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Li X, Ding Z, Tong Y. Correlations of m 6A Methylation-Related lncRNAs with the Prognosis of Papillary Thyroid Carcinoma. Int J Gen Med 2024; 17:775-790. [PMID: 38476625 PMCID: PMC10929225 DOI: 10.2147/ijgm.s449827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Purpose Papillary thyroid carcinoma (PTC) is the most common subtype of thyroid cancer. Recurrence makes the prognosis for some patients with PTC worse. Increasing evidence have suggested that N6-methyladenosine (m6A) RNA methylation plays an important role in tumorigenesis. However, the significance of m6A-related lncRNAs in the malignant progression of PTC remains unknown. In this study, we explored the significance of M6A-related lncrnas in the malignant progression of PTC. Patients and Methods Transcriptome and clinical data of PTC were achieved and integrated from The Cancer Genome Atlas (TCGA). Firstly, a Spearman correlation analysis was performed to obtain m6A RNA methylation-associated lncRNAs. Next, We constructed a prognostic signature and assessed the accuracy of the signature by receiver operating characteristic (ROC) curve and Kaplan Meier survival analyses. Furthermore, functional enrichment analysis was performed on the high- and low-risk groups. Finally, we determined prognostic gene expression in clinical samples using quantitative reverse transcription polymerase chain reaction (RT-qPCR). Results We identified 56 differentially expressed lncRNAs associated with m6A RNA methylation. Univariate Cox and Least Absolute Shrinkage and Selection Operator (LASSO) regression analyses showed that the survival-related lncRNAs associated with m6A RNA methylation were detected, which showed superior calibration and discrimination. Moreover, the biological processes related to energy metabolism were significantly activated in the high-risk group. Finally, the co-expressed genes of lncRNAs in the risk model were significantly enriched in biological processes related to copper ion response. Finally, we validated the expression levels of three prognostic genes in clinical samples using RT-qPCR. Conclusion Our study revealed m6A RNA methylation-associated lncRNAs were significantly associated with disease-free survival in patients with papillary thyroid cancer, which would improve our understanding of the relationship between m6A RNA methylation-associated lncRNAs and PTC.
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Affiliation(s)
- Xiang Li
- Department of General Surgery, The Affiliated Hospital of Jiujiang University, Jiujiang, People's Republic of China
| | - Zigang Ding
- Department of General Surgery, The Affiliated Hospital of Jiujiang University, Jiujiang, People's Republic of China
| | - Yun Tong
- Department of Pain, The Affiliated Hospital of Jiujiang University, Jiujiang, People's Republic of China
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2
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Shree B, Das K, Sharma V. Emerging role of transforming growth factor-β-regulated long non-coding RNAs in prostate cancer pathogenesis. CANCER PATHOGENESIS AND THERAPY 2023; 1:195-204. [PMID: 38327834 PMCID: PMC10846338 DOI: 10.1016/j.cpt.2022.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/01/2022] [Accepted: 12/20/2022] [Indexed: 02/09/2024]
Abstract
Prostate cancer (PCa) is the most common malignancy in men. Despite aggressive therapy involving surgery and hormonal treatments, the recurrence and emergence of metastatic castration-resistant prostate cancer (CRPCa) remain a major challenge. Dysregulation of the transforming growth factor-β (TGF-β) signaling pathway is crucial to PCa development and progression. This also contributes to androgen receptor activation and the emergence of CRPC. In addition, TGF-β signaling regulates long non-coding RNA (lncRNA) expression in multiple cancers, including PCa. Here, we discuss the complex regulatory network of lncRNAs and TGF-β signaling in PCa and their potential applications in diagnosing, prognosis, and treating PCa. Further investigations on the role of lncRNAs in the TGF-β pathway will help to better understand PCa pathogenesis.
