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Xu C, Li F, Liu Z, Yan C, Xiao J. Pan-cancer analysis of the prognostic and immunological role of SNX29: a potential target for survival and immunotherapy. BMC Med Genomics 2023; 16:34. [PMID: 36829159 PMCID: PMC9951530 DOI: 10.1186/s12920-023-01466-2] [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: 07/25/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND There is growing evidence that the SNX family is critical for clinical prognosis, immune infiltration and drug sensitivity in many types of tumors. The relationships between the SNX29 gene and clinical prognosis as well as pan-cancer cell infiltration and drug sensitivity have not been fully elucidated. METHODS In the current study, we explored the correlation between SNX29 expression and 33 types of malignancies via TCGA and GTEx. The relationship between SNX29 expression and prognostic outcome in the pan-caner cohort was also analyzed. Immune infiltration, microsatellite instability, tumor mutational burden and potential therapeutic targets of SNX29 were investigated by analyzing public databases. RESULTS The expression of SNX29 was found to be significantly upregulated in most tumor tissues compared to normal tissues. SNX29 expression was associated with prognosis and clinical stage. In the immune infiltration analysis, a significant relationship was found between SNX29 expression and the level of immune infiltration. In addition, we found associations between the SNX29 gene and tumor mutation burden, microsatellite instability, immunoinhibition-related genes and autophagy-related genes. Finally, the expression of SNX29 was significantly associated with the sensitivity of various tumor cell lines to 8 antitumor drugs. These results suggest that SNX29 expression is important in determining the progression, immune infiltration and drug sensitivity of various cancers. CONCLUSION This study provides novel insights into the potential pan-cancer targets of SNX29.
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Affiliation(s)
- Chengfei Xu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China.,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Fanghan Li
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Zilin Liu
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China.,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China
| | - Chuanjing Yan
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.
| | - Jiangwei Xiao
- Department of Gastrointestinal Surgery, Clinical Medical College and The First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,School of Clinical Medicine, Chengdu Medical College, Chengdu, 610500, People's Republic of China. .,First Affiliated Hospital of Chengdu Medical College, Chengdu, 610500, People's Republic of China.
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Ren W, Yang S, Chen X, Guo J, Zhao H, Yang R, Nie Z, Ding L, Zhang L. NCAPG2 Is a Novel Prognostic Biomarker and Promotes Cancer Stem Cell Maintenance in Low-Grade Glioma. Front Oncol 2022; 12:918606. [PMID: 35898895 PMCID: PMC9309203 DOI: 10.3389/fonc.2022.918606] [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: 04/12/2022] [Accepted: 06/15/2022] [Indexed: 11/13/2022] Open
Abstract
Gliomas account for 75% of all primary malignant brain tumors in adults and are associated with high mortality. Mounting evidence has shown that NCAPG2 is differentially expressed in various cancers. However, the prognostic value and immune functions of NCAPG2 in low-grade glioma (LGG) remain unresolved. In the present study, we revealed that NCAPG2 was up-regulated in LGG, and its higher expression was associated with adverse clinical outcomes and poor clinical characteristics, including WHO grade, IDH mutation, 1p/19q codeletion, and primary therapy outcome. The results of the Cox regression analysis revealed that NCAPG2 was an independent factor for the prognosis of low-grade glioma. Meanwhile, we also established a nomogram based on NCAPG2 to predict the 1-, 3-, or 5-year survival in LGG patients. Furthermore, we found that Copy number variation (CNV) and DNA hypomethylation results in its overexpression in LGG. In addition, functional annotation confirmed that NCAPG2 was mainly involved in the immune regulation and WNT signaling pathways. Finally, we determined that increased expression of NCAPG2 was correlated with infiltration levels of various immune cells and immune checkpoint in LGG. Importantly, we found that NCAPG2 was highly expressed in glioma stem cells lines and knockdown of NCAPG2 significantly inhibited the self-renewal ability of GSC. This is the first study to identify NCAPG2 as a new potential prognostic biomarker and characterize the functional roles of NCAPG2 in the progression of LGG, and provides a novel potential diagnostic and therapeutic biomarker for LGG in the future.
