1
|
Wang S, Qi X, Liu D, Xie D, Jiang B, Wang J, Wang X, Wu G. The implications for urological malignancies of non-coding RNAs in the the tumor microenvironment. Comput Struct Biotechnol J 2024; 23:491-505. [PMID: 38249783 PMCID: PMC10796827 DOI: 10.1016/j.csbj.2023.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/08/2023] [Accepted: 12/16/2023] [Indexed: 01/23/2024] Open
Abstract
Urological malignancies are a major global health issue because of their complexity and the wide range of ways they affect patients. There's a growing need for in-depth research into these cancers, especially at the molecular level. Recent studies have highlighted the importance of non-coding RNAs (ncRNAs) – these don't code for proteins but are crucial in controlling genes – and the tumor microenvironment (TME), which is no longer seen as just a background factor but as an active player in cancer progression. Understanding how ncRNAs and the TME interact is key for finding new ways to diagnose and predict outcomes in urological cancers, and for developing new treatments. This article reviews the basic features of ncRNAs and goes into detail about their various roles in the TME, focusing specifically on how different ncRNAs function and act in urological malignancies.
Collapse
Affiliation(s)
- Shijin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaochen Qi
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Dequan Liu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Deqian Xie
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Bowen Jiang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Jin Wang
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Xiaoxi Wang
- Department of Clinical Laboratory Medicine, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| | - Guangzhen Wu
- Department of Urology, The First Affiliated Hospital of Dalian Medical University, Dalian 116011, Liaoning, China
| |
Collapse
|
2
|
Maharati A, Moghbeli M. Long non-coding RNAs as the critical regulators of PI3K/AKT, TGF-β, and MAPK signaling pathways during breast tumor progression. J Transl Med 2023; 21:556. [PMID: 37596669 PMCID: PMC10439650 DOI: 10.1186/s12967-023-04434-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023] Open
Abstract
Breast cancer (BC) as one of the most common causes of human deaths among women, is always considered one of the global health challenges. Despite various advances in diagnostic and therapeutic methods, a significant percentage of BC patients have a poor prognosis due to the lack of therapeutic response. Therefore, investigating the molecular mechanisms involved in BC progression can improve the therapeutic and diagnostic strategies in these patients. Cytokine and growth factor-dependent signaling pathways play a key role during BC progression. In addition to cytokines and growth factors, long non-coding RNAs (lncRNAs) have also important roles in regulation of such signaling pathways. Therefore, in the present review we discussed the role of lncRNAs in regulation of PI3K/AKT, MAPK, and TGF-β signaling pathways in breast tumor cells. It has been shown that lncRNAs mainly have an oncogenic role through the promotion of these signaling pathways in BC. This review can be an effective step in introducing the lncRNAs inhibition as a probable therapeutic strategy to reduce tumor growth by suppression of PI3K/AKT, MAPK, and TGF-β signaling pathways in BC patients. In addition, considering the oncogenic role and increased levels of lncRNAs expressions in majority of the breast tumors, lncRNAs can be also considered as the reliable diagnostic markers in BC patients.
Collapse
Affiliation(s)
- Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| |
Collapse
|
3
|
Li G, Zhu J, Zhai L. Exploring molecular markers and drug candidates for colorectal cancer through comprehensive bioinformatics analysis. Aging (Albany NY) 2023; 15:7038-7055. [PMID: 37466419 PMCID: PMC10415558 DOI: 10.18632/aging.204891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 06/30/2023] [Indexed: 07/20/2023]
Abstract
Colorectal cancer (CRC) often has a poor prognosis and identifying useful and novel agents for treating CRC is urgently required. This study aimed to examine molecular markers associated with CRC prognosis and to identify potential drug candidates. The differentially expressed genes (DEGs) of CRC in TCGA were identified. The genes associated with CRC, summarized from NCBI-gene, OMIM, and the DEGs, were used to construct a co-expression network by WGCNA. Moreover, the co-expression genes from modules of interest were used to carry out functional enrichment. A total of 2742 DEGs, including 1674 upregulated and 1068 downregulated genes, were identified. Thirteen co-expression modules were constructed with WGCNA. Brown and blue co-expression modules with significant differences in disease phenotype were found. Functional enrichment analysis showed that genes in the brown module were mainly related to cell cycle, cell proliferation, DNA replication, and RNA transport. The genes in the blue module were mainly associated with fatty acid degradation, sulfur metabolism, PPAR signaling pathway and bile secretion. In addition, both the genes in brown and blue were associated with tumor staging. Some prognostic markers and candidate small molecules drugs for CRC treatment were identified. In conclusion, we revealed molecular biomarker profiles in CRC by systematic bioinformatics analysis, constructed regulatory networks of mRNA, ncRNA and transcriptional regulators (TFs), and identified potential drugs targeting hub proteins and TFs.
Collapse
Affiliation(s)
- Guangyao Li
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Wuhu, Wuhu, Anhui, People’s Republic of China
| | - JiangPeng Zhu
- Department of Gastrointestinal Surgery, The Second People’s Hospital of Wuhu, Wuhu, Anhui, People’s Republic of China
| | - Lulu Zhai
- Department of General Surgery, Renmin Hospital of Wuhan University, Wuhan 430060, Hubei, People’s Republic of China
| |
Collapse
|
4
|
Meyers TJ, Yin J, Herrera VA, Pressman AR, Hoffmann TJ, Schaefer C, Avins AL, Choquet H. Transcriptome-wide association study identifies novel candidate susceptibility genes for migraine. HGG ADVANCES 2023; 4:100211. [PMID: 37415806 PMCID: PMC10319829 DOI: 10.1016/j.xhgg.2023.100211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/05/2023] [Indexed: 07/08/2023] Open
Abstract
Genome-wide association studies (GWASs) have identified more than 130 genetic susceptibility loci for migraine; however, how most of these loci impact migraine development is unknown. To identify novel genes associated with migraine and interpret the transcriptional products of those genes, we conducted a transcriptome-wide association study (TWAS). We performed tissue-specific and multi-tissue TWAS analyses to assess associations between imputed gene expression from 53 tissues and migraine susceptibility using FUSION software. Meta-analyzed GWAS summary statistics from 26,052 migraine cases and 487,214 controls, all of European ancestry and from two cohorts (the Kaiser Permanente GERA and the UK Biobank), were used. We evaluated the associations for genes after conditioning on variant-level effects from GWAS, and we tested for colocalization of GWAS migraine-associated loci and expression quantitative trait loci (eQTLs). Across tissue-specific and multi-tissue analyses, we identified 53 genes for which genetically predicted gene expression was associated with migraine after correcting for multiple testing. Of these 53 genes, 10 (ATF5, CNTNAP1, KTN1-AS1, NEIL1, NEK4, NNT, PNKP, RUFY2, TUBG2, and VAT1) did not overlap known migraine-associated loci identified from GWAS. Tissue-specific analysis identified 45 gene-tissue pairs and cardiovascular tissues represented the highest proportion of the Bonferroni-significant gene-tissue pairs (n = 22 [49%]), followed by brain tissues (n = 6 [13%]), and gastrointestinal tissues (n = 4 [9%]). Colocalization analyses provided evidence of shared genetic variants underlying eQTL and GWAS signals in 18 of the gene-tissue pairs (40%). Our TWAS reports novel genes for migraine and highlights the important contribution of brain, cardiovascular, and gastrointestinal tissues in migraine susceptibility.
Collapse
Affiliation(s)
- Travis J. Meyers
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Victor A. Herrera
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Alice R. Pressman
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Sutter Health, San Francisco, CA 94107, USA
| | - Thomas J. Hoffmann
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Catherine Schaefer
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| | - Andrew L. Avins
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA 94612, USA
| |
Collapse
|
5
|
Kapinova A, Mazurakova A, Halasova E, Dankova Z, Büsselberg D, Costigliola V, Golubnitschaja O, Kubatka P. Underexplored reciprocity between genome-wide methylation status and long non-coding RNA expression reflected in breast cancer research: potential impacts for the disease management in the framework of 3P medicine. EPMA J 2023; 14:249-273. [PMID: 37275549 PMCID: PMC10236066 DOI: 10.1007/s13167-023-00323-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 06/07/2023]
Abstract
Breast cancer (BC) is the most common female malignancy reaching a pandemic scale worldwide. A comprehensive interplay between genetic alterations and shifted epigenetic regions synergistically leads to disease development and progression into metastatic BC. DNA and histones methylations, as the most studied epigenetic modifications, represent frequent and early events in the process of carcinogenesis. To this end, long non-coding RNAs (lncRNAs) are recognized as potent epigenetic modulators in pathomechanisms of BC by contributing to the regulation of DNA, RNA, and histones' methylation. In turn, the methylation status of DNA, RNA, and histones can affect the level of lncRNAs expression demonstrating the reciprocity of mechanisms involved. Furthermore, lncRNAs might undergo methylation in response to actual medical conditions such as tumor development and treated malignancies. The reciprocity between genome-wide methylation status and long non-coding RNA expression levels in BC remains largely unexplored. Since the bio/medical research in the area is, per evidence, strongly fragmented, the relevance of this reciprocity for BC development and progression has not yet been systematically analyzed. Contextually, the article aims at:consolidating the accumulated knowledge on both-the genome-wide methylation status and corresponding lncRNA expression patterns in BC andhighlighting the potential benefits of this consolidated multi-professional approach for advanced BC management. Based on a big data analysis and machine learning for individualized data interpretation, the proposed approach demonstrates a great potential to promote predictive diagnostics and targeted prevention in the cost-effective primary healthcare (sub-optimal health conditions and protection against the health-to-disease transition) as well as advanced treatment algorithms tailored to the individualized patient profiles in secondary BC care (effective protection against metastatic disease). Clinically relevant examples are provided, including mitochondrial health control and epigenetic regulatory mechanisms involved.
Collapse
Affiliation(s)
- Andrea Kapinova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Alena Mazurakova
- Department of Anatomy, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Erika Halasova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Zuzana Dankova
- Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| | - Dietrich Büsselberg
- Weill Cornell Medicine-Qatar, Education City, Qatar Foundation, 24144 Doha, Qatar
| | | | - Olga Golubnitschaja
- Predictive, Preventive, and Personalised (3P) Medicine, Department of Radiation Oncology, University Hospital Bonn, Rheinische Friedrich-Wilhelms-Universität Bonn, 53127 Bonn, Germany
| | - Peter Kubatka
- Department of Medical Biology, Jessenius Faculty of Medicine, Comenius University in Bratislava, 036 01 Martin, Slovakia
| |
Collapse
|
6
|
Han B, He J, Chen Q, Yuan M, Zeng X, Li Y, Zeng Y, He M, Zhou Q, Feng D, Ma D. ELFN1-AS1 promotes GDF15-mediated immune escape of colorectal cancer from NK cells by facilitating GCN5 and SND1 association. Discov Oncol 2023; 14:56. [PMID: 37147528 PMCID: PMC10163203 DOI: 10.1007/s12672-023-00675-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/27/2023] [Indexed: 05/07/2023] Open
Abstract
The ability of colorectal cancer (CRC) cells to escape from natural killer (NK) cell immune surveillance leads to anti-tumor treatment failure. The long non-coding RNA (lncRNA) ELFN1-AS1 is aberrantly expressed in multiple tumors suggesting a role as an oncogene in cancer development. However, whether ELFN1-AS1 regulates immune surveillance in CRC is unclear. Here, we determined that ELFN1-AS1 enhanced the ability of CRC cells to escape from NK cell surveillance in vitro and in vivo. In addition, we confirmed that ELFN1-AS1 in CRC cells attenuated the activity of NK cell by down-regulating NKG2D and GZMB via the GDF15/JNK pathway. Furthermore, mechanistic investigations demonstrated that ELFN1-AS1 enhanced the interaction between the GCN5 and SND1 protein and this influenced H3k9ac enrichment at the GDF15 promotor to stimulate GDF15 production in CRC cells. Taken together, our findings indicate that ELFN1-AS1 in CRC cells suppresses NK cell cytotoxicity and ELFN1-AS1 is a potential therapeutic target for CRC.
