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Lucchini S, Constantinou M, Marino S. Unravelling the mosaic: Epigenetic diversity in glioblastoma. Mol Oncol 2024. [PMID: 39148319 DOI: 10.1002/1878-0261.13706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 06/21/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024] Open
Abstract
Glioblastoma is the most common primary malignant brain tumour. Despite decades of intensive research in the disease, its prognosis remains poor, with an average survival of only 14 months after diagnosis. The remarkable level of intra- and interpatient heterogeneity is certainly contributing to the lack of progress in tackling this tumour. Epigenetic dysregulation plays an important role in glioblastoma biology and significantly contributes to intratumour heterogeneity. However, it is becoming increasingly clear that it also contributes to intertumour heterogeneity, which historically had mainly been linked to diverse genetic events occurring in different patients. In this review, we explore how DNA methylation, chromatin remodelling, microRNA (miRNA) dysregulation, and long noncoding RNA (lncRNA) alterations contribute to intertumour heterogeneity in glioblastoma, including its implications for advanced tumour stratification, which is the essential first step for developing more effective patient-specific therapeutic approaches.
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Affiliation(s)
- Sara Lucchini
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Myrianni Constantinou
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
| | - Silvia Marino
- Brain Tumour Research Centre, Blizard Institute, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Brain Tumour Centre, Faculty of Medicine and Dentistry, Queen Mary University of London, UK
- Barts Health NHS Trust, London, UK
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2
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Pokorná M, Černá M, Boussios S, Ovsepian SV, O’Leary VB. lncRNA Biomarkers of Glioblastoma Multiforme. Biomedicines 2024; 12:932. [PMID: 38790894 PMCID: PMC11117901 DOI: 10.3390/biomedicines12050932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules of 200 nucleotides or more in length that are not translated into proteins. Their expression is tissue-specific, with the vast majority involved in the regulation of cellular processes and functions. Many human diseases, including cancer, have been shown to be associated with deregulated lncRNAs, rendering them potential therapeutic targets and biomarkers for differential diagnosis. The expression of lncRNAs in the nervous system varies in different cell types, implicated in mechanisms of neurons and glia, with effects on the development and functioning of the brain. Reports have also shown a link between changes in lncRNA molecules and the etiopathogenesis of brain neoplasia, including glioblastoma multiforme (GBM). GBM is an aggressive variant of brain cancer with an unfavourable prognosis and a median survival of 14-16 months. It is considered a brain-specific disease with the highly invasive malignant cells spreading throughout the neural tissue, impeding the complete resection, and leading to post-surgery recurrences, which are the prime cause of mortality. The early diagnosis of GBM could improve the treatment and extend survival, with the lncRNA profiling of biological fluids promising the detection of neoplastic changes at their initial stages and more effective therapeutic interventions. This review presents a systematic overview of GBM-associated deregulation of lncRNAs with a focus on lncRNA fingerprints in patients' blood.
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Affiliation(s)
- Markéta Pokorná
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK;
- Faculty of Medicine, Health, and Social Care, Canterbury Christ Church University, Canterbury CT2 7PB, UK
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
- Kent Medway Medical School, University of Kent, Canterbury CT2 7LX, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
| | - Saak V. Ovsepian
- Faculty of Engineering and Science, University of Greenwich London, Chatham Maritime, Kent ME4 4TB, UK;
- Faculty of Medicine, Tbilisi State University, Tbilisi 0177, Georgia
| | - Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
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3
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Hao W, Yang W, Yang Y, Cheng T, Wei T, Tang L, Qian N, Yang Y, Li X, Jiang H, Wang M. Identification of lncRNA-miRNA-mRNA Networks in the Lenticular Nucleus Region of the Brain Contributes to Hepatolenticular Degeneration Pathogenesis and Therapy. Mol Neurobiol 2024; 61:1673-1686. [PMID: 37759104 PMCID: PMC10896925 DOI: 10.1007/s12035-023-03631-1] [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: 04/12/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023]
Abstract
Long non-coding RNAs (lncRNAs) are a recently discovered group of non-coding RNAs that play a crucial role in the regulation of various human diseases, especially in the study of nervous system diseases which has garnered significant attention. However, there is limited knowledge on the identification and function of lncRNAs in hepatolenticular degeneration (HLD). The objective of this study was to identify novel lncRNAs and determine their involvement in the networks associated with HLD. We conducted a comprehensive analysis of RNA sequencing (RNA-seq) data, reverse transcription-quantitative polymerase chain reaction (RT-qPCR), and computational biology to identify novel lncRNAs and explore their potential mechanisms in HLD. We identified 212 differently expressed lncRNAs, with 98 upregulated and 114 downregulated. Additionally, 32 differently expressed mRNAs were found, with 15 upregulated and 17 downregulated. We obtained a total of 1131 pairs of co-expressed lncRNAs and mRNAs by Pearson correlation test and prediction and annotation of the lncRNA-targeted miRNA-mRNA network. The differential lncRNAs identified in this study were found to be involved in various biological functions and signaling pathways. These include translational initiation, motor learning, locomotors behavior, dioxygenase activity, integral component of postsynaptic membrane, neuroactive ligand-receptor interaction, nuclear factor-kappa B (NF-κB) signaling pathway, cholinergic synapse, sphingolipid signaling pathway, and Parkinson's disease signaling pathway, as revealed by the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Six lncRNAs, including XR_001782921.1 (P < 0.01), XR_ 001780581.1 (P < 0.01), ENSMUST_00000207119 (P < 0.01), XR_865512.2 (P < 0.01), TCONS_00005916 (P < 0.01), and TCONS_00020683 (P < 0.01), showed significant differences in expression levels between the model group and normal group by RT-qPCR. Among these, four lncRNAs (TCONS_00020683, XR_865512.2, XR_001780581.1, and ENSMUST00000207119) displayed a high degree of conservation. This study provides a unique perspective for the pathogenesis and therapy of HLD by constructing the lncRNA-miRNA-mRNA network. This insight provides a foundation for future exploration in this field.
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Affiliation(s)
- Wenjie Hao
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Wenming Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China.
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China.