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Affiliation(s)
- Wenjun Ren
- Department of Cardiovascular Surgery, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Shu Yang
- Department of Neurology, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Xi Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Jishu Guo
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Heng Zhao
- Department of Neurology, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Ruihan Yang
- Department of Neurology, The First People’s Hospital of Yunnan Province, Kunming, China
| | - Zhi Nie
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Li Ding
- Department of Neurology, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Lei Zhang, ; Li Ding,
| | - Lei Zhang
- Department of Neurology, The First People’s Hospital of Yunnan Province, Kunming, China
- *Correspondence: Lei Zhang, ; Li Ding,
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Chen X, Jiang X, Wang H, Wang C, Wang C, Pan C, Zhou F, Tian J, Niu X, Nie Z, Chen W, Huang X, Pu J, Li C. DNA methylation-regulated SNX20 overexpression correlates with poor prognosis, immune cell infiltration, and low-grade glioma progression. Aging (Albany NY) 2022; 14:5211-5222. [PMID: 35771139 PMCID: PMC9271302 DOI: 10.18632/aging.204144] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 06/14/2022] [Indexed: 12/22/2022]
Abstract
We revealed that SNX20 was up-regulated in LGG, and its higher expression was associated with adverse clinical outcomes and poor clinical characteristics, including WHO grade, IDH mutation, 1p/19q codeletion, and primary therapy outcome. The results of the Cox regression analysis revealed that SNX20 was an independent factor for the prognosis of low-grade glioma. Meanwhile, we also established a nomogram based on SNX20 to predict the 1-, 3-, or 5-year survival in LGG patients. Furthermore, we found that DNA hypomethylation results in its overexpression in LGG. In addition, functional annotation confirmed that SNX20 was mainly involved in the immune response and inflammatory response related signaling pathways, including the T cell receptor signaling pathway, natural killer cell-mediated cytotoxicity, and the NF-kappa B signaling pathway. Finally, we determined that increased expression of SNX20 was correlated with infiltration levels of various immune cells and immune checkpoint in LGG. Importantly, we found that SNX20 was highly expressed in glioma cell lines. Depletion of SNX20 significantly inhibits glioma cell proliferation and migration abilities. This is the first study to identify SNX20 as a new potential prognostic biomarker and characterize the functional roles of SNX20 in the progression of LGG, and provides a novel potential diagnostic and therapeutic biomarker for LGG in the future.
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Affiliation(s)
- Xi Chen
- Department of Neurosurgery, The second Affiliated Hospital of Kunming Medical University, Kunming 650223, China
| | - Xiulin Jiang
- Key Laboratory of Animal Models and Human Disease Mechanisms of Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Kunming 650223, Yunnan, China
| | - Heping Wang
- Department of Neurosurgery, The second Affiliated Hospital of Kunming Medical University, Kunming 650223, China
| | - Chunyan Wang
- Department of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Chenyang Wang
- Department of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Chenglong Pan
- Department of Pathology, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Fan Zhou
- Hematology and Rheumatology Department, The Pu'er People's Hospital, Pu'er 665000, China
| | - Jintao Tian
- Department of Neurosurgery, The second Affiliated Hospital of Kunming Medical University, Kunming 650223, China
| | - Xiaoqun Niu
- Department of Respiratory Medicine, The 2nd Affiliated Hospital of Kunming Medical University, Kunming, Yunnan Province, China
| | - Zhi Nie
- Department of Neurology, First Affiliated Hospital of Kunming Medical University, Kunming 650032, Yunnan, China
| | - Wei Chen
- Hematology and Rheumatology Department, The Pu'er People's Hospital, Pu'er 665000, China
| | - Xiaobin Huang
- Department of Neurosurgery, The second Affiliated Hospital of Kunming Medical University, Kunming 650223, China
| | - Jun Pu
- Department of Neurosurgery, The second Affiliated Hospital of Kunming Medical University, Kunming 650223, China
| | - Chen Li
- Department of Biology, Chemistry, Pharmacy, Free University of Berlin, Berlin 14195, Germany
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Wu GJ, Ren K, He M, Xu JX, Li ZQ, Bo D, Xue Q. SNX20 Expression Correlates with Immune Cell Infiltration and Can Predict Prognosis in Lung Adenocarcinoma. Int J Gen Med 2021; 14:7599-7611. [PMID: 34764676 PMCID: PMC8575493 DOI: 10.2147/ijgm.s337198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/20/2021] [Indexed: 11/28/2022] Open
Abstract
Background Sorting nexin-20 (SNX20) is a member of the sorting nexin family of proteins. It plays a crucial role in the regulation of innate immunity. However, the prognostic risk, potential mechanisms, immunotherapy, and other functions of SNX20 in lung adenocarcinoma (LUAD) remain unclear. Methods We analyzed and validated the expression and prognostic role of SNX20 in LUAD through a combination of The Cancer Genome Atlas, Gene Expression Omnibus, Oncomine, TIMER, and Human Protein Atlas databases. Further, we analyzed the correlation between SNX20 expression and clinical characteristics of LUAD, and the prognostic value of SNX20 in LUAD was evaluated. Using fitted SNX20 expression and other clinical parameters, a predictive model with predictive performance for the overall survival of patients with LUAD was constructed. The potential biological function of SNX20 in LUAD was explored using gene set enrichment analysis. In addition, we analyzed the correlation between SNX20 expression and the immune microenvironment and survival. Results SNX20 was downregulated in most cancer types, was associated with poor prognosis in LUAD and could be an independent prognostic factor for patients with LUAD. The predictive model developed by us had good predictive power for determining the overall survival of patients with LUAD. Biofunctional analysis revealed that genes co-expressed with SNX20 mainly promoted the immune process and inhibited the cell proliferation process in LUAD. We observed that high expression of SNX20 was accompanied by a better immune microenvironment and survival in patients with LUAD. Furthermore, the LUAD immune response was elevated with an increase in SNX20 expression. Finally, we found that SNX20 expression was significantly associated with various tumor-infiltrating immune cells, and it was widely involved in regulating various immune molecules in LUAD and affecting immune infiltration in the tumor microenvironment. Conclusion Our results suggested that SNX20 is a potential immune-related biomarker and therapeutic target associated with the prognosis of patients with LUAD. This provided a new strategy for the development of immunotherapeutic and prognostic markers in LUAD.
