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Vieira FG, Bispo R, Lopes MB. Integration of Multi-Omics Data for the Classification of Glioma Types and Identification of Novel Biomarkers. Bioinform Biol Insights 2024; 18:11779322241249563. [PMID: 38812741 PMCID: PMC11135104 DOI: 10.1177/11779322241249563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 04/09/2024] [Indexed: 05/31/2024] Open
Abstract
Glioma is currently one of the most prevalent types of primary brain cancer. Given its high level of heterogeneity along with the complex biological molecular markers, many efforts have been made to accurately classify the type of glioma in each patient, which, in turn, is critical to improve early diagnosis and increase survival. Nonetheless, as a result of the fast-growing technological advances in high-throughput sequencing and evolving molecular understanding of glioma biology, its classification has been recently subject to significant alterations. In this study, we integrate multiple glioma omics modalities (including mRNA, DNA methylation, and miRNA) from The Cancer Genome Atlas (TCGA), while using the revised glioma reclassified labels, with a supervised method based on sparse canonical correlation analysis (DIABLO) to discriminate between glioma types. We were able to find a set of highly correlated features distinguishing glioblastoma from lower-grade gliomas (LGGs) that were mainly associated with the disruption of receptor tyrosine kinases signaling pathways and extracellular matrix organization and remodeling. Concurrently, the discrimination of the LGG types was characterized primarily by features involved in ubiquitination and DNA transcription processes. Furthermore, we could identify several novel glioma biomarkers likely helpful in both diagnosis and prognosis of the patients, including the genes PPP1R8, GPBP1L1, KIAA1614, C14orf23, CCDC77, BVES, EXD3, CD300A, and HEPN1. Collectively, this comprehensive approach not only allowed a highly accurate discrimination of the different TCGA glioma patients but also presented a step forward in advancing our comprehension of the underlying molecular mechanisms driving glioma heterogeneity. Ultimately, our study also revealed novel candidate biomarkers that might constitute potential therapeutic targets, marking a significant stride toward personalized and more effective treatment strategies for patients with glioma.
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Affiliation(s)
- Francisca G Vieira
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
| | - Regina Bispo
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Department of Mathematics, NOVA School of Science and Technology, Caparica, Portugal
| | - Marta B Lopes
- Center for Mathematics and Applications (NOVA Math), NOVA School of Science and Technology, Caparica, Portugal
- Department of Mathematics, NOVA School of Science and Technology, Caparica, Portugal
- UNIDEMI, Department of Mechanical and Industrial Engineering, NOVA School of Science and Technology, Caparica, Portugal
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Song QH, Zhao KX, Huang S, Chen T, He L. Escape from X-chromosome inactivation and sex differences in Alzheimer's disease. Rev Neurosci 2024; 35:341-354. [PMID: 38157427 DOI: 10.1515/revneuro-2023-0108] [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: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 01/03/2024]
Abstract
Sex differences exist in the onset and progression of Alzheimer's disease. Globally, women have a higher prevalence, while men with Alzheimer's disease experience earlier mortality and more pronounced cognitive decline than women. The cause of sex differences in Alzheimer's disease remains unclear. Accumulating evidence suggests the potential role of X-linked genetic factors in the sex difference of Alzheimer's disease (AD). During embryogenesis, a remarkable process known as X-chromosome inactivation (XCI) occurs in females, leading to one of the X chromosomes undergoing transcriptional inactivation, which balances the effects of two X chromosomes in females. Nevertheless, certain genes exceptionally escape from XCI, which provides a basis for dual expression dosage of specific genes in females. Based on recent research findings, we explore key escape genes and their potential therapeutic use associated with Alzheimer's disease. Also, we discuss their possible role in driving the sex differences in Alzheimer's disease. This will provide new perspectives for precision medicine and gender-specific treatment of AD.
