1
|
Tataranu LG, Turliuc S, Rizea RE, Dricu A, Alexandru O, Staicu GA, Kamel A. A Synopsis of Biomarkers in Glioblastoma: Past and Present. Curr Issues Mol Biol 2024; 46:6903-6939. [PMID: 39057054 PMCID: PMC11275428 DOI: 10.3390/cimb46070412] [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: 06/05/2024] [Revised: 06/27/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024] Open
Abstract
Accounting for 48% of malignant brain tumors in adults, glioblastoma has been of great interest in the last decades, especially in the biomolecular and neurosurgical fields, due to its incurable nature and notable neurological morbidity. The major advancements in neurosurgical technologies have positively influenced the extent of safe tumoral resection, while the latest progress in the biomolecular field of GBM has uncovered new potential therapeutical targets. Although GBM currently has no curative therapy, recent progress has been made in the management of this disease, both from surgical and molecular perspectives. The main current therapeutic approach is multimodal and consists of neurosurgical intervention, radiotherapy, and chemotherapy, mostly with temozolomide. Although most patients will develop treatment resistance and tumor recurrence after surgical removal, biomolecular advancements regarding GBM have contributed to a better understanding of this pathology and its therapeutic management. Over the past few decades, specific biomarkers have been discovered that have helped predict prognosis and treatment responses and contributed to improvements in survival rates.
Collapse
Affiliation(s)
- Ligia Gabriela Tataranu
- Neurosurgical Department, University of Medicine and Pharmacy “Carol Davila”, 020022 Bucharest, Romania;
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania;
| | - Serban Turliuc
- Medical Department, University of Medicine and Pharmacy “G. T. Popa”, 700115 Iasi, Romania;
| | - Radu Eugen Rizea
- Neurosurgical Department, University of Medicine and Pharmacy “Carol Davila”, 020022 Bucharest, Romania;
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania;
| | - Anica Dricu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania (O.A.); (G.-A.S.)
| | - Oana Alexandru
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania (O.A.); (G.-A.S.)
| | - Georgiana-Adeline Staicu
- Department of Biochemistry, Faculty of Medicine, University of Medicine and Pharmacy, 200349 Craiova, Romania (O.A.); (G.-A.S.)
| | - Amira Kamel
- Neurosurgical Department, Clinical Emergency Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania;
| |
Collapse
|
2
|
Choi BM, Cheong JH, Ryu JI, Won YD, Min KW, Han MH. Significant Genes Associated with Mortality and Disease Progression in Grade II and III Glioma. Biomedicines 2024; 12:858. [PMID: 38672212 PMCID: PMC11048596 DOI: 10.3390/biomedicines12040858] [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: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND The Wnt/β-catenin pathway plays a critical role in the tumorigenesis and maintenance of glioma stem cells. This study aimed to evaluate significant genes associated with the Wnt/β-catenin pathway involved in mortality and disease progression in patients with grade II and III glioma, using the Cancer Genome Atlas (TCGA) database. METHODS We obtained clinicopathological information and mRNA expression data from 515 patients with grade II and III gliomas from the TCGA database. We performed a multivariate Cox regression analysis to identify genes independently associated with glioma prognosis. RESULTS The analysis of 34 genes involved in Wnt/β-catenin signaling demonstrated that four genes (CER1, FRAT1, FSTL1, and RPSA) related to the Wnt/β-catenin pathway were significantly associated with mortality and disease progression in patients with grade II and III glioma. We also identified additional genes related to the four significant genes of the Wnt/β-catenin pathway mentioned above. The higher expression of BMP2, RPL18A, RPL19, and RPS12 is associated with better outcomes in patients with glioma. CONCLUSIONS Using a large-scale open database, we identified significant genes related to the Wnt/β-catenin signaling pathway associated with mortality and disease progression in patients with grade II and III gliomas.
