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Connerty P, Lock RB. The tip of the iceberg-The roles of long noncoding RNAs in acute myeloid leukemia. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1796. [PMID: 37267628 PMCID: PMC10909534 DOI: 10.1002/wrna.1796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) are traditionally defined as RNA transcripts longer than 200 nucleotides that have no protein coding potential. LncRNAs have been identified to be dysregulated in various types of cancer, including the deadly hematopoietic cancer-acute myeloid leukemia (AML). Currently, survival rates for AML have reached a plateau necessitating new therapeutic targets and biomarkers to improve treatment options and survival from the disease. Therefore, the identification of lncRNAs as novel biomarkers and therapeutic targets for AML has major benefits. In this review, we assess the key studies which have recently identified lncRNAs as important molecules in AML and summarize the current knowledge of lncRNAs in AML. We delve into examples of the specific roles of lncRNA action in AML such as driving proliferation, differentiation block and therapy resistance as well as their function as tumor suppressors and utility as biomarkers. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patrick Connerty
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneySydneyNew South WalesAustralia
- School of Clinical MedicineUNSW Medicine & Health, UNSW SydneySydneyNew South WalesAustralia
- University of New South Wales Centre for Childhood Cancer ResearchUNSW SydneySydneyNew South WalesAustralia
| | - Richard B. Lock
- Children's Cancer Institute, Lowy Cancer Research CentreUNSW SydneySydneyNew South WalesAustralia
- School of Clinical MedicineUNSW Medicine & Health, UNSW SydneySydneyNew South WalesAustralia
- University of New South Wales Centre for Childhood Cancer ResearchUNSW SydneySydneyNew South WalesAustralia
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2
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Budeus B, Unger K, Hess J, Sentek H, Klein D. Comparative computational analysis to distinguish mesenchymal stem cells from fibroblasts. Front Immunol 2023; 14:1270493. [PMID: 37822926 PMCID: PMC10562561 DOI: 10.3389/fimmu.2023.1270493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 08/30/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction Mesenchymal stem cells (MSCs) are considered to be the most promising stem cell type for cell-based therapies in regenerative medicine. Based on their potential to home to diseased body sites following a therapeutically application, these cells could (i) differentiate then into organ-specific cell types to locally restore injured cells or, most prominently, (ii) foster tissue regeneration including immune modulations more indirectly by secretion of protective growth factors and cytokines. As tissue-resident stem cells of mesenchymal origin, these cells are morphologically and even molecularly- at least concerning the classical marker genes- indistinguishable from similar lineage cells, particularly fibroblasts. Methods Here we used microarray-based gene expression and global DNA methylation analyses as well as accompanying computational tools in order to specify differences between MSCs and fibroblasts, to further unravel potential identity genes and to highlight MSC signaling pathways with regard to their trophic and immunosuppressive action. Results We identified 1352 differentially expressed genes, of which in the MSCs there is a strong signature for e.g., KRAS signaling, known to play essential role in stemness maintenance, regulation of coagulation and complement being decisive for resolving inflammatory processes, as well as of wound healing particularly important for their regenerative capacity. Genes upregulated in fibroblasts addressed predominately transcription and biosynthetic processes and mapped morphological features of the tissue. Concerning the cellular identity, we specified the already known HOX code for MSCs, established a potential HOX code for fibroblasts, and linked certain HOX genes to functional cell-type-specific properties. Accompanied methylation profiles revealed numerous regions, especially in HOX genes, being differentially methylated, which might provide additional biomarker potential. Discussion Conclusively, transcriptomic together with epigenetic signatures can be successfully be used for the definition (cellular identity) of MSCs versus fibroblasts as well as for the determination of the superior functional properties of MSCs, such as their immunomodulatory potential.
