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Liu Z, Yang L, Wu W, Chen Z, Xie Z, Shi D, Cai N, Zhuo S. Prognosis and therapeutic significance of IGF-1R-related signaling pathway gene signature in glioma. Front Cell Dev Biol 2024; 12:1375030. [PMID: 38665430 PMCID: PMC11043541 DOI: 10.3389/fcell.2024.1375030] [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: 01/23/2024] [Accepted: 03/28/2024] [Indexed: 04/28/2024] Open
Abstract
Background Glioma is the most common cancer of the central nervous system with poor therapeutic response and clinical prognosis. Insulin-like growth factor 1 receptor (IGF-1R) signaling is implicated in tumor development and progression and induces apoptosis of cancer cells following functional inhibition. However, the relationship between the IGF-1R-related signaling pathway genes and glioma prognosis or immunotherapy/chemotherapy is poorly understood. Methods LASSO-Cox regression was employed to develop a 16-gene risk signature in the TCGA-GBMLGG cohort, and all patients with glioma were divided into low-risk and high-risk subgroups. The relationships between the risk signature and the tumor immune microenvironment (TIME), immunotherapy response, and chemotherapy response were then analyzed. Immunohistochemistry was used to evaluate the HSP90B1 level in clinical glioma tissue. Results The gene risk signature yielded superior predictive efficacy in prognosis (5-year area under the curve: 0.875) and can therefore serve as an independent prognostic indicator in patients with glioma. The high-risk subgroup exhibited abundant immune infltration and elevated immune checkpoint gene expression within the TIME. Subsequent analysis revealed that patients in the high-risk subgroup benefited more from chemotherapy. Immunohistochemical analysis confirmed that HSP90B1 was overexpressed in glioma, with significantly higher levels observed in glioblastoma than in astrocytoma or oligodendrocytoma. Conclusion The newly identified 16-gene risk signature demonstrates a robust predictive capacity for glioma prognosis and plays a pivotal role in the TIME, thereby offering valuable insights for the exploration of novel biomarkers and targeted therapeutics.
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Affiliation(s)
- Zhen Liu
- Department of Neurosurgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Liangwang Yang
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
| | - Wenqi Wu
- Department of Neurology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zejun Chen
- Department of Neurosurgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zhengxing Xie
- Department of Neurosurgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Daoming Shi
- Department of General Surgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Ning Cai
- Department of Neurosurgery, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Shenghua Zhuo
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, Hainan, China
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Zhuo S, Tang C, Yang L, Chen Z, Chen T, Wang K, Yang K. Independent prognostic biomarker FERMT3 associated with immune infiltration and immunotherapy response in glioma. Ann Med 2023; 55:2264325. [PMID: 37795794 PMCID: PMC10557566 DOI: 10.1080/07853890.2023.2264325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Accepted: 09/25/2023] [Indexed: 10/06/2023] Open
Abstract
BACKGROUND Adult glioma progresses rapidly and has a poor clinical outcome. The focal adhesion protein Kindlin-3 (encoded by the FERMT3 gene) participates in tumor development, drug resistance, and progression. However, the relationship between Kindlin-3 and glioma prognosis or immune microenvironment is poorly understood. METHODS We comprehensively analyzed the expression, prognostic value, mutation landscape, functional enrichment, immune infiltration, and therapeutic role of FERMT3 in glioma using multiple datasets and validated Kindlin-3 expression in clinical tissue specimens by immunohistochemistry and multiple immunofluorescence staining. RESULTS FERMT3 is an independent predictor of glioma prognosis and is highly expressed in glioblastoma tissues. Functional enrichment analyses indicated that FERMT3 participates in multiple immune-related pathways such as immune response and cytokine production. Furthermore, FERMT3 expression was positively correlated with the infiltration of several immune cells, immune scores, and the expression of genes related to immune checkpoints. Further analyses revealed that overexpression of FERMT3 was linked to a better response to anti-PD1 therapy. Data from single-cell RNA-seq reveal that FERMT3 was largely expressed in microglial cells and tissue-resident macrophages. Multiple immunofluorescence staining confirmed the overexpression of Kindlin-3 in the glioma-associated microglia/macrophages (GAMs). CONCLUSION The findings of this study provide a new perspective on the role of Kindlin-3 in glioma and may have a significant impact on the discovery of novel biomarkers and targeting of GAMs in the future.