Collapse
Affiliation(s)
- Bo Mi Choi
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| | - Kyueng-Whan Min
- Department of Pathology, Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu 11759, Gyeonggi-do, Republic of Korea
| | - Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri 11923, Gyeonggi-do, Republic of Korea; (B.M.C.); (J.H.C.); (J.I.R.); (Y.D.W.)
| |
Collapse
|
3
|
Cao Q, Wang X, Liu J, Dong Y, Wu X, Mi Y, Liu K, Zhang M, Shi Y, Fan R. ICBP90, an epigenetic regulator, induces DKK3 promoter methylation, promotes glioma progression, and reduces sensitivity to cis-platinum. Exp Cell Res 2024; 436:113976. [PMID: 38401687 DOI: 10.1016/j.yexcr.2024.113976] [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] [Received: 10/25/2023] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 02/26/2024]
Abstract
Glioma is the most common brain malignancy, characterized by high morbidity, high mortality, and treatment-resistance. Inverted CCAAT box Binding Protein of 90 kDa (ICBP90) has been reported to be involved in tumor progression and the maintenance of DNA methylation. Herein, we constructed ICBP90 over-expression and knockdown glioma cell lines, and found that ICBP90 knockdown inhibited glioma cell proliferation, migration, and invasion. ICBP90 silencing potentially enhanced cellular sensitivity to cis-platinum (DDP) and exacerbated DDP-induced pyroptosis, manifested by the elevated levels of gasdermin D-N-terminal and cleaved caspase 1; whereas, ICBP90 over-expression exhibited the opposite effects. Consistently, ICBP90 knockdown inhibited tumor growth in an in vivo mouse xenograft study using U251 cells stably expressing sh-ICBP90 and oe-ICBP90. Further experiments found that ICBP90 reduced the expression of Dickkopf 3 homolog (DKK3), a negative regulator of β-catenin, by binding its promoter and inducing DNA methylation. ICBP90 knockdown prevented the nuclear translocation of β-catenin and suppressed the expression of c-Myc and cyclin D1. Besides, DKK3 over-expression restored the effects of ICBP90 over-expression on cell proliferation, migration, invasion, and DDP sensitivity. Our findings suggest that ICBP90 inhibits the expression of DKK3 in glioma by maintaining DKK3 promoter methylation, thereby conducing to ICBP90-mediated carcinogenesis and drug insensitivity.
Collapse
Affiliation(s)
- Qinchen Cao
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xinxin Wang
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Jie Liu
- Department of Magnetic Resonance Imaging, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yang Dong
- Department of Neurosurgery, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Xiaolong Wu
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yin Mi
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ke Liu
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Mingzhi Zhang
- Department of Medical Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Yonggang Shi
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Ruitai Fan
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China.
| |
Collapse
|
4
|
Ghosh D, Pryor B, Jiang N. Cellular signaling in glioblastoma: A molecular and clinical perspective. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2024; 386:1-47. [PMID: 38782497 DOI: 10.1016/bs.ircmb.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Glioblastoma multiforme (GBM) is the most aggressive brain tumor with an average life expectancy of less than 15 months. Such high patient mortality in GBM is pertaining to the presence of clinical and molecular heterogeneity attributed to various genetic and epigenetic alterations. Such alterations in critically important signaling pathways are attributed to aberrant gene signaling. Different subclasses of GBM show predominance of different genetic alterations and therefore, understanding the complex signaling pathways and their key molecular components in different subclasses of GBM is extremely important with respect to clinical management. In this book chapter, we summarize the common and important signaling pathways that play a significant role in different subclasses and discuss their therapeutic targeting approaches in terms of preclinical studies and clinical trials.
Collapse
Affiliation(s)
- Debarati Ghosh
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States.
