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Kim G, Siprashvili Z, Yang X, Meyers JM, Ji A, Khavari PA, Ducoli L. In vivo CRISPRi screen identified lncRNA portfolio crucial for cutaneous squamous cell carcinoma tumor growth. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.16.618774. [PMID: 39464078 PMCID: PMC11507908 DOI: 10.1101/2024.10.16.618774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
Abstract
Cutaneous squamous cell carcinoma (cSCC) accounts for 20% of all skin cancer deaths globally, making it the second-highest subtype of skin cancer. The prevalence of cSCC in humans, as well as the poor capacity for an efficient prognosis, highlights the need to uncover alternative actors and mechanisms at the foundation of skin cancer development. Significant advances have been made to better understand some key factors in cSCC progression. However, little is known about the role of noncoding RNAs, particularly of a specific category called long noncoding RNA (lncRNA). By performing pseudobulk analysis of single-cell sequencing data from normal and cSCC human skin tissues, we determined a global portfolio of lncRNAs specifically expressed in keratinocyte subpopulations. Integration of CRISPR interference screens in vitro and the xenograft model identified several lncRNAs impacting the growth of cSCC cancer lines both in vitro and in vivo. Among these, we further validated LINC00704 and LINC01116 as proliferation-regulating lncRNAs in cSCC lines and potential biomarkers of cSCC progression. Taken together, our study provides a comprehensive signature of lncRNAs with roles in regulating cSCC progression.
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Sarkar SS, Sharma M, Saproo S, Naidu S. LINC01116-dependent upregulation of RNA polymerase I transcription drives oncogenic phenotypes in lung adenocarcinoma. J Transl Med 2024; 22:904. [PMID: 39369230 PMCID: PMC11453068 DOI: 10.1186/s12967-024-05715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 09/30/2024] [Indexed: 10/07/2024] Open
Abstract
BACKGROUND Hyperactive RNA Polymerase I (Pol I) transcription is canonical in cancer, associated with malignant proliferation, poor prognosis, epithelial-mesenchymal transition, and chemotherapy resistance. Despite its significance, the molecular mechanisms underlying Pol I hyperactivity remain unclear. This study aims to elucidate the role of long noncoding RNAs (lncRNAs) in regulating Pol I transcription in lung adenocarcinoma (LUAD). METHODS Bioinformatics analyses were applied to identify lncRNAs interacting with Pol I transcriptional machinery. Fluorescence in situ hybridization was employed to examine the nucleolar localization of candidate lncRNA in LUAD cells. RNA immunoprecipitation assay validated the interaction between candidate lncRNA and Pol I components. Chromatin isolation by RNA purification and Chromatin Immunoprecipitation (ChIP) were utilized to confirm the interactions of candidate lncRNA with Pol I transcriptional machinery and the rDNA core promoter. Functional analyses, including lncRNA knock-in and knockdown, inhibition of Pol I transcription, quantitative PCR, cell proliferation, clonogenicity, apoptosis, cell cycle, wound-healing, and invasion assays, were performed to determine the effect of candidate lncRNA on Pol I transcription and associated malignant phenotypes in LUAD cells. ChIP assays and luminometry were used to investigate the transcriptional regulation of the candidate lncRNA. RESULTS We demonstrate that oncogenic LINC01116 scaffolds essential Pol I transcription factors TAF1A and TAF1D, to the ribosomal DNA promoter, and upregulate Pol I transcription. Crucially, LINC01116-driven Pol I transcription activation is essential for its oncogenic activities. Inhibition of Pol I transcription abrogated LINC01116-induced oncogenic phenotypes, including increased proliferation, cell cycle progression, clonogenicity, reduced apoptosis, increased migration and invasion, and drug sensitivity. Conversely, LINC01116 knockdown reversed these effects. Additionally, we show that LINC01116 upregulation in LUAD is driven by the oncogene c-Myc, a known Pol I transcription activator, indicating a functional regulatory feedback loop within the c-Myc-LINC01116-Pol I transcription axis. CONCLUSION Collectively, our findings reveal, for the first time, that LINC01116 enhances Pol I transcription by scaffolding essential transcription factors to the ribosomal DNA promoter, thereby driving oncogenic activities in LUAD. We propose the c-Myc-LINC01116-Pol I axis as a critical oncogenic pathway and a potential therapeutic target for modulating Pol I transcription in LUAD.
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Affiliation(s)
- Shashanka Shekhar Sarkar
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Mansi Sharma
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Sheetanshu Saproo
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Srivatsava Naidu
- Department of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India.