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Affiliation(s)
- Bakhya Shree
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad 500078, India
| | - Koyel Das
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad 500078, India
| | - Vivek Sharma
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad 500078, India
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3
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Xu H, Tang Y, He C, Tian Y, Ni R. Prognostic value of lncRNA HOXA-AS3 in cervical cancer by targeting miR-29a-3p and its regulatory effect on tumor progression. J Obstet Gynaecol Res 2022; 48:2594-2602. [PMID: 35817473 DOI: 10.1111/jog.15360] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/22/2022] [Accepted: 06/28/2022] [Indexed: 02/06/2023]
Abstract
BACKGROUND With the promotion of human papillomavirus (HPV) vaccine, cervical cancer has become a current research hotspot, and lncRNA has been confirmed to be used in the research of different diseases. This article systematically expounds the regulation and potential mechanisms of HOXA cluster antisense RNA 3 (HOXA-AS3) in cervical cancer, and discusses its possibility as a prognostic biomarker for cervical cancer. METHODS Relative expression levels of HOXA-AS3 and miR-29a-3p in tissues and cells were determined by real-time quantitative polymerase chain reaction (RT-qPCR). The survival of cervical cancer patients was analyzed by Kaplan-Meier method and the cumulative survival function table was drawn. The proliferation, migration, and invasion levels of HOXA-AS3 in cells were detected according to cell counting kit-8 (CCK-8) and transwell method. The dual-luciferase reporter gene assay confirmed the mechanism of action between HOXA-AS3 and miR-29a-3p. RESULTS HOXA-AS3 was elevated and miR-29a-3p was decreased in tissues and cells of cervical cancer patients. Knockdown of HOXA-AS3 could inhibit the progression of cervical cancer and was more conducive to patient survival. Bioinformatics analysis confirmed that HOXA-AS3 negatively regulates cervical cancer development by sponging miR-29a-3p. CONCLUSION In this research, knockdown of HOXA-AS3 could alleviate the process of cervical cancer by sponging miR-29a-3p, suggesting that HOXA-AS3 may be a potential prognostic target of cervical cancer, which could provide a theoretical basis for future clinical research of cervical cancer.
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Affiliation(s)
- Hui Xu
- Department of Obstetrics and Gynecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Yan Tang
- Department of Obstetrics and Gynecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Chuanyong He
- Department of Obstetrics and Gynecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Yong Tian
- Department of Obstetrics and Gynecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Rong Ni
- Department of Obstetrics and Gynecology, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
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4
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Yang B, Wang Z, Deng Y, Xiao L, Zhang K. LncRNA LAMTOR5-AS1 sponges miR-210-3p and regulates cervical cancer progression. J Obstet Gynaecol Res 2022; 48:3171-3178. [PMID: 36173004 DOI: 10.1111/jog.15439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/16/2022] [Accepted: 09/11/2022] [Indexed: 11/28/2022]
Abstract
AIM Cervical cancer has attracted increasing attention in recent years, and the incidence has shown a trend of younger age. Therefore, it is an effective method to regulate the progression of cervical cancer through new prognostic biomarkers. The purpose of this study was to evaluate the potential of lncRNA LAMTOR5-AS1 (LAMTOR5-AS1) as a prognostic biomarker and reveal its regulatory role in cervical cancer. METHODS A total of 120 patients with cervical cancer were selected as research subjects to verify the prognostic effect of LAMTOR5-AS1 in a series of experiments. The expression of LAMTOR5-AS1 in cervical cancer tissues and cells was determined by polymerase chain reaction assay. The proliferation, migration, and invasion ability of cervical cancer cells were evaluated by Cell Counting Kit-8 (CCK-8) and Transwell assay. Luciferase reporter gene detection was used to determine the mechanism of LAMTOR5-AS1 targeting miR-210-3p, and to reflect the prognostic value of LAMTOR5-AS1 according to statistical methods. RESULTS LAMTOR5-AS1 decreased in cervical cancer tissues, while miR-210-3p expression increased. In the study of cervical cancer cells, it was found that the LAMTOR5-AS1 sponge miR-210-3p was associated with the malignant progression of cervical cancer. Overexpression of LAMTOR5-AS1 could effectively inhibit the development of cervical cancer cells and might be chosen as a prognostic biomarker of cervical cancer. CONCLUSIONS LAMTOR5-AS1 sponges miR-210-3p and modulates the progression of cervical cancer, which predict the prognosis of cervical cancer patients.