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Affiliation(s)
- Shenghua Zhuo
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, China
- International Center for Aging and Cancer, Hainan Medical University, Haikou, China
| | - Caiying Tang
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Liangwang Yang
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Zhimin Chen
- Department of Neurosurgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Taixue Chen
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, China
| | - Kai Wang
- International Center for Aging and Cancer, Hainan Medical University, Haikou, China
| | - Kun Yang
- Department of Neurosurgery, First Affiliated Hospital of Hainan Medical University, Haikou, China
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Tan K, Song Y, Xu M, You Z. Clinical evidence for a role of E2F1-induced replication stress in modulating tumor mutational burden and immune microenvironment. DNA Repair (Amst) 2023; 129:103531. [PMID: 37453246 DOI: 10.1016/j.dnarep.2023.103531] [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: 07/18/2022] [Revised: 06/05/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
DNA replication stress (RS) is frequently induced by oncogene activation and is believed to promote tumorigenesis. However, clinical evidence for the role of oncogene-induced RS in tumorigenesis remains scarce, and the mechanisms by which RS promotes cancer development remain incompletely understood. By performing a series of bioinformatic analyses on the oncogene E2F1, other RS-inducing factors, and replication fork processing factors in TCGA cancer database using previously established tools, we show that hyperactivity of E2F1 likely promotes the expression of several of these factors in virtually all types of cancer to induce RS and cytosolic self-DNA production. In addition, the expression of these factors positively correlates with that of ATR and Chk1 that govern the cellular response to RS, the tumor mutational load, and tumor infiltration of immune-suppressive CD4+Th2 cells and myeloid-derived suppressor cells (MDSCs). Consistently, high expression of these factors is associated with poor patient survival. Our study provides new insights into the role of E2F1-induced RS in tumorigenesis and suggests therapeutic approaches for E2F1-overexpressing cancers by targeting genomic instability, cytosolic self-DNA and the tumor immune microenvironment.
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Affiliation(s)
- Ke Tan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212013, China; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yizhe Song
- McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Tan K, Fang Z, Kong L, Cheng C, Hwang S, Xu M. Pan-cancer analyses reveal GTSE1 as a biomarker for the immunosuppressive tumor microenvironment. Medicine (Baltimore) 2023; 102:e34996. [PMID: 37653815 PMCID: PMC10470696 DOI: 10.1097/md.0000000000034996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 09/02/2023] Open
Abstract
G2 and S phase-expressed-1 (GTSE1) has been reported to be associated with poor prognosis in many cancer types. However, the knowledge of GTSE1 across 33 cancer types remains scarce, and the mechanisms by which GTSE1 promotes cancer development remain incompletely understood. R language and TIMER2.0 were used to analyze the clinical relevance of GTSE1 across > 10,000 subjects representing 33 cancer types based on the cancer genome atlas databases. The expression of GTSE1 was upregulated in almost all cancer types and hyperactivity of GTSE1 is likely to induce DNA repair response and positively correlates with the tumor mutational burden and microsatellite instability which are both promising predictive biomarkers for immunotherapy. GTSE1 was upregulated in TP53 mutation patients. Additionally, GTSE1 also positively correlates with tumor purity and tumor infiltration of immune-suppressive myeloid-derived suppressor cells. Consistently, high expression of GTSE1 is associated with poor patient survival in many cancer types. Conclusion: Our study provides new insights into the diagnostic and prognostic role of GTSE1 in cancers and suggests therapeutic approaches for GTSE1-overexpressing cancers by targeting DNA repair response, and the tumor immune microenvironment.
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Affiliation(s)
- Ke Tan
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Zixuan Fang
- Department of Clinical Medicine, Clinical Medical College of Yangzhou University, Yangzhou, Jiangsu, China
| | - Lingzhen Kong
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO
| | - Chen Cheng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO
| | - Sydney Hwang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
- Digestive Disease Research Institute, Jiangsu University, Zhenjiang, Jiangsu, China
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Gao S, Zhang H, Lai L, Zhang J, Li Y, Miao Z, Rahman SU, Zhang H, Qian A, Zhang W. S100A10 might be a novel prognostic biomarker for head and neck squamous cell carcinoma based on bioinformatics analysis. Comput Biol Med 2022; 149:106000. [DOI: 10.1016/j.compbiomed.2022.106000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/29/2022] [Accepted: 08/14/2022] [Indexed: 12/09/2022]
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Systems Biology and Bioinformatics approach to Identify blood based signatures molecules and drug targets of patient with COVID-19. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100840. [PMID: 34981034 PMCID: PMC8716147 DOI: 10.1016/j.imu.2021.100840] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection results in the development of a highly contagious respiratory ailment known as new coronavirus disease (COVID-19). Despite the fact that the prevalence of COVID-19 continues to rise, it is still unclear how people become infected with SARS-CoV-2 and how patients with COVID-19 become so unwell. Detecting biomarkers for COVID-19 using peripheral blood mononuclear cells (PBMCs) may aid in drug development and treatment. This research aimed to find blood cell transcripts that represent levels of gene expression associated with COVID-19 progression. Through the development of a bioinformatics pipeline, two RNA-Seq transcriptomic datasets and one microarray dataset were studied and discovered 102 significant differentially expressed genes (DEGs) that were shared by three datasets derived from PBMCs. To identify the roles of these DEGs, we discovered disease-gene association networks and signaling pathways, as well as we performed gene ontology (GO) studies and identified hub protein. Identified significant gene ontology and molecular pathways improved our understanding of the pathophysiology of COVID-19, and our identified blood-based hub proteins TPX2, DLGAP5, NCAPG, CCNB1, KIF11, HJURP, AURKB, BUB1B, TTK, and TOP2A could be used for the development of therapeutic intervention. In COVID-19 subjects, we discovered effective putative connections between pathological processes in the transcripts blood cells, suggesting that blood cells could be used to diagnose and monitor the disease’s initiation and progression as well as developing drug therapeutics.