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Gan L, Zheng L, Zou J, Luo P, Chen T, Zou J, Li W, Chen Q, Cheng L, Zhang F, Qian B. Critical roles of lncRNA-mediated autophagy in urologic malignancies. Front Pharmacol 2024; 15:1405199. [PMID: 38939836 PMCID: PMC11208713 DOI: 10.3389/fphar.2024.1405199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Accepted: 05/23/2024] [Indexed: 06/29/2024] Open
Abstract
Urologic oncology is a significant public health concern on a global scale. Recent research indicates that long chain non-coding RNAs (lncRNAs) and autophagy play crucial roles in various cancers, including urologic malignancies. This article provides a summary of the latest research findings, suggesting that lncRNA-mediated autophagy could either suppress or promote tumors in prostate, kidney, and bladder cancers. The intricate network involving different lncRNAs, target genes, and mediated signaling pathways plays a crucial role in urological malignancies by modulating the autophagic process. Dysregulated expression of lncRNAs can disrupt autophagy, leading to tumorigenesis, progression, and enhanced resistance to therapy. Consequently, targeting particular lncRNAs that control autophagy could serve as a dependable diagnostic tool and a promising prognostic biomarker in urologic oncology, while also holding potential as an effective therapeutic approach.
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Affiliation(s)
- Lifeng Gan
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Liying Zheng
- Department of Graduate, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
| | - Junrong Zou
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Peiyue Luo
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Tao Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Jun Zou
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Wei Li
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Qi Chen
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Le Cheng
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Fangtao Zhang
- The First Clinical College, Gannan Medical University, Ganzhou, Jiangxi, China
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
| | - Biao Qian
- Department of Urology, The First Affiliated Hospital of Gannan Medical University, Ganzhou, Jiangxi, China
- Key Laboratory of Urology and Andrology of Ganzhou, Ganzhou, Jiangxi, China
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Ma K, Chu J, Liu Y, Sun L, Zhou S, Li X, Ji C, Zhang N, Guo X, Liang S, Cui T, Hu Q, Wang J, Liu Y, Liu L. Hepatocellular Carcinoma LINC01116 Outcompetes T Cells for Linoleic Acid and Accelerates Tumor Progression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2400676. [PMID: 38460179 PMCID: PMC11151013 DOI: 10.1002/advs.202400676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Indexed: 03/11/2024]
Abstract
Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer with a highly immunosuppressive tumor microenvironment and a typical pattern of disturbances in hepatic lipid metabolism. Long non-coding RNAs are shown to play an important role in the regulation of gene expression, but much remains unknown between tumor microenvironment and lipid metabolism as a bridging molecule. Here, long intergenic nonprotein coding RNA 01116 (LINC01116) acts as this molecular which is frequently upregulated in HCC patients and associated with HCC progression in vitro and in vivo is identified. Mechanistically, LINC01116 stabilizes EWS RNA-binding protein 1 (EWSR1) by preventing RAD18 E3 Ubiquitin Protein Ligase (RAD18) -mediated ubiquitination. The enhanced EWSR1 protein upregulates peroxisome proliferator activated receptor alpha (PPARA) and fatty acid binding protein1 (FABP1) expression, a long-chain fatty acid (LCFA) transporter, and thus cancer cells outcompete T cells for LCFAs, especially linoleic acid, for seeding their own growth, leading to T cell malfunction and HCC malignant progression. In a preclinical animal model, the blockade of LINC01116 leads to enhanced efficacy of anti-PD1 treatment accompanied by increased cytotoxic T cell and decreased exhausted T cell infiltration. Collectively, LINC01116 is an immunometabolic lncRNA and the LINC01116-EWSR1-PPARA-FABP1 axis may be targetable for cancer immunotherapy.
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Affiliation(s)
- Kun Ma
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| | - Junhui Chu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Yufeng Liu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Linmao Sun
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Shuo Zhou
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Xianying Li
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Changyong Ji
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Ning Zhang
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| | - Xinyu Guo
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
| | - Shuhang Liang
- Department of Gastrointestinal SurgeryAnhui Province Key Laboratory of Hepatopancreatobiliary SurgeryThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
| | - Tianming Cui
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Qingsong Hu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Jiabei Wang
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Yao Liu
- Department of Hepatobiliary SurgeryCentre for Leading Medicine and Advanced Technologies of IHMThe First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiAnhui230001China
- Anhui Province Key Laboratory of Hepatopancreatobiliary SurgeryHefeiAnhui230001China
- Anhui Provincial Clinical Research Center for Hepatobiliary DiseasesHefeiAnhui230001China
| | - Lianxin Liu
- Department of General SurgeryKey Laboratory of Hepatosplenic SurgeryMinistry of EducationThe First Affiliated Hospital of Harbin Medical UniversityHarbin150001China
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Zhang M, Wang Z, Wu Y, Chen M, Li J, Liu G. Hypoxia-induced factor-1α promotes radioresistance of esophageal cancer cells by transcriptionally activating LINC01116 and suppressing miR-3612 under hypoxia. J Biochem Mol Toxicol 2024; 38:e23551. [PMID: 37983895 DOI: 10.1002/jbt.23551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 08/02/2023] [Accepted: 09/27/2023] [Indexed: 11/22/2023]
Abstract
Esophageal cancer (EC) is a challenging tumor to treat with radiotherapy, often exhibiting resistance to this treatment modality. To explore the factors influencing radioresistance, we focused on the role of hypoxia-induced factor-1α (HIF-1α), and its interaction with the long noncoding RNA long intergenic nonprotein coding RNA 1116 (LINC01116). We analyzed the LINC01116 expression in EC and EC cell lines/human normal esophageal epithelial cell line (Het-1A). LINC01116 was silenced/overexpressed in EC109/KYSE30 cells under hypoxia, followed by radioresistance assessment. We measured HIF-1α levels in hypoxic EC cells and further validated the binding of HIF-1α with LINC01116, analyzing their interaction in EC cells. We then performed experiments in EC109 cells by transfection them with sh-HIF-1α/oe-LINC01116 to verify the effects. Additonally, we analyzed the localization of LINC01116 and its binding with miR-3612, followed by a combined experiment performed to validate the results. Our findings indicated that LINC01116 was highly expressed in EC and further elevated in hypoxic EC cells. LINC01116 was expressed at a high level in EC, which was further elevated in EC cells under hypoxic conditions. Knockdown of LINC01116 triggered EC cell apoptosis, thus suppressing radioresistance. Further investigation revealed that HIF-1α transcriptionally activated LINC01116 expression under hypoxia, and silencing HIF-1α lowered EC cell radioresistance by downregulating LINC01116. Under hypoxic conditions, LINC01116 could function as a sponge for miR-3612 and inhibit its expression. This interaction between LINC01116 and miR-3612 played a crucial role in mediating radioresistance in EC cells. Briefly, under hypoxic conditions, HIF-1α facilitates radioresistance of EC cells by transcriptionally activating LINC01116 expression and downregulating miR-3612.