Collapse
Affiliation(s)
- Bin Han
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Jinsong He
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Qing Chen
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
- Department of Gastroenterology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Min Yuan
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Xi Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Yuanting Li
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Yan Zeng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Meibo He
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China
| | - Qilin Zhou
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Dan Feng
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
- Institute of Pharmacy, North Sichuan Medical College, Nanchong, China.
| | - Daiyuan Ma
- GCP Center/Institute of Drug Clinical Trials, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
- Department of Oncology, Affiliated Hospital of North Sichuan Medical College, Nanchong, China.
| |
Collapse
|
7
|
Mas AM, Huarte M. Long Noncoding RNA Signatures as Cancer Biomarkers. J Clin Oncol 2023; 41:3059-3062. [PMID: 37043713 DOI: 10.1200/jco.23.00381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023] Open
Affiliation(s)
- Aina M Mas
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| | - Maite Huarte
- Center for Applied Medical Research, University of Navarra, Pamplona, Spain
- Institute of Health Research of Navarra (IdiSNA), Pamplona, Spain
| |
Collapse
|
8
|
García-Caballero D, Hart JR, Vogt PK. The MYC-regulated lncRNA LNROP (ENSG00000254887) enables MYC-driven cell proliferation by controlling the expression of OCT2. Cell Death Dis 2023; 14:168. [PMID: 36849510 PMCID: PMC9971199 DOI: 10.1038/s41419-023-05683-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 03/01/2023]
Abstract
MYC controls most of the non-coding genome. Several long noncoding transcripts were originally identified in the human B cell line P496-3 and then shown to be required for MYC-driven proliferation of Burkitt lymphoma-derived RAMOS cells. In this study, we used RAMOS cells exclusively as a representative of the human B cell lineage. One of the MYC-controlled lncRNAs required for RAMOS cell proliferation is ENSG00000254887 which we will term LNROP (long non-coding regulator of POU2F2). In the genome, LNROP is located in close proximity of POU2F2, the gene encoding OCT2. OCT2 is a transcription factor with important roles in sustaining the proliferation of human B cells. Here we show that LNROP is a nuclear RNA and a direct target of MYC. Downregulation of LNROP attenuates the expression of OCT2. This effect of LNROP on the expression of OCT2 is unidirectional as downregulation of OCT2 does not alter the expression of LNROP. Our data suggest that LNROP is a cis-acting regulator of OCT2. To illustrate the downstream reach of LNROP, we chose a prominent target of OCT2, the tyrosine phosphatase SHP-1. Downregulation of OCT2 elevates the expression of SHP-1. Our data suggest the following path of interactions: LNROP enables the proliferation of B cells by positively and unidirectionally regulating the growth-stimulatory transcription factor OCT2. In actively proliferating B cells, OCT2 attenuates the expression and anti-proliferative activity of SHP-1.
Collapse
Affiliation(s)
- Daniel García-Caballero
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.
| | - Jonathan R Hart
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Peter K Vogt
- Scripps Research, Department of Molecular Medicine, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| |
Collapse
|
9
|
Liu XM, Xia SY, Long W, Li HJ, Yang GQ, Sun W, Li SY, Du XH. Potent bromodomain and extraterminal domain inhibitor JAB-8263 suppresses MYC expression and exerts anti-tumor activity in colorectal cancer models. World J Gastrointest Oncol 2023; 15:332-342. [PMID: 36908321 PMCID: PMC9994054 DOI: 10.4251/wjgo.v15.i2.332] [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: 11/20/2022] [Revised: 12/21/2022] [Accepted: 12/31/2022] [Indexed: 02/14/2023] Open
Abstract
BACKGROUND The overexpression of the MYC gene plays an important role in the occurrence, development and evolution of colorectal cancer (CRC). Bromodomain and extraterminal domain (BET) inhibitors can decrease the function BET by recognizing acetylated lysine residues, thereby downregulating the expression of MYC.
AIM To investigate the inhibitory effect and mechanism of a BET inhibitor on CRC cells.
METHODS The effect of the BET inhibitor JAB-8263 on the proliferation of various CRC cell lines was studied by CellTiter-Glo method and colony formation assay. The effect of JAB-8263 on the cell cycle and apoptosis of CRC cells was studied by propidium iodide staining and Annexin V/propidium iodide flow assay, respectively. The effect of JAB-8263 on the expression of c-MYC, p21 and p16 in CRC cells was detected by western blotting assay. The anti-tumor effect of JAB-8263 on CRC cells in vivo and evaluation of the safety of the compound was predicted by constructing a CRC cell animal tumor model.
RESULTS JAB-8263 dose-dependently suppressed CRC cell proliferation and colony formation in vitro. The MYC signaling pathway was dose-dependently inhibited by JAB-8263 in human CRC cell lines. JAB-8263 dose-dependently induced cell cycle arrest and apoptosis in the MC38 cell line. SW837 xenograft model was treated with JAB-8263 (0.3 mg/kg for 29 d), and the average tumor volume was significantly decreased compared to the vehicle control group (P < 0.001). The MC38 syngeneic murine model was treated with JAB-8263 (0.2 mg/kg for 29 d), and the average tumor volume was significantly decreased compared to the vehicle control group (P = 0.003).
CONCLUSION BET could be a potential effective drug target for suppressing CRC growth, and the BET inhibitor JAB-8263 can effectively suppress c-MYC expression and exert anti-tumor activity in CRC models.
Collapse
Affiliation(s)
- Xin-Mo Liu
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100039, China
- Medical School of Chinese PLA, Beijing 100039, China
| | - Shao-You Xia
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100039, China
- Medical School of Chinese PLA, Beijing 100039, China
| | - Wei Long
- Department of Chemistry, Jacobio Pharmaceuticals, Beijing 102600, China
| | - Hai-Jun Li
- Department of Chemistry, Jacobio Pharmaceuticals, Beijing 102600, China
| | - Gui-Qun Yang
- Department of Pharmacology, Jacobio Pharmaceuticals, Beijing 102600, China
| | - Wen Sun
- Department of Anesthesiology, the Second Affiliated Hospital of Tianjin University of Traditional Chinese Medicine, Tianjin 300250, China
| | - Song-Yan Li
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100039, China
- Medical School of Chinese PLA, Beijing 100039, China
| | - Xiao-Hui Du
- Department of General Surgery, Chinese PLA General Hospital, Beijing 100039, China
- Medical School of Chinese PLA, Beijing 100039, China
| |
Collapse
|
10
|
Winkle M, Tayari MM, Kok K, Duns G, Grot N, Kazimierska M, Seitz A, de Jong D, Koerts J, Diepstra A, Dzikiewicz-Krawczyk A, Steidl C, Kluiver J, van den Berg A. The lncRNA KTN1-AS1 co-regulates a variety of Myc-target genes and enhances proliferation of Burkitt lymphoma cells. Hum Mol Genet 2022; 31:4193-4206. [PMID: 35866590 DOI: 10.1093/hmg/ddac159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/22/2022] [Accepted: 07/07/2022] [Indexed: 01/21/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in many normal and oncogenic pathways through a diverse repertoire of transcriptional and posttranscriptional regulatory mechanisms. LncRNAs that are under tight regulation of well-known oncogenic transcription factors such as c-Myc (Myc) are likely to be functionally involved in their disease-promoting mechanisms. Myc is a major driver of many subsets of B cell lymphoma and to date remains an undruggable target. We identified three Myc-induced and four Myc-repressed lncRNAs by use of multiple in vitro models of Myc-driven Burkitt lymphoma and detailed analysis of Myc binding profiles. We show that the top Myc-induced lncRNA KTN1-AS1 is strongly upregulated in different types of B cell lymphoma compared with their normal counterparts. We used CRISPR-mediated genome editing to confirm that the direct induction of KTN1-AS1 by Myc is dependent on the presence of a Myc E-box-binding motif. Knockdown of KTN1-AS1 revealed a strong negative effect on the growth of three BL cell lines. Global gene expression analysis upon KTN1-AS1 depletion shows a strong enrichment of key genes in the cholesterol biosynthesis pathway as well as co-regulation of many Myc-target genes, including a moderate negative effect on the levels of Myc itself. Our study suggests a critical role for KTN1-AS1 in supporting BL cell growth by mediating co-regulation of a variety of Myc-target genes and co-activating key genes involved in cholesterol biosynthesis. Therefore, KTN1-AS1 may represent a putative novel therapeutic target in lymphoma.
Collapse
Affiliation(s)
- Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Translational Molecular Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mina M Tayari
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands.,Department of Human Genetics, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL, USA
| | - Klaas Kok
- Department of Genetics, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Gerben Duns
- Department of Lymphoid Cancer Research, BC Cancer Center, Vancouver, BC, Canada
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Marta Kazimierska
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Annika Seitz
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Debora de Jong
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Jasper Koerts
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Arjan Diepstra
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | | | - Christian Steidl
- Department of Lymphoid Cancer Research, BC Cancer Center, Vancouver, BC, Canada
| | - Joost Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen (UMCG), Groningen, the Netherlands
| |
Collapse
|
11
|
The Theory of Carcino-Evo-Devo and Its Non-Trivial Predictions. Genes (Basel) 2022; 13:genes13122347. [PMID: 36553613 PMCID: PMC9777766 DOI: 10.3390/genes13122347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
To explain the sources of additional cell masses in the evolution of multicellular organisms, the theory of carcino-evo-devo, or evolution by tumor neofunctionalization, has been developed. The important demand for a new theory in experimental science is the capability to formulate non-trivial predictions which can be experimentally confirmed. Several non-trivial predictions were formulated using carcino-evo-devo theory, four of which are discussed in the present paper: (1) The number of cellular oncogenes should correspond to the number of cell types in the organism. The evolution of oncogenes, tumor suppressor and differentiation gene classes should proceed concurrently. (2) Evolutionarily new and evolving genes should be specifically expressed in tumors (TSEEN genes). (3) Human orthologs of fish TSEEN genes should acquire progressive functions connected with new cell types, tissues and organs. (4) Selection of tumors for new functions in the organism is possible. Evolutionarily novel organs should recapitulate tumor features in their development. As shown in this paper, these predictions have been confirmed by the laboratory of the author. Thus, we have shown that carcino-evo-devo theory has predictive power, fulfilling a fundamental requirement for a new theory.
Collapse
|
12
|
NUP153 promotes HCC cells proliferation via c-Myc-mediated downregulation of P15 INK4b. Dig Liver Dis 2022; 54:1706-1715. [PMID: 35288064 DOI: 10.1016/j.dld.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 12/30/2022]
Abstract
BACKGROUND AND AIM Nucleoporin NUP153 (NUP153) is involved in the regulation of nuclear transportation, mitosis, and tumor progression in various cancer cells. we aimed to investigate the roles of NUP153 in hepatocellular carcinoma (HCC). METHODS NUP153 expression level and its relationship with clinical prognosis were analyzed based on The Cancer Genome Atlas (TCGA). Quantitative real-time PCR (qRT-PCR), Western Blot (WB), and Immunohistochemistry (IHC) were used to assess NUP153 expression in tissues and cell lines. Loss-of-function experiments were implemented for exploring the roles of NUP153 in HCC cells. Ultimately, how NUP153 exerted biological functions was plumbed by performing rescue assays in HCC. RESULTS NUP153 expressed highly in HCC tissues and cell lines. Silencing NUP153 inhibited cellular multiplication, G1/S transition, migration, and triggered cytoskeletal rearrangement of Huh7 and HepG2 cells. Knockdown NUP153 caused up-regulation of mRNA and protein levels of P15, and siRNA deprivation of P15 partially reversed the function of low-level NUP153 in HCC. Meanwhile, silencing NUP153 caused down-regulation of mRNA and protein levels of c-Myc. Furthermore, the up-regulation of P15 and cell G1/S phase arrest induced by silencing NUP153 were partially reversed by overexpression of c-Myc. CONCLUSIONS NUP153 increases the proliferation ability of cells via the c-Myc/P15 axis in HCC.
Collapse
|
13
|
Shaath H, Vishnubalaji R, Elango R, Kardousha A, Islam Z, Qureshi R, Alam T, Kolatkar PR, Alajez NM. Long non-coding RNA and RNA-binding protein interactions in cancer: Experimental and machine learning approaches. Semin Cancer Biol 2022; 86:325-345. [PMID: 35643221 DOI: 10.1016/j.semcancer.2022.05.013] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 05/16/2022] [Accepted: 05/20/2022] [Indexed: 01/27/2023]
Abstract
Understanding the complex and specific roles played by non-coding RNAs (ncRNAs), which comprise the bulk of the genome, is important for understanding virtually every hallmark of cancer. This large group of molecules plays pivotal roles in key regulatory mechanisms in various cellular processes. Regulatory mechanisms, mediated by long non-coding RNA (lncRNA) and RNA-binding protein (RBP) interactions, are well documented in several types of cancer. Their effects are enabled through networks affecting lncRNA and RBP stability, RNA metabolism including N6-methyladenosine (m6A) and alternative splicing, subcellular localization, and numerous other mechanisms involved in cancer. In this review, we discuss the reciprocal interplay between lncRNAs and RBPs and their involvement in epigenetic regulation via histone modifications, as well as their key role in resistance to cancer therapy. Other aspects of RBPs including their structural domains, provide a deeper knowledge on how lncRNAs and RBPs interact and exert their biological functions. In addition, current state-of-the-art knowledge, facilitated by machine and deep learning approaches, unravels such interactions in better details to further enhance our understanding of the field, and the potential to harness RNA-based therapeutics as an alternative treatment modality for cancer are discussed.