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China.
| | - Yue Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Ting Cheng
- Department of Graduate, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Taohua Wei
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Lulu Tang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Nannan Qian
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Yulong Yang
- Key Laboratory of Xin'an Medicine of the Ministry of Education, Anhui University of Chinese Medicine, Hefei, China
| | - Xiang Li
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
| | - Hailin Jiang
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
| | - Meixia Wang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, China
- Center for Xin'an Medicine and Modernization of Traditional Chinese Medicine of IHM, Anhui University of Chinese Medicine, Hefei, China
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4
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Bao L. Roles, underlying mechanisms and clinical significances of LINC01503 in human cancers. Pathol Res Pract 2024; 254:155125. [PMID: 38241778 DOI: 10.1016/j.prp.2024.155125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 12/05/2023] [Accepted: 01/08/2024] [Indexed: 01/21/2024]
Abstract
Long intergenic non-coding RNA 01503 (LINC01503) is a long non-coding RNA (lncRNA) located on human chromosome 9q34.11. There is compelling evidence indicating that LINC01503 is upregulated in multiple types of tumors and functions as a tumor stimulator. The upregulation of LINC01503 was significantly associated with the risk of 12 tumors and showed a strong correlation with clinicopathological characteristics and poor prognosis in 9 tumors. The expression of LINC01503 is regulated by transcription factors such as TP63, EGR1, c-MYC, GATA1 and AR. The downstream regulatory mechanisms of LINC01503 are complex and multifaceted. LINC01503, as a competing endogenous RNA (ceRNA), regulates gene expression by competitively inhibiting miRNA. LINC01503 may also regulate gene expression via interacting with biomolecules or recruiting chromatin-modifying complexes. In addition, LINC01503 can abnormally activate the ERK/MAPK, PI3K/AKT and Wnt/β-catenin signaling pathways to enhance tumor progression. Here, this review presents an overview of the latest research progress of LINC01503 in the field of oncology, summarizes its comprehensive network involved in multiple cancer molecular mechanisms, and explores its potential applications in cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Lei Bao
- College of Basic Medical Science, China Three Gorges University, Yichang 443002, China.
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5
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Jacob JR, Singh R, Okamoto M, Chakravarti A, Palanichamy K. miRNA-194-3p represses NF-κB in gliomas to attenuate iPSC genes and proneural to mesenchymal transition. iScience 2024; 27:108650. [PMID: 38226170 PMCID: PMC10788216 DOI: 10.1016/j.isci.2023.108650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/01/2023] [Accepted: 12/04/2023] [Indexed: 01/17/2024] Open
Abstract
Severe tumor heterogeneity drives the aggressive and treatment refractory nature of glioblastomas (GBMs). While limiting GBM heterogeneity offers promising therapeutic potential, the underlying mechanisms that regulate GBM plasticity remain poorly understood. We utilized 14 patient-derived and four commercially available cell lines to uncover miR-194-3p as a key epigenetic determinant of stemness and transcriptional subtype in GBM. We demonstrate that miR-194-3p degrades TAB2, an important mediator of NF-κB activity, decreasing NF-κB transcriptional activity. The loss in NF-κB activity following miR-194-3p overexpression or TAB2 silencing decreased expression of induced pluripotent stem cell (iPSC) genes, inhibited the oncogenic IL-6/STAT3 signaling axis, suppressed the mesenchymal transcriptional subtype in relation to the proneural subtype, and induced differentiation from the glioma stem cell (GSC) to monolayer (ML) phenotype. miR-194-3p/TAB2/NF-κB signaling axis acts as an epigenetic switch that regulates GBM plasticity and targeting this signaling axis represents a potential strategy to limit transcriptional heterogeneity in GBMs.
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Affiliation(s)
- John Ryan Jacob
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Rajbir Singh
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Masa Okamoto
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
- Department of Radiation Oncology, Gunma University Graduate School of Medicine, Gunma 371-8511, Japan
| | - Arnab Chakravarti
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Kamalakannan Palanichamy
- Department of Radiation Oncology, The Ohio State University College of Medicine and Comprehensive Cancer Center, Columbus, OH 43210, USA
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Chaim OM, Miki S, Prager BC, Ma J, Jeong AY, Lara J, Tran NK, Smith JM, Rich JN, Gutkind JS, Miyamoto S, Furnari FB, Brown JH. Gα12 signaling regulates transcriptional and phenotypic responses that promote glioblastoma tumor invasion. Sci Rep 2023; 13:22412. [PMID: 38104152 PMCID: PMC10725435 DOI: 10.1038/s41598-023-49164-4] [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: 08/30/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
In silico interrogation of glioblastoma (GBM) in The Cancer Genome Atlas (TCGA) revealed upregulation of GNA12 (Gα12), encoding the alpha subunit of the heterotrimeric G-protein G12, concomitant with overexpression of multiple G-protein coupled receptors (GPCRs) that signal through Gα12. Glioma stem cell lines from patient-derived xenografts also showed elevated levels of Gα12. Knockdown (KD) of Gα12 was carried out in two different human GBM stem cell (GSC) lines. Tumors generated in vivo by orthotopic injection of Gα12KD GSC cells showed reduced invasiveness, without apparent changes in tumor size or survival relative to control GSC tumor-bearing mice. Transcriptional profiling of GSC-23 cell tumors revealed significant differences between WT and Gα12KD tumors including reduced expression of genes associated with the extracellular matrix, as well as decreased expression of stem cell genes and increased expression of several proneural genes. Thrombospondin-1 (THBS1), one of the genes most repressed by Gα12 knockdown, was shown to be required for Gα12-mediated cell migration in vitro and for in vivo tumor invasion. Chemogenetic activation of GSC-23 cells harboring a Gα12-coupled DREADD also increased THBS1 expression and in vitro invasion. Collectively, our findings implicate Gα12 signaling in regulation of transcriptional reprogramming that promotes invasiveness, highlighting this as a potential signaling node for therapeutic intervention.
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Affiliation(s)
- Olga Meiri Chaim
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA.
- Department of Cell Biology, Federal University of Paraná, Curitiba, Brazil.