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Affiliation(s)
- Bettina Budeus
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Kristian Unger
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Julia Hess
- Research Unit Radiation Cytogenetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Clinical Cooperation Group Personalized Radiotherapy in Head and Neck Cancer, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Hanna Sentek
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Diana Klein
- Institute for Cell Biology (Cancer Research), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
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Kałuzińska-Kołat Ż, Kołat D, Kośla K, Płuciennik E, Bednarek AK. Delineating the glioblastoma stemness by genes involved in cytoskeletal rearrangements and metabolic alterations. World J Stem Cells 2023; 15:302-322. [PMID: 37342224 PMCID: PMC10277965 DOI: 10.4252/wjsc.v15.i5.302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 02/03/2023] [Accepted: 03/08/2023] [Indexed: 05/26/2023] Open
Abstract
Literature data on glioblastoma ongoingly underline the link between metabolism and cancer stemness, the latter is one responsible for potentiating the resistance to treatment, inter alia due to increased invasiveness. In recent years, glioblastoma stemness research has bashfully introduced a key aspect of cytoskeletal rearrangements, whereas the impact of the cytoskeleton on invasiveness is well known. Although non-stem glioblastoma cells are less invasive than glioblastoma stem cells (GSCs), these cells also acquire stemness with greater ease if characterized as invasive cells and not tumor core cells. This suggests that glioblastoma stemness should be further investigated for any phenomena related to the cytoskeleton and metabolism, as they may provide new invasion-related insights. Previously, we proved that interplay between metabolism and cytoskeleton existed in glioblastoma. Despite searching for cytoskeleton-related processes in which the investigated genes might have been involved, not only did we stumble across the relation to metabolism but also reported genes that were found to be implicated in stemness. Thus, dedicated research on these genes in GSCs seems justifiable and might reveal novel directions and/or biomarkers that could be utilized in the future. Herein, we review the previously identified cytoskeleton/metabolism-related genes through the prism of glioblastoma stemness.
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Affiliation(s)
- Żaneta Kałuzińska-Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Damian Kołat
- Department of Experimental Surgery, Medical University of Lodz, Lodz 90-136, Lodzkie, Poland
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Katarzyna Kośla
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Elżbieta Płuciennik
- Department of Functional Genomics, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
| | - Andrzej K Bednarek
- Department of Molecular Carcinogenesis, Medical University of Lodz, Lodz 90-752, Lodzkie, Poland
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Wu W, Li Q, Zhu Z, Li C, Lu P, Zhou X, Huang Y, Liu Y, Wang M, Gong J. HTR1D functions as a key target of HOXA10-AS/miR-340-3p axis to promote the malignant outcome of pancreatic cancer via PI3K-AKT signaling pathway. Int J Biol Sci 2022; 18:3777-3794. [PMID: 35813473 PMCID: PMC9254475 DOI: 10.7150/ijbs.70546] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/12/2022] [Indexed: 11/05/2022] Open
Abstract
Competing endogenous RNAs (ceRNAs) are a newly discovered class of molecular regulators involved in many diseases, especially tumors. Therefore, exploration of the potential ceRNA regulatory network regarding the occurrence and development of pancreatic cancer will provide a new theoretical basis for its diagnosis and treatment. Based on the above background, we applied a bioinformatics approach to mine the public database The Cancer Genome Atlas (TCGA) and performed a series of subsequent molecular biology assays to confirm the hypothesis that HOXA10-AS/ miR-340-3p/HTR1D axis could modulate the malignant progression of pancreatic cancer. Here, our present study demonstrated that the expression level of HTR1D, positively correlated with the level of lncRNA HOXA10-AS and negatively associated with the level of miR-340-3p, was significantly increased in pancreatic cancer cell lines (PCs) compared with that in normal HPDE6-C7 cells. Knocking down HTR1D obviously inhibited the proliferation and migration of PCs and promoted apoptosis by upregulating p-AKT. Elevated miR-340-3p blocked the progression of pancreatic cancer by downregulating HTR1D. Lessened level of lncRNA HOXA10-AS reduced the sponging of miR-340-3p, resulting in an increase of miR-340-3p and a subsequent decrease of HTR1D to ultimately suppress the malignant biological behaviors of cancer. These data illustrated that the HOXA10-AS/miR-340-3p/HTR1D ceRNA axis acted a crucial part in the malignant biological behavior of pancreatic cancer in an AKT-dependent manner.
