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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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Xu K, Li D, Qian J, Zhang Y, Zhang M, Zhou H, Hou X, Jiang J, Zhang Z, Sun H, Shi G, Dai H, Liu H. Single-cell disulfidptosis regulator patterns guide intercellular communication of tumor microenvironment that contribute to kidney renal clear cell carcinoma progression and immunotherapy. Front Immunol 2024; 15:1288240. [PMID: 38292868 PMCID: PMC10824999 DOI: 10.3389/fimmu.2024.1288240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 01/03/2024] [Indexed: 02/01/2024] Open
Abstract
Background Disulfidptosis, an emerging type of programmed cell death, plays a pivotal role in various cancer types, notably impacting the progression of kidney renal clear cell carcinoma (KIRC) through the tumor microenvironment (TME). However, the specific involvement of disulfidptosis within the TME remains elusive. Methods Analyzing 41,784 single cells obtained from seven samples of KIRC through single-cell RNA sequencing (scRNA-seq), this study employed nonnegative matrix factorization (NMF) to assess 24 disulfidptosis regulators. Pseudotime analysis, intercellular communication mapping, determination of transcription factor activities (TFs), and metabolic profiling of the TME subgroup in KIRC were conducted using Monocle, CellChat, SCENIC, and scMetabolism. Additionally, public cohorts were utilized to predict prognosis and immune responses within the TME subgroup of KIRC. Results Through NMF clustering and differential expression marker genes, fibroblasts, macrophages, monocytes, T cells, and B cells were categorized into four to six distinct subgroups. Furthermore, this investigation revealed the correlation between disulfidptosis regulatory factors and the biological traits, as well as the pseudotime trajectories of TME subgroups. Notably, disulfidptosis-mediated TME subgroups (DSTN+CD4T-C1 and FLNA+CD4T-C2) demonstrated significant prognostic value and immune responses in patients with KIRC. Multiple immunohistochemistry (mIHC) assays identified marker expression within both cell clusters. Moreover, CellChat analysis unveiled diverse and extensive interactions between disulfidptosis-mediated TME subgroups and tumor epithelial cells, highlighting the TNFSF12-TNFRSF12A ligand-receptor pair as mediators between DSTN+CD4T-C1, FLNA+CD4T-C2, and epithelial cells. Conclusion Our study sheds light on the role of disulfidptosis-mediated intercellular communication in regulating the biological characteristics of the TME. These findings offer valuable insights for patients with KIRC, potentially guiding personalized immunotherapy approaches.
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Affiliation(s)
- Kangjie Xu
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Dongling Li
- Nephrology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Jinke Qian
- Urology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Yanhua Zhang
- Obstetrics and Gynecology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Minglei Zhang
- Oncology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Hai Zhou
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Xuefeng Hou
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Jian Jiang
- Central Laboratory Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Zihang Zhang
- Pathology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Hang Sun
- Urology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Guodong Shi
- Medical Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
| | - Hua Dai
- Yangzhou University Clinical Medical College, Jiangsu Key Laboratory of Experimental & Translational Non-coding RNA Research, Yancheng, Jiangsu, China
| | - Hui Liu
- Urology Department, Binhai County People’s Hospital, Yancheng, Jiangsu, China
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Li H, Dai X, Zhou L, Nie J, Cheng H, Gao P. Ferroptosis-related gene MTF-1 as a novel prognostic biomarker in low-grade glioma and its correlation with immune infiltration. Heliyon 2023; 9:e21159. [PMID: 38027604 PMCID: PMC10643104 DOI: 10.1016/j.heliyon.2023.e21159] [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: 05/31/2023] [Revised: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
Background Metal-responsive transcription factor-1 performs a necessary position in a range of cancers. It is unknown, though, how the prognosis of patients with low-grade gliomas is related to immune infiltration. Method The Cancer Genome Atlas database was used in this investigation to evaluate MTF-1 transcription in low-grade glioma and healthy brain tissues, and immunohistochemistry was used to confirm MTF-1 levels. By using functional enrichment analysis and R software, the putative biological roles and signaling pathways connected to MTF-1 in LGG as well as its prognostic significance were investigated. Further research was done on the connection involving MTF-1 and tumor mutational burden in LGG. Finally, the research evaluated how MTF-1 and immune cell infiltration are related. Results We noticed that the WHO grade, 1p/19q codeletion, and older age were all substantially linked with MTF-1 overexpression in low-grade gliomas. OS and disease-specific survival were significantly lowered as a result of MTF-1 transcription. MTF-1 was recognized as an independent OS prognostic predictor with a poor prognosis by multifactorial Cox analysis. Functional enrichment analysis revealed that the primary enrichment pathways were chemical carcinogenesis-receptor activation and the generation of miRNAs implicated in gene suppression by miRNA. Additionally, there was a negative correlation between MTF-1 overexpression and the degree of immune cell infiltration in neutrophils and DC. Conclusion MTF-1 may be a novel prognostic biomarker.