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Affiliation(s)
- Mengyan Zhang
- Oncology Department, Guangzhou No.1 People's Hospital, Guangzhou City, Guangdong Province, P.R. China
- Thoracic Radiotherapy Department, Fujian Medical University Cancer Hospital Fujian Cancer Hospital, Fuzhou City, Fujian Province, P.R. China
| | - Zhiping Wang
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou City, Fujian Province, P.R. China
| | - Yahua Wu
- Thoracic Radiotherapy Department, Fujian Medical University Union Hospital, Fuzhou City, Fujian Province, P.R. China
| | - Mingqiu Chen
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou City, Fujian Province, P.R. China
| | - Jiancheng Li
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou City, Fujian Province, P.R. China
| | - Guolong Liu
- Oncology Department, Guangzhou No.1 People's Hospital, Guangzhou City, Guangdong Province, P.R. China
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Liu J, Qi Y, Hou S, Zhang S, Wang Z. Linc01116 Silencing Inhibits the Proliferation and Invasion, Promotes Apoptosis of Chordoma Cells via Regulating the Expression of Mir-9-5p/PKG1. Curr Mol Med 2024; 24:1056-1071. [PMID: 37489776 DOI: 10.2174/1566524023666230719121758] [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: 11/18/2022] [Revised: 06/09/2023] [Accepted: 06/19/2023] [Indexed: 07/26/2023]
Abstract
BACKGROUND Long intergenic non-protein coding RNA 1116 (LINC01116) plays a carcinogenic role in a variety of cancers. The study aims to investigate the roles of LINC01116 and hsa-miR-9-5p (miR-9-5p) and fathom their interaction in chordoma. METHODS The predicted binding sites between miR-9-5p with LINC01116 and phosphoglycerate kinase 1 (PGK1) by starBase were confirmed through dual-luciferase reporter assay. The behaviors of chordoma cells undergoing transfection with siLINC01116 or miR-9-5p inhibitor were determined by Cell Counting Kit-8 (CCK-8), colony formation, Transwell, and flow cytometry assays. The glucose consumption, lactate production, and adenosine triphosphate (ATP) production of chordoma cells were examined with specific kits. Quantitative real-time polymerase chain reaction (qRT-PCR) and Western blot were performed to determine relevant gene expressions in chordoma cells. RESULTS Silencing of LINC01116 facilitated the apoptosis and expressions of Bcl-2- associated X (Bax), cleaved caspase-3 (C caspase-3) and miR-9-5p while repressing the cell cycle, viability, proliferation, invasion, glucose consumption, lactate production, ATP production, and expressions of PGK1 and Bcl-2. Meanwhile, LINC01116 sponged miR-9-5p, which could target PGK1. Moreover, the miR-9-5p inhibitor acted contrarily and reversed the role of siLINC01116 in chordoma cells. Besides, LINC01116 downregulation facilitated apoptosis and attenuated the proliferation and invasion of chordoma cells as well as PGK1 expression by upregulating miR-9-5p expression. CONCLUSION LINC01116/miR-9-5p plays a regulatory role in the progression of chordoma cells and is a potential biomarker for chordoma.