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Affiliation(s)
- Qing-Hua Song
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ke-Xuan Zhao
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Shuai Huang
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Tong Chen
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
| | - Ling He
- Department of Pharmacology, China Pharmaceutical University, No. 24 Tong Jia Xiang, Nanjing 210009, Jiangsu Province, China
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Song Z, Zhao Z, Zhu S, Jin Q, Zhang S, Wang Z, Shen B, Wang Z, Zhao Z. Arylsulfatase D is a prognostic biomarker that promotes glioma cells progression through JAK2/STAT3 pathway and M2 macrophage infiltration. Front Oncol 2023; 13:1228426. [PMID: 37766864 PMCID: PMC10521731 DOI: 10.3389/fonc.2023.1228426] [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: 05/24/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Background Arylsulfatase D (ARSD) belongs to the sulfatase family and plays a crucial role in maintaining the proper structure of bone and cartilage matrix. Although several researches have revealed the functions of ARSD in tumor progression, the prognostic value of ARSD in glioma and the related mechanisms have not been fully investigated. Methods We performed a pan-cancer analysis of ARSD, and investigated the relationship between expression of ARSD and overall survival (OS) in multiple glioma datasets. ROC curves and nomograms were created to investigate the predictive capacity of ARSD. Immune and analysis were conducted to investigate the mechanisms underlying the roles of ARSD in glioma. Glioma tissue samples were collected to verify the expression of ARSD in glioma, while the functions of ARSD were explored using cell experiment. M2 macrophage infiltration assay was used to determine the relation between ARSD and tumor immune microenvironment. Results Survival analysis indicated that individuals with high ARSD expression in glioma had a shorter survival time. Cox analysis showed that ARSD had a good ability for predicting prognosis in glioma. Immune analysis suggested that ARSD could regulate immune cell infiltration and affect the Cancer-Immunity Cycle to create an immunosuppressive environment. Combined with cell experiment and bioinformatic analysis, we found that ARSD can promote glioma progression through regulation of JAK2/STAT3 pathway and M2 macrophage infiltration. Conclusion Our study found that ARSD can promote glioma development by regulating immune microenvironment and JAK2/STAT3 signaling pathway, which provided a potential therapy target for glioma treatment.
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Affiliation(s)
- Zihan Song
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zijun Zhao
- Spine Center, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Siyu Zhu
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Qianxu Jin
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Shiyang Zhang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zairan Wang
- Department of Neurosurgery, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bowei Shen
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zijian Wang
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
| | - Zongmao Zhao
- Department of Neurosurgery, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
- Department of Neurosurgery, The Fourth Hospital of Hebei Medical University, Shijiazhuang, Hebei, China
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Shang D, Lan T, Wang Y, Li X, Liu Q, Dong H, Xu B, Cheng H, Zhou R. PGCLCs of human 45,XO reveal pathogenetic pathways of neurocognitive and psychosocial disorders. Cell Biosci 2022; 12:194. [DOI: 10.1186/s13578-022-00925-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 11/03/2022] [Indexed: 12/03/2022] Open
Abstract
Abstract
Background
Neurocognitive disorders and psychosocial difficulties are common in patients with Turner syndrome and multiple neurodegenerative diseases, yet there is no effective cure. Human primordial germ cells (hPGCs) are pluripotent germline stem cells in early embryo, which pass genetic information from one generation to the next, whereas all somatic cells will die along with the end of life. However, it is not known whether patient hPGCs with Turner syndrome contain information of neurocognitive and psychosocial illness.
Results
In this report, we used a high-density of culture system of embryoids derived from iPSCs of a patient with Turner syndrome to ask how pathogenetic pathways are associated with onset of neurocognitive and psychosocial disorders. The hPGC-Like Cells (hPGCLCs) were in vitro specified from iPSCs of 45,XO, 46,XX and 46,XY by the high-density induction of embryoids. Amazingly, we found that the specification process of the hPGCLCs in 45,XO, compared to those in 46,XX and 46,XY, enriched several common pathogenetic pathways regulating neurocognitive and psychosocial disorders, that shared among multiple neurodegenerative diseases and Turner syndrome. The downregulated chemical synaptic transmission pathways, including glutamatergic, GABAergic, and nicotine cholinergic synapses, indicated synaptic dysfunctions, while upregulated pathways that were associated with imbalance of mitochondrial respiratory chain complexes and apoptosis, may contribute to neuronal dysfunctions. Notably, downregulation of three types of ubiquitin ligases E1-E2-E3 and lysosome-associated sulfatases and RAB9A, owing to haploinsufficiency and parental preference of the X chromosome expression, indicated that two pathways of cellular degradation, lysosome and ubiquitin–proteasome, were impaired in the specification process of 45,XO hPGCLCs. This would lead to accumulation of undesired proteins and aggregates, which is a typically pathological hallmark in neurodegenerative diseases.
Conclusions
Our data suggest that the specification process of the hPGCLCs in 45,XO, compared to those in 46,XX and 46,XY, enriched pathogenetic pathways that are associated with the onset of neurocognitive and psychosocial disorders.
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