| | - Shunichiro Miki
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA
| | - Briana C Prager
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Cleveland Clinic Lerner College of Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Jianhui Ma
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA
| | - Anthony Y Jeong
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
| | - Jacqueline Lara
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
| | - Nancy K Tran
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
| | - Jeffrey M Smith
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
| | - Jeremy N Rich
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Neurology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - J Silvio Gutkind
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
- Moores Cancer Center, University of California at San Diego, La Jolla, CA, USA
| | - Shigeki Miyamoto
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
| | - Frank B Furnari
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, CA, USA
| | - Joan Heller Brown
- Department of Pharmacology, University of California San Diego, Biomedical Sciences Building, 9500 Gilman Drive #0636, La Jolla, CA, 92093-0636, USA
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Fan Y, Gao Z, Xu J, Wang H, Guo Q, Li B, Li M, Xu H, Qi Y, Zhao S, Qiu W, Pan Z, Wang Q, Xue H, Zhao R, Guo X, Li G. SPI1-mediated MIR222HG transcription promotes proneural-to-mesenchymal transition of glioma stem cells and immunosuppressive polarization of macrophages. Theranostics 2023; 13:3310-3329. [PMID: 37351164 PMCID: PMC10283056 DOI: 10.7150/thno.82590] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 05/07/2023] [Indexed: 06/24/2023] Open
Abstract
Background: Glioma stem cells (GSCs) are a key factor in glioblastoma (GBM) development and treatment resistance. GSCs can be divided into the mesenchymal (MES) and proneural (PN) subtypes, and these two subtypes of GSCs can undergo interconversion under certain conditions. MES GSCs have higher malignancy and radioresistance and are closely associated with an immunosuppressive microenvironment. Long noncoding RNAs (lncRNAs) play a broad role in GBM, while the role of GSCs subtype remains unknown. Methods: We performed RNA sequencing to explore the lncRNA expression profile in MES- and PN-subtype GBM tissues. The biological function of a host gene-MIR222HG-in GBM development was confirmed in vitro and in vivo. Specifically, RNA sequencing, RNA pulldown, mass spectrometry, RIP, ChIP, luciferase reporter assays and Co-IP were performed. Results: MIR222HG, the expression of which can be induced by SPI1, has high levels in MES GBM tissues. Functionally, we demonstrated that MIR222HG promotes the MES transition and radioresistance in GSCs in vivo and in vitro. Mechanistically, MIR222HG can bind to the YWHAE/HDAC5 complex to promote the MES transition of GSCs through H4 deacetylation. Moreover, cotranscribed miR221 and miR222 can be delivered to macrophages via exosomes to target SOCS3, causing immunosuppressive polarization. Finally, PLX-4720 sensitivity is associated with SPI1 expression and acts on MES GSCs to enhance radiosensitivity. Conclusions: This study demonstrates that targeting SPI1 to block transcription of the MIR222HG cluster helps to reduce radioresistance and combat the immunosuppressive microenvironment in GBM. PLX-4720 is a potential GBM drug and radiosensitizer.
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Affiliation(s)
- Yang Fan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Zijie Gao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Jianye Xu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
- Tianjin Neurological Institute, Key Laboratory of Post-Neuroinjury Neuro-repair and Regeneration in Central Nervous System, Ministry of Education and Tianjin City, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Huizhi Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Qindong Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Boyan Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Ming Li
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
- Department of Neurosurgery, The Affiliated Taian City Central Hospital of Qingdao University, Taian 271000, Shandong, China
| | - Hao Xu
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
- Department of Neurosurgery, The Affiliated Yantai Yuhuangding Hospital of Qingdao University, Yantai 264000, Shandong, China
| | - Yanhua Qi
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Shulin Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Wei Qiu
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Ziwen Pan
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Qingtong Wang
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Hao Xue
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Rongrong Zhao
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Xing Guo
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
| | - Gang Li
- Department of Neurosurgery, Qilu Hospital, Cheeloo College of Medicine and Institute of Brain and Brain-Inspired Science, Shandong University, Jinan 250012, Shandong, China
- Shandong Key Laboratory of Brain Function Remodeling, Jinan 250012, Shandong, China
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8
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Vasileva NS, Kuligina EV, Dymova MA, Savinovskaya YI, Zinchenko ND, Ageenko AB, Mishinov SV, Dome AS, Stepanov GA, Richter VA, Semenov DV. Transcriptome Changes in Glioma Cells Cultivated under Conditions of Neurosphere Formation. Cells 2022; 11:cells11193106. [PMID: 36231068 PMCID: PMC9563256 DOI: 10.3390/cells11193106] [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: 08/11/2022] [Revised: 09/23/2022] [Accepted: 09/27/2022] [Indexed: 11/16/2022] Open
Abstract
Glioma is the most common and heterogeneous primary brain tumor. The development of a new relevant preclinical models is necessary. As research moves from cultures of adherent gliomas to a more relevant model, neurospheres, it is necessary to understand the changes that cells undergo at the transcriptome level. In the present work, we used three patient-derived gliomas and two immortalized glioblastomas, while their cultivation was carried out under adherent culture and neurosphere (NS) conditions. When comparing the transcriptomes of monolayer (ML) and NS cell cultures, we used Enrichr genes sets enrichment analysis to describe transcription factors (TFs) and the pathways involved in the formation of glioma NS. It was observed that NS formation is accompanied by the activation of five common gliomas of TFs, SOX2, UBTF, NFE2L2, TCF3 and STAT3. The sets of transcripts controlled by TFs MYC and MAX were suppressed in NS. Upregulated genes are involved in the processes of the epithelial-mesenchymal transition, cancer stemness, invasion and migration of glioma cells. However, MYC/MAX-dependent downregulated genes are involved in translation, focal adhesion and apical junction. Furthermore, we found three EGFR and FGFR signaling feedback regulators common to all analyzed gliomas-SPRY4, ERRFI1, and RAB31-which can be used for creating new therapeutic strategies of suppressing the invasion and progression of gliomas.
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Affiliation(s)
- Natalia S. Vasileva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Elena V. Kuligina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Maya A. Dymova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Yulya I. Savinovskaya
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Nikita D. Zinchenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Alisa B. Ageenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Sergey V. Mishinov
- Novosibirsk Research Institute of Traumatology and Orthopedics n.a. Ya.L. Tsivyan, Department of Neurosurgery, Frunze Street 17, Novosibirsk 630091, Russia
| | - Anton S. Dome
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Grigory A. Stepanov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Vladimir A. Richter
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
| | - Dmitry V. Semenov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Lavrentyev Avenue 8, Novosibirsk 630090, Russia
- Correspondence: ; Tel.: +73-833635189
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9
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Long non-coding RNA LINC01018 inhibits human glioma cell proliferation and metastasis by directly targeting miRNA-182-5p. J Neurooncol 2022; 160:67-78. [PMID: 36094613 DOI: 10.1007/s11060-022-04113-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 08/04/2022] [Indexed: 10/14/2022]
Abstract
AIM Accumulating evidence suggests that lncRNAs are potential biomarkers and key regulators of tumor development and progression. However, the precise function of most lncRNAs in glioma remains unknown. In this study, we explored the role of long intergenic non-protein coding RNA 1018 (LINC01018) in human glioma. METHODS Expression levels of LINC01018 and miR-182-5p in clinical glioma tissues and cell lines were detected by quantitative real-time PCR (qRT-PCR). Cell proliferation, migration, and invasion were determined by Cell Counting Kit-8 (CCK-8) assay and Transwell assay. Epithelial-mesenchymal transition (EMT) related proteins were measured by Western blotting. Direct relationship between LINC01018 and miR-182-5p was tested by dual-luciferase reporter assay, RNA immunoprecipitation assay (RIP), and rescue assays. Lastly, bioinformatics analyses were conducted to predict the downstream factors of LINC01018/miR-182-5p axis in glioma. RESULTS LINC01018 was significantly down-regulated in glioma tissues and cell lines. Overexpression of LINC01018 dramatically inhibited cell proliferation, migration, and invasion and reverse EMT process in glioma. LINC01018 directly target to miR-182-5p. Forced up-regulation of miR-182-5p reversed the inhibitory effects on proliferative and metastatic abilities of glioma cells with LINC01018 overexpression. Lastly, the bioinformatics analyses revealed that LINC01018/miR-182-5p axis mediated a cluster of downstream genes (ADRA2C, RAB6B, RAB27B, RAPGEF5, STEAP2, TAGLN3, and UNC13C), which were potential key factors in the development of glioma. CONCLUSION LINC01018 inhibits cell proliferation and metastasis in human glioma by targeting miR-182-5p, and should be considered as a potential therapeutic target in this cancer.
