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Constantinou M, Nicholson J, Zhang X, Maniati E, Lucchini S, Rosser G, Vinel C, Wang J, Lim YM, Brandner S, Nelander S, Badodi S, Marino S. Lineage specification in glioblastoma is regulated by METTL7B. Cell Rep 2024; 43:114309. [PMID: 38848215 PMCID: PMC11220825 DOI: 10.1016/j.celrep.2024.114309] [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: 11/08/2023] [Revised: 04/10/2024] [Accepted: 05/16/2024] [Indexed: 06/09/2024] Open
Abstract
Glioblastomas are the most common malignant brain tumors in adults; they are highly aggressive and heterogeneous and show a high degree of plasticity. Here, we show that methyltransferase-like 7B (METTL7B) is an essential regulator of lineage specification in glioblastoma, with an impact on both tumor size and invasiveness. Single-cell transcriptomic analysis of these tumors and of cerebral organoids derived from expanded potential stem cells overexpressing METTL7B reveal a regulatory role for the gene in the neural stem cell-to-astrocyte differentiation trajectory. Mechanistically, METTL7B downregulates the expression of key neuronal differentiation players, including SALL2, via post-translational modifications of histone marks.
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Affiliation(s)
- Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - James Nicholson
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Xinyu Zhang
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Eleni Maniati
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6AS, UK
| | - Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Gabriel Rosser
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Claire Vinel
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Jun Wang
- Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6AS, UK
| | - Yau Mun Lim
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, and Department of Neurodegenerative Disease, Queen Square, Institute of Neurology, University College London, Queen Square, London, UK
| | - Sebastian Brandner
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London Hospitals NHS Foundation Trust, and Department of Neurodegenerative Disease, Queen Square, Institute of Neurology, University College London, Queen Square, London, UK
| | - Sven Nelander
- Department of Immunology Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Sara Badodi
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University London, London, UK.
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Zhang L, Liu X, Zhou S, Wang P, Zhang X. Glycolysis Modulation by METTL7B Shapes Acute Lymphoblastic Leukemia Cell Proliferation and Chemotherapy Response. Hum Cell 2024; 37:478-490. [PMID: 38294636 DOI: 10.1007/s13577-024-01025-6] [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: 09/22/2023] [Accepted: 01/01/2024] [Indexed: 02/01/2024]
Abstract
Acute lymphoblastic leukemia (ALL) is a devastating hematological malignancy characterized by uncontrolled proliferation of immature lymphoid cells. While advances in treatment have improved patient outcomes, challenges remain in enhancing therapeutic efficacy and understanding underlying molecular mechanisms. Methyltransferase-like 7B (METTL7B), known for its methyltransferase activity, has been implicated in various solid tumors, yet its role in ALL remains unexplored. Here, we reveal that high METTL7B expression is correlated with poorer prognosis in ALL patients. Employing genetic manipulation strategies, we demonstrate that METTL7B depletion reduces ALL cell proliferation and enhances chemosensitivity. Mechanistically, we uncover METTL7B's involvement in modulating glycolysis, a crucial metabolic pathway supporting ALL cell growth. Furthermore, METTL7B's methyltransferase activity is identified as a determinant of its impact on glycolysis and proliferation. This study sheds light on METTL7B's multifaceted role in ALL, highlighting its potential as a therapeutic target and offering insights into the metabolic rewiring crucial for ALL progression.
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Affiliation(s)
- Li Zhang
- Department of Human Anatomy, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Xiao Liu
- Department of Hematology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Shuai Zhou
- Department of Human Anatomy, School of Basic Medical Sciences, Binzhou Medical University, Yantai, Shandong, China
| | - Peng Wang
- Department of Critical Care Unit, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Xuan Zhang
- Department of Geriatric Respiratory Disease, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China.
