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Bakulin A, Teyssier NB, Kampmann M, Khoroshkin M, Goodarzi H. pyPAGE: A framework for Addressing biases in gene-set enrichment analysis-A case study on Alzheimer's disease. PLoS Comput Biol 2024; 20:e1012346. [PMID: 39236079 PMCID: PMC11421795 DOI: 10.1371/journal.pcbi.1012346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/24/2024] [Accepted: 07/22/2024] [Indexed: 09/07/2024] Open
Abstract
Inferring the driving regulatory programs from comparative analysis of gene expression data is a cornerstone of systems biology. Many computational frameworks were developed to address this problem, including our iPAGE (information-theoretic Pathway Analysis of Gene Expression) toolset that uses information theory to detect non-random patterns of expression associated with given pathways or regulons. Our recent observations, however, indicate that existing approaches are susceptible to the technical biases that are inherent to most real world annotations. To address this, we have extended our information-theoretic framework to account for specific biases and artifacts in biological networks using the concept of conditional information. To showcase pyPAGE, we performed a comprehensive analysis of regulatory perturbations that underlie the molecular etiology of Alzheimer's disease (AD). pyPAGE successfully recapitulated several known AD-associated gene expression programs. We also discovered several additional regulons whose differential activity is significantly associated with AD. We further explored how these regulators relate to pathological processes in AD through cell-type specific analysis of single cell and spatial gene expression datasets. Our findings showcase the utility of pyPAGE as a precise and reliable biomarker discovery in complex diseases such as Alzheimer's disease.
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Affiliation(s)
- Artemy Bakulin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
| | - Noam B. Teyssier
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
| | - Martin Kampmann
- Institute for Neurodegenerative Diseases, University of California San Francisco, California, United States of America
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
| | - Matvei Khoroshkin
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, United States of America
- Department of Urology, University of California San Francisco, San Francisco, California, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California, United States of America
- Bakar Computational Health Sciences Institute, University of California San Francisco, San Francisco, California, United States of America
- Arc Institute, Palo Alto, California, United States of America
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Yu X, Bu C, Yang X, Jiang W, He X, Sun R, Guo H, Shang L, Ou C. Exosomal non-coding RNAs in colorectal cancer metastasis. Clin Chim Acta 2024; 556:117849. [PMID: 38417779 DOI: 10.1016/j.cca.2024.117849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 02/24/2024] [Accepted: 02/25/2024] [Indexed: 03/01/2024]
Abstract
Colorectal cancer (CRC) is a type of gastrointestinal cancer with high morbidity and mortality rates, and is often accompanied by distant metastases. Metastasis is a major cause of shortened survival time and poor treatment outcomes for patients with CRC. However, the molecular mechanisms underlying the metastasis of CRC remain unclear. Exosomes are a class of small extracellular vesicles that originate from almost all human cells and can transmit biological information (e.g., nucleic acids, lipids, proteins, and metabolites) from secretory cells to target recipient cells. Recent studies have revealed that non-coding RNAs (ncRNAs) can be released by exosomes into the tumour microenvironment or specific tissues, and play a pivotal role in tumorigenesis by regulating a series of key molecules or signalling pathways, particularly those involved in tumour metastasis. Exosomal ncRNAs have potential as novel therapeutic targets for CRC metastasis, and can also be used as liquid biopsy biomarkers because of their specificity and sensitivity. Therefore, further investigations into the biological function and clinical value of exosomal ncRNAs will be of great value for the prevention, early diagnosis, and treatment of CRC metastasis.
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Affiliation(s)
- Xiaoqian Yu
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Chiwen Bu
- Department of General Surgery, People's Hospital of Guanyun County, Lianyungang 222200, Jiangsu, China
| | - Xuejie Yang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Wenying Jiang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Ru Sun
- Department of Blood Transfusion, Affiliated Hospital of North Sichuan Medical College, Xichang 637000, Sichuan, China
| | - Hongbin Guo
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China
| | - Li Shang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan, China.
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3
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Li B, Yao B, Guo X, Wang Z, Xie W, Wu X, Wang F, Mei Y. c-Myc-induced long noncoding RNA MIRE cooperates with hnRNPK to stabilize ELF2 mRNA and promotes clear cell renal cell carcinogenesis. Cancer Gene Ther 2023; 30:1215-1226. [PMID: 37248433 DOI: 10.1038/s41417-023-00631-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 05/16/2023] [Accepted: 05/17/2023] [Indexed: 05/31/2023]
Abstract
Elevated expression of c-Myc is associated with a variety of human cancers including clear cell renal cell carcinoma (ccRCC). Increasing evidence suggests that long noncoding RNAs (lncRNAs) are an important class of molecules that regulate both tumor initiation and progression. Here, we report the lncRNA c-Myc-induced regulator of ELF2 (MIRE) as a transcriptional target of c-Myc. MIRE functions as an oncogenic molecule in ccRCC by increasing ELF2 expression. Mechanistically, MIRE promotes phase separation of the RNA binding protein hnRNPK and facilitates the binding of hnRNPK to ELF2 mRNA, thereby resulting in the stabilization of ELF2 mRNA. Interestingly, MIRE is also under transcriptional control by ELF2, establishing an ELF2-MIRE positive feedback loop. Together, these findings provide new insights into the mechanisms by which c-Myc promotes tumorigenesis. They also implicate MIRE as an important regulator of ccRCC carcinogenesis.
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Affiliation(s)
- Bingyan Li
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Bo Yao
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Xiaorui Guo
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Zhongyu Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
| | - Wei Xie
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China
- DeepBio Technology Ltd Co., 515 ShenNan Road, Shanghai, 201612, China
| | - Xianning Wu
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Fang Wang
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
| | - Yide Mei
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
- The CAS Key Laboratory of Innate Immunity and Chronic Disease, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, Anhui, China.
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4
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Rasmussen A, Okholm T, Knudsen M, Vang S, Dyrskjøt L, Hansen T, Pedersen J. Circular stable intronic RNAs possess distinct biological features and are deregulated in bladder cancer. NAR Cancer 2023; 5:zcad041. [PMID: 37554968 PMCID: PMC10405568 DOI: 10.1093/narcan/zcad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/02/2023] [Indexed: 08/10/2023] Open
Abstract
Until recently, intronic lariats were regarded as short-lasting splicing byproducts with no apparent function; however, increasing evidence of stable derivatives suggests regulatory roles. Yet little is known about their characteristics, functions, distribution, and expression in healthy and tumor tissue. Here, we profiled and characterized circular stable intronic sequence RNAs (sisRNAs) using total RNA-Seq data from bladder cancer (BC; n = 457, UROMOL cohort), healthy tissue (n = 46), and fractionated cell lines (n = 5). We found that the recently-discovered full-length intronic circles and the stable lariats formed distinct subclasses, with a surprisingly high intronic circle fraction in BC (∼45%) compared to healthy tissues (0-20%). The stable lariats and their host introns were characterized by small transcript sizes, highly conserved BP regions, enriched BP motifs, and localization in multiple cell fractions. Additionally, circular sisRNAs showed tissue-specific expression patterns. We found nine circular sisRNAs as differentially expressed across early-stage BC patients with different prognoses, and sisHNRNPK expression correlated with progression-free survival. In conclusion, we identify distinguishing biological features of circular sisRNAs and point to specific candidates (incl. sisHNRNPK, sisWDR13 and sisMBNL1) that were highly expressed, had evolutionary conserved sequences, or had clinical correlations, which may facilitate future studies and further insights into their functional roles.
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Affiliation(s)
- Asta M Rasmussen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
| | - Trine Line H Okholm
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology & Immunology, University of California, San Francisco, CA, USA
| | - Michael Knudsen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Søren Vang
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
| | - Thomas B Hansen
- Department of Molecular Biology and Genetics (MBG), Aarhus University, Aarhus 8000, Denmark
| | - Jakob S Pedersen
- Department of Clinical Medicine, Aarhus University, Aarhus 8000, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus N 8200, Denmark
- Bioinformatics Research Center (BiRC), Aarhus University, Aarhus 8000, Denmark
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5
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Zhang T, Leng Y, Duan M, Li Z, Ma Y, Huang C, Shi Q, Wang Y, Wang C, Liu D, Zhao X, Cheng S, Liu A, Zhou Y, Liu J, Pan Z, Zhang H, Shen L, Zhao H. LncRNA GAS5-hnRNPK axis inhibited ovarian cancer progression via inhibition of AKT signaling in ovarian cancer cells. Discov Oncol 2023; 14:157. [PMID: 37639158 PMCID: PMC10462600 DOI: 10.1007/s12672-023-00764-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 08/04/2023] [Indexed: 08/29/2023] Open
Abstract
BACKGROUND The incidence of ovarian cancer ranks third among gynecologic malignancies, but the mortality rate ranks first. METHODS The expression of GAS5 is low in ovarian cancer and is associated with the low survival of ovarian cancer patients according to public ovarian cancer databases. GAS5 overexpression inhibited ovarian malignancy by affecting the proliferation and migratory abilities in OVCAR3 and A2780 cells. GAS5 overexpression increased the rate of cell apoptosis, and the cells were blocked in the G1 phase as assessed by flow cytometry. RESULTS We found that hnRNPK was a potential target gene, which was regulated negatively by GAS5 based on RNA-pulldown and mass spectrometry analysis. Mechanistically, GAS5 affected the inhibition of the PI3K/AKT/mTOR pathways and bound the protein of hnRNPK, which influenced hnRNPK stability. Furthermore, rescue assays demonstrated hnRNPK was significantly involved in the progression of ovarian cancer. CONCLUSIONS Our study showed one of the mechanisms that GAS5 inhibited ovarian cancer metastasis by down-regulating hnRNPK expression, and GAS5 can be used to predict the prognosis of ovarian cancer patients.
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Affiliation(s)
- Te Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
- Biomedical Research Institute, Hubei University of Medicine, 442000, Shiyan, Hubei, China
| | - Yahui Leng
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Mengjing Duan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
- Hengdian Central Health Center, Huangpi District, Wuhan, Hubei, China
| | - Zihang Li
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yongqing Ma
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Chengyang Huang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Qin Shi
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yi Wang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Chengcheng Wang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Dandan Liu
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xuan Zhao
- The Second Clinical College, Xi'an Medical University, Xi'an, Shaanxi, China
| | - Shuang Cheng
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Ao Liu
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Yang Zhou
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Jiaqi Liu
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zhongqiu Pan
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Huimei Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China
| | - Li Shen
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China.
- Department of Clinical Oncology, Taihe Hospital, Hubei University of Medicine, 30 South Renmin Road, 442000, Shiyan, Hubei, China.
| | - Hongyan Zhao
- Hubei Key Laboratory of Embryonic Stem Cell Research, Hubei University of Medicine, Shiyan, Hubei, China.
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Chongqing Medical University, Chongqing, China.
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6
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Xu T, Li ZY, Liu M, Zhang SB, Ding HH, Wu JY, Lin SY, Liu J, Wei JY, Zhang XQ, Xin WJ. CircFhit Modulates GABAergic Synaptic Transmission via Regulating the Parental Gene Fhit Expression in the Spinal Dorsal Horn in a Rat Model of Neuropathic Pain. Neurosci Bull 2023; 39:947-961. [PMID: 36637791 PMCID: PMC10264304 DOI: 10.1007/s12264-022-01014-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 01/14/2023] Open
Abstract
Effective treatments for neuropathic pain are lacking due to our limited understanding of the mechanisms. The circRNAs are mainly enriched in the central nervous system. However, their function in various physiological and pathological conditions have yet to be determined. Here, we identified circFhit, an exon-intron circRNA expressed in GABAergic neurons, which reduced the inhibitory synaptic transmission in the spinal dorsal horn to mediate spared nerve injury-induced neuropathic pain. Moreover, we found that circFhit decreased the expression of GAD65 and induced hyperexcitation in NK1R+ neurons by promoting the expression of its parental gene Fhit in cis. Mechanistically, circFhit was directly bound to the intronic region of Fhit, and formed a circFhit/HNRNPK complex to promote Pol II phosphorylation and H2B monoubiquitination by recruiting CDK9 and RNF40 to the Fhit intron. In summary, we revealed that the exon-intron circFhit contributes to GABAergic neuron-mediated NK1R+ neuronal hyperexcitation and neuropathic pain via regulating Fhit in cis.
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Affiliation(s)
- Ting Xu
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China
| | - Zhen-Yu Li
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China
| | - Meng Liu
- Department of Anesthesia and Pain Medicine, Guangzhou First People's Hospital, Guangzhou, 510000, China
| | - Su-Bo Zhang
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
| | - Huan-Huan Ding
- Department of Physiology, Xuzhou Medical University, Xuzhou, 221004, China
| | - Jia-Yan Wu
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China
| | - Su-Yan Lin
- Department of Neurology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510000, China.
| | - Jun Liu
- Department of Neurology, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, 510000, China
| | - Jia-You Wei
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China
- Guangdong Provincial Engineering Research Center of Molecular Imaging, Guangdong Provincial Key Laboratory of Biomedical Imaging, and Department of Interventional Medicine, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai, 519000, China
| | - Xue-Qin Zhang
- The Affiliated Brain Hospital (Guangzhou Huiai Hospital) and School of Health Management, Guangzhou Medical University, Guangzhou, 510182, China.
| | - Wen-Jun Xin
- Neuroscience Program of Zhongshan School of Medicine and the Fifth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510080, China.
- Guangdong Province Key Laboratory of Brain Function and Disease, Sun Yat-sen University, Guangzhou, 510120, China.
- Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Guangzhou, 510000, China.
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Shao Y, Chan Y, Zhao R. SH3BP5-AS1/IGF2BP2/VDAC2 Axis Promotes the Apoptosis and Ferroptosis of Bladder Cancer Cells. Bladder Cancer 2023; 9:29-40. [PMID: 38994477 PMCID: PMC11181683 DOI: 10.3233/blc-211629] [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: 12/13/2021] [Accepted: 04/24/2022] [Indexed: 11/15/2022]
Abstract
BACKGROUND Bladder cancer (BC) is the most common malignant tumor in the urinary system with a high incidence, imposing a burden on the healthcare system worldwide. The participation of long non-coding RNAs (lncRNAs) in BC has attracted increasing attention. OBJECTIVE The aim in the current study was to explore the potential mechanism involving SH3BP5-AS1 in modulating BC cell proliferation, apoptosis and ferroptosis. METHODS qPCR and WB analysis measured the expression of RNAs and proteins. Functional and mechanism experiments were performed to investigate RNA impacts on cell proliferation, apoptosis and ferroptosis, and explore the correlation between RNA and protein expression. RESULTS SH3BP5-AS1 was down-regulated in BC cells, and SH3BP5-AS1 overexpression could inhibit BC cell proliferation but facilitate the cell apoptosis. SH3BP5-AS1 was also found to facilitate the ferroptosis of BC cells. Additionally, SH3BP5-AS1 was confirmed to recruit IGF2BP2 to regulate VDAC2 expression in the m6A-dependent manner. VDAC2 was detected to be down-regulated in BC cells and was verified to inhibit BC cell growth. Moreover, it was indicated from rescue assays that SH3BP5-AS1 could modulate VDAC2 expression to promote the ferroptosis of BC cells. CONCLUSION SH3BP5-AS1 could affect BC cell proliferation, apoptosis and ferroptosis via IGF2BP2/VDAC2, providing a novel molecular perspective for understanding BC.
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Affiliation(s)
- Yong Shao
- Department of Urology Third Ward, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Yunhui Chan
- Department of Urology Third Ward, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
| | - Rong Zhao
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, China
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Yu J, Chen X, Li J, Wang F. CERS6 antisense RNA 1 promotes colon cancer via upregulating mitochondrial calcium uniporter. Eur J Clin Invest 2023; 53:e13951. [PMID: 36628448 DOI: 10.1111/eci.13951] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/27/2022] [Accepted: 12/26/2022] [Indexed: 01/12/2023]
Abstract
BACKGROUND Colon cancer (CC) belongs to a common cancer of digestive system. Long non-coding RNAs (lncRNAs) are dysregulated in numerous cancers and affect their development. The function of lncRNA CERS6 antisense RNA 1 (CERS6-AS1) in CC remains unclear. MATERIALS AND METHODS CERS6-AS1 expression in colon adenocarcinoma tissues and CC cell lines was assessed by The Cancer Genome Atlas database and quantitative real-time polymerase chain reaction analysis. The function of CERS6-AS1 in CC was analysed by 5-ethynyl-2'-deoxyuridine, colony formation, flow cytometry, terminal deoxynucleotidyl transferase dUTP nick end labelling, wound healing, Transwell and immunofluorescence assays. Mechanistic analyses including RNA pull down, RNA-binding protein immunoprecipitation and luciferase reporter assay revealed the interaction between RNAs. RESULTS CERS6-AS1 expression was aberrantly upregulated in colon adenocarcinoma tissues and CC cell lines. CERS6-AS1 knockdown inhibited CC cell malignant phenotypes and in vivo tumour growth. CERS6-AS1 served as the competing endogenous RNA of microRNA-16-5p in CC, and microRNA-16-5p inhibition partly rescued the effects of CERS6-AS1 depletion on CC development. Mitochondrial calcium uniporter was targeted by microRNA-16-5p. Mitochondrial calcium uniporter upregulation completely remedied the influence of CERS6-AS1 silencing in CC progression. Moreover, CERS6-AS1 enhanced the stability of mitochondrial calcium uniporter messenger RNA via recruiting RNA-binding protein embryonic lethal abnormal vision like 1. CONCLUSION CERS6-AS1 promotes the development of CC via upregulating mitochondrial calcium uniporter expression.
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Affiliation(s)
- Juan Yu
- Endoscopic Diagnosis and Treatment Center, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Xiaoguang Chen
- Endoscopic Diagnosis and Treatment Center, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Li
- Endoscopic Diagnosis and Treatment Center, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
| | - Furang Wang
- Endoscopic Diagnosis and Treatment Center, Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, China
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9
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Chen QW, Cai QQ, Yang Y, Dong S, Liu YY, Chen ZY, Kang CL, Qi B, Dong YW, Wu W, Zhuang LP, Shen YH, Meng ZQ, Wu XZ. LncRNA BC promotes lung adenocarcinoma progression by modulating IMPAD1 alternative splicing. Clin Transl Med 2023; 13:e1129. [PMID: 36650118 PMCID: PMC9845120 DOI: 10.1002/ctm2.1129] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 11/14/2022] [Accepted: 11/17/2022] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND The therapeutic value of targeted therapies in patients with lung cancer is reduced when tumours acquire secondary resistance after an initial period of successful treatment. However, the molecular events behind the resistance to targeted therapies in lung cancer remain largely unknown. AIMS To discover the important role and mechanism of lncRNA BC in promoting tumor metastasis and influencing clinical prognosis of LUAD. MATERIALS & METHODS Microarrays were used to screen a comprehensive set of lncRNAs with differential expression profiles in lung cancer cells. The functional role and mechanism of lncRNA were further investigated by gain- and loss-of-function assays. RNA pull-down, protein assays, and mass spectrometry were used to identify proteins that interacted with lncRNA. TaqMan PCR was used to measure lncRNA in lung adenocarcinoma and adjacent nontumor tissues from 428 patients. The clinical significance of lncRNA identified was statistically confirmed in this cohort of patients. RESULTS In this study, we show that the long non-coding RNA BC009639 (BC) is involved in acquired resistance to EGFR-targeted therapies. Among the 235 long non-coding RNAs that were differentially expressed in lung cancer cell lines, with different metastatic potentials, BC promoted growth, invasion, metastasis, and resistance to EGFR-tyrosine kinase inhibitors (EGFR-TKIs), both in vitro and in vivo. BC was highly expressed in 428 patients with lung adenocarcinoma (LUAD) and high BC expression correlated with reduced efficacy of EGFR-TKI therapy. To uncover the molecular mechanism of BC-mediated EGFR-TKI resistance in lung cancer, we screened and identified nucleolin and hnRNPK that interact with BC. BC formed the splicing complex with nucleolin and hnRNPK to facilitate the production of a non-protein-coding inositol monophosphatase domain containing 1 (IMPAD1) splice variant, instead of the protein-coding variant. The BC-mediated alternative splicing (AS) of IMPAD1 resulted in the induction of the epithelial-mesenchymal transition and resistance to EGFR-TKI in lung cancer. High BC expression correlated with clinical progress and poor survival among 402 patients with LUAD. DISSCUSSION Through alternative splicing, BC boosted the non-coding IMPAD1-203 transcript variant while suppressing the IMPAD1-201 variant. In order to control the processing of pre-mRNA, BC not only attracted RNA binding proteins (NCL, IGF2BP1) or splicing factors (hnRNPK), but also controlled the formation of the splicing-regulator complex by creating RNA-RNA-duplexes. CONCLUSION Our results reveal an important role for BC in mediating resistance to EGFR-targeted therapy in LUAD through IMPAD1 AS and in implication for the targeted therapy resistance.
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Affiliation(s)
- Qi Wen Chen
- Department of Integrative OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Qian Qian Cai
- Shanghai Key Laboratory of Molecular ImagingShanghai University of Medicine and Health SciencesShanghaiP. R. China
| | - Ying Yang
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
| | - Shu Dong
- Department of Integrative OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Yuan Yuan Liu
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
| | - Zhong Yi Chen
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
| | - Chun Lan Kang
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
| | - Bing Qi
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
| | - Yi Wei Dong
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
| | - Wei Wu
- Department of PathologyShanghai Pulmonary Hospital, Tongji University School of MedicineShanghaiP. R. China
| | - Li Ping Zhuang
- Department of Integrative OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Ye Hua Shen
- Department of Integrative OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Zhi Qiang Meng
- Department of Integrative OncologyFudan University Shanghai Cancer CenterShanghaiP. R. China
- Department of Oncology, Shanghai Medical CollegeFudan UniversityShanghaiP. R. China
| | - Xing Zhong Wu
- Key Laboratory of Glycoconjugate Research Ministry of Public Health, Department of Biochemistry and Molecular Biology, School of Basic Medical SciencesFudan UniversityShanghaiP. R. China
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10
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Manzoor Y, Hasan M, Zafar A, Dilshad M, Ahmed MM, Tariq T, Hassan SG, Hassan SG, Shaheen A, Caprioli G, Shu X. Incubating Green Synthesized Iron Oxide Nanorods for Proteomics-Derived Motif Exploration: A Fusion to Deep Learning Oncogenesis. ACS OMEGA 2022; 7:47996-48006. [PMID: 36591177 PMCID: PMC9798745 DOI: 10.1021/acsomega.2c05948] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
The nanotechnological arena has revolutionized the diagnostic efficacies by investigating the protein corona. This displays provoking proficiencies in determining biomarkers and diagnostic fingerprints for early detection and advanced therapeutics. The green synthesized iron oxide nanoparticles were prepared via Withania coagulans and were well characterized using UV-visible spectroscopy, X-ray diffraction analysis, Fourier transform infrared spectroscopy, and nano-LC mass spectrophotometry. Iron oxides were rod-shaped with an average size of 17.32 nm and have crystalline properties. The as-synthesized nanotool mediated firm nano biointeraction with the proteins in treatment with nine different cancers. The resultant of the proteome series was filtered oddly that highlighted the variant proteins within the differentially expressed proteins on behalf of nano-bioinformatics. Further magnification focused on S13_N, RS15, RAB, and 14_3_3 domains and few abundant motifs that aid scanning biomarkers. The entire set of variant proteins contracting to common proteins elucidates the underlining mechanical proteins that are marginally assessed using the robotic nanotechnology. Additionally, the iron rods indirectly possess a prognostic effect in manipulating expression of proteins through a smarter route. Thereby, such biologically designed nanotools provide a dual approach for medical studies.
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Affiliation(s)
- Yasmeen Manzoor
- Department
of Biotechnology, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Murtaza Hasan
- Department
of Biotechnology, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
- College of
Chemistry and Chemical Engineering, Zhongkai
Agriculture University and Engineering Guangzhou, Guangzhou 510225, PR China
| | - Ayesha Zafar
- Department
of Biotechnology, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
- Department
of Biomedical Engineering, College of Future Technology, Peking University, Beijing 510225, PR China
| | - Momina Dilshad
- Department
of Biotechnology, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Muhammad Mahmood Ahmed
- Department
of Bioinformatics, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Tuba Tariq
- Department
of Biotechnology, The Institute of Biochemistry, Biotechnology and
Bioinformatics, The Islamia University of
Bahawalpur, Bahawalpur 63100, Pakistan
| | - Shahzad Gul Hassan
- National
Institute of Cardiovascular Diseases (NICVD) Cantonment, Karachi 75510, Pakistan
| | - Shahbaz Gul Hassan
- College
of Information Science and Engineering, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Aqeela Shaheen
- Deaprtment
of Chemistry, Govt, Sadiq College Women
University, Bahawalpur 63100, Pakistan
| | - Giovanni Caprioli
- Chemistry
Interdisciplinary Project (CHip), School of Pharmacy, University of Camerino, Via Madonna delle Carceri, Camerino 62032, Italy
| | - Xugang Shu
- College of
Chemistry and Chemical Engineering, Zhongkai
Agriculture University and Engineering Guangzhou, Guangzhou 510225, PR China
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11
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hnRNP K Degrades Viral Nucleocapsid Protein and Induces Type I IFN Production to Inhibit Porcine Epidemic Diarrhea Virus Replication. J Virol 2022; 96:e0155522. [PMID: 36317879 PMCID: PMC9682996 DOI: 10.1128/jvi.01555-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a re-emerging enteric coronavirus currently spreading in several nations and inflicting substantial financial damages on the swine industry. The currently available coronavirus vaccines do not provide adequate protection against the newly emerging viral strains. It is essential to study the relationship between host antiviral factors and the virus and to investigate the mechanisms underlying host immune response against PEDV infection. This study shows that heterogeneous nuclear ribonucleoprotein K (hnRNP K), the host protein determined by the transcription factor KLF15, inhibits the replication of PEDV by degrading the nucleocapsid (N) protein of PEDV in accordance with selective autophagy. hnRNP K was found to be capable of recruiting the E3 ubiquitin ligase, MARCH8, aiming to ubiquitinate N protein. Then, it was found that the ubiquitinated N protein could be delivered into autolysosomes for degradation by the cargo receptor NDP52, thereby inhibiting PEDV proliferation. Moreover, based on the enhanced MyD88 expression, we found that hnRNP K activated the interferon 1 (IFN-1) signaling pathway. Overall, the data obtained revealed a new mechanism of hnRNP K-mediated virus restriction wherein hnRNP K suppressed PEDV replication by degradation of viral N protein using the autophagic degradation pathway and by induction of IFN-1 production based on upregulation of MyD88 expression. IMPORTANCE The spread of the highly virulent PEDV in many countries is still leading to several epidemic and endemic outbreaks. To elucidate effective antiviral mechanisms, it is important to study the relationship between host antiviral factors and the virus and to investigate the mechanisms underlying host immune response against PEDV infection. In the work, we detected hnRNP K as a new host restriction factor which can hinder PEDV replication through degrading the nucleocapsid protein based on E3 ubiquitin ligase MARCH8 and the cargo receptor NDP52. In addition, via the upregulation of MyD88 expression, hnRNP K could also activate the interferon (IFN) signaling pathway. This study describes a previously unknown antiviral function of hnRNP K and offers a new vision toward host antiviral factors that regulate innate immune response as well as a protein degradation pathway against PEDV infection.