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Affiliation(s)
- Junqi Liu
- Department of Otorhinolaryngology, Xuanwu Hospital Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, 100053, China
| | - Yan Qi
- Department of Otorhinolaryngology, Xuanwu Hospital Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, 100053, China
| | - Siyuan Hou
- Department of Otorhinolaryngology, Xuanwu Hospital Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, 100053, China
| | - Siyuan Zhang
- Department of Otorhinolaryngology, Xuanwu Hospital Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, 100053, China
| | - Zhenlin Wang
- Department of Otorhinolaryngology, Xuanwu Hospital Capital Medical University, 45 Changchun Street, Xicheng District, Beijing, 100053, China
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Ghasemian A, Omear HA, Mansoori Y, Mansouri P, Deng X, Darbeheshti F, Zarenezhad E, Kohansal M, Pezeshki B, Wang Z, Tang H. Long non-coding RNAs and JAK/STAT signaling pathway regulation in colorectal cancer development. Front Genet 2023; 14:1297093. [PMID: 38094755 PMCID: PMC10716712 DOI: 10.3389/fgene.2023.1297093] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/10/2023] [Indexed: 10/17/2024] Open
Abstract
Colorectal cancer (CRC) is one of the main fatal cancers. Cell signaling such as Janus kinase/signal transducer and activator of transcription (JAK/STAT) signaling substantially influences the process of gene expression and cell growth. Long non-coding RNAs (lncRNAs) play regulatory roles in cell signaling, cell proliferation, and cancer fate. Hence, lncRNAs can be considered biomarkers in cancers. The inhibitory or activating effects of different lncRNAs on the JAK/STAT pathway regulate cancer cell proliferation or tumor suppression. Additionally, lncRNAs regulate immune responses which play a role in immunotherapy. Mechanisms of lncRNAs in CRC via JAK/STAT regulation mainly include cell proliferation, invasion, metastasis, apoptosis, adhesion, and control of inflammation. More profound findings are warranted to specifically target the lncRNAs in terms of activation or suppression in hindering CRC cell proliferation. Here, to understand the lncRNA cross-talk in CRC through the JAK/STAT signaling pathway, we collected the related in vitro and in vivo data. Future insights may pave the way for the development of novel diagnostic tools, therapeutic interventions, and personalized treatment strategies for CRC patients.
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Affiliation(s)
- Abdolmajid Ghasemian
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Hadeel A. Omear
- College of Science, University of Tikrit University, Tikrit, Iraq
| | - Yaser Mansoori
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Pardis Mansouri
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Xinpei Deng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Farzaneh Darbeheshti
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Elham Zarenezhad
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Maryam Kohansal
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Babak Pezeshki
- Noncommunicable Diseases Research Center, Fasa University of Medical Sciences, Fasa, Iran
| | - Zhangling Wang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
| | - Hailin Tang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, China
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Poller W, Sahoo S, Hajjar R, Landmesser U, Krichevsky AM. Exploration of the Noncoding Genome for Human-Specific Therapeutic Targets-Recent Insights at Molecular and Cellular Level. Cells 2023; 12:2660. [PMID: 37998395 PMCID: PMC10670380 DOI: 10.3390/cells12222660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023] Open
Abstract
While it is well known that 98-99% of the human genome does not encode proteins, but are nevertheless transcriptionally active and give rise to a broad spectrum of noncoding RNAs [ncRNAs] with complex regulatory and structural functions, specific functions have so far been assigned to only a tiny fraction of all known transcripts. On the other hand, the striking observation of an overwhelmingly growing fraction of ncRNAs, in contrast to an only modest increase in the number of protein-coding genes, during evolution from simple organisms to humans, strongly suggests critical but so far essentially unexplored roles of the noncoding genome for human health and disease pathogenesis. Research into the vast realm of the noncoding genome during the past decades thus lead to a profoundly enhanced appreciation of the multi-level complexity of the human genome. Here, we address a few of the many huge remaining knowledge gaps and consider some newly emerging questions and concepts of research. We attempt to provide an up-to-date assessment of recent insights obtained by molecular and cell biological methods, and by the application of systems biology approaches. Specifically, we discuss current data regarding two topics of high current interest: (1) By which mechanisms could evolutionary recent ncRNAs with critical regulatory functions in a broad spectrum of cell types (neural, immune, cardiovascular) constitute novel therapeutic targets in human diseases? (2) Since noncoding genome evolution is causally linked to brain evolution, and given the profound interactions between brain and immune system, could human-specific brain-expressed ncRNAs play a direct or indirect (immune-mediated) role in human diseases? Synergistic with remarkable recent progress regarding delivery, efficacy, and safety of nucleic acid-based therapies, the ongoing large-scale exploration of the noncoding genome for human-specific therapeutic targets is encouraging to proceed with the development and clinical evaluation of novel therapeutic pathways suggested by these research fields.