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Affiliation(s)
- Huaixu Li
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
| | - Xingliang Dai
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
- Department of Research & Development, East China Institute of Digital Medical Engineering, Shangrao, 334000, PR China
| | - Lv Zhou
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
| | - Jianyu Nie
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
| | - Hongwei Cheng
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
| | - Peng Gao
- Department of Neurosurgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, 210002, PR 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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Hao Z, Yin X, Ding R, Chen L, Hao C, Duan H. A novel oncolytic virus-based biomarker participates in prognosis and tumor immune infiltration of glioma. Front Microbiol 2023; 14:1249289. [PMID: 37808305 PMCID: PMC10556503 DOI: 10.3389/fmicb.2023.1249289] [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: 06/28/2023] [Accepted: 09/07/2023] [Indexed: 10/10/2023] Open
Abstract
Background Glioma is the most common central nervous malignancy. Due to its poor survival outcomes, it is essential to identify novel individualized therapy. Oncolytic virus (OV) treatment is a key therapy regulating tumor microenvironment in malignant glioma. Herein, we aim to identify the key genes after OV infection and its role in glioma. Methods Performing an RNA-seq analysis, the differentially expressed genes (DEGs) between EV-A71-infection and mock group were screened with GFold values. DAVID online analysis was performed to identify the functional classification. Overall survival (OS) or disease-free survival (DFS) was evaluated to analyze the relation between PTBP1 expression levels and prognosis of glioma patients. Additionally, the ssGSEA and TIMER algorithms were applied for evaluating immune cell infiltration in glioma. Results Following EV-A71 infection in glioma cells, PTBP1, one of the downregulated DEGs, was found to be associated with multiple categories of GO and KEGG enrichment analysis. We observed elevated expression levels of PTBP1 across various tumor grades of glioma in comparison to normal brain samples. High PTBP1 expression had a notable impact on the OS of patients with low-grade glioma (LGG). Furthermore, we observed an obvious association between PTBP1 levels and immune cell infiltration in LGG. Notably, PTBP1 was regarded as an essential prognostic biomarker in immune cells of LGG. Conclusion Our research uncovered a critical role of PTBP1 in outcomes and immune cell infiltration of glioma patients, particularly in those with LGG.
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Affiliation(s)
- Zheng Hao
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Xiaofeng Yin
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Rui Ding
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Laizhao Chen
- Department of Neurosurgery, Second Hospital of Shanxi Medical University, Taiyuan, China
| | - Chunyan Hao
- Department of Geriatrics, First Hospital of Shanxi Medical University, Taiyuan, China
| | - Hubin Duan
- Department of Neurosurgery, First Hospital of Shanxi Medical University, Taiyuan, China
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Ren J, Xu B, Ren J, Liu Z, Cai L, Zhang X, Wang W, Li S, Jin L, Ding L. The Importance of M1-and M2-Polarized Macrophages in Glioma and as Potential Treatment Targets. Brain Sci 2023; 13:1269. [PMID: 37759870 PMCID: PMC10526262 DOI: 10.3390/brainsci13091269] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/25/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
Glioma is the most common and malignant tumor of the central nervous system. Glioblastoma (GBM) is the most aggressive glioma, with a poor prognosis and no effective treatment because of its high invasiveness, metabolic rate, and heterogeneity. The tumor microenvironment (TME) contains many tumor-associated macrophages (TAMs), which play a critical role in tumor proliferation, invasion, metastasis, and angiogenesis and indirectly promote an immunosuppressive microenvironment. TAM is divided into tumor-suppressive M1-like (classic activation of macrophages) and tumor-supportive M2-like (alternatively activated macrophages) polarized cells. TAMs exhibit an M1-like phenotype in the initial stages of tumor progression, and along with the promotion of lysing tumors and the functions of T cells and NK cells, tumor growth is suppressed, and they rapidly transform into M2-like polarized macrophages, which promote tumor progression. In this review, we discuss the mechanism by which M1- and M2-polarized macrophages promote or inhibit the growth of glioblastoma and indicate the future directions for treatment.
