51
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Huang Y, Zheng Y, Yao L, Qiao F, Hou Y, Hu X, Li D, Shao Z. RNA binding protein POP7 regulates ILF3 mRNA stability and expression to promote breast cancer progression. Cancer Sci 2022; 113:3801-3813. [PMID: 35579257 DOI: 10.1111/cas.15430] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 05/07/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
RNA Binding Proteins(RBPs)play pivotal roles in breast cancer (BC) development. As a RBP, Processing of precursor 7 (POP7) is one of the subunits of RNase P and RNase MRP, however, its exact function and mechanism in BC remain unknown. Here, we showed that expression of POP7 was frequently increased in breast cancer cells and in primary breast tumors. Up-regulated POP7 significantly promoted BC cell proliferation in vitro and primary tumor growth in vivo. POP7 also increased cell migration, invasion in vitro and lung metastasis in vivo. Through RNA-immunoprecipitation coupled with sequencing (RIP-seq), we found that POP7 bound preferentially to intron regions and POP7-binding peak associated genes were mainly enriched in cancer-related pathways. Further, POP7 regulated Interleukin Enhancer Binding Factor 3 (ILF3) expression through influencing its mRNA stability. Knockdown of ILF3 significantly impaired the increased malignant potential of POP7 over-expressing cells, suggesting that POP7 enhances BC progression through regulating ILF3 expression. Collectively, our findings provide the first evidence for the important role of POP7 and its regulation of ILF3 in promoting breast cancer progression.
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Affiliation(s)
- Yanni Huang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yizi Zheng
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Thyroid and Breast Surgery, Shenzhen Second People's Hospital/First Affiliated Hospital of Shenzhen University Health Science Center, Shenzhen, China
| | - Ling Yao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Feng Qiao
- Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Yifeng Hou
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Hu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Daqiang Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Zhiming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University, Shanghai Cancer Center, Fudan University, Shanghai, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
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NEAT1 can be a diagnostic biomarker in the breast cancer and gastric cancer patients by targeting XIST, hsa-miR-612, and MTRNR2L8: integrated RNA targetome interaction and experimental expression analysis. Genes Environ 2022; 44:16. [PMID: 35581633 PMCID: PMC9112444 DOI: 10.1186/s41021-022-00244-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 04/01/2022] [Indexed: 12/19/2022] Open
Abstract
Background The most frequent malignancy in women is breast cancer (BC). Gastric cancer (GC) is also the leading cause of cancer-related mortality. Long non-coding RNAs (lncRNAs) are thought to be important neurotic regulators in malignant tumors. In this study, we aimed to evaluate the expression level of NEAT1 and the interaction of this non-coding RNA with correlated microRNAs, lncRNAs, and mRNAs or protein coding genes, experimentally and bioinformatically. Methods For the bioinformatics analyses, we performed RNA-RNA and protein–protein interaction analyses, using ENCORI and STRING. The expression analyses were performed by five tools: Microarray data analysis, TCGA data analysis (RNA-seq, R Studio), GEPIA2, ENCORI, and real-time PCR experiment. qRT-PCR experiment was performed on 50 GC samples and 50 BC samples, compared to adjacent control tissue. Results Based on bioinformatics and experimental analyses, lncRNA NEAT1 have a significant down-regulation in the breast cancer samples with tumor size lower than 2 cm. Also, it has a significant high expression in the gastric cancer patients. Furthermore, NEAT1 have a significant interaction with XIST, hsa-miR-612 and MTRNR2L8. High expression of NEAT1 have a correlation with the lower survival rate of breast cancer samples and higher survival rate of gastric cancer patients. Conclusion This integrated computational and experimental investigation revealed some new aspects of the lncRNA NEAT1 as a potential prognostic biomarker for the breast cancer and gastric cancer samples. Further investigations about NEA1 and correlated mRNAs, lncRNAs, and microRNAs – specially the mentioned RNAs in this study – can lead the researchers to more clear information about the role of NEAT1 in the breast cancer and gastric cancer.
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53
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Jafari H, Hussain S, Campbell MJ. Nuclear Receptor Coregulators in Hormone-Dependent Cancers. Cancers (Basel) 2022; 14:2402. [PMID: 35626007 PMCID: PMC9139824 DOI: 10.3390/cancers14102402] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 05/09/2022] [Indexed: 12/10/2022] Open
Abstract
Nuclear receptors (NRs) function collectively as a transcriptional signaling network that mediates gene regulatory actions to either maintain cellular homeostasis in response to hormonal, dietary and other environmental factors, or act as orphan receptors with no known ligand. NR complexes are large and interact with multiple protein partners, collectively termed coregulators. Coregulators are essential for regulating NR activity and can dictate whether a target gene is activated or repressed by a variety of mechanisms including the regulation of chromatin accessibility. Altered expression of coregulators contributes to a variety of hormone-dependent cancers including breast and prostate cancers. Therefore, understanding the mechanisms by which coregulators interact with and modulate the activity of NRs provides opportunities to develop better prognostic and diagnostic approaches, as well as novel therapeutic targets. This review aims to gather and summarize recent studies, techniques and bioinformatics methods used to identify distorted NR coregulator interactions that contribute as cancer drivers in hormone-dependent cancers.
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Affiliation(s)
- Hedieh Jafari
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Shahid Hussain
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
| | - Moray J. Campbell
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH 43210, USA;
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Pu F, Liu J, Jing D, Chen F, Huang X, Shi D, Wu W, Lin H, Zhao L, Zhang Z, Lv X, Wang B, Zhang Z, Shao Z. LncCCAT1 interaction protein PKM2 upregulates SREBP2 phosphorylation to promote osteosarcoma tumorigenesis by enhancing the Warburg effect and lipogenesis. Int J Oncol 2022; 60:44. [PMID: 35244192 PMCID: PMC8923656 DOI: 10.3892/ijo.2022.5334] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 12/30/2021] [Indexed: 11/25/2022] Open
Abstract
Pyruvate kinase M2 (PKM2) plays an important role in the consumption of glucose and the production of lactic acid, the striking feature of cancer metabolism. The association of PKM2 with osteosarcoma (OS) has been reported but its role in OS has yet to be elucidated. To study this, PKM2‑bound RNAs in HeLa cells, a type of cancer cells widely used in the study of molecular function and mechanism, were obtained. Peak calling analysis revealed that PKM2 binds to long noncoding RNAs (lncRNAs), which are associated with cancer pathogenesis and development. Validation of the PKM2‑lncRNA interaction in the human OS cell line revealed that lncRNA colon cancer associated transcript‑1 (lncCCAT1) interacted with PKM2, which upregulated the phosphorylation of sterol regulatory element‑binding protein 2 (SREBP2). These factors promoted the Warburg effect, lipogenesis, and OS cell growth. PKM2 appears to be a key regulator in OS by binding to lncCCAT1. This further extends the biological functions of PKM2 in tumorigenesis and makes it a novel potential therapeutic for OS.
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Affiliation(s)
- Feifei Pu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jianxiang Liu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Doudou Jing
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Fengxia Chen
- Department of Radiation and Medical Oncology, Zhongnan Hospital, Wuhan University, Wuhan, Hubei 430071, P.R. China
| | - Xin Huang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Deyao Shi
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Wei Wu
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Hui Lin
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Lei Zhao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zhenhao Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xiao Lv
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Baichuan Wang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zhicai Zhang
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Zengwu Shao
- Department of Orthopedics, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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Expression and functions of long non-coding RNA NEAT1 and isoforms in breast cancer. Br J Cancer 2022; 126:551-561. [PMID: 34671127 PMCID: PMC8854383 DOI: 10.1038/s41416-021-01588-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 09/08/2021] [Accepted: 10/05/2021] [Indexed: 02/07/2023] Open
Abstract
NEAT1 is a highly abundant nuclear architectural long non-coding RNA. There are two overlapping NEAT1 isoforms, NEAT1_1 and NEAT1_2, of which the latter is an essential scaffold for the assembly of a class of nuclear ribonucleoprotein bodies called paraspeckles. Paraspeckle formation is elevated by a wide variety of cellular stressors and in certain developmental processes, either through transcriptional upregulation of the NEAT1 gene or through a switch from NEAT1_1 to NEAT1_2 isoform production. In such conditions, paraspeckles modulate cellular processes by sequestering proteins or RNA molecules. NEAT1 is abnormally expressed in many cancers and a growing body of evidence suggests that, in many cases, high NEAT1 levels are associated with therapy resistance and poor clinical outcome. Here we review the current knowledge of NEAT1 expression and functions in breast cancer, highlighting its established role in postnatal mammary gland development. We will discuss possible isoform-specific roles of NEAT1_1 and NEAT1_2 in different breast cancer subtypes, which critically needs to be considered when studying NEAT1 and breast cancer.
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56
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Zhu YS, Zhu J. Molecular and cellular functions of long non-coding RNAs in prostate and breast cancer. Adv Clin Chem 2022; 106:91-179. [PMID: 35152976 DOI: 10.1016/bs.acc.2021.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Long noncoding RNAs (lncRNAs) are defined as noncoding RNA transcripts with a length greater than 200 nucleotides. Research over the last decade has made great strides in our understanding of lncRNAs, especially in the biology of their role in cancer. In this article, we will briefly discuss the biogenesis and characteristics of lncRNAs, then review their molecular and cellular functions in cancer by using prostate and breast cancer as examples. LncRNAs are abundant, diverse, and evolutionarily, less conserved than protein-coding genes. They are often expressed in a tumor and cell-specific manner. As a key epigenetic factor, lncRNAs can use a wide variety of molecular mechanisms to regulate gene expression at each step of the genetic information flow pathway. LncRNAs display widespread effects on cell behavior, tumor growth, and metastasis. They act intracellularly and extracellularly in an autocrine, paracrine and endocrine fashion. Increased understanding of lncRNA's role in cancer has facilitated the development of novel biomarkers for cancer diagnosis, led to greater understanding of cancer prognosis, enabled better prediction of therapeutic responses, and promoted identification of potential targets for cancer therapy.
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Affiliation(s)
- Yuan-Shan Zhu
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States.
| | - Jifeng Zhu
- Clinical and Translational Science Center, Weill Cornell Medicine, New York, NY, United States
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57
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Zhou H, Wang Y, Liu Z, Zhang Z, Xiong L, Wen Y. Recent advances of NEAT1-miRNA interactions in cancer. Acta Biochim Biophys Sin (Shanghai) 2022; 54:153-162. [PMID: 35538025 PMCID: PMC9827865 DOI: 10.3724/abbs.2021022] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
With high incidence rate, cancer is the main cause of death in humans. Non-coding RNAs, as novel master regulators, especially long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), play important roles in the regulation of tumorigenesis. lncRNA NEAT1 has recently gained much attention, as it is dysregulated in a broad spectrum of cancers, where it acts as either an oncogene or a tumor suppressor gene. Accumulating evidence shows that NEAT1 is correlated with the process of carcinogenesis, including proliferation, invasion, survival, drug resistance, and metastasis. NEAT1 is considered to be a biomarker and a novel therapeutic target for the diagnosis and prognosis of different cancer types. The mechanisms by which NEAT1 plays a critical role in cancers are mainly via interactions with miRNAs. NEAT1-miRNA regulatory networks play significant roles in tumorigenesis, which has attracted much attention from researchers around the world. In this review, we summarize the interaction of NEAT1 with miRNAs in the regulation of protein-coding genes in cancer. A better understanding of the NEAT1-miRNA interactions in cancer will help develop new diagnostic biomarkers and therapeutic approaches.
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Affiliation(s)
| | | | | | | | | | - Yu Wen
- Correspondence address. Tel: +86-731-85294099; E-mail:
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Feng J, Zhu F, Ye D, Zhang Q, Guo X, Du C, Kang J. Sin3a drives mesenchymal-to-epithelial transition through cooperating with Tet1 in somatic cell reprogramming. Stem Cell Res Ther 2022; 13:29. [PMID: 35073971 PMCID: PMC8785580 DOI: 10.1186/s13287-022-02707-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 11/28/2021] [Indexed: 12/16/2022] Open
Abstract
Background Identifying novel regulatory factors and uncovered mechanisms of somatic cell reprogramming will be helpful for basic research and clinical application of induced pluripotent stem cells (iPSCs). Sin3a, a multifunctional transcription regulator, has been proven to be involved in the maintenance of pluripotency in embryonic stem cells (ESCs), but the role of Sin3a in somatic cell reprogramming remains unclear. Methods RNA interference of Sin3a during somatic cell reprogramming was realized by short hairpin RNAs. Reprogramming efficiency was evaluated by the number of alkaline phosphatase (AP)-positive colonies and Oct4-GFP-positive colonies. RNA sequencing was performed to identify the influenced biological processes after Sin3a knockdown and further confirmed by quantitative RT-PCR (qRT-PCR), western blotting and flow cytometry. The interaction between Sin3a and Tet1 was detected by coimmunoprecipitation. The enrichment of Sin3a and Tet1 at the epithelial gene promoters was measured by chromatin immunoprecipitation. Furthermore, DNA methylation patterns at the gene loci were investigated by hydroxymethylated DNA immunoprecipitation. Finally, Sin3a mutants that disrupt the interaction of Sin3a and Tet1 were also introduced to assess the importance of the Sin3a–Tet1 interaction during the mesenchymal-to-epithelial transition (MET) process. Results We found that Sin3a was gradually increased during OSKM-induced reprogramming and that knockdown of Sin3a significantly impaired MET at the early stage of reprogramming and iPSC generation. Mechanistic studies showed that Sin3a recruited Tet1 to facilitate the hydroxymethylation of epithelial gene promoters. Moreover, disrupting the interaction of Sin3a and Tet1 significantly blocked MET and iPSC generation. Conclusions Our studies revealed that Sin3a was a novel mediator of MET during early reprogramming, where Sin3a functioned as an epigenetic coactivator, cooperating with Tet1 to activate the epithelial program and promote the initiation of somatic cell reprogramming. These findings highlight the importance of Sin3a in the MET process and deepen our understanding of the epigenetic regulatory network of early reprogramming. Supplementary Information The online version contains supplementary material available at 10.1186/s13287-022-02707-4.
