1
|
Lee JS, Dan T, Zhang H, Cheng Y, Rehfeld F, Brugarolas J, Mendell JT. An ultraconserved snoRNA-like element in long noncoding RNA CRNDE promotes ribosome biogenesis and cell proliferation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604857. [PMID: 39091767 PMCID: PMC11291168 DOI: 10.1101/2024.07.23.604857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Cancer cells frequently upregulate ribosome production to support tumorigenesis. While small nucleolar RNAs (snoRNAs) are critical for ribosome biogenesis, the roles of other classes of noncoding RNAs in this process remain largely unknown. Here we performed CRISPRi screens to identify essential long noncoding RNAs (lncRNAs) in renal cell carcinoma (RCC) cells. This revealed that an alternatively-spliced isoform of lncRNA Colorectal Neoplasia Differentially Expressed containing an ultraconserved element (UCE), referred to as CRNDE UCE, is required for RCC cell proliferation. CRNDE UCE localizes to the nucleolus and promotes 60S ribosomal subunit biogenesis. The UCE of CRNDE functions as an unprocessed C/D box snoRNA that directly interacts with ribosomal RNA precursors. This facilitates delivery of eIF6, a key 60S biogenesis factor, which binds to CRNDE UCE through a sequence element adjacent to the UCE. These findings highlight the functional versatility of snoRNA sequences and expand the known mechanisms through which noncoding RNAs orchestrate ribosome biogenesis.
Collapse
Affiliation(s)
- Jong-Sun Lee
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tu Dan
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - He Zhang
- Quantitative Biomedical Research Center, Peter O’Donnell Jr. School of Public Health, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yujing Cheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Frederick Rehfeld
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - James Brugarolas
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Kidney Cancer Program, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Joshua T. Mendell
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| |
Collapse
|
2
|
Heydari R, Karimi P, Meyfour A. Long non-coding RNAs as pathophysiological regulators, therapeutic targets and novel extracellular vesicle biomarkers for the diagnosis of inflammatory bowel disease. Biomed Pharmacother 2024; 176:116868. [PMID: 38850647 DOI: 10.1016/j.biopha.2024.116868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a chronic relapsing disease of the gastrointestinal (GI) system that includes two groups, Crohn's disease (CD) and ulcerative colitis (UC). To cope with these two classes of IBD, the investigation of pathogenic mechanisms and the discovery of new diagnostic and therapeutic approaches are crucial. Long non-coding RNAs (lncRNAs) which are non-coding RNAs with a length of longer than 200 nucleotides have indicated significant association with the pathology of IBD and strong potential to be used as accurate biomarkers in diagnosing and predicting responses to the IBD treatment. In the current review, we aim to investigate the role of lncRNAs in the pathology and development of IBD. We first describe recent advances in research on dysregulated lncRNAs in the pathogenesis of IBD from the perspective of epithelial barrier function, intestinal immunity, mitochondrial function, and intestinal autophagy. Then, we highlight the possible translational role of lncRNAs as therapeutic targets, diagnostic biomarkers, and predictors of therapeutic response in colon tissues and plasma samples. Finally, we discuss the potential of extracellular vesicles and their lncRNA cargo in the pathophysiology, diagnosis, and treatment of IBD.
Collapse
Affiliation(s)
- Raheleh Heydari
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Padideh Karimi
- CRTD/Center for Regenerative Therapies Dresden, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Dresden 01307, Germany
| | - Anna Meyfour
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
3
|
Sun J, Guo H, Zhang S, Nie Y, Zhou S, Zeng Y, Sun Y. Machine learning-based integration develops an immunogenic cell death-derived lncRNA signature for predicting prognosis and immunotherapy response in lung adenocarcinoma. Sci Rep 2024; 14:11724. [PMID: 38778157 PMCID: PMC11111459 DOI: 10.1038/s41598-024-62569-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 05/19/2024] [Indexed: 05/25/2024] Open
Abstract
Accumulating evidence demonstrates that lncRNAs are involved in the regulation of the immune microenvironment and early tumor development. Immunogenic cell death occurs mainly through the release or increase of tumor-associated antigen and tumor-specific antigen, exposing "danger signals" to stimulate the body's immune response. Given the recent development of immunotherapy in lung adenocarcinoma, we explored the role of tumor immunogenic cell death-related lncRNAs in lung adenocarcinoma for prognosis and immunotherapy benefit, which has never been uncovered yet. Based on the lung adenocarcinoma cohorts from the TCGA database and GEO database, the study developed the immunogenic cell death index signature by several machine learning algorithms and then validated the signature for prognosis and immunotherapy benefit of lung adenocarcinoma patients, which had a more stable performance compared with published signatures in predicting the prognosis, and demonstrated predictive value for benefiting from immunotherapy in multiple cohorts of multiple cancers, and also guided the utilization of chemotherapy drugs.
Collapse
Affiliation(s)
- Jiazheng Sun
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Hehua Guo
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Respiratory Medicine, The First People's Hospital of Jiangxia District, Wuhan, China
| | - Siyu Zhang
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yalan Nie
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sirui Zhou
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yulan Zeng
- Department of Respiratory Medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| | - Yalu Sun
- Department of Rehabilitation Medicine, Affiliated Hospital of Jining Medical University, Jining, China.
| |
Collapse
|
4
|
Yang T, Zhang R, Cui Z, Zheng B, Zhu X, Yang X, Huang Q. Glycolysis‑related lncRNA may be associated with prognosis and immune activity in grade II‑III glioma. Oncol Lett 2024; 27:238. [PMID: 38601183 PMCID: PMC11005085 DOI: 10.3892/ol.2024.14371] [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: 11/19/2023] [Accepted: 03/04/2024] [Indexed: 04/12/2024] Open
Abstract
Glucose metabolism, as a novel theory to explain tumor cell behavior, has been intensively studied in various tumors. The present study explored the long non-coding RNAs (lncRNAs) related to glycolysis in grade II-III glioma, aiming to provide a promising target for further research. Pearson correlation analysis was used to identify glycolysis-related lncRNAs. Univariate/multivariate Cox regression analysis and the Least Absolute Shrinkage and Selection Operator algorithm were applied to identify glycolysis-related lncRNAs to construct a prognosis prediction model. Subsequently, multi-dimensional evaluations were used to verify whether the risk model could predict the prognosis and survival rate of patients with grade II-III glioma. Finally, it was verified by functional experiments. The present study finally identified seven glycolysis-related lncRNAs (CRNDE, AC022034.1, RHOQ-AS1, AL159169.2, AL133215.2, AC007098.1 and LINC02587) to construct a prognosis prediction model. The present study further investigated the underlying immune microenvironment, somatic landscape and functional enrichment pathways. