1
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Luo M, Zhao C, Zhao Y, wang Y, Li P. Identification of homer protein homolog 3 as a prognostic marker of colon adenocarcinoma. Heliyon 2024; 10:e33344. [PMID: 39035486 PMCID: PMC11259827 DOI: 10.1016/j.heliyon.2024.e33344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/23/2024] Open
Abstract
Background Homer protein homolog 3 (HOMER3), a factor implicated in both physiological and pathological processes, has been studied extensively to determine the relationship between its expression level and the prognosis of various malignancies. However, the significance and clinicopathological role of HOMER3 in colorectal adenocarcinoma remain unclear. Methods In this study, bioinformatics techniques were used to find the correlation between high HOMER3 expression levels and clinicopathological features of colorectal adenocarcinoma (COAD) patients. Results Cellular experiments confirmed the differential expression of HOMER3 in tumor cells compared to normal cells. HOMER3 overexpression was significantly associated with COAD staging and carcinoembryonic antigen (CEA) levels. Patients with high HOMER3 expression levels have a poor prognosis. HOMER3 expression levels can be distinguished more accurately between tumor and non-tumor tissues (AUC = 0.634). The HOMER3 gene variation rate in COAD tissue was 0.7 %. Moreover, 16 of the 22 DNA methylation sites in HOMER3 were associated with COAD prognosis. Our findings confirmed that HOMER3 was positively correlated with immune cell infiltration and immune checkpoints (PD-1, CTLA-4, LMTK3, and LAG3) in COAD, Specifically, we will clearly state that while there is statistical significance, the actual strength of the correlations is weak. During KEGG enrichment analysis, HOMER3 was enriched along with DLG4 and SHANK1 in glutamatergic synapses. Additionally, upstream microRNAs that could bind to HOMER3 were predicted. These findings suggest that HOMER3 might be involved in COAD development and immune regulation. Conclusions HOMER3 acts as a potential biomarker that can facilitate innovative developments in the diagnosis and prognostic assessment of COAD.
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Affiliation(s)
- Min Luo
- Institute for Translational Medicine, Qingdao University, Qingdao, 266000, China
- The Third Affiliated Hospital of Zunyi Medical University, The First People's Hospital of Zunyi, Zunyi, Guizhou, 563000, China
| | - Cheng Zhao
- Institute for Translational Medicine, Qingdao University, Qingdao, 266000, China
| | - Yanhua Zhao
- Institute for Translational Medicine, Qingdao University, Qingdao, 266000, China
| | - yin wang
- Institute for Translational Medicine, Qingdao University, Qingdao, 266000, China
| | - Peifeng Li
- Institute for Translational Medicine, Qingdao University, Qingdao, 266000, China
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2
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Banushi B, Joseph SR, Lum B, Lee JJ, Simpson F. Endocytosis in cancer and cancer therapy. Nat Rev Cancer 2023:10.1038/s41568-023-00574-6. [PMID: 37217781 DOI: 10.1038/s41568-023-00574-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/24/2023]
Abstract
Endocytosis is a complex process whereby cell surface proteins, lipids and fluid from the extracellular environment are packaged, sorted and internalized into cells. Endocytosis is also a mechanism of drug internalization into cells. There are multiple routes of endocytosis that determine the fate of molecules, from degradation in the lysosomes to recycling back to the plasma membrane. The overall rates of endocytosis and temporal regulation of molecules transiting through endocytic pathways are also intricately linked with signalling outcomes. This process relies on an array of factors, such as intrinsic amino acid motifs and post-translational modifications. Endocytosis is frequently disrupted in cancer. These disruptions lead to inappropriate retention of receptor tyrosine kinases on the tumour cell membrane, changes in the recycling of oncogenic molecules, defective signalling feedback loops and loss of cell polarity. In the past decade, endocytosis has emerged as a pivotal regulator of nutrient scavenging, response to and regulation of immune surveillance and tumour immune evasion, tumour metastasis and therapeutic drug delivery. This Review summarizes and integrates these advances into the understanding of endocytosis in cancer. The potential to regulate these pathways in the clinic to improve cancer therapy is also discussed.