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Affiliation(s)
- Bo Yang
- Department of Gynecologic Oncology (5), Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Ziyi Wang
- Department of Gynecologic Oncology (5), Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Yuping Deng
- Department of Gynecologic Oncology (5), Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Lingzhi Xiao
- Department of Gynecologic Oncology (5), Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
| | - Keqiang Zhang
- Department of Gynecologic Oncology (5), Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
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Gilloteaux DJ, Jamison JM, Summers JL, Taper HS. Xenografts on nude mouse diaphragm of human DU145 prostate carcinoma cells: mesothelium removal by outgrowths and angiogenesis. Ultrastruct Pathol 2022; 46:413-438. [PMID: 36165802 DOI: 10.1080/01913123.2022.2115596] [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: 10/14/2022]
Abstract
Human prostate carcinoma DU145 cells, androgen-independent malignant cells, implanted in the athymic nu/nu male mouse, developed numerous tumors on peritoneal and retro-peritoneal organs whose growth aspects and vascular supply have yet to be investigated with fine structure techniques. A series of necropsies from moribund implanted mice diaphragms were examined with light, scanning, and transmission electron microscopy. DU145 xenografts installations, far away from the implanted site, were described as the smallest installation to large diaphragm outgrowths in moribund mice. Carcinomas did not show extracellular matrix and, reaching more than 0.15 mm in thickness, they revealed new structures in these outgrowths. Voids to be gland-like structures with mediocre secretion and, unexpectedly, intercellular spaces connected with fascicles of elongated DU145 cells that merged with a vascular supply originated from either the tumor cells and/or some perimysium vessels. In the largest carcinomas, most important vascular invasions coincidently accompanied the mouse lethality, similarly to human cancers. This androgen-independent model would be useful to study tumor outgrowth's changes related to testing anticancer strategy, including anti-angiogenic therapies involving toxicity, simultaneously with those of other vital organs with combined biomolecular and fine structure techniques.
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Affiliation(s)
- Dr Jacques Gilloteaux
- Department of Anatomical Sciences, St Georges' University International School of Medicine, KB Taylor Global Scholar's Program, Newcastle upon Tyne, UK, NE1 8JG.,Unit of Research in Molecular Physiology (URPhyM), NARILIS, Université de Namur, Namur, Belgium, 5000.,Department of Anatomical Sciences, Ohio Medical University (NEOMed/Northeastern Ohio Universities College of Medicine, Rootstown, OH, USA, 44272
| | - James M Jamison
- Department of Urology, Ohio Medical University (NEOMed/Northeastern Ohio Universities College of Medicine, Rootstown, OH, USA, 44272.,St Thomas Hospital, The Apatone Development Center, Summa Research Foundation, Akron, OH, USA, 44310
| | - Jack L Summers
- Department of Urology, Ohio Medical University (NEOMed/Northeastern Ohio Universities College of Medicine, Rootstown, OH, USA, 44272.,St Thomas Hospital, The Apatone Development Center, Summa Research Foundation, Akron, OH, USA, 44310
| | - Henryk S Taper
- Laboratoire de Pharmacologie Toxicologique et Cancérologique, School of Pharmacy, Université Catholique de Louvain, Brussels, Belgium, 1200
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m6A-Related lncRNA Signature Is Involved in Immunosuppression and Predicts the Patient Prognosis of the Age-Associated Ovarian Cancer. J Immunol Res 2022; 2022:3258400. [PMID: 35991123 PMCID: PMC9385364 DOI: 10.1155/2022/3258400] [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: 04/07/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 11/18/2022] Open
Abstract