| | - Brett Pryor
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Nancy Jiang
- Wellesley College, Wellesley, MA, United States
| |
Collapse
|
5
|
Huang Y, Liu H, Liu B, Chen X, Li D, Xue J, Li N, Zhu L, Yang L, Xiao J, Liu C. Quantified pathway mutations associate epithelial-mesenchymal transition and immune escape with poor prognosis and immunotherapy resistance of head and neck squamous cell carcinoma. BMC Med Genomics 2024; 17:49. [PMID: 38331768 PMCID: PMC10854145 DOI: 10.1186/s12920-024-01818-6] [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: 06/14/2023] [Accepted: 01/23/2024] [Indexed: 02/10/2024] Open
Abstract
BACKGROUND Pathway mutations have been calculated to predict the poor prognosis and immunotherapy resistance in head and neck squamous cell carcinoma (HNSCC). To uncover the unique markers predicting prognosis and immune therapy response, the accurate quantification of pathway mutations are required to evaluate epithelial-mesenchymal transition (EMT) and immune escape. Yet, there is a lack of score to accurately quantify pathway mutations. MATERIAL AND METHODS Firstly, we proposed Individualized Weighted Hallmark Gene Set Mutation Burden (IWHMB, https://github.com/YuHongHuang-lab/IWHMB ) which integrated pathway structure information and eliminated the interference of global Tumor Mutation Burden to accurately quantify pathway mutations. Subsequently, to further elucidate the association of IWHMB with EMT and immune escape, support vector machine regression model was used to identify IWHMB-related transcriptomic features (IRG), while Adversarially Regularized Graph Autoencoder (ARVGA) was used to further resolve IRG network features. Finally, Random walk with restart algorithm was used to identify biomarkers for predicting ICI response. RESULTS We quantified the HNSCC pathway mutation signatures and identified pathway mutation subtypes using IWHMB. The IWHMB-related transcriptomic features (IRG) identified by support vector machine regression were divided into 5 communities by ARVGA, among which the Community 1 enriching malignant mesenchymal components promoted EMT dynamically and regulated immune patterns associated with ICI responses. Bridge Hub Gene (BHG) identified by random walk with restart was key to IWHMB in EMT and immune escape, thus, more predictive for ICI response than other 70 public signatures. CONCLUSION In summary, the novel pathway mutation scoring-IWHMB suggested that the elevated malignancy mediated by pathway mutations is a major cause of poor prognosis and immunotherapy failure in HNSCC, and is capable of identifying novel biomarkers to predict immunotherapy response.
Collapse
Affiliation(s)
- Yuhong Huang
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Han Liu
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Bo Liu
- Institute for Genome Engineered Animal Models of Human Diseases, Dalian Medical University, Dalian, China
| | - Xiaoyan Chen
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Danya Li
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Junyuan Xue
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Nan Li
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Lei Zhu
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China
| | - Liu Yang
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China
| | - Jing Xiao
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China.
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China.
| | - Chao Liu
- Department of Oral Pathology, Dalian Medical University School of Stomatology, Dalian, China.
- Academician Laboratory of Immunology and Oral Development & Regeneration, Dalian Medical University, Dalian, China.
| |
Collapse
|
6
|
Mourtada J, Thibaudeau C, Wasylyk B, Jung AC. The Multifaceted Role of Human Dickkopf-3 (DKK-3) in Development, Immune Modulation and Cancer. Cells 2023; 13:75. [PMID: 38201279 PMCID: PMC10778571 DOI: 10.3390/cells13010075] [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] [Received: 11/14/2023] [Revised: 12/22/2023] [Accepted: 12/26/2023] [Indexed: 01/12/2024] Open
Abstract
The human Dickkopf (DKK) family includes four main secreted proteins, DKK-1, DKK-2, DKK-3, and DKK-4, as well as the DKK-3 related protein soggy (Sgy-1 or DKKL1). These glycoproteins play crucial roles in various biological processes, and especially modulation of the Wnt signaling pathway. DKK-3 is distinct, with its multifaceted roles in development, stem cell differentiation and tissue homeostasis. Intriguingly, DKK-3 appears to have immunomodulatory functions and a complex role in cancer, acting as either a tumor suppressor or an oncogene, depending on the context. DKK-3 is a promising diagnostic and therapeutic target that can be modulated by epigenetic reactivation, gene therapy and DKK-3-blocking agents. However, further research is needed to optimize DKK-3-based therapies. In this review, we comprehensively describe the known functions of DKK-3 and highlight the importance of context in understanding and exploiting its roles in health and disease.
Collapse
Affiliation(s)
- Jana Mourtada
- Laboratoire de Biologie Tumorale, Institut de Cancérologie Strasbourg Europe, 67200 Strasbourg, France; (J.M.); (C.T.)
- Laboratoire STREINTH (Stress Response and Innovative Therapies), INSERM U1113 IRFAC, Université de Strasbourg, 67200 Strasbourg, France
| | - Chloé Thibaudeau
- Laboratoire de Biologie Tumorale, Institut de Cancérologie Strasbourg Europe, 67200 Strasbourg, France; (J.M.); (C.T.)