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12
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LINC00472 inhibits cell migration by enhancing intercellular adhesion and regulates H3K27ac level via interacting with P300 in renal clear cell carcinoma. Cell Death Dis 2022; 8:454. [PMID: 36371410 PMCID: PMC9653443 DOI: 10.1038/s41420-022-01243-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/21/2022] [Accepted: 10/26/2022] [Indexed: 11/14/2022]
Abstract
Renal clear cell carcinoma (RCCC) is the most common type of renal cell carcinoma, which is also difficult to diagnose and easy to metastasize. Currently, there is still a lack of effective clinical diagnostic indicators and treatment targets. This study aims to find effective diagnostic markers and therapeutic targets from the perspective of noncoding RNA. In this study, we found that the expression of Long noncoding RNA LINC00472 was significantly decreased in RCCC and showed a downward trend with the progression of cancer stage. Patients with low LINC00472 expression have poor prognosis. Inhibition of LINC00472 significantly increased cell proliferation and migration, while overexpression of LINC00472 obviously inhibited cell proliferation and enhanced intercellular adhesion. Transcriptome sequencing analysis demonstrated that LINC00472 was highly correlated with extracellular matrix and cell metastasis-related pathways, and the consistent results were obtained by The Cancer Genome Atlas (TCGA) data analysis. Additionally, we discovered that the integrin family protein ITGB8 is a potential target gene of LINC00472. Mechanistically, we found that the change of LINC00472 affected the acetylation level of H3K27 site in cells, and we speculate that this effect is likely to be generated through the interaction with acetyltransferase P300. In conclusion, LINC00472 has an important impact on the proliferation and metastasis of renal clear cells, and probably participate in the regulation of histone modification, and it may be used as a potential diagnostic marker of RCCC.
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13
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Cui M, Liu Y, Cheng L, Li T, Deng Y, Liu D. Research progress on anti-ovarian cancer mechanism of miRNA regulating tumor microenvironment. Front Immunol 2022; 13:1050917. [DOI: 10.3389/fimmu.2022.1050917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Ovarian cancer is the most deadly malignancy among women, but its complex pathogenesis is unknown. Most patients with ovarian cancer have a poor prognosis due to high recurrence rates and chemotherapy resistance as well as the lack of effective early diagnostic methods. The tumor microenvironment mainly includes extracellular matrix, CAFs, tumor angiogenesis and immune-associated cells. The interaction between tumor cells and TME plays a key role in tumorigenesis, progression, metastasis and treatment, affecting tumor progression. Therefore, it is significant to find new tumor biomarkers and therapeutic targets. MicroRNAs are non-coding RNAs that post-transcriptionally regulate the expression of target genes and affect a variety of biological processes. Studies have shown that miRNAs regulate tumor development by affecting TME. In this review, we summarize the mechanisms by which miRNAs affect ovarian cancer by regulating TME and highlight the key role of miRNAs in TME, which provides new targets and theoretical basis for ovarian cancer treatment.
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14
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Wang JX, Zhao X, Xu SQ. Screening Key lncRNAs of Ankylosing Spondylitis Using Bioinformatics Analysis. J Inflamm Res 2022; 15:6087-6096. [DOI: 10.2147/jir.s387258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022] Open
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15
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Liu P, Fan B, Othmane B, Hu J, Li H, Cui Y, Ou Z, Chen J, Zu X. m 6A-induced lncDBET promotes the malignant progression of bladder cancer through FABP5-mediated lipid metabolism. Am J Cancer Res 2022; 12:6291-6307. [PMID: 36168624 PMCID: PMC9475447 DOI: 10.7150/thno.71456] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/13/2022] [Indexed: 12/23/2022] Open
Abstract
The limited effect of adjuvant therapy for advanced bladder cancer (BCa) leads to a poor prognosis. Increasing evidence has shown that RNA N6-methyladenosine (m6A) modification plays important functional roles in tumorigenesis. Nevertheless, the role and mechanism of m6A-modified noncoding RNAs (ncRNAs) in BCa remain largely unknown. Methods: RT-PCR, western blotting and ONCOMINE dataset were used to determine the dominant m6A-related enzyme in BCa. M6A-lncRNA epitranscriptomic microarray was used to screen candidate targets of METTL14. RT-PCR, MeRIP and TCGA dataset were carried out to confirm the downstream target of METTL14. CHIRP/MS was conducted to identify the candidate proteins binding to lncDBET. RT-PCR, western blotting, RIP and KEGG analysis were used to confirm the target of lncDBET. The levels of METTL14, lncDBET and FABP5 were tested in vitro and in vivo. CCK-8, EdU, transwell and flow cytometry assays were performed to determine the oncogenic function of METTL14, lncDBET and FABP5, and their regulatory networks. Results: We identified that the m6A level of total RNA was elevated and that METTL14 was the dominant m6A-related enzyme in BCa. m6A modification mediated by METTL14 promoted the malignant progression of BCa by promoting the expression of lncDBET. Upregulated lncDBET activated the PPAR signalling pathway to promote the lipid metabolism of cancer cells through direct interaction with FABP5, thus promoting the malignant progression of BCa in vitro and in vivo. Conclusions: Our study establishes METTL14/lncDBET/FABP5 as a critical oncogenic axis in BCa.
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Affiliation(s)
- Peihua Liu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Benyi Fan
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Belaydi Othmane
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Jiao Hu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Huihuang Li
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Yu Cui
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Zhenyu Ou
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Jinbo Chen
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
| | - Xiongbing Zu
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan 410008, PR China
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16
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The Long Noncoding RNA MEG3 Retains Epithelial-Mesenchymal Transition by Sponging miR-146b-5p to Regulate SLFN5 Expression in Breast Cancer Cells. J Immunol Res 2022; 2022:1824166. [PMID: 36033389 PMCID: PMC9411926 DOI: 10.1155/2022/1824166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022] Open
Abstract
More and more studies have shown that long noncoding RNAs (lncRNAs) play essential roles in malignant tumors. The lncRNA MEG3 serves as a crucial molecule in breast cancer development, but the specific molecular mechanism needs to be further explored. We previously reported that Schlafen family member 5 (SLFN5) inhibits breast cancer malignant development by regulating epithelial-mesenchymal transition (EMT), invasion, and proliferation/apoptosis. Herein, we demonstrated that MEG3 was downregulated in pan-cancers and correlated with SLFN5 expression positively in breast cancer by bioinformatics analysis of TCGA and UCSC Xena data. Intervention with MEG3 positively affected SLFN5 expression in breast cancer cells. MEG3 repressed EMT and migration/invasion, similar to our previously reported functions of SLFN5 in breast cancer. Through bioinformatics analysis of starBase and LncBase data, 12 miRNAs were found to regulate both SLFN5 and MEG3, in which miR-146b-5p was confirmed to be regulated by MEG3 using MEG3 siRNA and overexpression method. MiR-146b-5p could bind to both SLFN5 3′UTR and MEG3, and inhibit their expression in a competing endogenous RNA mechanism, assayed by luciferase reporter and RNA pull down methods. Therefore, we conclude that MEG3 positively modulates SLFN5 expression by sponging miR-146b-5p and inhibits breast cancer development.
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17
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LncRNA-Profile-Based Screening of Extracellular Vesicles Released from Brain Endothelial Cells after Oxygen–Glucose Deprivation. Brain Sci 2022; 12:brainsci12081027. [PMID: 36009090 PMCID: PMC9405926 DOI: 10.3390/brainsci12081027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/23/2022] [Accepted: 07/27/2022] [Indexed: 01/27/2023] Open
Abstract
Brain microvascular endothelial cells (BMECs) linked by tight junctions play important roles in cerebral ischemia. Intercellular signaling via extracellular vesicles (EVs) is an underappreciated mode of cell–cell crosstalk. This study aims to explore the potential function of long noncoding RNAs (lncRNAs) in BMECs’ secreted EVs. We subjected primary human and rat BMECs to oxygen and glucose deprivation (OGD). EVs were enriched for RNA sequencing. A comparison of the sequencing results revealed 146 upregulated lncRNAs and 331 downregulated lncRNAs in human cells and 1215 upregulated lncRNAs and 1200 downregulated lncRNAs in rat cells. Next, we analyzed the genes that were coexpressed with the differentially expressed (DE) lncRNAs on chromosomes and performed Gene Ontology (GO) and signaling pathway enrichment analyses. The results showed that the lncRNAs may play roles in apoptosis, the TNF signaling pathway, and leukocyte transendothelial migration. Next, three conserved lncRNAs between humans and rats were analyzed and confirmed using PCR. The binding proteins of these three lncRNAs in human astrocytes were identified via RNA pulldown and mass spectrometry. These proteins could regulate mRNA stability and translation. Additionally, the lentivirus was used to upregulate them in human microglial HMC3 cells. The results showed NR_002323.2 induced microglial M1 activation. Therefore, these results suggest that BMECs’ EVs carry the lncRNAs, which may regulate gliocyte function after cerebral ischemia.
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18
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D’Souza MH, Mrozowich T, Badmalia MD, Geeraert M, Frederickson A, Henrickson A, Demeler B, Wolfinger M, Patel T. Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res 2022; 50:5881-5898. [PMID: 35639511 PMCID: PMC9177966 DOI: 10.1093/nar/gkac414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.
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Affiliation(s)
- Michael H D’Souza
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Mitchell Geeraert
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
- NorthWest Biophysics Consortium, University of Lethbridge, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, Währingerstrasse 29, 1090 Vienna, Austria
- Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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Zhou Z, Ren X, Zheng L, Li A, Zhou W. LncRNA NEAT1 stabilized Wnt3a via U2AF2 and activated Wnt/β-catenin pathway to alleviate ischemia stroke induced injury. Brain Res 2022; 1788:147921. [PMID: 35452660 DOI: 10.1016/j.brainres.2022.147921] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 04/08/2022] [Accepted: 04/15/2022] [Indexed: 11/26/2022]
Abstract
BACKGROUND Ischaemic stroke is the leading cause of mortality and disability in the world. LncRNA NEAT1 has been shown to play an important role in ischaemic injury, but the molecular mechanism remains unclear. METHODS qRT-PCR was used to determine the expression of lncRNA NEAT1 in OGD/R-induced BV-2 cells. Cell viability was assessed by an MTT assay, and cell apoptosis was assessed by flow cytometry. The expression of related proteins was evaluated by Western blotting and ELISA. The interactions among lncRNA NEAT1, U2AF2 and Wnt3a mRNA was demonstrated by RIP and RNA pulldown assays. XAV-939 was used as an inhibitor of the Wnt/β-catenin pathway. RESULTS LncRNA NEAT1 was found to be downregulated in OGD/R-induced BV-2 cells. Overexpression of lncRNA NEAT1 protected BV-2 cells against OGD/R-induced injury. LncRNA NEAT1 enhanced the stability of Wnt3a mRNA via U2AF2. Knockdown of Wnt3a or blockade of the Wnt/β-catenin pathway rescued the effect of lncRNA NEAT1. CONCLUSIONS LncRNA NEAT1 protected cells against OGD/R-induced apoptosis and the inflammatory response by activating the Wnt/β-catenin pathway through upregulation of Wnt3a in a U2AF2-dependent manner. LncRNA NEAT1 could be a promising therapeutic candidate for ischaemic stroke treatment in the future.
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Affiliation(s)
- Zhiwen Zhou
- Departments of Neurology, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha 410016, Hunan Province, PR China
| | - Xiang Ren
- Departments of Neurology, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha 410016, Hunan Province, PR China
| | - Lijun Zheng
- Departments of Neurology, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha 410016, Hunan Province, PR China
| | - Aiping Li
- Departments of Neurology, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha 410016, Hunan Province, PR China
| | - Wensheng Zhou
- Departments of Neurology, Hunan Provincial People's Hospital, The First-Affiliated Hospital of Hunan Normal University, Changsha 410016, Hunan Province, PR China.
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20
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Deletion of Hnrnpk Gene Causes Infertility in Male Mice by Disrupting Spermatogenesis. Cells 2022; 11:cells11081277. [PMID: 35455958 PMCID: PMC9028439 DOI: 10.3390/cells11081277] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/03/2022] [Accepted: 04/07/2022] [Indexed: 02/07/2023] Open
Abstract
HnRNPK is a heterogeneous nuclear ribonucleoprotein (hnRNP) that has been firmly implicated in transcriptional and post-transcriptional regulation. However, the molecular mechanisms by which hnRNPK orchestrates transcriptional or post-transcriptional regulation are not well understood due to early embryonic lethality in homozygous knockout mice, especially in a tissue-specific context. Strikingly, in this study, we demonstrated that hnRNPK is strongly expressed in the mouse testis and mainly localizes to the nucleus in spermatogonia, spermatocytes, and round spermatids, suggesting an important role for hnRNPK in spermatogenesis. Using a male germ cell-specific hnRNPK-depleted mouse model, we found that it is critical for testicular development and male fertility. The initiation of meiosis of following spermatogenesis was not affected in Hnrnpk cKO mice, while most germ cells were arrested at the pachytene stage of the meiosis and no mature sperm were detected in epididymides. The further RNA-seq analysis of Hnrnpk cKO mice testis revealed that the deletion of hnRNPK disturbed the expression of genes involved in male reproductive development, among which the meiosis genes were significantly affected, and Hnrnpk cKO spermatocytes failed to complete the meiotic prophase. Together, these results identify hnRNPK as an essential regulator of spermatogenesis and male fertility.
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21
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Li T, Qin P, Chen B, Niu X, Wang Y, Niu Y, Wei C, Hou D, Ma H, Han R, Li H, Liu X, Kang X, Li Z. A novel 27-bp indel in the intron region of the YBX3 gene is associated with growth traits in chickens. Br Poult Sci 2022; 63:590-596. [PMID: 35382648 DOI: 10.1080/00071668.2022.2059340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. The DNA/RNA binding protein YBX3 is associated with gene transcription, DNA repair, and the progression of various diseases and is highly conserved from bacteria to humans.2. The following experiment found a 27-bp insertion/deletion polymorphism in the intron region of the YBX3 gene through resequencing. In cross-designed, F2 resource groups, the indel was significantly associated with broiler weight and body size at 0, 2, 4, 6, 8, 10 and 12 weeks of age and several other traits (semi evisceration weight (SEW), evisceration weight (EW), semi evisceration rate (SER), evisceration rate (ER), head weight (HW), claw weight (CLW), wing weight (DWW), gizzard weight (GW), pancreas weight (PW), chest muscle weight (CMW), leg weight (LW), leg muscle weight (LMW), shedding weight (SW), carcass weight (CW) and pectoral area (PA)) (P<0.05).3. The insertion-insertion (II) genotype was significantly associated with the greatest growth traits and carcass traits, whereas the values associated with the insertion-deletion (ID) genotype were the lowest in the F2 reciprocal cross chickens.4. The mutation sites were genotyped in 3611 individuals from 13 different chicken breeds and cross-designed F2 resource groups. The II genotype is the most important in commercial broilers, and the I allele frequency observed in these breeds was relatively high. However, there is still considerable potential in breeding dual-purpose chickens and commercial laying hens.5. The mRNA expression of the YBX3 gene in tissues from different breeds and developmental stages demonstrated that the 27-bp indel may affect the entire development process of poultry by affecting muscle development. These findings are beneficial for elucidating the function of the YBX3 gene and facilitating enhanced reproduction in the chicken industry.
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Affiliation(s)
- Tong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Panpan Qin
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Bingjie Chen
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xinran Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Yufang Niu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Chengjie Wei
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Dan Hou
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Haoxiang Ma
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.,Henan Innovative Engineering Research Centre of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.,Henan Innovative Engineering Research Centre of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450002, China.,Henan Innovative Engineering Research Centre of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou 450002, China
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22
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circDlgap4 Alleviates Cerebral Ischaemic Injury by Binding to AUF1 to Suppress Oxidative Stress and Neuroinflammation. Mol Neurobiol 2022; 59:3218-3232. [PMID: 35294732 DOI: 10.1007/s12035-022-02796-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 03/09/2022] [Indexed: 10/18/2022]
Abstract
Ischaemic stroke is one of the most common causes of mortality and morbidity.circDlgap4 has been implicated in ischemia/reperfusion injury through an unknown mechanism. Here, we studied the function of circDlgap4/AUF1 in ischaemic stroke and its underlying molecular mechanism. N2a cells and primary mouse cortical neurons were subjected to OGD to mimic neuronal injury during ischemia. BV-2 cells were treated with LPS to mimic neuroinflammation. The MTT assay was used to assess cell viability, while flow cytometry was used to measure cell apoptosis. qRT-PCR, western blotting, immunohistochemistry, and immunostaining were employed to determine the levels of circDlgap4, AUF1, NRF2/HO-1, proinflammatory cytokines, NF-κB pathway-related proteins, and IBA-1. RIP and RNA pulldown assays were employed to validate the interactions of circDlgap4/AUF1, AUF1/NRF2, and AUF1/cytokine mRNAs. mRNA degradation was used to determine the effects on mRNA stability. The tMCAO model was used as an in vivo model of ischaemic stroke. TCC staining and neurological scoring were performed to evaluate ischaemic injury. circDlgap4 was decreased following OGD and during tMCAO. circDlgap4 overexpression inhibited OGD-induced cell death and oxidative stress and LPS-induced increases in proinflammatory cytokines by increasing NRF2/HO-1. Knockdown of AUF1 blocked the effects of circDlgap4 overexpression. Mechanistically, RIP, RNA pulldown, and mRNA degradation assay results showed circDlgap4/AUF1/NRF2 mRNA formed a complex to stabilize NRF2 mRNA. Furthermore, AUF1 directly interacted with TNF-α, IL-1β, and COX-2 mRNAs, and circDlgap4/AUF1 binding promoted the degradation of these mRNAs. Finally, circDlgap4 ameliorated ischaemic injury in vivo. circDlgap4 alleviates ischaemic stroke injury by suppressing oxidative stress and neuroinflammation by binding to AUF1.
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23
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Miki Y, Iwabuchi E, Takagi K, Suzuki T, Sasano H, Yaegashi N, Ito K. Co-expression of nuclear heterogeneous nuclear ribonucleic protein K and estrogen receptor α in endometrial cancer. Pathol Res Pract 2022; 231:153795. [DOI: 10.1016/j.prp.2022.153795] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 11/16/2022]
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24
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Liu J, Li Z, Zhang T, Wang C, Chen W, Zhang D, Wang J. Long Noncoding RNA LINC00941 Promotes Cell Proliferation and Invasion by Interacting with hnRNPK in Oral Squamous Cell Carcinoma. Nutr Cancer 2022; 74:2983-2995. [PMID: 35037538 DOI: 10.1080/01635581.2022.2027473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Oral squamous cell carcinoma (OSCC) is a prevalent carcinoma of the head, neck and mouth. Recently studies involving the role of long noncoding RNAs (lncRNAs) that play key regulatory roles in altering gene expression has been reported in the context of promoting tumorigenesis. However, the functions of lncRNAs in the context of oral squamous cell carcinoma have not been extensively described. In this study, we report a never identified before lncRNA, LINC00941, which was highly expressed in OSCC tissues and cells. Expression of LINC00941 promoted cell proliferation, migration, invasion, and metastasis of OSCC cells In Vitro by inducing epithelial-mesenchymal transition (EMT) and activating the Wnt/β-catenin signaling cascade. In silico analyses revealed heterogeneous nuclear ribonucleoprotein K (hnRNPK) to be a strong positive regulator of LINC00941 activity. Experimental verification of this association revealed a direct interaction of LINC00941 and hnRNPK to induce cell growth and invasion by activating EMT in OSCC cells. Therefore, our study reports that LINC00941 promotes progression of OSCC by its interaction with hnRNPK, and it may present a promising strategy for diagnosis and treatment of OSCC.
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Affiliation(s)
- Jie Liu
- Department of Oral Surgery, Liaocheng People's Hospital, LiaoCheng, Shandong, China.,Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Zhenxing Li
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Ting Zhang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Chunhui Wang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Wen Chen
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Danfeng Zhang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Junyu Wang
- Department of Neurosurgery, Changzheng Hospital, Second Military Medical University, Shanghai, China
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25
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Puvvula PK, Buczkowski S, Moon AM. hnRNPK-derived cell-penetrating peptide inhibits cancer cell survival. Mol Ther Oncolytics 2021; 23:342-354. [PMID: 34820504 PMCID: PMC8586514 DOI: 10.1016/j.omto.2021.10.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/28/2021] [Accepted: 10/15/2021] [Indexed: 11/30/2022] Open
Abstract
hnRNPK is a multifunctional protein that plays an important role in cancer cell proliferation and metastasis via its RNA- and DNA-binding properties. Previously we showed that cell-penetrating peptides derived from the RGG RNA-binding domain of SAFA (hnRNPU) disrupt cancer cell proliferation and survival. Here we explore the efficacy of a peptide derived from the RGG domain of hnRNPK. This peptide acts in a dominant-negative manner on several hnRNPK functions to induce death of multiple types of cancer cells. The peptide phenocopies the effect of hnRNPK knockdown on its mRNA-stability targets such as KLF4 and EGR1 and alters the levels and locations of long non-coding RNAs (lncRNAs) and proteins required for nuclear and paraspeckle formation and function. The RGG-derived peptide also decreases euchromatin as evidenced by loss of active marks and polymerase II occupancy. Our findings reveal the potential therapeutic utility of the hnRNPK RGG-derived peptide in a range of cancers.
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Affiliation(s)
- Pavan Kumar Puvvula
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Corresponding author: Pavan Kumar Puvvula, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
| | - Stephanie Buczkowski
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
| | - Anne M. Moon
- Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
- The Mindich Child Health and Development Institute, Hess Center for Science and Medicine at Mount Sinai, New York, NY, USA
- Corresponding author: Anne M. Moon, MD, PhD, Department of Molecular and Functional Genomics, Weis Center for Research, Geisinger Clinic, Danville, PA, USA.
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26
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Yao J, Tu Y, Shen C, Zhou Q, Xiao H, Jia D, Sun Q. Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN. Cell Mol Life Sci 2021; 78:7617-7633. [PMID: 34689235 PMCID: PMC11073023 DOI: 10.1007/s00018-021-03992-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
The majority of lncRNAs and a small fraction of mRNAs localize in the cell nucleus to exert their functions. A SIRLOIN RNA motif was previously reported to drive its nuclear localization by the RNA-binding protein hnRNPK. However, the underlying mechanism remains unclear. Here, we report crystal structures of hnRNPK in complex with SIRLOIN, and with the nuclear import receptor (NIR) Impα1, respectively. The protein hnRNPK bound to SIRLOIN with multiple weak interactions, and interacted Impα1 using an independent high-affinity site. Forming a complex with hnRNPK and Impα1 was essential for the nuclear import and stress granule localization of SIRLOIN in semi-permeabilized cells. Nuclear import of SIRLOIN enhanced with increasing NIR concentrations, but its stress granule localization peaked at a low NIR concentration. Collectively, we propose a mechanism of SIRLOIN localization, in which NIRs functioned as drivers/regulators, and hnRNPK as an adaptor.
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Affiliation(s)
- Jialin Yao
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Yingfeng Tu
- Division of Neurology, Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Congcong Shen
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Qiao Zhou
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Hengyi Xiao
- Aging Research Lab, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Da Jia
- Division of Neurology, Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Qingxiang Sun
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China.
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27
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Li D, Zhang Z, Xia C, Niu C, Zhou W. Non-Coding RNAs in Glioma Microenvironment and Angiogenesis. Front Mol Neurosci 2021; 14:763610. [PMID: 34803608 PMCID: PMC8595242 DOI: 10.3389/fnmol.2021.763610] [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: 08/24/2021] [Accepted: 10/11/2021] [Indexed: 12/17/2022] Open
Abstract
Glioma, especially glioblastoma, is the most common and lethal brain tumor. In line with the complicated vascularization processes and the strong intratumoral heterogeneity, tumor-associated blood vessels in glioma are regulated by multiple types of cells through a variety of molecular mechanisms. Components of the tumor microenvironment, including tumor cells and tumor-associated stromata, produce various types of molecular mediators to regulate glioma angiogenesis. As critical regulatory molecules, non-coding RNAs (ncRNAs) inside cells or secreted to the tumor microenvironment play essential roles in glioma angiogenesis. In this review, we briefly summarize recent studies about the production, delivery, and functions of ncRNAs in the tumor microenvironment, as well as the molecular mechanisms underlying the regulation of angiogenesis by ncRNAs. We also discuss the ncRNA-based therapeutic strategies in the anti-angiogenic therapy for glioma treatment.