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Affiliation(s)
- Wu Wu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Qujin Li
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Zhu Zhu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Chunming Li
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Peilin Lu
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Xi Zhou
- Department of Gastroenterology, Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
| | - Yujing Huang
- Department of Dermatology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yan Liu
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Gastroenterology, The Fifth People's Hospital of Chengdu, Chengdu, Sichuan, China
| | - Menghao Wang
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jianping Gong
- Department of Hepatobiliary Surgery, The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
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+HOXA10-AS Promotes Malignant Phenotypes of Gastric Cancer via Upregulating HOXA10. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:1846687. [PMID: 35222681 PMCID: PMC8866012 DOI: 10.1155/2022/1846687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/16/2021] [Accepted: 12/29/2021] [Indexed: 12/07/2022]
Abstract
Objective To study the role of long noncoding RNA HOXA10-AS in gastric cancer (GC) and its underlying mechanism which is one of the most common and fetal malignancies. Long noncoding RNA HOXA10-AS is highly expressed and acts in an oncogenic role in cancers. However, its roles in GC are still unknown. Methods The expression of HOXA10-AS and HOXA10 in GC tissues from the TCGA database was analyzed. Western blot and qRT-PCR assays were applied to examine the expression of HOXA10-AS and HOXA10. Cell proliferation was evaluated with CCK-8 and EdU incorporation assays. Cell apoptosis was analyzed by flow cytometry. Migratory and invasive capacities were evaluated with wound healing and transwell assays. Results HOXA10-AS and HOXA10 were upregulated in GC, and their expressions were positively correlated. Knockdown of HOXA10-AS inhibited HOXA10 expression in GC cells. Furthermore, knockdown of HOXA10-AS restrained GC cell proliferation, migration, and invasion but promoted apoptosis. In addition, overexpression of HOXA10-AS promoted malignant phenotypes of GC cells, but all these effects could be reversed by knockdown of HOXA10. Conclusion HOXA10-AS promoted GC cell proliferation, migration and invasion and enhanced apoptosis via upregulating HOXA10. Our study implies a novel regulatory mechanism of malignant phenotypes and provides potential therapeutic targets for GC.
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Wang X, Nie P, Zhu D. LncRNA HOXA10-AS Activated by E2F1 Facilitates Proliferation and Migration of Nasopharyngeal Carcinoma Cells Through Sponging miR-582-3p to Upregulate RAB31. Am J Rhinol Allergy 2022; 36:348-359. [PMID: 35072529 DOI: 10.1177/19458924211064400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a kind of head and neck cancer with a characteristic regional distribution. Increasing evidence has illustrated that long noncoding RNAs (lncRNAs) exert the regulatory function in tumor development. Nevertheless, the specific functions of lncRNA HOXA10 antisense RNA (HOXA10-AS) in NPC remain to be clarified. In this research, quantitative reverse transcription polymerase chain reaction detected HOXA10-AS expression in NPC cells. Cell counting kit-8, colony formation, and transwell assays were utilized to measure the proliferation and migration of NPC cells. Moreover, mechanism assays detected the interaction of different genes. Briefly, HOXA10-AS was highly expressed in NPC cells. HOXA10-AS down-regulation restrained NPC cell proliferation and migration. Further, HOXA10-AS could bind to miR-582-3p by acting as a competing endogenous RNA. Besides, Ras-related protein Rab-31 (RAB31) was proven as the target gene of miR-582-3p. Additionally, E2F transcription factor 1 (E2F1) acted as a transcription factor to activate HOXA10-AS expression. In the final rescue assays, we observed that the effect of HOXA10-AS depletion on NPC cell growth could be fully reversed by RAB31 overexpression or miR-582-3p inhibition. In short, our research proved that HOXA10-AS activated by E2F1 facilitated proliferation and migration of NPC cells through sponging miR-582-3p to upregulate RAB31.
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Affiliation(s)
- Xinyan Wang
- Jinan Fourth People's Hospital, Jinan, China
| | - Peilan Nie
- Jinan Fourth People's Hospital, Jinan, China
| | - Dongmei Zhu
- Jinan Fourth People's Hospital, Jinan, China
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Shao W, Ding Q, Guo Y, Xing J, Huo Z, Wang Z, Xu Q, Guo Y. A Pan-Cancer Landscape of HOX-Related lncRNAs and Their Association With Prognosis and Tumor Microenvironment. Front Mol Biosci 2021; 8:767856. [PMID: 34805277 PMCID: PMC8602076 DOI: 10.3389/fmolb.2021.767856] [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: 08/31/2021] [Accepted: 10/20/2021] [Indexed: 12/27/2022] Open
Abstract
The highly conserved homology cassette family (HOX) as well as 18 referenced long non-coding antisense transcripts (HOXATs) play vital roles in the development of some cancers. Nevertheless, their expression patterns as well as their association with cancer prognosis and the tumor microenvironment (TME) in pan-cancers are still unclear. Here, based on public databases, the expression levels of HOXATs, their prognostic potentials, and correlation with tumor mutation burden (TMB), immune cell infiltration, immune subtype, immune response-related genes, and stemness scores corresponding to 33 tumor types were analyzed systematically using R language. The results of the analysis indicated that different cancer tissues show different HOXAT expression profiles. Further, HOXAT expression showed association with cancer prognosis and immune and stemness regulation. Gene set enrichment analysis also demonstrated that HOXATs participate in cancer- and immune-related pathways, and based on their expression levels, HOTAIRM1 and HOXB-AS1 showed potential involvement in oncogenesis as well as possible involvement in immune regulation across a variety of cancer types. Further investigation also confirmed a significantly higher expression of HOXB-AS1 in GBM than in lower grade glioma tissues. Importantly, in vitro cell function experiments indicated that HOXB-AS1 supports cancer stem cell and plays a fundamental role in glioma metastasis. In conclusion, our results provide valuable resources that can guide the investigation of the mechanisms related to the role of HOXATs in cancers as well as therapeutic analysis in this regard.