- Laboratoire STREINTH (Stress Response and Innovative Therapies), INSERM U1113 IRFAC, Université de Strasbourg, 67200 Strasbourg, France
| | - Bohdan Wasylyk
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), 67404 Illkirch Graffenstaden, France;
- Institut National de la Santé et de la Recherche Médicale (INSERM), U 1258, 67404 Illkirch Graffenstaden, France
- Centre Nationale de la Recherche Scientifique (CNRS), UMR 7104, 67404 Illkirch Graffenstaden, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Alain C. Jung
- Laboratoire de Biologie Tumorale, Institut de Cancérologie Strasbourg Europe, 67200 Strasbourg, France; (J.M.); (C.T.)
- Laboratoire STREINTH (Stress Response and Innovative Therapies), INSERM U1113 IRFAC, Université de Strasbourg, 67200 Strasbourg, France
| |
Collapse
|
7
|
Yoon HG, Cheong JH, Ryu JI, Won YD, Min KW, Han MH. The genes significantly associated with an improved prognosis and long-term survival of glioblastoma. PLoS One 2023; 18:e0295061. [PMID: 38019838 PMCID: PMC10686432 DOI: 10.1371/journal.pone.0295061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Accepted: 11/14/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND AND PURPOSE Glioblastoma multiforme (GBM) is the most devastating brain tumor with less than 5% of patients surviving 5 years following diagnosis. Many studies have focused on the genetics of GBM with the aim of improving the prognosis of GBM patients. We investigated specific genes whose expressions are significantly related to both the length of the overall survival and the progression-free survival in patients with GBM. METHODS We obtained data for 12,042 gene mRNA expressions in 525 GBM tissues from the Cancer Genome Atlas (TCGA) database. Among those genes, we identified independent genes significantly associated with the prognosis of GBM. Receiver operating characteristic (ROC) curve analysis was performed to determine the genes significant for predicting the long-term survival of patients with GBM. Bioinformatics analysis was also performed for the significant genes. RESULTS We identified 33 independent genes whose expressions were significantly associated with the prognosis of 525 patients with GBM. Among them, the expressions of five genes were independently associated with an improved prognosis of GBM, and the expressions of 28 genes were independently related to a poorer prognosis of GBM. The expressions of the ADAM22, ATP5C1, RAC3, SHANK1, AEBP1, C1RL, CHL1, CHST2, EFEMP2, and PGCP genes were either positively or negatively related to the long-term survival of GBM patients. CONCLUSIONS Using a large-scale and open database, we found genes significantly associated with both the prognosis and long-term survival of patients with GBM. We believe that our findings may contribute to improving the understanding of the mechanisms underlying GBM.
Collapse
Affiliation(s)
- Hong Gyu Yoon
- Department of Neurosurgery, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Kyueng-Whan Min
- Department of Pathology Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu, Gyeonggi-do, Republic of Korea
| | - Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| |
Collapse
|
8
|
Han MH, Baek JM, Min KW, Cheong JH, Ryu JI, Won YD, Kwon MJ, Koh SH. DKK3 expression is associated with immunosuppression and poor prognosis in glioblastoma, in contrast to lower-grade gliomas. BMC Neurol 2023; 23:183. [PMID: 37149563 PMCID: PMC10163766 DOI: 10.1186/s12883-023-03236-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/30/2023] [Indexed: 05/08/2023] Open
Abstract
PURPOSE We previously reported that expression of dickkopf-3 (DKK3), which is involved in the Wnt/β-catenin pathway, is significantly associated with prognosis in patients with glioblastoma multiforme (GBM). The aim of this study was to compare the association of DKK3 with other Wnt/β-catenin pathway-related genes and immune responses between lower grade glioma (LGG) and GBM. METHODS We obtained the clinicopathological data of 515 patients with LGG (World Health Organization [WHO] grade II and III glioma) and 525 patients with GBM from the Cancer Genome Atlas (TCGA) database. We performed Pearson's correlation analysis to investigate the relationships between Wnt/β-catenin-related gene expression in LGG and GBM. Linear regression analysis was performed to identify the association between DKK3 expression and immune cell fractions in all grade II to IV gliomas. RESULTS A total of 1,040 patients with WHO grade II to IV gliomas were included in the study. As the grade of glioma increased, DKK3 showed a tendency to be more strongly positively correlated with the expression of other Wnt/β-catenin pathway-related genes. DKK3 was not associated with immunosuppression in LGG but was associated with downregulation of immune responses in GBM. We hypothesized that the role of DKK3 in the Wnt/β-catenin pathway might be different between LGG and GBM. CONCLUSION According to our findings, DKK3 expression had a weak effect on LGG but a significant effect on immunosuppression and poor prognosis in GBM. Therefore, DKK3 expression seems to play different roles, through the Wnt/β-catenin pathway, between LGG and GBM.