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Affiliation(s)
- Wolfgang Poller
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 13353 Berlin, Germany
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
| | - Susmita Sahoo
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1030, New York, NY 10029, USA;
| | - Roger Hajjar
- Gene & Cell Therapy Institute, Mass General Brigham, 65 Landsdowne St, Suite 143, Cambridge, MA 02139, USA;
| | - Ulf Landmesser
- Department for Cardiology, Angiology and Intensive Care Medicine, Deutsches Herzzentrum Charité (DHZC), Charité-Universitätsmedizin Berlin, 12200 Berlin, Germany;
- German Center for Cardiovascular Research (DZHK), Site Berlin, 10785 Berlin, Germany
- Berlin Institute of Health, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany
| | - Anna M. Krichevsky
- Department of Neurology, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA;
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Kyrgiafini MA, Giannoulis T, Chatziparasidou A, Christoforidis N, Mamuris Z. Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility. Int J Mol Sci 2023; 24:15002. [PMID: 37834450 PMCID: PMC10573971 DOI: 10.3390/ijms241915002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Male infertility is a global health issue, affecting over 20 million men worldwide. Genetic factors are crucial in various male infertility forms, including teratozoospermia. Nonetheless, the genetic causes of male infertility remain largely unexplored. In this study, we employed whole-genome sequencing and RNA expression analysis to detect differentially expressed (DE) long-noncoding RNAs (lncRNAs) in teratozoospermia, along with mutations that are exclusive to teratozoospermic individuals within these DE lncRNAs regions. Bioinformatic tools were used to assess variants' impact on lncRNA structure, function, and lncRNA-miRNA interactions. Our analysis identified 1166 unique mutations in teratozoospermic men within DE lncRNAs, distinguishing them from normozoospermic men. Among these, 64 variants in 23 lncRNAs showed potential regulatory roles, 7 variants affected 4 lncRNA structures, while 37 variants in 17 lncRNAs caused miRNA target loss or gain. Pathway Enrichment and Gene Ontology analyses of the genes targeted by the affected miRNAs revealed dysregulated pathways in teratozoospermia and a link between male infertility and cancer. This study lists novel variants and lncRNAs associated for the first time with teratozoospermia. These findings pave the way for future studies aiming to enhance diagnosis and therapy in the field of male infertility.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Alexia Chatziparasidou
- Embryolab IVF Unit, St. 173-175 Ethnikis Antistaseos, Kalamaria, 55134 Thessaloniki, Greece
| | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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10
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Karimi Taheri M, Ghanbari S, Gholipour A, Givi T, Sadeghizadeh M. LINC01116 affects patient survival differently and is dissimilarly expressed in ER+ and ER- breast cancer samples. Cancer Rep (Hoboken) 2023; 6:e1848. [PMID: 37321964 PMCID: PMC10432450 DOI: 10.1002/cnr2.1848] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/18/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Breast cancer is the most commonly detected cancer and one of the leading causes of cancer mortality. Emerging evidence supports that aberrant expression of lncRNAs is correlated with tumor progression and various aspects of tumor development. AIM This study aimed to evaluate the expression pattern of LINC01116 in breast cancer tissues and investigate the impact of LINC01116 on patients' survival. METHODS AND RESULTS Microarray and qRT-PCR data analysis were performed, and the KM-plotter database was used in this study. In addition, the gain of function approach was performed to examine the effect of LINC01116 on breast cancer cells in-vitro. The results exhibited that LINC01116 is meaningfully upregulated in the ER+ tumor specimens compared to the ER- ones. Also, relative to normal tissues, the expression of LINC01116 in ER+ and ER- tumor tissues significantly increased and decreased, respectively. ROC curve analysis revealed the power of LINC01116 in distinguishing ER+ from ER- samples. Additionally, the Kaplan-Meier survival analysis showed that the LINC01116 expression positively correlates with survival probability in all as well as ER+ patients. However, this correlation was negative in ER- patients. Furthermore, our results showed that the overexpression of LINC01116 induces TGF-β signaling in ER- cells (MDA-MB-231), and microarray data analysis revealed that LINC01116 is significantly upregulated in 17β-Estradiol treated MCF7 cells. CONCLUSION In conclusion, our results suggest that LINC01116 can be a potential biomarker in distinguishing ER+ and ER- tissues and has different effects on patients' survival based on ER status by affecting TGF-β and ER signaling.
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Affiliation(s)
| | - Sogol Ghanbari
- Molecular Genetics DepartmentBiological Sciences Faculty, Tarbiat Modares UniversityTehranIran
| | - Akram Gholipour
- Cardiogenetic Research Center, Rajaie Cardiovascular Medical and Research CenterIran University of Medical SciencesTehranIran
| | - Taraneh Givi
- Molecular Genetics DepartmentBiological Sciences Faculty, Tarbiat Modares UniversityTehranIran
| | - Majid Sadeghizadeh
- Molecular Genetics DepartmentBiological Sciences Faculty, Tarbiat Modares UniversityTehranIran
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11
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Chao C, Tang R, Zhao J, Di D, Qian Y, Wang B. Oncogenic roles and related mechanisms of the long non-coding RNA MINCR in human cancers. Front Cell Dev Biol 2023; 11:1087337. [PMID: 37215074 PMCID: PMC10196036 DOI: 10.3389/fcell.2023.1087337] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 04/24/2023] [Indexed: 05/24/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play vital roles in regulating epigenetic mechanisms and gene expression levels, and their dysregulation is closely associated with a variety of diseases such as cancer. Several studies have demonstrated that lncRNAs are dysregulated during tumor progression. Recently, the MYC-induced long non-coding RNA MINCR, a newly identified lncRNA, has been demonstrated to act as an oncogene in different cancers, including gallbladder cancer, hepatocellular cancer, colorectal cancer, non-small cell lung cancer, oral squamous cell carcinoma, nasopharyngeal cancer, and glioma. Moreover, MINCR has been reported to act as a biomarker in the prognosis of patients with different cancers. In this review, we summarize and analyze the oncogenic roles of MINCR in a variety of human cancers in terms of its clinical significance, biological functions, cellular activities, and regulatory mechanism. Our analysis of the literature suggests that MINCR has potential as a novel biomarker and therapeutic target in human cancers.