Background Epithelial ovarian cancers are age-associated diseases, usually diagnosed at an advanced stage. lncRNA has been discovered to interplay with N6-methyladenosine (m6A), working in tandem to promote cancer progression and worsening patient outcomes. This study is aimed at investigating the roles and mechanism of m6A-related lncRNA signature on ovarian cancers. Methods We retrieved TCGA and CGGA sequencing data to identify m6A-related lncRNA signature and constructed an m6A score (MS) using the LASSO algorithm. A clinical nomogram was then established to predict the overall survival of patients. Subsequently, GSEA analyses were conducted to obtain pathways involved. Expression of HLA genes, 28 tumor-infiltrating lymphocyte infiltration, and anticancer cycle were analyzed the immunological differences between high-MS and low-MS groups. Finally, immune checkpoint gene expressions and IC50 of chemotherapeutic drugs were calculated, and CMap was run to identify the potential compounds and their corresponding mechanisms. Results We identified 16 m6A-related lncRNAs and constructed an MS model. The high-MS group showed a poor prognosis. A clinical nomogram consists of MS, and age was constructed and predicted the 1-, 3-, and 5-year survival with high accuracy. GSEA analyses presented downregulated antigen processing and presentation pathways. Immunocyte infiltrating analyses demonstrated that high-MS was associated with high infiltration of Treg cells, macrophages, and low Th1/Th2 rate. Also, high expression of immune checkpoint genes NRP1, TNFSF9, and VSIR was observed in the high-MS group. Finally, the high-MS group also predicted low IC50 of vinorelbine and vorinostat. Conclusion This study constructed a robust prediction model for prognostic management and revealed the cross-talk between m6A and immunosuppression. Besides, the m6A lncRNA signature can predict the chemotherapeutic drug response. These will shed light on the development of novel therapeutic strategies and render survival benefits for ovarian patients.
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Chen G, Wang K, Li G, Wang L, Xiao Y, Chen B. Long Noncoding RNA LAMTOR5-AS1 Interference Affects MicroRNA-506-3p/E2F6-Mediated Behavior of Non-Small Cell Lung Cancer Cells. Oncol Res 2022; 28:945-959. [PMID: 34588094 PMCID: PMC8790135 DOI: 10.3727/096504021x16328213967104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Long noncoding RNA LAMTOR5 antisense RNA 1 (LAMTOR5-AS1) has been certified as a risk predictor and diagnostic biomarker of prostate cancer. However, the expression and exact roles of LAMTOR5-AS1 in non-small cell lung cancer (NSCLC) remain unclear. Thus, we measured LAMTOR5-AS1 expression in NSCLC and gauged its clinical value. The detailed roles and downstream working mechanism of LAMTOR5-AS1 in NSCLC were comprehensively unraveled. qRT-PCR was applied to measure gene expression. Functionally, utilizing small interfering RNA, LAMTOR5-AS1 was ablated, and the functional alterations were addressed by means of different experiments. The targeting activities between LAMTOR5-AS1 and microRNA-506-3p (miR-506-3p) and between miR-506-3p and E2F transcription factor 6 (E2F6) were confirmed by RNA immunoprecipitation and luciferase reporter assays. LAMTOR5-AS1 overexpression in NSCLC was verified in TCGA datasets and our own cohort and manifested an evident relationship with poor prognosis. Interference with LAMTOR5-AS1 led to repression of the proliferation, cloning, and metastasis abilities of NSCLC cells in vitro. We further confirmed an obvious increase in LAMTOR5-AS1-silenced NSCLC cell apoptosis. Furthermore, the absence of LAMTOR5-AS1 restricted tumor growth in vivo. Mechanistically, LAMTOR5-AS1 sponged miR-506-3p in NSCLC cells. Furthermore, E2F6, a downstream target of miR-506-3p, was under the control of LAMTOR5-AS1, which was realized by decoying miR-506-3p. Rescue experiments showed that miR-506-3p suppression or E2F6 reintroduction was capable of remitting LAMTOR5-AS1 deficiency-triggered anticarcinogenic actions in NSCLC. Our study confirmed the exact roles of LAMTOR5-AS1 for the first time and revealed that LAMTOR5-AS1 knockdown disrupts the malignancy of NSCLC by targeting the miR-506-3p/E2F6 axis. Targeting the LAMTOR5-AS1/miR-506-3p/E2F6 pathway may be instrumental for managing patients with NSCLC.