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3
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Zhu W, Chen Z, Fu M, Li Q, Chen X, Li X, Luo N, Tang W, Yang F, Zhang Y, Zhang Y, Peng X, Hu G. Cuprotosis clusters predict prognosis and immunotherapy response in low-grade glioma. Apoptosis 2024; 29:169-190. [PMID: 37713112 PMCID: PMC10830610 DOI: 10.1007/s10495-023-01880-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
Abstract
Cuprotosis, an emerging mode of cell death, has recently caught the attention of researchers worldwide. However, its impact on low-grade glioma (LGG) patients has not been fully explored. To gain a deeper insight into the relationship between cuprotosis and LGG patients' prognosis, we conducted this study in which LGG patients were divided into two clusters based on the expression of 18 cuprotosis-related genes. We found that LGG patients in cluster A had better prognosis than those in cluster B. The two clusters also differed in terms of immune cell infiltration and biological functions. Moreover, we identified differentially expressed genes (DEGs) between the two clusters and developed a cuprotosis-related prognostic signature through the least absolute shrinkage and selection operator (LASSO) analysis in the TCGA training cohort. This signature divided LGG patients into high- and low-risk groups, with the high-risk group having significantly shorter overall survival (OS) time than the low-risk group. Its predictive reliability for prognosis in LGG patients was confirmed by the TCGA internal validation cohort, CGGA325 cohort and CGGA693 cohort. Additionally, a nomogram was used to predict the 1-, 3-, and 5-year OS rates of each patient. The analysis of immune checkpoints and tumor mutation burden (TMB) has revealed that individuals belonging to high-risk groups have a greater chance of benefiting from immunotherapy. Functional experiments confirmed that interfering with the signature gene TNFRSF11B inhibited LGG cell proliferation and migration. Overall, this study shed light on the importance of cuprotosis in LGG patient prognosis. The cuprotosis-related prognostic signature is a reliable predictor for patient outcomes and immunotherapeutic response and can help to develop new therapies for LGG.
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Affiliation(s)
- Wenjun Zhu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Ziqi Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Min Fu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Qianxia Li
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xin Chen
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Xiaoyu Li
- Department of Oncology, Hubei Cancer Hospital, Wuhan, 430030, China
| | - Na Luo
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wenhua Tang
- Department of Oncology and Southwest Cancer Center, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing, 400038, China
| | - Feng Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yiling Zhang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yuanyuan Zhang
- Department of Radiology, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Xiaohong Peng
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
| | - Guangyuan Hu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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Li J, Guo Q, Xing R. Construction and validation of an immune infiltration-related risk model for predicting prognosis and immunotherapy response in low grade glioma. BMC Cancer 2023; 23:727. [PMID: 37543576 PMCID: PMC10403952 DOI: 10.1186/s12885-023-11222-5] [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: 11/02/2022] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
BACKGROUND Low grade glioma (LGG) is considered a heterogeneous tumor with highly variable survival and limited efficacy of immunotherapy. To identify high-risk subsets and apply immunotherapy effectively in LGG, the status and function of immune infiltration in the glioma microenvironment must be explored. METHODS Four independent glioma cohorts comprising 1,853 patients were enrolled for bioinformatics analysis. We used ConsensusClusterPlus to cluster patients into four different immune subtypes based on immune infiltration. The immune-infiltration signature (IIS) was constructed by LASSO regression analysis. Somatic mutation and copy number variation (CNV) analyses were performed to explore genomic and transcriptomic traits in the high- and low- risk groups. The correlation between response to programmed cell death 1 (PD-1) blockade and the IIS risk score was confirmed in an in vivo glioma model. RESULTS Patients were clustered into four different immune subtypes based on immune infiltration, and the high immune infiltration subtype was associated with worse survival in LGG. The high immune infiltration subtype had stronger inflammatory response, immune response and immune cell chemotaxis. The IIS, consisting of EMP3, IQGAP2, METTL7B, SLC1A6 and TNFRSF11B, could predict LGG malignant progression, which was validated with internal clinical samples. M2 macrophage infiltration positively correlated with the IIS risk score. The high-risk group had significantly more somatic mutations and CNVs. The IIS risk score was related to immunomodulatory molecules and could predict immunotherapy clinical benefit. In vivo, immunotherapy-sensitive glioma model exhibited higher IIS risk score and more infiltration of immune cells, especially M2 macrophages. The IIS risk score was decreased in an immunotherapy-sensitive glioma model after anti-PD1 immunotherapy. CONCLUSION Different immune subtypes of LGG had unique immune cell infiltration characteristics, and the high immune infiltration subtype was associated with immunosuppressive signaling pathways. A novel IIS prognostic model based on immune infiltration status was constructed for immunophenotypic classification, risk stratification, prognostication and immunotherapy response prediction in LGG.
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Affiliation(s)
- Jinna Li
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110000, China
| | - Qing Guo
- Department of Neurosurgery, The First Hospital of China Medical University, Shenyang, 110000, China.
| | - Rui Xing
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, 110000, China.