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Affiliation(s)
- Dongxue Li
- Intelligent Pathology Institute, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Zhe Zhang
- Basic Medical College, Qingdao University, Qingdao, China
| | - Chengyu Xia
- Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Chaoshi Niu
- Department of Neurosurgery, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Wenchao Zhou
- Intelligent Pathology Institute, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China.,Department of Pathology, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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28
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Chen Q, Li Y, Gao W, Chen L, Xu W, Zhu X. Exosome-Mediated Crosstalk Between Tumor and Tumor-Associated Macrophages. Front Mol Biosci 2021; 8:764222. [PMID: 34722637 PMCID: PMC8549832 DOI: 10.3389/fmolb.2021.764222] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/18/2022] Open
Abstract
Exosomes are nanosized vesicles, derived from the endolysosomal compartment of cells and can shuttle diverse biomolecules such as nucleic acids, proteins, lipids, amino acids, and metabolites, which can reflect their origin cells. Delivery of these cargoes to recipient cells enables exosomes to influence diverse cellular functions. As one of the most abundant immune cells in the tumor microenvironment, tumor-associated macrophages (TAMs) are educated by the tumor milieu, which is rich in cancer cells and stroma components, to exert functions such as the promotion of tumor growth, immunosuppression, angiogenesis, and cancer cell dissemination. Herein, we focus on exosomes-mediated intercellular communication between tumor cells and TAM in the tumor microenvironment, which may provide new targets for anti-tumor treatment. In this review, we highlight the most recent studies on the effect of tumor/macrophage-derived exosomes on macrophage/tumor function in different cancer types.
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Affiliation(s)
- Qi Chen
- Department of Oncology and Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,International Genome Center, Jiangsu University, Zhenjiang, China
| | - Yuefeng Li
- Affiliated People Hospital of Jiangsu University, Zhenjiang, China
| | - Wujiang Gao
- Department of Oncology and Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Lu Chen
- Department of Oncology and Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Wenlin Xu
- Department of Oncology and Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Xiaolan Zhu
- Department of Oncology and Central Laboratory, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China.,International Genome Center, Jiangsu University, Zhenjiang, China.,Reproduction Medicine Center, Fourth Affiliated Hospital of Jiangsu University, Zhenjiang, China
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29
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Huang Y, Chu P, Bao G. Silencing of Long Non-coding RNA TTN-AS1 Inhibits Hepatocellular Carcinoma Progression by the MicroRNA-134/ITGB1 Axis. Dig Dis Sci 2021; 66:3916-3928. [PMID: 33387127 DOI: 10.1007/s10620-020-06737-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022]
Abstract
BACKGROUND Hepatocellular carcinoma (HCC) causes considerable mortality worldwide. Long non-coding RNA (lncRNA) TTN-AS1 has been recently identified as an oncogene in several cancers, but its role in HCC and the molecules remain largely unknown. AIMS The study aims to probe the function of lncRNA TTN-AS1 in HCC progression and the molecules involved. METHODS Differentially expressed lncRNAs between HCC and the adjacent normal tissues were analyzed using a microarray. TTN-AS1 expression in HCC and normal tissues and cells was determined. Targeting relationships between TTN-AS1 and miR-134 and between miR-134 and ITGB1 were validated. Artificial up-regulation or down-regulation of TTN-AS1, miR-134 and ITGB1 was introduced in HCC cells to probe their effects on the biological behaviors of HCC cells. Xenograft tumors were induced in nude mice for in vivo experiments. RESULTS TTN-AS1 and ITGB1 were highly expressed, while miR-134 was poorly expressed in HCC tissues. TTN-AS1 enforced ITGB1 expression through sequestering miR-134. Silencing of TTN-AS1 or over-expression of miR-134 inhibited proliferation, invasion, migration, and resistance to death of Huh7 cells. Following miR-134 silencing, further down-regulation of ITGB1 suppressed the malignant behaviors of HUH7 cells. The similar results were reproduced in vivo. CONCLUSION The current study provided evidence that TTN-AS1 might promote HCC progression through sponging miR-134 and the following ITGB1 up-regulation. TTN-AS1 may serve as a potential target for HCC treatment.
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Affiliation(s)
- Yong Huang
- Department of Hepatobiliary Surgery, Zaozhuang Municipal Hospital, No 41, Longtou Road, Shizhong District, Zaozhuang, 277101, Shandong, People's Republic of China
| | - Peng Chu
- Department of Hepatobiliary Surgery, Zaozhuang Municipal Hospital, No 41, Longtou Road, Shizhong District, Zaozhuang, 277101, Shandong, People's Republic of China
| | - Guangjian Bao
- Department of Hepatobiliary Surgery, Zaozhuang Municipal Hospital, No 41, Longtou Road, Shizhong District, Zaozhuang, 277101, Shandong, People's Republic of China.
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30
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Zhang R, Wang J, Xiao Z, Zou C, An Q, Li H, Zhou X, Wu Z, Shi D, Deng Y, Yang S, Wei Y. The Expression Profiles of mRNAs and lncRNAs in Buffalo Muscle Stem Cells Driving Myogenic Differentiation. Front Genet 2021; 12:643497. [PMID: 34306003 PMCID: PMC8294193 DOI: 10.3389/fgene.2021.643497] [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: 12/18/2020] [Accepted: 05/25/2021] [Indexed: 11/13/2022] Open
Abstract
Buffalo breeding has become an important branch of the beef cattle industry. Hence, it is of great significance to study buffalo meat production and meat quality. However, the expression profiles of mRNA and long non-coding RNAs (lncRNA) molecules in muscle stem cells (MuSCs) development in buffalo have not been explored fully. We, therefore, performed mRNA and lncRNA expression profiling analysis during the proliferation and differentiation phases of MuSCs in buffalo. The results showed that there were 4,820 differentially expressed genes as well as 12,227 mRNAs and 1,352 lncRNAs. These genes were shown to be enriched in essential biological processes such as cell cycle, p53 signaling pathway, RNA transport and calcium signaling pathway. We also identified a number of functionally important genes, such as MCMC4, SERDINE1, ISLR, LOC102394806, and LOC102403551, and found that interference with MYLPF expression significantly inhibited the differentiation of MuSCs. In conclusion, our research revealed the characteristics of mRNA and lncRNA expression during the differentiation of buffalo MuSCs. This study can be used as an important reference for the study of RNA regulation during muscle development in buffalo.
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Affiliation(s)
- Ruimen Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Jinling Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Zhengzhong Xiao
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Chaoxia Zou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Qiang An
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Xiaoqing Zhou
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Zhuyue Wu
- The Animal Husbandry Research Institute of Guangxi Autonomous, Nanning, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Yanfei Deng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
| | - Sufang Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China.,International Zhuang Medical Hospital Affiliated to Guangxi University Chinese Medicine, Nanning, China
| | - Yingming Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Animal Reproduction Institute, Guangxi University, Nanning, China
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31
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Sun J, He D, Fu Y, Zhang R, Guo H, Wang Z, Wang Y, Gao T, Wei Y, Guo Y, Pang Q, Liu Q. A novel lncRNA ARST represses glioma progression by inhibiting ALDOA-mediated actin cytoskeleton integrity. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2021; 40:187. [PMID: 34099027 PMCID: PMC8183030 DOI: 10.1186/s13046-021-01977-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 05/09/2021] [Indexed: 12/03/2022]
Abstract
Background Glioma is one of the most aggressive malignant brain tumors that is characterized with inevitably infiltrative growth and poor prognosis. ARST is a novel lncRNA whose expression level is significantly decreased in the patients with glioblastoma multiforme. However, the exact mechanisms of ARST in gliomagenesis are largely unknown. Methods The expressions of ARST in the glioma samples and cell lines were analyzed by qRT-PCR. FISH was utilized to detect the distribution of ARST in the glioma cells. CCK-8, EdU and flow cytometry were used to examine cellular viability, proliferation and apoptosis. Transwell and wound-healing assays were performed to determine the migratory and invasive abilities of the cells. Intracranial tumorigenesis models were established to explore the roles of ARST in vivo. RNA pulldown assay was used to examine proteins that bound to ARST. The activities of key enzymes in the glycolysis and production of lactate acid were measured by colorimetry. In addition, RIP, Co-IP, western blot and immunofluorescence were used to investigate the interaction and regulation between ARST, F-actin, ALDOA and cofilin. Results In this study, we reported that ARST was downregulated in the gliomas. Overexpression of ARST in the glioma cells significantly suppressed various cellular vital abilities such as cell growth, proliferation, migration and invasion. The tumorigenic capacity of these cells in vivo was reduced as well. We further demonstrated that the tumor suppressive effects of ARST could be mediated by a direct binding to a glycolytic enzyme aldolase A (ALDOA), which together with cofilin, keeping the polymerization and depolymerization of actin filaments in an orderly dynamic equilibrium. Upregulation of ARST interrupted the interaction between ALDOA and actin cytoskeleton, which led to a rapid cofilin-dependent loss of F-actin stress fibers. Conclusions Taken together, it is concluded that ARST performs its function via a non-metabolic pathway associated with ALDOA, which otherwise modifies the morphology and invasive properties of the glioma cells. This has added new perspective to its role in tumorigenesis, thus providing potential target for glioma diagnosis, therapy, and prognosis. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-021-01977-9.
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Affiliation(s)
- Jun Sun
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Dong He
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yibing Fu
- Department of Obstetrics and Gynecology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Rui Zhang
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Hua Guo
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Zhaojuan Wang
- Department of Physiology, Shandong Medical College, Jinan, 250012, Shandong, People's Republic of China
| | - Yanan Wang
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.,Department of Pathology, Tai-an Municipal Hospital, Jinan, 250012, Shandong, People's Republic of China
| | - Taihong Gao
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yanbang Wei
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Yuji Guo
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China
| | - Qi Pang
- Department of Neurosurgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
| | - Qian Liu
- Department of Histology and Embryology, School of Basic Medical Science, Cheeloo College of Medicine, Shandong University, Jinan, 250012, Shandong, People's Republic of China.
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Lang C, Yin C, Lin K, Li Y, Yang Q, Wu Z, Du H, Ren D, Dai Y, Peng X. m 6 A modification of lncRNA PCAT6 promotes bone metastasis in prostate cancer through IGF2BP2-mediated IGF1R mRNA stabilization. Clin Transl Med 2021; 11:e426. [PMID: 34185427 PMCID: PMC8181202 DOI: 10.1002/ctm2.426] [Citation(s) in RCA: 82] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 04/28/2021] [Accepted: 05/04/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Bone metastasis is the leading cause of tumor-related death in prostate cancer (PCa) patients. Long noncoding RNAs (lncRNAs) have been well documented to be involved in the progression of multiple cancers. Nevertheless, the role of lncRNAs in PCa bone metastasis remains largely unclear. METHODS The expression of prostate cancer-associated transcripts was analyzed in published datasets and further verified in clinical samples and cell lines by RT-qPCR and in situ hybridization assays. Colony formation assay, MTT assay, cell cycle analysis, EdU assay, Transwell migration and invasion assays, wound healing assay, and in vivo experiments were carried out to investigate the function of prostate cancer-associated transcript 6 (PCAT6) in bone metastasis and tumor growth of PCa. Bioinformatic analysis, RNA pull-down, and RIP assays were conducted to identify the proteins binding to PCAT6 and the potential targets of PCAT6. The therapeutic potential of targeting PCAT6 by antisense oligonucleotides (ASO) was further explored in vivo. RESULTS PCAT6 was upregulated in PCa tissues with bone metastasis and increased PCAT6 expression predicted poor prognosis in PCa patients. Functional experiments found that PCAT6 knockdown significantly inhibited PCa cell invasion, migration, and proliferation in vitro, as well as bone metastasis and tumor growth in vivo. Mechanistically, METTL3-mediated m6 A modification contributed to PCAT6 upregulation in an IGF2BP2-dependent manner. Furthermore, PCAT6 upregulated IGF1R expression by enhancing IGF1R mRNA stability through the PCAT6/IGF2BP2/IGF1R RNA-protein three-dimensional complex. Importantly, PCAT6 inhibition by ASO in vivo showed therapeutic potential against bone metastasis in PCa. Finally, the clinical correlation of METTL3, IGF2BP2, IGF1R, and PCAT6 was further demonstrated in PCa tissues and cells. CONCLUSIONS Our study uncovers a novel molecular mechanism by which the m6 A-induced PCAT6/IGF2BP2/IGF1R axis promotes PCa bone metastasis and tumor growth, suggesting that PCAT6 may serve as a promising prognostic marker and therapeutic target against bone-metastatic PCa.