Collapse
Affiliation(s)
- Hibah Shaath
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Radhakrishnan Vishnubalaji
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ramesh Elango
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Ahmed Kardousha
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar
| | - Zeyaul Islam
- Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Rizwan Qureshi
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Tanvir Alam
- College of Science and Engineering, Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Prasanna R Kolatkar
- College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; Diabetes Research Center (DRC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, PO Box 34110, Doha, Qatar
| | - Nehad M Alajez
- Translational Cancer and Immunity Center (TCIC), Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar; College of Health & Life Sciences, Hamad Bin Khalifa University (HBKU), Qatar Foundation (QF), PO Box 34110, Doha, Qatar.
| |
Collapse
|
14
|
Pathophysiology of Ischemic Stroke: Noncoding RNA Role in Oxidative Stress. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5815843. [PMID: 36132228 PMCID: PMC9484962 DOI: 10.1155/2022/5815843] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/12/2022] [Accepted: 08/20/2022] [Indexed: 11/29/2022]
Abstract
Stroke is a neurological disease that causes significant disability and death worldwide. Ischemic stroke accounts for 75% of all strokes. The pathophysiological processes underlying ischemic stroke include oxidative stress, the toxicity of excitatory amino acids, ion disorder, enhanced apoptosis, and inflammation. Noncoding RNAs (ncRNAs) may have a vital role in regulating the pathophysiological processes of ischemic stroke, as confirmed by the altered expression of ncRNAs in blood samples from acute ischemic stroke patients, animal models, and oxygen-glucose-deprived (OGD) cell models. Due to specific changes in expression, ncRNAs can potentially be biomarkers for the diagnosis, treatment, and prognosis of ischemic stroke. As an important brain cell component, glial cells mediate the occurrence and progression of oxidative stress after ischemic stroke, and ncRNAs are an irreplaceable part of this mechanism. This review highlights the impact of ncRNAs in the oxidative stress process of ischemic stroke. It focuses on specific ncRNAs that underlie the pathophysiology of ischemic stroke and have potential as diagnostic biomarkers and therapeutic targets.
Collapse
|
15
|
Gu Y, Huang K, Zhang M, Teng F, Ge L, Zhou J, Xu J, Jia X. Long Noncoding RNA CTD-2589M5.4 Inhibits Ovarian Cancer Cell Proliferation, Migration, and Invasion Via Downregulation of the Extracellular Matrix-Receptor Interaction Pathway. Cancer Biother Radiopharm 2022; 37:580-588. [PMID: 34242057 DOI: 10.1089/cbr.2020.4429] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Background: The authors' previous study showed that the long noncoding RNA CTD-2589M5.4 was significantly upregulated in multidrug-resistant ovarian cancer cells. However, the role of CTD-2589M5.4 in the progression of ovarian cancer remains unclear. The purpose of this current study was to illuminate the biological function and possible mechanism of CTD-2589M5.4 in ovarian cancer development. Materials and Methods: The expression of CTD-2589M5.4 was examined via real-time quantitative PCR in primary ovarian cancer tissues (POCTs) and ovarian cancer cell lines. The biological function of CTD-2589M5.4 was analyzed via CCK-8 proliferation, wound healing, transwell, and flow cytometry assays in CTD-2589M5.4-overexpressed/silenced and control ovarian cancer cells. The mechanism of CTD-2589M5.4 function in ovarian cancer progression was analyzed utilizing high-throughput RNA-sequencing, Kyoto Encyclopedia of Genes and Genomes analysis, qRT-PCR, Western blot, and rescue experiments. Results: CTD-2589M5.4 expression was decreased in the POCTs and ovarian cancer cells compared with the normal ovarian tissues (p < 0.05) and normal ovarian epithelial cells (p < 0.05). Overexpression of CTD-2589M5.4 inhibited the proliferation, invasion, and migration of ovarian cancer cells, while knockdown of CTD-2589M5.4 had the opposite effect. Furthermore, a total of 750 and 233 genes were notably upregulated and downregulated, respectively, in the CTD-2589M5.4-overexpressed A2780 cells, while the extracellular matrix (ECM)-receptor interaction pathway was significantly downregulated. In addition, overexpression of fibronectin 1 significantly abrogated the tumor suppressive function of CTD-2589M5.4. Conclusions: This study demonstrated that CTD-2589M5.4 could inhibit ovarian cancer cell proliferation, invasion, and migration, at least partially by way of downregulating the ECM-receptor interaction pathway, therefore providing a potential therapeutic target for the prevention and/or treatment of ovarian cancer.
Collapse
Affiliation(s)
- Yuanyuan Gu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China.,Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Ke Huang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Min Zhang
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Fang Teng
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Lili Ge
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Juan Zhou
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Juan Xu
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| | - Xuemei Jia
- Department of Gynecology, Women's Hospital of Nanjing Medical University (Nanjing Maternity and Child Health Care Hospital), Nanjing, China
| |
Collapse
|
16
|
CREB1 contributes colorectal cancer cell plasticity by regulating lncRNA CCAT1 and NF-κB pathways. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1481-1497. [PMID: 35696016 DOI: 10.1007/s11427-022-2108-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
The CREB1 gene encodes an exceptionally pleiotropic transcription factor that frequently dysregulated in human cancers. CREB1 can regulate tumor cell status of proliferation and/or migration; however, the molecular basis for this switch involvement in cell plasticity has not fully been understood yet. Here, we first show that knocking out CREB1 triggers a remarkable effect of epithelial-mesenchymal transition (EMT) and leads to the occurrence of inhibited proliferation and enhanced motility in HCT116 colorectal cancer cells. By monitoring 45 cellular signaling pathway activities, we find that multiple growth-related pathways decline significantly while inflammatory pathways including NF-κB are largely upregulated in comparing between the CREB1 wild-type and knocked out cells. Mechanistically, cells with CREB1 knocked out show downregulation of MYC as a result of impaired CREB1-dependent transcription of the oncogenic lncRNA CCAT1. Interestingly, the unbalanced competition between the coactivator CBP/p300 for CREB1 and p65 leads to the activation of the NF-κB pathway in cells with CREB1 disrupted, which induces an obvious EMT phenotype of the cancer cells. Taken together, these studies identify previously unknown mechanisms of CREB1 in CRC cell plasticity via regulating lncRNA CCAT1 and NF-κB pathways, providing a critical insight into a combined strategy for CREB1-targeted tumor therapies.
Collapse
|
17
|
Chen W, Liu Y, Kang S, Lv X, Fu W, Zhang J, Song C. LINC00092 Modulates Oxidative Stress and Glycolysis of Breast Cancer Cells via Pyruvate Carboxylase-Mediated AKT/mTOR Pathway. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2022; 2022:5215748. [PMID: 35799892 PMCID: PMC9256459 DOI: 10.1155/2022/5215748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/23/2022]
Abstract
Background The discovery of noncoding RNAs (ncRNAs) offers new options for cancer-targeted therapy. This study is aimed at exploring the regulatory function of LINC00092 on breast cancer (BC) oxidative stress and glycolysis, along with internal mechanism concerning pyruvate carboxylase (PC). Methods Bioinformatics analysis was used to explore LINC00092 (or friend leukemia virus integration 1 (FLI1)) expression on BC progression, as well as oxidative stress and glycolysis in BC. After LINC00092 overexpression or silence, BC cell viability, proliferation, migration, invasion, oxidative stress, glycolysis, and AKT/mTOR pathway were detected. Following 2-DG, SC79, or MK2206 treatment, effects of LINC00092 on BC cells were measured. Moreover, regulatory activity of LINC00092 in PC expression was analyzed. Whether PC participated in the modulation of LINC00092 on BC cell functions was explored. Results LINC00092 was lowly expressed in BC and negatively related to BC progression. FLI1 bound to LINC00092 promoter to positively modulate LINC00092. LINC00092 overexpression inhibited BC cell proliferation, migration, invasion, oxidative stress, glycolysis, and AKT/mTOR pathway and likewise suppressed BC growth in vivo. Silence of LINC00092 had opposite influences. 2-DG partially reversed the LINC00092 silence-resulted increase of BC cell proliferation. SC79 alleviated the function of LINC00092 overexpression on BC cell functions. MK2206 had the contrary influence of SC79. Besides, LINC00092 bound to PC to modulate ubiquitination degradation of PC protein. PC took part in the influences of LINC00092 on BC cell functions. Conclusions LINC0092 modulates oxidative stress and glycolysis of BC cells via the PC-mediated AKT/mTOR pathway, which is possibly a target for BC diagnosis and therapy.
Collapse
Affiliation(s)
- Wei Chen
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Yushan Liu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Shaohong Kang
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Xinying Lv
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Wenfen Fu
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
| | - Jie Zhang
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province 350001, China
| | - Chuangui Song
- Department of Breast Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Department of General Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian Province 350001, China
- Breast Cancer Institute, Fujian Medical University, Fuzhou, Fujian Province 350001, China
| |
Collapse
|
18
|
Dysregulated Expression of Long Non-Coding RNA MINCR and EZH2 in Colorectal Cancer. IRANIAN BIOMEDICAL JOURNAL 2022; 26:64-9. [PMID: 34923811 PMCID: PMC8784897 DOI: 10.52547/ibj.26.1.64] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
BACKGROUND As critical regulators, lncRNAs have attracted attention from researchers for diagnostic, prognostic, and therapeutic purposes in human carcinogenesis via interfering with mRNAs such as EZH2. Nevertheless, the potent roles and molecular mechanisms of these RNAs in CRC are not clearly known. METHODS In this study, the tissue expressions of lncRNA MINCR and EZH2 mRNA between colorectal tumors and polyps were compared with the adjacent normal tissues collected from 114 Iranian patients, using real-time PCR method. Furthermore, the correlation of the expression levels of MINCR and EZH2 with other clinical parameters was evaluated. RESULTS The significant overexpression of MINCR and EZH2 were observed in the CRC tissues compared to control tissues (p < 0.0001). This observation confirmed the association of these expression enhancements with the pathological stage of CRC patients. CONCLUSION Our findings revealed that the expression of MINCR significantly alters during CRC development, and it can be identified as a potential biomarker for the detection of CRC.
Collapse
|
19
|
[EEFSEC knockdown inhibits proliferation, migration and invasion of prostate cancer cells in vitro]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:1787-1794. [PMID: 35012909 PMCID: PMC8752429 DOI: 10.12122/j.issn.1673-4254.2021.12.05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
OBJECTIVE To investigate the role of selenocysteine-tRNA specific eukaryotic elongation factor (EEFSEC) in regulating the proliferation, migration, and invasion of human prostate cancer 22Rv1 cells. METHODS We detected EEFSEC mRNA expression levels in human normal prostate cell line RWPE1 and human prostate cancer cell lines 22Rv1, LNCaP, Vcap and PC-3 using qRT-PCR and EEFSEC protein expression in surgical specimens of prostate cancer and adjacent tissues using Western blotting. 22Rv1 cells were infected with a lentiviral vector carrying EEFSEC shRNA or a control lentivirus and the interference efficiency was determined using Western blotting. XTT assay was used to assess the changes in the viability of the infected cells, and Transwell chamber assay was used to examine the changes in cell migration and invasion. The effect of EEFSEC knockdown on cell cycle progression was determined with flow cytometry and by detecting the expressions of cell cycle proteins using qRT-PCR. RESULTS EEFSEC was significantly upregulated in prostate cancer cells (P < 0.05), and a high expression of EEFSEC was associated with a poor prognosis of the patients with prostate cancer. In 22Rv1 cells, EEFSEC knockdown significantly suppressed the proliferation (P < 0.001), migration (P < 0.001) and invasion (P < 0.001) of the cells, resulted in cell cycle arrest in G0/G1 phase, obviously inhibited the expression of C-myc and CCNB1, and significantly increased the expression of p15. CONCLUSION EEFSEC knockdown can inhibit the proliferation, migration, and invasion of prostate cancer cells in vitro possibly by down-regulating the expression of C-myc.