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Russell DA, Chau MK, Shi Y, Levasseur IN, Maldonato BJ, Totah RA. METTL7A (TMT1A) and METTL7B (TMT1B) Are Responsible for Alkyl S-Thiol Methyl Transferase Activity in Liver. Drug Metab Dispos 2023; 51:1024-1034. [PMID: 37137720 PMCID: PMC10353073 DOI: 10.1124/dmd.123.001268] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/19/2023] [Accepted: 04/27/2023] [Indexed: 05/05/2023] Open
Abstract
S-methylation of drugs containing thiol-moieties often alters their activity and results in detoxification. Historically, scientists attributed methylation of exogenous aliphatic and phenolic thiols to a putative S-adenosyl-L-methionine (SAM)-dependent membrane-associated enzyme referred to as thiol methyltransferase (TMT). This putative TMT appeared to have a broad substrate specificity and methylated the thiol metabolite of spironolactone, mertansine, ziprasidone, captopril, and the active metabolites of the thienopyridine prodrugs, clopidogrel, and prasugrel. Despite TMT's role in the S-methylation of clinically relevant drugs, the enzyme(s) responsible for this activity remained unknown. We recently identified methyltransferase-like protein 7B (METTL7B) as an alkyl thiol methyltransferase. METTL7B is an endoplasmic reticulum-associated protein with similar biochemical properties and substrate specificity to the putative TMT. Yet, the historic TMT inhibitor 2,3-dichloro-α-methylbenzylamine (DCMB) did not inhibit METTL7B, indicating that multiple enzymes contribute to TMT activity. Here we report that methyltransferase-like protein 7A (METTL7A), an uncharacterized member of the METTL7 family, is also a SAM-dependent thiol methyltransferase. METTL7A exhibits similar biochemical properties to METTL7B and putative TMT, including inhibition by DCMB (IC50 = 1.17 μM). Applying quantitative proteomics to human liver microsomes and gene modulation experiments in HepG2 and HeLa cells, we determined that TMT activity correlates closely with METTL7A and METTL7B protein levels. Furthermore, purification of a novel His-GST-tagged recombinant protein and subsequent activity experiments prove that METTL7A can selectively methylate exogenous thiol-containing substrates, including 7α-thiospironolactone, dithiothreitol, 4-chlorothiophenol, and mertansine. We conclude that the METTL7 family encodes for two enzymes, METTL7A and METTL7B, which are now renamed thiol methyltransferase 1A (TMT1A) and thiol methyltransferase 1B (TMT1B), respectively, that are responsible for thiol methylation activity in human liver microsomes. SIGNIFICANCE STATEMENT: We identified methyltransferase-like protein 7A (thiol methyltransferase 1A) and methyltransferase-like protein 7B (thiol methyltransferase 1B) as the enzymes responsible for the microsomal alkyl thiol methyltransferase (TMT) activity. These are the first two enzymes directly associated with microsomal TMT activity. S-methylation of commonly prescribed thiol-containing drugs alters their pharmacological activity and/or toxicity, and identifying the enzymes responsible for this activity will improve our understanding of the drug metabolism and pharmacokinetic (DMPK) properties of alkyl- or phenolic thiol-containing therapeutics.
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Affiliation(s)
- Drake A Russell
- University of Washington, Department of Medicinal Chemistry, Seattle, Washington
| | - Marvin K Chau
- University of Washington, Department of Medicinal Chemistry, Seattle, Washington
| | - Yuanyuan Shi
- University of Washington, Department of Medicinal Chemistry, Seattle, Washington
| | - Ian N Levasseur
- University of Washington, Department of Medicinal Chemistry, Seattle, Washington
| | - Benjamin J Maldonato
- University of Washington, Department of Medicinal Chemistry, Seattle, Washington
| | - Rheem A Totah
- University of Washington, Department of Medicinal Chemistry, Seattle, Washington
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Denford SE, Wilhelm BT. Defining the elusive oncogenic role of the methyltransferase TMT1B. Front Oncol 2023; 13:1211540. [PMID: 37456227 PMCID: PMC10339810 DOI: 10.3389/fonc.2023.1211540] [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: 04/24/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023] Open
Abstract
Methyltransferases are enzymes fundamental to a wide range of normal biological activities that can become dysregulated during oncogenesis. For instance, the recent description of the methyltransferase-like (METTL) family of enzymes, has demonstrated the importance of the N6-adenosine-methyltransferase (m6A) modification in transcripts in the context of malignant transformation. Because of their importance, numerous METTL family members have been biochemically characterized to identify their cellular substrates, however some members such as METTL7B, recently renamed TMT1B and which is the subject of this review, remain enigmatic. First identified in the stacked Golgi, TMT1B is also localized to the endoplasmic reticulum as well as lipid droplets and has been reported as being upregulated in a wide range of cancer types including lung cancer, gliomas, and leukemia. Interestingly, despite evidence that TMT1B might act on protein substrates, it has also been shown to act on small molecule alkyl thiol substrates such as hydrogen sulfide, and its loss has been found to affect cellular proliferation and migration. Here we review the current evidence for TMT1B's activity, localization, and potential biological role in the context of both normal and cancerous cell types.
