1
|
Huang Z, Huang J, Lin Y, Deng Y, Yang L, Zhang X, Huang H, Sun Q, Liu H, Liang H, Lv Z, He B, Hu F. Construction and validation of a TAMRGs prognostic signature for gliomas by integrated analysis of scRNA and bulk RNA sequencing data. Brain Res 2024; 1846:149237. [PMID: 39270996 DOI: 10.1016/j.brainres.2024.149237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 09/06/2024] [Accepted: 09/10/2024] [Indexed: 09/15/2024]
Abstract
BACKGROUND This study aimed to construct and validate a prognostic model based on tumor associated macrophage-related genes (TAMRGs) by integrating single-cell RNA sequencing (scRNA-seq) and bulk RNA sequencing (bulk RNA-seq) data. METHODS The scRNA-seq data of three inhouse glioma tissues were used to identify the tumor-associated macrophages (TAMs) marker genes, the DEGs from the The Cancer Genome Atlas (TCGA) - Genotype-Tissue Expression (GTEx) dataset were used to further select TAMs marker genes. Subsequently, a TAMRG-score was constructed by Least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analysis in the TCGA dataset and validated in the Chinese Glioma Genome Atlas (CGGA) dataset. RESULTS We identified 186 TAMs marker genes, and a total of 6 optimal prognostic genes including CKS2, LITAF, CTSB, TWISTNB, PPIF and G0S2 were selected to construct a TAMRG-score. The high TAMRG-score was significantly associated with worse prognosis (log-rank test, P<0.001). Moreover, the TAMRG-score outperformed the other three models with AUC of 0.808. Immune cell infiltration, TME scores, immune checkpoints, TMB and drug susceptibility were significantly different between TAMRG-score groups. In addition, a nomogram were constructed by combing the TAMRG-score and clinical information (Age, Grade, IDH mutation and 1p19q codeletion) to predict the survival of glioma patients with AUC of 0.909 for 1-year survival. CONCLUSION The high TAMRG-score group was associated with a poor prognosis. A nomogram by incorporating TMARG-score could precisely predict glioma survival, and provide evidence for personalized treatment of glioma.
Collapse
Affiliation(s)
- Zhicong Huang
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China
| | - Jingyao Huang
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China
| | - Ying Lin
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China
| | - Ying Deng
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China
| | - Longkun Yang
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China
| | - Xing Zhang
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China
| | - Hao Huang
- Department of Epidemiology, School of Public Health, Shenzhen University Medical School, Shenzhen, Guangdong, PR China
| | - Qian Sun
- Department of Neurosurgery, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Hui Liu
- Department of Neurosurgery, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Hongsheng Liang
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Zhonghua Lv
- Department of Neurosurgery, The Tumor Hospital Affiliated to Harbin Medical University, Harbin, Heilongjiang, PR China.
| | - Baochang He
- Department of Epidemiology and Health Statistics, Fujian Provincial Key Laboratory of Environment Factors and Cancer, School of Public Health, Fujian Medical University, Fujian, PR China.
| | - Fulan Hu
- Department of Epidemiology, School of Public Health, Shenzhen University Medical School, Shenzhen, Guangdong, PR China.
| |
Collapse
|
2
|
Awuah WA, Ahluwalia A, Ghosh S, Roy S, Tan JK, Adebusoye FT, Ferreira T, Bharadwaj HR, Shet V, Kundu M, Yee ALW, Abdul-Rahman T, Atallah O. The molecular landscape of neurological disorders: insights from single-cell RNA sequencing in neurology and neurosurgery. Eur J Med Res 2023; 28:529. [PMID: 37974227 PMCID: PMC10652629 DOI: 10.1186/s40001-023-01504-w] [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: 08/10/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Single-cell ribonucleic acid sequencing (scRNA-seq) has emerged as a transformative technology in neurological and neurosurgical research, revolutionising our comprehension of complex neurological disorders. In brain tumours, scRNA-seq has provided valuable insights into cancer heterogeneity, the tumour microenvironment, treatment resistance, and invasion patterns. It has also elucidated the brain tri-lineage cancer hierarchy and addressed limitations of current models. Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis have been molecularly subtyped, dysregulated pathways have been identified, and potential therapeutic targets have been revealed using scRNA-seq. In epilepsy, scRNA-seq has explored the cellular and molecular heterogeneity underlying the condition, uncovering unique glial subpopulations and dysregulation of the immune system. ScRNA-seq has characterised distinct cellular constituents and responses to spinal cord injury in spinal cord diseases, as well as provided molecular signatures of various cell types and identified interactions involved in vascular remodelling. Furthermore, scRNA-seq has shed light on the molecular complexities of cerebrovascular diseases, such as stroke, providing insights into specific genes, cell-specific expression patterns, and potential therapeutic interventions. This review highlights the potential of scRNA-seq in guiding precision medicine approaches, identifying clinical biomarkers, and facilitating therapeutic discovery. However, challenges related to data analysis, standardisation, sample acquisition, scalability, and cost-effectiveness need to be addressed. Despite these challenges, scRNA-seq has the potential to transform clinical practice in neurological and neurosurgical research by providing personalised insights and improving patient outcomes.
