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Aass KR, Nedal TMV, Tryggestad SS, Haukås E, Slørdahl TS, Waage A, Standal T, Mjelle R. Paired miRNA- and messenger RNA-sequencing identifies novel miRNA-mRNA interactions in multiple myeloma. Sci Rep 2022; 12:12147. [PMID: 35840794 PMCID: PMC9287335 DOI: 10.1038/s41598-022-16448-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/11/2022] [Indexed: 01/15/2023] Open
Abstract
Multiple myeloma (MM) is an incurable cancer of terminally differentiated plasma cells that proliferate in the bone marrow. miRNAs are promising biomarkers for risk stratification in MM and several miRNAs are shown to have a function in disease pathogenesis. However, to date, surprisingly few miRNA-mRNA interactions have been described for and functionally validated in MM. In this study, we performed miRNA-seq and mRNA-seq on CD138 + cells isolated from bone marrow aspirates of 86 MM patients to identify novel interactions between sRNAs and mRNAs. We detected 9.8% significantly correlated miRNA-mRNA pairs of which 5.17% were positively correlated and 4.65% were negatively correlated. We found that miRNA-mRNA pairs that were predicted by in silico target-prediction algorithms were more negatively correlated than non-target pairs, indicating functional miRNA targeting and that correlation between miRNAs and mRNAs from patients can be used to identify miRNA-targets. mRNAs for negatively correlated miRNA-mRNA target pairs were associated with gene ontology terms such as autophagy, protein degradation and endoplasmic stress response, reflecting important processes in MM. Targets for two specific miRNAs, miR-125b-5p and miR-365b-3p, were functionally validated in MM cell line transfection experiments followed by RNA-sequencing and qPCR. In summary, we identified functional miRNA-mRNA target pairs by correlating miRNA and mRNA data from primary MM cells. We identified several target pairs that are of potential interest for further studies. The data presented here may serve as a hypothesis-generating knowledge base for other researchers in the miRNA/MM field. We also provide an interactive web application that can be used to exploit the miRNA-target interactions as well as clinical parameters associated to these target-pairs.
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Affiliation(s)
- Kristin Roseth Aass
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Tonje Marie Vikene Nedal
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Synne Stokke Tryggestad
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway
| | - Einar Haukås
- grid.412835.90000 0004 0627 2891Department of Hematology, Stavanger University Hospital, 4011 Stavanger, Norway
| | - Tobias S. Slørdahl
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Anders Waage
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Therese Standal
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Centre of Molecular Inflammation Research, Norwegian University of Science and Technology, Gastrosenteret, Prinsesse Kristinas gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.52522.320000 0004 0627 3560Department of Hematology, St. Olavs University Hospital, 7030 Trondheim, Norway
| | - Robin Mjelle
- grid.5947.f0000 0001 1516 2393Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Erling Skjalgssons gt. 1, 7491 Trondheim, Norway ,grid.5947.f0000 0001 1516 2393Bioinformatics Core Facility - BioCore, Norwegian University of Science and Technology NTNU, 7491 Trondheim, Norway
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Long Intergenic Noncoding RNA 00641 Promotes Growth and Invasion of Colorectal Cancer through Regulating miR-450b-5p/GOLPH3 Axis. JOURNAL OF ONCOLOGY 2022; 2022:8259135. [PMID: 35756081 PMCID: PMC9217543 DOI: 10.1155/2022/8259135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/26/2022] [Accepted: 05/24/2022] [Indexed: 11/18/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) have a vital function in tumor onset and progress. For instance, long intergenic noncoding RNA 00641 (LINC00641) has been linked to cancer modulation. Nonetheless, the precise biological roles of LINC00641 in colorectal cancer (CRC) remain elusive. Methods The expression levels of LINC00641 as well as the docking sites for LINC00641 and miR-450b-5p were analyzed using public data resources and web-based analytic tools. The putative downstream targets of miR-450b-5p were also predicted. Next, we evaluated the biological functions and the contents of LINC00641 in CRC both in vivo and in vitro. We next explored the influence of LINC00641 on the growth, migration, and infiltration of CRC cells via cell proliferation, migration, and invasion experiments. Besides, qRT-PCR, western blotting, flow cytometry, luciferase enzyme reporter assay, and in vivo tumorigenicity assays were conducted. Results Our results confirmed that LINC00641 was markedly upmodulated in CRC tissues and CRC cell lines, and the upmodulation was linked to poor survival. Notably, the proliferative and migratory abilities of HCT-116 and SW480 cells were significantly inhibited by the knockdown of LINC00641 both in vitro and in vivo, illustrating that LINC00641 exerted a tumor-promotion role in CRC. Mechanistically, LINC00641 could competitively bind miR-450b-5p, thereby expunging its inhibitory effect on GOLPH3 expression. Moreover, miR-450-5p and GOLPH3 were able to reverse LINC00641-mediated cellular processes. Conclusions Overall, the findings of this study suggest that LINC00641 promotes the proliferative and migratory abilities of CRC through sponging the miR-450b-5p/GOLPH3 axis.