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Affiliation(s)
- Blerida Banushi
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Shannon R Joseph
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Benedict Lum
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Jason J Lee
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia
| | - Fiona Simpson
- Frazer Institute, University of Queensland, Woolloongabba, Queensland, Australia.
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3
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Shayeghpour A, Forghani-Ramandi MM, Solouki S, Hosseini A, Hosseini P, Khodayar S, Hasani M, Aghajanian S, Siami Z, Zarei Ghobadi M, Mozhgani SH. Identification of novel miRNAs potentially involved in the pathogenesis of adult T-cell leukemia/lymphoma using WGCNA followed by RT-qPCR test of hub genes. Infect Agent Cancer 2023; 18:12. [PMID: 36841815 PMCID: PMC9968414 DOI: 10.1186/s13027-023-00492-0] [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: 08/11/2022] [Accepted: 02/17/2023] [Indexed: 02/27/2023] Open
Abstract
BACKGROUND Adult T-cell Lymphoma/Leukemia (ATLL) is characterized by the malignant proliferation of T-cells in Human T-Lymphotropic Virus Type 1 and a high mortality rate. Considering the emerging roles of microRNAs (miRNAs) in various malignancies, the analysis of high-throughput miRNA data employing computational algorithms helps to identify potential biomarkers. METHODS Weighted gene co-expression network analysis was utilized to analyze miRNA microarray data from ATLL and healthy uninfected samples. To identify miRNAs involved in the progression of ATLL, module preservation analysis was used. Subsequently, based on the target genes of the identified miRNAs, the STRING database was employed to construct protein-protein interaction networks (PPIN). Real-time quantitative PCR was also performed to validate the expression of identified hub genes in the PPIN network. RESULTS After constructing co-expression modules and then performing module preservation analysis, four out of 15 modules were determined as ATLL-specific modules. Next, the hub miRNA including hsa-miR-18a-3p, has-miR-187-5p, hsa-miR-196a-3p, and hsa-miR-346 were found as hub miRNAs. The protein-protein interaction networks were constructed for the target genes of each hub miRNA and hub genes were identified. Among them, UBB, RPS15A, and KMT2D were validated by Reverse-transcriptase PCR in ATLL patients. CONCLUSION The results of the network analysis of miRNAs and their target genes revealed the major players in the pathogenesis of ATLL. Further studies are required to confirm the role of these molecular factors and to discover their potential benefits as treatment targets and diagnostic biomarkers.
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Affiliation(s)
- Ali Shayeghpour
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Setayesh Solouki
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Amin Hosseini
- Department of Computer, Faculty of Engineering, Raja University, Qazvin, Iran
| | - Parastoo Hosseini
- grid.411705.60000 0001 0166 0922Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran ,grid.411705.60000 0001 0166 0922Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | - Sara Khodayar
- grid.411705.60000 0001 0166 0922Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahsa Hasani
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Sepehr Aghajanian
- grid.411705.60000 0001 0166 0922School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Zeinab Siami
- grid.411705.60000 0001 0166 0922Department of Infectious Diseases, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | | | - Sayed-Hamidreza Mozhgani
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran. .,Non-Communicable Disease Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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4
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Iglesia RP, Prado MB, Alves RN, Escobar MIM, Fernandes CFDL, Fortes ACDS, Souza MCDS, Boccacino JM, Cangiano G, Soares SR, de Araújo JPA, Tiek DM, Goenka A, Song X, Keady JR, Hu B, Cheng SY, Lopes MH. Unconventional Protein Secretion in Brain Tumors Biology: Enlightening the Mechanisms for Tumor Survival and Progression. Front Cell Dev Biol 2022; 10:907423. [PMID: 35784465 PMCID: PMC9242006 DOI: 10.3389/fcell.2022.907423] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/26/2022] [Indexed: 11/28/2022] Open
Abstract
Non-canonical secretion pathways, collectively known as unconventional protein secretion (UPS), are alternative secretory mechanisms usually associated with stress-inducing conditions. UPS allows proteins that lack a signal peptide to be secreted, avoiding the conventional endoplasmic reticulum-Golgi complex secretory pathway. Molecules that generally rely on the canonical pathway to be secreted may also use the Golgi bypass, one of the unconventional routes, to reach the extracellular space. UPS studies have been increasingly growing in the literature, including its implication in the biology of several diseases. Intercellular communication between brain tumor cells and the tumor microenvironment is orchestrated by various molecules, including canonical and non-canonical secreted proteins that modulate tumor growth, proliferation, and invasion. Adult brain tumors such as gliomas, which are aggressive and fatal cancers with a dismal prognosis, could exploit UPS mechanisms to communicate with their microenvironment. Herein, we provide functional insights into the UPS machinery in the context of tumor biology, with a particular focus on the secreted proteins by alternative routes as key regulators in the maintenance of brain tumors.