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Zhang YB, Zheng SF, Ma LJ, Lin P, Shang-Guan HC, Lin YX, Kang DZ, Yao PS. Elevated Hexose-6-Phosphate Dehydrogenase Regulated by OSMR-AS1/hsa-miR-516b-5p Axis Correlates with Poor Prognosis and Dendritic Cells Infiltration of Glioblastoma. Brain Sci 2022; 12:brainsci12081012. [PMID: 36009075 PMCID: PMC9405636 DOI: 10.3390/brainsci12081012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 07/18/2022] [Accepted: 07/22/2022] [Indexed: 02/04/2023] Open
Abstract
Objective Glioblastoma (GBM), a type of malignant glioma, is the most aggressive type of brain tumor and is associated with high mortality. Hexose-6-phosphate dehydrogenase (H6PD) has been detected in multiple tumors and is involved in tumor initiation and progression. However, the specific role and mechanism of H6PD in GBM remain unclear. Methods We performed pan-cancer analysis of expression and prognosis of H6PD in GBM using the Genotype-Tissue Expression Project (GTEx) and The Cancer Genome Atlas (TCGA). Subsequently, noncoding RNAs regulating H6PD expression were obtained by comprehensive analysis, including gene expression, prognosis, correlation, and immune infiltration. Finally, tumor immune infiltrates related to H6PD and survival were performed. Results Higher expression of H6PD was statistically significantly associated with an unfavorable outcome in GBM. Downregulation of hsa-miR-124-3p and hsa-miR-516b-5p in GBM was detected from GSE90603. Subsequently, OSMR-AS1 was observed in the regulation of H6PD via hsa-miR-516b-5p. Moreover, higher H6PD expression significantly correlated with immune infiltration of dendritic cells, immune checkpoint expression, and biomarkers of dendritic cells. Conclusions The OSMR-AS1/ miR-516b-5p axis was identified as the highest-potential upstream ncRNA-related pathway of H6PD in GBM. Furthermore, the present findings demonstrated that H6PD blockading might possess antitumor roles via regulating dendritic cell infiltration and immune checkpoint expression.
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Affiliation(s)
- Yi-Bin Zhang
- Department of Neurosurgery, Neurosurgical Research Institute, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China; (Y.-B.Z.); (S.-F.Z.); (H.-C.S.-G.); (Y.-X.L.)
| | - Shu-Fa Zheng
- Department of Neurosurgery, Neurosurgical Research Institute, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China; (Y.-B.Z.); (S.-F.Z.); (H.-C.S.-G.); (Y.-X.L.)
| | - Lin-Jie Ma
- Department of Neurology and Neurosurgery, Changji Traditional Chinese Medicine Hospital, Changji 831100, China;
| | - Peng Lin
- Department of Pain, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China;
| | - Huang-Cheng Shang-Guan
- Department of Neurosurgery, Neurosurgical Research Institute, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China; (Y.-B.Z.); (S.-F.Z.); (H.-C.S.-G.); (Y.-X.L.)
| | - Yuan-Xiang Lin
- Department of Neurosurgery, Neurosurgical Research Institute, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China; (Y.-B.Z.); (S.-F.Z.); (H.-C.S.-G.); (Y.-X.L.)
- Fujian Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
| | - De-Zhi Kang
- Department of Neurosurgery, Neurosurgical Research Institute, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China; (Y.-B.Z.); (S.-F.Z.); (H.-C.S.-G.); (Y.-X.L.)
- Fujian Key Laboratory of Precision Medicine for Cancer, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Key Laboratory of Radiation Biology of Fujian Higher Education Institutions, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Fujian Provincial Institutes of Brain Disorders and Brain Sciences, First Affiliated Hospital, Fujian Medical University, Fuzhou 350005, China
- Correspondence: (D.-Z.K.); (P.-S.Y.); Tel.: +8613859099988 (D.-Z.K.); +8618650084102 (P.-S.Y.); Fax: +86-591-83569369 (D.-Z.K. &P.-S.Y.)
| | - Pei-Sen Yao
- Department of Neurosurgery, Neurosurgical Research Institute, First Affiliated Hospital, Fujian Medical University, Fuzhou 350004, China; (Y.-B.Z.); (S.-F.Z.); (H.-C.S.-G.); (Y.-X.L.)
- Department of Neurology and Neurosurgery, Changji Traditional Chinese Medicine Hospital, Changji 831100, China;
- Correspondence: (D.-Z.K.); (P.-S.Y.); Tel.: +8613859099988 (D.-Z.K.); +8618650084102 (P.-S.Y.); Fax: +86-591-83569369 (D.-Z.K. &P.-S.Y.)
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Entezari M, Sadrkhanloo M, Rashidi M, Asnaf SE, Taheriazam A, Hashemi M, Ashrafizadeh M, Zarrabi A, Rabiee N, Hushmandi K, Mirzaei S, Sethi G. Non-coding RNAs and macrophage interaction in tumor progression. Crit Rev Oncol Hematol 2022; 173:103680. [PMID: 35405273 DOI: 10.1016/j.critrevonc.2022.103680] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 03/25/2022] [Accepted: 04/06/2022] [Indexed: 12/12/2022] Open
Abstract
The macrophages are abundantly found in TME and their M2 polarization is in favor of tumor malignancy. On the other hand, non-coding RNAs (ncRNAs) can modulate macrophage polarization in TME to affect cancer progression. The miRNAs can dually induce/suppress M2 polarization of macrophages and by affecting various molecular pathways, they modulate tumor progression and therapy response. The lncRNAs can affect miRNAs via sponging and other molecular pathways to modulate macrophage polarization. A few experiments have also examined role of circRNAs in targeting signaling networks and affecting macrophages. The therapeutic targeting of these ncRNAs can mediate TME remodeling and affect macrophage polarization. Furthermore, exosomal ncRNAs derived from tumor cells or macrophages can modulate polarization and TME remodeling. Suppressing biogenesis and secretion of exosomes can inhibit ncRNA-mediated M2 polarization of macrophages and prevent tumor progression. The ncRNAs, especially exosomal ncRNAs can be considered as non-invasive biomarkers for tumor diagnosis.