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Affiliation(s)
- Jiangbin Ren
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Bangjie Xu
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Jianghao Ren
- Department of Thoracic Surgery, Shanghai Chest Hospital, Shanghai Jiaotong University, Shanghai 200030, China;
| | - Zhichao Liu
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Lingyu Cai
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Xiaotian Zhang
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Weijie Wang
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Shaoxun Li
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Luhao Jin
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
| | - Lianshu Ding
- Department of neurosurgery, The Affiliated Huaian No. 1 People’s Hospital of Nanjing Medical University, Nanjing Medical University, Huai’an 223000, China; (J.R.); (B.X.); (Z.L.); (L.C.); (X.Z.); (W.W.); (S.L.); (L.J.)
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Nurzat Y, Dai D, Hu J, Zhang F, Lin Z, Huang Y, Gang L, Ji H, Zhang X. Prognostic biomarker CCR6 and its correlation with immune infiltration in cutaneous melanoma. Front Oncol 2023; 13:1162406. [PMID: 37182147 PMCID: PMC10166847 DOI: 10.3389/fonc.2023.1162406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 04/03/2023] [Indexed: 05/16/2023] Open
Abstract
Background Cutaneous melanoma (CM) is an aggressive type of skin cancer. Even after standard treatment, the recurrence and malignant progression of CM were almost inevitable. The overall survival (OS) of patients with CM varied widely, making it critical for prognostic prediction. Based on the correlation between CCR6 and melanoma incidence, we aimed to investigate the prognostic role of CCR6 and its relationship with immune infiltration in CM. Methods We obtained RNA sequencing data from The Cancer Genome Atlas (TCGA) to analyze the CM expression. Functional enrichment analyses, immune infiltration analyses, immune checkpoint analyses, and clinicopathology analyses were performed. Univariate and multivariate Cox regression analyses were used to identify independent prognostic factors. A nomogram model had been developed. Kaplan-Meier survival analysis and log-rank test were used to estimate the relationship between OS and CCR6 expression. Results CCR6 was significantly upregulated in CM. Functional enrichment analyses revealed that CCR6 was correlated with immune response. Most immune cells and immune checkpoints were positively correlated with CCR6 expression. Kaplan-Meier analyses showed that high CCR6 expression was associated with a good outcome in CM and its subtypes. Cox regression showed that CCR6 was an independent prognostic factor in patients with CM (HR = 0.550, 95% CI = 0.332-0.912, p<0.05). Conclusions CCR6 is considered to be a new prognostic biomarker for patients with CM, and our study provides a potential therapeutic target for CM treatment.
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Affiliation(s)
- Yeltai Nurzat
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Damao Dai
- Department of Plastic and Cosmetic Surgery, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Julong Hu
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Feiyu Zhang
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Zaihuan Lin
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yang Huang
- Department of Operating Room, Shenzhen People’s Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, Guangdong, China
| | - Liang Gang
- Department of Plastic Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Hang Ji
- Department of Plastic Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaowen Zhang
- State Key Laboratory of Respiratory Disease, Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
- Department of Allergy and Clinical Immunology, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Department of Cancer, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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Kuang Y, Jiang B, Zhu H, Zhou Y, Huang H, Li C, Zhang W, Li X, Cao Y. Classification related to immunogenic cell death predicts prognosis, immune microenvironment characteristics, and response to immunotherapy in lower-grade gliomas. Front Immunol 2023; 14:1102094. [PMID: 37153540 PMCID: PMC10154552 DOI: 10.3389/fimmu.2023.1102094] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Background Immunogenic cell death (ICD) is a form of cell death that elicits immune responses against the antigens found in dead or dying tumor cells. Growing evidence implies that ICD plays a significant role in triggering antitumor immunity. The prognosis for glioma remains poor despite many biomarkers being reported, and identifying ICD-related biomarkers is