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Affiliation(s)
- Ce Chao
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Renzhe Tang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Jiamin Zhao
- Department of Respiratory Medicine, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Dongmei Di
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Yongxiang Qian
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
| | - Bin Wang
- Department of Cardiothoracic Surgery, The Third Affiliated Hospital of Soochow University, Changzhou, China
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12
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Identification and Characterization of an Ageing-Associated 13-lncRNA Signature That Predicts Prognosis and Immunotherapy in Hepatocellular Carcinoma. JOURNAL OF ONCOLOGY 2023; 2023:4615297. [PMID: 36844873 PMCID: PMC9957638 DOI: 10.1155/2023/4615297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/28/2022] [Accepted: 10/13/2022] [Indexed: 02/19/2023]
Abstract
Background In cancer pathology, cell senescence not only alters cell function but also reshapes the immune microenvironments in tumours. However, the association between cell senescence, tumour microenvironment, and disease progression of hepatocellular carcinoma (HCC) is yet to be fully understood. Therefore, the role of cell senescence-related genes and long noncoding RNAs (lncRNAs) in evaluating the clinical prognosis and immune cell infiltration (ICI) of HCC patients requires further investigation. Methods The limma R package was utilised to investigate differentially expressed genes according to the multiomics data. The CIBERSORT R package was utilised to assess ICI, and unsupervised cluster analysis was conducted using the R software's ConsensusClusterPlus package. A polygenic prognostic model of lncRNAs was constructed by conducting univariate and least absolute shrinkage and selection operator (Lasso) cox proportional-hazards regression analyses. The time-dependent receiver operating characteristic (ROC) curves were used for validation. We utilised the survminer R package to evaluate the tumour mutational burden (TMB). Moreover, the gene set enrichment analysis (GSEA) helped in pathway enrichment analysis, and the immune infiltration level of the model was evaluated using the IMvigor210 cohort. Results The identification of 36 prognosis-related genes was achieved based on their differential expression between healthy and liver cancer tissues. Liver cancer individuals were categorised into 3 independent senescence subtypes using the gene list, revealing considerable survival differences (variations). We observed that the prognosis of patients in the ARG-ST2 subtype was substantially better as compared to that in the ARG-ST3 subtype. Differences were observed in gene expression profiles among the three subtypes, with the differentially expressed genes predominantly associated with cell cycle control. The enrichment of upregulated genes in the ARG-ST3 subtype was observed in pathways related to biological processes, for instance, organelle fission, nuclear division, and chromosome recombination. ICI in the ARG-ST1 and ARG-ST2 subtypes, with relatively better prognosis, was substantially higher as compared to the ARG-ST3 subtype. Furthermore, a risk-score model, which can be employed as a reliable prognostic factor in an independent manner for individuals suffering from liver cancer, was constructed based on 13 cell senescence-related lncRNAs (MIR99AHG, LINC01224, LINC01138, SLC25A30AS1, AC006369.2, SOCS2AS1, LINC01063, AC006037.2, USP2AS1, FGF14AS2, LINC01116, KIF25AS1, and AC002511.2). The individuals with higher risk scores had noticeably poor prognoses in contrast with those having low-risk scores. Moreover, increased levels of TMB and ICI were observed in individuals with low-risk scores and gaining more benefit from immune checkpoint therapy. Conclusion Cell senescence is an essential factor in HCC onset and progression. We identified 13 senescence-related lncRNAs as HCC prognostic markers, which can help understand their function in the onset and progression of HCC and guide clinical diagnosis and treatment.
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13
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Zhang T, Tang X, Zhu Y, Wang C, Jiang Z, Yang N, Wang T, Shu L, Xu Y, Sun L. IGF2BP2 enhances LincRNA01116 stability via m 6 A: A potential biomarker and therapeutic target for patients with pre-eclampsia. J Cell Biochem 2023; 124:239-253. [PMID: 36538649 DOI: 10.1002/jcb.30358] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 11/23/2022] [Accepted: 11/29/2022] [Indexed: 02/24/2023]
Abstract
Pre-eclampsia (PE) is a serious complication in pregnant women characterized by failure of placental remodeling and is one of the primary causes of changes in the placental structure and function. The aberrant expression of long noncoding RNA is associated with the occurrence and progression of PE. This study found that linc01116 expression was significantly downregulated in PE patients and was related to poor uterine spiral artery remodeling. Knockdown of linc01116 remarkably decreased the angiogenesis of trophoblast cells in vitro and in vivo. Mechanistically, IGF2BP2 regulated linc01116 RNA stability via m6 A methylation. Bioinformatics and other experiments further revealed that linc01116 upregulates AAMP expression by adsorbing miR-210-3p in trophoblast cells. In conclusion, this study revealed the critical role of linc01116 in regulating trophoblast angiogenesis. Furthermore, the study provides new clues for detecting placental pathology in PE.