Collapse
|
20
|
Li A, Yu WH, Hsu CL, Huang HC, Juan HF. Modular signature of long non-coding RNA association networks as a prognostic biomarker in lung cancer. BMC Med Genomics 2021; 14:290. [PMID: 34872564 PMCID: PMC8650235 DOI: 10.1186/s12920-021-01137-0] [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: 11/24/2021] [Accepted: 11/30/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Increasing amount of long non-coding RNAs (lncRNAs) have been found involving in many biological processes and played salient roles in cancers. However, up until recently, functions of most lncRNAs in lung cancer have not been fully discovered, particularly in the co-regulated lncRNAs. Thus, this study aims to investigate roles of lncRNA modules and uncover a module-based biomarker in lung adenocarcinoma (LUAD). RESULTS We used gene expression profiles from The Cancer Genome Atlas (TCGA) to construct the lncRNA association networks, from which the highly-associated lncRNAs are connected as modules. It was found that the expression of some modules is significantly associated with patient's survival, including module N1 (HR = 0.62, 95% CI = 0.46-0.84, p = 0.00189); N2 (HR = 0.68, CI = 0.50-0.93, p = 0.00159); N4 (HR = 0.70, CI = 0.52-0.95, p = 0.0205) and P3 (HR = 0.68, CI = 0.50-0.92, p = 0.0123). The lncRNA signature consisting of these four prognosis-related modules, a 4-modular lncRNA signature, is associated with favourable prognosis in TCGA-LUAD (HR = 0.51, CI = 0.37-0.69, p value = 2.00e-05). Afterwards, to assess the performance of the generic modular signature as a prognostic biomarker, we computed the time-dependent area under the receiver operating characteristics (AUC) of this 4-modular lncRNA signature, which showed AUC equals 68.44% on 336th day. In terms of biological functions, these modules are correlated with several cancer hallmarks and pathways, including Myc targets, E2F targets, cell cycle, inflammation/immunity-related pathways, androgen/oestrogen response, KRAS signalling, DNA repair and epithelial-mesenchymal transition (EMT). CONCLUSION Taken together, we identified four novel LUAD prognosis-related lncRNA modules, and assessed the performance of the 4-modular lncRNA signature being a prognostic biomarker. Functionally speaking, these modules involve in oncogenic hallmarks as well as pathways. The results unveiled the co-regulated lncRNAs in LUAD and may provide a framework for further lncRNA studies in lung cancer.
Collapse
Affiliation(s)
- Albert Li
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Wen-Hsuan Yu
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan
| | - Chia-Lang Hsu
- Department of Medical Research, National Taiwan University Hospital, Taipei, 10002, Taiwan
| | - Hsuan-Cheng Huang
- Institute of Biomedical Informatics, National Yang Ming Chiao Tung University, Taipei, 11221, Taiwan.
| | - Hsueh-Fen Juan
- Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University, Taipei, 10617, Taiwan. .,Department of Life Science, National Taiwan University, Taipei, 10617, Taiwan. .,Center for Computational and Systems Biology, National Taiwan University, Taipei, 10617, Taiwan.
| |
Collapse
|
21
|
Ji Z, Tang T, Chen M, Dong B, Sun W, Wu N, Chen H, Feng Q, Yang X, Jin R, Jiang L. C-Myc-activated long non-coding RNA LINC01050 promotes gastric cancer growth and metastasis by sponging miR-7161-3p to regulate SPZ1 expression. J Exp Clin Cancer Res 2021; 40:351. [PMID: 34749766 PMCID: PMC8573944 DOI: 10.1186/s13046-021-02155-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Growing evidence shows that long non-coding RNAs (lncRNAs) play significant roles in cancer development. However, the functions of most lncRNAs in human gastric cancer are still not fully understood. Here, we explored the role of a novel c-Myc-activated lncRNA, LINC01050, in gastric cancer progression. METHODS The expression of LINC01050 in the context of gastric cancer was assessed using The Cancer Genome Atlas datasets. Its functions in gastric cancer were investigated through gain- and loss-of-function experiments combined with the Cell Counting Kit-8 assays, colony-forming assays, Transwell assays, flow cytometry, Western blot analyses, and xenograft tumor and mouse metastasis models. Potential LINC01050 transcription activators were screened via bioinformatics and validated by chromatin immunoprecipitation and luciferase assays. The interaction between LINC01050 and miR-7161-3p and the targets of miR-7161-3p were predicted by bioinformatics analysis and confirmed by a luciferase assay, RNA immunoprecipitation, RNA pull-down, and rescue experiments. RESULTS LINC01050 was significantly up-regulated in gastric cancer, and its high expression was positively correlated with a poor prognosis. The transcription factor c-Myc was found to directly bind to the LINC01050 promoter region and activate its transcription. Furthermore, overexpression of LINC01050 was confirmed to promote gastric cancer cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro and tumor growth in vivo. At the same time, its knockdown inhibited gastric cancer cell proliferation, migration, invasion, and epithelial-mesenchymal transition in vitro along with tumor growth and metastasis in vivo. Moreover, mechanistic investigations revealed that LINC01050 functions as a molecular sponge to absorb cytosolic miR-7161-3p, which reduces the miR-7161-3p-mediated translational repression of SPZ1, thus contributing to gastric cancer progression. CONCLUSIONS Taken together, our results identified a novel gastric cancer-associated lncRNA, LINC01050, which is activated by c-Myc. LINC01050 may be considered a potential therapeutic target for gastric cancer.
Collapse
Affiliation(s)
- Ziwei Ji
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Tianbin Tang
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Mengxia Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Buyuan Dong
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Wenjing Sun
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Nan Wu
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Hao Chen
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Qian Feng
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Xingyi Yang
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China
| | - Rong Jin
- Department of Gastroenterology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| | - Lei Jiang
- Central Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, 325000, China.
| |
Collapse
|
22
|
Li B, Zhang G, Wang Z, Yang Y, Wang C, Fang D, Liu K, Wang F, Mei Y. c-Myc-activated USP2-AS1 suppresses senescence and promotes tumor progression via stabilization of E2F1 mRNA. Cell Death Dis 2021; 12:1006. [PMID: 34707111 PMCID: PMC8551278 DOI: 10.1038/s41419-021-04330-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 12/16/2022]
Abstract
The c-Myc oncoprotein plays a prominent role in cancer initiation, progression, and maintenance. Long noncoding RNAs (lncRNAs) are recently emerging as critical regulators of the c-Myc signaling pathway. Here, we report the lncRNA USP2-AS1 as a direct transcriptional target of c-Myc. Functionally, USP2-AS1 inhibits cellular senescence and acts as an oncogenic molecule by inducing E2F1 expression. Mechanistically, USP2-AS1 associates with the RNA-binding protein G3BP1 and facilitates the interaction of G3BP1 to E2F1 3′-untranslated region, thereby leading to the stabilization of E2F1 messenger RNA. Furthermore, USP2-AS1 is shown as a mediator of the oncogenic function of c-Myc via the regulation of E2F1. Together, these findings suggest that USP2-AS1 is a negative regulator of cellular senescence and also implicates USP2-AS1 as an important player in mediating c-Myc function.
Collapse
Affiliation(s)
- Bingyan Li
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Guang Zhang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Zhongyu Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Yang Yang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Chenfeng Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Debao Fang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Kaiyue Liu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China
| | - Fang Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.
| | - Yide Mei
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. .,Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China.
| |
Collapse
|
23
|
Huang H, Li L, Wen K. Interactions between long non‑coding RNAs and RNA‑binding proteins in cancer (Review). Oncol Rep 2021; 46:256. [PMID: 34676873 PMCID: PMC8548813 DOI: 10.3892/or.2021.8207] [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] [Received: 08/27/2021] [Accepted: 10/12/2021] [Indexed: 12/30/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) fulfill important roles in the majority of cellular processes. Previous studies have demonstrated that lncRNAs are involved in the pathogenesis of various diseases, including cancer. However, to date, the functions of only a small number of the known lncRNAs have been well-documented. lncRNAs comprise a class of multifunctional non-coding transcripts that are able to interact with different types of biomolecules. Interactions between lncRNAs and RNA-binding proteins (RBPs) provide an important mechanism through which lncRNAs exert their regulatory functions, mainly through findings on ‘generalized RBPs’. Regulatory effects on lncRNAs mediated by RBPs have also been explored. Taking account of the research that has been completed to date, the continued and in-depth study of the bidirectional interactions between lncRNAs and RBPs will prove to be of major importance for understanding the pathogenesis of cancer and for developing effective therapies. The present review aims to explore the interactions between lncRNAs and RBPs that have been investigated in cancer, taking into consideration several different aspects, including the regulation of expression, subcellular localization and the mediation of diverse functions.
Collapse
Affiliation(s)
- Handong Huang
- Department of Gastrointestinal Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Lu Li
- Department of Ophthalmology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| | - Kunming Wen
- Department of Gastrointestinal Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou 563000, P.R. China
| |
Collapse
|
24
|
The Role of lncRNA in the Development of Tumors, including Breast Cancer. Int J Mol Sci 2021; 22:ijms22168427. [PMID: 34445129 PMCID: PMC8395147 DOI: 10.3390/ijms22168427] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/03/2021] [Accepted: 08/03/2021] [Indexed: 12/28/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) are the largest groups of ribonucleic acids, but, despite the increasing amount of literature data, the least understood. Given the involvement of lncRNA in basic cellular processes, especially in the regulation of transcription, the role of these noncoding molecules seems to be of great importance for the proper functioning of the organism. Studies have shown a relationship between disturbed lncRNA expression and the pathogenesis of many diseases, including cancer. The present article presents a detailed review of the latest reports and data regarding the importance of lncRNA in the development of cancers, including breast carcinoma.
Collapse
|
25
|
Wang H, Zhu Y, Chen H, Yang N, Wang X, Li B, Ying P, He H, Cai Y, Zhang M, Niu S, Li Y, Lu Z, Peng X, Zou D, Zhong R, Chang J, Dai M, Tian J, Miao X. Colorectal cancer risk variant rs7017386 modulates two oncogenic lncRNAs expression via ATF1-mediated long-range chromatin loop. Cancer Lett 2021; 518:140-151. [PMID: 34274452 DOI: 10.1016/j.canlet.2021.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 06/26/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023]
Abstract
The activating transcription factor 1 (ATF1) has been identified as a vital pathogenic factor in the progression of colorectal cancer (CRC), whiles, the precise regulatory mechanisms remain elusive. Here, we comprehensively characterized the ATF1 cistrome by RNA-seq and ChIP-seq assays in CRC cell lines. As the results, we identified 358 genes differentially regulated and 15,029 ATF1 binding sites and demonstrated that ATF1 was widely involved in major signaling pathways in CRC, such as Wnt, TNF, Jak-STAT. Subsequently, by the expression quantitative trait loci (eQTL) analyses, we found that rs7017386 was associated with the expression of CCAT1 and PVT1 in the Wnt pathway. By a two-stage population study with 6,131 CRC cases and 10,022 healthy controls, we identified the variant was associated with CRC risk. Mechanistically, we found rs7017386 allele-specifically enhanced the binding affinity of ATF1 and promoted the expressions of PVT1 and CCAT1, via forming a long-range chromatin loop. Moreover, those two lncRNAs could synergistically facilitate c-Myc expression to activate the Wnt pathway in CRC progression. Our findings not only demonstrated the transcriptomic profiling of ATF1 in CRC, but also provided important clues for the etiology of CRC.
Collapse
Affiliation(s)
- Haoxue Wang
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ying Zhu
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hongda Chen
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Yang
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoyang Wang
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bin Li
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Pingting Ying
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Heng He
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yimin Cai
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ming Zhang
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Siyuan Niu
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yue Li
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zequn Lu
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiating Peng
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danyi Zou
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Rong Zhong
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jiang Chang
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Dai
- Office of Cancer Screening, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianbo Tian
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Xiaoping Miao
- Department of Epidemiology and Biostatistics, And the Ministry of Education Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
26
|
Baruch E, Nizri-Megnaji T, Berkowitz O, Ginsberg D. A novel E2F1-regulated lncRNA, LAPAS1, is required for S phase progression and cell proliferation. Oncotarget 2021; 12:1072-1082. [PMID: 34084281 PMCID: PMC8169067 DOI: 10.18632/oncotarget.27962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 05/03/2021] [Indexed: 11/25/2022] Open
Abstract
The transcription factor E2F1 induces both proliferation and apoptosis and is a critical downstream target of the tumor suppressor RB. Long non-coding RNAs (lncRNAs) are major regulators of many cellular processes, including cell cycle progression and cell proliferation. However, the mode of action as well as the transcriptional regulation of most lncRNAs are only beginning to be understood. Here, we report that a novel human lncRNA, LAPAS1, is an E2F1- regulated lncRNA that affects S phase progression. Inhibition of LAPAS1 expression increases percentage of S phase cells, and its silencing in synchronized cells delays their progression through S phase. In agreement with its suggested role in cell cycle progression, prolonged inhibition of LAPAS1 attenuates proliferation of human cancer cells. Our data demonstrate that LAPAS1 predominantly functions in trans to repress expression of Sphingolipid Transporter 2 (SPNS2). Importantly, knockdown of SPNS2 rescues the effect of LAPAS1 silencing on cell cycle and cell proliferation. Notably, low levels of LAPAS1 are associated with increased survival of kidney cancer patients. Summarily, we identify LAPAS1 as a novel E2F-regulated lncRNA that has a potential role in human cancer and regulates cell-cycle progression and cell proliferation, at least in part, via regulation of SPNS2.