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Affiliation(s)
- Rebeca Piatniczka Iglesia
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Mariana Brandão Prado
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Rodrigo Nunes Alves
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Isabel Melo Escobar
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Camila Felix de Lima Fernandes
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Ailine Cibele dos Santos Fortes
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria Clara da Silva Souza
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Jacqueline Marcia Boccacino
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Giovanni Cangiano
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Samuel Ribeiro Soares
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - João Pedro Alves de Araújo
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Deanna Marie Tiek
- The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Anshika Goenka
- The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Xiao Song
- The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Jack Ryan Keady
- The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Bo Hu
- The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Shi Yuan Cheng
- The Robert H. Lurie Comprehensive Cancer Center, The Ken and Ruth Davee Department of Neurology, Lou and Jean Malnati Brain Tumor Institute at Northwestern Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Marilene Hohmuth Lopes
- Laboratory of Neurobiology and Stem Cells, Department of Cell and Developmental Biology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Marilene Hohmuth Lopes,
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5
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Hou W, Li GS, Gao L, Lu HP, Zhou HF, Kong JL, Chen G, Xia S, Wei HY. SYNJ2 is a novel and potential biomarker for the prediction and treatment of cancers: from lung squamous cell carcinoma to pan-cancer. BMC Med Genomics 2022; 15:114. [PMID: 35581615 PMCID: PMC9112447 DOI: 10.1186/s12920-022-01266-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 05/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The roles and clinical values of synaptojanin 2 (SYNJ2) in lung squamous cell carcinoma (LUSC) remain unclear. METHODS A total of 2824 samples from multi-center were collected to identify the expression of SYNJ2 in LUSC by using Wilcoxon rank-sum test, t-test, and standardized mean difference (SMD), and 194 in-house samples were also included to validate SYNJ2 expression in LUSC. The clinical roles of SYNJ2 were investigated via receiver operating characteristic (ROC) curves, univariate Cox regression analysis, and Kaplan-Meier plots. The underlying mechanisms of SYNJ2 in LUSC were explored by gene set enrichment analysis and immune correlation analysis. Further, a pan-cancer analysis based on 10,238 sapiens was performed to promote the understating of the expression and clinical significance of SYNJ2 in multiple human cancers. RESULTS SYNJ2 was found to be significantly upregulated in LUSC at both mRNA and protein levels (p < 0.05, SMD = 0.89 [95% CI 0.34-1.45]) via public and in-house samples. Overexpressed SYNJ2 predicted poor prognosis for LUSC patients (hazard ratio = 2.38 [95% CI 1.42-3.98]). The cancer-promoting effect of SYNJ2 may be related to protein digestion and absorption and extracellular matrix-receptor interaction. SYNJ2 expression was closely related to immune cell infiltration, indicating its role in the immune response. Moreover, the distinct expression levels and essential clinical relevance of SYNJ2 in a series of cancers were initially revealed in this study. CONCLUSIONS This study disclosed the clinical significance of SYNJ2 in LUSC and multiple cancers, demonstrating the novel and potential biomarker for predicting and treating cancers.