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MESH Headings
- Adenosine/analogs & derivatives
- Adenosine/chemistry
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Bone Neoplasms/genetics
- Bone Neoplasms/metabolism
- Bone Neoplasms/secondary
- Cell Cycle
- Cell Movement
- Cell Proliferation
- Gene Expression Regulation, Neoplastic
- Humans
- Male
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Prognosis
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- RNA Stability
- RNA, Long Noncoding/chemistry
- RNA, Long Noncoding/genetics
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/metabolism
- Survival Rate
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
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Affiliation(s)
- Chuandong Lang
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Chi Yin
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Kaiyuan Lin
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Yue Li
- Department of Experimental ResearchState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineSun Yat‐sen University Cancer CenterGuangzhouChina
| | - Qing Yang
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Zhengquan Wu
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Hong Du
- Department of Pathologythe First People's Hospital of Guangzhou CityGuangzhouChina
| | - Dong Ren
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Yuhu Dai
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
| | - Xinsheng Peng
- Department of Orthopaedic Surgerythe First Affiliated HospitalSun Yat‐Sen UniversityGuangzhouChina
- Guangdong Provincial Key Laboratory of Orthopedics and TraumatologyGuangzhouChina
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Podvin S, Jones A, Liu Q, Aulston B, Mosier C, Ames J, Winston C, Lietz CB, Jiang Z, O’Donoghue AJ, Ikezu T, Rissman RA, Yuan SH, Hook V. Mutant Presenilin 1 Dysregulates Exosomal Proteome Cargo Produced by Human-Induced Pluripotent Stem Cell Neurons. ACS OMEGA 2021; 6:13033-13056. [PMID: 34056454 PMCID: PMC8158845 DOI: 10.1021/acsomega.1c00660] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/16/2021] [Indexed: 05/28/2023]
Abstract
The accumulation and propagation of hyperphosphorylated tau (p-Tau) is a neuropathological hallmark occurring with neurodegeneration of Alzheimer's disease (AD). Extracellular vesicles, exosomes, have been shown to initiate tau propagation in the brain. Notably, exosomes from human-induced pluripotent stem cell (iPSC) neurons expressing the AD familial A246E mutant form of presenilin 1 (mPS1) are capable of inducing tau deposits in the mouse brain after in vivo injection. To gain insights into the exosome proteome cargo that participates in propagating tau pathology, this study conducted proteomic analysis of exosomes produced by human iPSC neurons expressing A246E mPS1. Significantly, mPS1 altered the profile of exosome cargo proteins to result in (1) proteins present only in mPS1 exosomes and not in controls, (2) the absence of proteins in the mPS1 exosomes which were present only in controls, and (3) shared proteins which were upregulated or downregulated in the mPS1 exosomes compared to controls. These results show that mPS1 dysregulates the proteome cargo of exosomes to result in the acquisition of proteins involved in the extracellular matrix and protease functions, deletion of proteins involved in RNA and protein translation systems along with proteasome and related functions, combined with the upregulation and downregulation of shared proteins, including the upregulation of amyloid precursor protein. Notably, mPS1 neuron-derived exosomes displayed altered profiles of protein phosphatases and kinases involved in regulating the status of p-tau. The dysregulation of exosome cargo proteins by mPS1 may be associated with the ability of mPS1 neuron-derived exosomes to propagate tau pathology.
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Affiliation(s)
- Sonia Podvin
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Alexander Jones
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Qing Liu
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Brent Aulston
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Charles Mosier
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Janneca Ames
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Charisse Winston
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Christopher B. Lietz
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Zhenze Jiang
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Anthony J. O’Donoghue
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
| | - Tsuneya Ikezu
- Department
of Pharmacology and Experimental Therapeutics, Department of Neurology,
Alzheimer’s Disease Research Center, Boston University, School of Medicine, Boston 02118, Massachusetts, United States
| | - Robert A. Rissman
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
- Veterans
Affairs San Diego Healthcare System,
La Jolla, San Diego 92161, California, United States
| | - Shauna H. Yuan
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
| | - Vivian Hook
- Skaggs
School of Pharmacy and Pharmaceutical Sciences, University of California San Diego,
La Jolla, San Diego 92093, California, United States
- Biomedical
Sciences Graduate Program, University of
California, San Diego, La Jolla, San Diego 92093, California, United States
- Department
of Neurosciences, School of Medicine, University
of California, San Diego, La Jolla, San Diego 92093, California, United States
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Razavi ZS, Asgarpour K, Mahjoubin-Tehran M, Rasouli S, Khan H, Shahrzad MK, Hamblin MR, Mirzaei H. Angiogenesis-related non-coding RNAs and gastrointestinal cancer. MOLECULAR THERAPY-ONCOLYTICS 2021; 21:220-241. [PMID: 34095461 PMCID: PMC8141508 DOI: 10.1016/j.omto.2021.04.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Gastrointestinal (GI) cancers are among the main reasons for cancer death globally. The deadliest types of GI cancer include colon, stomach, and liver cancers. Multiple lines of evidence have shown that angiogenesis has a key role in the growth and metastasis of all GI tumors. Abnormal angiogenesis also has a critical role in many non-malignant diseases. Therefore, angiogenesis is considered to be an important target for improved cancer treatment. Despite much research, the mechanisms governing angiogenesis are not completely understood. Recently, it has been shown that angiogenesis-related non-coding RNAs (ncRNAs) could affect the development of angiogenesis in cancer cells and tumors. The broad family of ncRNAs, which include long non-coding RNAs, microRNAs, and circular RNAs, are related to the development, promotion, and metastasis of GI cancers, especially in angiogenesis. This review discusses the role of ncRNAs in mediating angiogenesis in various types of GI cancers and looks forward to the introduction of mimetics and antagonists as possible therapeutic agents.
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Affiliation(s)
| | - Kasra Asgarpour
- Department of Medicine, University of Western Ontario, London, ON, Canada
| | - Maryam Mahjoubin-Tehran
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Susan Rasouli
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Mohammad Karim Shahrzad
- Department of Internal Medicine and Endocrinology, Shohadae Tajrish Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Michael R Hamblin
- Laser Research Centre, Faculty of Health Science, University of Johannesburg, Doornfontein 2028, South Africa
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
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Bu J, Guo R, Xu XZ, Luo Y, Liu JF. LncRNA SNHG16 promotes epithelial-mesenchymal transition by upregulating ITGA6 through miR-488 inhibition in osteosarcoma. J Bone Oncol 2021; 27:100348. [PMID: 33598394 PMCID: PMC7868993 DOI: 10.1016/j.jbo.2021.100348] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/12/2020] [Accepted: 01/05/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Osteosarcoma is a primary cause of cancer-associated death in children and adolescents worldwide. Long non-coding RNAs SNHG16 (lncRNA SNHG16) and integrin subunit-a 6 (ITGA6) are recently reported to be involved in the tumorigenesis of osteosarcoma by multiple mechanisms. However, the correlation between SNHG16 and ITGA6 in osteosarcoma remains undetermined. METHODS Expression of miR-488, SNHG16 and ITGA6, as well as epithelial-mesenchymal transition (EMT) associated markers in osteosarcoma tissues and cell lines were examined by qRT-PCR or Western blotting. Effects of miR-488, SNHG16 and ITGA6 on cell migration, invasion were evaluated by wound-healing assay and transwell assay. Bioinformatics analysis and dual-luciferase reported assays were applied to assess the interaction among miR-488, SNHG16 and ITGA6. RNA immunoprecipitation (RIP) was also used to verify SNHG16 and miR-488 interaction. Finally, animal study was used to detect the effect of SNHG16 on osteosarcoma in vivo. RESULTS SNHG16 and ITGA6 were significantly increased while miR-488 was decreased in osteosarcoma. ITGA6 was screened as a target gene of miR-488, and SNHG16 was sponged by miR-488 in osteosarcoma cells. MiR-488 overexpression and SNHG16 knockdown suppressed migration, invasion and EMT of osteosarcoma cells. Moreover, rescue assays proved that the influences of SNHG16 on osteosarcoma cells migration, invasion and EMT were dependent on miR-488 and ITGA6. In addition, the promotive effects of SNHG16 on osteosarcoma tumor growth and metastasis were further supported by xenograft tumor growth assay. CONCLUSION SNHG16 promoted migration, invasion and EMT of osteosarcoma by sponging miR-488 to release ITGA6.
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Affiliation(s)
- Jie Bu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| | - Ru Guo
- Department of Pediatrics, Maternal and Child Health Care Hospital of Hunan Province, Changsha 410008, Hunan Province, People's Republic of China
| | - Xue-Zheng Xu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| | - Yi Luo
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
| | - Jian-Fan Liu
- Department of Orthopaedics, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha 410013, Hunan Province, People's Republic of China
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36
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Lee WJ, Shin CH, Ji H, Jeong SD, Park MS, Won HH, Pandey PR, Tsitsipatis D, Gorospe M, Kim HH. hnRNPK-regulated LINC00263 promotes malignant phenotypes through miR-147a/CAPN2. Cell Death Dis 2021; 12:290. [PMID: 33731671 PMCID: PMC7969774 DOI: 10.1038/s41419-021-03575-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/23/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022]
Abstract
Malignant characteristics of cancers, represented by rapid cell proliferation and high metastatic potential, are a major cause of high cancer-related mortality. As a multifunctional RNA-binding protein, heterogeneous nuclear ribonucleoprotein K (hnRNPK) is closely associated with cancer progression in various types of cancers. In this study, we sought to identify hnRNPK-regulated long intergenic non-coding RNAs (lincRNAs) that play a critical role in the regulation of cancer malignancy. We found that hnRNPK controlled malignant phenotypes including invasiveness, proliferation, and clonogenicity. RNA sequencing and functional studies revealed that LINC00263, a novel target of hnRNPK, is involved in the oncogenic functions of hnRNPK. Knockdown of LINC00263 mitigated the malignant capabilities. Conversely, increased malignant phenotypes were observed in LINC00263-overexpressing cells. Since LINC00263 was mainly localized in the cytosol and highly enriched in Argonaute 2-immunoprecipitation (Ago2-IP), we hypothesized that LINC00263 acts as a competitive endogenous RNA (ceRNA), and thus sought to identify LINC00263-associated microRNAs. Using small RNA sequencing followed by antisense oligonucleotide pull-down, miR-147a was selected for further study. We found that miR-147a negatively regulates LINC00263 via direct interaction, thus suppressing malignant capabilities. Moreover, knockdown of hnRNPK and LINC00263 upregulated miR-147a, indicating that LINC00263 serves as a ceRNA for miR-147a. By analyzing RNA sequencing data and miRNA target prediction, calpain 2 (CAPN2) was identified as a putative target of miR-147a. Ago2-IP and luciferase reporter assay revealed that miR-147a suppressed CAPN2 expression by directly binding to the 3′UTR of CAPN2 mRNA. In addition, we found that the weakened malignant capabilities following knockdown of hnRNPK or LINC00263 were restored by miR-147a inhibition or CAPN2 overexpression. Furthermore, our findings were validated in various other types of cancer cells including lung cancer, colorectal cancer, neuroblastoma, and melanoma. Collectively, we demonstrate that hnRNPK-regulated LINC00263 plays an important role in cancer malignancy by acting as a miR-147a decoy and thus upregulating CAPN2.
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Affiliation(s)
- Woo Joo Lee
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Chang Hoon Shin
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Haein Ji
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Seong Dong Jeong
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Mi-So Park
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Hong-Hee Won
- Department of Digital Health, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea
| | - Poonam R Pandey
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Dimitrios Tsitsipatis
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Myriam Gorospe
- Laboratory of Genetics and Genomics, National Institute on Aging Intramural Research Program, National Institutes of Health, Baltimore, MD, 21224, USA
| | - Hyeon Ho Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul, 06351, Republic of Korea. .,Research Institute for Future Medicine, Samsung Medical Center, Seoul, 06351, Republic of Korea.
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37
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Fan X, Xie X, Yang M, Wang Y, Wu H, Deng T, Weng X, Wen W, Nie G. YBX3 Mediates the Metastasis of Nasopharyngeal Carcinoma via PI3K/AKT Signaling. Front Oncol 2021; 11:617621. [PMID: 33816248 PMCID: PMC8010247 DOI: 10.3389/fonc.2021.617621] [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: 10/17/2020] [Accepted: 02/02/2021] [Indexed: 01/11/2023] Open
Abstract
The metastasis of nasopharyngeal carcinoma (NPC) is a complex process associated with oncogenic dysfunction, the deciphering of which remains a challenge and requires more in-depth studies. Y-box protein 3 (YBX3) is a DNA/RNA binding protein associated with gene transcription, DNA repair, and the progression of various diseases. However, whether and how YBX3 affects the metastasis of NPC remains unknown. Thus, in this study, we aimed to investigate the role of YBX3 in the metastasis of NPC and determine its underlying mechanism. Interestingly, it was found that the expression of YBX3, which was associated with NPC metastasis, was upregulated in the clinical NPC tissues and cell lines. Moreover, we found that knockdown of YBX3 expression by lentivirus shRNA significantly suppressed NPC cells migration in vitro and metastasis in vivo. Mechanistically, RNA sequencing results suggested that the genes regulated by YBX3 were significantly enriched in cell adhesion molecules, cAMP signaling pathway, calcium signaling pathway, focal adhesion, PI3K/AKT signaling pathway, Ras signaling pathway, Rap1 signaling pathway, NF-κB signaling pathway, and Chemokine signaling pathway. Of these, PI3K/AKT signaling pathway contained the most genes. Accordingly, YBX3 knockdown decreased the activation of PI3K/AKT signaling pathway, thereby inhibit epithelial-to-mesenchymal transition (EMT) and MMP1. These results have demonstrated that YBX3 are involved in the metastasis of NPC through regulating PI3K/AKT signaling pathway, and serve as a potential therapeutic target for patients with NPC.
