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Du Z, Jiang Y, Yang Y, Kang X, Yan J, Liu B, Yang M. A multi-omics analysis-based model to predict the prognosis of low-grade gliomas. Sci Rep 2024; 14:9427. [PMID: 38658591 PMCID: PMC11043340 DOI: 10.1038/s41598-024-58434-8] [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: 08/04/2023] [Accepted: 03/29/2024] [Indexed: 04/26/2024] Open
Abstract
Lower-grade gliomas (LGGs) exhibit highly variable clinical behaviors, while classic histology characteristics cannot accurately reflect the authentic biological behaviors, clinical outcomes, and prognosis of LGGs. In this study, we carried out analyses of whole exome sequencing, RNA sequencing and DNA methylation in primary vs. recurrent LGG samples, and also combined the multi-omics data to construct a prognostic prediction model. TCGA-LGG dataset was searched for LGG samples. 523 samples were used for whole exome sequencing analysis, 532 for transcriptional analysis, and 529 for DNA methylation analysis. LASSO regression was used to screen genes with significant association with LGG survival from the frequently mutated genes, differentially expressed genes, and differentially methylated genes, whereby a prediction model for prognosis of LGG was further constructed and validated. The most frequently mutated diver genes in LGGs were IDH1 (77%), TP53 (48%), ATRX (37%), etc. Top significantly up-regulated genes were C6orf15, DAO, MEOX2, etc., and top significantly down-regulated genes were DMBX1, GPR50, HMX2, etc. 2077 genes were more and 299 were less methylated in recurrent vs. primary LGG samples. Thirty-nine genes from the above analysis were included to establish a prediction model of survival, which showed that the high-score group had a very significantly shorter survival than the low-score group in both training and testing sets. ROC analysis showed that AUC was 0.817 for the training set and 0.819 for the testing set. This study will be beneficial to accurately predict the survival of LGGs to identify patients with poor prognosis to take specific treatment as early, which will help improve the treatment outcomes and prognosis of LGG.
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Affiliation(s)
- Zhijie Du
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Yuehui Jiang
- Nanjing Drum Tower Hospital Clinical College of Nanjing University of Chinese Medicine, Nanjing, China
| | - Yueling Yang
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xiaoyu Kang
- Nanjing Hospital of Chinese Medicine Affiliated to Nanjing University of Chinese Medicine, Nanjing, China
| | - Jing Yan
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Baorui Liu
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China
| | - Mi Yang
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, Nanjing Drum Tower Hospital Clinical College of Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
- The Comprehensive Cancer Centre of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.
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Zhu L, Yuan F, Wang X, Zhu R, Guo W. Cuproptosis-related gene-located DNA methylation in lower-grade glioma: Prognosis and tumor microenvironment. Cancer Biomark 2024; 40:185-198. [PMID: 38578883 DOI: 10.3233/cbm-230341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
Cuproptosis a novel copper-dependent cell death modality, plays a crucial part in the oncogenesis, progression and prognosis of tumors. However, the relationships among DNA-methylation located in cuproptosis-related genes (CRGs), overall survival (OS) and the tumor microenvironment remain undefined. In this study, we systematically assessed the prognostic value of CRG-located DNA-methylation for lower-grade glioma (LGG). Clinical and molecular data were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We employed Cox hazard regression to examine the associations between CRG-located DNA-methylation and OS, leading to the development of a prognostic signature. Kaplan-Meier survival and time-dependent receiver operating characteristic (ROC) analyses were utilized to gauge the accuracy of the signature. Gene Set Enrichment Analysis (GSEA) was applied to uncover potential biological functions of differentially expressed genes between high- and low-risk groups. A three CRG-located DNA-methylation prognostic signature was established based on TCGA database and validated in GEO dataset. The 1-year, 3-year, and 5-year area under the curve (AUC) of ROC curves in the TCGA dataset were 0.884, 0.888, and 0.859 while those in the GEO dataset were 0.943, 0.761 and 0.725, respectively. Cox-regression-analyses revealed the risk signature as an independent risk factor for LGG patients. Immunogenomic profiling suggested that the signature was associated with immune infiltration level and immune checkpoints. Functional enrichment analysis indicated differential enrichment in cell differentiation in the hindbrain, ECM receptor interactions, glycolysis and reactive oxygen species pathway across different groups. We developed and verified a novel CRG-located DNA-methylation signature to predict the prognosis in LGG patients. Our findings emphasize the potential clinical implications of CRG-located DNA-methylation indicating that it may serve as a promising therapeutic target for LGG patients.