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Affiliation(s)
- Sarah E. Denford
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
| | - Brian T. Wilhelm
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
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Lin Y, Zhang Y, Tuo Z, Gao L, Ding D, Bi L, Yu D, Lv Z, Wang J, Chen X. ORC6, a novel prognostic biomarker, correlates with T regulatory cell infiltration in prostate adenocarcinoma: a pan-cancer analysis. BMC Cancer 2023; 23:285. [PMID: 36978046 PMCID: PMC10053432 DOI: 10.1186/s12885-023-10763-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
BACKGROUND The origin recognition complex (ORC), a six-subunit DNA-binding complex, participates in DNA replication in cancer cells. Specifically in prostate cancers, ORC participates the androgen receptor (AR) regulated genomic amplification and tumor proliferation throughout the entire cell cycle. Of note, ORC6, the smallest subunit of ORC, has been reported to be dysregulated in some types of cancers (including prostate cancer), however, its prognostic and immunological significances remain yet to be elucidated. METHODS In the current study, we comprehensively investigated the potential prognostic and immunological role of ORC6 in 33 human tumors using multiple databases, such as TCGA, Genotype-Tissue Expression, CCLE, UCSC Xena, cBioPortal, Human Protein Atlas, GeneCards, STRING, MSigDB, TISIDB, and TIMER2 databases. RESULTS ORC6 expression was significantly upregulated in 29 types of cancers compared to the corresponding normal adjacent tissues. ORC6 overexpression correlated with higher stage and worse prognostic outcomes in most cancer types analyzed. Additionally, ORC6 was involved in the cell cycle pathway, DNA replication, and mismatch repair pathways in most tumor types. A negative correlation was observed between the tumor endothelial cell infiltration and ORC6 expression in almost all tumors, whereas the immune infiltration of T regulatory cell was noted to be statistically positively correlated with the expression of ORC6 in prostate cancer tissues. Furthermore, in most tumor types, immunosuppression-related genes, especially TGFBR1 and PD-L1 (CD274), exhibited a specific correlation with the expression of ORC6. CONCLUSIONS This comprehensive pan-cancer analysis revealed that ORC6 expression serves as a prognostic biomarker and that ORC6 is involved in the regulation of various biological pathways, the tumor microenvironment, and the immunosuppression status in several human cancers, suggesting its potential diagnostic, prognostic, and therapeutic value in pan-cancer, especially in prostate adenocarcinoma.