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Chen Y, Guo Y, Li S, Xu J, Wang X, Ning W, Ma L, Qu Y, Zhang M, Zhang H. Identification of N6-Methyladenosine-Related lncRNAs as a Prognostic Signature in Glioma. Front Oncol 2022; 12:789283. [PMID: 35311131 PMCID: PMC8927984 DOI: 10.3389/fonc.2022.789283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most abundant modification in long noncoding RNAs (lncRNAs). Current studies have shown that the abnormal expression of m6A-related genes is closely associated with the tumorigenesis and progression of glioma. However, the role of m6A-related lncRNAs in glioma development is still unclear. Herein, we screened 566 m6A-related lncRNAs in glioma from The Cancer Genome Atlas (TCGA) database. The expression pattern of these lncRNAs could cluster samples into two groups, in which various classical tumor-related functions and the tumor immune microenvironment were significantly different. Subsequently, a nine-factor m6A-related lncRNA prognostic signature (MLPS) was constructed by using a LASSO regression analysis in the training set and was validated in the test set and independent datasets. The AUC values of the MLPS were 0.881, 0.918 and 0.887 for 1-, 3- and 5-year survival in the training set, respectively, and 0.856, 0.916 and 0.909 for 1-, 3-, and 5-year survival in the test set, respectively. Stratification analyses of the MLPS illustrated its prognostic performance in gliomas with different characteristics. Correlation analyses showed that the infiltrations of monocytes and tumor-associated macrophages (TAMs) were significantly relevant to the risk score in the MLPS. Moreover, we detected the expression of four MLPS factors with defined sequences in glioma and normal cells by using RT-PCR. Afterwards, we investigated the functions of LNCTAM34A (one of the MLPS factors) in glioma cells, which have rarely been reported. Via in vitro experiments, LNCTAM34A was demonstrated to promote the proliferation, migration and epithelial-mesenchymal transition (EMT) of glioma cells. Overall, our study revealed the critical role of m6A-related lncRNAs in glioma and elucidated that LNCTAM34A could promote glioma proliferation, migration and EMT.
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Affiliation(s)
- Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jiacheng Xu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Mingshan Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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Han X, Zhang S. Role of Long Non-Coding RNA LINC00641 in Cancer. Front Oncol 2022; 11:829137. [PMID: 35155216 PMCID: PMC8828736 DOI: 10.3389/fonc.2021.829137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are non-protein coding RNAs with more than 200 nucleic acids in length. When lncRNAs are located in the nucleus, they regulate chromosome structure, participate in chromatin remodeling, and act as transcription regulators. When lncRNAs are exported to the cytoplasm, they regulate mRNA stability, regulate translation, and interfere with post-translational modification. In recent years, more and more evidences have shown that lncRNA can regulate the biological processes of tumor proliferation, apoptosis, invasion and metastasis, and can participate in a variety of tumor signaling pathways. Long-gene non-protein coding RNA641 (LINC00641), located on human chromosome 14q11.2, is differentially expressed in a variety of tumors and is related to overall survival and prognosis, etc. Interfering the expression of LINC00641 can lead to changes in tumor cell proliferation, invasion, metastasis, apoptosis and other biological behaviors. Therefore, LINC00641 is a promising new biomarker and potential clinical therapeutic target. In this review, the biological functions, related mechanisms and clinical significance of LINC00641 in many human cancers are described in detail.