Collapse
Affiliation(s)
- Esther Baruch
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat Gan, Israel
| | - Tali Nizri-Megnaji
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat Gan, Israel
| | - Oron Berkowitz
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat Gan, Israel.,Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Doron Ginsberg
- The Mina and Everard Goodman Faculty of Life Science, Bar-Ilan University, Ramat Gan, Israel
| |
Collapse
|
27
|
Dworschak GC, Reutter HM, Ludwig M. Currarino syndrome: a comprehensive genetic review of a rare congenital disorder. Orphanet J Rare Dis 2021; 16:167. [PMID: 33836786 PMCID: PMC8034116 DOI: 10.1186/s13023-021-01799-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 03/30/2021] [Indexed: 11/10/2022] Open
Abstract
Background The triad of a presacral mass, sacral agenesis and an anorectal anomaly constitutes the rare Currarino syndrome (CS), which is caused by dorsal–ventral patterning defects during embryonic development. The major causative CS gene is MNX1, encoding a homeobox protein. Main body In the majority of patients, CS occurs as an autosomal dominant trait; however, a female predominance observed, implies that CS may underlie an additional mode(s) of inheritance. Often, the diagnosis of CS is established solely by clinical findings, impacting a detailed analysis of the disease. Our combined data, evaluating more than 60 studies reporting patients with CS-associated mutations, revealed a slightly higher incidence rate in females with a female-to-male ratio of 1.39:1. Overall, MNX1 mutation analysis was successful in only 57.4% of all CS patients investigated, with no mutation detected in 7.7% of the familial and 68% of the sporadic patients. Our studies failed to detect the presence of an expressed MNX1 isoform that might explain at least some of these mutation-negative cases. Conclusion Aside from MNX1, other genes or regulatory regions may contribute to CS and we discuss several cytogenetic studies and whole-exome sequencing data that have implicated further loci/genes in its etiology. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-021-01799-0.
Collapse
Affiliation(s)
- Gabriel C Dworschak
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany. .,Institute of Anatomy and Cell Biology, Medical Faculty, University of Bonn, 53115, Bonn, Germany. .,Department of Pediatrics, University Hospital Bonn, 53127, Bonn, Germany.
| | - Heiko M Reutter
- Institute of Human Genetics, Medical Faculty, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.,Department of Neonatology and Pediatric Intensive Care, University Hospital Bonn, 53127, Bonn, Germany
| | - Michael Ludwig
- Department of Clinical Chemistry and Clinical Pharmacology, University of Bonn, 53127, Bonn, Germany
| |
Collapse
|
28
|
Miao Y, Zhang H, Su B, Wang J, Quan W, Li Q, Mi D. Construction and validation of an RNA-binding protein-associated prognostic model for colorectal cancer. PeerJ 2021; 9:e11219. [PMID: 33868829 PMCID: PMC8029696 DOI: 10.7717/peerj.11219] [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: 12/30/2020] [Accepted: 03/15/2021] [Indexed: 12/15/2022] Open
Abstract
Colorectal cancer (CRC) is one of the most prevalent and fatal malignancies, and novel biomarkers for the diagnosis and prognosis of CRC must be identified. RNA-binding proteins (RBPs) are essential modulators of transcription and translation. They are frequently dysregulated in various cancers and are related to tumorigenesis and development. The mechanisms by which RBPs regulate CRC progression are poorly understood and no clinical prognostic model using RBPs has been reported in CRC. We sought to identify the hub prognosis-related RBPs and to construct a prognostic model for clinical use. mRNA sequencing and clinical data for CRC were obtained from The Cancer Genome Atlas database (TCGA). Gene expression profiles were analyzed to identify differentially expressed RBPs using R and Perl software. Hub RBPs were filtered out using univariate Cox and multivariate Cox regression analysis. We used functional enrichment analysis, including Gene Ontology and Gene Set Enrichment Analysis, to perform the function and mechanisms of the identified RBPs. The nomogram predicted overall survival (OS). Calibration curves were used to evaluate the consistency between the predicted and actual survival rate, the consistency index (c-index) was calculated, and the prognostic effect of the model was evaluated. Finally, we identified 178 differently expressed RBPs, including 121 up-regulated and 57 down-regulated proteins. Our prognostic model was based on nine RBPs (PNLDC1, RRS1, HEXIM1, PPARGC1A, PPARGC1B, BRCA1, CELF4, AEN and NOVA1). Survival analysis showed that patients in the high-risk subgroup had a worse OS than those in the low-risk subgroup. The area under the curve value of the receiver operating characteristic curve of the prognostic model is 0.712 in the TCGA cohort and 0.638 in the GEO cohort. These results show that the model has a moderate diagnostic ability. The c-index of the nomogram is 0.77 in the TCGA cohort and 0.73 in the GEO cohort. We showed that the risk score is an independent prognostic biomarker and that some RBPs may be potential biomarkers for the diagnosis and prognosis of CRC.
Collapse
Affiliation(s)
- Yandong Miao
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Hongling Zhang
- Cancer Ward, Palliative Medical Center, New Kunhua Hospital, Kunming, Yunnan, China
| | - Bin Su
- Department of Oncology, The 920th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Kunming, Yunnan, China
| | - Jiangtao Wang
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China
| | - Wuxia Quan
- Qingyang People's Hospital, Qingyang, Gansu, China
| | - Qiutian Li
- Department of Oncology, The 920th Hospital of the Chinese People's Liberation Army Joint Logistic Support Force, Kunming, Yunnan, China
| | - Denghai Mi
- The First Clinical Medical College, Lanzhou University, Lanzhou, Gansu, China.,Gansu Academy of Traditional Chinese Medicine, Lanzhou, China
| |
Collapse
|
29
|
Hu X, Xiang L, He D, Zhu R, Fang J, Wang Z, Cao K. The long noncoding RNA KTN1-AS1 promotes bladder cancer tumorigenesis via KTN1 cis-activation and the consequent initiation of Rho GTPase-mediated signaling. Clin Sci (Lond) 2021; 135:555-574. [PMID: 33480975 DOI: 10.1042/cs20200908] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 01/07/2021] [Accepted: 01/22/2021] [Indexed: 12/14/2022]
Abstract
BACKGROUND Accumulating evidence support the hypothesis that long noncoding RNAs (lncRNAs) are involved in several physiological and pathological conditions, including cancer. Here, we investigated the potential role of lncRNAs in bladder cancer. METHODS We first looked at available datasets retrieved from the TCGA database and discovered that the lncRNA KTN 1 antisense RNA 1 (KTN1-AS1) was significantly up-regulated in several cancer types including bladder cancer, but was decreased in some other tumors. Therefore, we focused our attention on KTN1-AS1. Using both in vitro and in vivo systems that allowed the modulation of KTN1-AS1 and expression of other relevant proteins, we investigated in-depth the role of KTN1-AS1 in bladder cancer (and the mechanism behind). We further investigated the potential KTN1-AS1-interacting proteins using RNA immunoprecipitation, and explored the KTN1-AS1-related epigenetic landscape (with a particular emphasis on acetylation) using chromatin immunoprecipitation (ChIP) assays. RESULTS KTN1-AS1 silencing inhibited the proliferation, invasion, and migration of bladder cancer cells, while KTN1-AS1 overexpression had the obvious opposite effects. Mechanistically, KTN1-AS1 promoted the recruitment of EP300, a histone acetyltransferase that enriched acetylation of histone H3 at lysine 27 (H3K27Ac) in the KTN1 promoter region. This epigenetic modulation contributed to the up-regulation of KTN1, which affected bladder cancer growth and progression via the regulation of Rho GTPase (RAC1, RHOA, and CDC42)-mediated signaling. CONCLUSION Overall, our data support the idea that the lncRNA KTN1-AS1 promotes bladder cancer tumorigenesis via modulation of the KTN1/Rho GTPase axis and is a promising new therapeutic target for the treatment of bladder cancer.
Collapse
Affiliation(s)
- Xueying Hu
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Liang Xiang
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Dong He
- Department of Respiratory, The Second People's Hospital of Hunan Province, Changsha 410007, China
| | - Rongrong Zhu
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Jianing Fang
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Zhanwang Wang
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| | - Ke Cao
- Department of Oncology, Third Xiangya Hospital of Central South University, Changsha 410013, China
| |
Collapse
|
30
|
Abstract
Evidence accumulated over the past decade shows that long non-coding RNAs (lncRNAs) are widely expressed and have key roles in gene regulation. Recent studies have begun to unravel how the biogenesis of lncRNAs is distinct from that of mRNAs and is linked with their specific subcellular localizations and functions. Depending on their localization and their specific interactions with DNA, RNA and proteins, lncRNAs can modulate chromatin function, regulate the assembly and function of membraneless nuclear bodies, alter the stability and translation of cytoplasmic mRNAs and interfere with signalling pathways. Many of these functions ultimately affect gene expression in diverse biological and physiopathological contexts, such as in neuronal disorders, immune responses and cancer. Tissue-specific and condition-specific expression patterns suggest that lncRNAs are potential biomarkers and provide a rationale to target them clinically. In this Review, we discuss the mechanisms of lncRNA biogenesis, localization and functions in transcriptional, post-transcriptional and other modes of gene regulation, and their potential therapeutic applications.
Collapse
|
31
|
Yang Y, Deng X, Li Q, Wang F, Miao L, Jiang Q. Emerging roles of long noncoding RNAs in cholangiocarcinoma: Advances and challenges. Cancer Commun (Lond) 2020; 40:655-680. [PMID: 33142045 PMCID: PMC7743012 DOI: 10.1002/cac2.12109] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/10/2020] [Accepted: 10/21/2020] [Indexed: 12/19/2022] Open
Abstract
Cholangiocarcinoma (CCA), a cancer with a relatively low incidence rate, is usually associated with poor prognosis. Current modalities for the diagnosis and treatment of CCA patients are still far from satisfactory. In recent years, numerous long noncoding RNAs (lncRNAs) have been identified as crucial players in the development of various cancers, including CCA. Abnormally expressed lncRNAs in CCA, regulated by some upstream molecules, significantly influence the biological behavior of tumor cells and are involved in tumor development through various mechanisms, including interactions with functional proteins, participation in competing for endogenous RNA (ceRNA) regulatory networks, activation of cancer‐related signaling pathways and epigenetic modification of gene expression. Furthermore, several lncRNAs are closely associated with the clinicopathological features of CCA patients, and are promising biomarkers for diagnosing and prognostication of CCA. Some of these lncRNAs play an important role in chemotherapy drug resistance. In addition, lncRNAs have also been shown to be involved in the inflammation microenvironment of CCA and malignant outcome of CCA risk factors, such as cholestatic liver diseases. In view of the difficulty of diagnosing CCA, more attention should be paid to detectable lncRNAs in the serum or bile. This review summarizes the recent knowledge on lncRNAs in CCA and provides a new outlook on the molecular mechanisms of CCA development from the perspective of lncRNAs. Moreover, we also discussed the limitations of the current studies and differential expression of lncRNAs in different types of CCA.
Collapse
Affiliation(s)
- Yang Yang
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Xueting Deng
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Quanpeng Li
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Fei Wang
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Lin Miao
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China.,Nanjing Medical University, Nanjing, Jiangsu, 210000, P. R. China
| | - Qi Jiang
- Department of Gastroenterology, Dongtai People's Hospital, Yancheng, Jiangsu, 224000, P. R. China
| |
Collapse
|
32
|
Tong Y, Song Y, Xia C, Deng S. Theoretical and in silico Analyses Reveal MYC as a Dynamic Network Biomarker in Colon and Rectal Cancer. Front Genet 2020; 11:555540. [PMID: 33193630 PMCID: PMC7606845 DOI: 10.3389/fgene.2020.555540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 09/16/2020] [Indexed: 12/24/2022] Open
Abstract
In this article, we make a theoretical and in silico study for uncovering and evaluating biomarkers in colon and rectal cancer (CRC) by the dynamic network biomarker (DNB) theory. We propose a strategy to employ the theoretical concept of UICC TNM classification in CRC. To reveal the critical transition of CRC, the DNB algorithm was implemented to analyze the genome-wide dynamic network through temporal gene expression data. The relationship between gene sets and clinical features was evaluated by weighted gene co-expression network analysis. The results show that MYC was significantly associated with tumor amplification, tumor immune cells, and survival times. The candidate tumor suppressor genes were ZBTB16, MAL, LIFR, and SLIT2. Protein-protein interaction (PPI) analysis shows that these candidate tumor suppressor genes were significant in immune cells. Data from the Human Protein Atlas showed that a high expression of these candidate tumor suppressor genes was associated with favorable prognosis in TNM stages I-IV. In conclusion, this work provides significant and novel information regarding the TNM stage, cause, and consequences of elevated MYC expression in CRC. MYC expression levels had significant negative correlations with tumor suppressor genes and immune cells.