imminent for better-personalized management in patients with lower-grade glioma (LGG). Materials and methods We identified ICD-related differentially expressed genes (DEGs) by comparing gene expression profiles obtained across Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA) cohorts. On the foundation of ICD-related DEGs, two ICD-related clusters were identified through consensus clustering. Then, survival analysis, functional enrichment analysis, somatic mutation analysis, and immune characteristics analysis were performed in the two ICD-related subtypes. Additionally, we developed and validated a risk assessment signature for LGG patients. Finally, we selected one gene (EIF2AK3) from the above risk model for experimental validation. Results 32 ICD-related DEGs were screened, dividing the LGG samples from the TCGA database into two distinct subtypes. The ICD-high subgroup showed worse overall survival (OS), greater immune infiltration, more active immune response process, and higher expression levels of HLA genes than the ICD-low subgroup. Additionally, nine ICD-related DEGs were identified to build the prognostic signature, which was highly correlated with the tumor-immune microenvironment and could unambiguously be taken as an independent prognostic factor and further verified in an external dataset. The experimental results indicated that EIF2AK3 expression was higher in tumors than paracancerous tissues, and high-expression EIF2AK3 was enriched in WHO III and IV gliomas by qPCR and IHC, and Knockdown of EIF2AK3 suppressed cell viability and mobility in glioma cells. Conclusion We established novel ICD-related subtypes and risk signature for LGG, which may be beneficial to improving clinical outcome prediction and guiding individualized immunotherapy.
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Affiliation(s)
- Yirui Kuang
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bincan Jiang
- Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - Hecheng Zhu
- Department of Oncology Radiology, Changsha Kexin Cancer Hospital, Changsha, Hunan, China
| | - Yi Zhou
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Haoxuan Huang
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Can Li
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenlong Zhang
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xuewen Li
- Department of Oncology Radiology, Changsha Kexin Cancer Hospital, Changsha, Hunan, China
| | - Yudong Cao
- Department of Neurosurgery, National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
- *Correspondence: Yudong Cao,
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Lu W, Xie B, Tan G, Dai W, Ren J, Pervaz S, Li K, Li F, Wang Y, Wang M. Elafin is related to immune infiltration and could predict the poor prognosis in ovarian cancer. Front Endocrinol (Lausanne) 2023; 14:1088944. [PMID: 36742380 PMCID: PMC9893492 DOI: 10.3389/fendo.2023.1088944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 01/02/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Ovarian cancer (OC) is the most lethal gynecologic malignancy, yet the clinical results for OC patients are still variable. Therefore, we examined how elafin expression affects the patients' prognoses and immunotherapy responses in OC, which may facilitate treatment selection and improve prognosis. METHODS The elafin mRNA expression profile was downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus. Elafin's prognostic potential and its relationship with clinical variables were investigated using Kaplan-Meier survival curves, time-dependent receiver operating characteristic curves as well as univariate and multivariate Cox regression models. As validation, protein expression in the tumor and adjacent tissues of OC patients was investigated by using immunohistochemistry (IHC). Comprehensive analyses were then conducted to explore the correlation between immune infiltration and elafin expression. RESULTS A higher mRNA expression of elafin was associated with an unfavorable prognosis in TCGA cohort and was validated in GSE31245 and IHC. Moreover, elafin was indicated as an independent risk factor for OC. A significantly higher protein expression of elafin was detected in the adjacent tissues of OC patients with shorter overall survival (OS). The immune-related pathways were mainly enriched in the high-elafin-mRNA-expression group. However, the mRNA expression of elafin was favorably correlated with indicators of the immune filtration and immunotherapy response, which also proved better immunotherapy outcomes. CONCLUSION The high elafin expression was associated with an unfavorable OS, while it also indicated better immunotherapy responses. Thus, the detection of elafin is beneficial to diagnosis and treatment selection.