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Affiliation(s)
- Wei Shao
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Juan Xing
- Henan Provincial Nanyang Central Hospital, Nanyang, China
| | - Zheng Huo
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Zhan Wang
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-Reactor, Nanyang Normal University, Nanyang, China
| | - Yue Guo
- Henan Provincial Nanyang Central Hospital, Nanyang, China
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Li X, Zhang J, Zhang M, Qi X, Wang S, Teng J. Construction and comprehensive analysis of a competitive endogenous RNA network to reveal potential biomarkers for the malignant differentiation of glioma. Medicine (Baltimore) 2021; 100:e27248. [PMID: 34596120 PMCID: PMC8483826 DOI: 10.1097/md.0000000000027248] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 08/27/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Long noncoding RNAs (lncRNAs) can act as microRNA (miRNA) sponges to regulate protein-coding gene expression; therefore, lncRNAs are considered major components of the competitive endogenous RNA (ceRNA) network and have attracted growing attention. This study explored the regulatory mechanisms and functional roles of lncRNAs as ceRNAs in the malignant differentiation of low-grade glioma (LGG) to glioblastoma (GBM) and their potential impact on the prognosis of patients with GBM. METHODS LncRNA and messenger RNA (mRNA) data were extracted from the Cancer Genome Atlas (TCGA) database from 156 GBM samples and 529 LGG samples. Separately, the miRNA expression data were downloaded from the Gene Expression Omnibus database, with the GSE112009 dataset containing miRNA expression data from 10 GBM samples and 15 LGG samples. Weighted gene coexpression network analysis was performed to screen the glioma grade-related lncRNAs. Then, a ceRNA network was established. The database for annotation, visualization, and integrated discovery was adopted to conduct functional enrichment analysis based on 57 upregulated differentially expressed mRNAs in the ceRNA network. Finally, Kaplan-Meier curves were created for the survival analysis of 13 hub lncRNA by combining the clinical data of GBM patients in TCGA. RESULTS A ceRNA network including 16 lncRNAs, 18 miRNAs, and 78 mRNAs specific to the malignant differentiation of LGG to GBM was established. The 57 upregulated differentially expressed mRNAs in the ceRNA network were significantly enriched in 35 gene ontology terms and 5 pathways. The survival analysis showed that 2 lncRNAs (LINC00261 and HOXA10-AS) were prognostic biomarkers for patients with GBM in TCGA. CONCLUSION The proposed ceRNA network may help elucidate the regulatory mechanism by which lncRNAs function as ceRNAs and contribute to the malignant differentiation of LGG to GBM. Importantly, the candidate lncRNAs, miRNAs, and mRNAs involved in the ceRNA network can be further evaluated as potential therapeutic targets and prognostic biomarkers for GBM.
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Affiliation(s)
- Xin Li
- Weifang Traditional Chinese Medicine Hospital, WeiFang, China
| | - Jingwen Zhang
- School of Acupuncture and Massage, Shandong University of Traditional Chinese Medicine, JiNan, China
| | - Min Zhang
- School of Statistics, Renmin University of China, Beijing, China
| | - Xianghua Qi
- Affiliated Hospital of Shandong University of Traditional Chinese Medicine, JiNan, China
| | - Shiyuan Wang
- School of Traditional Chinese Medicine, Shandong University of Traditional Chinese Medicine, JiNan, China
| | - Jing Teng
- First School of Clinical Medicine, Shandong University of Traditional Chinese Medicine, JiNan, China
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Huang T, Chen Y, Zeng Y, Xu C, Huang J, Hu W, Chen X, Fu H. Long non-coding RNA PSMA3-AS1 promotes glioma progression through modulating the miR-411-3p/HOXA10 pathway. BMC Cancer 2021; 21:844. [PMID: 34294084 PMCID: PMC8296684 DOI: 10.1186/s12885-021-08465-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Glioma is a common type of brain tumor and is classified as low and high grades according to morphology and molecules. Growing evidence has proved that long non-coding RNAs (lncRNAs) play pivotal roles in numerous tumors or diseases including glioma. Proteasome 20S subunit alpha 3 antisense RNA 1 (PSMA3-AS1), as a member of lncRNAs, has been disclosed to play a tumor-promoting role in cancer progression. However, the role of PSMA3-AS1 in glioma remains unknown. Therefore, we concentrated on researching the regulatory mechanism of PSMA3-AS1 in glioma. METHODS PSMA3-AS1 expression was detected using RT-qPCR. Functional assays were performed to measure the effects of PSMA3-AS1 on glioma progression. After that, ENCORI ( http://starbase.sysu.edu.cn/ ) database was used to predict potential genes that could bind to PSMA3-AS1, and miR-411-3p was chosen for further studies. The interaction among PSMA3-AS1, miR-411-3p and homeobox A10 (HOXA10) were confirmed through mechanism assays. RESULTS PSMA3-AS1 was verified to be up-regulated in glioma cells and promote glioma progression. Furthermore, PSMA3-AS1 could act as a competitive endogenous RNA (ceRNA) for miR-411-3p to regulate HOXA10 and thus affecting glioma progression. CONCLUSION PSMA3-AS1 stimulated glioma progression via the miR-411-3p/HOXA10 pathway, which might offer a novel insight for the therapy and treatment of glioma.