Collapse
Affiliation(s)
- Yanqiu Tong
- Department of Broadcasting and TV, Chongqing Jiaotong University, Chongqing, China
- Laboratory of Forensic Medicine and Biomedical Informatics, Chongqing Medical University, Chongqing, China
| | - Yang Song
- Department of Medical Informatics, Chongqing Medical University, Chongqing, China
| | - Chuanhui Xia
- School of Materials Science and Engineering, Chongqing Jiaotong University, Chongqing, China
| | - Shixiong Deng
- Laboratory of Forensic Medicine and Biomedical Informatics, Chongqing Medical University, Chongqing, China
| |
Collapse
|
33
|
MYC as a Multifaceted Regulator of Tumor Microenvironment Leading to Metastasis. Int J Mol Sci 2020; 21:ijms21207710. [PMID: 33081056 PMCID: PMC7589112 DOI: 10.3390/ijms21207710] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 12/12/2022] Open
Abstract
The Myc family of oncogenes is deregulated in many types of cancer, and their over-expression is often correlated with poor prognosis. The Myc family members are transcription factors that can coordinate the expression of thousands of genes. Among them, c-Myc (MYC) is the gene most strongly associated with cancer, and it is the focus of this review. It regulates the expression of genes involved in cell proliferation, growth, differentiation, self-renewal, survival, metabolism, protein synthesis, and apoptosis. More recently, novel studies have shown that MYC plays a role not only in tumor initiation and growth but also has a broader spectrum of functions in tumor progression. MYC contributes to angiogenesis, immune evasion, invasion, and migration, which all lead to distant metastasis. Moreover, MYC is able to promote tumor growth and aggressiveness by recruiting stromal and tumor-infiltrating cells. In this review, we will dissect all of these novel functions and their involvement in the crosstalk between tumor and host, which have demonstrated that MYC is undoubtedly the master regulator of the tumor microenvironment. In sum, a better understanding of MYC’s role in the tumor microenvironment and metastasis development is crucial in proposing novel and effective cancer treatment strategies.
Collapse
|
34
|
Olivero CE, Dimitrova N. Identification and characterization of functional long noncoding RNAs in cancer. FASEB J 2020; 34:15630-15646. [PMID: 33058262 PMCID: PMC7756267 DOI: 10.1096/fj.202001951r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/29/2020] [Accepted: 10/01/2020] [Indexed: 12/12/2022]
Abstract
Long noncoding RNAs (lncRNAs) have emerged as key regulators in a variety of cellular processes that influence disease states. In particular, many lncRNAs are genetically or epigenetically deregulated in cancer. However, whether lncRNA alterations are passengers acquired during cancer progression or can act as tumorigenic drivers is a topic of ongoing investigation. In this review, we examine the current methodologies underlying the identification of cancer-associated lncRNAs and highlight important considerations for evaluating their biological significance as cancer drivers.
Collapse
Affiliation(s)
- Christiane E Olivero
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| |
Collapse
|
35
|
Peng W, Zhang C, Peng J, Huang Y, Peng C, Tan Y, Ji D, Zhang Y, Zhang D, Tang J, Feng Y, Sun Y. Lnc-FAM84B-4 acts as an oncogenic lncRNA by interacting with protein hnRNPK to restrain MAPK phosphatases-DUSP1 expression. Cancer Lett 2020; 494:94-106. [PMID: 32866608 DOI: 10.1016/j.canlet.2020.08.036] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/01/2020] [Accepted: 08/25/2020] [Indexed: 12/11/2022]
Abstract
The mitogen activated protein kinase (MAPK) pathway has been reported to be involved in many cancer developments. Normally, MAPK activity is self-limited between rapid phosphorylation and dephosphorylation. In abnormal conditions, however, this dynamic equilibrium is broken, trigging tumor-suppressing or -promoting roles. While dual-specificity MAPK phosphatases (MKP/DUSPs) are important for cascade control in MAPK pathway, their role in colorectal cancer (CRC) remains largely unknown. Here, we investigated lnc-FAM84B-4 and DUSP1 to systematically elucidate their underlying roles in MAPK singling pathway and functions in CRC. Upregulated lnc-FAM84B-4 was identified by re-mining CRC microarray. Functional assays were performed in vitro and in vivo. RNA-Seq, RNA pull-down, and RIP assays were used to investigate the mechanisms of Lnc-FAM84B-4 in regulating expression of DUSP1. The results indicated that Lnc-FAM84B-4 regulates MAPK pathway by restraining DUSP1 expression. Mechanistically, RNA pull-down followed by mass spectrum determined hnRNPK functions as a binding partner of lnc-FAM84B-4 in mediating DUSP1 expression. Our findings demonstrate the important role of lnc-FAM84B-4-hnRNPK-DUSP1 axis in CRC development, and suggest a therapeutic target for CRC treatment.
Collapse
Affiliation(s)
- Wen Peng
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Chuan Zhang
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Jianing Peng
- Nanjing Foreign Language School, British Columbia Academy, Nanjing, Jiangsu, 210008, PR China
| | - Yuanjian Huang
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Chaofan Peng
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Yuqian Tan
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Dongjian Ji
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Yue Zhang
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Dongsheng Zhang
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China
| | - Junwei Tang
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China.
| | - Yifei Feng
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China.
| | - Yueming Sun
- The First School of Clinical Medicine, Nanjing Medical University, PR China, Department of General Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, 210029, PR China.
| |
Collapse
|
36
|
Li C, Zhao W, Pan X, Li X, Yan F, Liu S, Feng J, Lu J. LncRNA KTN1-AS1 promotes the progression of non-small cell lung cancer via sponging of miR-130a-5p and activation of PDPK1. Oncogene 2020; 39:6157-6171. [PMID: 32820252 DOI: 10.1038/s41388-020-01427-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 08/01/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022]
Abstract
Non-small cell lung cancer (NSCLC) is the major cause of cancer-associated death worldwide, but its underlying mechanisms remain to be fully elucidated. Long noncoding RNAs (lncRNAs) are known to play an important role in the aberrant regulation of gene expression in many cancers, including NSCLC. Here, we investigated the involvement of the lncRNA KTN1-AS1 in NSCLC. We found that KTN1-AS1 expression was upregulated in NSCLC tissue and was positively associated with poor prognosis. KTN1-AS1 knockdown inhibited cell growth and proliferation, increased apoptosis, and modulated the expression of cell cycle- and apoptosis-related proteins (cyclin A1, cyclin-dependent kinase 2, Bcl2, and Bax) in NSCLC cell lines and tumour xenografts in nude mice. KTN1-AS1 bound to and directly regulated the expression of miR-130a-5p. Notably, miR-130a-5p overexpression suppressed NSCLC cell proliferation and increased apoptosis in vitro and in vivo, and this effect was reversed by KTN1-AS1 overexpression. Finally, we showed that KTN1-AS1 modulated the expression of 3-phosphoinositide-dependent protein kinase 1 (PDPK1), a miR-130a-5p target and key regulator of autophagy in NSCLC cells. Taken together, our results suggest that the KTN1-AS1/miR-130a-5p/PDPK1 pathway may be a potential therapeutic target for NSCLC.
Collapse
Affiliation(s)
- Chenchen Li
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
| | - Wei Zhao
- School of Laboratory Medicine/Sichuan Provincial Engineering Laboratory for Prevention and Control Technology of Veterinary Drug Residue in Animal-origin Food, Chengdu Medical College, Chengdu, People's Republic of China
| | - Xuan Pan
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
| | - Xiaoyou Li
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
| | - Fei Yan
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
| | - Siwen Liu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China
| | - Jifeng Feng
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China.
| | - Jianwei Lu
- Department of Medical Oncology, The Affiliated Cancer Hospital of Nanjing Medical University & Jiangsu Cancer Hospital& Jiangsu Institute of Cancer Research, Nanjing, People's Republic of China.
| |
Collapse
|
37
|
Liao Y, Jung SH, Kim T. A-to-I RNA editing as a tuner of noncoding RNAs in cancer. Cancer Lett 2020; 494:88-93. [PMID: 32822814 DOI: 10.1016/j.canlet.2020.08.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 07/11/2020] [Accepted: 08/07/2020] [Indexed: 12/26/2022]
Abstract
Recent advancement in RNA technology and computation biology shows the abundance and impact of RNA editing at the genome-wide level. Of RNA editing events, Adenosine-to-inosine (A-to-I) RNA editing is one of the most frequent types of RNA editing catalyzed by ADAR proteins. Indeed, A-to-I RNA editing occurs at the various coding and noncoding regions, triggering abnormal signaling pathways involved in cancer pathogenesis. Noncoding RNAs such as microRNA and long noncoding RNA have emerged as key regulators of pathways in cancer. The RNA editing including A-to-I editing is enriched in noncoding regions because of the abundance of noncoding RNAs accounting for 99% of total transcripts in the human genome. The effects of A-to-I editing in coding genes have been investigated and reported. However, those in noncoding RNAs have been less known in spite of the high frequency of editing events in noncoding regions. In this review, we will briefly discuss current findings and potential directions of A-to-I RNA editing research of noncoding RNAs and cancer. We will also introduce the concept of A-to-I editing, ADAR proteins, RNA editing technologies and databases.
Collapse
Affiliation(s)
- Yuanfan Liao
- Department of Anatomy, Histology and Developmental Biology, Base for International Science and Technology Cooperation, Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University, Health Science Center, Shenzhen, 518055, China
| | - Seung Ho Jung
- Applied Neuroscience, Warfighter Interface Division, 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Dayton, OH, 45433, USA; ORISE, Oak Ridge, TN, 37830, USA.
| | - Taewan Kim
- Department of Anatomy, Histology and Developmental Biology, Base for International Science and Technology Cooperation, Carson Cancer Stem Cell Vaccines R&D Center, International Cancer Center, Shenzhen University, Health Science Center, Shenzhen, 518055, China; The Ohio State University Comprehensive Cancer Center, Columbus, OH, 43210, USA.
| |
Collapse
|
38
|
Chen Q, Shen H, Zhu X, Liu Y, Yang H, Chen H, Xiong S, Chi H, Xu W. A nuclear lncRNA Linc00839 as a Myc target to promote breast cancer chemoresistance via PI3K/AKT signaling pathway. Cancer Sci 2020; 111:3279-3291. [PMID: 32619088 PMCID: PMC7469761 DOI: 10.1111/cas.14555] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/18/2020] [Accepted: 06/23/2020] [Indexed: 12/16/2022] Open
Abstract
Chemoresistance has become a leading cause of mortality in breast cancer patients and is one of the major obstacles for improving the clinical outcome. Long noncoding RNAs play important roles in breast cancer tumorigenesis and chemoresistance. However, the involvement and regulation of lncRNAs in breast cancer chemoresistance are not completely understood. Here, we reported that Linc00839 was localized in the nucleus and upregulated in chemoresistant breast cancer cells and tissues, and high level of Linc00839 was associated with a poor prognosis. Knockdown of Linc00839 significantly suppressed proliferation, invasion, and migration, sensitized cells to paclitaxel in vitro and inhibited transplant tumor development in vivo. Mechanistically, we found that Myc could directly bind to the promoter region of Linc00839 and activate its transcription. Furthermore, Linc00839 overexpression increased the expression of Myc and the RNA‐binding protein Lin28B and activated the PI3K/AKT signaling pathway. We also discovered that Lin28B positively interacted with Linc00839 and was upregulated in breast cancer tissues. Taken together, for the first time, we showed that Linc00839 was activated by Myc and promoted proliferation and chemoresistance in breast cancer through binding with Lin28B. These findings provide new insight into the regulatory mechanism of Linc00839 and propose a Myc/Linc00839/Lin28B feedback loop that could be used as a novel therapeutic target for breast cancer.