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Affiliation(s)
- Maliheh Entezari
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | | | - Mohsen Rashidi
- Department Pharmacology, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran; The Health of Plant and Livestock Products Research Center, Mazandaran University of Medical Sciences, Sari, Iran
| | - Sholeh Etehad Asnaf
- Department of Cell and Molecular Biology, Faculty of Biological Sciences, North Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Afshin Taheriazam
- Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Department of Orthopedics, Faculty of medicine, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Mehrdad Hashemi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran; Farhikhtegan Medical Convergence sciences Research Center, Farhikhtegan Hospital Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Milad Ashrafizadeh
- Faculty of Engineering and Natural Sciences, Sabanci University, Orta Mahalle, Üniversite Caddesi No. 27, Orhanlı, Tuzla, Istanbul, Turkey
| | - Ali Zarrabi
- Department of Biomedical Engineering, Faculty of Engineering and Natural Sciences, Istinye University, Istanbul 34396, Turkey
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Kiavash Hushmandi
- Department of Food Hygiene and Quality Control, Division of Epidemiology & Zoonoses, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran.
| | - Sepideh Mirzaei
- Department of Biology, Faculty of Science, Islamic Azad University, Science and Research Branch, Tehran, Iran.
| | - Gautam Sethi
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Cancer Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore.
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12
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Wei P, Jiang J, Xiao M, Zeng M, Liu X, Zhao B, Chen F. The transcript ENST00000444125 of lncRNA LINC01503 promotes cancer stem cell properties of glioblastoma cells via reducing FBXW1 mediated GLI2 degradation. Exp Cell Res 2022; 412:113009. [PMID: 34990616 DOI: 10.1016/j.yexcr.2022.113009] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 12/22/2021] [Accepted: 01/02/2022] [Indexed: 11/04/2022]
Abstract
LINC010503 is a novel oncogenic lncRNA in multiple cancers. In this study, we further explored the expression of LINC010503 transcripts and their regulations on the glioblastoma (GBM) stem cell (GSC) properties. LINC01503 transcription patterns in GBM and normal brain tissues were compared using RNA-seq data from Genotype-Tissue Expression (GTEx) and The Cancer Genome Atlas (TCGA)-GBM. GBM cell lines (U251 and U87) were used as in vitro cell models for cellular and molecular studies. The results showed that ENST00000444125 was the dominant transcript of LINC01503 in both normal and tumor tissues. Its expression was significantly elevated in the tumor group and associated with poor survival outcomes. LINC01503 had both cytoplasmic and nuclear distribution. It positively modulated the expression of multiple GSC markers, including CD133, SOX2, NESTIN, ALDH1A1, and MSI1, and tumorsphere formation in U251 and U87 cells. RNA pull-down and RIP-qPCR assay confirmed an interaction between ENST00000444125 and GLI2. ENST00000444125 positively regulated the half-life of the GLI2 protein in GBM cells. ENST00000444125 overexpression reduced GLI2 ubiquitination and partially attenuated FBXW1 overexpression induced GLI2 ubiquitination. ENST00000444125 overexpression could activate Wnt/β-catenin signaling in GBM cells. However, these activating effects were remarkedly hampered when GLI2 was knocked down. In conclusion, this study revealed that LINC01503 might have isoform-specific dysregulation in GBM. Among the two major transcripts expressed in GBM cells, ENST00000444125 might be the major functional transcript. Its upregulation might enhance the GSC properties of GBM cells via reducing FBXW1-mediated proteasomal degradation of GLI2.
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Affiliation(s)
- Pan Wei
- Department of Neurosurgery, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China
| | - Jing Jiang
- Department of Gastroenterology, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China
| | - Ming Xiao
- Department of Neurosurgery, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China
| | - Mengfei Zeng
- Department of Neurosurgery, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China
| | - Xingzhi Liu
- Department of Neurosurgery, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China
| | - Baihao Zhao
- Department of Neurosurgery, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China
| | - Fang Chen
- Department of Neurosurgery, The First People(')s Hospital of LongQuanYi District, Chengdu, Sichuan, 610100, China.
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Wu J, Ren X, Wang N, Zhou R, Chen M, Cai Y, Lin S, Zhang H, Xie X, Dang C, Zhang S, Zhou Z. A Mutation-Related Long Noncoding RNA Signature of Genome Instability Predicts Immune Infiltration and Hepatocellular Carcinoma Prognosis. Front Genet 2021; 12:779554. [PMID: 34880908 PMCID: PMC8645863 DOI: 10.3389/fgene.2021.779554] [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: 09/19/2021] [Accepted: 11/03/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Long noncoding RNAs (lncRNAs) have been discovered to play a regulatory role in genomic instability (GI), which participates in the carcinogenesis of various cancers, including hepatocellular carcinoma (HCC). We endeavored to establish a GI-derived lncRNA signature (GILncSig) as a potential biomarker and explore its impact on immune infiltration and prognostic significance. Methods: Combining expression and somatic mutation profiles from The Cancer Genome Atlas database, we identified GI-related lncRNAs and conducted functional analyses on co-expressed genes. Based on Cox regression analysis, a GILncSig was established in the training cohort (n = 187), and an independent testing patient cohort (n = 183) was used to validate its predictive ability. Kaplan-Meier method and receiver operating characteristic curves were adopted to evaluate the performance. The correlation between GI and immune infiltration status was investigated based on the CIBERSORT algorithm and single sample gene set enrichment analysis. In addition, a comprehensive nomogram integrating the GILncSig and clinicopathological variables was constructed to efficiently assess HCC patient prognosis in clinical applications. Results: A total of 88 GI-related lncRNAs were screened out and the functional analyses indicated diversified effects on HCC progression. The GILncSig was established using four independent lncRNAs (AC116351.1, ZFPM2-AS1, AC145343.1, and MIR210HG) with significant prognostic value (p < 0.05). Following evaluation with the GILncSig, low-risk patients had significantly better clinical outcomes than high-risk patients in the training cohort (p < 0.001), which was subsequently validated in the independent testing cohort. High-risk group exhibited more immunocyte infiltration including B cells memory, macrophages M0 and neutrophils and higher expression of HLA gene set and immune checkpoint genes. Compared to existing HCC signatures, the GILncSig showed better prognosis predictive performance [area under the curve (AUC) = 0.709]. Furthermore, an integrated nomogram was constructed and validated to efficiently and reliably evaluate HCC patient prognosis (3-years survival AUC = 0.710 and 5-years survival AUC = 0.707). Conclusion: The GILncSig measuring GI and impacting immune infiltration serves as a potential biomarker and independent predictor of HCC patient prognosis. Our results highlight further investigation of GI and HCC molecular mechanisms.