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Affiliation(s)
- Wei Hou
- Guangxi Key Laboratory of Thalassemia Research, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.,Key Laboratory of Thalassemia Medicine, Chinese Academy of Medical Sciences, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Guo-Sheng Li
- Guangxi Key Laboratory of Thalassemia Research, Life Sciences Institute, Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Li Gao
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hui-Ping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hua-Fu Zhou
- Department of Cardiothoracic Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Jin-Liang Kong
- Ward of Pulmonary and Critical Care Medicine, Department of Respiratory Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Shuang Xia
- Department of Human Anatomy, Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
| | - Hong-Yu Wei
- Department of Organic Chemistry and Medicinal Chemistry, Pharmaceutical College, Guangxi Medical University, Nanning, 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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6
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Chen J, Sun S, Ren L, Hua L, Wang D, Xie Q, Wirsching HG, Deng J, Weller M, Gong Y. m 6A Regulator Expression Segregates Meningiomas Into Biologically Distinct Subtypes. Front Oncol 2022; 11:760892. [PMID: 35004283 PMCID: PMC8727752 DOI: 10.3389/fonc.2021.760892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/29/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Meningiomas are the most common primary intracranial tumors in adults. According to the 2021 World Health Organization (WHO) classification of central nervous system tumors, approximately 80% of meningiomas are WHO grade 1, that is, histopathologically benign, whereas about 20% are WHO grade 2 or grade 3, showing signs of atypia or malignancy. The dysregulation of N6-methylation (m6A) regulators is associated with disorders of diverse critical biological processes in human cancer. This study aimed to explore whether m6A regulator expression was associated with meningioma molecular subtypes and immune infiltration. METHODS We evaluated the m6A modification patterns of 160 meningioma samples based on 19 m6A regulators and correlated them with immune infiltration characteristics. Novel molecular subtypes were defined based on prognostic hub gene expression. RESULTS Two meningioma clusters were identified based on the expression of 19 m6A regulators. In cluster 1, 607 differentially expressed genes (DEGs) were upregulated and 519 were downregulated. A total of 1,126 DEGs comprised three gene expression modules characterized by turquoise, blue, and gray. Functional annotation suggested that the turquoise module was involved in Wnt-related and other important cancer-related pathways. We identified 32 hub genes in this module by constructing a protein-protein interaction network. The meningioma samples were divided into two molecular subtypes. EPN1, EXOSC4, H2AX, and MZT2B not only showed significant differences between meningioma molecular subtypes but also had the potential to be the marker genes of specific meningioma subtypes. CONCLUSION m6A regulator gene expression may be a novel prognostic marker in meningioma.
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Affiliation(s)
- Jiawei Chen
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Shuchen Sun
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Leihao Ren
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Lingyang Hua
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Daijun Wang
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Qing Xie
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Jiaojiao Deng
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China
| | - Michael Weller
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Ye Gong
- Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China.,Institute of Neurosurgery, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Brain Function Restoration and Neural Regeneration, Fudan University, Shanghai, China.,Department of Critical Care Medicine, Huashan Hospital, Fudan University, Shanghai, China
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7
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Shin J, Nile A, Oh JW. Role of adaptin protein complexes in intracellular trafficking and their impact on diseases. Bioengineered 2021; 12:8259-8278. [PMID: 34565296 PMCID: PMC8806629 DOI: 10.1080/21655979.2021.1982846] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/15/2021] [Accepted: 09/15/2021] [Indexed: 02/07/2023] Open
Abstract
Adaptin proteins (APs) play a crucial role in intracellular cell trafficking. The 'classical' role of APs is carried out by AP1‒3, which bind to clathrin, cargo, and accessory proteins. Accordingly, AP1-3 are crucial for both vesicle formation and sorting. All APs consist of four subunits that are indispensable for their functions. In fact, based on studies using cells, model organism knockdown/knock-out, and human variants, each subunit plays crucial roles and contributes to the specificity of each AP. These studies also revealed that the sorting and intracellular trafficking function of AP can exert varying effects on pathology by controlling features such as cell development, signal transduction related to the apoptosis and proliferation pathways in cancer cells, organelle integrity, receptor presentation, and viral infection. Although the roles and functions of AP1‒3 are relatively well studied, the functions of the less abundant and more recently identified APs, AP4 and AP5, are still to be investigated. Further studies on these APs may enable a better understanding and targeting of specific diseases.APs known or suggested locations and functions.