Collapse
Affiliation(s)
- Qi Chen
- Department of Breast Diseases, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,School of medicine, Jiangsu University, Zhenjiang, China
| | - Huiling Shen
- Department of Oncology, Affiliated People Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaolan Zhu
- Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yueqin Liu
- Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Hui Yang
- Department of Breast Diseases, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Hui Chen
- School of medicine, Jiangsu University, Zhenjiang, China
| | - Shangwan Xiong
- School of medicine, Jiangsu University, Zhenjiang, China
| | - Huamao Chi
- Department of Breast Diseases, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenlin Xu
- Department of Breast Diseases, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,School of medicine, Jiangsu University, Zhenjiang, China
| |
Collapse
|
39
|
Neitzel C, Demuth P, Wittmann S, Fahrer J. Targeting Altered Energy Metabolism in Colorectal Cancer: Oncogenic Reprogramming, the Central Role of the TCA Cycle and Therapeutic Opportunities. Cancers (Basel) 2020; 12:E1731. [PMID: 32610612 PMCID: PMC7408264 DOI: 10.3390/cancers12071731] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is among the most frequent cancer entities worldwide. Multiple factors are causally associated with CRC development, such as genetic and epigenetic alterations, inflammatory bowel disease, lifestyle and dietary factors. During malignant transformation, the cellular energy metabolism is reprogrammed in order to promote cancer cell growth and proliferation. In this review, we first describe the main alterations of the energy metabolism found in CRC, revealing the critical impact of oncogenic signaling and driver mutations in key metabolic enzymes. Then, the central role of mitochondria and the tricarboxylic acid (TCA) cycle in this process is highlighted, also considering the metabolic crosstalk between tumor and stromal cells in the tumor microenvironment. The identified cancer-specific metabolic transformations provided new therapeutic targets for the development of small molecule inhibitors. Promising agents are in clinical trials and are directed against enzymes of the TCA cycle, including isocitrate dehydrogenase, pyruvate dehydrogenase kinase, pyruvate dehydrogenase complex (PDC) and α-ketoglutarate dehydrogenase (KGDH). Finally, we focus on the α-lipoic acid derivative CPI-613, an inhibitor of both PDC and KGDH, and delineate its anti-tumor effects for targeted therapy.
Collapse
Affiliation(s)
| | | | | | - Jörg Fahrer
- Division of Food Chemistry and Toxicology, Department of Chemistry, Technical University of Kaiserslautern, 67663 Kaiserslautern, Germany; (C.N.); (P.D.); (S.W.)
| |
Collapse
|
40
|
A Driver Never Works Alone-Interplay Networks of Mutant p53, MYC, RAS, and Other Universal Oncogenic Drivers in Human Cancer. Cancers (Basel) 2020; 12:cancers12061532. [PMID: 32545208 PMCID: PMC7353041 DOI: 10.3390/cancers12061532] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/03/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022] Open
Abstract
The knowledge accumulating on the occurrence and mechanisms of the activation of oncogenes in human neoplasia necessitates an increasingly detailed understanding of their systemic interactions. None of the known oncogenic drivers work in isolation from the other oncogenic pathways. The cooperation between these pathways is an indispensable element of a multistep carcinogenesis, which apart from inactivation of tumor suppressors, always includes the activation of two or more proto-oncogenes. In this review we focus on representative examples of the interaction of major oncogenic drivers with one another. The drivers are selected according to the following criteria: (1) the highest frequency of known activation in human neoplasia (by mutations or otherwise), (2) activation in a wide range of neoplasia types (universality) and (3) as a part of a distinguishable pathway, (4) being a known cause of phenotypic addiction of neoplastic cells and thus a promising therapeutic target. Each of these universal oncogenic factors—mutant p53, KRAS and CMYC proteins, telomerase ribonucleoprotein, proteasome machinery, HSP molecular chaperones, NF-κB and WNT pathways, AP-1 and YAP/TAZ transcription factors and non-coding RNAs—has a vast network of molecular interrelations and common partners. Understanding this network allows for the hunt for novel therapeutic targets and protocols to counteract drug resistance in a clinical neoplasia treatment.
Collapse
|
41
|
Role of long non-coding RNAs and MYC interaction in cancer metastasis: A possible target for therapeutic intervention. Toxicol Appl Pharmacol 2020; 399:115056. [PMID: 32445756 DOI: 10.1016/j.taap.2020.115056] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/13/2020] [Accepted: 05/16/2020] [Indexed: 01/17/2023]
Abstract
The c-MYC is one of the most commonly discussed oncogenes in almost all cancers. c-MYC, as a proto-oncogene in normal cells, has found to be tightly controlled and regulated, both genetically and epigenetically. Evasion of the controlled checkpoint mechanisms during cancer causes a deregulated expression of c-MYC. Overexpression of c-MYC causes the onset of many hallmarks of cancer. Despite c-MYC being centrally located in several cancers, it is not feasible to target c-MYC in therapeutic resistant cancers. Similarly, long non-coding RNAs (lncRNAs) are deregulated during the genesis and progression of different cancers. LncRNAs contribute to almost 27% human genome and recent findings by tumor genome sequencing revealed many of the lncRNAs loci that are modified, deleted, amplified, and mutated during the different stages of cancer development. Recent studies also reported that multiple lncRNAs regulate c-MYC by different mechanisms and vice versa. Thus, oncogenic lncRNAs and c-MYC interaction are positioned to provide an interesting choice for therapeutic interventions in cancers. In this mini-review, we summarize the recent discoveries and explain how the interaction between oncogenic lncRNAs and c-MYC could be used as a possible target for therapeutic intervention in cancers, especially the therapeutic resistant metastatic cancers.
Collapse
|
42
|
Mechanisms of Long Non-Coding RNAs in Cancers and Their Dynamic Regulations. Cancers (Basel) 2020; 12:cancers12051245. [PMID: 32429086 PMCID: PMC7281179 DOI: 10.3390/cancers12051245] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/12/2020] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Long non-coding RNA (lncRNA), which is a kind of noncoding RNA, is generally characterized as being more than 200 nucleotide transcripts in length. LncRNAs exhibit many biological activities, including, but not limited to, cancer development. In this review, a search of the PubMed database was performed to identify relevant studies published in English. The term "lncRNA or long non-coding RNA" was combined with a range of search terms related to the core focus of the review: mechanism, structure, regulation, and cancer. The eligibility of the retrieved studies was mainly based on the abstract. The decision as to whether or not the study was included in this review was made after a careful assessment of its content. The reference lists were also checked to identify any other study that could be relevant to this review. We first summarized the molecular mechanisms of lncRNAs in tumorigenesis, including competing endogenous RNA (ceRNA) mechanisms, epigenetic regulation, decoy and scaffold mechanisms, mRNA and protein stability regulation, transcriptional and translational regulation, miRNA processing regulation, and the architectural role of lncRNAs, which will help a broad audience better understand how lncRNAs work in cancer. Second, we introduced recent studies to elucidate the structure of lncRNAs, as there is a link between lncRNA structure and function and visualizing the architectural domains of lncRNAs is vital to understanding their function. Third, we explored emerging evidence for regulators of lncRNA expression, lncRNA turnover, and lncRNA modifications (including 5-methylcytidine, N6-methyladenosine, and adenosine to inosine editing), highlighting the dynamics of lncRNAs. Finally, we used autophagy in cancer as an example to interpret the diverse mechanisms of lncRNAs and introduced clinical trials of lncRNA-based cancer therapies.
Collapse
|
43
|
Grixti JM, Ayers D. Long noncoding RNAs and their link to cancer. Noncoding RNA Res 2020; 5:77-82. [PMID: 32490292 PMCID: PMC7256057 DOI: 10.1016/j.ncrna.2020.04.003] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 04/22/2020] [Accepted: 04/22/2020] [Indexed: 02/09/2023] Open
Abstract
The central dogma of molecular biology, developed from the study of simple organisms such as Escherichia coli, has up until recently been that RNA functions mainly as an information intermediate between a DNA sequence (gene), localized in the cell nucleus, serving as a template for the transcription of messenger RNAs, which in turn translocate into the cytoplasm and act as blueprints for the translation of their encoded proteins. There are a number of classes of non-protein coding RNAs (ncRNAs) which are essential for gene expression to function. The specific number of ncRNAs within the human genome is unknown. ncRNAs are classified on the basis of their size. Transcripts shorter than 200 nucleotides, referred to as ncRNAs, which group includes miRNAs, siRNAs, piRNAs, etc, have been extensively studied. Whilst transcripts with a length ranging between 200 nt up to 100 kilobases, referred to as lncRNAs, make up the second group, and are recently receiving growing concerns. LncRNAs play important roles in a variety of biological processes, regulating physiological functions of organisms, including epigenetic control of gene regulation, transcription and post-transcription, affecting various aspects of cellular homeostasis, including proliferation, survival, migration and genomic stability. LncRNAs are also capable of tuning gene expression and impact cellular signalling cascades, play crucial roles in promoter-specific gene regulation, and X-chromosome inactivation. Furthermore, it has been reported that lncRNAs interact with DNA, RNA, and/or protein molecules, and regulate chromatin organisation, transcriptional and post-transcriptional regulation. Consequently, they are differentially expressed in tumours, and they are directly linked to the transformation of healthy cells into tumour cells. As a result of their key functions in a wide range of biological processes, lncRNAs are becoming rising stars in biology and medicine, possessing potential active roles in various oncologic diseases, representing a gold mine of potential new biomarkers and drug targets.
Collapse
Affiliation(s)
- Justine M Grixti
- Institute of Integrative Biology, Faculty of Health & Life Sciences, University of Liverpool, Liverpool, L69 6ZB, UK, United Kingdom
| | - Duncan Ayers
- Centre for Molecular Medicine and Biobanking, University of Malta, Msida, MSD2080, Malta.,Faculty of Biology, Medicine and Health Sciences, The University of Manchester, Manchester, M13 9PL, UK, United Kingdom
| |
Collapse
|
44
|
Wang W, Tang X, Qu H, He Q. Translation regulatory long non-coding RNA 1 represents a potential prognostic biomarker for colorectal cancer. Oncol Lett 2020; 19:4077-4087. [PMID: 32391108 PMCID: PMC7204641 DOI: 10.3892/ol.2020.11532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 03/05/2020] [Indexed: 12/22/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) have attracted a lot of attention for their role in the development, progression and prognosis of colorectal cancer (CRC). However, little is known on the clinical significance of the translation regulatory lncRNA 1 (TRERNA1) in CRC. The present study aimed to explore the clinical value of TRERNA1 in patients with CRC. A total of 89 cancer-associated lncRNA genes were analyzed using the RT2 lncRNA PCR array Human Cancer PathwayFinder. Following the PCR array, reverse transcription-quantitative (RT-q)PCR was conducted to identify the differential expression of TRERNA1 between 130 CRC and corresponding non-tumorous adjacent tissues. Additionally, the association between TRERNA1 expression and clinical characteristics was analyzed. Furthermore, TRERNA1 expression was knocked down via small interfering RNAs. The results of the PCR array and RT-qPCR revealed that TRERNA1 expression was significantly upregulated in CRC tissues compared with in adjacent normal tissues. TRERNA1 upregulation was positively associated with distant metastasis, perineural invasion, TNM stage, node metastasis stage and tumor diameter. Multivariate analysis revealed that patients with higher TRERNA1 expression had a shorter overall survival (OS) time and a less favorable prognosis compared with those in the low TRERNA1 expression group. Knockdown of TRERNA1 inhibited invasion and metastasis of CRC cells via regulating Snail expression. In conclusion, TRERNA1 expression was upregulated in CRC tissues. High expression levels of TRERNA1 may be associated with poor OS times, a less favorable prognosis and lymph node metastasis in patients with CRC. TRERNA1 may therefore serve as a useful and novel biomarker for CRC lymph node metastasis and prognosis.
Collapse
Affiliation(s)
- Weijia Wang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China.,Department of General Surgery, Linyi People's Hospital, Linyi, Shandong 276000, P.R. China
| | - Xiaolong Tang
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Hui Qu
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| | - Qingsi He
- Department of General Surgery, Qilu Hospital of Shandong University, Jinan, Shandong 250012, P.R. China
| |
Collapse
|
45
|
Liu C, Li X, Hao Y, Wang F, Cheng Z, Geng H, Geng D. STAT1-induced upregulation of lncRNA KTN1-AS1 predicts poor prognosis and facilitates non-small cell lung cancer progression via miR-23b/DEPDC1 axis. Aging (Albany NY) 2020; 12:8680-8701. [PMID: 32396871 PMCID: PMC7244022 DOI: 10.18632/aging.103191] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/17/2020] [Indexed: 12/25/2022]
Abstract
Several of the thousands of long noncoding RNAs (lncRNAs) have been functionally characterized in various tumors. In this study, we aimed to explore the function and possible molecular mechanism of lncRNA KTN1 antisense RNA 1 (KTN1-AS1) involved in non-small cell lung cancer (NSCLC). We identified a novel NSCLC-related lncRNA, KTN1 antisense RNA 1 (KTN1-AS1) which was demonstrated to be distinctly highly expressed in NSCLC. KTN1-AS1 upregulation was induced by STAT1. Clinical study also suggested that higher levels of KTN1-AS1 were associated with advanced clinical progression and a shorter five-year overall survival. Functionally, loss-of-function assays with in vitro and in vivo experiments revealed that KTN1-AS1 promoted the proliferation, migration, invasion and EMT progress of NSCLC cells, and suppressed apoptosis. Mechanistic studies indicated that miR-23b was a direct target of KTN1-AS1, which functioned as a ceRNA to subsequently facilitate miR-23b’s target gene DEPDC1 expression in NSCLC cells. Rescue experiments confirmed that KTN1-AS1 overexpression could increase the colony formation and migration ability suppressed by miR-23b upregulation in NSCLC cells. Overall, our findings imply that STAT1-induced upregulation of KTN1-AS1 display tumor-promotive roles in NSCLC progression via regulating miR-23b/DEPDC1 axis, suggesting that KTN1-AS1 may be a novel biomarker and therapeutic target for NSCLC patients.