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Affiliation(s)
- Guojie Chen
- *Department of Oncology, The First People’s Hospital of Yancheng, The Fourth Affiliated Hospital of Nantong University, Jiangsu, P. R. China
| | - Kai Wang
- *Department of Oncology, The First People’s Hospital of Yancheng, The Fourth Affiliated Hospital of Nantong University, Jiangsu, P. R. China
| | - Guoshu Li
- †Department of Respiratory Medicine, Shanghai Tenth People’s Hospital, Tongji University School of Medicine, Shanghai, P. R. China
| | - Leidong Wang
- ‡Department of Pathology, Binzhou Medical University Hospital, Shandong, P. R. China
| | - Yangyang Xiao
- §Department of Clinical Laboratory, Binzhou Medical University Hospital, Shandong, P. R. China
| | - Bo Chen
- ¶Department of Infectious Disease, The First People’s Hospital of Yancheng, The Fourth Affiliated Hospital of Nantong University, Jiangsu, P. R. China
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Rafat M, Yadegar N, Dadashi Z, Shams K, Mohammadi M, Abyar M. The prominent role of miR-942 in carcinogenesis of tumors. Adv Biomed Res 2022; 11:63. [PMID: 36133499 PMCID: PMC9483553 DOI: 10.4103/abr.abr_226_21] [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: 07/27/2021] [Revised: 10/14/2021] [Accepted: 10/27/2021] [Indexed: 12/04/2022] Open
Abstract
As a family of short noncoding RNAs, MicroRNAs have been identified as possible biomarkers for cancer discovery and assist in therapy control due to their epigenetic involvement in gene expression and other cellular biological processes. In the present review, the evidence for reaching the clinical effect and the molecular mechanism of miR-942 in various kinds of cancer is amassed. Dysregulation of miR-942 amounts in different kinds of malignancies, as bladder cancer, esophageal squamous cell carcinoma, breast cancer, cervical cancer, gastric cancer, colorectal cancer, Kaposi's sarcoma, melanoma, Hepatocellular carcinoma, nonsmall-cell lung cancer, oral squamous cell carcinoma, osteosarcoma, ovarian cancer, pancreatic ductal adenocarcinoma, renal cell carcinoma, and prostate cancer has stated a considerable increase or decrease in its level indicating its function as oncogene or tumor suppressor. MiR-942 is included in cell proliferation, migration, and invasion through cell cycle pathways, including pathways of transforming growth factor-beta signaling pathways, Wnt pathway, JAK/STAT pathway, PI3K/AKT pathway, apoptosis pathway, hippo signaling pathway, lectin pathway, interferon-gamma signaling, signaling by G-protein coupled receptor, developmental genes, nuclear factor-kappa B pathway, Mesodermal commitment pathway, and T-cell receptor signaling in cancer. An important biomarker, MiR-942 is a potential candidate for prediction in several cancers. The present investigation introduced miR-942 as a prognostic marker for early discovery of tumor progression, metastasis, and development.