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Affiliation(s)
- Xiaoqin Fan
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.,Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xina Xie
- Guangdong Key Laboratory of Systems Biology and Synthetic Biology for Urogenital Tumors, Institute of Translational Medicine, Shenzhen Second People's Hospital, First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Ming Yang
- Department of Otolaryngology, Shenzhen First People's Hospital, The Affiliated Hospital of Jinan University, Guangzhou, China
| | - Yujie Wang
- Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Hanwei Wu
- Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Tingting Deng
- Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Xin Weng
- Department of Pathology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
| | - Weiping Wen
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Guohui Nie
- Department of Otolaryngology, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.,Department of Otolaryngology, Shenzhen Second People's Hospital, The First Affiliated Hospital of Shenzhen University, Shenzhen, China
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Iwabuchi E, Miki Y, Suzuki T, Hirakawa H, Ishida T, Sasano H. Heterogeneous Nuclear Ribonucleoprotein K Is Involved in the Estrogen-Signaling Pathway in Breast Cancer. Int J Mol Sci 2021; 22:ijms22052581. [PMID: 33806648 PMCID: PMC7962001 DOI: 10.3390/ijms22052581] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 02/24/2021] [Accepted: 03/01/2021] [Indexed: 01/22/2023] Open
Abstract
Heterogeneous nuclear ribonucleoprotein K (hnRNPK) transcripts are abundant in estrogen receptor (ER)- or progesterone receptor (PR)-positive breast cancer. However, the biological functions of hnRNPK in the ER-mediated signaling pathway have remained largely unknown. Therefore, this study analyzes the functions of hnRNPK expression in the ER-mediated signaling pathway in breast cancer. We initially evaluated hnRNPK expression upon treatment with estradiol (E2) and ICI 182,780 in the ERα-positive breast carcinoma cell line MCF-7. The results revealed that E2 increased hnRNPK; however, hnRNPK expression was decreased with ICI 182,780 treatment, indicating estrogen dependency. We further evaluated the effects of hnRNPK knockdown in the ER-mediated signaling pathway in MCF-7 cells using small interfering RNAs. The results revealed that hnRNPK knockdown decreased ERα expression and ERα target gene pS2 by E2 treatment. As hnRNPK interacts with several other proteins, we explored the interaction between hnRNPK and ERα, which was demonstrated using immunoprecipitation and proximity ligation assay. Subsequently, we immunolocalized hnRNPK in patients with breast cancer, which revealed that hnRNPK immunoreactivity was significantly higher in ERα-positive carcinoma cells and significantly lower in Ki67-positive or proliferative carcinoma cells. These results indicated that hnRNPK directly interacted with ERα and was involved in the ER-mediated signaling pathway in breast carcinoma. Furthermore, hnRNPK expression could be an additional target of endocrine therapy in patients with ERα-positive breast cancer.
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Affiliation(s)
- Erina Iwabuchi
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan;
| | - Yasuhiro Miki
- Department of Disaster Obstetrics and Gynecology, International Research Institute of Disaster Science (IRIDes), Tohoku University, Sendai 980-8575, Japan;
| | - Takashi Suzuki
- Department of Pathology and Histotechnology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan;
| | - Hisashi Hirakawa
- Department of Surgery, Tohoku Kosai Hospital, Sendai 980-0803, Japan;
| | - Takanori Ishida
- Department of Breast and Endocrine Surgical Oncology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan;
| | - Hironobu Sasano
- Department of Pathology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan;
- Correspondence: ; Tel.: +81-22-717-8050
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Abstract
Long non-coding RNAs (LncRNAs) can bind to other proteins or RNAs to regulate gene expression, and its role in tumors has been extensively studied. A common RNA binding protein, UPF1, is also a key factor in a variety of RNA decay pathways. RNA decay pathways serve to control levels of particular RNA molecules. The expression of UPF1 is often dysregulated in tumors, an observation which suggests that UPF1 contributes to development of a variety of tumors. Herein, we review evidence from studies of fourteen lncRNAs interact with UPF1. The interaction between lncRNA and UPFI provide fundamental basis for cell transformation and tumorigenic growth.
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Affiliation(s)
- Junjian He
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
| | - Xiaoxin Ma
- Department of Obstetrics and Gynecology, Shengjing Hospital of China Medical University, Shenyang, China.,Key Laboratory of Maternal-Fetal Medicine of Liaoning Province, Key Laboratory of Obstetrics and Gynecology of Higher Education of Liaoning Province, Shenyang, China
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40
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Xie W, Zhu H, Zhao M, Wang L, Li S, Zhao C, Zhou Y, Zhu B, Jiang X, Liu W, Ren C. Crucial roles of different RNA-binding hnRNP proteins in Stem Cells. Int J Biol Sci 2021; 17:807-817. [PMID: 33767590 PMCID: PMC7975692 DOI: 10.7150/ijbs.55120] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/07/2021] [Indexed: 11/05/2022] Open
Abstract
The self-renewal, pluripotency and differentiation of stem cells are regulated by various genetic and epigenetic factors. As a kind of RNA binding protein (RBP), the heterogeneous nuclear ribonucleoproteins (hnRNPs) can act as "RNA scaffold" and recruit mRNA, lncRNA, microRNA and circRNA to affect mRNA splicing and processing, regulate gene transcription and post-transcriptional translation, change genome structure, and ultimately play crucial roles in the biological processes of cells. Recent researches have demonstrated that hnRNPs are irreplaceable for self-renewal and differentiation of stem cells. hnRNPs function in stem cells by multiple mechanisms, which include regulating mRNA stability, inducing alternative splicing of mRNA, epigenetically regulate gene expression, and maintaining telomerase activity and telomere length. The functions and the underlying mechanisms of hnRNPs in stem cells deserve further investigation.
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Affiliation(s)
- Wen Xie
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Hecheng Zhu
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,Changsha Kexin Cancer Hospital, Changsha, Hunan 410205, China
| | - Ming Zhao
- Changsha Kexin Cancer Hospital, Changsha, Hunan 410205, China
| | - Lei Wang
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Shasha Li
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Cong Zhao
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Yao Zhou
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Bin Zhu
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Xingjun Jiang
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Weidong Liu
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
| | - Caiping Ren
- Cancer Research Institute, Department of Neurosurgery, School of Basic Medical Science, Xiangya Hospital, Central South University, Changsha 410008, China.,The Key Laboratory of Carcinogenesis of the Chinese Ministry of Health and the Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha 410008, China
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41
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Qian X, Xu C, Wu B, Tang H, Zhao P, Qi Z. SNORD126 Promotes Hepatitis C Virus Infection by Upregulating Claudin-1 via Activation of PI3K-AKT Signaling Pathway. Front Microbiol 2020; 11:565590. [PMID: 33042070 PMCID: PMC7522514 DOI: 10.3389/fmicb.2020.565590] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022] Open
Abstract
Hepatitis C virus (HCV) infection involves a variety of viral and host factors, some of which promote the infection process. A small nucleolar RNA, C/D box 126 (SNORD126), was previously shown to be associated with hepatocellular carcinoma (HCC). However, the role of SNORD126 in HCV infection, which is one of the primary reasons for HCC development, has not been elucidated. In the present study, using small nucleolar RNA profiling, we observed that SNORD126 was significantly downregulated during HCV infection in both Huh7 and Huh7.5.1 cells. In addition, overexpression of SNORD126 enhanced HCV entry into host cells, whereas SNORD126 knockdown showed the opposite effect, suggesting that SNORD126 promotes HCV infection, especially through viral entry. Further functional analysis revealed that SNORD126 could enhance the expression level of claudin-1 (CLDN1), a key HCV entry factor, by increasing the levels of phosphorylated AKT. Additionally, the function of SNORD126 in HCV infection was associated with ribonucleoprotein (RNP) complexes. In summary, our findings demonstrate that oncogenic SNORD126 levels are decreased during HCV infection probably due to the host defense reaction, and SNORD126 may be important to promote viral entry by increasing CLDN1 expression through activation of the PI3K-AKT pathway, the mechanism of which is partly associated with SNORD126-mediated snoRNA RNP (snoRNP) function. Our work here provides initial evidence that endogenous snoRNA takes part in HCV infection and shows potential as a diagnostic or antiviral agent.
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Affiliation(s)
- Xijing Qian
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Chen Xu
- Spine Center, Department of Orthopedics, Changzheng Hospital Affiliated to Second Military Medical University, Shanghai, China
| | - Bingan Wu
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Hailin Tang
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Ping Zhao
- Department of Microbiology, Second Military Medical University, Shanghai, China
| | - Zhongtian Qi
- Department of Microbiology, Second Military Medical University, Shanghai, China
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Saberiyan M, Mirfakhraie R, Gholami D, Dehdehi L, Teimori H. Investigating the regulatory function of the ANO1-AS2 on the ANO1 gene in infertile men with asthenozoospermia and terato-asthenozoospermia. Exp Mol Pathol 2020; 117:104528. [PMID: 32916161 DOI: 10.1016/j.yexmp.2020.104528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 08/30/2020] [Accepted: 09/05/2020] [Indexed: 12/21/2022]
Abstract
Long non-coding RNAs (lncRNAs) have a particular expression in the testicular tissue and exhibit a regulatory function on the reproduction system. ANO1-AS2 (linc02584), as an lncRNA is located near the anoctamin1 (ANO1) gene. ANO1 is an important component of the transmembrane system exhibiting expression modifications in the idiopathic infertile men. Therefore, the present study was conducted to investigate the relationship between ANO1-AS2 and ANO1 gene expression with sperm motility and morphology in the patients with asthenozoospermia (AZ) and terato- asthenozoospermia (TAZ). The study population included 32 patients with AZ, 35 patients with TAZ, and 34 people with normozoospermia (NZ, control). The expression levels of ANO1 gene and ANO1-AS2 in the spermatozoa were measured by the quantitative real-time polymerase chain reaction (PCR). Docking analysis was performed to investigate the interactions of the ANO1 gene promoter and intermediate elements with ANO1-AS2. ANO1 gene expression was significantly (P < 0.05) downregulated in the patients however; ANO1-AS2 expression was significantly upregulated (P < 0.05). The subsequent analysis confirmed the inverse correlation between ANO1 and ANO1-AS2. ANO1 gene expression level was significantly positively correlated with sperm motility and morphology (P < 0.05). Moreover, ANO1-AS2 expression showed an inverse correlation with sperm motility and morphology (P < 0.05). Docking analysis confirmed that ANO1-AS2 could stably interact with ANO1 gene promoter. In conclusion, ANO1-AS2 is likely to downregulate the ANO1 gene by interacting with ANO1 gene promoter, which can influence the sperm motility and morphology.
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Affiliation(s)
- Mohammadreza Saberiyan
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Reza Mirfakhraie
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Delnya Gholami
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Leila Dehdehi
- Clinical Research Developmental Unit, Hajar Hospital, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Hossein Teimori
- Cellular and Molecular Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran.
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43
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LINC00689 participates in proliferation, chemoresistance and metastasis via miR-31-5p/YAP/β-catenin axis in colorectal cancer. Exp Cell Res 2020; 395:112176. [PMID: 32682784 DOI: 10.1016/j.yexcr.2020.112176] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/27/2022]
Abstract
As a kind of high-incidence malignant tumors in the digestive tract, colorectal cancer (CRC) has extremely morbidity and mortality in the population. LncRNAs have been proved to regulate the proliferation, chemoresistance and metastasis of tumors including CRC. LINC00689 and miR-31-5p in CRC were found misregulated in CRC by TCGA analysis. However, the mechanism of LINC00689 and miR-31-5p in regulating CRC remains unknown. The expression levels of LINC00689, miR-31-5p and LATS2 in CRC tissues and cell lines were examined by qRT-PCR assay. Cell proliferation, metastasis (including invasion and migration) were quantified by MTT assay, colony formation and Transwell assay, respectively. Western blotting assay was then performed to verify the levels of YAP/β-catenin and metastasis-related proteins. Dual-luciferase reporter assay and RIP assay were performed to evaluate the interaction between LINC00689 (LATS2) and miR-31-5p. Moreover, the function of LINC00689 and miR-31-5p were confirmed by CRC xenograft in nude mice. LINC00689 was decreased while miR-31-5p was increased in CRC. The overexpression of LINC00689 or the knockdown of miR-31-5p inhibited cell proliferation, chemoresistance and metastasis of CRC cells. Meanwhile, the up-regulated LATS2 suppressed the activity of YAP/β-catenin pathway to repress CRC occurrence. Silencing LATS2 reversed the inhibition effects of overexpression of LINC00689 or knockdown of miR-31-5p on proliferation, chemoresistance and metastasis of CRC cells. LINC00689 indeed acted as a miR-31-5p sponge to inhibit CRC proliferation, chemoresistance and metastasis through up-regulating LATS2 and repressing YAP/β-catenin signaling pathway.