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Affiliation(s)
- Jiabao Feng
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Fugui Zhu
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Dan Ye
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Qingquan Zhang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China
| | - Xudong Guo
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China. .,Institute for Advanced Study, Tongji University, Shanghai, 200092, People's Republic of China.
| | - Changsheng Du
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China.
| | - Jiuhong Kang
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Key Laboratory of Signaling and Disease Research, Frontier Science Center for Stem Cell Research, National Stem Cell Translational Resource Center, School of Life Sciences and Technology, Tongji University, 1239 Siping Road, Shanghai, 200092, People's Republic of China.
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Zhang H, Zhuang P, Welchko RM, Dai M, Meng F, Turner DL. Regulation of retinal amacrine cell generation by miR-216b and Foxn3. Development 2022; 149:273765. [PMID: 34919141 PMCID: PMC8917416 DOI: 10.1242/dev.199484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 12/07/2021] [Indexed: 01/19/2023]
Abstract
The mammalian retina contains a complex mixture of different types of neurons. We find that microRNA miR-216b is preferentially expressed in postmitotic retinal amacrine cells in the mouse retina, and expression of miR-216a/b and miR-217 in retina depend in part on Ptf1a, a transcription factor required for amacrine cell differentiation. Surprisingly, ectopic expression of miR-216b directed the formation of additional amacrine cells and reduced bipolar neurons in the developing retina. We identify the Foxn3 mRNA as a retinal target of miR-216b by Argonaute PAR-CLIP and reporter analysis. Inhibition of Foxn3, a transcription factor, in the postnatal developing retina by RNAi increased the formation of amacrine cells and reduced bipolar cell formation. Foxn3 disruption by CRISPR in embryonic retinal explants also increased amacrine cell formation, whereas Foxn3 overexpression inhibited amacrine cell formation prior to Ptf1a expression. Co-expression of Foxn3 partially reversed the effects of ectopic miR-216b on retinal cell formation. Our results identify Foxn3 as a novel regulator of interneuron formation in the developing retina and suggest that miR-216b likely regulates Foxn3 and other genes in amacrine cells.
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Affiliation(s)
- Huanqing Zhang
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Pei Zhuang
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Ryan M. Welchko
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Manhong Dai
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109-2200, USA
| | - Fan Meng
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109-2200, USA,Department of Psychiatry, University of Michigan, Ann Arbor, MI 48109, USA
| | - David L. Turner
- Michigan Neuroscience Institute, University of Michigan, Ann Arbor, MI 48109-2200, USA,Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA,Author for correspondence ()
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Long non-coding RNA CTSLP8 mediates ovarian cancer progression and chemotherapy resistance by modulating cellular glycolysis and regulating c-Myc expression through PKM2. Cell Biol Toxicol 2022; 38:1027-1045. [PMID: 34510316 PMCID: PMC9750935 DOI: 10.1007/s10565-021-09650-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 08/29/2021] [Indexed: 01/25/2023]
Abstract
PURPOSE Long non-coding RNAs (lncRNAs) play vital roles in tumor progression and resistance. Ovarian cancer (OC), a common gynecological cancer, is associated with poor prognosis as it can progress to peritoneal metastasis and develop resistance to chemotherapy. This study aimed to examine the role of lncRNAs in the development of chemotherapy resistance in OC. METHODS The clinical samples were divided into chemotherapy-sensitive and chemotherapy-resistant groups based on the chemotherapy response at follow-up. The glycolysis levels in the two groups were analyzed using positron emission tomography/computed tomography (PET/CT) scanning and immunohistochemistry. GEO dataset analysis revealed the expression of CTSLP8 in chemotherapy-resistant patients with OC. Two pairs of normal and diamminodichloroplatinum (DDP)-resistant cells were transfected with CTSLP8 overexpression and knockdown constructs to examine the functions of CTSLP8 in the OC cells and elucidate the underlying mechanisms. The in vivo effect of CTSLP8 overexpression and knockdown on the chemotherapy response of tumors was examined using a mouse subcutaneous tumor model. The tissue chips were subjected to fluorescence in situ hybridization and immunohistochemical (IHC) staining to examine the correlation among CTSLP8 expression, DDP resistance, and prognosis in OC. RESULTS The dataset analysis demonstrated that CTSLP8 was upregulated in chemotherapy-resistant tumor tissues. CTSLP8 promoted the proliferation and development of DDP resistance in the OC cells. Moreover, CTSLP8 promoted c-Myc expression by facilitating the binding of PKM2 to the promoter region of c-Myc, thereby upregulating glycolysis. The analysis of tissue chips revealed that the upregulation of CTSLP8 was associated with the development of DDP resistance and poor prognosis in patients with OC. CONCLUSIONS These findings indicate that CTSLP8 forms a complex with PKM2 to regulate c-Myc, and this action results in the upregulation of cellular glycolysis, consequently promoting OC progression and development of chemotherapy resistance. HEADLIGHTS 1. CTSLP8 was upregulated in the chemotherapy-resistant tumor tissues. 2. CTSLP8 promoted the proliferation and cisplatin resistance in the OC cells. 3. CTSLP8 promoted glycolysis by facilitating the binding of PKM2 to the promoter region of c-Myc. 4. Inhibition of CTSLP8 or the combination of c-Myc inhibitors with cisplatin were potential therapeutic strategies for chemotherapy-resistant of OC.
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Xie J, Zhang X, Zheng J, Hong X, Tong X, Liu X, Xue Y, Wang X, Zhang Y, Liu S. Two novel RNA-binding proteins identification through computational prediction and experimental validation. Genomics 2021; 114:149-160. [PMID: 34921931 DOI: 10.1016/j.ygeno.2021.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 08/05/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022]
Abstract
Since RBPs play important roles in the cell, it's particularly important to find new RBPs. We performed iRIP-seq and CLIP-seq to verify two proteins, CLIP1 and DMD, predicted by RBPPred whether are RBPs or not. The experimental results confirm that these two proteins have RNA-binding activity. We identified significantly enriched binding motifs UGGGGAGG, CUUCCG and CCCGU for CLIP1 (iRIP-seq), DMD (iRIP-seq) and DMD (CLIP-seq), respectively. The computational KEGG and GO analysis show that the CLIP1 and DMD share some biological processes and functions. Besides, we found that the SNPs between DMD and its RNA partners may be associated with Becker muscular dystrophy, Duchenne muscular dystrophy, Dilated cardiomyopathy 3B and Cardiovascular phenotype. Among the thirteen cancers data, CLIP1 and another 300 oncogenes always co-occur, and 123 of these 300 genes interact with CLIP1. These cancers may be associated with the mutations occurred in both CLIP1 and the genes it interacts with.
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Affiliation(s)
- Juan Xie
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaoli Zhang
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jinfang Zheng
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xu Hong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiaoxue Tong
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xudong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yaqiang Xue
- Laboratory for Genome Regulation and Human Health, ABLife Inc., Wuhan, Hubei 430075, China
| | - Xuelian Wang
- ABLife BioBigData Institute, Wuhan, Hubei 430075, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, Hubei 430075, China
| | - Shiyong Liu
- School of Physics, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China.
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Park MK, Zhang L, Min KW, Cho JH, Yeh CC, Moon H, Hormaechea-Agulla D, Mun H, Ko S, Lee JW, Jathar S, Smith AS, Yao Y, Giang NT, Vu HH, Yan VC, Bridges MC, Kourtidis A, Muller F, Chang JH, Song SJ, Nakagawa S, Hirose T, Yoon JH, Song MS. NEAT1 is essential for metabolic changes that promote breast cancer growth and metastasis. Cell Metab 2021; 33:2380-2397.e9. [PMID: 34879239 PMCID: PMC8813003 DOI: 10.1016/j.cmet.2021.11.011] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 08/27/2021] [Accepted: 11/16/2021] [Indexed: 01/08/2023]
Abstract
Accelerated glycolysis is the main metabolic change observed in cancer, but the underlying molecular mechanisms and their role in cancer progression remain poorly understood. Here, we show that the deletion of the long noncoding RNA (lncRNA) Neat1 in MMTV-PyVT mice profoundly impairs tumor initiation, growth, and metastasis, specifically switching off the penultimate step of glycolysis. Mechanistically, NEAT1 directly binds and forms a scaffold bridge for the assembly of PGK1/PGAM1/ENO1 complexes and thereby promotes substrate channeling for high and efficient glycolysis. Notably, NEAT1 is upregulated in cancer patients and correlates with high levels of these complexes, and genetic and pharmacological blockade of penultimate glycolysis ablates NEAT1-dependent tumorigenesis. Finally, we demonstrate that Pinin mediates glucose-stimulated nuclear export of NEAT1, through which it exerts isoform-specific and paraspeckle-independent functions. These findings establish a direct role for NEAT1 in regulating tumor metabolism, provide new insights into the Warburg effect, and identify potential targets for therapy.
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Affiliation(s)
- Mi Kyung Park
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Zhang
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kyung-Won Min
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung-si, Gangwon-do 25457, Republic of Korea
| | - Jung-Hyun Cho
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Chih-Chen Yeh
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyesu Moon
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Republic of Korea
| | - Daniel Hormaechea-Agulla
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hyejin Mun
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Seungbeom Ko
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Ji Won Lee
- Department of Biology, College of Natural Sciences, Gangneung-Wonju National University, Gangneung-si, Gangwon-do 25457, Republic of Korea
| | - Sonali Jathar
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA; Laboratory of lncRNA Biology, National Center for Cell Science, Pune, Maharashtra 411007, India
| | - Aubrey S Smith
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Yixin Yao
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Nguyen Thu Giang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong Ha Vu
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Victoria C Yan
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mary C Bridges
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Antonis Kourtidis
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC 29425, USA
| | - Florian Muller
- Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jeong Ho Chang
- Department of Biology Education, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Su Jung Song
- Soonchunhyang Institute of Medi-bio Science, Soonchunhyang University, Cheonan-si, Chungcheongnam-do 31151, Republic of Korea
| | - Shinichi Nakagawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
| | - Tetsuro Hirose
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | - Je-Hyun Yoon
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA.
| | - Min Sup Song
- Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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Low expression of ECT2 confers radiotherapy resistance through transcription coupled nucleolar DNA damage repair. Int J Radiat Oncol Biol Phys 2021; 112:1229-1242. [DOI: 10.1016/j.ijrobp.2021.12.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 11/11/2021] [Accepted: 12/08/2021] [Indexed: 11/23/2022]
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Zhang Y, Guan B, WU Y, Du F, Zhuang J, Yang Y, Guan G, Liu X. LncRNAs Associated with Chemoradiotherapy Response and Prognosis in Locally Advanced Rectal Cancer. J Inflamm Res 2021; 14:6275-6292. [PMID: 34866926 PMCID: PMC8636753 DOI: 10.2147/jir.s334096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/05/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND There are only limited studies on the long non-coding RNAs (lncRNAs) associated with neoadjuvant chemoradiotherapy (NCRT) response and prognosis of locally advanced rectal cancer (LARC) patients. This study identified lncRNAs associated with NCRT response and prognosis in CRC patients and explored their potential predictive mechanisms. METHODS The study subjected the LncRNA expression profiles from our previous gene chip data to LASSO and identified a four-lncRNA signature that predicted NCRT response and prognosis. A Cox regression model was subsequently performed to identify the prognostic risk factors. The function of LINC00909, the lncRNA with the most powerful predictive ability, was finally identified in vivo and in vitro using CRC cell lines. RESULTS A comparison of the relative lncRNA expression of NCRT-responsive and non-responsive patients revealed four hub lncRNAs: DBET, LINC00909, FLJ33534, and HSD52 with AUC = 0.68, 0.73, 0.73, and 0.70, respectively (all p < 0.05). COX regression analysis further demonstrated that DBET, LINC00909 and FLJ33534 were associated with the DFS in CRC patients. The expression of the four lncRNAs was also significant in LARC patients who had not undergone NCRT (all p < 0.05). A risk score model was subsequently constructed based on the results of the multivariate COX analysis and used to predict NCRT response and prognosis in the CRC and LARC patients. The expression and prognosis of DBET, LINC00909 and FLJ33534 in the CRC tissues were further validated in the R2 platform and Oncomine database. Notably, overexpression of the LINC00909 increased the cell line resistance to the 5-FU and radiotherapy in vivo and in vitro. CONCLUSION DBET, LINC00909, and FLJ33534 are potential novel biomarkers for predicting NCRT response and prognosis in CRC patients. In particular, LINC00909 is an effective oncogene in CRC that could be used as a novel therapeutic target to enhance NCRT response.