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Affiliation(s)
- Jianhua Wu
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xueting Ren
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Nan Wang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ruina Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Mengsha Chen
- Department of Anesthesia, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yifan Cai
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuai Lin
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Hao Zhang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Xin Xie
- Department of Nuclear Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Shuqun Zhang
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Zhangjian Zhou
- Department of Oncology, The Second Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Shen Z, Liu S, Liu J, Liu J, Yao C. Weighted Gene Co-Expression Network Analysis and Treatment Strategies of Tumor Recurrence-Associated Hub Genes in Lung Adenocarcinoma. Front Genet 2021; 12:756235. [PMID: 34868230 PMCID: PMC8636777 DOI: 10.3389/fgene.2021.756235] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/06/2021] [Indexed: 12/16/2022] Open
Abstract
Despite the recent progress of lung adenocarcinoma (LUAD) therapy, tumor recurrence remained to be a challenging factor that impedes the effectiveness of treatment. The objective of the present study was to predict the hub genes affecting LUAD recurrence via weighted gene co-expression network analysis (WGCNA). Microarray samples from LUAD dataset of GSE32863 were analyzed, and the modules with the highest correlation to tumor recurrence were selected. Functional enrichment analysis was conducted, followed by establishment of a protein-protein interaction (PPI) network. Subsequently, hub genes were identified by overall survival analyses and further validated by evaluation of expression in both myeloid populations and tissue samples of LUAD. Gene set enrichment analysis (GSEA) was then carried out, and construction of transcription factors (TF)-hub gene and drug-hub gene interaction network was also achieved. A total of eight hub genes (ACTR3, ARPC5, RAB13, HNRNPK, PA2G4, WDR12, SRSF1, and NOP58) were finally identified to be closely correlated with LUAD recurrence. In addition, TFs that regulate hub genes have been predicted, including MYC, PML, and YY1. Finally, drugs including arsenic trioxide, cisplatin, Jinfukang, and sunitinib were mined for the treatment of the eight hub genes. In conclusion, our study may facilitate the invention of targeted therapeutic drugs and shed light on the understanding of the mechanism for LUAD recurrence.
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Affiliation(s)
- Zhengze Shen
- Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Shengwei Liu
- Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Jie Liu
- JiangJin Central Hosptial of Chongqing, Chongqing, China
| | - Jingdong Liu
- Department of Pharmacy, First People's Hospital of Chongqing Liangjiang New District, Chongqing, China
| | - Caoyuan Yao
- Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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15
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Wu ZH, Li ZW, Yang DL, Liu J. Development and Validation of a Pyroptosis-Related Long Non-coding RNA Signature for Hepatocellular Carcinoma. Front Cell Dev Biol 2021; 9:713925. [PMID: 34869306 PMCID: PMC8634266 DOI: 10.3389/fcell.2021.713925] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 10/05/2021] [Indexed: 01/07/2023] Open
Abstract
Background: Hepatocellular carcinoma (HCC) is a highly aggressive malignant disease, and numerous studies have demonstrated that an inflammatory environment can induce normal cells to transform into cancerous. Methods: We integrated genomic data to comprehensively assess the association between pyroptosis and tumor microenvironment (TME) cell-infiltrating characteristics in HCC, as well as the potential molecular function and clinical significance of lncRNA. Results: The analysis of CNV alteration frequency displayed that CNV changes were common in 33 PRGs, and most were focused on copy number amplification. As a result of lasso regression analysis, nine differentially expressed lncRNAs (AL031985.3, NRAV, OSMR-AS1, AC073611.1, MKLN1-AS, AL137186.2, AL049840.4, MIR4435-2HG, and AL118511.1) were selected as independent prognosis factors of HCC patients. Patients at high risk have poorer survival than those in the low-risk group in training and testing cohorts. A low-risk score was significantly associated with an IC50 of chemotherapeutics such as bortezomib (p < 0.001), but a high-risk score was significantly linked to docetaxel (p < 0.001), implying that signature served as a prospective predictor for chemosensitivity. Conclusion: This work suggests pyroptosis-related lncRNAs features and their potential mechanisms on tumor microenvironment. The exploration may assist in identifying novel biomarkers and assist patients in predicting their prognosis, clinical diagnosis, and management.
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Affiliation(s)
- Zeng-Hong Wu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zi-Wei Li
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Dong-Liang Yang
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jia Liu
- Department of Infectious Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Liang Q, Wu J, Zhao X, Shen S, Zhu C, Liu T, Cui X, Chen L, Wei C, Cheng P, Cheng W, Wu A. Establishment of tumor inflammasome clusters with distinct immunogenomic landscape aids immunotherapy. Am J Cancer Res 2021; 11:9884-9903. [PMID: 34815793 PMCID: PMC8581407 DOI: 10.7150/thno.63202] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 10/06/2021] [Indexed: 12/22/2022] Open
Abstract
Inflammasome signaling is a reaction cascade that influences immune response and cell death. Although the inflammasomes participate in tumorigenesis, their role as an oncogenic booster or a tumor suppresser is still controversial. Therefore, it is important to comprehensively investigate the inflammasome signaling status across various cancers to clarify its clinical and therapeutic significance. Methods: A total of 9881 patients across 33 tumor types from The Cancer Genome Atlas database were included in this study. Five gene sets were identified to step-wisely profile inflammasome signaling. Unsupervised clustering was used for sample classification based on gene set enrichment. Machine learning and in vitro and in vivo experiments were used to confirm the implications of inflammasome classification. Results: A hundred and forty-one inflammasome-signaling-related genes were identified to construct five gene sets representing the sensing, activation, and termination steps of the inflammasome signaling. Six inflammasome clusters were robustly established with distinct molecular, biological, clinical, and therapeutic features. Importantly, clusters with inflammasome signaling activation were found to be immunosuppressive and resistant to ICB treatment. Inflammasome inhibition reverted the therapeutic failure of ICB in inflammasome-activated tumors. Moreover, based on the proposed classification and therapeutic implications, an open website was established to provide tumor patients with comprehensive information on inflammasome signaling. Conclusions: Our study conducted a systematical investigation on inflammasome signaling in various tumor types. These findings highlight the importance of inflammasome evaluation in tumor classification and provide a foundation for improving relevant therapeutic regimens.