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Affiliation(s)
- Tingting Zhang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Xiaotong Tang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yuanyuan Zhu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Cong Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Ziyan Jiang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Nana Yang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Tianjun Wang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lijun Shu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Yetao Xu
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
| | - Lizhou Sun
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, People's Republic of China
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14
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Jiang H, Sun J, Liu F, Wu X, Wen Z. An Immune-Related Long Noncoding RNA Pair as a New Biomarker to Predict the Prognosis of Patients in Breast Cancer. Front Genet 2022; 13:895200. [PMID: 35812755 PMCID: PMC9257047 DOI: 10.3389/fgene.2022.895200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Immune-related long non-coding RNAs (irlncRNAs) might remodel the tumor immune microenvironment by changing the inherent properties of tumor cells and the expression of immune genes, which have been used to predict the efficacy of immunotherapy and the prognosis of various tumors. However, the value of irlncRNAs in breast cancer (BRCA) remains unclear.Materials and Methods: Initially, transcriptome data and immune-related gene sets were downloaded from The Cancer Genome Atlas (TCGA) database. The irlncRNAs were extracted from the Immunology Database and Analysis Portal (ImmPort) database. Differently expressed irlncRNAs (DEirlncRNAs) were further identified by utilizing the limma R package. Then, univariate and multivariate Cox regression analyses were conducted to select the DEirlncRNAs associated with the prognosis of BRCA patients. In addition, the univariate and least absolute shrinkage and selection operator (LASSO) Cox regression analyses were performed to determine the DEirlncRNA pairs with the independent prediction capability of prognosis in BRCA patients. Finally, the chosen DEirlncRNA pair would be evaluated in terms of survival time, clinicopathological characteristics, tumor-infiltrating immune cells, immune checkpoints (ICs), signaling pathways, and potential small-molecule drugs.Results: A total of 21 DEirlncRNA pairs were extracted, and among them, lncRNA MIR4435-2HG and lncRNA U62317.1 were chosen to establish a risk signature that served as an independent prognostic biomarker in BRCA patients. Patients in the high-risk group had a worse prognosis than those in the low-risk group, and they also had an abundance of infiltration of CD4+ T and CD8+ T cells to enhance the immune response to tumor cells. Furthermore, the risk signature showed a strong correlation with ICs, signaling pathways, and potential small-molecule drugs.Conclusion: Our research revealed that the risk signature independent of specific DEirlncRNA pair expression was closely associated with the prognosis and tumor immune microenvironment in BRCA patients and had the potential to function as an independent prognostic biomarker and a predictor of immunotherapy for BRCA patients, which would provide new insights for BRCA accurate treatment.
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Affiliation(s)
- Hanwen Jiang
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingxian Sun
- Department of Neurosurgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Fucong Liu
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xincai Wu
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhaohui Wen
- Department of Neurology, Brain Ultrasound, The First Affiliated Hospital of Harbin Medical University, Harbin, China
- *Correspondence: Zhaohui Wen,
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15
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Ying Y, Liu D, Zhao Y, Zhong Y, Xu X, Luo J, Zhang Z. LINC01116 Promotes Migration and Invasion of Oral Squamous Cell Carcinoma by Acting as a Competed Endogenous RNA in Regulation of MMP1 Expression. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:2857022. [PMID: 35756415 PMCID: PMC9232319 DOI: 10.1155/2022/2857022] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/28/2022] [Indexed: 02/06/2023]
Abstract
Oral squamous cell carcinoma (OSCC) has increasingly become a worldwide health concern, and its survival rate has not been much improved partially due to a deficiency of precise molecular markers. Dysregulation of LINC01116, a long noncoding RNA sequence, has been observed in several types of cancer. However, the role played by LINC01116 in OSCC has not yet been fully elaborated. This study explored how LINC01116 was involved in the regulation of OSCC progression by analyzing expressions of LINC01116 in OSCC patients. The findings demonstrated upregulation of LINC01116 in OSCC tissues as opposed to regular oral mucosa, and overexpression of LINC01116 was correlated with advanced tumor status. LINC01116 knockdown using shRNA markedly reduced the OSCC cell invasion and migration in vitro. Moreover, the expression of LINC01116 was negatively correlated with that of microRNA-9-5p (miR-9). Luciferase reporter and loss-of-function assays demonstrated that LINC01116 functioned as a competing endogenous RNA (ceRNA) that could effectively sponge miR-9, thus regulating the derepression of matrix metalloproteinase 1 (MMP1). Furthermore, we confirmed that LINC01116 knockdown did not affect the expression of MMP1 messenger RNA (mRNA). Collectively, it is demonstrated in this study that overexpression of LINC01116 can promote the OSCC progression. The LINC01116-miR-9-MMP1 axis provides a novel insight into the OSCC pathogenesis and offers potential therapeutic targets against OSCC.