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Affiliation(s)
- Yiyi Zhang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People’s Republic of China
| | - Bingjie Guan
- Department of Radiation Oncology, Fujian Medical University Union Hospital, Fuzhou, People’s Republic of China
| | - Yong WU
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People’s Republic of China
| | - Fan Du
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330006, People’s Republic of China
| | - Jinfu Zhuang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People’s Republic of China
| | - Yuanfeng Yang
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People’s Republic of China
| | - Guoxian Guan
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People’s Republic of China
| | - Xing Liu
- Department of Colorectal Surgery, The First Affiliated Hospital of Fujian Medical University, Fuzhou, People’s Republic of China
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Xu R, Yu SS, Yao RR, Tang RC, Liang JW, Pang X, Zhang J. Interferon-Inducible LINC02605 Promotes Antiviral Innate Responses by Strengthening IRF3 Nuclear Translocation. Front Immunol 2021; 12:755512. [PMID: 34804040 PMCID: PMC8602795 DOI: 10.3389/fimmu.2021.755512] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 10/11/2021] [Indexed: 11/26/2022] Open
Abstract
Non-coding RNAs represent a class of important regulators in immune response. Previously, LINC02605 was identified as a candidate regulator in innate immune response by lncRNA microarray assays. In this study, we systematically analyzed the functions and the acting mechanisms of LINC02605 in antiviral innate immune response. LINC02605 was up-regulated by RNA virus, DNA virus, and type I IFNs in NF-κB and Jak-stat dependent manner. Overexpression of LINC02605 promotes RNA virus-induced type I interferon production and inhibited viral replication. Consistently, knockdown of LINC02605 resulted in reduced antiviral immune response and increased viral replication. Mechanistically, LINC02605 released the inhibition of hsa-miR-107 on the expression of phosphatase and tensin homolog (PTEN). By microRNA mimics and inhibitors, hsa-miR-107 was demonstrated to not only inhibit PTEN’s expression but also negatively regulate the antiviral immune response. Knockdown of LINC02605 led to the reduction of PTEN expression both in mRNA and protein levels. Overexpression of LINC02605 had an opposite impact. Moreover, LINC02605 attenuated the serine 97 phosphorylation level of interferon regulatory factor 3 (IRF3) by promoting PTEN expression. Nucleoplasmic fragmentation assay showed that knocking down LINC02605 inhibited the nuclear translocation of IRF3, rendering the host cells more susceptible to viral invasion, while overexpression showed opposite effects. Therefore, LINC02605 is an induced lncRNA by viral infection and plays a positive feedback in antiviral immune response through modulating the nuclear translocation of IRF3.
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Affiliation(s)
- Rui Xu
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Shuang-Shuang Yu
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Ran-Ran Yao
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Rong-Chun Tang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Jia-Wei Liang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Xuewen Pang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
| | - Jun Zhang
- Department of Immunology, School of Basic Medical Sciences, NHC Key Laboratory of Medical Immunology, Ministry of Health (Peking University), Peking University Health Science Center, Beijing, China
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Geng F, Jia WC, Li T, Li N, Wei W. Knockdown of lncRNA NEAT1 suppresses proliferation and migration, and induces apoptosis of cervical cancer cells by regulating the miR‑377/FGFR1 axis. Mol Med Rep 2021; 25:10. [PMID: 34779493 PMCID: PMC8600400 DOI: 10.3892/mmr.2021.12526] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 03/08/2021] [Indexed: 11/16/2022] Open
Abstract
To investigate the role of NEAT1 and the microRNA (miR)-377/fibroblast growth factor receptor 1 (FGFR1) axis in cervical cancer (CC), the expression levels of NEAT1, FGFR1 and miR-377 were detected in CC tissues and cell lines. NEAT1 or FGFR1 was knocked down by transfection with short hairpin RNA (sh)-NEAT1 or sh-FGFR1, and miR-377 was overexpressed by transfection with miR-377 mimics in HeLa and C33A cells. Cell viability and migration were measured using MTT and Transwell assays, respectively. Cell apoptosis was determined by flow cytometry. A dual luciferase reporter assay was performed to confirm the presence of binding sites between miR-377 and FGFR1. The results revealed that the expression levels of NEAT1 and FGFR1 were significantly elevated, whereas miR-377 expression was markedly decreased in CC tissues and cell lines. In HeLa and C33A cells, after NEAT1 knockdown, miR-377 expression was increased, cell viability and migration were inhibited, and apoptosis was induced. Similarly, silencing FGFR1 inhibited cell viability and migration, and induced apoptosis of HeLa and C33A cells. A dual luciferase reporter gene assay verified a targeting relationship between NEAT1 and miR-377. Inhibition of miR-377 or overexpression of FGFR1 reversed the effects of NEAT1 knockdown on cell function in HeLa and C33A cells. Moreover, a dual luciferase reporter assay confirmed that FGFR1 was a direct target of miR-377. In conclusion, suppression of NEAT1 inhibited cell viability and migration, and promoted apoptosis of CC cells, and these effects were achieved through regulation of the miR-377/FGFR1 axis.
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Affiliation(s)
- Feng Geng
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Wen-Cong Jia
- Department of Obstetrics and Gynecology, Binzhou Second People's Hospital, Binzhou, Shandong 256800, P.R. China
| | - Tao Li
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Na Li
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
| | - Wei Wei
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, P.R. China
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Molaei Ramshe S, Ghaedi H, Omrani MD, Geranpayeh L, Alipour B, Ghafouri-Fard S. Up-regulation of FOXN3-AS1 in invasive ductal carcinoma of breast cancer patients. Heliyon 2021; 7:e08179. [PMID: 34703931 PMCID: PMC8526775 DOI: 10.1016/j.heliyon.2021.e08179] [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: 11/06/2020] [Revised: 06/12/2021] [Accepted: 10/11/2021] [Indexed: 11/04/2022] Open
Abstract
Oncogenic and tumor-suppressive roles of long non-coding RNA make them an appropriate target for expression analysis in cancer studies. In this study, we selected two lncRNAs (EMX2OS and FOXN3-AS1) that are resided near the GWAS-identified SNPs for breast cancer (rs2901157 and rs141061110). These transcripts have been identified in different cancer types as either oncogenes or tumor suppressors. In the present investigation, we aimed to quantify the expression level of EMX2OS and FOXN3-AS1 in 44 breast cancer samples and normal adjacent tissues (ANCTs). The FOXN3-AS1 expression level was significantly increased in breast cancer samples compared with ANCTs (P value = 0.02), Also its amounts could distinguish two sets of samples with an accuracy of 70% (P value = 0.009). We have found an association between FOXN3-AS1 expression and tumor size (P value = 0.02). On the other hand, no significant differences were found in the EMX2OS expression level between two sets of samples (P value = 0.44); however, EMX2OS expression level has a significant association with the age of the patients (P value = 0.03). According to our result, FOXN3-AS1 can be demonstrated as a probable diagnostic marker in breast cancer so we suggest further functional studies to find the precise role of these lncRNAs in breast cancer progression.
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Affiliation(s)
- Samira Molaei Ramshe
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mir Davood Omrani
- Urogenital Stem Cell Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Behnam Alipour
- Department of Laboratory Sciences, Faculty of Paramedicine, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Li K, Yao T, Zhang Y, Li W, Wang Z. NEAT1 as a competing endogenous RNA in tumorigenesis of various cancers: Role, mechanism and therapeutic potential. Int J Biol Sci 2021; 17:3428-3440. [PMID: 34512157 PMCID: PMC8416723 DOI: 10.7150/ijbs.62728] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/24/2021] [Indexed: 12/24/2022] Open
Abstract
The nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA (lncRNA) that is upregulated in a variety of human cancer types. Increasing evidence has shown that the elevation of NEAT1 in cancer cells promotes cell growth, migration, and invasion and inhibits cell apoptosis. It is also known that lncRNAs act as a competing endogenous RNA (ceRNA) by sponging microRNAs (miRNAs) to alter the expression levels of their target genes in the development of cancers. Therefore, it is important to understand the molecular mechanisms underlying this observation. In this review, specific emphasis was placed on NEAT1's role in tumor development. We also summarize and discuss the feedback roles of NEAT1/miRNA/target network in the progression of various cancers. As our understanding of the role of NEAT1 during tumorigenesis improves, its therapeutic potential as a biomarker and/or target for cancer also becomes clearer.
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Affiliation(s)
- Kun Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Tongyue Yao
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Yu Zhang
- Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
| | - Wen Li
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China
| | - Ziqiang Wang
- Department of Nuclear Medicine, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Jinan 250014, China.,Biomedical Sciences College & Shandong Medicinal Biotechnology Centre, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan 250062, China
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Downregulation of PART1 Inhibits Proliferation and Differentiation of Hep3B Cells by Targeting hsa-miR-3529-3p/FOXC2 Axis. JOURNAL OF ONCOLOGY 2021; 2021:7792223. [PMID: 34484336 PMCID: PMC8410447 DOI: 10.1155/2021/7792223] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/23/2021] [Accepted: 08/13/2021] [Indexed: 11/23/2022]
Abstract
Background Long noncoding RNAs (lncRNAs) are an important subtype of noncoding RNAs (ncRNAs) and microRNA sponges regulate protein-coding gene expression. The lncRNA prostate androgen-regulated transcript 1 (PART1) was implicated in the process of several cancer pathogeneses. However, studies on the regulation of PART1 expression and its mechanism in liver cancer are lacking. Methods qRT-PCR and western blot were used to detect PART1 levels in liver cancer serums and cell lines. Cell proliferation, migration, and invasion were detected using CCK8 assays, cell clones, and transwell assays. Interaction between PART1 and miR-3529-3p and forkhead box protein C2 (FOXC2) was confirmed using dual-luciferase reporter assays. Results We revealed that expression levels of PART1 and FOXC2 are significantly upregulated and the miR-3529-3p expression level significantly decreases in the serum while high expression level of PART1 is positively associated with tumour size, BCLC stage, and TNM stage. shRNA of PART1 can significantly reduce the ability of cell migration and invasion by regulating AKT signalling associated with the reduction of MMP-2 and MMP-9 protein expression. Dual-luciferase reporter assays showed that PART1 can sponge miR-3529-3p, which targets FOXC2 in liver cancer cells. The promoting or suppressing effect of PART1 for Hep3B cell proliferation, invasion, and migration is revised by miR-3529-3p mimics and inhibitors. Conclusion Results showed that downregulation of PART1 can partially inhibit proliferation and differentiation by targeting hsa-miR-3529-3p/FOXC2 axis.
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Zuo S, Wang B, Liu J, Kong D, Cui H, Jia Y, Wang C, Xu X, Chen G, Wang Y, Yang L, Zhang K, Ai D, Du J, Shen Y, Yu Y. ER-anchored CRTH2 antagonizes collagen biosynthesis and organ fibrosis via binding LARP6. EMBO J 2021; 40:e107403. [PMID: 34223653 PMCID: PMC8365266 DOI: 10.15252/embj.2020107403] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Revised: 05/11/2021] [Accepted: 05/20/2021] [Indexed: 02/06/2023] Open
Abstract
Excessive deposition of extracellular matrix, mainly collagen protein, is the hallmark of organ fibrosis. The molecular mechanisms regulating fibrotic protein biosynthesis are unclear. Here, we find that chemoattractant receptor homologous molecule expressed on TH2 cells (CRTH2), a plasma membrane receptor for prostaglandin D2, is trafficked to the endoplasmic reticulum (ER) membrane in fibroblasts in a caveolin-1-dependent manner. ER-anchored CRTH2 binds the collagen mRNA recognition motif of La ribonucleoprotein domain family member 6 (LARP6) and promotes the degradation of collagen mRNA in these cells. In line, CRTH2 deficiency increases collagen biosynthesis in fibroblasts and exacerbates injury-induced organ fibrosis in mice, which can be rescued by LARP6 depletion. Administration of CRTH2 N-terminal peptide reduces collagen production by binding to LARP6. Similar to CRTH2, bumetanide binds the LARP6 mRNA recognition motif, suppresses collagen biosynthesis, and alleviates bleomycin-triggered pulmonary fibrosis in vivo. These findings reveal a novel anti-fibrotic function of CRTH2 in the ER membrane via the interaction with LARP6, which may represent a therapeutic target for fibrotic diseases.
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Affiliation(s)
- Shengkai Zuo
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Bei Wang
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Jiao Liu
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Deping Kong
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Hui Cui
- School of Life Science and TechnologyShanghai Tech UniversityShanghaiChina
| | - Yaonan Jia
- School of Pharmaceutical SciencesZhengzhou UniversityZhengzhouChina
| | - Chenyao Wang
- Department of Inflammation and ImmunityLerner Research InstituteCleveland ClinicClevelandOHUSA
| | - Xin Xu
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Guilin Chen
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Yuanyang Wang
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Linlin Yang
- Department of PharmacologySchool of Basic Medical SciencesZhengzhou UniversityZhengzhouChina
| | - Kai Zhang
- Department of Biochemistry and Molecular BiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Ding Ai
- Department of Physiology and PathophysiologySchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Jie Du
- Beijing Anzhen Hospital of Capital Medical University and Beijing Institute of Heart Lung and Blood Vessel DiseasesBeijingChina
| | - Yujun Shen
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
| | - Ying Yu
- Tianjin Key Laboratory of Inflammatory BiologyCenter for Cardiovascular DiseasesKey Laboratory of Immune Microenvironment and Disease (Ministry of Education)Department of PharmacologyThe Province and Ministry Co‐sponsored Collaborative Innovation Center for Medical EpigeneticsSchool of Basic Medical SciencesTianjin Medical UniversityTianjinChina
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Muluhngwi P, Klinge CM. Identification and Roles of miR-29b-1-3p and miR29a-3p-Regulated and Non-Regulated lncRNAs in Endocrine-Sensitive and Resistant Breast Cancer Cells. Cancers (Basel) 2021; 13:3530. [PMID: 34298743 PMCID: PMC8307416 DOI: 10.3390/cancers13143530] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/30/2021] [Accepted: 07/07/2021] [Indexed: 01/05/2023] Open
Abstract
Despite improvements in the treatment of endocrine-resistant metastatic disease using combination therapies in patients with estrogen receptor α (ERα) primary tumors, the mechanisms underlying endocrine resistance remain to be elucidated. Non-coding RNAs (ncRNAs), including microRNAs (miRNA) and long non-coding RNAs (lncRNA), are targets and regulators of cell signaling pathways and their exosomal transport may contribute to metastasis. Previous studies have shown that a low expression of miR-29a-3p and miR-29b-3p is associated with lower overall breast cancer survival before 150 mos. Transient, modest overexpression of miR-29b1-3p or miR-29a-3p inhibited MCF-7 tamoxifen-sensitive and LCC9 tamoxifen-resistant cell proliferation. Here, we identify miR-29b-1/a-regulated and non-regulated differentially expressed lncRNAs in MCF-7 and LCC9 cells using next-generation RNA seq. More lncRNAs were miR-29b-1/a-regulated in LCC9 cells than in MCF-7 cells, including DANCR, GAS5, DSCAM-AS1, SNHG5, and CRND. We examined the roles of miR-29-regulated and differentially expressed lncRNAs in endocrine-resistant breast cancer, including putative and proven targets and expression patterns in survival analysis using the KM Plotter and TCGA databases. This study provides new insights into lncRNAs in endocrine-resistant breast cancer.