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Affiliation(s)
- Tianzao Huang
- Department of Neurosurgery, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Yingxian Chen
- Department of Neurosurgery, The Jinjiang Municipal Hospital, Quanzhou, Fujian, China
| | - Yile Zeng
- Department of Neurosurgery, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Chaoyang Xu
- Department of Neurosurgery, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Jinzhong Huang
- Department of Neurosurgery, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Weipeng Hu
- Department of Neurosurgery, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Xiangrong Chen
- Department of Neurosurgery, the Second Affiliated Hospital, Fujian Medical University, Quanzhou, 362000, Fujian, China
| | - Huangde Fu
- Department of Neurosurgery, The Second Nanning People's Hospital, 13 Dancun Road, Jiangnan District, Nanning, 530031, Guangxi, China.
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Novikova EL, Kulakova MA. There and Back Again: Hox Clusters Use Both DNA Strands. J Dev Biol 2021; 9:28. [PMID: 34287306 PMCID: PMC8293171 DOI: 10.3390/jdb9030028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 12/25/2022] Open
Abstract
Bilaterian animals operate the clusters of Hox genes through a rich repertoire of diverse mechanisms. In this review, we will summarize and analyze the accumulated data concerning long non-coding RNAs (lncRNAs) that are transcribed from sense (coding) DNA strands of Hox clusters. It was shown that antisense regulatory RNAs control the work of Hox genes in cis and trans, participate in the establishment and maintenance of the epigenetic code of Hox loci, and can even serve as a source of regulatory peptides that switch cellular energetic metabolism. Moreover, these molecules can be considered as a force that consolidates the cluster into a single whole. We will discuss the examples of antisense transcription of Hox genes in well-studied systems (cell cultures, morphogenesis of vertebrates) and bear upon some interesting examples of antisense Hox RNAs in non-model Protostomia.
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Affiliation(s)
- Elena L. Novikova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
| | - Milana A. Kulakova
- Department of Embryology, St. Petersburg State University, Universitetskaya nab. 7–9, 199034 Saint Petersburg, Russia;
- Laboratory of Evolutionary Morphology, Zoological Institute RAS, Universitetskaya nab. 1, 199034 Saint Petersburg, Russia
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Kałuzińska Ż, Kołat D, Bednarek AK, Płuciennik E. PLEK2, RRM2, GCSH: A Novel WWOX-Dependent Biomarker Triad of Glioblastoma at the Crossroads of Cytoskeleton Reorganization and Metabolism Alterations. Cancers (Basel) 2021; 13:cancers13122955. [PMID: 34204789 PMCID: PMC8231639 DOI: 10.3390/cancers13122955] [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: 03/19/2021] [Revised: 04/30/2021] [Accepted: 06/11/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma is one of the deadliest human cancers. Its malignancy depends on cytoskeleton reorganization, which is related to, e.g., epithelial-to-mesenchymal transition and metastasis. The malignant phenotype of glioblastoma is also affected by the WWOX gene, which is lost in nearly a quarter of gliomas. Although the role of WWOX in the cytoskeleton rearrangement has been found in neural progenitor cells, its function as a modulator of cytoskeleton in gliomas was not investigated. Therefore, this study aimed to investigate the role of WWOX and its collaborators in cytoskeleton dynamics of glioblastoma. Methodology on RNA-seq data integrated the use of databases, bioinformatics tools, web-based platforms, and machine learning algorithm, and the obtained results were validated through microarray data. PLEK2, RRM2, and GCSH were the most relevant WWOX-dependent genes that could serve as novel biomarkers. Other genes important in the context of cytoskeleton (BMP4, CCL11, CUX2, DUSP7, FAM92B, GRIN2B, HOXA1, HOXA10, KIF20A, NF2, SPOCK1, TTR, UHRF1, and WT1), metabolism (MTHFD2), or correlation with WWOX (COL3A1, KIF20A, RNF141, and RXRG) were also discovered. For the first time, we propose that changes in WWOX expression dictate a myriad of alterations that affect both glioblastoma cytoskeleton and metabolism, rendering new therapeutic possibilities.