Collapse
Affiliation(s)
- Wireko Andrew Awuah
- Faculty of Medicine, Sumy State University, Zamonstanksya 7, Sumy, 40007, Ukraine
| | | | - Shankaneel Ghosh
- Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
| | - Sakshi Roy
- School of Medicine, Queen's University Belfast, Belfast, UK
| | | | | | - Tomas Ferreira
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | | | - Vallabh Shet
- Faculty of Medicine, Bangalore Medical College and Research Institute, Bangalore, Karnataka, India
| | - Mrinmoy Kundu
- Institute of Medical Sciences and SUM Hospital, Bhubaneswar, India
| | | | - Toufik Abdul-Rahman
- Faculty of Medicine, Sumy State University, Zamonstanksya 7, Sumy, 40007, Ukraine
| | - Oday Atallah
- Department of Neurosurgery, Hannover Medical School, Carl-Neuberg-Strasse 1, 30625, Hannover, Germany
| |
Collapse
|
3
|
Oh JH, Cho JY. Comparative oncology: overcoming human cancer through companion animal studies. Exp Mol Med 2023; 55:725-734. [PMID: 37009802 PMCID: PMC10167357 DOI: 10.1038/s12276-023-00977-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/20/2023] [Accepted: 01/25/2023] [Indexed: 04/04/2023] Open
Abstract
Comparative oncology is a field of study that has been recently adopted for studying cancer and developing cancer therapies. Companion animals such as dogs can be used to evaluate novel biomarkers or anticancer targets before clinical translation. Thus, the value of canine models is increasing, and numerous studies have been conducted to analyze similarities and differences between many types of spontaneously occurring cancers in canines and humans. A growing number of canine cancer models as well as research-grade reagents for these models are becoming available, leading to substantial growth in comparative oncology research spanning from basic science to clinical trials. In this review, we summarize comparative oncology studies that have been conducted on the molecular landscape of various canine cancers and highlight the importance of the integration of comparative biology into cancer research.
Collapse
Affiliation(s)
- Ji Hoon Oh
- Department of Biochemistry, Brain Korea 21 Project and Research Institute for Veterinary Science, Seoul National University College of Veterinary Medicine, Seoul, 08826, Republic of Korea
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea
| | - Je-Yoel Cho
- Department of Biochemistry, Brain Korea 21 Project and Research Institute for Veterinary Science, Seoul National University College of Veterinary Medicine, Seoul, 08826, Republic of Korea.
- Comparative Medicine Disease Research Center, Seoul National University, Seoul, 08826, Republic of Korea.