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Affiliation(s)
- Juhyun Shin
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Arti Nile
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
| | - Jae-Wook Oh
- Department of Stem Cell and Regenerative Biotechnology and Animal Resources Research Center, Konkuk University, Seoul, Republic of Korea
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8
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das Chagas PF, de Sousa GR, Veronez LC, Martins-da-Silva A, Corrêa CAP, Cruzeiro GAV, Nagano LFP, Queiroz RGDP, Marie SKN, Brandalise SR, Scrideli CA, Tone LG, Valera ET. Identification of ITPR1 as a Hub Gene of Group 3 Medulloblastoma and Coregulated Genes with Potential Prognostic Values. J Mol Neurosci 2021; 72:633-641. [PMID: 34822110 DOI: 10.1007/s12031-021-01942-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/04/2021] [Indexed: 01/03/2023]
Abstract
The Group 3 Medulloblastoma (Grp3-MB) is an aggressive molecular subtype with a high incidence of metastasis and deaths. In this study, were used an RNA sequencing data (RNA-Seq) from a Brazilian cohort of MBs to identify hub genes associated with the metastatic risk. Data validation were performed by using multiple large datasets from MBs (GSE85217, GSE37418, and EGAS00001001953). DESeq2 package in R software was used to identify the differentially expressed genes (DEGs) in our RNA-Seq data. The DEGs data were accessed to construct the modules/graphs of co-expression and to identify hub genes through Cytoscape platform. The coregulated genes were enriched by the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, and the protein-protein interaction (PPI) network was visualized by Cytoscape. The Kaplan-Meier plotter and ROC curves were used to validate the diagnostic and prognostic values of specific biomarkers identified through this model. We identified that inositol 1,4,5-trisphosphate receptor type 1 (ITPR1) as a downregulated hub gene, with a high diagnostic accuracy to Grp3-MBs and associated with tumor metastasis. In addition, we identified genes significantly correlated with ITPR1 that were associated with metastasis in Grp3-MB (ATP1A2, MTTL7A, and RGL1) and worst overall survival in MBs (ANTXR1 and RGL1). Our findings suggest that the ITPR1 hub gene is potentially involved in the metastatic process for Grp3-MB. Our data also provide evidence of targets that may serve as prognostic predictors and/or regulators for the metastatic process that maybe explored for further research of individualized therapy to Grp3-MBs.
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Affiliation(s)
- Pablo Ferreira das Chagas
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.