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Affiliation(s)
- Liucun Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Fa Yuan
- School of Life Sciences, Shanghai University, Shanghai, China
- School of Life Sciences, Shanghai University, Shanghai, China
| | - Xue Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Rui Zhu
- School of Life Sciences, Shanghai University, Shanghai, China
- Department of Clinical Laboratory Medicine, Shanghai Tenth People's Hospital of Tongji University, Shanghai, China
| | - Wenna Guo
- School of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
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Bilgen N, Çınar Kul B, Akkurt MY, Bakıcı C, Buckley RM, Lyons LA, Coghill LM, Çıldır ÖŞ, Kutlu F. Cardiomyopathy associated 5 ( CMYA5) implicated as a genetic risk factor for radial hemimelia in Siamese cats. J Feline Med Surg 2023; 25:1098612X231193557. [PMID: 37791865 PMCID: PMC10812016 DOI: 10.1177/1098612x231193557] [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] [Indexed: 10/05/2023]
Abstract
OBJECTIVES The present study aimed to determine the inheritance pattern and genetic cause of congenital radial hemimelia (RH) in cats. METHODS Clinical and genetic analyses were conducted on a Siamese cat family (n = 18), including two siblings with RH. Radiographs were obtained for the affected kittens and echocardiograms of an affected kitten and sire. Whole genome sequencing was completed on the two cases and the parents. Genomic data were compared with the 99 Lives Cat Genome data set of 420 additional domestic cats with whole genome and whole exome sequencing data. Variants were considered as homozygous in the two cases of the siblings with RH and heterozygous in the parents. Candidate variants were genotyped by Sanger sequencing in the extended pedigree. RESULTS Radiographs of the female kitten revealed bilateral absence of the radii and bowing of the humeri, while the male kitten showed a dysplastic right radius. Echocardiography suggested the female kitten had restrictive cardiomyopathy with a positive left atrial-to-aortic root ratio (LA:Ao = 1.83 cm), whereas hypertrophic cardiomyopathy was more likely in the sire, showing diastolic dysfunction using tissue Doppler imaging (59.06 cm/s). Twenty-two DNA variants were unique and homozygous in the affected kittens and heterozygous in the parents. Seven variants clustered in one chromosomal region, including two frameshift variants in cardiomyopathy associated 5 (CMYA5) and five variants in junction mediating and regulatory protein, P53 cofactor (JMY ), including a missense and an in-frame deletion. CONCLUSIONS AND RELEVANCE The present study suggested an autosomal recessive mode of inheritance with variable expression for RH in the Siamese cat family. Candidate variants for the phenotype were identified, implicating their roles in bone development. These genes should be considered as potentially causal for other cats with RH. Siamese cat breeders should consider genetically testing their cats for these variants to prevent further dissemination of the suspected variants within the breed.