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Affiliation(s)
- Weiyu Lu
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Biao Xie
- Department of Biostatistics, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Guangqing Tan
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Wanying Dai
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Jingyi Ren
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Sadaf Pervaz
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Kun Li
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
| | - Fangfang Li
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Yingxiong Wang
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
| | - Meijiao Wang
- Department of Physiology, School of Basic Medical Science, Chongqing Medical University, Chongqing, China
- Joint International Research Laboratory of Reproduction and Development of the Ministry of Education of China, School of Public Health and Management, Chongqing Medical University, Chongqing, China
- *Correspondence: Meijiao Wang,
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10
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Mao C, Huang C, Hu Z, Qu S. Transcription factor CASZ1 increases an oncogenic transcriptional process in tumorigenesis and progression of glioma cells. MedComm (Beijing) 2022; 3:e182. [PMID: 36276925 PMCID: PMC9583698 DOI: 10.1002/mco2.182] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 09/08/2022] [Accepted: 09/15/2022] [Indexed: 11/28/2022] Open
Abstract
As a transcription factor, the role of CASZ1 in different entities is inconsistent. Glioma is one of the leading causes of cancer death worldwide. Its prognostic relevance and biological functions in glioma remain obscure. We focused on the role, mechanism, and prognostic value of CASZ1 in glioma cells. Herein, CASZ1 was identified as a novel potential oncogene in glioma tissues from GEO and TCGA datasets. CASZ1 was highly expressed in glioma tissues, predicting poor prognosis in glioma patients. Knockdown of CASZ1 inhibited proliferation and invasion in vitro, whereas upregulation of CASZ1 presented opposite results. Overexpression of CASZ1 increased transcriptional process of target gene p75NTR. CASZ1 was the potential transcriptional regulators for p75NTR. In addition, the p75NTR expression is essential for CASZ1 to exert its function as an oncogene. Our findings indicate that highly expressed CASZ1 in glioma cells acts as a pro‐oncogene factor in gliomas via regulating transcriptional process of target gene p75NTR, which was identified as an unfavorable prognostic marker in patients with gliomas. CASZ1 is expected to become a novel target for the treatment of gliomas.
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Affiliation(s)
- Chaofu Mao
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Chengying Huang
- Department of Obstetrics and Gynecology, Baiyun Branch Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
| | - Zhicheng Hu
- Department of Burn Surgery First Affiliated Hospital Sun Yat‐sen University Guangzhou Guangdong People's Republic of China
| | - Shanqiang Qu
- Department of Neurosurgery Nanfang Hospital Southern Medical University Guangzhou Guangdong People's Republic of China
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11
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Jia J, Han Z, Wang X, Zheng X, Wang S, Cui Y. H2B gene family: A prognostic biomarker and correlates with immune infiltration in glioma. Front Oncol 2022; 12:966817. [PMID: 36387186 PMCID: PMC9641242 DOI: 10.3389/fonc.2022.966817] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 09/28/2022] [Indexed: 11/02/2023] Open
Abstract
The current prognosis of glioma is unfavorable and effective treatments remain limited. However, bioinformatics has created new opportunities for improving glioma treatment. Research indicates that H2B is involved in the pathological process of cancer. Thus, this study conducted bioinformatic analyses of the H2B gene family to evaluate whether these genes can play a role in predicting prognosis and are associated with immune infiltration. High expression of H2B genes was observed in cholangiocarcinoma, esophageal carcinoma, glioblastoma multiforme (GBM), head and neck squamous cell carcinoma, and other cancers. In addition, a rise in H2B gene expression was correlated with an increase in glioma grade. In the Cancer Genome Atlas (TCGA), the Chinese Glioma Genome Atlas (CGGA) database and multiple datasets from the Gene Expression Omnibus (GEO), high expression of H2B gene family members predicted poor prognosis of a variety of tumors including glioma. In particular, high H2BC5, H2BC9, H2BC11, and H2BC21 expression was associated with poor glioma prognosis. H2BC9, H2BC11, and H2BC12 expression were also positively correlated with both immune and stromal scores. Enrichment analysis indicated that H2B family genes may be involved in the pathological process of glioma using various pathways including the cell cycle and immune response. H2B-specific siRNAs were used to verify the role of H2BC5, H2BC9, H2BC11, and H2BC21 expression on cell cycle distribution. In summary, H2BC5, H2BC9, H2BC11, and H2BC21 were independent prognostic indicators of glioma, and H2BC9 and H2BC11 may correlate with tumor immunity.