| | - Graziella Ribeiro de Sousa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Luciana Chain Veronez
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Andrea Martins-da-Silva
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Carolina Alves Pereira Corrêa
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Gustavo Alencastro Veiga Cruzeiro
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil.,Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luis Fernando Peinado Nagano
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil
| | - Rosane Gomes de Paula Queiroz
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Suely Kazue Nagahashi Marie
- Laboratory of Cellular and Molecular Biology, Department of Neurology, Faculdade de Medicina FMUSP, Universidade de SãoPaulo, São Paulo, SP, Brazil
| | | | - Carlos Alberto Scrideli
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.,Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Luiz Gonzaga Tone
- Department of Genetics, Ribeirão Preto Medical School, University of São Paulo, Avenida Bandeirantes, Ribeirão Preto, CEP, 390014049-900, Brazil.,Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
| | - Elvis Terci Valera
- Department of Pediatrics, Ribeirão Preto Medical School, Clinics Hospital, University of São Paulo Ribeirão Preto, Ribeirão, Brazil
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Lu X, Li C, Xu W, Wu Y, Wang J, Chen S, Zhang H, Huang H, Huang H, Liu W. Malignant Tumor Purity Reveals the Driven and Prognostic Role of CD3E in Low-Grade Glioma Microenvironment. Front Oncol 2021; 11:676124. [PMID: 34557404 PMCID: PMC8454269 DOI: 10.3389/fonc.2021.676124] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 07/02/2021] [Indexed: 12/23/2022] Open
Abstract
The tumor microenvironment (TME) contributes to the initiation and progression of many neoplasms. However, the impact of low-grade glioma (LGG) purity on carcinogenesis remains to be elucidated. We selected 509 LGG patients with available genomic and clinical information from the TCGA database. The percentage of tumor infiltrating immune cells and the tumor purity of LGG were evaluated using the ESTIMATE and CIBERSORT algorithms. Stromal-related genes were screened through Cox regression, and protein-protein interaction analyses and survival-related genes were selected in 487 LGG patients from GEO database. Hub genes involved in LGG purity were then identified and functionally annotated using bioinformatics analyses. Prognostic implications were validated in 100 patients from an Asian real-world cohort. Elevated tumor purity burden, immune scores, and stromal scores were significantly associated with poor outcomes and increased grade in LGG patients from the TCGA cohort. In addition, CD3E was selected with the most significant prognostic value (Hazard Ratio=1.552, P<0.001). Differentially expressed genes screened according to CD3E expression were mainly involved in stromal related activities. Additionally, significantly increased CD3E expression was found in 100 LGG samples from the validation cohort compared with adjacent normal brain tissues. High CD3E expression could serve as an independent prognostic indicator for survival of LGG patients and promotes malignant cellular biological behaviors of LGG. In conclusion, tumor purity has a considerable impact on the clinical, genomic, and biological status of LGG. CD3E, the gene for novel membrane immune biomarker deeply affecting tumor purity, may help to evaluate the prognosis and develop individual immunotherapy strategies for LGG patients. Evaluating the ratio of differential tumor purity and CD3E expression levels may provide novel insights into the complex structure of the LGG microenvironment and targeted drug development.
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Affiliation(s)
- Xiuqin Lu
- Department of Nursing and Health Management, Shanghai University of Medicine & Health Sciences, Shanghai, China
| | - Chuanyu Li
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Wenhao Xu
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical University, Fudan University, Shanghai, China
| | - Yuanyuan Wu
- Department of Gastroenterology, Naval Medical Center of People’s Liberation Army (PLA) of China, Naval Military Medical University, Shanghai, China
| | - Jian Wang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shuxian Chen
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hailiang Zhang
- Department of Urology, Fudan University Shanghai Cancer Center, Shanghai Medical University, Fudan University, Shanghai, China
| | - Huadong Huang
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Haineng Huang
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
| | - Wangrui Liu
- Department of Nursing and Health Management, Shanghai University of Medicine & Health Sciences, Shanghai, China
- Department of Neurosurgery, Affiliated Hospital of Youjiang Medical University for Nationalities, Guangxi, China
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10