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Affiliation(s)
- Nüket Bilgen
- Faculty of Veterinary Medicine, Department of Genetics, Ankara University, Ankara, Türkiye
| | - Bengi Çınar Kul
- Faculty of Veterinary Medicine, Department of Genetics, Ankara University, Ankara, Türkiye
| | - Mustafa Yenal Akkurt
- Faculty of Veterinary Medicine, Department of Genetics, Ankara University, Ankara, Türkiye
| | - Caner Bakıcı
- Faculty of Veterinary Medicine, Department of Anatomy, Ankara University, Ankara, Türkiye
| | - Reuben M Buckley
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Leslie A Lyons
- Department of Veterinary Medicine and Surgery, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Lyndon M Coghill
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO, USA
| | - Özge Şebnem Çıldır
- Faculty of Veterinary Medicine, Department of Genetics, Kafkas University, Kars, Türkiye
| | - Furkan Kutlu
- Faculty of Veterinary Medicine, Department of Genetics, Ankara University, Ankara, Türkiye
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Li J, Wang S, He Q, Lin F, Tao C, Ding Y, Wang J, Zhao J, Wang W. High ECM2 Expression Predicts Poor Clinical Outcome and Promotes the Proliferation, Migration, and Invasiveness of Glioma. Brain Sci 2023; 13:851. [PMID: 37371331 DOI: 10.3390/brainsci13060851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/04/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
OBJECTIVE Glioma is the most prevalent and fatal intracranial malignant tumor. Extracellular matrix protein 2 (ECM2) has rarely been studied in gliomas. Therefore, we explored the role of ECM2 in lower-grade gliomas (LGGs). METHODS The RNA-seq and clinicopathology data were obtained from the TCGA database. The immunohistochemical (IHC) staining was used to verify the expression of ECM2. Functional enrichment analyses, immune-related analyses, drug sensitivity, and mutation profile analyses were further conducted. Cox regression and Kaplan-Meier curves were utilized for survival analyses, while four external datasets were used to validate the prognostic role of ECM2. Furthermore, qRT-PCR, CCK-8, wound healing, and transwell assays were performed to confirm the function of ECM2 in gliomas. RESULTS The study found a significant upregulation of ECM2 expression with increasing glioma grades and a significant association between ECM2 expression and tumor immune infiltration. Cox regression verified the prognostic role of ECM2 in LGG patients (HR = 1.656, 95%CI = 1.055-2.600, p = 0.028). High ECM2 expression was significantly associated with poor outcome (p < 0.001). Four external datasets validated its prognostic value. After the knockdown of ECM2, the functional experiments showed a significant decrease in proliferation, migration, and invasion in glioma cell lines. CONCLUSION The study suggested the potential of ECM2 as a novel immune-associated prognostic biomarker and therapeutic target for glioma patients.
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Affiliation(s)
- Junsheng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing 100070, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing 100070, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing 100070, China
| | - Siyu Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Qiheng He
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing 100070, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing 100070, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing 100070, China
| | - Fa Lin
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing 100070, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing 100070, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing 100070, China
| | - Chuming Tao
- Department of Neurosurgery, Second Affiliated Hospital of Soochow University, Suzhou 215004, China
| | - Yaowei Ding
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
| | - Jia Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing 100070, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing 100070, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing 100070, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing 100070, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing 100070, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing 100070, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing 101408, China
| | - Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing 100070, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing 100070, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing 100070, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing 100070, China
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Deng L, Zeng S, Yi Q, Song L. High expression of six-transmembrane epithelial antigen of prostate 3 promotes the migration and invasion and predicts unfavorable prognosis in glioma. PeerJ 2023; 11:e15136. [PMID: 37009153 PMCID: PMC10065001 DOI: 10.7717/peerj.15136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023] Open
Abstract
Recent studies have suggested that ferroptosis, a form of iron-dependent regulated cell death, might play essential roles in tumor initiation and progression. Six-transmembrane epithelial antigen of prostate 3 (STEAP3) is a ferrireductase involved in the regulation of intracellular iron homeostasis. However, the clinical significance and biological function of STEAP3 in human cancers remain poorly understood. Through a comprehensive bioinformatics analysis, we found that STEAP3 mRNA and protein expression were up-regulated in GBM, LUAD, and UCEC, and down-regulated in LIHC. Survival analysis indicated that STEAP3 had prognostic significance only in glioma. Multivariate Cox regression analysis revealed that high STEPA3 expression was correlated with poor prognosis. STEAP3 expression was significantly negatively correlated with promoter methylation level, and patients with lower STEAP3 methylation level had worse prognosis than those with higher STEAP3 methylation level. Single-cell functional state atlas showed that STEAP3 regulated epithelial-to-mesenchymal transition (EMT) in GBM. Furthermore, the results of wound healing and transwell invasion assays demonstrated that knocking down STEAP3 inhibited the migration and invasion of T98G and U251 cells. Functional enrichment analysis suggested that genes co-expressed with STEAP3 mainly participated in inflammation and immune-related pathways. Immunological analysis revealed that STEAP3 expression was significantly correlated with immune infiltration cells, including macrophages and neutrophils, especially the M2 macrophages. Individuals with low STEAP3 expression were more likely to respond to immunotherapy than those with high STEAP3 expression. These results suggest that STEAP3 promotes glioma progression and highlight its pivotal role in regulating immune microenvironment.