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Affiliation(s)
- Yukang Ying
- Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000 Zhejiang Province, China
| | - Dong Liu
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Anhui Medical University, Hefei, 230000 Anhui Province, China
| | - Yue Zhao
- Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000 Zhejiang Province, China
| | - Yuan Zhong
- Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000 Zhejiang Province, China
| | - Xuhui Xu
- Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000 Zhejiang Province, China
| | - Jun Luo
- Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000 Zhejiang Province, China
| | - Zhenxing Zhang
- Department of Stomatology, Taizhou Central Hospital (Taizhou University Hospital), Taizhou, 318000 Zhejiang Province, China
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16
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Deforzh E, Uhlmann EJ, Das E, Galitsyna A, Arora R, Saravanan H, Rabinovsky R, Wirawan AD, Teplyuk NM, El Fatimy R, Perumalla S, Jairam A, Wei Z, Mirny L, Krichevsky AM. Promoter and enhancer RNAs regulate chromatin reorganization and activation of miR-10b/HOXD locus, and neoplastic transformation in glioma. Mol Cell 2022; 82:1894-1908.e5. [PMID: 35390275 PMCID: PMC9271318 DOI: 10.1016/j.molcel.2022.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/27/2022] [Accepted: 03/10/2022] [Indexed: 01/06/2023]
Abstract
miR-10b is silenced in normal neuroglial cells of the brain but commonly activated in glioma, where it assumes an essential tumor-promoting role. We demonstrate that the entire miR-10b-hosting HOXD locus is activated in glioma via the cis-acting mechanism involving 3D chromatin reorganization and CTCF-cohesin-mediated looping. This mechanism requires two interacting lncRNAs, HOXD-AS2 and LINC01116, one associated with HOXD3/HOXD4/miR-10b promoter and another with the remote enhancer. Knockdown of either lncRNA in glioma cells alters CTCF and cohesin binding, abolishes chromatin looping, inhibits the expression of all genes within HOXD locus, and leads to glioma cell death. Conversely, in cortical astrocytes, enhancer activation is sufficient for HOXD/miR-10b locus reorganization, gene derepression, and neoplastic cell transformation. LINC01116 RNA is essential for this process. Our results demonstrate the interplay of two lncRNAs in the chromatin folding and concordant regulation of miR-10b and multiple HOXD genes normally silenced in astrocytes and triggering the neoplastic glial transformation.
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Affiliation(s)
- Evgeny Deforzh
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Erik J Uhlmann
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Eashita Das
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksandra Galitsyna
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 143026, Russia
| | - Ramil Arora
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Harini Saravanan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aditya D Wirawan
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Nadiya M Teplyuk
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Rachid El Fatimy
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Sucika Perumalla
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anirudh Jairam
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leonid Mirny
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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17
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Yang L, Guo G, Yu X, Wen Y, Lin Y, Zhang R, Zhao D, Huang Z, Wang G, Yan Y, Zhang X, Chen D, Xing W, Wang W, Zeng W, Zhang L. Mutation-Derived Long Noncoding RNA Signature Predicts Survival in Lung Adenocarcinoma. Front Oncol 2022; 12:780631. [PMID: 35372012 PMCID: PMC8965709 DOI: 10.3389/fonc.2022.780631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
Background Genomic instability is one of the representative features of cancer evolution. Recent research has revealed that long noncoding RNAs (lncRNAs) play a critical role in maintaining genomic instability. Our work proposed a gene signature (GILncSig) based on genomic instability-derived lncRNAs to probe the possibility of lncRNA signatures as an index of genomic instability, providing a potential new approach to identify genomic instability-related cancer biomarkers. Methods Lung adenocarcinoma (LUAD) gene expression data from an RNA-seq FPKM dataset, somatic mutation information and relevant clinical materials were downloaded from The Cancer Genome Atlas (TCGA). A prognostic model consisting of genomic instability-related lncRNAs was constructed, termed GILncSig, to calculate the risk score. We validated GILncSig using data from the Gene Expression Omnibus (GEO) database. In this study, we used R software for data analysis. Results Through univariate and multivariate Cox regression analyses, five genomic instability-associated lncRNAs (LINC01671, LINC01116, LINC01214, lncRNA PTCSC3, and LINC02555) were identified. We constructed a lncRNA signature (GILncSig) related to genomic instability. LUAD patients were classified into two risk groups by GILncSig. The results showed that the survival rate of LUAD patients in the low-risk group was higher than that of those in the high-risk group. Then, we verified GILncSig in the GEO database. GILncSig was associated with the genomic mutation rate of LUAD. We also used GILncSig to divide TP53 mutant-type patients and TP53 wild-type patients into two groups and performed prognostic analysis. The results suggested that compared with TP53 mutation status, GILncSig may have better prognostic significance. Conclusions By combining the lncRNA expression profiles associated with somatic mutations and the corresponding clinical characteristics of LUAD, a lncRNA signature (GILncSig) related to genomic instability was established.
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Affiliation(s)
- Longjun Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guangran Guo
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiangyang Yu
- Department of Thoracic Surgery, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yingsheng Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yongbin Lin
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Rusi Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dechang Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Zirui Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Gongming Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Yan Yan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Huizhou Municipal Central Hospital, Huizhou, China
| | - Xuewen Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Dongtai Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Wei Xing
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Weidong Wang
- Department of Thoracic Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Weian Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Anesthesiology, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Lanjun Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.,Department of Thoracic Surgery, Sun Yat-sen University Cancer Center, Guangzhou, China
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