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Cao R, Shao J, Zhang W, Lin Y, Huang Z, Li Z. Silencing long intergenic non-protein coding RNA 00987 inhibits proliferation, migration, and invasion of osteosarcoma cells by sponging miR-376a-5p to regulate FNBP1 expression. Discov Oncol 2021; 12:18. [PMID: 35201476 PMCID: PMC8777572 DOI: 10.1007/s12672-021-00412-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 05/24/2021] [Indexed: 01/19/2023] Open
Abstract
High expression of long intergenic non-protein coding RNA 987 (LINC00987) is strongly associated with low overall survival of osteosarcoma; however, its role in osteosarcoma remains unclear. This study explored the biological function and underlying mechanism of LINC00987 in osteosarcoma. In this study, LINC00987 expression in osteosarcoma cells was analyzed using Cancer Cell Line Encyclopedia and qRT-PCR. The proliferation and migration and invasion in osteosarcoma cells were evaluated using Cell Counting Kit-8 and Transwell assays, respectively. Bioinformatic analysis was used to predict the LINC00987-bound miRNAs and miR-376a-5p-bound mRNAs. Dual-luciferase reporter assays were used to assess the interaction between miR-376a-5p, LINC00987, and forming-binding protein 1 (FNBP1). FNBP1 expression was measured by western blotting. LINC00987 was found to be upregulated in osteosarcoma cells. LINC00987 silencing suppressed proliferation, migration, and invasion of osteosarcoma cells. Additionally, miR-376a-5p expression was downregulated in osteosarcoma cells. miR-376a-5p knockdown reversed the effect of LINC00987 silencing on the biological function of osteosarcoma cell. miR-376a-5p was found to target LINC00987 and FNBP1. FNBP1protein level was increased in osteosarcoma cells; however, it was inhibited by silencing LINC00987 and enhanced by silencing miR-376a-5p. In conclusions, this study suggests LINC00987 silencing inhibits osteosarcoma cell proliferation, migration, and invasion by sponging miR-376a-5p to regulate FNBP1 expression. LINC00987 as a potential therapeutic target for osteosarcoma.
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Affiliation(s)
- Riliang Cao
- Department of Orthopedics, First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Tianhe District, Guangzhou, 510630, China
| | - Jianli Shao
- Department of Orthopedics, First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Tianhe District, Guangzhou, 510630, China
| | - Wencai Zhang
- Department of Orthopedics, First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Tianhe District, Guangzhou, 510630, China
| | - Yongxin Lin
- Department of Orthopedics, First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Tianhe District, Guangzhou, 510630, China
| | - Zerong Huang
- Department of Orthopedics, First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Tianhe District, Guangzhou, 510630, China
| | - Zhizhong Li
- Department of Orthopedics, First Affiliated Hospital of Jinan University, 613 W. Huangpu Avenue, Tianhe District, Guangzhou, 510630, China.
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11
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Wang XW, Sun Q, Xu SB, Xu C, Xia CJ, Zhao QM, Zhang HH, Tan WQ, Zhang L, Yao SD. A 3-DNA methylation signature as a novel prognostic biomarker in patients with sarcoma by bioinformatics analysis. Medicine (Baltimore) 2021; 100:e26040. [PMID: 34011115 PMCID: PMC8137010 DOI: 10.1097/md.0000000000026040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Accepted: 05/04/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Tumor-specific DNA methylation can potentially be a useful indicator in cancer diagnostics and monitoring. Sarcomas comprise a heterogeneous group of mesenchymal neoplasms which cause life-threatening tumors occurring throughout the body. Therefore, potential molecular detection and prognostic evaluation is very important for early diagnosis and treatment. METHODS We performed a retrospective study analyzing DNA methylation of 261 patients with sarcoma from The Cancer Genome Atlas (TCGA) database. Cox regression analyses were conducted to identify a signature associated with the overall survival (OS) of patients with sarcoma, which was validated in a validation dataset. RESULTS Three DNA methylation signatures were identified to be significantly associated with OS. Kaplan-Meier analysis showed that the 3-DNA methylation signature could significantly distinguish the high- and low-risk patients in both training (first two-thirds) and validation datasets (remaining one-third). Receiver operating characteristic (ROC) analysis confirmed that the 3-DNA methylation signature exhibited high sensitivity and specificity in predicting OS of patients. Also, the Kaplan-Meier analysis and the area under curve (AUC) values indicated that the 3-DNA methylation signature was independent of clinical characteristics, including age at diagnosis, sex, anatomic location, tumor residual classification, and histological subtypes. CONCLUSIONS The current study showed that the 3-DNA methylation model could efficiently function as a novel and independent prognostic biomarker and therapeutic target for patients with sarcoma.