Collapse
Affiliation(s)
- Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Jeong Min Baek
- Department of Translational Medicine, Graduate School of Biomedical Science & Engineering, Hanyang University, Hanyang University, Seoul, South Korea
| | - Kyueng-Whan Min
- Department of Pathology Uijeongbu Eulji Medical Center, Eulji University School of Medicine, Uijeongbu, Gyeonggi-do, Republic of Korea.
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, Gyeonggi-do, Republic of Korea
| | - Mi Jung Kwon
- Department of Pathology, Hallym University Sacred Heart Hospital, Hallym University College of Medicine, Anyang, Gyeonggi-do, Republic of Korea
| | - Seong-Ho Koh
- Department of Neurology, Hanyang University Guri Hospital, 11923 Gyeongchun-ro, Guri-Si, Gyeonggi-do, Republic of Korea.
| |
Collapse
|
9
|
Xu Q, Wang C, Yin G. Immune-related gene signature to predict TACE refractoriness in patients with hepatocellular carcinoma based on artificial neural network. Front Genet 2023; 13:993509. [PMID: 36685822 PMCID: PMC9846524 DOI: 10.3389/fgene.2022.993509] [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: 07/13/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
Background: Transarterial chemoembolization (TACE) is the standard treatment option for intermediate-stage hepatocellular carcinoma (HCC), while response varies among patients. This study aimed to identify novel immune-related genes (IRGs) and establish a prediction model for TACE refractoriness in HCC patients based on machine learning methods. Methods: Gene expression data were downloaded from GSE104580 dataset of Gene Expression Omnibus (GEO) database, differential analysis was first performed to screen differentially expressed genes (DEGs). The least absolute shrinkage and selection operator (LASSO) regression analysis was performed to further select significant DEGs. Weighted gene co-expression network analysis (WGCNA) was utilized to build a gene co-expression network and filter the hub genes. Final signature genes were determined by the intersection of LASSO analysis results, WGCNA results and IRGs list. Based on the above results, the artificial neural network (ANN) model was constructed in the training cohort and verified in the validation cohort. Receiver operating characteristics (ROC) analysis was used to assess the prediction accuracy. Correlation of signature genes with tumor microenvironment scores, immune cells and immune checkpoint molecules were further analyzed. The tumor immune dysfunction and exclusion (TIDE) score was used to evaluate the response to immunotherapy. Results: One hundred and forty-seven samples were included in this study, which was randomly divided into the training cohort (n = 103) and validation cohort (n = 44). In total, 224 genes were identified as DEGs. Further LASSO regression analysis screened out 25 genes from all DEGs. Through the intersection of LASSO results, WGCNA results and IRGs list, S100A9, TREM1, COLEC12, and IFIT1 were integrated to construct the ANN model. The areas under the curves (AUCs) of the model were .887 in training cohort and .765 in validation cohort. The four IRGs also correlated with tumor microenvironment scores, infiltrated immune cells and immune checkpoint genes in various degrees. Patients with TACE-Response, lower expression of COLEC12, S100A9, TREM1 and higher expression of IFIT1 had better response to immunotherapy. Conclusion: This study constructed and validated an IRG signature to predict the refractoriness to TACE in patients with HCC, which may have the potential to provide insights into the TACE refractoriness in HCC and become the immunotherapeutic targets for HCC patients with TACE refractoriness.