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Affiliation(s)
- Jingnan Jia
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
| | - Zhaocheng Han
- Department of Chinese Medicine, JiRen Hospital of Chinese Medicine, Zhengzhou, China
| | - Xueke Wang
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
| | | | - Shurui Wang
- Department of Encephalopathy, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
| | - Yinglin Cui
- The Second Clinical Medical School, Henan University of Chinese Medicine, Zhengzhou, China
- Department of Encephalopathy, Henan Province Hospital of Traditional Chinese Medicine, Zhengzhou, China
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12
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Xu W, Geng R, Zhao Y, Ma X, Bai Y, Jiang Y, Zhao L, Li Y. Microfibrillar-associated protein 2 is a prognostic marker that correlates with the immune microenvironment in glioma. Front Genet 2022; 13:989521. [PMID: 36204318 PMCID: PMC9531167 DOI: 10.3389/fgene.2022.989521] [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: 07/08/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Aims: microfibrillar-associated protein 2 (MFAP2), a component of the extracellular matrix, plays key roles in regulating growth factor signal transduction and various malignant tumors. However, the clinicopathological features of microfibrillar-associated protein 2 in gliomas have not been elucidated to date. Methods: TCGA and CGGA databases were used to study the expression of microfibrillar-associated protein 2 in glioma and its relationship with clinicopathological features of patients with glioma. Western blotting was performed to detect the expression of microfibrillar-associated protein 2 protein in tissue samples from glioma patients. Gene set enrichment analysis (GSEA) was applied to detect biological processes and signal pathways related to microfibrillar-associated protein 2. Single-sample gene set enrichment analysis, TIMER 2.0, and TISIDB databases were used to evaluate the role of microfibrillar-associated protein 2 in tumor immune characteristics. The prognostic role of microfibrillar-associated protein 2 in glioma was analyzed using the Kaplan-Meier method and Cox regression. Survival data were used to establish a nomogram prediction model. Results: microfibrillar-associated protein 2 expression was significantly elevated in gliomas. receiver operating characteristic analysis revealed good discrimination of microfibrillar-associated protein 2 between glioma and normal tissues. High expression of microfibrillar-associated protein 2 was associated with malignant phenotypes, such as histological type. Based on gene set enrichment analysis, we identified pathways associated with high microfibrillar-associated protein 2 expression. High microfibrillar-associated protein 2 expression was related to the infiltration of tumor immune cells, including Th2 cells and macrophages, and correlated with key markers of T-cell exhaustion. Based on the TISIDB database, microfibrillar-associated protein 2 was observed to be associated with chemokines, chemokine receptors, and multiple immunoinhibitors in glioma. Kaplan–Meier survival analyses revealed that high microfibrillar-associated protein 2 expression predicted poor overall survival, DSS, and PFS in patients with glioma. By combining microfibrillar-associated protein 2 and other prognostic factors, a nomogram prognostic prediction model was constructed, which demonstrated an ideal prediction effect. Conclusion: microfibrillar-associated protein 2 is a potential prognostic marker that plays a key role in glioma development given its association with malignant phenotypes, cancer-related pathways and tumor immunity.
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Affiliation(s)
- Wanzhen Xu
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
| | - Ren Geng
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
| | - Yao Zhao
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
| | - Xiaoshan Ma
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
| | - Yang Bai
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
| | - Yining Jiang
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
| | - Liyan Zhao
- Department of Clinical Laboratory, Second Hospital of Jilin University, Changchun, China
- *Correspondence: Liyan Zhao, ; Yunqian Li,
| | - Yunqian Li
- Department of Neurosurgery, First Hospital of Jilin University, Changchun, China
- *Correspondence: Liyan Zhao, ; Yunqian Li,
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13
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He D, Qin Z, Liu Z, Ji X, Gao J, Guo H, Yang F, Fan H, Wei Y, Wang Z, Liu Q, Pang Q. Comprehensive Analysis of the Prognostic Value and Immune Infiltration of Butyrophilin Subfamily 2/3 (BTN2/3) Members in Pan-Glioma. Front Oncol 2022; 12:816760. [PMID: 36033440 PMCID: PMC9399357 DOI: 10.3389/fonc.2022.816760] [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: 12/08/2021] [Accepted: 04/15/2022] [Indexed: 11/13/2022] Open
Abstract
The BTN2/3 subfamilies are overexpressed in many cancers, including pan-glioma (low- and high-grade gliomas). However, the expression and prognosis of BTN2/3 subfamilies and tumor-infiltrating lymphocytes in pan-glioma remain unknown. In the present study, we systematically explored and validated the expression and prognostic value of BTN2/3 subfamily members in pan-glioma [The Cancer Genome Atlas–glioblastoma and low-grade glioma (TCGA-GBMLGG) merge cohort] using multiple public databases. We used clinical specimens for high-throughput verification and cell lines for qRT-PCR verification, which confirmed the expression profiles of BTN2/3 subfamilies. In addition, the function of the BTN2/3 subfamily members and the correlations between BTN2/3 subfamily expression and pan-glioma immune infiltration levels were investigated. We found that BTN2/3 subfamily members were rarely mutated. BTN2/3 subfamilies were overexpressed in pan-glioma; high expression of BTN2/3 subfamily members was correlated with poor prognosis. In addition, BTN2/3 subfamilies might positively regulate proliferation, and the overexpression of BTN2/3 subfamilies influenced cell cycle, differentiation, and glioma stemness. In terms of immune infiltrating levels, BTN2/3 subfamily expression was positively associated with CD4+ T-cell, B-cell, neutrophil, macrophage, and dendritic cell infiltrating levels. These findings suggest that BTN2/3 subfamily expression is correlated with prognosis and immune infiltration levels in glioma. Therefore, the BTN2/3 subfamilies can be used as biomarkers for pan-glioma and prognostic biomarkers for determining the prognosis and immune infiltration levels in pan-glioma.