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Colapietro A, Rossetti A, Mancini A, Martellucci S, Ocone G, Pulcini F, Biordi L, Cristiano L, Mattei V, Delle Monache S, Marampon F, Gravina GL, Festuccia C. Multiple Antitumor Molecular Mechanisms Are Activated by a Fully Synthetic and Stabilized Pharmaceutical Product Delivering the Active Compound Sulforaphane (SFX-01) in Preclinical Model of Human Glioblastoma. Pharmaceuticals (Basel) 2021; 14:1082. [PMID: 34832864 PMCID: PMC8626029 DOI: 10.3390/ph14111082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 09/23/2021] [Accepted: 10/18/2021] [Indexed: 12/11/2022] Open
Abstract
Frequent relapses and therapeutic resistance make the management of glioblastoma (GBM, grade IV glioma), extremely difficult. Therefore, it is necessary to develop new pharmacological compounds to be used as a single treatment or in combination with current therapies in order to improve their effectiveness and reduce cytotoxicity for non-tumor cells. SFX-01 is a fully synthetic and stabilized pharmaceutical product containing the α-cyclodextrin that delivers the active compound 1-isothiocyanato-4-methyl-sulfinylbutane (SFN) and maintains biological activities of SFN. In this study, we verified whether SFX-01 was active in GBM preclinical models. Our data demonstrate that SFX-01 reduced cell proliferation and increased cell death in GBM cell lines and patient-derived glioma initiating cells (GICs) with a stem cell phenotype. The antiproliferative effects of SFX-01 were associated with a reduction in the stemness of GICs and reversion of neural-to-mesenchymal trans-differentiation (PMT) closely related to epithelial-to-mesenchymal trans-differentiation (EMT) of epithelial tumors. Commonly, PMT reversion decreases the invasive capacity of tumor cells and increases the sensitivity to pharmacological and instrumental therapies. SFX-01 induced caspase-dependent apoptosis, through both mitochondrion-mediated intrinsic and death-receptor-associated extrinsic pathways. Here, we demonstrate the involvement of reactive oxygen species (ROS) through mediating the reduction in the activity of essential molecular pathways, such as PI3K/Akt/mTOR, ERK, and STAT-3. SFX-01 also reduced the in vivo tumor growth of subcutaneous xenografts and increased the disease-free survival (DFS) and overall survival (OS), when tested in orthotopic intracranial GBM models. These effects were associated with reduced expression of HIF1α which, in turn, down-regulates neo-angiogenesis. So, SFX-01 may have potent anti-glioma effects, regulating important aspects of the biology of this neoplasia, such as hypoxia, stemness, and EMT reversion, which are commonly activated in this neoplasia and are responsible for therapeutic resistance and glioma recurrence. SFX-01 deserves to be considered as an emerging anticancer agent for the treatment of GBM. The possible radio- and chemo sensitization potential of SFX-01 should also be evaluated in further preclinical and clinical studies.
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Affiliation(s)
- Alessandro Colapietro
- Laboratory of Radiobiology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.R.); (A.M.); (G.O.); (G.L.G.)
| | - Alessandra Rossetti
- Laboratory of Radiobiology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.R.); (A.M.); (G.O.); (G.L.G.)
| | - Andrea Mancini
- Laboratory of Radiobiology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.R.); (A.M.); (G.O.); (G.L.G.)
| | - Stefano Martellucci
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy; (S.M.); (V.M.)
- Laboratory of Vascular Biology and Stem Cells, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.P.); (S.D.M.)
| | - Giuseppe Ocone
- Laboratory of Radiobiology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.R.); (A.M.); (G.O.); (G.L.G.)
| | - Fanny Pulcini
- Laboratory of Vascular Biology and Stem Cells, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.P.); (S.D.M.)
| | - Leda Biordi
- Laboratory of Medical Oncology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Loredana Cristiano
- Department of Clinical Medicine, Public Health, Division of Human Anatomy, University of L’Aquila, 67100 L’Aquila, Italy;
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100 Rieti, Italy; (S.M.); (V.M.)
| | - Simona Delle Monache
- Laboratory of Vascular Biology and Stem Cells, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (F.P.); (S.D.M.)
| | - Francesco Marampon
- Department of Radiological, Oncological and Pathological Sciences, La Sapienza University of Rome, 00185 Rome, Italy;
| | - Giovanni Luca Gravina
- Laboratory of Radiobiology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.R.); (A.M.); (G.O.); (G.L.G.)
- Department of Biotechnological and Applied Clinical Sciences, Division of Radiotherapy, University of L’Aquila, 67100 L’Aquila, Italy
| | - Claudio Festuccia
- Laboratory of Radiobiology, Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (A.C.); (A.R.); (A.M.); (G.O.); (G.L.G.)
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18
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Huang K, Yue X, Zheng Y, Zhang Z, Cheng M, Li L, Chen Z, Yang Z, Bian E, Zhao B. Development and Validation of an Mesenchymal-Related Long Non-Coding RNA Prognostic Model in Glioma. Front Oncol 2021; 11:726745. [PMID: 34540695 PMCID: PMC8446619 DOI: 10.3389/fonc.2021.726745] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/16/2021] [Indexed: 12/29/2022] Open
Abstract
Glioma is well known as the most aggressive and prevalent primary malignant tumor in the central nervous system. Molecular subtypes and prognosis biomarkers remain a promising research area of gliomas. Notably, the aberrant expression of mesenchymal (MES) subtype related long non-coding RNAs (lncRNAs) is significantly associated with the prognosis of glioma patients. In this study, MES-related genes were obtained from The Cancer Genome Atlas (TCGA) and the Ivy Glioblastoma Atlas Project (Ivy GAP) data sets of glioma, and MES-related lncRNAs were acquired by performing co-expression analysis of these genes. Next, Cox regression analysis was used to establish a prognostic model, that integrated ten MES-related lncRNAs. Glioma patients in TCGA were divided into high-risk and low-risk groups based on the median risk score; compared with the low-risk groups, patients in the high-risk group had shorter survival times. Additionally, we measured the specificity and sensitivity of our model with the ROC curve. Univariate and multivariate Cox analyses showed that the prognostic model was an independent prognostic factor for glioma. To verify the predictive power of these candidate lncRNAs, the corresponding RNA-seq data were downloaded from the Chinese Glioma Genome Atlas (CGGA), and similar results were obtained. Next, we performed the immune cell infiltration profile of patients between two risk groups, and gene set enrichment analysis (GSEA) was performed to detect functional annotation. Finally, the protective factors DGCR10 and HAR1B, and risk factor SNHG18 were selected for functional verification. Knockdown of DGCR10 and HAR1B promoted, whereas knockdown of SNHG18 inhibited the migration and invasion of gliomas. Collectively, we successfully constructed a prognostic model based on a ten MES-related lncRNAs signature, which provides a novel target for predicting the prognosis for glioma patients.