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Errafii K, Al-Akl NS, Khalifa O, Arredouani A. Comprehensive analysis of LncRNAs expression profiles in an in vitro model of steatosis treated with Exendin-4. J Transl Med 2021; 19:235. [PMID: 34078383 PMCID: PMC8173795 DOI: 10.1186/s12967-021-02885-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 05/14/2021] [Indexed: 12/12/2022] Open
Abstract
Background and aims The hallmark of non-alcoholic fatty liver disease (NAFLD) is the excessive hepatic lipid accumulation. Currently, no pharmacotherapy exists for NAFLD. However, the glucagon-like peptide-1 receptor agonists have recently emerged as potential therapeutics. Here, we sought to identify the long non-coding RNAs (LncRNAs) associated with the steatosis improvement induced by the GLP-1R agonist Exendin-4 (Ex-4) in vitro. Methods Steatosis was induced in HepG2 cells with oleic acid. The transcriptomic profiling was performed using total RNA extracted from untreated, steatotic, and Ex-4-treated steatotic cells. We validated a subset of differentially expressed LncRNAs with qRT-PCR and identified the most significantly enriched cellular functions associated with the relevant LncRNAs. Results We confirm that Ex-4 improves steatosis in HepG2 cells. We found 379 and 180 differentially expressed LncRNAs between untreated and steatotic cells and between steatotic and Ex-4-treated steatotic cells, respectively. Interestingly, 22 upregulated LncRNAs in steatotic cells became downregulated with Ex-4 exposure, while 50 downregulated LncRNAs in steatotic cells became upregulated in the presence of Ex-4. Although some LncRNAs, such as MALAT1, H19, and NEAT1, were previously associated with NAFLD, the association of others with steatosis and the positive effect of Ex-4 is being reported for the first time. Functional enrichment analysis identified many critical pathways, including fatty acid and pyruvate metabolism, and insulin, PPAR, Wnt, TGF-β, mTOR, VEGF, NOD-like, and Toll-like receptors signaling pathways. Conclusion Our results suggest that LncRNAs may play essential roles in the mechanisms underlying steatosis improvement in response to GLP-1R agonists and warrant further functional studies. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02885-4.
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Affiliation(s)
- Khaoula Errafii
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.,Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box: 34110, Doha, Qatar
| | - Neyla S Al-Akl
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box: 34110, Doha, Qatar
| | - Olfa Khalifa
- Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box: 34110, Doha, Qatar
| | - Abdelilah Arredouani
- College of Health and Life Sciences, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar. .,Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, PO Box: 34110, Doha, Qatar.
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Yan X, Cong B, Chen Q, Liu L, Luan X, Du J, Cao M. Silencing lncRNA HOXA10-AS decreases cell proliferation of oral cancer and HOXA10-antisense RNA can serve as a novel prognostic predictor. J Int Med Res 2021; 48:300060520934254. [PMID: 32776855 PMCID: PMC7418258 DOI: 10.1177/0300060520934254] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Objective Long noncoding (lnc)RNAs regulate multiple biological processes including cancer. Oral squamous cell carcinoma (OSCC) is a common malignancy with poor prognosis. We aimed to identify the function of lncRNA HOXA10 antisense RNA (HOXA10-AS) and its clinical significance. Methods We used differential expression analysis to identify aberrantly expressed lncRNAs associated with OSCC. We identified key genes related to HOXA10-AS and their biological functions using bioinformatics tools and functional enrichment analyses. We predicted the function of HOXA10-AS using gene set enrichment and variation analyses and analyzed proliferation markers at the mRNA and protein levels. Finally, we silenced HOXA10-AS using antisense oligonucleotide and assessed proliferation ability using a cell counting kit (CCK8) and clone formation assays. Results In total, 506 aberrantly expressed lncRNAs were identified. HOXA10-AS was identified as a risk factor for OSCC and its expression was positively associated with tumor grade. We identified hub genes involved in regulating proliferation and predicted that HOXA10-AS is associated with an active cell cycle and increased proliferation. Silencing HOXA10-AS decreased proliferation in OSCC cell lines. Conclusions HOXA10-AS is involved in cell proliferation and silencing it decreases proliferation. Thus, HOXA10-AS could serve as prognostic biomarker and therapeutic target for OSCC.