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Lin D, Chen Y, Negi S, Cheng D, Ouyang Z, Sexton D, Li K, Zhang B. CellDepot: A unified repository for scRNA-seq data and visual exploration. J Mol Biol 2021; 434:167425. [PMID: 34971674 DOI: 10.1016/j.jmb.2021.167425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/09/2021] [Accepted: 12/20/2021] [Indexed: 11/29/2022]
Abstract
CellDepot containing over 270 datasets from 8 species and many tissues serves as an integrated web application to empower scientists in exploring single-cell RNA-seq (scRNA-seq) datasets and comparing the datasets among various studies through a user-friendly interface with advanced visualization and analytical capabilities. To begin with, it provides an efficient data management system that users can upload single cell datasets and query the database by multiple attributes such as species and cell types. In addition, the graphical multi-logic, multi-condition query builder and convenient filtering tool backed by MySQL database system, allows users to quickly find the datasets of interest and compare the expression of gene(s) across these. Moreover, by embedding the cellxgene VIP tool, CellDepot enables fast exploration of individual dataset in the manner of interactivity and scalability to gain more refined insights such as cell composition, gene expression profiles, and differentially expressed genes among cell types by leveraging more than 20 frequently applied plotting functions and high-level analysis methods in single cell research. In summary, the web portal available at http://celldepot.bxgenomics.com, prompts large scale single cell data sharing, facilitates meta-analysis and visualization, and encourages scientists to contribute to the single-cell community in a tractable and collaborative way. Finally, CellDepot is released as open-source software under MIT license to motivate crowd contribution, broad adoption, and local deployment for private datasets.
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Affiliation(s)
- Dongdong Lin
- Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
| | - Yirui Chen
- Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
| | - Soumya Negi
- Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
| | - Derrick Cheng
- BioInfoRx, Inc., 510 Charmany Dr, Suite 275A, Madison, WI 53719, USA.
| | - Zhengyu Ouyang
- BioInfoRx, Inc., 510 Charmany Dr, Suite 275A, Madison, WI 53719, USA.
| | - David Sexton
- Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
| | - Kejie Li
- Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
| | - Baohong Zhang
- Research Department, Biogen, Inc., 225 Binney St, Cambridge, MA 02142, USA.
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Huang Z, Li Y, Hong W, Chen X, Pan Y, Weng Y, Liu W, Wang L, Qiu S. Identification of a ferroptosis-associated gene signature and the related therapeutic targets in head and neck squamous carcinoma. Int Immunopharmacol 2021; 102:108431. [PMID: 34906855 DOI: 10.1016/j.intimp.2021.108431] [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: 04/30/2021] [Revised: 11/30/2021] [Accepted: 11/30/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) has a poor prognosis due to its high rates of recurrence and metastasis. Herein, we designed and validated an individualized ferroptosis-associated gene signature (FGS) and further probed the potential survival mechanisms along with therapeutic targets for HNSCC. METHODS The FGS risk score was constructed using stepwise regression analysis and validated in the GSE41613 cohort. Characterization of the tumor microenvironment (TME) in patients with HNSCC, involving immune cells and immunomodulatory genes, was performed to investigate the survival mechanisms and therapeutic targets associated with FGS. To validate the role of FGS in TME, multiplex fluorescent immunohistochemistry (mfIHC) was performed on tissue sections from 55 patients with oral squamous carcinoma. RESULTS The risk score obtained from FGS showed good predictive power as an independent predictor of overall survival. From the tumor immune dysfunction and exclusion (TIDE) prediction, it was found that patients at low risk may benefit from immunotherapy. Furthermore, FGS was significantly associated with CD276, which was highly expressed in fibroblasts that enriched in angiogenesis and epithelial-mesenchymal transition pathways at a single-cell resolution, suggesting CD276 may play a critical mediator of the immunosuppressive microenvironment. Lastly, we identified ATG5 as a critical gene in FGS. And the immune-bioinformatics analysis combined with experimental validation showed a negative correlation between ATG5 expression and CD8 + T cells. CONCLUSION The FGS model provides a novel and effective method to predict the prognosis of patients with HNSCC and their survival can be prolonged through TME-related therapeutic targets.
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Affiliation(s)
- Zongwei Huang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Ying Li
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Wenquan Hong
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Xiaochuan Chen
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Yuhui Pan
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Youliang Weng
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Wei Liu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Lihua Wang
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China
| | - Sufang Qiu
- Department of Radiation Oncology, Fujian Medical University Cancer Hospital, Fujian Cancer Hospital, Fuzhou, China.
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