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Affiliation(s)
- Kebing Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Xiaoyu Yue
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Yinfei Zheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhengwei Zhang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Meng Cheng
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Lianxin Li
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhigang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Zhihao Yang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Erbao Bian
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
| | - Bing Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.,Cerebral Vascular Disease Research Center, Anhui Medical University, Hefei, China
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19
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Sharma RK, Calderon C, Vivas-Mejia PE. Targeting Non-coding RNA for Glioblastoma Therapy: The Challenge of Overcomes the Blood-Brain Barrier. FRONTIERS IN MEDICAL TECHNOLOGY 2021; 3:678593. [PMID: 35047931 PMCID: PMC8757885 DOI: 10.3389/fmedt.2021.678593] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant form of all primary brain tumors, and it is responsible for around 200,000 deaths each year worldwide. The standard therapy for GBM treatment includes surgical resection followed by temozolomide-based chemotherapy and/or radiotherapy. With this treatment, the median survival rate of GBM patients is only 15 months after its initial diagnosis. Therefore, novel and better treatment modalities for GBM treatment are urgently needed. Mounting evidence indicates that non-coding RNAs (ncRNAs) have critical roles as regulators of gene expression. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are among the most studied ncRNAs in health and disease. Dysregulation of ncRNAs is observed in virtually all tumor types, including GBMs. Several dysregulated miRNAs and lncRNAs have been identified in GBM cell lines and GBM tumor samples. Some of them have been proposed as diagnostic and prognostic markers, and as targets for GBM treatment. Most ncRNA-based therapies use oligonucleotide RNA molecules which are normally of short life in circulation. Nanoparticles (NPs) have been designed to increase the half-life of oligonucleotide RNAs. An additional challenge faced not only by RNA oligonucleotides but for therapies designed for brain-related conditions, is the presence of the blood-brain barrier (BBB). The BBB is the anatomical barrier that protects the brain from undesirable agents. Although some NPs have been derivatized at their surface to cross the BBB, optimal NPs to deliver oligonucleotide RNA into GBM cells in the brain are currently unavailable. In this review, we describe first the current treatments for GBM therapy. Next, we discuss the most relevant miRNAs and lncRNAs suggested as targets for GBM therapy. Then, we compare the current drug delivery systems (nanocarriers/NPs) for RNA oligonucleotide delivery, the challenges faced to send drugs through the BBB, and the strategies to overcome this barrier. Finally, we categorize the critical points where research should be the focus in order to design optimal NPs for drug delivery into the brain; and thus move the Oligonucleotide RNA-based therapies from the bench to the clinical setting.
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Affiliation(s)
- Rohit K. Sharma
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Carlos Calderon
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
| | - Pablo E. Vivas-Mejia
- Comprehensive Cancer Center, University of Puerto Rico, San Juan, PR, United States
- Department of Biochemistry, University of Puerto Rico, Medical Sciences Campus, San Juan, PR, United States
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20
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Sorokin M, Raevskiy M, Zottel A, Šamec N, Skoblar Vidmar M, Matjašič A, Zupan A, Mlakar J, Suntsova M, Kuzmin DV, Buzdin A, Jovčevska I. Large-Scale Transcriptomics-Driven Approach Revealed Overexpression of CRNDE as a Poor Survival Prognosis Biomarker in Glioblastoma. Cancers (Basel) 2021; 13:3419. [PMID: 34298634 PMCID: PMC8303503 DOI: 10.3390/cancers13143419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma is the most common and malignant brain malignancy worldwide, with a 10-year survival of only 0.7%. Aggressive multimodal treatment is not enough to increase life expectancy and provide good quality of life for glioblastoma patients. In addition, despite decades of research, there are no established biomarkers for early disease diagnosis and monitoring of patient response to treatment. High throughput sequencing technologies allow for the identification of unique molecules from large clinically annotated datasets. Thus, the aim of our study was to identify significant molecular changes between short- and long-term glioblastoma survivors by transcriptome RNA sequencing profiling, followed by differential pathway-activation-level analysis. We used data from the publicly available repositories The Cancer Genome Atlas (TCGA; number of annotated cases = 135) and Chinese Glioma Genome Atlas (CGGA; number of annotated cases = 218), and experimental clinically annotated glioblastoma tissue samples from the Institute of Pathology, Faculty of Medicine in Ljubljana corresponding to 2-58 months overall survival (n = 16). We found one differential gene for long noncoding RNA CRNDE whose overexpression showed correlation to poor patient OS. Moreover, we identified overlapping sets of congruently regulated differential genes involved in cell growth, division, and migration, structure and dynamics of extracellular matrix, DNA methylation, and regulation through noncoding RNAs. Gene ontology analysis can provide additional information about the function of protein- and nonprotein-coding genes of interest and the processes in which they are involved. In the future, this can shape the design of more targeted therapeutic approaches.
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Affiliation(s)
- Maxim Sorokin
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1000 Brussels, Belgium;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Mikhail Raevskiy
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Alja Zottel
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
| | - Neja Šamec
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
| | | | - Alenka Matjašič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Jernej Mlakar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Maria Suntsova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Denis V. Kuzmin
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Anton Buzdin
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1000 Brussels, Belgium;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- OmicsWay Corp., Walnut, CA 91789, USA
| | - Ivana Jovčevska
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
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21
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Liu S, Zeng F, Fan G, Dong Q. Identification of Hub Genes and Construction of a Transcriptional Regulatory Network Associated With Tumor Recurrence in Colorectal Cancer by Weighted Gene Co-expression Network Analysis. Front Genet 2021; 12:649752. [PMID: 33897765 PMCID: PMC8058478 DOI: 10.3389/fgene.2021.649752] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/15/2021] [Indexed: 12/26/2022] Open
Abstract
Tumor recurrence is one of the most important risk factors that can negatively affect the survival rate of colorectal cancer (CRC) patients. However, the key regulators dictating this process and their exact mechanisms are understudied. This study aimed to construct a gene co-expression network to predict the hub genes affecting CRC recurrence and to inspect the regulatory network of hub genes and transcription factors (TFs). A total of 177 cases from the GSE17536 dataset were analyzed via weighted gene co-expression network analysis to explore the modules related to CRC recurrence. Functional annotation of the key module genes was assessed through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. The protein and protein interaction network was then built to screen hub genes. Samples from the Cancer Genome Atlas (TCGA) were further used to validate the hub genes. Construction of a TFs-miRNAs–hub genes network was also conducted using StarBase and Cytoscape approaches. After identification and validation, a total of five genes (TIMP1, SPARCL1, MYL9, TPM2, and CNN1) were selected as hub genes. A regulatory network of TFs-miRNAs-targets with 29 TFs, 58 miRNAs, and five hub genes was instituted, including model GATA6-MIR106A-CNN1, SP4-MIR424-TPM2, SP4-MIR326-MYL9, ETS1-MIR22-TIMP1, and ETS1-MIR22-SPARCL1. In conclusion, the identification of these hub genes and the prediction of the Regulatory relationship of TFs-miRNAs-hub genes may provide a novel insight for understanding the underlying mechanism for CRC recurrence.
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Affiliation(s)
- Shengwei Liu
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China.,Chongqing Key Laboratory of Biochemistry and Molecular Pharmacology, School of Pharmacy, Chongqing Medical University, Chongqing, China
| | - Fanping Zeng
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Guangwen Fan
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Qiyong Dong
- Department of Pharmacy, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
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