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Affiliation(s)
- Dong He
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Zhen Qin
- Department of Clinical Laboratory, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan, China
| | - Zihao Liu
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Xiaoshuai Ji
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Jiajia Gao
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Qianfoshan Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hua Guo
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Fan Yang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Haitao Fan
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yanbang Wei
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Zixiao Wang
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
| | - Qian Liu
- Department of Histology and Embryology, Cheeloo College of Medicine, School of Basic Medical Sciences Shandong University, Jinan, China
- *Correspondence: Qian Liu, ; Qi Pang,
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- *Correspondence: Qian Liu, ; Qi Pang,
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14
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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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15
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Noor H, Zaman A, Teo C, Sughrue ME. PODNL1 Methylation Serves as a Prognostic Biomarker and Associates with Immune Cell Infiltration and Immune Checkpoint Blockade Response in Lower-Grade Glioma. Int J Mol Sci 2021; 22:ijms222212572. [PMID: 34830454 PMCID: PMC8625785 DOI: 10.3390/ijms222212572] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/15/2021] [Accepted: 11/18/2021] [Indexed: 12/27/2022] Open
Abstract
Lower-grade glioma (LGG) is a diffuse infiltrative tumor of the central nervous system, which lacks targeted therapy. We investigated the role of Podocan-like 1 (PODNL1) methylation in LGG clinical outcomes using the TCGA-LGG transcriptomics dataset. We identified four PODNL1 CpG sites, cg07425555, cg26969888, cg18547299, and cg24354933, which were associated with unfavorable overall survival (OS) and disease-free survival (DFS) in univariate and multivariate analysis after adjusting for age, gender, tumor-grade, and IDH1-mutation. In multivariate analysis, the OS and DFS hazard ratios ranged from 0.44 to 0.58 (p < 0.001) and 0.62 to 0.72 (p < 0.001), respectively, for the four PODNL1 CpGs. Enrichment analysis of differential gene and protein expression and analysis of 24 infiltrating immune cell types showed significantly increased infiltration in LGGs and its histological subtypes with low-methylation levels of the PODNL1 CpGs. High PODNL1 expression and low-methylation subgroups of the PODNL1 CpG sites were associated with significantly increased PD-L1, PD-1, and CTLA4 expressions. PODNL1 methylation may thus be a potential indicator of immune checkpoint blockade response, and serve as a biomarker for determining prognosis and immune subtypes in LGG.
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Affiliation(s)
- Humaira Noor
- Cure Brain Cancer Biomarkers and Translational Research Group, Prince of Wales Clinical School, University of New South Wales, Sydney, NSW 2031, Australia
- Adult Cancer Program, Lowy Cancer Research Centre, UNSW Sydney, Randwick, NSW 2031, Australia
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Correspondence:
| | - Ashraf Zaman
- Faculty of Medicine, University of New South Wales, Randwick, NSW 2031, Australia;
- Garvan-Weizmann Centre for Cellular Genomics, Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Charles Teo
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
| | - Michael E. Sughrue
- Centre for Minimally Invasive Neurosurgery, Prince of Wales Private Hospital, Randwick, NSW 2031, Australia; (C.T.); (M.E.S.)
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