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9
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Pu Y, Tan Y, Zang C, Zhao F, Cai C, Kong L, Deng H, Chao F, Xia R, Xie M, Ge F, Pan Y, Cai S, Huang D. LAMTOR5-AS1 regulates chemotherapy-induced oxidative stress by controlling the expression level and transcriptional activity of NRF2 in osteosarcoma cells. Cell Death Dis 2021; 12:1125. [PMID: 34862368 PMCID: PMC8642434 DOI: 10.1038/s41419-021-04413-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 10/27/2021] [Accepted: 11/15/2021] [Indexed: 12/22/2022]
Abstract
Long-noncoding RNAs (lncRNAs) play roles in regulating cellular functions. High-throughput sequencing analysis identified a new lncRNA, termed LAMTOR5-AS1, the expression of which was much higher in the chemosensitive osteosarcoma (OS) cell line G-292 than in the chemoresistant cell line SJSA-1. Further investigations revealed that LAMTOR5-AS1 significantly inhibits the proliferation and multidrug resistance of OS cells. In vitro assays demonstrated that LAMTOR5-AS1 mediates the interaction between nuclear factor erythroid 2-related factor 2 (NFE2L2, NRF2) and kelch-like ECH-associated protein 1 (KEAP1), which regulate the oxidative stress. Further mechanistic studies revealed that LAMTOR5-AS1 inhibited the ubiquitination degradation pathway of NRF2, resulting in a higher level of NRF2 but a loss of NRF2 transcriptional activity. High level of NRF2 in return upregulated the downstream gene heme oxygenase 1 (HO-1). Moreover, NRF2 controls its own activity by promoting LAMTOR5-AS1 expression, whereas the feedback regulation is weakened in drug-resistant cells due to high antioxidant activity. Overall, we propose that LAMTOR5-AS1 globally regulates chemotherapy-induced cellular oxidative stress by controlling the expression and activity of NRF2.
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Affiliation(s)
- Youguang Pu
- grid.59053.3a0000000121679639Department of Cancer Epigenetics Program, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Yiao Tan
- grid.59053.3a0000000121679639Department of Urology Surgery, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Chunbao Zang
- grid.59053.3a0000000121679639Department of Radiation Oncology, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Fangfang Zhao
- grid.59053.3a0000000121679639Department of Cancer Epigenetics Program, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Cifeng Cai
- grid.412899.f0000 0000 9117 1462College of Life and Environmental Science, Wenzhou University, 325035 Wenzhou, Zhejiang People’s Republic of China
| | - Lingsuo Kong
- grid.59053.3a0000000121679639Department of Anesthesiology, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Hui Deng
- grid.59053.3a0000000121679639Department of Cancer Epigenetics Program, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Fengmei Chao
- grid.59053.3a0000000121679639Department of Cancer Epigenetics Program, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Ran Xia
- grid.59053.3a0000000121679639Department of Cancer Epigenetics Program, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Minghua Xie
- grid.59053.3a0000000121679639Department of Thoracic Tumor Surgery Department, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001 Hefei, Anhui People’s Republic of China
| | - Fangfang Ge
- grid.443626.10000 0004 1798 4069Department of Provincial Clinical College, Wannan Medical College, 241002 Wuhu, Anhui People’s Republic of China
| | - Yueyin Pan
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, People's Republic of China.
| | - Shanbao Cai
- Department of Orthopedic Surgery, Anhui Provincial Cancer Hospital, West Branch of the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, People's Republic of China.
| | - Dabing Huang
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, 230001, Hefei, Anhui, People's Republic of China.