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Affiliation(s)
- Xiaodong Yan
- Department of Stomatology, Zibo Central Hospital, Zibo, Shandong, China
| | - Bin Cong
- Department of Stomatology, The Third Hospital of Jinan, Jinan, Shandong, China
| | - Qinchao Chen
- Department of Stomatology, Zibo Central Hospital, Zibo, Shandong, China
| | - Lingyun Liu
- Department of Stomatology, Zibo Central Hospital, Zibo, Shandong, China
| | - Xidi Luan
- Department of Orthopaedics, Zibo Mining Group Central Hospital, Zibo, Shandong, China
| | - Jianxin Du
- Department of Stomatology, Zibo Central Hospital, Zibo, Shandong, China
| | - Meng Cao
- Department of Stomatology, Zibo Central Hospital, Zibo, Shandong, China
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FAM225B Is a Prognostic lncRNA for Patients with Recurrent Glioblastoma. DISEASE MARKERS 2020; 2020:8888085. [PMID: 33299501 PMCID: PMC7704151 DOI: 10.1155/2020/8888085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/22/2020] [Accepted: 10/29/2020] [Indexed: 12/22/2022]
Abstract
Objective The overall survival of patients with recurrent glioblastoma (rGBM) is quite different, so clinical outcome prediction is necessary to guide personalized clinical treatment for patients with rGBM. The expression level of lncRNA FAM225B was analyzed to determine its prognostic value in rGBMs. Methods We collected 109 samples of Chinese Glioma Genome Atlas (CGGA) RNA sequencing dataset and divided into training set and validation set. Then, we analyzed the expression of FAM225B, clinical characteristics, and overall survival (OS) information. Kaplan-Meier survival analysis was used to estimate the OS distributions. The prognostic value of FAM225B in rGBMs was tested by univariate and multivariate Cox regression analyses. Moreover, we analyzed the biological processes and signaling pathways of FAM225B. Results We found that FAM225B was upregulated in rGBMs (P = 0.0009). The expression of FAM225B increased with the grades of gliomas (P < 0.0001). The OS of rGBMs in the low-expression group was significantly longer than that in the high-expression group (P = 0.0041). Similar result was found in the training set (P = 0.0340) and verified in the validation set (P = 0.0292). In multivariate Cox regression analysis, FAM225B was identified to be an independent prognostic factor for rGBMs (P = 0.003). Biological process and KEGG pathway analyses implied FAM225B mainly played a functional role on transcription, regulation of transcription, cell migration, focal adhesion, etc. Conclusions FAM225B is expected to be as a new prognostic biomarker for the identification of rGBM patients with poor outcome. And our study provided a potential therapeutic target for rGBMs.
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Roly ZY, Godini R, Estermann MA, Major AT, Pocock R, Smith CA. Transcriptional landscape of the embryonic chicken Müllerian duct. BMC Genomics 2020; 21:688. [PMID: 33008304 PMCID: PMC7532620 DOI: 10.1186/s12864-020-07106-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background Müllerian ducts are paired embryonic tubes that give rise to the female reproductive tract in vertebrates. Many disorders of female reproduction can be attributed to anomalies of Müllerian duct development. However, the molecular genetics of Müllerian duct formation is poorly understood and most disorders of duct development have unknown etiology. In this study, we describe for the first time the transcriptional landscape of the embryonic Müllerian duct, using the chicken embryo as a model system. RNA sequencing was conducted at 1 day intervals during duct formation to identify developmentally-regulated genes, validated by in situ hybridization. Results This analysis detected hundreds of genes specifically up-regulated during duct morphogenesis. Gene ontology and pathway analysis revealed enrichment for developmental pathways associated with cell adhesion, cell migration and proliferation, ERK and WNT signaling, and, interestingly, axonal guidance. The latter included factors linked to neuronal cell migration or axonal outgrowth, such as Ephrin B2, netrin receptor, SLIT1 and class A semaphorins. A number of transcriptional modules were identified that centred around key hub genes specifying matrix-associated signaling factors; SPOCK1, HTRA3 and ADGRD1. Several novel regulators of the WNT and TFG-β signaling pathway were identified in Müllerian ducts, including APCDD1 and DKK1, BMP3 and TGFBI. A number of novel transcription factors were also identified, including OSR1, FOXE1, PRICKLE1, TSHZ3 and SMARCA2. In addition, over 100 long non-coding RNAs (lncRNAs) were expressed during duct formation. Conclusions This study provides a rich resource of new candidate genes for Müllerian duct development and its disorders. It also sheds light on the molecular pathways engaged during tubulogenesis, a fundamental process in embryonic development.