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Affiliation(s)
- Penn Muluhngwi
- Department of Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA;
| | - Carolyn M. Klinge
- Department of Biochemistry & Molecular Genetics, University of Louisville School of Medicine, Louisville, KY 40292, USA
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Adedokun B, Du Z, Gao G, Ahearn TU, Lunetta KL, Zirpoli G, Figueroa J, John EM, Bernstein L, Zheng W, Hu JJ, Ziegler RG, Nyante S, Bandera EV, Ingles SA, Press MF, Deming-Halverson SL, Rodriguez-Gil JL, Yao S, Ogundiran TO, Ojengbede O, Blot W, Troester MA, Nathanson KL, Hennis A, Nemesure B, Ambs S, Fiorica PN, Sucheston-Campbell LE, Bensen JT, Kushi LH, Torres-Mejia G, Hu D, Fejerman L, Bolla MK, Dennis J, Dunning AM, Easton DF, Michailidou K, Pharoah PDP, Wang Q, Sandler DP, Taylor JA, O'Brien KM, Kitahara CM, Falusi AG, Babalola C, Yarney J, Awuah B, Addai-Wiafe B, Chanock SJ, Olshan AF, Ambrosone CB, Conti DV, Ziv E, Olopade OI, Garcia-Closas M, Palmer JR, Haiman CA, Huo D. Cross-ancestry GWAS meta-analysis identifies six breast cancer loci in African and European ancestry women. Nat Commun 2021; 12:4198. [PMID: 34234117 PMCID: PMC8263739 DOI: 10.1038/s41467-021-24327-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 06/02/2021] [Indexed: 02/06/2023] Open
Abstract
Our study describes breast cancer risk loci using a cross-ancestry GWAS approach. We first identify variants that are associated with breast cancer at P < 0.05 from African ancestry GWAS meta-analysis (9241 cases and 10193 controls), then meta-analyze with European ancestry GWAS data (122977 cases and 105974 controls) from the Breast Cancer Association Consortium. The approach identifies four loci for overall breast cancer risk [1p13.3, 5q31.1, 15q24 (two independent signals), and 15q26.3] and two loci for estrogen receptor-negative disease (1q41 and 7q11.23) at genome-wide significance. Four of the index single nucleotide polymorphisms (SNPs) lie within introns of genes (KCNK2, C5orf56, SCAMP2, and SIN3A) and the other index SNPs are located close to GSTM4, AMPD2, CASTOR2, and RP11-168G16.2. Here we present risk loci with consistent direction of associations in African and European descendants. The study suggests that replication across multiple ancestry populations can help improve the understanding of breast cancer genetics and identify causal variants.
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Affiliation(s)
- Babatunde Adedokun
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | - Zhaohui Du
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Guimin Gao
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Thomas U Ahearn
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Gary Zirpoli
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Jonine Figueroa
- Usher Institute and CRUK Edinburgh Centre, University of Edinburgh, Edinburgh, UK
| | - Esther M John
- Departments of Epidemiology & Population Health and of Medicine (Oncology) and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
| | - Leslie Bernstein
- Biomarkers of Early Detection and Prevention, Department of Population Sciences, Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA, USA
| | - Wei Zheng
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jennifer J Hu
- Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Regina G Ziegler
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Sarah Nyante
- Department of Radiology, University of North Carolina, Chapel Hill, NC, USA
| | - Elisa V Bandera
- Cancer Prevention and Control Program, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
| | - Sue A Ingles
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael F Press
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sandra L Deming-Halverson
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Jorge L Rodriguez-Gil
- Genomics, Development and Disease Section, Genetic Disease Research Branch, National Human Genome Research Institute, NIH, Bethesda, MD, USA
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Temidayo O Ogundiran
- Department of Surgery, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - Oladosu Ojengbede
- Center for Population and Reproductive Health, College of Medicine, University of Ibadan, Ibadan, Nigeria
| | - William Blot
- Division of Epidemiology, Department of Medicine, Vanderbilt Epidemiology Center, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA
| | - Melissa A Troester
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Katherine L Nathanson
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Anselm Hennis
- University of the West Indies, Bridgetown, Barbados
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Barbara Nemesure
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY, USA
| | - Stefan Ambs
- Laboratory of Human Carcinogenesis, National Cancer Institute, Bethesda, MD, USA
| | - Peter N Fiorica
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA
| | - Lara E Sucheston-Campbell
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, OH, USA
| | - Jeannette T Bensen
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Lawrence H Kushi
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Gabriela Torres-Mejia
- Center for Population Health Research, Instituto Nacional de Salud Publica, Cuernavaca, Mexico
| | - Donglei Hu
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Laura Fejerman
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Manjeet K Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Biostatistics Unit, The Cyprus Institute of Neurology & Genetics, Nicosia, Cyprus
| | - Paul D P Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Dale P Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Jack A Taylor
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Katie M O'Brien
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC, USA
| | - Cari M Kitahara
- Radiation Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Adeyinka G Falusi
- Institute for Advanced Medical Research and Training, College of Medicine, University of Ibadan, Ibadan, Oyo, Nigeria
| | - Chinedum Babalola
- Department of Pharmaceutical Chemistry, University of Ibadan, Ibadan, Oyo, Nigeria
| | | | | | | | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, USA
| | - Andrew F Olshan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Christine B Ambrosone
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - David V Conti
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Elad Ziv
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Olufunmilayo I Olopade
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA
| | | | - Julie R Palmer
- Slone Epidemiology Center, Boston University, Boston, MA, USA
| | - Christopher A Haiman
- Department of Preventative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
| | - Dezheng Huo
- Center for Clinical Cancer Genetics and Global Health, Department of Medicine, University of Chicago, Chicago, IL, USA.
- Department of Public Health Sciences, University of Chicago, Chicago, IL, USA.
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Abstract
Metastasis is a major contributor to cancer-associated deaths. It is characterized by a multistep process that occurs through the acquisition of molecular and phenotypic changes enabling cancer cells from a primary tumour to disseminate and colonize at distant organ sites. Over the past decade, the discovery and characterization of long noncoding RNAs (lncRNAs) have revealed the diversity of their regulatory roles, including key contributions throughout the metastatic cascade. Here, we review how lncRNAs promote metastasis by functioning in discrete pro-metastatic steps including the epithelial-mesenchymal transition, invasion and migration and organotrophic colonization, and by influencing the metastatic tumour microenvironment, often by interacting within ribonucleoprotein complexes or directly with other nucleic acid entities. We discuss well-characterized lncRNAs with in vivo phenotypes and highlight mechanistic commonalities such as convergence with the TGFβ-ZEB1/ZEB2 axis or the nuclear factor-κB pathway, in addition to lncRNAs with controversial mechanisms and the influence of methodologies on mechanistic interpretation. Furthermore, some lncRNAs can help identify tumours with increased metastatic risk and spur novel therapeutic strategies, with several lncRNAs having shown potential as novel targets for antisense oligonucleotide therapy in animal models. In addition to well-characterized examples of lncRNAs functioning in metastasis, we discuss controversies and ongoing challenges in lncRNA biology. Finally, we present areas for future study for this rapidly evolving field.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
| | - Ha X Dang
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA
| | - Daniel A Lim
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, CA, USA
- San Francisco Veterans Affairs Medical Center, San Francisco, CA, USA
| | - Felix Y Feng
- Department of Radiation Oncology, University of California, San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
- Division of Hematology and Oncology, Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
- Department of Urology, University of California, San Francisco, San Francisco, CA, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO, USA.
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO, USA.
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO, USA.
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO, USA.
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74
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Wang X, Ji Y, Feng P, Liu R, Li G, Zheng J, Xue Y, Wei Y, Ji C, Chen D, Li J. The m6A Reader IGF2BP2 Regulates Macrophage Phenotypic Activation and Inflammatory Diseases by Stabilizing TSC1 and PPAR γ. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:2100209. [PMID: 34258163 PMCID: PMC8261491 DOI: 10.1002/advs.202100209] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/06/2021] [Indexed: 05/20/2023]
Abstract
Phenotypic polarization of macrophages is regulated by a milieu of cues in the local tissue microenvironment. Currently, little is known about how the intrinsic regulators modulate proinflammatory (M1) versus prohealing (M2) macrophages activation. Here, it is observed that insulin-like growth factor 2 messenger RNA (mRNA)-binding protein 2 (IGF2BP2)-deleted macrophages exhibit enhanced M1 phenotype and promote dextran sulfate sodium induced colitis development. However, the IGF2BP2-/- macrophages are refractory to interleukin-4 (IL-4) induced activation and alleviate cockroach extract induced pulmonary allergic inflammation. Molecular studies indicate that IGF2BP2 switches M1 macrophages to M2 activation by targeting tuberous sclerosis 1 via an N6-methyladenosine (m6A)-dependent manner. Additionally, it is also shown a signal transducer and activators of transcription 6 (STAT6)-high mobility group AT-hook 2-IGF2BP2-peroxisome proliferator activated receptor-γ axis involves in M2 macrophages differentiation. These findings highlight a key role of IGF2BP2 in regulation of macrophages activation and imply a potential therapeutic target of macrophages in the inflammatory diseases.
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Affiliation(s)
- Xia Wang
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Yuge Ji
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Panpan Feng
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Rucheng Liu
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Guosheng Li
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Junjie Zheng
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Yaqiang Xue
- ABLife BioBigData InstituteWuhanHubei430075China
| | - Yaxun Wei
- Center for Genoem AnalysisABLife Inc.WuhanHubei430075China
| | - Chunyan Ji
- Department of HematologyQilu HospitalCheeloo College of MedicineShandong UniversityJinanShandong250012China
| | - Dawei Chen
- Laboratory of Medical ChemistryInterdisciplinary Cluster for Applied Genoproteomics (GIGA) Stem CellsUniversity of LiègeCHU, Sart‐TilmanLiège4000Belgium
| | - Jingxin Li
- Department of PhysiologySchool of Basic Medical SciencesCheeloo College of MedicineShandong UniversityJinanShandong250012China
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75
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Zampedri C, Martínez-Flores WA, Melendez-Zajgla J. The Use of Zebrafish Xenotransplant Assays to Analyze the Role of lncRNAs in Breast Cancer. Front Oncol 2021; 11:687594. [PMID: 34123857 PMCID: PMC8190406 DOI: 10.3389/fonc.2021.687594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 05/04/2021] [Indexed: 12/19/2022] Open
Abstract
Breast cancer represents a great challenge since it is the first cause of death by cancer in women worldwide. LncRNAs are a newly described class of non-coding RNAs that participate in cancer progression. Their use as cancer markers and possible therapeutic targets has recently gained strength. Animal xenotransplants allows for in vivo monitoring of disease development, molecular elucidation of pathogenesis and the design of new therapeutic strategies. Nevertheless, the cost and complexities of mice husbandry makes medium to high throughput assays difficult. Zebrafishes (Danio rerio) represent a novel model for these assays, given the ease with which xenotransplantation trials can be performed and the economic and experimental advantages it offers. In this review we propose the use of xenotransplants in zebrafish to study the role of breast cancer lncRNAs using low to medium high throughput assays.
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Affiliation(s)
- Cecilia Zampedri
- Functional Genomics Laboratories, Instituto Nacional de Medicina Genomica, Mexico City, Mexico
| | | | - Jorge Melendez-Zajgla
- Functional Genomics Laboratories, Instituto Nacional de Medicina Genomica, Mexico City, Mexico
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76
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Liu QL, Luo M, Huang C, Chen HN, Zhou ZG. Epigenetic Regulation of Epithelial to Mesenchymal Transition in the Cancer Metastatic Cascade: Implications for Cancer Therapy. Front Oncol 2021; 11:657546. [PMID: 33996581 PMCID: PMC8117142 DOI: 10.3389/fonc.2021.657546] [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: 01/23/2021] [Accepted: 04/09/2021] [Indexed: 02/05/2023] Open
Abstract
Metastasis is the end stage of cancer progression and the direct cause of most cancer-related deaths. The spreading of cancer cells from the primary site to distant organs is a multistep process known as the metastatic cascade, including local invasion, intravasation, survival in the circulation, extravasation, and colonization. Each of these steps is driven by the acquisition of genetic and/or epigenetic alterations within cancer cells, leading to subsequent transformation of metastatic cells. Epithelial–mesenchymal transition (EMT), a cellular process mediating the conversion of cell from epithelial to mesenchymal phenotype, and its reverse transformation, termed mesenchymal–epithelial transition (MET), together endow metastatic cells with traits needed to generate overt metastases in different scenarios. The dynamic shift between these two phenotypes and their transitional state, termed partial EMT, emphasizes the plasticity of EMT. Recent advances attributed this plasticity to epigenetic regulation, which has implications for the therapeutic targeting of cancer metastasis. In this review, we will discuss the association between epigenetic events and the multifaceted nature of EMT, which may provide insights into the steps of the cancer metastatic cascade.