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Haswell JR, Mattioli K, Gerhardinger C, Maass PG, Foster DJ, Peinado P, Wang X, Medina PP, Rinn JL, Slack FJ. Genome-wide CRISPR interference screen identifies long non-coding RNA loci required for differentiation and pluripotency. PLoS One 2021; 16:e0252848. [PMID: 34731163 PMCID: PMC8565776 DOI: 10.1371/journal.pone.0252848] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 08/26/2021] [Indexed: 12/26/2022] Open
Abstract
Although many long non-coding RNAs (lncRNAs) exhibit lineage-specific expression, the vast majority remain functionally uncharacterized in the context of development. Here, we report the first described human embryonic stem cell (hESC) lines to repress (CRISPRi) or activate (CRISPRa) transcription during differentiation into all three germ layers, facilitating the modulation of lncRNA expression during early development. We performed an unbiased, genome-wide CRISPRi screen targeting thousands of lncRNA loci expressed during endoderm differentiation. While dozens of lncRNA loci were required for proper differentiation, most differentially expressed lncRNAs were not, supporting the necessity for functional screening instead of relying solely on gene expression analyses. In parallel, we developed a clustering approach to infer mechanisms of action of lncRNA hits based on a variety of genomic features. We subsequently identified and validated FOXD3-AS1 as a functional lncRNA essential for pluripotency and differentiation. Taken together, the cell lines and methodology described herein can be adapted to discover and characterize novel regulators of differentiation into any lineage.
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Affiliation(s)
- Jeffrey R. Haswell
- Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Kaia Mattioli
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Chiara Gerhardinger
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
| | - Philipp G. Maass
- Genetics and Genome Biology Program, SickKids Research Institute, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel J. Foster
- Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- Department of Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Paola Peinado
- Department of Biochemistry and Molecular Biology, University of Granada, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - Xiaofeng Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, United States of America
| | - Pedro P. Medina
- Department of Biochemistry and Molecular Biology, University of Granada, Centre for Genomics and Oncological Research (GENYO), Granada, Spain
| | - John L. Rinn
- Department of Biochemistry, University of Colorado, BioFrontiers Institute, Boulder, Colorado, United States of America
| | - Frank J. Slack
- Department of Pathology, HMS Initiative for RNA Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts, United States of America
- * E-mail:
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Wang D, Dai C, Zhang X, Gu C, Liu M, Liu H, Yang F, Wu H, Wang Y. Identification and Functional Analysis of Long Non-coding RNAs in Human Pulmonary Microvascular Endothelial Cells Subjected to Cyclic Stretch. Front Physiol 2021; 12:655971. [PMID: 33868024 PMCID: PMC8047408 DOI: 10.3389/fphys.2021.655971] [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: 01/19/2021] [Accepted: 02/16/2021] [Indexed: 11/13/2022] Open
Abstract
Background: Despite decades of intense research, the pathophysiology and pathogenesis of acute respiratory distress syndrome (ARDS) are not adequately elucidated, which hamper the improvement of effective and convincing therapies for ARDS patients. Mechanical ventilation remains to be one of the primary supportive approaches for managing ARDS cases. Nevertheless, mechanical ventilation leads to the induction of further aggravating lung injury which is known as leading to ventilator-induced lung injury (VILI). It has been reported that lncRNAs play important roles in various cellular process through transcriptional, posttranscriptional, translational, and epigenetic regulations. However, to our knowledge, there is no investigation of the expression profile and functions of transcriptome-level endothelium-related lncRNAs in VILI yet. Methods: To screen the differential expression of lncRNAs and mRNAs in Human pulmonary microvascular endothelial cells (HPMECs) subjected to cyclic stretch, we constructed a cellular model of VILI, followed by transcriptome profiling using Affymetrix Human Transcriptome Array 2.0. Bioinformatics analyses, including functional and pathway enrichment analysis, protein-protein interaction network, lncRNA-mRNA coexpression network, and cis-analyses, were performed to reveal the potential functions and underlying mechanisms of differentially expressed lncRNAs. Results: In total, 199 differentially expressed lncRNAs (DELs) and 97 differential expressed mRNAs were screened in HPMECs subjected to 20% cyclic stretch for 2 h. The lncRNA-mRNA coexpression network suggested that DELs mainly enriched in response to hypoxia, response to oxidative stress, inflammatory response, cellular response to hypoxia, and NF-kappa B signaling pathway. LncRNA n335470, n406639, n333984, and n337322 might regulate inflammation and fibrosis induced by cyclic stretch through cis- or trans-acting mechanisms. Conclusion: This study provides the first transcriptomic landscape of differentially expressed lncRNAs in HPMECs subjected to cyclic stretch, which provides novel insights into the molecular mechanisms and potential directions for future basic and clinical research of VILI.