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Affiliation(s)
- Langmei Deng
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Shuangshuang Zeng
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiaoli Yi
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Liying Song
- Department of Pharmacy, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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Ozair A, Bhat V, Alisch RS, Khosla AA, Kotecha RR, Odia Y, McDermott MW, Ahluwalia MS. DNA Methylation and Histone Modification in Low-Grade Gliomas: Current Understanding and Potential Clinical Targets. Cancers (Basel) 2023; 15:cancers15041342. [PMID: 36831683 PMCID: PMC9954183 DOI: 10.3390/cancers15041342] [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: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/14/2023] [Indexed: 02/22/2023] Open
Abstract
Gliomas, the most common type of malignant primary brain tumor, were conventionally classified through WHO Grades I-IV (now 1-4), with low-grade gliomas being entities belonging to Grades 1 or 2. While the focus of the WHO Classification for Central Nervous System (CNS) tumors had historically been on histopathological attributes, the recently released fifth edition of the classification (WHO CNS5) characterizes brain tumors, including gliomas, using an integration of histological and molecular features, including their epigenetic changes such as histone methylation, DNA methylation, and histone acetylation, which are increasingly being used for the classification of low-grade gliomas. This review describes the current understanding of the role of DNA methylation, demethylation, and histone modification in pathogenesis, clinical behavior, and outcomes of brain tumors, in particular of low-grade gliomas. The review also highlights potential diagnostic and/or therapeutic targets in associated cellular biomolecules, structures, and processes. Targeting of MGMT promoter methylation, TET-hTDG-BER pathway, association of G-CIMP with key gene mutations, PARP inhibition, IDH and 2-HG-associated processes, TERT mutation and ARL9-associated pathways, DNA Methyltransferase (DNMT) inhibition, Histone Deacetylase (HDAC) inhibition, BET inhibition, CpG site DNA methylation signatures, along with others, present exciting avenues for translational research. This review also summarizes the current clinical trial landscape associated with the therapeutic utility of epigenetics in low-grade gliomas. Much of the evidence currently remains restricted to preclinical studies, warranting further investigation to demonstrate true clinical utility.
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Affiliation(s)
- Ahmad Ozair
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Faculty of Medicine, King George’s Medical University, Lucknow 226003, India
| | - Vivek Bhat
- St. John’s Medical College, Bangalore 560034, India
| | - Reid S. Alisch
- Department of Neurosurgery, University of Wisconsin-Madison, Madison, WI 53792, USA
| | - Atulya A. Khosla
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
| | - Rupesh R. Kotecha
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Yazmin Odia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
| | - Michael W. McDermott
- Herbert Wertheim College of Medicine, Florida International University, Miami, FL 33199, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
| | - Manmeet S. Ahluwalia
- Miami Cancer Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Miami Neuroscience Institute, Baptist Health South Florida, Miami, FL 33176, USA
- Correspondence: (M.W.M.); (M.S.A.)