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Affiliation(s)
- Yuan Lin
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Ying Zhang
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhouting Tuo
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Liang Gao
- Center for Clinical Medicine, Huatuo Institute of Medical Innovation (HTIMI), Berlin, Germany
| | - Demao Ding
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Liangkuan Bi
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Dexin Yu
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
| | - Zhengmei Lv
- Department of Histology and Embryology, School of Basic Medical Sciences, Anhui Medical University, Anhui, China
| | - Jiani Wang
- School of Health Administration, Anhui Medical University, Hefei, China
- Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, Berlin, Germany
- Berlin Institute of Health, Institute for Social Medicine, Epidemiology and Health Economics, Berlin, Germany
| | - Xin Chen
- Department of Urology, The Second Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
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Quantitative Evaluation of Stem-like Markers of Human Glioblastoma Using Single-Cell RNA Sequencing Datasets. Cancers (Basel) 2023; 15:cancers15051557. [PMID: 36900348 PMCID: PMC10001303 DOI: 10.3390/cancers15051557] [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: 01/06/2023] [Revised: 02/17/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Targeting glioblastoma (GBM) stem-like cells (GSCs) is a common interest in both the laboratory investigation and clinical treatment of GBM. Most of the currently applied GBM stem-like markers lack validation and comparison with common standards regarding their efficiency and feasibility in various targeting methods. Using single-cell RNA sequencing datasets from 37 GBM patients, we obtained a large pool of 2173 GBM stem-like marker candidates. To evaluate and select these candidates quantitatively, we characterized the efficiency of the candidate markers in targeting the GBM stem-like cells by their frequencies and significance of being the stem-like cluster markers. This was followed by further selection based on either their differential expression in GBM stem-like cells compared with normal brain cells or their relative expression level compared with other expressed genes. The cellular location of the translated protein was also considered. Different combinations of selection criteria highlight different markers for different application scenarios. By comparing the commonly used GSCs marker CD133 (PROM1) with markers selected by our method regarding their universality, significance, and abundance, we revealed the limitations of CD133 as a GBM stem-like marker. Overall, we propose BCAN, PTPRZ1, SOX4, etc. for laboratory-based assays with samples free of normal cells. For in vivo targeting applications that require high efficiency in targeting the stem-like subtype, the ability to distinguish GSCs from normal brain cells, and a high expression level, we recommend the intracellular marker TUBB3 and the surface markers PTPRS and GPR56.
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Cheng X, Liu Z, Liang W, Zhu Q, Wang C, Wang H, Zhang J, Li P, Gao Y. ECM2, a prognostic biomarker for lower grade glioma, serves as a potential novel target for immunotherapy. Int J Biochem Cell Biol 2023; 158:106409. [PMID: 36997057 DOI: 10.1016/j.biocel.2023.106409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 03/31/2023]
Abstract
Extracellular matrix protein 2 (ECM2), which regulates cell proliferation and differentiation, has recently been reported as a prognostic indicator for multiple cancers, but its value in lower grade glioma (LGG) remains unknown. In this study, LGG transcriptomic data of 503 cases in The Cancer Genome Atlas (TCGA) database and 403 cases in The Chinese Glioma Genome Atlas (CGGA) database were collected to analyze ECM2 expression patterns and the relationship with clinical characteristics, prognosis, enriched signaling pathways, and immune-related markers. In addition, a total of 12 laboratory samples were used for experimental validation. Wilcoxon or Kruskal-Wallis tests demonstrated highly expressed ECM2 in LGG was positively associated with malignant histological features and molecular features such as recurrent LGG and isocitrate dehydrogenase (IDH) wild-type. Also, Kaplan-Meier (KM) curves proved high ECM2 expression could predict shorter overall survival in LGG patients, as multivariate analysis and meta-analysis claimed ECM2 was a deleterious factor for LGG prognosis. In addition, the enrichment of immune-related pathways for ECM2, for instance JAK-STAT pathway, was obtained by Gene Set Enrichment Analysis (GSEA) analysis. Furthermore, positive relationships between ECM2 expression with immune cells infiltration and cancer-associated fibroblasts (CAFs), iconic markers (CD163), and immune checkpoints (CD274, encoding PD-L1) were proved by Pearson correlation analysis. Finally, laboratory experiments of RT-qPCR and immunohistochemistry showed high expression of ECM2, as well as CD163 and PD-L1 in LGG samples. This study identifies ECM2, for the first time, as a subtype marker and prognostic indicator for LGG. ECM2 could also provide a reliable guarantee for further personalized therapy, synergizing with tumor immunity, to break through the current limitations and thus reinvigorating immunotherapy for LGG. AVAILABILITY OF DATA AND MATERIALS: Raw data from all public databases involved in this study are stored in the online repository (chengMD2022/ECM2 (github.com)).
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10
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The prognostic signature based on glycolysis-immune related genes for acute myeloid leukemia patients. Immunobiology 2023; 228:152355. [PMID: 36868006 DOI: 10.1016/j.imbio.2023.152355] [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: 07/13/2022] [Revised: 02/15/2023] [Accepted: 02/17/2023] [Indexed: 02/23/2023]
Abstract
Acute myeloid leukemia (AML) is widely considered an immunoresponsive malignancy. However, potential association between glycolysis-immune related genes and AML patients' prognosis has been seldom studied. AML-related data was downloaded from TCGA and GEO databases. We grouped patients according to Glycolysis status, Immune Score and combination analysis, basing on which overlapped differentially expressed genes (DEGs) were identified. The Risk Score model was then established. The results showed that totally 142 overlapped genes were probably correlated with glycolysis-immunity in AML patients, among which 6 optimal genes were screened to construct Risk Score. High Risk Score was an independent poor prognostic factor for AML. In conclusion, we established a relatively reliable prognostic signature of AML based on glycolysis-immunity related genes, including METTL7B, HTR7, ITGAX, TNNI2, SIX3 and PURG.