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Affiliation(s)
- Dong Wang
- Department of Anesthesiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Chenyang Dai
- Department of Ophthalmology, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaoning Zhang
- Department of Anesthesiology, Shandong Provincial Qianfoshan Hospital, Shandong University, Cheeloo College of Medicine, Jinan, China
| | - Changping Gu
- Department of Anesthesiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Mengjie Liu
- Department of Anesthesiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Huan Liu
- Department of Anesthesiology, Shandong Provincial Qianfoshan Hospital, Shandong University, Cheeloo College of Medicine, Jinan, China
| | - Fan Yang
- Department of Anesthesiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Haifeng Wu
- Department of Anesthesiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China
| | - Yuelan Wang
- Department of Anesthesiology, The First Affiliated Hospital of Shandong First Medical University & Shandong Provincial Qianfoshan Hospital, Shandong Institute of Anesthesia and Respiratory Critical Medicine, Jinan, China.,Department of Anesthesiology, Shandong Provincial Qianfoshan Hospital, Shandong University, Cheeloo College of Medicine, Jinan, China
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Chen Z, Huang J, Feng Y, Li Z, Jiang Y. Profiling of specific long non-coding RNA signatures identifies ST8SIA6-AS1 AS a novel target for breast cancer. J Gene Med 2021; 23:e3286. [PMID: 33037712 DOI: 10.1002/jgm.3286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 09/24/2020] [Accepted: 09/26/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Breast cancer is the most commonly diagnosed cancer among women and is also the leading cause of cancer death for which the treatment and methods of diagnosis remain unsatisfied. Long non-coding RNA (lncRNA) plays an important role in the occurrence and development of tumors, including breast cancer. We aimed to seek new and efficient treatment targets by analyzing the lncRNA expression profiles of breast cancer. METHODS A competitive endogenous RNA microarray was used to investigate the profiles of differentially expressed lncRNAs. Quantitative real-time polymerase chain reaction analysis (qRT-PCR) validated the top differentially expressed lncRNAs in 107 pairs of breast cancer tissues and adjacent normal tissues. cis- and trans-regulation mRNAs of lncRNAs were used to perform enrichment analysis. Cell function assays were used to explore the functions of ST8SIA6-AS1. RESULTS Seven lncRNAs, comprising ST8SIA6-AS1, lnc-HIST1H2BJ-5:1, lnc-PRICKLE2-3:2, RP1-86C11.7, RP11-15F12.1, ZNF670-ZNF695 and lnc-STRN3-12:1, were shown to be significantly up-regulated in breast cancer. lncRNA ST8SIA6-AS1 was associated with TNM staging and Ki-67 index. The cell function assays showed that ST8SIA6-AS1 can promote the proliferation, migration and invasion of breast cancer cells. The functions of ST8SIA6-AS1 were explored and the competing endogenous RNA mode showed that miR-4252 was a potential candidate. Its target genes were further predicted. The lncRNA-protein mode showed three potential candidate RNA binding proteins: NONO, QKI and RBMX. CONCLUSIONS lncRNA ST8SIA6-AS1 can promote the proliferation, migration and invasion of breast cancer cells. By hypothesizing two different functional modes of ST8SIA6-AS1, we found lncRNA ST8SIA6-AS1 may contribute to breast cancer progression through miR-4252 or interacting with RNA binding proteins: NONO, QKI and RBMX.
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Affiliation(s)
- Zhanghan Chen
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jie Huang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yanling Feng
- Department of Pathology, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zehuan Li
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Ying Jiang
- Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.,Department of General Surgery, Xiamen Branch, Zhongshan Hospital, Fudan University, Fujian, China
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