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Affiliation(s)
- Qiu-Luo Liu
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Maochao Luo
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Canhua Huang
- Department of Biotherapy, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hai-Ning Chen
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Zong-Guang Zhou
- Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Collaborative Innovation Center for Biotherapy, Chengdu, China
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77
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Wang MQ, Zhu WJ, Gao P. New insights into long non-coding RNAs in breast cancer: Biological functions and therapeutic prospects. Exp Mol Pathol 2021; 120:104640. [PMID: 33878314 DOI: 10.1016/j.yexmp.2021.104640] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/24/2021] [Accepted: 04/16/2021] [Indexed: 11/29/2022]
Abstract
Breast cancer (BC) has become one of the most common malignant tumors in the world, seriously endangering women's health and life. However, the underlying molecular mechanisms of BC remain unclear. Over the past decade, long non-coding RNAs (lncRNAs) were gradually discovered and appreciated to play pivotal regulatory role in the progression of BC. It has been demonstrated that lncRNAs are implicated in regulating plenty of biological phenomena including cell proliferation, apoptosis, invasion and metastasis by interacting with DNA, RNA or proteins. In addition to these, the function of lncRNAs in tumor resistance has increasingly attracted more attention. In this review, we summarized the emerging impact of lncRNAs on the occurrence and progression of human BC, specifically focusing on the functions and mechanisms of them, with the aim of exploring the potential value of lncRNAs as oncogenic drivers or tumor suppressors. Furthermore, the potential clinical application of lncRNAs as diagnostic biomarkers and therapeutic targets in BC was also discussed.
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Affiliation(s)
- Meng-Qi Wang
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, CheeLoo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China
| | - Wen-Jie Zhu
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, CheeLoo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China.
| | - Peng Gao
- Key Laboratory for Experimental Teratology of Ministry of Education, Department of Pathology, School of Basic Medical Sciences, CheeLoo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Department of Pathology, Qilu Hospital, Shandong University, Jinan, Shandong 250012, China.
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78
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Cisneros-Villanueva M, Hidalgo-Pérez L, Cedro-Tanda A, Peña-Luna M, Mancera-Rodríguez MA, Hurtado-Cordova E, Rivera-Salgado I, Martínez-Aguirre A, Jiménez-Morales S, Alfaro-Ruiz LA, Arellano-Llamas R, Tenorio-Torres A, Domínguez-Reyes C, Villegas-Carlos F, Ríos-Romero M, Hidalgo-Miranda A. LINC00460 Is a Dual Biomarker That Acts as a Predictor for Increased Prognosis in Basal-Like Breast Cancer and Potentially Regulates Immunogenic and Differentiation-Related Genes. Front Oncol 2021; 11:628027. [PMID: 33912452 PMCID: PMC8074675 DOI: 10.3389/fonc.2021.628027] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/10/2021] [Indexed: 12/23/2022] Open
Abstract
Breast cancer (BRCA) is a serious public health problem, as it is the most frequent malignant tumor in women worldwide. BRCA is a molecularly heterogeneous disease, particularly at gene expression (mRNAs) level. Recent evidence shows that coding RNAs represent only 34% of the total transcriptome in a human cell. The rest of the 66% of RNAs are non−coding, so we might be missing relevant biological, clinical or regulatory information. In this report, we identified two novel tumor types from TCGA with LINC00460 deregulation. We used survival analysis to demonstrate that LINC00460 expression is a marker for poor overall (OS), relapse-free (RFS) and distant metastasis-free survival (DMFS) in basal-like BRCA patients. LINC00460 expression is a potential marker for aggressive phenotypes in distinct tumors, including HPV-negative HNSC, stage IV KIRC, locally advanced lung cancer and basal-like BRCA. We show that the LINC00460 prognostic expression effect is tissue-specific, since its upregulation can predict poor OS in some tumors, but also predicts an improved clinical course in BRCA patients. We found that the LINC00460 expression is significantly enriched in the Basal-like 2 (BL2) TNBC subtype and potentially regulates the WNT differentiation pathway. LINC00460 can also modulate a plethora of immunogenic related genes in BRCA, such as SFRP5, FOSL1, IFNK, CSF2, DUSP7 and IL1A and interacts with miR-103-a-1, in-silico, which, in turn, can no longer target WNT7A. Finally, LINC00460:WNT7A ratio constitutes a composite marker for decreased OS and DMFS in Basal-like BRCA, and can predict anthracycline therapy response in ER-BRCA patients. This evidence confirms that LINC00460 is a master regulator in BRCA molecular circuits and influences clinical outcome.
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Affiliation(s)
- Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Laboratorio de Epigenética del Cáncer, Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Mexico
| | - Lizbett Hidalgo-Pérez
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Programa de Doctorado en Ciencias Biomédicas, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, Mexico
| | - Alberto Cedro-Tanda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Mónica Peña-Luna
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | | | - Eduardo Hurtado-Cordova
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Irene Rivera-Salgado
- Departamento de Anatomía Patológica, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos, Ciudad de México, México
| | - Alejandro Martínez-Aguirre
- Departamento de Anatomía Patológica, Hospital Central Sur de Alta Especialidad, Petróleos Mexicanos, Ciudad de México, México
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Luis Alberto Alfaro-Ruiz
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | - Rocío Arellano-Llamas
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
| | | | | | | | - Magdalena Ríos-Romero
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México.,Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Ciudad de México, México
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Ciudad de México, México
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79
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MCPIP1-mediated NFIC alternative splicing inhibits proliferation of triple-negative breast cancer via cyclin D1-Rb-E2F1 axis. Cell Death Dis 2021; 12:370. [PMID: 33824311 PMCID: PMC8024338 DOI: 10.1038/s41419-021-03661-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 03/18/2021] [Accepted: 03/23/2021] [Indexed: 12/12/2022]
Abstract
Triple-negative breast cancer (TNBC) is the most aggressive subtype with the worst prognosis and the highest metastatic and recurrence potential, which represents 15–20% of all breast cancers in Chinese females, and the 5-year overall survival rate is about 80% in Chinese women. Recently, emerging evidence suggested that aberrant alternative splicing (AS) plays a crucial role in tumorigenesis and progression. AS is generally controlled by AS-associated RNA binding proteins (RBPs). Monocyte chemotactic protein induced protein 1 (MCPIP1), a zinc finger RBP, functions as a tumor suppressor in many cancers. Here, we showed that MCPIP1 was downregulated in 80 TNBC tissues and five TNBC cell lines compared to adjacent paracancerous tissues and one human immortalized breast epithelial cell line, while its high expression levels were associated with increased overall survival in TNBC patients. We demonstrated that MCPIP1 overexpression dramatically suppressed cell cycle progression and proliferation of TNBC cells in vitro and repressed tumor growth in vivo. Mechanistically, MCPIP1 was first demonstrated to act as a splicing factor to regulate AS in TNBC cells. Furthermore, we demonstrated that MCPIP1 modulated NFIC AS to promote CTF5 synthesis, which acted as a negative regulator in TNBC cells. Subsequently, we showed that CTF5 participated in MCPIP1-mediated antiproliferative effect by transcriptionally repressing cyclin D1 expression, as well as downregulating its downstream signaling targets p-Rb and E2F1. Conclusively, our findings provided novel insights into the anti-oncogenic mechanism of MCPIP1, suggesting that MCPIP1 could serve as an alternative treatment target in TNBC.
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80
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Breast Cancer and the Other Non-Coding RNAs. Int J Mol Sci 2021; 22:ijms22063280. [PMID: 33807045 PMCID: PMC8005115 DOI: 10.3390/ijms22063280] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022] Open
Abstract
Breast cancer is very heterogenous and the most common gynaecological cancer, with various factors affecting its development. While its impact on human lives and national health budgets is still rising in almost all global areas, many molecular mechanisms affecting its onset and development remain unclear. Conventional treatments still prove inadequate in some aspects, and appropriate molecular therapeutic targets are required for improved outcomes. Recent scientific interest has therefore focused on the non-coding RNAs roles in tumour development and their potential as therapeutic targets. These RNAs comprise the majority of the human transcript and their broad action mechanisms range from gene silencing to chromatin remodelling. Many non-coding RNAs also have altered expression in breast cancer cell lines and tissues, and this is often connected with increased proliferation, a degraded extracellular environment, and higher endothelial to mesenchymal transition. Herein, we summarise the known abnormalities in the function and expression of long non-coding RNAs, Piwi interacting RNAs, small nucleolar RNAs and small nuclear RNAs in breast cancer, and how these abnormalities affect the development of this deadly disease. Finally, the use of RNA interference to suppress breast cancer growth is summarised.
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81
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Inhibition of lncRNA-NEAT1 sensitizes 5-Fu resistant cervical cancer cells through de-repressing the microRNA-34a/LDHA axis. Biosci Rep 2021; 41:227998. [PMID: 33645623 PMCID: PMC8298262 DOI: 10.1042/bsr20200533] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/25/2022] Open
Abstract
Cervical cancer is one of the most diagnosed malignancies among females. The 5-fluorouracil (5-Fu) is a widely used chemotherapeutic agent against diverse cancers. Despite the initially encouraging progresses, a fraction of cervical cancer patients developed 5-Fu resistance. We detected that nuclear-rich transcripts 1 (NEAT1) was significantly up-regulated in cervical cancer tissues and cell lines. Moreover, NEAT1 was positively associated with 5-Fu resistance. Furthermore, expression of NEAT1 was significantly up-regulated in 5-Fu resistant CaSki cervical cancer cells. Knocking down NEAT1 by shRNA dramatically promoted the sensitivity of 5-Fu resistant CaSki cells. We observed a negative correlation between long noncoding RNA (lncRNA)-NEAT1 and miR-34a in cervical cancer patient tissues. Overexpression of miR-34a significantly sensitized 5-Fu resistant cells. Bioinformatics analysis uncovered that NEAT1 functions as a competitive endogenous RNA (ceRNA) of miR-34a in cervical cancer cells via sponging it at multiple sites to suppress expression of miR-34a. This negative association between NEAT1 and miR-34a was further verified in cervical cancer tissues. We found the 5-Fu resistant cells displayed significantly increased glycolysis rate. Overexpression of miR-34a suppressed cellular glycolysis rate and sensitized 5-Fu resistant cells through direct targeting the 3′-untranslated region (UTR) of LDHA, a glycolysis key enzyme. Importantly, knocking down NEAT1 successfully down-regulated LDHA expressions and glycolysis rate of cervical cancer cells by up-regulating miR-34a, a process could be further rescued by miR-34a inhibition. Finally, we demonstrated inhibition of NEAT1 significantly sensitized cervical cancer cells to 5-Fu through the miR-34a/LDHA pathway. In summary, the present study suggests a new molecular mechanism for the NEAT1-mediated 5-Fu resistance via the miR-34a/LDHA-glycolysis axis.
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82
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Thankachan S, Bhardwaj BK, Venkatesh T, Suresh PS. Long Non-coding RNA NEAT1 as an Emerging Biomarker in Breast and Gynecologic Cancers: a Systematic Overview. Reprod Sci 2021; 28:2436-2447. [PMID: 33569749 DOI: 10.1007/s43032-021-00481-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/31/2021] [Indexed: 02/06/2023]
Abstract
Long non-coding RNAs (lncRNAs) are emerging regulators of cellular pathways, especially in cancer development. Among the lncRNAs, nuclear paraspeckle assembly transcript 1 (NEAT1) forms a scaffold for a nuclear body; the paraspeckle and aberrant expression of NEAT1 have been reported in breast and gynecologic cancers (ovarian, cervical, endometrial, and vulvar). Abundantly expressed NEAT1 in breast and gynecologic cancers generally contribute to tumor development by sponging its corresponding tumor-suppressive microRNAs or interacting with various regulatory proteins. The distinct expression of NEAT1 and its contribution to tumorigenic pathways make it a promising therapeutic target in breast and gynecologic cancers. Herein, we summarize the functions and molecular mechanisms of NEAT1 in human breast, ovarian, cervical, endometrial, and vulvar cancers. Furthermore, we emphasize its critical role in the formation of paraspeckle development and its functions. Conclusively, NEAT1 is a considerable biomarker with a bright prospect and can be therapeutically targeted to manage breast and gynecologic cancers.
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Affiliation(s)
- Sanu Thankachan
- School of Biotechnology, National Institute of Technology, Calicut, Kerala, 673601, India
| | | | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kasargod, Kerala, 671316, India
| | - Padmanaban S Suresh
- School of Biotechnology, National Institute of Technology, Calicut, Kerala, 673601, India.
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83
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Wei J, Li DK, Hu X, Cheng C, Zhang Y. Galectin-1-RNA interaction map reveals potential regulatory roles in angiogenesis. FEBS Lett 2021; 595:623-636. [PMID: 33483966 DOI: 10.1002/1873-3468.14047] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/29/2020] [Accepted: 12/30/2020] [Indexed: 12/17/2022]
Abstract
Hyperactive angiogenesis contributes to the immunosuppressive microenvironment important for immunotherapy. Galectin-1, encoded by LGALS1, can trigger the vascular signaling programs and mediate the anti-angiogenic treatment response. However, the mechanism through which galectin-1 regulates angiogenesis is poorly understood. It has been suggested that galectin-1 may associate with mRNAs in cells. This study applied the iRIP-seq methodology to study the potential role of galectin-1 as an RNA-binding protein. We found that galectin-1 interacts with a large number of mRNAs, with a preference for binding near stop codons and a preference for UGCA/UGGA and GAGCAG as binding motifs. Galectin-1 binds to the mRNAs of angiogenesis-associated genes including VEGFA, EGR1, and LAMA5, suggesting that galectin-1 may regulate angiogenesis via its mRNA-binding activity. We further show that shLGALS1 inhibits capillary tube formation in an in vitro angiogenesis assay and alters the expression levels of several galectin-1-bound angiogenesis-associated mRNAs. These results uncover a previously unrecognized mRNA-binding activity of galectin-1.