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Affiliation(s)
- Zahida Yesmin Roly
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Rasoul Godini
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Martin A Estermann
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Andrew T Major
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Roger Pocock
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia
| | - Craig A Smith
- Department of Anatomy and Developmental Biology, Monash Biomedicine Discovery Institute, Monash University, Wellington Road, Clayton, VIC, 3800, Australia.
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16
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Liu Z, Wan Y, Yang M, Qi X, Dong Z, Huang J, Xu J. Identification of methylation-driven genes related to the prognosis of papillary renal cell carcinoma: a study based on The Cancer Genome Atlas. Cancer Cell Int 2020; 20:235. [PMID: 32536823 PMCID: PMC7291558 DOI: 10.1186/s12935-020-01331-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/08/2020] [Indexed: 02/07/2023] Open
Abstract
Background Aberrant DNA methylation patterns are involved in the pathogenesis of papillary renal cell carcinoma (pRCC). This study aimed to investigate the potential of methylation-driven genes as biomarkers in determining the prognosis of pRCC by bioinformatics analysis. Methods DNA methylation and transcriptome profiling data were downloaded from The Cancer Genome Atlas database. Methylation-driven genes (MDGs) were obtained using MethylMix R package. A Cox regression model was used to screen for pRCC prognosis-related MDGs, and a linear risk model based on MDG methylation profiles was constructed. A combined methylation and gene expression survival analysis was performed to further explore the prognostic value of MDGs independently. Results A total of 31 MDGs were obtained. Univariate and multivariate Cox regression analysis identified eight genes (CASP1, CD68, HOXD3, HHLA2, HOXD9, HOXA10-AS, TMEM71, and PLA2G16), which were used to construct a predictive model associated with overall survival in pRCC patients. Combined DNA methylation and gene expression survival analysis revealed that C19orf33, GGT6, GIPC2, HHLA2, HOXD3, HSD17B14, PLA2G16, and TMEM71 were significantly associated with patients’ survival. Conclusion Through the analysis of MDGs in pRCC, this study identified potential biomarkers for precision treatment and prognosis prediction, and provided the basis for future research into the molecular mechanism of pRCC.
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Affiliation(s)
- Zeyu Liu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Yuxiang Wan
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Ming Yang
- School of Traditional Chinese Medicine, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Xuewei Qi
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Zhenzhen Dong
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Jinchang Huang
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
| | - Jingnan Xu
- Third Affiliated Hospital, Beijing University of Chinese Medicine, Beijing, 100029 China
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Adato O, Orenstein Y, Kopolovic J, Juven-Gershon T, Unger R. Quantitative Analysis of Differential Expression of HOX Genes in Multiple Cancers. Cancers (Basel) 2020; 12:E1572. [PMID: 32545894 PMCID: PMC7352544 DOI: 10.3390/cancers12061572] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/06/2020] [Accepted: 06/11/2020] [Indexed: 12/12/2022] Open
Abstract
Transcription factors encoded by Homeobox (HOX) genes play numerous key functions during early embryonic development and differentiation. Multiple reports have shown that mis-regulation of HOX gene expression plays key roles in the development of cancers. Their expression levels in cancers tend to differ based on tissue and tumor type. Here, we performed a comprehensive analysis comparing HOX gene expression in different cancer types, obtained from The Cancer Genome Atlas (TCGA), with matched healthy tissues, obtained from Genotype-Tissue Expression (GTEx). We identified and quantified differential expression patterns that confirmed previously identified expression changes and highlighted new differential expression signatures. We discovered differential expression patterns that are in line with patient survival data. This comprehensive and quantitative analysis provides a global picture of HOX genes' differential expression patterns in different cancer types.
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Affiliation(s)
- Orit Adato
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel;
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel;
| | - Juri Kopolovic
- Department of Pathology, Hadassah Medical Center, Jerusalem 9112102, Israel;
| | - Tamar Juven-Gershon
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel;
| | - Ron Unger
- The Mina & Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan 5290002, Israel;
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