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Affiliation(s)
- Xue Han
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Shitai Zhang
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China
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miR-206 Inhibits Laryngeal Carcinoma Cell Multiplication, Migration, and Invasion. JOURNAL OF HEALTHCARE ENGINEERING 2021; 2021:5614861. [PMID: 34868522 PMCID: PMC8642001 DOI: 10.1155/2021/5614861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/22/2021] [Accepted: 10/28/2021] [Indexed: 12/29/2022]
Abstract
Laryngeal carcinoma (LC) is one of the common human cancer types. MicroRNAs (miRNAs) were reported to be the essential regulators in cancer diagnosis, treatment, and prognosis. It was reported that miR-206 expression was reduced in various neoplastic diseases. However, the role and functional mechanism of miR-206 in LC progression remain unclear. In this research, miR-206 was found to be associated with tumor-node-metastasis (TNM) staging. In addition, the area under the curve (AUC) of miR-206 was 0.902 for diagnosis of LC and 0.854 for differential diagnosis of stage I-II and stage III-IV patients. Low expression of miR-206 was associated with poor prognosis of LC patients. miR-206 expression was an independent factor affecting the prognosis of LC patients, as revealed by the Cox regression analysis. In vitro experiments demonstrated that miR-206 overexpression reduced cell multiplication, invasion, and migration and increased cell apoptosis in LC cells. Moreover, SOX9 was a target of miR-206, and miR-206 negatively regulated SOX9 expression. Collectively, miR-206 might be a promising biomarker with diagnostic and prognostic value for LC, and the miR-206/SOX9 axis might be a candidate target for LC therapy.
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Huang H, Tang Y, Ye X, Chen W, Xie H, Chen S. The influence of lncRNAs on the prognosis of prostate cancer based on TCGA database. Transl Androl Urol 2021; 10:1302-1313. [PMID: 33850764 PMCID: PMC8039585 DOI: 10.21037/tau-21-154] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Prostate adenocarcinoma (PRAD) is a common male urinary system cancer globally with a poor prognosis. Our research aims to explore the role of LncRNA in the occurrence and prognosis of prostate cancer and its underlying mechanism. Methods The biomaRt package screened for the differentially expressed lncRNA. The survival package was used to identify lncRNAs related to prognosis. The survminer package completed the Kaplan-Meier survival curves. WGCNA (Weighted Gene Co-Expression Network Analysis) screened for the co-expressed genes. The ClusterProfiler package implemented the analysis results of GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes). Results We performed differential expression analysis on the TCGA (The Cancer Genome Atlas) database to determine the association between LncRNA and Prostate cancer. The data of 500 Prostate cancer patients were tested. 6 LncRNAs (AC245884.1, LINC01524, AL807752.4, AP000844.2, AC016590.1, LINC00641) were selected as independent prognostic factors using statistical analysis methods, and their value was tested through multivariate COX analysis and Kaplan-Meier survival analysis. Through the study of co-expressed genes, the biological processes of these lncRNA enrichment are the perception and conduction of smell and taste. The specific carcinogenic and cancer-promoting mechanisms need further study. Conclusions This study shows that lncRNA has a certain predictive effect on prostate cancer occurrence and prognosis and can be a new biomarker for prostate cancer survival and potential treatment targets.
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Affiliation(s)
- Hang Huang
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yufan Tang
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xueting Ye
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Wei Chen
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Hui Xie
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Shengye Chen
- Department of Urology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
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