Collapse
|
10
|
Al Shareef Z, Ershaid MNA, Mudhafar R, Soliman SSM, Kypta RM. Dickkopf-3: An Update on a Potential Regulator of the Tumor Microenvironment. Cancers (Basel) 2022; 14:cancers14235822. [PMID: 36497305 PMCID: PMC9738550 DOI: 10.3390/cancers14235822] [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: 09/12/2022] [Revised: 11/10/2022] [Accepted: 11/16/2022] [Indexed: 11/29/2022] Open
Abstract
Dickkopf-3 (Dkk-3) is a member of the Dickkopf family protein of secreted Wingless-related integration site (Wnt) antagonists that appears to modulate regulators of the host microenvironment. In contrast to the clear anti-tumorigenic effects of Dkk-3-based gene therapies, the role of endogenous Dkk-3 in cancer is context-dependent, with elevated expression associated with tumor promotion and suppression in different settings. The receptors and effectors that mediate the diverse effects of Dkk-3 have not been characterized in detail, contributing to an ongoing mystery of its mechanism of action. This review compares the various functions of Dkk-3 in the tumor microenvironment, where Dkk-3 has been found to be expressed by subpopulations of fibroblasts, endothelial, and immune cells, in addition to epithelial cells. We also discuss how the activation or inhibition of Dkk-3, depending on tumor type and context, might be used to treat different types of cancers.
Collapse
Affiliation(s)
- Zainab Al Shareef
- College of Medicine, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- Correspondence: ; Tel.: +971-6505-7250
| | - Mai Nidal Asad Ershaid
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Rula Mudhafar
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Sameh S. M. Soliman
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
- College of Pharmacy, University of Sharjah, Sharjah P.O. Box 27272, United Arab Emirates
| | - Robert M. Kypta
- CIC BioGUNE, Basque Research and Technology Alliance, BRTA, Bizkaia Technology Park, 48160 Derio, Spain
- Department of Surgery and Cancer, Imperial College London, London W12 0NN, UK
| |
Collapse
|
11
|
Han MH, Min KW, Noh YK, Kim JM, Cheong JH, Ryu JI, Won YD, Koh SH, Park YM. Identification of genes from ten oncogenic pathways associated with mortality and disease progression in glioblastoma. Front Oncol 2022; 12:965638. [PMID: 36033456 PMCID: PMC9399757 DOI: 10.3389/fonc.2022.965638] [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: 06/09/2022] [Accepted: 07/20/2022] [Indexed: 11/28/2022] Open
Abstract
Glioblastoma multiforme (GBM) is the most malignant brain tumor with an extremely poor prognosis. The Cancer Genome Atlas (TCGA) database has been used to confirm the roles played by 10 canonical oncogenic signaling pathways in various cancers. The purpose of this study was to evaluate the expression of genes in these 10 canonical oncogenic signaling pathways, which are significantly related to mortality and disease progression in GBM patients. Clinicopathological information and mRNA expression data of 525 patients with GBM were obtained from TCGA database. Gene sets related to the 10 oncogenic signaling pathways were investigated via Gene Set Enrichment Analysis. Multivariate Cox regression analysis was performed for all the genes significantly associated with mortality and disease progression for each oncogenic signaling pathway in GBM patients. We found 12 independent genes from the 10 oncogenic signaling pathways that were significantly related to mortality and disease progression in GBM patients. Considering the roles of these 12 significant genes in cancer, we suggest possible mechanisms affecting the prognosis of GBM. We also observed that the expression of 6 of the genes significantly associated with a poor prognosis of GBM, showed negative correlations with CD8+ T-cells in GBM tissue. Using a large-scale open database, we identified 12 genes belonging to 10 well-known oncogenic canonical pathways, which were significantly associated with mortality and disease progression in patients with GBM. We believe that our findings will contribute to a better understanding of the mechanisms underlying the pathophysiology of GBM in the future.
Collapse
Affiliation(s)
- Myung-Hoon Han
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Kyueng-Whan Min
- Department of Pathology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
- *Correspondence: Kyueng-Whan Min, ; Yung-Kyun Noh,
| | - Yung-Kyun Noh
- Department of Computer Science, Hanyang University, Seoul, South Korea
- School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea
- *Correspondence: Kyueng-Whan Min, ; Yung-Kyun Noh,
| | - Jae Min Kim
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Jin Hwan Cheong
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Je Il Ryu
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Yu Deok Won
- Department of Neurosurgery, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Seong-Ho Koh
- Department of Neurology, Hanyang University Guri Hospital, Hanyang University College of Medicine, Guri, South Korea
| | - Young Mi Park
- Department of Pediatrics, Gangneung Asan Hospital, Ulsan University College of Medicine, Gangneung-si, South Korea
| |
Collapse
|