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Gu S, Shu L, Zhou L, Wang Y, Xue H, Jin L, Xia Z, Dai X, Gao P, Cheng H. Interfering with CALCRL expression inhibits glioma proliferation, promotes apoptosis, and predicts prognosis in low-grade gliomas. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:1277. [PMID: 36618798 PMCID: PMC9816851 DOI: 10.21037/atm-22-5154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022]
Abstract
Background CALCRL is involved in a variety of key biological processes, including cell proliferation, apoptosis, angiogenesis, and inflammation. However, the role of CALCRL in glioma remains unknown. The purpose of this study was to investigate the effect of differential CALCRL expression on the malignant progression of glioma and its value in glioma prognosis. Methods Sequencing data from glioma and normal tissues were downloaded from The Cancer Genome Atlas (TCGA) and Genotype-Tissue Expression (GTEx) databases, and the downloaded data were statistically analyzed using bioinformatics tools and the corresponding R package. The expression of CALCRL in normal brain tissue and different grades of glioma tissue was detected by pathological and immunohistochemical staining of clinical glioma specimens. The expression of CALCRL in different glioma cell lines was detected by quantitative real-time polymerase chain reaction (qRT-PCR), and the U87 cell line with high expression was selected to construct the CALCRL knockdown model by transfection with short hairpin (shRNA). The cell proliferation ability was detected by Celigo assay and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, the ability of cell clone formation was detected by clone formation assay, and the level of apoptosis was detected by flow cytometry. Results The expression of CALCRL in glioma was significantly upregulated compared with that of normal tissue, especially in low-grade glioma (LGG) compared to glioblastoma, and the differential expression of CALCRL correlated significantly with the prognosis of LGG. Clinical pathology and immunohistochemistry showed that the expression of CALCRL was related to the pathological grade of glioma, and the highest expression was found in World Health Organization (WHO) grade Ⅲ glioma. The results of qRT-PCR showed that CALCRL expression was highest in the U87 cell line. After knockdown of CALCRL expression, the proliferation and clonogenic ability of U87 cells were significantly decreased, and the apoptosis rate was significantly increased. Conclusions CALCRL is highly expressed in LGG. Interfering with CALCRL expression inhibits glioma cell proliferation and promotes apoptosis, and thus has potential as a biomarker and therapeutic target for the prognosis of those with LGGs.
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Affiliation(s)
- Shengcai Gu
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Lei Shu
- Department of Clinical Medicine, the First Clinical College of Anhui Medical University, Hefei, China
| | - Lv Zhou
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuxin Wang
- Department of Clinical Medicine, the First Clinical College of Anhui Medical University, Hefei, China
| | - Hanying Xue
- Department of Clinical Medicine, the First Clinical College of Anhui Medical University, Hefei, China
| | - Lan Jin
- Department of Clinical Medicine, the First Clinical College of Anhui Medical University, Hefei, China
| | - Zhiyu Xia
- Department of Clinical Medicine, the First Clinical College of Anhui Medical University, Hefei, China
| | - Xingliang Dai
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peng Gao
- Department of Neurosurgery, Affiliated Jinling Hospital, Medical School of Nanjing University, Nanjing, China
| | - Hongwei Cheng
- Department of Neurosurgery, the First Affiliated Hospital of Anhui Medical University, Hefei, China
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Li J, Wang J, Liu D, Tao C, Zhao J, Wang W. Establishment and validation of a novel prognostic model for lower-grade glioma based on senescence-related genes. Front Immunol 2022; 13:1018942. [PMID: 36341390 PMCID: PMC9633681 DOI: 10.3389/fimmu.2022.1018942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/07/2022] [Indexed: 01/10/2023] Open
Abstract
Objective Increasing studies have indicated that senescence was associated with tumorigenesis and progression. Lower-grade glioma (LGG) presented a less invasive nature, however, its treatment efficacy and prognosis prediction remained challenging due to the intrinsic heterogeneity. Therefore, we established a senescence-related signature and investigated its prognostic role in LGGs. Methods The gene expression data and clinicopathologic features were from The Cancer Genome Atlas (TCGA) database. The experimentally validated senescence genes (SnGs) from the CellAge database were obtained. Then LASSO regression has been performed to build a prognostic model. Cox regression and Kaplan-Meier survival curves were performed to investigate the prognostic value of the SnG-risk score. A nomogram model has been constructed for outcome prediction. Immunological analyses were further performed. Data from the Chinese Glioma Genome Atlas (CGGA), Repository of Molecular Brain Neoplasia Data (REMBRANDT), and GSE16011 were used for validation. Results The 6-SnG signature has been established. The results showed SnG-risk score could be considered as an independent predictor for LGG patients (HR=2.763, 95%CI=1.660-4.599, P<0.001). The high SnG-risk score indicated a worse outcome in LGG (P<0.001). Immune analysis showed a positive correlation between the SnG-risk score and immune infiltration level, and the expression of immune checkpoints. The CGGA datasets confirmed the prognostic role of the SnG-risk score. And Kaplan-Meier analyses in the additional datasets (CGGA, REMBRANDT, and GSE16011) validated the prognostic role of the SnG-signature (P<0.001 for all). Conclusion The SnG-related prognostic model could predict the survival of LGG accurately. This study proposed a novel indicator for predicting the prognosis of LGG and provided potential therapeutic targets.