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44
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HOTAIRM1 regulates neuronal differentiation by modulating NEUROGENIN 2 and the downstream neurogenic cascade. Cell Death Dis 2020; 11:527. [PMID: 32661334 PMCID: PMC7359305 DOI: 10.1038/s41419-020-02738-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 06/15/2020] [Accepted: 06/18/2020] [Indexed: 12/25/2022]
Abstract
Neuronal differentiation is a timely and spatially regulated process, relying on precisely orchestrated gene expression control. The sequential activation/repression of genes driving cell fate specification is achieved by complex regulatory networks, where transcription factors and noncoding RNAs work in a coordinated manner. Herein, we identify the long noncoding RNA HOTAIRM1 (HOXA Transcript Antisense RNA, Myeloid-Specific 1) as a new player in neuronal differentiation. We demonstrate that the neuronal-enriched HOTAIRM1 isoform epigenetically controls the expression of the proneural transcription factor NEUROGENIN 2 that is key to neuronal fate commitment and critical for brain development. We also show that HOTAIRM1 activity impacts on NEUROGENIN 2 downstream regulatory cascade, thus contributing to the achievement of proper neuronal differentiation timing. Finally, we identify the RNA-binding proteins HNRNPK and FUS as regulators of HOTAIRM1 biogenesis and metabolism. Our findings uncover a new regulatory layer underlying NEUROGENIN 2 transitory expression in neuronal differentiation and reveal a previously unidentified function for the neuronal-induced long noncoding RNA HOTAIRM1.
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Abstract
Currently, cardiovascular diseases continue to be the leading cause of death worldwide; therefore, atherosclerosis remains one of the most crucial public health problems. This chronic and complex disease is considered to be a result of aberrant lipid homeostasis and inflammation of the inner wall of arteries that leads to plaque development. In recent years, a specific class of non-coding RNAs that are characterised by transcript lengths longer than 200 nucleotides, called long non-coding RNAs (lncRNAs), has emerged. Moreover, a growing body of evidence indicates that deregulation of lncRNA expression may contribute to the development of many diseases. Despite continuous efforts in deciphering the molecular basis of atherosclerotic plaque (AP) formation, many aspects of this process remain elusive. Therefore, continuing efforts in this area should remain the highest priority in the coming years. Establishment of a standardised experimental pipeline and validation of lncRNAs as possible relevant biomarkers for cardiovascular disease would enable the translation of gathered findings into clinical practice.
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Affiliation(s)
- Weronika Kraczkowska
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland.
| | - Paweł Piotr Jagodziński
- Department of Biochemistry and Molecular Biology, Poznań University of Medical Science, 6 Święcickiego Street, 60-781, Poznan, Poland
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RNA-binding motifs of hnRNP K are critical for induction of antibody diversification by activation-induced cytidine deaminase. Proc Natl Acad Sci U S A 2020; 117:11624-11635. [PMID: 32385154 DOI: 10.1073/pnas.1921115117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Activation-induced cytidine deaminase (AID) is the key enzyme for class switch recombination (CSR) and somatic hypermutation (SHM) to generate antibody memory. Previously, heterogeneous nuclear ribonucleoprotein K (hnRNP K) was shown to be required for AID-dependent DNA breaks. Here, we defined the function of major RNA-binding motifs of hnRNP K, GXXGs and RGGs in the K-homology (KH) and the K-protein-interaction (KI) domains, respectively. Mutation of GXXG, RGG, or both impaired CSR, SHM, and cMyc/IgH translocation equally, showing that these motifs were necessary for AID-dependent DNA breaks. AID-hnRNP K interaction is dependent on RNA; hence, mutation of these RNA-binding motifs abolished the interaction with AID, as expected. Some of the polypyrimidine sequence-carrying prototypical hnRNP K-binding RNAs, which participate in DNA breaks or repair bound to hnRNP K in a GXXG and RGG motif-dependent manner. Mutation of the GXXG and RGG motifs decreased nuclear retention of hnRNP K. Together with the previous finding that nuclear localization of AID is necessary for its function, lower nuclear retention of these mutants may worsen their functional deficiency, which is also caused by their decreased RNA-binding capacity. In summary, hnRNP K contributed to AID-dependent DNA breaks with all of its major RNA-binding motifs.
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47
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RNA-Binding Proteins as Important Regulators of Long Non-Coding RNAs in Cancer. Int J Mol Sci 2020; 21:ijms21082969. [PMID: 32340118 PMCID: PMC7215867 DOI: 10.3390/ijms21082969] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 12/20/2022] Open
Abstract
The majority of the genome is transcribed into pieces of non-(protein) coding RNA, among which long non-coding RNAs (lncRNAs) constitute a large group of particularly versatile molecules that govern basic cellular processes including transcription, splicing, RNA stability, and translation. The frequent deregulation of numerous lncRNAs in cancer is known to contribute to virtually all hallmarks of cancer. An important regulatory mechanism of lncRNAs is the post-transcriptional regulation mediated by RNA-binding proteins (RBPs). So far, however, only a small number of known cancer-associated lncRNAs have been found to be regulated by the interaction with RBPs like human antigen R (HuR), ARE/poly(U)-binding/degradation factor 1 (AUF1), insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1), and tristetraprolin (TTP). These RBPs regulate, by various means, two aspects in particular, namely the stability and the localization of lncRNAs. Importantly, these RBPs themselves are commonly deregulated in cancer and might thus play a major role in the deregulation of cancer-related lncRNAs. There are, however, still many open questions, for example regarding the context specificity of these regulatory mechanisms that, in part, is based on the synergistic or competitive interaction between different RBPs. There is also a lack of knowledge on how RBPs facilitate the transport of lncRNAs between different cellular compartments.
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48
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Qin C, Xu PP, Zhang X, Zhang C, Liu CB, Yang DG, Gao F, Yang ML, Du LJ, Li JJ. Pathological significance of tRNA-derived small RNAs in neurological disorders. Neural Regen Res 2020; 15:212-221. [PMID: 31552886 PMCID: PMC6905339 DOI: 10.4103/1673-5374.265560] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a type of RNA that is not translated into proteins. Transfer RNAs (tRNAs), a type of ncRNA, are the second most abundant type of RNA in cells. Recent studies have shown that tRNAs can be cleaved into a heterogeneous population of ncRNAs with lengths of 18–40 nucleotides, known as tRNA-derived small RNAs (tsRNAs). There are two main types of tsRNA, based on their length and the number of cleavage sites that they contain: tRNA-derived fragments and tRNA-derived stress-induced RNAs. These RNA species were first considered to be byproducts of tRNA random cleavage. However, mounting evidence has demonstrated their critical functional roles as regulatory factors in the pathophysiological processes of various diseases, including neurological diseases. However, the underlying mechanisms by which tsRNAs affect specific cellular processes are largely unknown. Therefore, this study comprehensively summarizes the following points: (1) The biogenetics of tsRNA, including their discovery, classification, formation, and the roles of key enzymes. (2) The main biological functions of tsRNA, including its miRNA-like roles in gene expression regulation, protein translation regulation, regulation of various cellular activities, immune mediation, and response to stress. (3) The potential mechanisms of pathophysiological changes in neurological diseases that are regulated by tsRNA, including neurodegeneration and neurotrauma. (4) The identification of the functional diversity of tsRNA may provide valuable information regarding the physiological and pathophysiological mechanisms of neurological disorders, thus providing a new reference for the clinical treatment of neurological diseases. Research into tsRNAs in neurological diseases also has the following challenges: potential function and mechanism studies, how to accurately quantify expression, and the exact relationship between tsRNA and miRNA. These challenges require future research efforts.
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Affiliation(s)
- Chuan Qin
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Pei-Pei Xu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Xin Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chao Zhang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Chang-Bin Liu
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - De-Gang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Feng Gao
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Ming-Liang Yang
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Liang-Jie Du
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
| | - Jian-Jun Li
- School of Rehabilitation Medicine, Capital Medical University; China Rehabilitation Science Institute; Center of Neural Injury and Repair, Beijing Institute for Brain Disorders; Department of Spinal and Neural Functional Reconstruction, China Rehabilitation Research Center; Beijing Key Laboratory of Neural Injury and Rehabilitation, Beijing, China
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49
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Sun XH, Fan WJ, An ZJ, Sun Y. Inhibition of Long Noncoding RNA CRNDE Increases Chemosensitivity of Medulloblastoma Cells by Targeting miR-29c-3p. Oncol Res 2019; 28:95-102. [PMID: 31753063 PMCID: PMC7851516 DOI: 10.3727/096504019x15742472027401] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Long noncoding RNA CRNDE (CRNDE) recently emerged as a carcinogenic promoter in various cancers including medulloblastoma. However, the functions and molecular mechanisms of CRNDE to the acquired drug resistance of medulloblastoma are still unclear. The transcript levels of CRNDE were examined in four medulloblastoma cell lines exposed to cisplatin treatment, and IC50 values were calculated. Effects of CRNDE knockdown or miR-29c-3p overexpression on cell viability, colony formation, apoptosis, migration, and invasion were assessed using the CCK-8, colony formation assay, flow cytometry, and Transwell assays, respectively. RNA pulldown and RNA-binding protein immunoprecipitation (RIP) were performed to confirm the molecular interactions between CRNDE and miR-29c-3p involved in medulloblastoma cells. The in vivo role of CRNDE knockdown or miR-29c-3p overexpression on tumor growth and apoptosis was evaluated in a xenograft mouse model of human medulloblastoma. The transcript levels of lncRNA CRNDE were significantly higher in cisplatin-treated tumor cells with higher IC50 values. Depletion of CRNDE inhibited tumor cell proliferation and colony formation, induced cell apoptosis, and suppressed migration and invasion in medulloblastoma cells. Moreover, overexpression of miR-29c-3p inhibited tumor cell proliferation and colony formation, migration, and invasion, and enhanced apoptosis and chemosensitivity to cisplatin. In addition, CRNDE was found to act as a miR-29c-3p sponge. Furthermore, in vivo experiments showed the CRNDE/miR-29c-3p interactions involved in medulloblastoma. Our study demonstrates that CRNDE acts as a critical mediator of proliferation, apoptosis, migration, invasion, and resistance to chemotherapeutics via binding to and negatively regulating miR-29c-3p in medulloblastoma cells. These results provide novel molecular targets for treatment of medulloblastoma.
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Affiliation(s)
- Xiao-Hui Sun
- Medical Department, Qingdao Infectious Disease HospitalQingdao, ShandongP.R. China
| | - Wen-Jie Fan
- Department of Anesthesia, Qingdao Women and Children's HospitalQingdao, ShandongP.R. China
| | - Zong-Jian An
- Department of Pediatric Neurosurgery, Qingdao Women and Children's HospitalQingdao, ShandongP.R. China
| | - Yong Sun
- Department of Pediatric Neurosurgery, Qingdao Women and Children's HospitalQingdao, ShandongP.R. China
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Bermúdez M, Aguilar-Medina M, Lizárraga-Verdugo E, Avendaño-Félix M, Silva-Benítez E, López-Camarillo C, Ramos-Payán R. LncRNAs as Regulators of Autophagy and Drug Resistance in Colorectal Cancer. Front Oncol 2019; 9:1008. [PMID: 31632922 PMCID: PMC6783611 DOI: 10.3389/fonc.2019.01008] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 09/19/2019] [Indexed: 12/11/2022] Open
Abstract
Colorectal cancer (CRC) is a common malignancy with 1. 8 million cases in 2018. Autophagy helps to maintain an adequate cancer microenvironment in order to provide nutritional supplement under adverse conditions such as starvation and hypoxia. Additionally, most of the cases of CRC are unresponsive to chemotherapy, representing a significant challenge for cancer therapy. Recently, autophagy induced by therapy has been shown as a unique mechanism of resistance to anticancer drugs. In this regard, long non-coding RNAs (lncRNAs) analysis are important for cancer detection, progression, diagnosis, therapy response, and prognostic values. With increasing development of quantitative detection techniques, lncRNAs derived from patients' non-invasive samples (i.e., blood, stools, and urine) has become into a novel approach in precision oncology. Tumorspecific GAS5, HOTAIR, H19, and MALAT are novels CRC related lncRNAs detected in patients. Nonetheless, the effect and mechanism of lncRNAs in cancer autophagy and chemoresistance have not been extensively characterized. Chemoresistance and autophagy are relevant for cancer treatment and lncRNAs play a pivotal role in resistance acquisition for several drugs. LncRNAs such as HAGLROS, KCNQ1OT1, and H19 are examples of lncRNAs related to chemoresistance leaded by autophagy. Finally, clinical implications of lncRNAs in CRC are relevant, since they have been associated with tumor differentiation, tumor size, histological grade, histological types, Dukes staging, degree of differentiation, lymph node metastasis, distant metastasis, recurrent free survival, and overall survival (OS).
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Affiliation(s)
- Mercedes Bermúdez
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | - Maribel Aguilar-Medina
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | - Erik Lizárraga-Verdugo
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | - Mariana Avendaño-Félix
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Mexico
| | | | - Cesar López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - Rosalío Ramos-Payán
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, Mexico
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