen F, Li W. IFI30 expression is an independent unfavourable prognostic factor in glioma. J Cell Mol Med 2020; 24:12433-12443. [PMID: 32969157 PMCID: PMC7686962 DOI: 10.1111/jcmm.15758] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Revised: 10/24/2019] [Accepted: 08/05/2020] [Indexed: 12/21/2022] Open
Abstract
Gamma-interferon-inducible lysosomal thiol reductase, the only known lysosomal thiol reductase, is encoded by gene IFI30 and expressed constitutively in antigen-presenting cells. Our comprehensive study on IFI30 in gliomas found its expression to be high in glioblastomas and in gliomas with a mesenchymal subtype or wild-type isocitrate dehydrogenase, all of which indicated the malignancy and poor outcomes of gliomas. Kaplan-Meier survival analysis ascertained that high IFI30 expression conferred poor outcomes. The IFI30 expression levels also showed high efficiency in predicting 1-, 3- and 5-year overall survival. Univariable and multivariable Cox regression analyses were performed to define IFI30 as an independent prognostic marker. Biological process analysis suggested that IFI30 was involved in immune responses. ESTIMATE and CIBERSORT were applied to evaluate immune cell infiltration, with results indicating that samples with higher IFI30 expression had higher infiltration of immune cells, including regulatory T cells and M0 macrophages. Correlation analysis showed that IFI30 was significantly positively correlated with immune checkpoints that suppress effective antitumour immune responses. Immunohistochemical staining was also performed to confirm the association between IFI30 expression and the immune phenotype. The suggested correlation between high IFI30 expression and an immunosuppressive phenotype contributes to our knowledge about the glioma microenvironment and might provide clues for the development of novel therapeutic targets.
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Affiliation(s)
- Xiu Liu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chunyan Song
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shoubo Yang
- Department of Neuro-Oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qiang Ji
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Feng Chen
- Department of Neuro-Oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenbin Li
- Department of Neuro-Oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
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Li Y, Deng G, Qi Y, Zhang H, Gao L, Jiang H, Ye Z, Liu B, Chen Q. Bioinformatic Profiling of Prognosis-Related Genes in Malignant Glioma Microenvironment. Med Sci Monit 2020; 26:e924054. [PMID: 32843610 PMCID: PMC7780890 DOI: 10.12659/msm.924054] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Gliomas are the most common primary tumors of the brain and spinal cord. The tumor microenvironment (TME) is the cellular environment in which tumors exist. This study aimed to identify the role of the TME and the effects of genes involved in the TME of malignant glioma. MATERIAL AND METHODS The ESTIMATE algorithms in the R package were used to calculate the immune and stromal scores of samples in the TCGA and GSE4290 datasets. The associations of stromal and immune scores with clinicopathological characteristics and overall survival of malignant glioma patients were assessed by analysis of variance and Kaplan-Meier analysis. Differentially expressed genes (DEGs) were obtained through the median immune and stromal score using the R package "limma". Functional enrichment analysis and the PPI network MCODE were used to analyze DEGs. RESULTS Increased immune and stromal scores were closely related with advanced glioma grade and poor prognosis (all P<0.01). In total, 558 DEGs were found and most were related to tumor prognosis. Functional enrichment analysis showed that DEGs were associated with cell-matrix regulation and immune response. Four hub modules related to tumor angiogenesis, collagen formation, and immune response were found and analyzed. Previously overlooked microenvironment-related genes such as LAMB1, FN1, ACTN1, TRIM, SERPINH1, CYBA, LAIR1, and LILRB2 showed prognostic values in malignant glioma patients. CONCLUSIONS The glioma stromal/immune scores are closely related to glioma grade, histology, and survival time. Some glioma microenvironment-related genes including LAMB1, FN1, ACTN1, TRIM6, SERPINH1, CYBA, LAIR1, and LILRB2 show prognostic values in malignant gliomas and serve as potential biomarkers.