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Affiliation(s)
- Gu Jie Wu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.,Medical College of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Kuan Ren
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.,Medical College of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Min He
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.,Medical College of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Jian Xun Xu
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.,Medical College of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Zhen Qing Li
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.,Medical College of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Ding Bo
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China.,Medical College of Nantong University, Nantong, 226001, Jiangsu, People's Republic of China
| | - Qun Xue
- Department of Thoracic Surgery, Affiliated Hospital of Nantong University, Nantong, 226001, Jiangsu Province, People's Republic of China
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Xia F, Yu Z, Deng A, Gao G. Identification of molecular subtyping system and four-gene prognostic signature with immune-related genes for uveal melanoma. Exp Biol Med (Maywood) 2021; 247:246-262. [PMID: 34743576 DOI: 10.1177/15353702211053801] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Immunotherapy is the most promising treatment for uveal melanoma patients with metastasis. Tumor microenvironment plays an essential role in tumor progression and greatly affects the efficacy of immunotherapy. This research constructed an immune-related subtyping system and discovered immune prognostic genes to further understand the immune mechanism in uveal melanoma. Immune-related genes were determined from literature. Gene expression profiles of uveal melanoma were clustered using consensus clustering based on immune-related genes. Subtypes were further divided by applying immune landscape, and weighted correlation network analysis was performed to construct immune gene modules. Univariate Cox regression analysis was conducted to generate a prognostic model. Enriched immune cells were determined after gene set enrichment analysis. Three major immune subtypes (IS1, IS2, and IS3) were identified, and IS2 could be further divided into IS2A and IS2B. The subtypes were closely associated with uveal melanoma prognosis. IS3 group had the most favorable prognosis and was sensitive to PD-1 inhibitor. Immune genes in IS1 group showed an overall higher expression than IS3 group. Six immune gene modules were identified, and the enrichment score of immune genes varied within immune subtypes. Four immune prognostic genes (IL32, IRF1, SNX20, and VAV1) were found to be closely related to survival. This novel immune subtyping system and immune landscape provide a new understanding of immunotherapy in uveal melanoma. The four prognostic genes can predict prognosis of uveal melanoma patients and contribute to new development of targeted drugs.
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Affiliation(s)
- Fei Xia
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Clinical Medical Institute, Weifang Medical University, Weifang 261000, China
| | - Zhilong Yu
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Clinical Medical Institute, Weifang Medical University, Weifang 261000, China
| | - Aijun Deng
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Clinical Medical Institute, Weifang Medical University, Weifang 261000, China
| | - Guohong Gao
- Department of Ophthalmology, Affiliated Hospital of Weifang Medical University, Clinical Medical Institute, Weifang Medical University, Weifang 261000, China
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6
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Yuan Y, Jiang X, Tang L, Wang J, Liu Q, Zou X, Duan L. SNX20AR/MiRNA-301a-3p/SNX20 Axis Associated With Cell Proliferation and Immune Infiltration in Lung Adenocarcinoma. Front Mol Biosci 2021; 8:744363. [PMID: 34604311 PMCID: PMC8484765 DOI: 10.3389/fmolb.2021.744363] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/08/2021] [Indexed: 12/23/2022] Open
Abstract
Lung cancer is the most common tumor with severe morbidity and high mortality. Increasing evidence has demonstrated that SNX20 plays crucial roles in the progression of human cancer. However, the functions and mechanism of SNX20 in LUAD are still barely known. Here, we employ the TCGA, GEO and CCLE databases to examine the expression of SNX20 in human varies cancer, the results shown that SNX20 is down-regulated in lung Adenocarcinoma, SNX20 level was significantly positive correlated with poor prognosis and lung cancer immune cell infiltration. We found that over-expression of SNX20 significantly restrain NSCLC cell proliferation and migration. Subsequently, we discover a network regulating SNX20 in LUAD, further study found that the decreased of the SNX20 likely caused by DNA hypermethylation. Furthermore, we identified that SNX20AR/miRNA-301a-3p mediated decreased of SNX20 correlated with lung cancer progression and cancer immune infiltration in LUAD. Our findings suggested that ncRNAs play a crucial role in the regulatory network of SNX20. Collectively, our findings demonstrate the suppressor roles of the SNX20AR/miRNA-301a-3p/SNX20 axis in Lung Adenocarcinoma, represent that SNX20 have the potential of as an effective therapeutic target in future.
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Affiliation(s)
- Yixiao Yuan
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiulin Jiang
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Lin Tang
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Juan Wang
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Qianqian Liu
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Xiaolan Zou
- Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Lincan Duan
- Department of Graduate School of Kunming Medical University, Kunming, China.,Department of Thoracic Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
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