| |
Collapse
|
4
|
Zhu Z, Kiang KMY, Li N, Liu J, Zhang P, Jin L, He X, Zhang S, Leung GKK. Folate enzyme MTHFD2 links one-carbon metabolism to unfolded protein response in glioblastoma. Cancer Lett 2022; 549:215903. [PMID: 36089117 DOI: 10.1016/j.canlet.2022.215903] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/27/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022]
Abstract
The mitochondrial folate enzyme methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) has shown oncogenic roles in various cancers and may have non-metabolic functions. This study investigated the role of MTHFD2 in glioblastoma pathogenesis. We find that MTHFD2 expression is enriched in gliomas by analysing public databases and clinical specimens. RNA interference (RNAi) and inhibitor of MTHFD2 hamper the proliferation of glioblastoma and induce apoptosis in cell lines, glioma stem-like cells (GSCs) and patient-derived xenografts (PDX). Metabolomic analyses show that MTHFD2 depletion suppresses the central carbon metabolic pathways, including glycolysis, the pentose phosphate pathway (PPP), and the tricarboxylic acid (TCA) cycle. GSEA reveals a novel non-metabolic function of MTHFD2 in association with the unfolded protein response (UPR). MTHFD2 depletion activates the PERK/eIF2α axis which contributes to translation inhibition and apoptosis; these effects are attenuated by a PERK inhibitor. Mechanistically, MTHFD2 may be linked to UPR via the post-transcriptionally regulation of chaperone protein GRP78. In conclusion, MTHFD2 could be a promising therapeutic target for glioblastoma. Besides its canonical role, MTHFD2 may contribute to glioblastoma pathogenesis via UPR, highlighting a newly identified functional link between one-carbon metabolism and cell stress response.
Collapse
Affiliation(s)
- Zhiyuan Zhu
- Department of Functional Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Guangzhou, China; Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Karrie Mei-Yee Kiang
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Ning Li
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Jiaxin Liu
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Pingde Zhang
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Lei Jin
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China
| | - Xiaozheng He
- Department of Functional Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Guangzhou, China
| | - Shizhong Zhang
- Department of Functional Neurosurgery, Zhujiang Hospital, Southern Medical University, The National Key Clinical Specialty, The Engineering Technology Research Center of Education Ministry of China, Guangdong Provincial Key Laboratory on Brain Function Repair and Regeneration, The Neurosurgery Institute of Guangdong Province, Guangzhou, China.
| | - Gilberto Ka-Kit Leung
- Department of Surgery, LKS Faculty of Medicine, The University of Hong Kong, Queen Mary Hospital, Hong Kong, China.
| |
Collapse
|
5
|
Li M, Duan X, Xiao Y, Yuan M, Zhao Z, Cui X, Wu D, Shi J. BUB1 Is Identified as a Potential Therapeutic Target for Pancreatic Cancer Treatment. Front Public Health 2022; 10:900853. [PMID: 35769782 PMCID: PMC9235519 DOI: 10.3389/fpubh.2022.900853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/03/2022] [Indexed: 11/17/2022] Open
Abstract
Pancreatic cancer is one of the most challenging cancer types in clinical treatment worldwide. This study aimed to understand the tumorigenesis mechanism and explore potential therapeutic targets for patients with pancreatic cancer. Single-cell data and expression profiles of pancreatic cancer samples and normal tissues from multiple databases were included. Comprehensive bioinformatics analyses were applied to clarify tumor microenvironment and identify key genes involved in cancer development. Immense difference of cell types was shown between tumor and normal samples. Four cell types (B cell_1, B cell_2, cancer cell_3, and CD1C+_B dendritic cell_3) were screened to be significantly associated with prognosis. Three ligand-receptor pairs, including CD74-MIF, CD74-COPA, and CD74-APP, greatly contributed to tumorigenesis. High expression of BUB1 (BUB1 Mitotic Checkpoint Serine/Threonine Kinase) was closely correlated with worse prognosis. CD1C+_B dendritic cell_3 played a key role in tumorigenesis and cancer progression possibly through CD74-MIF. BUB1 can serve as a prognostic biomarker and a therapeutic target for patients with pancreatic cancer. The study provided a novel insight into studying the molecular mechanism of pancreatic cancer development and proposed a potential strategy for exploiting new drugs.
Collapse
Affiliation(s)
- Ming Li
- Department of General Surgery, Shijiazhuang People's Hospital, Shijiazhuang, China
| | - Xiaoyang Duan
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Hebei Tumor Hospital, Shijiazhuang, China
| | - Yajie Xiao
- Translational Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Meng Yuan
- Internal Medical, University of Occupational and Environmental Health, Fukuoka, Japan
| | - Zhikun Zhao
- Translational Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Xiaoli Cui
- Translational Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Dongfang Wu
- Translational Medicine, YuceBio Technology Co., Ltd., Shenzhen, China
| | - Jian Shi
- Department of Medical Oncology, The Fourth Hospital of Hebei Medical University, Hebei Tumor Hospital, Shijiazhuang, China
| |
Collapse
|