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Affiliation(s)
- Jiajun Wei
- Department of Neurology, Renmin Hospital of Wuhan University, China
| | - Daniel K Li
- Department of Biology and Biotechnology, School of Chemistry, Chemical Engineering and Life Sciences, Wuhan University of Technology, China
| | - Xinyu Hu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Chao Cheng
- ABLife BioBigData Institute, Wuhan, China
| | - Yi Zhang
- ABLife BioBigData Institute, Wuhan, China
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84
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Huang S, Dong D, Zhang Y, Chen Z, Geng J, Zhao Y. Long non-coding RNA nuclear paraspeckle assembly transcript 1 promotes activation of T helper 2 cells via inhibiting STAT6 ubiquitination. Hum Cell 2021; 34:800-807. [PMID: 33550532 DOI: 10.1007/s13577-021-00496-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 01/23/2021] [Indexed: 11/25/2022]
Abstract
T helper (Th) 2 cell-medicated immune response participates in various immune diseases, including systemic lupus erythematosus (SLE). Long non-coding RNA nuclear paraspeckle assembly transcript 1 (NEAT1) has been reported to be associated with T helper 2 (Th2) cell activation. Here, we demonstrated the molecular mechanism of NEAT1 in regulating Th2 cell activation. We found that NEAT1 was located in nucleus. NEAT1 overexpression promoted the levels of Th2-related cytokines IL-4, IL-5 and IL-13 in CD4+ T cells. Moreover, NEAT1 up-regulation reduced Th1-related cytokine INF-γ production and enhanced the levels of Th17-related cytokines IL-17 in CD4+ T cells. STAT6 deficiency reduced the levels of IL-4, IL-5, IL-13 and IL-17 enhanced the levels of INF-γ in CD4+ T cells, which was rescued by NEAT1 overexpression. Moreover, NEAT1 promoted STAT6 protein expression, whereas NEAT1 had no effect on the expression of STAT6 mRNA. Furthermore, NEAT1 interacted with STAT6, inhibited the ubiquitination of STAT6 in CD4+ T cells. In conclusion, our work has confirmed that NEAT1 promotes STAT6 expression by inhibiting STAT6 ubiquitination, thereby promoting Th2 cell activation. Thus, our work may highlight novel insights into the molecular mechanism of NEAT1 in regulating Th2 cell activation.
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Affiliation(s)
- Shuman Huang
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China
| | - Dong Dong
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Yaqian Zhang
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Zhuo Chen
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China
| | - Jing Geng
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.,Academy of Medical Science, Zhengzhou University, Zhengzhou, 450052, China
| | - Yulin Zhao
- The Rhinology Department, The First Affiliated Hospital of Zhengzhou University, No. 1 Jianshe East Road, Zhengzhou, 450052, China.
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85
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Chen Y, Li J, Xiao JK, Xiao L, Xu BW, Li C. The lncRNA NEAT1 promotes the epithelial-mesenchymal transition and metastasis of osteosarcoma cells by sponging miR-483 to upregulate STAT3 expression. Cancer Cell Int 2021; 21:90. [PMID: 33546665 PMCID: PMC7866772 DOI: 10.1186/s12935-021-01780-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Accepted: 01/20/2021] [Indexed: 02/06/2023] Open
Abstract
Background Osteosarcoma is one of the most prevalent primary bone tumours in adolescents. Accumulating evidence shows that aberrant expression of the long non-coding RNA (lncRNA) NEAT1 and microRNA-483 (miR-483) contribute to the epithelial-mesenchymal transition (EMT), invasion and metastasis of tumour cells. However, the potential regulatory effects of NEAT1 and miR-483 on the EMT of osteosarcoma remain elusive. Methods The expression of the NEAT1, miR-483, signal transducer and activator of transcription-1 (STAT1), STAT3, and EMT-associated markers was measured using qRT-PCR or western blotting. NEAT1 overexpression or knockdown was induced by lentivirus-mediated transfection. A luciferase reporter assay was employed to confirm the association between NEAT1/miR-483 and miR-483/STAT3. RNA immunoprecipitation (RIP) was also performed to verify the NEAT1 and miR-483 interaction. Wound healing and transwell assays were implemented to assess the migration and invasion of U2OS cells. Unilateral subcutaneous injection of U2OS into nude mice was performed to investigate tumour metastasis in vivo. Results The expression of miR-483 was downregulated in both osteosarcoma cell lines and osteosarcoma tissues. The overexpression of miR-483 suppressed the migration, invasion, and expression of EMT-associated proteins in U2OS cells, while simultaneous overexpression of STAT3 partially relieved this suppression. Mechanistically, miR-483 specifically targeted the 3′ untranslated region (3′UTR) of STAT3 and repressed its expression. However, NEAT1 sponged miR-438, increased STAT3 expression, and repressed STAT1 expression, subsequently increasing the EMT of osteosarcoma cells. The knockdown of NEAT1 in transplanted U2OS cells impaired the liver and lung metastases of osteosarcoma in nude mice. Moreover, NEAT1 silencing inhibited the mesenchymal- epithelial transition (MET) of osteosarcoma at metastasis sites. Conclusions The lncRNA NEAT1/miR-483/STAT3 axis plays a crucial role in regulating the metastasis of osteosarcoma and potentially represents one appealing therapeutic target for osteosarcoma treatment in the future.
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Affiliation(s)
- Yan Chen
- Department of Nephrology, The Second Affiliated Hospital of Nanchang University, Nanchang, 330006, People's Republic of China
| | - Jun Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Jia-Kun Xiao
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Lei Xiao
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Bin-Wu Xu
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China
| | - Chen Li
- Department of Orthopedic Surgery, The Second Affiliated Hospital of Nanchang University, No. 1 Minde Road, Nanchang, 330006, Jiangxi, People's Republic of China.
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86
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Ma T, Qiao T, Yuan Z, Wang G, Huang R, Wang M, Hu H, Zhu Y, Zou X, Wang X. Long Noncoding RNA JAKMIP2-AS1 Promotes the Growth of Colorectal Cancer and Indicates Poor Prognosis. Onco Targets Ther 2021; 14:763-772. [PMID: 33568916 PMCID: PMC7868292 DOI: 10.2147/ott.s289617] [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: 11/10/2020] [Accepted: 01/22/2021] [Indexed: 01/05/2023] Open
Abstract
Background The identification of cancer-associated long noncoding RNAs and the investigation of their molecular and biological functions are important for understanding the molecular biology and progression of cancer. JAKMIP2-AS1 has not been reported in the literature, especially in the context of colorectal cancer. The aim of the present study was to examine the expression pattern of JAKMIP2-AS1 in colorectal cancer (CRC) and evaluate its biological role and clinical significance in tumor progression. Methods JAKMIP2-AS1 expression was analyzed in 56 CRC tissues and nine CRC cell lines by quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Overexpression and RNA interference (RNAi) approaches were used to investigate the biological functions of JAKMIP2-AS1. The effect of JAKMIP2-AS1 on proliferation was evaluated by CCK-8, colony formation, and EdU assays. Subcutaneous injection of cells was used to study proliferation in BALB/c nude male mice. Proliferation-related protein levels were examined by immunohistochemical analysis. Differences between groups were tested for significance using Student's t-test (two-tailed). Results JAKMIP2-AS1 was highly expressed in both CRC samples and cell lines compared with the corresponding normal counterparts. The upregulation of JAKMIP2-AS1 expression promoted the proliferation of colorectal cancer cells. Moreover, patients with high levels of JAKMIP2-AS1 expression had a relatively poor prognosis. Inhibition of JAKMIP2-AS1 by RNAi decreased the proliferation of CRC cells in vitro and impeded cell growth in vivo. Ki-67 and PCNA levels were affected by JAKMIP2-AS1 knockdown or overexpression in vivo. Conclusion Our findings indicate that JAKMIP2-AS1 is significantly upregulated in CRC tissues and regulates CRC cell proliferation. Thus, JAKMIP2-AS1 may represent a new marker of poor prognosis and is a potential therapeutic target for CRC intervention.
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Affiliation(s)
- Tianyi Ma
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Tianyu Qiao
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Ziming Yuan
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Guiyu Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Rui Huang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Meng Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Hanqing Hu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Yihao Zhu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Xiaoming Zou
- Department of General Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China
| | - Xishan Wang
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, People's Republic of China.,Department of Colorectal Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100021, People's Republic of China
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87
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Chen J, Zhang J, Gao Y, Li Y, Feng C, Song C, Ning Z, Zhou X, Zhao J, Feng M, Zhang Y, Wei L, Pan Q, Jiang Y, Qian F, Han J, Yang Y, Wang Q, Li C. LncSEA: a platform for long non-coding RNA related sets and enrichment analysis. Nucleic Acids Res 2021; 49:D969-D980. [PMID: 33045741 PMCID: PMC7778898 DOI: 10.1093/nar/gkaa806] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 09/03/2020] [Accepted: 09/30/2020] [Indexed: 02/01/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have been proven to play important roles in transcriptional processes and various biological functions. Establishing a comprehensive collection of human lncRNA sets is urgent work at present. Using reference lncRNA sets, enrichment analyses will be useful for analyzing lncRNA lists of interest submitted by users. Therefore, we developed a human lncRNA sets database, called LncSEA, which aimed to document a large number of available resources for human lncRNA sets and provide annotation and enrichment analyses for lncRNAs. LncSEA supports >40 000 lncRNA reference sets across 18 categories and 66 sub-categories, and covers over 50 000 lncRNAs. We not only collected lncRNA sets based on downstream regulatory data sources, but also identified a large number of lncRNA sets regulated by upstream transcription factors (TFs) and DNA regulatory elements by integrating TF ChIP-seq, DNase-seq, ATAC-seq and H3K27ac ChIP-seq data. Importantly, LncSEA provides annotation and enrichment analyses of lncRNA sets associated with upstream regulators and downstream targets. In summary, LncSEA is a powerful platform that provides a variety of types of lncRNA sets for users, and supports lncRNA annotations and enrichment analyses. The LncSEA database is freely accessible at http://bio.liclab.net/LncSEA/index.php.
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Affiliation(s)
- Jiaxin Chen
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jian Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yu Gao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yanyu Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chenchen Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chao Song
- Department of Pharmacology, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Ziyu Ning
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Xinyuan Zhou
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Jianmei Zhao
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Minghong Feng
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yuexin Zhang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Ling Wei
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qi Pan
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Yong Jiang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Fengcui Qian
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Junwei Han
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China
| | - Yongsan Yang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Qiuyu Wang
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
| | - Chunquan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China
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88
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Zhang Y, Xu M, Sun Y, Chen Y, Chi P, Xu Z, Lu X. Identification of LncRNAs Associated With FOLFOX Chemoresistance in mCRC and Construction of a Predictive Model. Front Cell Dev Biol 2021; 8:609832. [PMID: 33585448 PMCID: PMC7876414 DOI: 10.3389/fcell.2020.609832] [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: 09/24/2020] [Accepted: 12/21/2020] [Indexed: 12/19/2022] Open
Abstract
Oxaliplatin, fluorouracil plus leucovorin (FOLFOX) regimen is the first-line chemotherapy of patients with metastatic colorectal cancer (mCRC). However, studies are limited regarding long non-coding RNAs (lncRNAs) associated with FOLFOX chemotherapy response and prognosis. This study aimed to identify lncRNAs associated with FOLFOX chemotherapy response and prognosis in mCRC patients and to construct a predictive model. We analyzed lncRNA expression in 11 mCRC patients treated with FOLFOX chemotherapy before surgery (four sensitive, seven resistant) by Gene Array Chip. The top eight lncRNAs (AC007193.8, CTD-2008N3.1, FLJ36777, RP11-509J21.4, RP3-508I15.20, LOC100130950, RP5-1042K10.13, and LINC00476) for chemotherapy response were identified according to weighted correlation network analysis (WGCNA). A competitive endogenous RNA (ceRNA) network was then constructed. The crucial functions of the eight lncRNAs enriched in chemotherapy resistance were mitogen-activated protein kinase (MAPK) and proteoglycans signaling pathway. Receiver operating characteristic (ROC) analysis demonstrated that the eight lncRNAs were potent predictors for chemotherapy resistance of mCRC patients. To further identify a signature model lncRNA chemotherapy response and prognosis, the validation set consisted of 196 CRC patients from our center was used to validate lncRNAs expression and prognosis by quantitative PCR (qPCR). The expression of the eight lncRNAs expression between CRC cancerous and adjacent non-cancerous tissues was also verified in the validation data set to determine the prognostic value. A generalized linear model was established to predict the probability of chemotherapy resistance and survival. Our findings showed that the eight-lncRNA signature may be a novel biomarker for the prediction of FOLFOX chemotherapy response and prognosis of mCRC patients.