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11
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Zhang P, Zhang T, Chen D, Gong L, Sun M. Prognosis and Novel Drug Targets for Key lncRNAs of Epigenetic Modification in Colorectal Cancer. Mediators Inflamm 2023; 2023:6632205. [PMID: 37091904 PMCID: PMC10116225 DOI: 10.1155/2023/6632205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/20/2022] [Accepted: 03/20/2023] [Indexed: 04/25/2023] Open
Abstract
Background Colorectal cancer (CRC) has been the 3rd most commonly malignant tumor of the gastrointestinal tract in the world. 5-Methylcytosine (m5C) and long noncoding RNAs (lncRNAs) have an essential role in predicting the prognosis and immune response for CRC patients. Therefore, we built a m5C-related lncRNA (m5CRlncRNA) model to investigate the prognosis and treatment methods for CRC patients. Methods Firstly, we secured the transcriptome and clinical data for CRC from The Cancer Genome Atlas (TCGA). Then, m5CRlncRNAs were recognized by coexpression analysis. Then, univariate Cox, least absolute shrinkage and selection operator (LASSO), and multivariate Cox regression analyses were utilized to build m5C-related prognostic characteristics. Besides, Kaplan-Meier analysis, ROC, PCA, C-index, enrichment analysis, and nomogram were performed to investigate the model. Additionally, immunotherapy responses and antitumor medicines were explored for CRC patients. Results A total of 8 m5C-related lncRNAs (AC093157.1, LINC00513, AC025171.4, AC090948.2, ZEB1-AS1, AC109449.1, AC009041.3, and LINC02516) were adopted to construct a risk model to investigate survival and prognosis for CRC patients. CRC samples were separated into low- and high-risk groups, with the latter having a worse prognosis. The m5C-related lncRNA model helps us to better distinguish immunotherapy responses and IC50 of antitumor medicines in different groups of CRC patients. Conclusion The research may give new perspectives on tailored therapy approaches as well as novel theories for forecasting the prognosis of CRC patients.
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Affiliation(s)
- Peng Zhang
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Tingting Zhang
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Denggang Chen
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Li Gong
- Department of Endocrinology, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Min Sun
- Department of General Surgery, Taihe Hospital, Hubei University of Medicine, Shiyan, China
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Li Z, Song Y, Zhang J. lncRNA PDCD4-AS1 Promotes the Progression of Glioma by Regulating miR-30b-3p/METTL7B Signaling. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2023; 2023:3492480. [PMID: 37151605 PMCID: PMC10162875 DOI: 10.1155/2023/3492480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/29/2022] [Indexed: 05/09/2023]
Abstract
Background Gliomas are the most common and most malignant primary tumors of the adult central nervous system, but their etiology and pathogenesis remain unclear. This study was aimed at investigating the expression and function of lncRNA PDCD4-AS1 in glioma and elucidating the mechanism by which PDCD4-AS1 regulates the biological features of glioma. Method The expression of PDCD4-AS1 was determined by bioinformatic analysis and qRT-PCR assay. PDCD4-AS1 was knocked down in glioma cells using siRNA transfection. The functional analysis of cells was conducted using CCK-8 proliferation, cell migration, and invasion assays, as well as cell cycle analysis. An in vivo tumorigenesis assay was performed to investigate the role of PDCD4-AS1 knockdown in glioma tumor growth. We performed bioinformatic analysis, RNA pull-down, and luciferase reporter assays to investigate the downstream targets of PDCD4-AS1. A rescue experiment was then performed to confirm the regulating mechanism. Results PDCD4-AS1 was found to be significantly upregulated in glioma patients' tumor tissues and cell lines. The silencing of PDCD4-AS1 inhibited glioma cell proliferation, invasion, migration, and induced cell cycle arrest. In vivo experiments showed that silencing PDCD4-AS1 inhibited glioma tumor growth. An investigation of the underlying mechanism suggested that PDCD4-AS1 positively regulated METTL7B expression by sponging miR-30b-3. Both the knockdown of miR-30b-3p and the overexpression of METTL7B could, respectively, reverse the malignant phenotype of cells affected by silencing PDCD4-AS1. Conclusion These results demonstrate that PDCD4-AS1 exerted an oncogenic role by regulating the miR-30b-3p/METTL7B axis.