Collapse
Affiliation(s)
- Changmin Liu
- Department of Oncology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Xiaoming Li
- Department of Hepatobiliary Surgery, Shandong Provincial ENT Hospital, Shandong Provincial ENT Hospital Affiliated to Shandong University, Jinan, Shandong, China
| | - Yanzhang Hao
- Department of Oncology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Feng Wang
- Department of Oncology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Zhiwen Cheng
- Department of Oncology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Haitao Geng
- Department of Oncology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| | - Dianzhong Geng
- Department of Oncology, Binzhou Medical University Hospital, Binzhou, Shandong, China
| |
Collapse
|
46
|
Silva-Fisher JM, Dang HX, White NM, Strand MS, Krasnick BA, Rozycki EB, Jeffers GGL, Grossman JG, Highkin MK, Tang C, Cabanski CR, Eteleeb A, Mudd J, Goedegebuure SP, Luo J, Mardis ER, Wilson RK, Ley TJ, Lockhart AC, Fields RC, Maher CA. Long non-coding RNA RAMS11 promotes metastatic colorectal cancer progression. Nat Commun 2020; 11:2156. [PMID: 32358485 PMCID: PMC7195452 DOI: 10.1038/s41467-020-15547-8] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 03/16/2020] [Indexed: 01/14/2023] Open
Abstract
Colorectal cancer (CRC) is the most common gastrointestinal malignancy in the U.S.A. and approximately 50% of patients develop metastatic disease (mCRC). Despite our understanding of long non-coding RNAs (lncRNAs) in primary colon cancer, their role in mCRC and treatment resistance remains poorly characterized. Therefore, through transcriptome sequencing of normal, primary, and distant mCRC tissues we find 148 differentially expressed RNAs Associated with Metastasis (RAMS). We prioritize RAMS11 due to its association with poor disease-free survival and promotion of aggressive phenotypes in vitro and in vivo. A FDA-approved drug high-throughput viability assay shows that elevated RAMS11 expression increases resistance to topoisomerase inhibitors. Subsequent experiments demonstrate RAMS11-dependent recruitment of Chromobox protein 4 (CBX4) transcriptionally activates Topoisomerase II alpha (TOP2α). Overall, recent clinical trials using topoisomerase inhibitors coupled with our findings of RAMS11-dependent regulation of TOP2α supports the potential use of RAMS11 as a biomarker and therapeutic target for mCRC.
Collapse
Affiliation(s)
- Jessica M Silva-Fisher
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Ha X Dang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- The McDonnell Genome Institute, St. Louis, MO, USA
| | - Nicole M White
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Matthew S Strand
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Bradley A Krasnick
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Emily B Rozycki
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Gejae G L Jeffers
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Julie G Grossman
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Maureen K Highkin
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Cynthia Tang
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Abdallah Eteleeb
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Jingqin Luo
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Division of Public Health Sciences, Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Richard K Wilson
- Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, OH, USA
| | - Timothy J Ley
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
| | | | - Ryan C Fields
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA.
- The McDonnell Genome Institute, St. Louis, MO, USA.
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO, USA.
| |
Collapse
|
47
|
Raffeiner P, Hart JR, García-Caballero D, Bar-Peled L, Weinberg MS, Vogt PK. An MXD1-derived repressor peptide identifies noncoding mediators of MYC-driven cell proliferation. Proc Natl Acad Sci U S A 2020; 117:6571-6579. [PMID: 32156728 PMCID: PMC7104257 DOI: 10.1073/pnas.1921786117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
MYC controls the transcription of large numbers of long noncoding RNAs (lncRNAs). Since MYC is a ubiquitous oncoprotein, some of these lncRNAs probably play a significant role in cancer. We applied CRISPR interference (CRISPRi) to the identification of MYC-regulated lncRNAs that are required for MYC-driven cell proliferation in the P493-6 and RAMOS human lymphoid cell lines. We identified 320 noncoding loci that play positive roles in cell growth. Transcriptional repression of any one of these lncRNAs reduces the proliferative capacity of the cells. Selected hits were validated by RT-qPCR and in CRISPRi competition assays with individual GFP-expressing sgRNA constructs. We also showed binding of MYC to the promoter of two candidate genes by chromatin immunoprecipitation. In the course of our studies, we discovered that the repressor domain SID (SIN3-interacting domain) derived from the MXD1 protein is highly effective in P493-6 and RAMOS cells in terms of the number of guides depleted in library screening and the extent of the induced transcriptional repression. In the cell lines used, SID is superior to the KRAB repressor domain, which serves routinely as a transcriptional repressor domain in CRISPRi. The SID transcriptional repressor domain is effective as a fusion to the MS2 aptamer binding protein MCP, allowing the construction of a doxycycline-regulatable CRISPRi system that allows controlled repression of targeted genes and will facilitate the functional analysis of growth-promoting lncRNAs.
Collapse
Affiliation(s)
- Philipp Raffeiner
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Jonathan R Hart
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | | | - Liron Bar-Peled
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037
| | - Marc S Weinberg
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
- Wits-SAMRC Antiviral Gene Therapy Research Unit, Department of Molecular Medicine and Hematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg 2000, South Africa
| | - Peter K Vogt
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037;
| |
Collapse
|
48
|
Chen Z, Chen X, Lei T, Gu Y, Gu J, Huang J, Lu B, Yuan L, Sun M, Wang Z. Integrative Analysis of NSCLC Identifies LINC01234 as an Oncogenic lncRNA that Interacts with HNRNPA2B1 and Regulates miR-106b Biogenesis. Mol Ther 2020; 28:1479-1493. [PMID: 32246902 DOI: 10.1016/j.ymthe.2020.03.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 03/13/2020] [Indexed: 12/31/2022] Open
Abstract
The discovery of long noncoding RNAs (lncRNAs) has increased our understanding of the development and progression of many cancers, but their contributions to non-small cell lung cancer (NSCLC) remain poorly understood. Here, we profiled lncRNA expression in NSCLC and investigated in detail the molecular function of one upregulated lncRNA, LINC01234. LINC01234 was overexpressed in NSCLC compared with normal lung tissue and correlated positively with poor prognosis. Downregulation of LINC01234 impaired cell proliferation in vitro and tumor growth in vivo. RNA pull-down/mass spectrometry experiments showed that LINC01234 interacted with the RNA-binding protein heterogeneous nuclear ribonucleoprotein A2/B1 (HNRNPA2B1), which, in turn, led to the recruitment of DiGeorge syndrome critical region gene 8 (DGCR8), a subunit of the microRNA (miRNA) microprocessor complex. Accordingly, depletion of either LINC01234 or HNRNPA2B1 reduced the processing of several miRNA precursors, including primary microRNA (pri-miR)-106b. miR-106b-5p enhanced NSCLC cell growth by downregulating cryptochrome 2 (CRY2), thereby increasing c-Myc expression. Finally, we found that activated c-Myc binds to the LINC01234 promoter to increase its transcription, creating a c-Myc-LINC01234-HNRNPA2B1-miR-106b-5p-CRY2-c-Myc positive-feedback loop. We identified numerous lncRNAs with dysregulated expression in NSCLC and demonstrated a novel oncogenic axis involving LINC01234, HNRNPA2B1, miR-106b-5p, CRY2, and c-Myc. Components of this axis may be potential novel targets for NSCLC.
Collapse
Affiliation(s)
- Zhenyao Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China
| | - Xin Chen
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China
| | - Tianyao Lei
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China
| | - Yu Gu
- Faculty of Mathematics, University of Waterloo, Waterloo, ON N2L 3G1, Canada
| | - Jinyao Gu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China
| | - Jiali Huang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China
| | - Binbin Lu
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China
| | - Li Yuan
- Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing 210029, Jiangsu, P.R. China
| | - Ming Sun
- Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX 77030, USA.
| | - Zhaoxia Wang
- Cancer Medical Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing 210011, Jiangsu, P.R. China.
| |
Collapse
|
49
|
Jiang Y, Wu K, Cao W, Xu Q, Wang X, Qin X, Wang X, Li Y, Zhang J, Chen W. Long noncoding RNA KTN1-AS1 promotes head and neck squamous cell carcinoma cell epithelial-mesenchymal transition by targeting miR-153-3p. Epigenomics 2020; 12:487-505. [PMID: 32267161 DOI: 10.2217/epi-2019-0173] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Aim: To explore the biological functions and clinicopathologic significance of the long noncoding RNA KTN1-AS1 in head and neck squamous cell carcinoma (HNSCC). Materials & methods: We assessed the effects of KTN1-AS1 and identified the target miRNA by bioinformatics analysis, luciferase reporter, RNA pull-down and RNA immunoprecipitation assays. The clinicopathologic features of KTN1-AS1 and its target miRNA were analyzed in HNSCC. Results:KTN1-AS1, a competing endogenous RNA, promoted cell proliferation, migration, invasion and epithelial-mesenchymal transition by sponging miR-153-3p in HNSCC. Dysregulation of SNAI1 and ZEB2 mediated the effect of KTN1-AS1 due to miR-153-3p exhaustion. The KTN1-AS1 and miR-153-3p combination can accurately diagnose HNSCC. Conclusion: The KTN1-AS1 and miR-153-3p combination could be a valuable diagnostic and prognostic predictor for HNSCC.
Collapse
Affiliation(s)
- Yingying Jiang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
- Department of Dentistry, Affiliated Hospital, Weifang Medical University, Weifang 261031, PR China
| | - Kun Wu
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
| | - Wei Cao
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
| | - Qin Xu
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, PR China
| | - Xu Wang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
| | - Xing Qin
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
| | - Xiaoning Wang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
| | - Yan Li
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
| | - Jianjun Zhang
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, PR China
| | - Wantao Chen
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China
- Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200011, PR China
- Department of Oral & Maxillofacial Surgery, First Affiliated Hospital of Zhengzhou University, Zhengzhou 450052, PR China
| |
Collapse
|
50
|
LncRNA RUNX1-IT1 which is downregulated by hypoxia-driven histone deacetylase 3 represses proliferation and cancer stem-like properties in hepatocellular carcinoma cells. Cell Death Dis 2020; 11:95. [PMID: 32024815 PMCID: PMC7002583 DOI: 10.1038/s41419-020-2274-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/13/2020] [Accepted: 01/14/2020] [Indexed: 12/24/2022]
Abstract
Hepatocellular carcinoma (HCC) is characterised by a hypoxic microenvironment and a high rate of heterogeneity and recurrence, and the presence of cancer stem cells (CSCs) in HCC may well explain both of these pathological properties. There is mounting evidence that long non-coding RNAs (lncRNAs) participate in carcinogenesis and maintain cancer stemness of HCC cells. However, the expression modes, regulatory mechanisms and potential roles of stemness-related lncRNAs in HCC are still obscure. LncRNA RUNX1-IT1 is the intronic transcript 1 of the RUNX1, which is also known as chromosome 21 open-reading frame 96 (C21orF96). Although the functions of the RUNX1 have been identified in different diseases, the function and its potential mechanisms of the lncRNA RUNX1-IT1 in HCC still remains to be largely unknown. In this study, we verified that the expression of LncRNA RUNX1-IT1 was decreased in GEO data set, HCC samples and correlated with unfavourable clinicopathologic characteristics and poor prognosis. RUNX1-IT1 repressed HCC cell proliferation, cell cycle progression, invasion and cancer stemness and induced apoptosis in vitro. Overexpression of RUNX1-IT1 impaired the growth, metastasis and stem-like features of HCC cells in vivo. Mechanistically, RUNX1-IT1 directly bound to miR-632 and acted as competing endogenous RNA to facilitate the expression of the miR-632 target gene GSK-3β and subsequently modulate the WNT/β-catenin pathway in HCC cells. Furthermore, hypoxia-driven histone deacetylase 3 (HDAC3), as an upstream regulatory mechanism, was critical for the downregulation of RUNX1-IT1 in HCC. Thus, lncRNA RUNX1-IT1, as a regulator of hypoxia, may function as a potential therapeutic target for conquering HCC.
Collapse
|