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Affiliation(s)
- Yiyi Zhang
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Meifang Xu
- Department of Pathology, Fujian Medical University Union Hospital, Fuzhou, China
| | - Yanwu Sun
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Ying Chen
- Department of Plastic Surgery, Fuzhou Dermatosis Prevention Hospital, Fuzhou, China
| | - Pan Chi
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Zongbin Xu
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
| | - Xingrong Lu
- Department of Colorectal Surgery, Fujian Medical University Union Hospital, Fuzhou, China
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89
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Huang Y, Wang X, Zheng Y, Chen W, Zheng Y, Li G, Lou W, Wang X. Construction of an mRNA-miRNA-lncRNA network prognostic for triple-negative breast cancer. Aging (Albany NY) 2021; 13:1153-1175. [PMID: 33428596 PMCID: PMC7835059 DOI: 10.18632/aging.202254] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 11/13/2020] [Indexed: 01/10/2023]
Abstract
The aim of this study was to establish a novel competing endogenous RNA (ceRNA) network able to predict prognosis in patients with triple-negative breast cancer (TNBC). Differential gene expression analysis was performed using the GEO2R tool. Enrichr and STRING were used to conduct protein-protein interaction and pathway enrichment analyses, respectively. Upstream lncRNAs and miRNAs were identified using miRNet and mirTarBase, respectively. Prognostic values, expression, and correlational relationships of mRNAs, lncRNAs, and miRNAs were examined using GEPIA, starBase, and Kaplan-Meier plotter. It total, 860 upregulated and 622 downregulated differentially expressed mRNAs were identified in TNBC. Ten overexpressed and two underexpressed hub genes were screened. Next, 10 key miRNAs upstream of these key hub genes were predicted, of which six upregulated miRNAs were significantly associated with poor prognosis and four downregulated miRNAs were associated with good prognosis in TNBC. NEAT1 and MAL2 were selected as key lncRNAs. An mRNA-miRNA-lncRNA network in TNBC was constructed. Thus, we successfully established a novel mRNA-miRNA-lncRNA regulatory network, each component of which is prognostic for TNBC.
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Affiliation(s)
- Yuan Huang
- Department of Breast Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang Province, Hangzhou 310022, China
| | - Xiaowei Wang
- Department of Colorectal Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Zhejiang Province, Hangzhou 310016, China
| | - Yiran Zheng
- School of Pharmaceutical Sciences, Soochow University, Jiangsu Province, Suzhou 215123, China
| | - Wei Chen
- Silergy Corporation, Zhejiang Province, Hangzhou 310012, China
| | - Yabing Zheng
- Department of Breast Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang Province, Hangzhou 310022, China
| | - Guangliang Li
- Department of Breast Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang Province, Hangzhou 310022, China
| | - Weiyang Lou
- Department of Breast Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Zhejiang Province, Hangzhou 310003, China
| | - Xiaojia Wang
- Department of Breast Medical Oncology, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Zhejiang Province, Hangzhou 310022, China
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Lin Z, Chen M, Wan Y, Lei L, Ruan H. miR-574-5p Targets FOXN3 to Regulate the Invasion of Nasopharyngeal Carcinoma Cells via Wnt/β-Catenin Pathway. Technol Cancer Res Treat 2020; 19:1533033820971659. [PMID: 33317407 PMCID: PMC7745553 DOI: 10.1177/1533033820971659] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miR) are a class of non-coding endogenous RNA molecules that suppress the translation of protein-coding genes by destabilizing target mRNAs. The MiR-574-5p has been reported to be involved in the several types of cancer. However, the expression of miR-574-5p and its mechanism in nasopharyngeal carcinoma (NPC) remain unclear. We found that the expression level of miR-574-5p was significantly increased in the NPC cell lines. We further demonstrated that Forkhead box N3 (FOXN3) was a target gene of miR-574-5p. FOXN3 overexpression and inhibition reversed the promoting or suppressing effect, respectively, of NPC cell proliferation, migration and invasion caused by miR-574-5p. Furthermore, miR-574-5p enhanced the β-catenin and TCF4 protein expression by repressing FOXN3 expression, resulting in the activation of the Wnt/β-catenin signaling pathway, but the activity of the Wnt/β-catenin signaling pathway was inhibited by a miR-574-5p inhibitor or FOXN3 overexpression, which reversed the effect of miR-574-5p. Wound-healing and Transwell assays also showed that miR-574-5p promotes the cell migration and invasion of NPC cells, whereas the promoting effect of miR-574-5p was also reversed by a miR-574-5p inhibitor or FOXN3 overexpression. Collectively, these data suggested that miR-574-5p promotes NPC cell proliferation, migration, and invasion at least partly by targeting the FOXN3/Wnt/β-Catenin signaling pathway.
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Affiliation(s)
- Zhonghao Lin
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Ningde, Fujian, China
| | - Miaoan Chen
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Ningde, Fujian, China
| | - Yawen Wan
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Ningde, Fujian, China
| | - Liguang Lei
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Mindong Hospital of Fujian Medical University, Ningde, Fujian, China
| | - Huiqing Ruan
- Department of Endocrinology, The Affiliated Mindong Hospital of Fujian Medical University, Ningde, Fujian, China
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91
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Wen S, Wei Y, Zen C, Xiong W, Niu Y, Zhao Y. Long non-coding RNA NEAT1 promotes bone metastasis of prostate cancer through N6-methyladenosine. Mol Cancer 2020; 19:171. [PMID: 33308223 PMCID: PMC7733260 DOI: 10.1186/s12943-020-01293-4] [Citation(s) in RCA: 171] [Impact Index Per Article: 42.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 12/06/2020] [Indexed: 02/07/2023] Open
Abstract
Background N6-methyladenosine (m6A) is the most prevalent messenger RNA modification in mammalian cells. However, the disease relevant function of m6A on specific oncogenic long non-coding RNAs (ncRNAs) is not well understood. Methods We analyzed the m6A status using patients samples and bone metastatic PDXs. Through m6A high-throughput sequencing, we identified the m6A sites on NEAT1–1 in prostate bone metastatic PDXs. Mass spec assay showed interaction among NEAT1–1, CYCLINL1 and CDK19. RNA EMSA, RNA pull-down, mutagenesis, CLIP, western blot, ChIP and ChIRP assays were used to investigate the molecular mechanisms underlying the functions of m6A on NEAT1–1. Loss-of function and rescued experiments were executed to detect the biological roles of m6A on NEAT1–1 in the PDX cell phenotypes in vivo. Results In this study, we identified 4 credible m6A sites on long ncRNA NEAT1–1. High m6A level of NEAT1–1 was related to bone metastasis of prostate cancer and m6A level of NEAT1–1 was a powerful predictor of eventual death. Transcribed NEAT1–1 served as a bridge to facility the binding between CYCLINL1 and CDK19 and promoted the Pol II ser2 phosphorylation. Importantly, depletion of NEAT1–1or decreased m6A of NEAT1–1 impaired Pol II Ser-2p level in the promoter of RUNX2. Overexpression of NEAT1–1 induced cancer cell metastasis to lung and bone; xenograft growth and shortened the survival of mice, but NEAT1–1 with m6A site mutation failed to do these. Conclusion Collectively, the findings indicate that m6A on ncRNA NEAT1–1 takes critical role in regulating Pol II ser2 phosphorylation and may be novel specific target for bone metastasis cancer therapy and diagnosis. New complex CYCLINL1/CDK19/NEAT1–1 might provide new insight into the potential mechanism of the pathogenesis and development of bone metastatic prostate cancer. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-020-01293-4.
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Affiliation(s)
- Simeng Wen
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China
| | - Yulei Wei
- Department of Gynecology and Obstetrics, Tianjin First Central Hospital, Tianjin, 300192, China
| | - Chong Zen
- Department of Urology, Central South University, Changsha, 410011, China
| | - Wei Xiong
- Department of Urology, Central South University, Changsha, 410011, China
| | - Yuanjie Niu
- Department of Urology, The Second Hospital of Tianjin Medical University, Tianjin Medical University, Tianjin, 300211, China.
| | - Yu Zhao
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, 55905, USA.
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15-lncRNA-Based Classifier-Clinicopathologic Nomogram Improves the Prediction of Recurrence in Patients with Hepatocellular Carcinoma. DISEASE MARKERS 2020; 2020:9180732. [PMID: 33520012 PMCID: PMC7817238 DOI: 10.1155/2020/9180732] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 09/07/2020] [Accepted: 10/15/2020] [Indexed: 02/06/2023]
Abstract
Background Our study aims to develop a lncRNA-based classifier and a nomogram incorporating the genomic signature and clinicopathologic factors to help to improve the accuracy of recurrence prediction for hepatocellular carcinoma (HCC) patients. Methods The lncRNA profiling data of 374 HCC patients and 50 normal healthy controls were downloaded from The Cancer Genome Atlas (TCGA). Using univariable Cox regression and least absolute shrinkage and selection operator (LASSO) analysis, we developed a 15-lncRNA-based classifier and compared our classifier to the existing six-lncRNA signature. Besides, a nomogram incorporating the genomic classifier and clinicopathologic factors was also developed. The predictive accuracy and discriminative ability of the genomic-clinicopathologic nomogram were determined by a concordance index (C-index) and calibration curve and were compared with the TNM staging system by the C-index and receiver operating characteristic (ROC) analysis. Decision curve analysis (DCA) was performed to estimate the clinical value of our nomogram. Results Fifteen relapse-free survival (RFS-) related lncRNAs were identified, and the classifier, consisting of the identified 15 lncRNAs, could effectively classify patients into the high-risk and low-risk subgroups. The prediction accuracy of the 15-lncRNA-based classifier for predicting 2-year and 5-year RFS was 0.791 and 0.834 in the training set and 0.684 and 0.747 in the validation set, respectively, which was better than the existing six-lncRNA signature. Moreover, the AUC of genomic-clinicopathologic nomogram in predicting RFS were 0.837 in the training set and 0.753 in the validation set, and the C-index of the genomic-clinicopathologic nomogram was 0.78 (0.72-0.83) in the training set and 0.71 (0.65-0.76) in the validation set, which was better than the traditional TNM stage and 15-lncRNA-based classifier. The decision curve analysis further demonstrated that our nomogram had a larger net benefit than the TNM stage and 15-lncRNA-based classifier. The results were confirmed externally. Conclusion Compared to the TNM stage, the 15-lncRNAs-based classifier-clinicopathologic nomogram is a more effective and valuable tool to identify HCC recurrence and may aid in clinical decision-making.
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NEAT1/miR-200b-3p/SMAD2 axis promotes progression of melanoma. Aging (Albany NY) 2020; 12:22759-22775. [PMID: 33202380 PMCID: PMC7746346 DOI: 10.18632/aging.103909] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 07/13/2020] [Indexed: 12/11/2022]
Abstract
Melanoma is a skin malignancy with a high mutation frequency of genetic alterations. MicroRNA (miR)-200b-3p is involved in various cancers, while in melanoma its bio-function remains unknown. In this study, we found that miR-200b-3p was down-regulated in melanoma tissues and cell lines compared to benign nevus cells. Overexpression of miR-200b-3p significantly inhibited the proliferation and invasion of melanoma cells. According to bioinformatics analysis and sequencing data, we supposed that SMAD family member 2 (SMAD2) was the target gene and nuclear enriched abundant transcript 1 (NEAT1) was the upstream long non-coding RNA (lncRNA) of miR-200b-3p. These predictions were verified by western blotting and quantitative real-time reverse transcription PCR (RT-qPCR). Luciferase reporter assays revealed that NEAT1 up-regulated SMAD2 by directly sponging miR-200b-3p. In vitro and in vivo, we demonstrated that both NEAT1 and SMAD2 could promote the proliferation and invasion of melanoma cells, and these effects were reversed by up-regulating miR-200b-3p. In addition, NEAT1/miR-200b-3p/SMAD2 axis promoted melanoma progression by activating EMT signaling pathway and immune responses. Taken together, the NEAT1/miR-200b-3p/SMAD2 signaling pathway promotes melanoma via activation of EMT, cell invasion and is related with immune responses, which provides new insights into the molecular mechanisms and therapeutic targets for melanoma.
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Yang Y, Zhang Y, Miao L, Liao W, Liao W. LncRNA PPP1R14B-AS1 Promotes Tumor Cell Proliferation and Migration via the Enhancement of Mitochondrial Respiration. Front Genet 2020; 11:557614. [PMID: 33262783 PMCID: PMC7686783 DOI: 10.3389/fgene.2020.557614] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/14/2020] [Indexed: 12/24/2022] Open
Abstract
PPP1R14B-AS1 is an antisense long non-coding RNA with unknown functions. Herein, gene differential analyses were performed using the data of patients with liver cancer and lung adenocarcinoma (LUAD) from The Cancer Genome Atlas database. PPP1R14B-AS1 was found to be upregulated and also overexpressed in 10 other types of cancers. In addition, PPP1R14B-AS1 overexpression was associated with poor overall prognosis in eight cancers. Furthermore, PPPAR14B-AS1 upregulation was positively associated with worsening development of liver and LUAD cancers and related to poor disease-free survival. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses suggested that PPP1R14B-AS1 strongly participated in regulating cell aerobic respiration processes, such as mitochondrial electron respiration chain and NADH dehydrogenation processes. Cell cytoplasmic and nuclear RNA purification assessment results revealed that PPP1R14B-AS existed in the cell nucleus and cytoplasm. The knockdown of PPP1R14B-AS1 in HepG2 and A549 cells using PPP1R14B-AS1-specific siRNAs decreased mitochondrial respiration as demonstrated by the reduction in basal respiration and ATP production. Moreover, PPP1R14B-AS1 downregulation did not obviously affect cell glycolysis ability. Finally, PPP1R14B-AS1 inhibition inhibited HepG2 and A549 cell migration and proliferation. In summary, our study found for the first time that PPP1R14B-AS1 could be a potential biomarker for cancer diagnosis and that PPP1R14B-AS1 inhibition could be a potentially effective therapy.