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Affiliation(s)
| | - Qi Sun
- Department of Orthopedic Surgery, Fuyang Orthopedics and Traumatology Hospital, Zhejiang Chinese Medical University
| | - Shi-Bin Xu
- Department of Orthopedic Surgery, The First People's Hospital of Xiaoshan District
| | - Chao Xu
- Department of Oncology, Zhejiang Cancer Hospital
| | - Chen-Jie Xia
- Department of Orthopedic Surgery, Li Hui-Li Hospital, Ningbo
| | - Qi-Ming Zhao
- Department of Plastic Surgery, Zhejiang Hospital
| | | | - Wei-Qiang Tan
- Department of Plastic Surgery, Sir Run Run Shaw Hospital, Zhejiang University College of Medicine
| | - Lei Zhang
- Department of Orthopedic Surgery, Xiaoshan Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Hangzhou
| | - Shu-Dong Yao
- Department of Nephrology, Huzhou Hospital of Traditional Chinese Medicine, Zhejiang Chinese Medical University, Huzhou, Zhejiang, China
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12
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Pan X, Liu W, Chai Y, Hu L, Wang J, Zhang Y. Identification of Hub Genes in Atypical Teratoid/Rhabdoid Tumor by Bioinformatics Analyses. J Mol Neurosci 2020; 70:1906-1913. [PMID: 32440821 DOI: 10.1007/s12031-020-01587-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 05/13/2020] [Indexed: 02/06/2023]
Abstract
Atypical teratoid/rhabdoid tumor (ATRT) is a devastating intracranial tumor in children. Currently, its molecular mechanisms cannot be studied effectively because patient samples are limited, and many factors are involved in its pathogenesis. In this study, we analyzed three gene expression profile data sets obtained from the Gene Expression Omnibus (GEO) database to identify genes that participate in ATRT. The datasets were integrated and analyzed using the RobustRankAggreg method to screen for differentially expressed genes (DEGs). We identified 197 DEGs, including 94 downregulated and 103 upregulated genes which were then used for gene set enrichment analysis. The results showed that the downregulated genes were mainly enriched in synaptic vesicle cycle, nicotine addiction, and GABAergic synapse, whereas the upregulated genes were enriched in the cell cycle, p53 signaling pathway, and cellular senescence. Consistent with these results, gene set enrichment analysis showed that E2F targets, G2M checkpoints, and MYC targets were significantly enriched in datasets. Protein-protein interaction (PPI) network revealed that CDK1, CCNA2, BUB1B, CDC20, KIF11, KIF20A, KIF2C, NCAPG, NDC80, NUSAP1, PBK, RRM2, TPX2, TOP2A, and TTK were hub genes. NetworkAnalyst algorithm was used to predict the transcription factor (TF), and the results showed that MYC, SOX2, and KDM5B could regulate these hub genes. In conclusion, the present study brings a new perspective of ATRT pathogenesis and the strategy targeted to cell cycle related gene may be promising treatments for the disease.
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Affiliation(s)
- Xin Pan
- Department of Neurosurgery, Yuquan Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 100040, China
| | - Wei Liu
- School of Clinical Medicine, Tsinghua University, Beijing, 10084, China
| | - Yi Chai
- School of Clinical Medicine, Tsinghua University, Beijing, 10084, China
| | - Libo Hu
- School of Clinical Medicine, Tsinghua University, Beijing, 10084, China
| | - Junhua Wang
- Department of Neurosurgery, Yuquan Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 100040, China
| | - Yuqi Zhang
- Department of Neurosurgery, Yuquan Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 100040, China.
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