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Affiliation(s)
- Yong Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Gang Deng
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Yangzhi Qi
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Huikai Zhang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Lun Gao
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Hongxiang Jiang
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Zhang Ye
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Baohui Liu
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
| | - Qianxue Chen
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, Hubei, China (mainland)
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Xu L, Pelosof L, Wang R, McFarland HI, Wu WW, Phue JN, Lee CT, Shen RF, Juhl H, Wu LH, Alterovitz WL, Petricon E, Rosenberg AS. NGS Evaluation of Colorectal Cancer Reveals Interferon Gamma Dependent Expression of Immune Checkpoint Genes and Identification of Novel IFNγ Induced Genes. Front Immunol 2020; 11:224. [PMID: 32265897 PMCID: PMC7103651 DOI: 10.3389/fimmu.2020.00224] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/28/2020] [Indexed: 12/28/2022] Open
Abstract
To evaluate the expression of immune checkpoint genes, their concordance with expression of IFNγ, and to identify potential novel ICP related genes (ICPRG) in colorectal cancer (CRC), the biological connectivity of six well documented ("classical") ICPs (CTLA4, PD1, PDL1, Tim3, IDO1, and LAG3) with IFNγ and its co-expressed genes was examined by NGS in 79 CRC/healthy colon tissue pairs. Identification of novel IFNγ- induced molecules with potential ICP activity was also sought. In our study, the six classical ICPs were statistically upregulated and correlated with IFNγ, CD8A, CD8B, CD4, and 180 additional immunologically related genes in IFNγ positive (FPKM > 1) tumors. By ICP co-expression analysis, we also identified three IFNγ-induced genes [(IFNγ-inducible lysosomal thiol reductase (IFI30), guanylate binding protein1 (GBP1), and guanylate binding protein 4 (GBP4)] as potential novel ICPRGs. These three genes were upregulated in tumor compared to normal tissues in IFNγ positive tumors, co-expressed with CD8A and had relatively high abundance (average FPKM = 362, 51, and 25, respectively), compared to the abundance of the 5 well-defined ICPs (Tim3, LAG3, PDL1, CTLA4, PD1; average FPKM = 10, 9, 6, 6, and 2, respectively), although IDO1 is expressed at comparably high levels (FPKM = 39). We extended our evaluation by querying the TCGA database which revealed the commonality of IFNγ dependent expression of the three potential ICPRGs in 638 CRCs, 103 skin cutaneous melanomas (SKCM), 1105 breast cancers (BC), 184 esophageal cancers (ESC), 416 stomach cancers (STC), and 501 lung squamous carcinomas (LUSC). In terms of prognosis, based on Pathology Atlas data, correlation of GBP1 and GBP4, but not IFI30, with 5-year survival rate was favorable in CRC, BC, SKCM, and STC. Thus, further studies defining the role of IFI30, GBP1, and GBP4 in CRC are warranted.
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Affiliation(s)
- Lai Xu
- Office of Oncologic Diseases, Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Lorraine Pelosof
- Office of Oncologic Diseases, Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Rong Wang
- Office of Biotechnology Products, Division of Biotechnology Review and Research III (DBRRIII), Office of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Hugh I. McFarland
- Office of Biotechnology Products, Division of Biotechnology Review and Research III (DBRRIII), Office of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Je-Nie Phue
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Chun-Ting Lee
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | | | - Lei-Hong Wu
- Division of Bioinformatics and Biostatistics (DBB), National Center for Toxicological Research (NCTR), FDA, Jefferson, AR, United States
| | - Wei-Lun Alterovitz
- HIVE, Center for Biologics Evaluation and Research (CBER), FDA, Silver Spring, MD, United States
| | - Emanuel Petricon
- Center for Applied Proteomics and Molecular Medicine (CAPMM), George Mason University, Fairfax, VA, United States
| | - Amy S. Rosenberg
- Office of Biotechnology Products, Division of Biotechnology Review and Research III (DBRRIII), Office of Pharmaceutical Quality (OPQ), Center for Drug Evaluation and Research (CDER), FDA, Silver Spring, MD, United States
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Zhu C, Chen X, Guan G, Zou C, Guo Q, Cheng P, Cheng W, Wu A. IFI30 Is a Novel Immune-Related Target with Predicting Value of Prognosis and Treatment Response in Glioblastoma. Onco Targets Ther 2020; 13:1129-1143. [PMID: 32103982 PMCID: PMC7008640 DOI: 10.2147/ott.s237162] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022] Open
Abstract
Purpose As a crucial part of anti-tumor immunotherapy, interferon-α/β (IFN-α/β) treatment has been broadly applied to clinical trials of glioma. However, less is known about implement of interferon-γ (IFN-γ) in glioma. Further investigating the valuable hub molecular of IFN-γ family might provide us a novel guidance for glioma therapy. Methods This study carried out an analysis on glioma patients from the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) cohorts. The analyses were performed by GraphPad Prism 8 and R language. All the validated experiments were performed three times independently. Results We identified IFI30 as the most stable independent prognostic gene among 20 classical IFN-γ stimulated genes (ISGs) in glioma patients. Furthermore, we found that IFI30 highly expressed in malignant subtypes of glioma and associated with chemotherapy response. We also found IFI30 could activate IL6-STAT6 signal pathway to decline the glioma cells' chemotherapy sensitivity by performing experiments. Gene ontology (GO) analysis showed IFI30 associated with enhanced leucocyte mediated immune and inflammatory response. Microenvironment analysis referred that high IFI30 expression accompanied with more infiltration of M2 type macrophages. Conclusion IFI30 is involved in the malignant progression and chemotherapy response of glioblastoma, which can be a potential target for treatment in glioblastoma patients.
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Affiliation(s)
- Chen Zhu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Xin Chen
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Gefei Guan
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Cunyi Zou
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Qing Guo
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Peng Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Wen Cheng
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
| | - Anhua Wu
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, Liaoning, People's Republic of China
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