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Affiliation(s)
- Yibin Yang
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Yuan Zhang
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Lihong Miao
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
| | - Weijie Liao
- School of Life Sciences, Tsinghua University, Beijing, China
| | - Weifang Liao
- School of Biology and Pharmaceutical Engineering, Wuhan Polytechnic University, Wuhan, China
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95
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NEAT1 and Paraspeckles in Cancer Development and Chemoresistance. Noncoding RNA 2020; 6:ncrna6040043. [PMID: 33143162 PMCID: PMC7712271 DOI: 10.3390/ncrna6040043] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 09/21/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Non-coding RNA were previously thought to be biologically useless molecules arising from simple transcriptional noise. These are now known to be an integral part of cellular biology and pathology. The wide range of RNA molecules have a diverse range of structures, functions, and mechanisms of action. However, structural long non-coding RNAs (lncRNAs) are a particular class of ncRNA that are proving themselves more and more important in cellular biology, as the exact structures that such RNAs form and stabilise become more understood. Nuclear Enriched Abundant Transcript 1 (NEAT1) is a specific structural RNA emerging as a critical component in the progress and development of cancer. NEAT1 forms part of multiple biological pathways, acting through a diverse group of mechanisms. The most important of these is the formation of the paraspeckle, through which it can influence the stability of a tumour to develop resistance to drugs. This review will thus cover the range of effects by which NEAT1 interacts with cancer progression in order to describe the various roles of NEAT1 in chemoresistance, as well as to identify drug targets that protein research alone could not provide.
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Cross-talk between the ER pathway and the lncRNA MAFG-AS1/miR-339-5p/ CDK2 axis promotes progression of ER+ breast cancer and confers tamoxifen resistance. Aging (Albany NY) 2020; 12:20658-20683. [PMID: 33098638 PMCID: PMC7655217 DOI: 10.18632/aging.103966] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/07/2020] [Indexed: 12/12/2022]
Abstract
Hormone receptor-positive breast cancer accounts for around 75% of breast cancers. The estrogen receptor pathway promotes tumor progression and endocrine resistance. Recently, the cross-talk between the ER signaling pathway and cell cycle regulation has been identified. It is necessary to determine the underlying molecular mechanisms involved in the ER signaling pathway and find new target genes for prognosis and drug resistance in ER+ breast cancer. In this study, lncRNA MAFG-AS1 was shown to be up-regulated and associated with poor prognosis in ER+ breast cancer. Functionally, down-regulation of MAFG-AS1 could inhibit cell proliferation and promote apoptosis. In addition, MAFG-AS1 which contained an estrogen-responsive element could promote CDK2 expression by sponging miR-339-5p. Subsequently, MAFG-AS1 and CDK2 were found to be up-regulated in tamoxifen-resistant MCF-7 cells. Cross-talk between the ER signaling pathway and cell cycle conducted by MAFG-AS1 and CDK2 could promote tamoxifen resistance. In conclusion, our study indicated that estrogen-responsive lncRNA MAFG-AS1 up-regulated CDK2 by sponging miR-339-5p, which promoted ER+ breast cancer proliferation. Cross-talk between the ER signaling pathway and cell cycle suggested that lncRNA MAFG-AS1 is a potential biomarker and therapeutic target in ER+ breast cancer. CDK2 inhibitors may be applied to endocrine resistance therapy.
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Huang J, Sachdeva M, Xu E, Robinson TJ, Luo L, Ma Y, Williams NT, Lopez O, Cervia LD, Yuan F, Qin X, Zhang D, Owzar K, Gokgoz N, Seto A, Okada T, Singer S, Andrulis IL, Wunder JS, Lazar AJ, Rubin BP, Pipho K, Mello SS, Giudice J, Kirsch DG. The Long Noncoding RNA NEAT1 Promotes Sarcoma Metastasis by Regulating RNA Splicing Pathways. Mol Cancer Res 2020; 18:1534-1544. [PMID: 32561656 PMCID: PMC7541426 DOI: 10.1158/1541-7786.mcr-19-1170] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 04/09/2020] [Accepted: 06/15/2020] [Indexed: 11/16/2022]
Abstract
Soft-tissue sarcomas (STS) are rare malignancies showing lineage differentiation toward diverse mesenchymal tissues. Half of all high-grade STSs develop lung metastasis with a median survival of 15 months. Here, we used a genetically engineered mouse model that mimics undifferentiated pleomorphic sarcoma (UPS) to study the molecular mechanisms driving metastasis. High-grade sarcomas were generated with Cre recombinase technology using mice with conditional mutations in Kras and Trp53 (KP) genes. After amputation of the limb bearing the primary tumor, mice were followed for the development of lung metastasis. Using RNA-sequencing of matched primary KP tumors and lung metastases, we found that the long noncoding RNA (lncRNA) Nuclear Enriched Abundant Transcript 1 (Neat1) is significantly upregulated in lung metastases. Furthermore, NEAT1 RNA ISH of human UPS showed that NEAT1 is upregulated within a subset of lung metastases compared with paired primary UPS. Remarkably, CRISPR/Cas9-mediated knockout of Neat1 suppressed the ability of KP tumor cells to colonize the lungs. To gain insight into the underlying mechanisms by which the lncRNA Neat1 promotes sarcoma metastasis, we pulled down Neat1 RNA and used mass spectrometry to identify interacting proteins. Interestingly, most Neat1 interacting proteins are involved in RNA splicing regulation. In particular, KH-Type Splicing Regulatory Protein (KHSRP) interacts with Neat1 and is associated with poor prognosis of human STS. Moreover, depletion of KHSRP suppressed the ability of KP tumor cells to colonize the lungs. Collectively, these results suggest that Neat1 and its interacting proteins, which regulate RNA splicing, are involved in mediating sarcoma metastasis. IMPLICATIONS: Understanding that lncRNA NEAT1 promotes sarcoma metastasis, at least in part, through interacting with the RNA splicing regulator KHSRP may translate into new therapeutic approaches for sarcoma.
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Affiliation(s)
- Jianguo Huang
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Mohit Sachdeva
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Eric Xu
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Timothy J Robinson
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Lixia Luo
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Yan Ma
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Nerissa T Williams
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina
| | - Omar Lopez
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
| | - Lisa D Cervia
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Fan Yuan
- Department of Biomedical Engineering, Duke University, Durham, North Carolina
| | - Xiaodi Qin
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Dadong Zhang
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
| | - Kouros Owzar
- Duke Cancer Institute, Duke University Medical Center, Durham, North Carolina
- Department of Biostatistics & Bioinformatics, Duke University, Durham, North Carolina
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Andrew Seto
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Tomoyo Okada
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel Singer
- Memorial Sloan Kettering Cancer Center, New York, New York
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Jay S Wunder
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- University of Toronto Musculoskeletal Oncology Unit, and Department of Surgery, University of Toronto, Toronto, Canada
| | - Alexander J Lazar
- Departments of Pathology, Genomic Medicine, and Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Brian P Rubin
- Robert J. Tomsich Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, Ohio
| | - Krista Pipho
- University of Rochester Medical Center, Rochester, New York
| | | | - Jimena Giudice
- Department of Cell Biology and Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
- McAllister Heart Institute, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina
| | - David G Kirsch
- Department of Radiation Oncology, Duke University Medical Center, Durham, North Carolina.
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina
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Wang Z, Li K, Huang W. Long non-coding RNA NEAT1-centric gene regulation. Cell Mol Life Sci 2020; 77:3769-3779. [PMID: 32219465 PMCID: PMC11104955 DOI: 10.1007/s00018-020-03503-0] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/02/2020] [Accepted: 03/09/2020] [Indexed: 12/28/2022]
Abstract
Nuclear paraspeckle assembly transcript 1 (NEAT1) is a long non-coding RNA that is widely expressed in a variety of mammalian cell types. An increasing number of studies have demonstrated that NEAT1 plays key roles in various biological and pathological processes; therefore, it is important to understand how its expression is regulated and how it regulates the expression of its target genes. Recently, we found that NEAT1 expression could be regulated by signal transducer and activator of transcription 3 and that altered NEAT1 expression epigenetically regulates downstream gene transcription during herpes simplex virus-1 infection and Alzheimer's disease, suggesting that NEAT1 acts as an important sensor and effector during stress and disease development. In this review, we summarize and discuss the molecules and regulatory patterns that control NEAT1 gene expression and the molecular mechanism via which NEAT1 regulates the expression of its target genes, providing novel insights into the central role of NEAT1 in gene regulation.
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Affiliation(s)
- Ziqiang Wang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China.
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China.
| | - Kun Li
- Department of Nuclear Medicine, Shandong Provincial Qianfoshan Hospital, The First Hospital Affiliated with Shandong First Medical University, Jinan, 250014, China
| | - Weiren Huang
- Department of Urology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, International Cancer Center, Shenzhen University School of Medicine, Shenzhen, 518039, China.
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Shenzhen, 518035, China.
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Zhao C, Mo L, Li C, Han S, Zhao W, Liu L. FOXN3 suppresses the growth and invasion of papillary thyroid cancer through the inactivation of Wnt/β-catenin pathway. Mol Cell Endocrinol 2020; 515:110925. [PMID: 32619584 DOI: 10.1016/j.mce.2020.110925] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/10/2020] [Accepted: 06/23/2020] [Indexed: 12/22/2022]
Abstract
Forkhead box N3 (FOXN3) is a subtype of FOX family that has been demonstrated to be implicated in several cancers. However, the role of FOXN3 in papillary thyroid carcinoma (PTC) and its mechanisms have not yet been investigated. Our results showed that FOXN3 was markedly down regulated in PTC tissues and cell lines. Overexpression of FOXN3 suppressed the proliferation, colony formation, migration, and invasion in PTC cells. Overexpression of FOXN3 also prevented EMT process in PTC cells, as shown by the increased E-cadherin expression level and decreased expression levels of N-cadherin and vimentin. In addition, overexpression of FOXN3 inhibited tumor growth of PTC in vivo. Furthermore, overexpression of FOXN3 caused significant decreases in expression levels of β-catenin, c-Myc, and cyclin D1. Additionally, activation of Wnt/β-catenin pathway reversed the effects of FOXN3 on PTC cells. In conclusion, these findings indicated that FOXN3 exerted a tumor suppressive activity in PTC, which was mediated by Wnt/β-catenin pathway.
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Affiliation(s)
- Chang'an Zhao
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China; Department of Pathology, School of Basic Medical Sciences Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Liping Mo
- Department of Pathology, School of Basic Medical Sciences Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Chao Li
- School of Public Health, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Shuiping Han
- Department of Pathology, School of Basic Medical Sciences Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Wenbo Zhao
- Department of Pathology, School of Basic Medical Sciences Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Lifeng Liu
- Department of Otolaryngology-Head and Neck Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China.
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Nie W, Wang S, He R, Xu Q, Wang P, Wu Y, Tian F, Yuan J, Zhu B, Chen G. A-to-I RNA editing in bacteria increases pathogenicity and tolerance to oxidative stress. PLoS Pathog 2020; 16:e1008740. [PMID: 32822429 PMCID: PMC7467310 DOI: 10.1371/journal.ppat.1008740] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2020] [Revised: 09/02/2020] [Accepted: 06/24/2020] [Indexed: 01/25/2023] Open
Abstract
Adenosine-to-inosine (A-to-I) RNA editing is an important posttranscriptional event in eukaryotes; however, many features remain largely unexplored in prokaryotes. This study focuses on a serine-to-proline recoding event (S128P) that originated in the mRNA of fliC, which encodes a flagellar filament protein; the editing event was observed in RNA-seq samples exposed to oxidative stress. Using Sanger sequencing, we show that the S128P editing event is induced by H2O2. To investigate the in vivo interaction between RNAs and TadA, which is the principal enzyme for A-to-I editing, genome-wide RNA immunoprecipitation–coupled high-throughput sequencing (iRIP-Seq) analysis was performed using HA-tagged TadA from Xanthomonas oryzae pv. oryzicola. We found that TadA can bind to the mRNA of fliC and the binding motif is identical to that previously reported by Bar-Yaacov and colleagues. This editing event increased motility and enhanced tolerance to oxidative stress due to changes in flagellar filament structure, which was modelled in 3D and measured by TEM. The change in filament structure due to the S128P mutant increased biofilm formation, which was measured by the 3D laser scanning confocal microscopy. RNA-seq revealed that a gene cluster that contributes to siderophore biosynthesis and Fe3+ uptake was upregulated in S128P compared with WT. Based on intracellular levels of reactive oxygen species and an oxidative stress survival assay, we found that this gene cluster can contribute to the reduction of the Fenton reaction and increases biofilm formation and bacterial virulence. This oxidative stress response was also confirmed in Pseudomonas putida. Overall, our work demonstrates that A-to-I RNA editing plays a role in bacterial pathogenicity and adaptation to oxidative stress. Adenosine-to-inosine (A-to-I) RNA editing is an important posttranscriptional event in eukaryotes that has only been recently documented in bacteria. In this study, we use multiple ‘omic’ approaches to show that A-to-I RNA editing can occur in fliC, a flagellar filament protein. We show that TadA, which encodes adenosine deaminase, can directly bind to mRNA of target genes through recognition of a GACG motif. This editing event changes a single amino acid residue from serine to proline in FliC, resulting in a structural change in the flagellar filament. This posttranscriptional editing event contributes to virulence and increases tolerance to oxidative stress by enhancing biofilm formation. Our results provide insight into a new mechanism that bacterial pathogens use to adapt to oxidative stress, which can also increase virulence.
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Affiliation(s)
- Wenhan Nie
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Sai Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui He
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, and SJTU-Yale Joint Center for Biostatistics and Data Science, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Peihong Wang
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yan Wu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Tian
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junhua Yuan
- Hefei National Laboratory for Physical Sciences at the Microscale and Department of Physics, University of Science and Technology of China, Hefei, Anhui, China
| | - Bo Zhu
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (BZ); (GC)
| | - Gongyou Chen
- Key Laboratory of Urban Agriculture by Ministry of Agriculture of China, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- * E-mail: (BZ); (GC)
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