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Affiliation(s)
- Junsheng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Jia Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Dongjing Liu
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Chuming Tao
- Department of Neurosurgery, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
- Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, China
- *Correspondence: Wen Wang, ; Jizong Zhao,
| | - Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China
- Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China
- Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
- *Correspondence: Wen Wang, ; Jizong Zhao,
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Li J, Wang J, Ding Y, Zhao J, Wang W. Prognostic biomarker SGSM1 and its correlation with immune infiltration in gliomas. BMC Cancer 2022; 22:466. [PMID: 35484511 PMCID: PMC9047296 DOI: 10.1186/s12885-022-09548-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/15/2022] [Indexed: 11/30/2022] Open
Abstract
Objective Glioma was the most common type of intracranial malignant tumor. Even after standard treatment, the recurrence and malignant progression of lower-grade gliomas (LGGs) were almost inevitable. The overall survival (OS) of patients with LGG varied widely, making it critical for prognostic prediction. Small G Protein Signaling Modulator 1 (SGSM1) has hardly been studied in gliomas. Therefore, we aimed to investigate the prognostic role of SGSM1 and its relationship with immune infiltration in LGGs. Methods We obtained RNA sequencing data from The Cancer Genome Atlas (TCGA) to analyze SGSM1 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. And nomogram model has been developed. Kaplan–Meier survival analysis and log-rank test were used to estimate the relationship between OS and SGSM1 expression. The survival analyses and Cox regression were validated in datasets from the Chinese Glioma Genome Atlas (CGGA). Results SGSM1 was significantly down-regulated in LGGs. Functional enrichment analyses revealed SGSM1 was correlated with immune response. Most immune cells and immune checkpoints were negatively correlated with SGSM1 expression. The Kaplan–Meier analyses showed that low SGSM1 expression was associated with a poor outcome in LGG and its subtypes. The Cox regression showed SGSM1 was an independent prognostic factor in patients with LGG (HR = 0.494, 95%CI = 0.311–0.784, P = 0.003). Conclusion SGSM1 was considered to be a new prognostic biomarker for patients with LGG. And our study provided a potential therapeutic target for LGG treatment.
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Affiliation(s)
- Junsheng Li
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Road 119, Fengtai District, Beijing, 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China.,Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Jia Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Road 119, Fengtai District, Beijing, 100070, China.,China National Clinical Research Center for Neurological Diseases, Beijing, China.,Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China.,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China.,Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China
| | - Yaowei Ding
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jizong Zhao
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Road 119, Fengtai District, Beijing, 100070, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China. .,Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China. .,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China. .,Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China. .,Savaid Medical School, University of the Chinese Academy of Sciences, Beijing, China.
| | - Wen Wang
- Department of Neurosurgery, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Road 119, Fengtai District, Beijing, 100070, China. .,China National Clinical Research Center for Neurological Diseases, Beijing, China. .,Center of Stroke, Beijing Institute for Brain Disorders, Beijing, China. .,Beijing Key Laboratory of Translational Medicine for Cerebrovascular Disease, Beijing, China. .,Beijing Translational Engineering Center for 3D Printer in Clinical Neuroscience, Beijing, China.
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