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Affiliation(s)
- Zuowei Li
- Shandong University of Traditional Chinese Medicine, Jinan 250011, China
- Department of Encephalopathy, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250011, China
| | - Yelin Song
- Department of Cardiovascular Medicine, Qingdao Hospital of Traditional Chinese Medicine, Qingdao 266011, China
| | - Jimei Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250011, China
- The 960th Hospital of the PLA Joint Logistics Support Force (Tai'an), Tai'an 271099, China
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Downregulation of hsa-miR-30b-3p Inhibits the Oncogenicity of Lung Adenocarcinoma by Targeting the METTL7B Gene. JOURNAL OF ONCOLOGY 2022; 2022:6883140. [PMID: 35646115 PMCID: PMC9142323 DOI: 10.1155/2022/6883140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 11/21/2022]
Abstract
Objective Lung adenocarcinoma (LUAD) is one of the malignant tumors with the highest morbidity and mortality rates worldwide. Although surgery-based combination therapy can greatly improve the prognosis of LUAD patients, the overall outcome is still poor, and there is an urgent need to develop new and effective treatment alternatives for LUAD. The microRNA (miRNA) miR-30b-3p is a typical multifunctional miRNA that has been reported to promote the development of various malignancies. In this study, we investigated the effects of miR-30b-3p on the biological properties of LUAD and the possible mechanisms involved to provide new ideas for the development of more effective treatment options for LUAD. Methods Fluorescence quantitative real-time polymerase chain reaction (qRT-PCR) was used to measure the expression of miR-30b-3p and its target METTL7B gene in tumor tissues and adjacent noncancerous lung tissues of LUAD patients and to determine their correlation. The effect of miR-30b-3p on the biological properties of LUAD was investigated, after transfection of miR-30b-3p mimics or scramble miRNA (negative control) in LUAD cells, using various approaches, including by measuring cell proliferation using CCK-8 and Edu assays, cell invasion by Transwell assay, and apoptosis and cell cycle distribution by flow cytometry. Additionally, rescue assays were performed to verify the effect of METTL7B on miR-30b-3p function. Results In LUAD patients, low expression of miR-30b-3p and high expression of METTL7B in tumor tissues were significantly and negatively correlated with those in adjacent noncancerous lung tissues of the LUAD patients. It was also found that miR-30b-3p inhibits the proliferation and invasion of LUAD cells, promotes apoptosis, and changes the cell cycle distribution. METTL7B is a target gene of miR-30b-3p. METTL7B overexpression significantly reversed the biological effects of miR-30b-3p overexpression, including inhibition of cell proliferation and invasion, promotion of apoptosis, and alteration of the cell cycle distribution. Conclusions The miR-30b-3p alters the biology of LUAD by negatively regulating METTL7B expression, indicating the importance of the miR-30b-3p/METTL7B pathway in the development of LUAD.
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Qian Y, Li Y, Chen K, Liu N, Hong X, Wu D, Xu Z, Zhou L, Xu L, Jia R, Ge YZ. Pan-Cancer Transcriptomic Analysis Identifies PLK1 Crucial for the Tumorigenesis of Clear Cell Renal Cell Carcinoma. J Inflamm Res 2022; 15:1099-1116. [PMID: 35210814 PMCID: PMC8859474 DOI: 10.2147/jir.s347732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 02/02/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yiguan Qian
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Yang Li
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Ke Chen
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Ning Liu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Xi Hong
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Di Wu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Zheng Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Liuhua Zhou
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Luwei Xu
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
| | - Ruipeng Jia
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
- Correspondence: Ruipeng Jia; Yu-Zheng Ge, Department of Urology, Nanjing First Hospital, Nanjing Medical UniversityNanjing, Jiangsu, People’s Republic of China, Tel +86-15850675660, Email ;
| | - Yu-Zheng Ge
- Department of Urology, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, People’s Republic of China
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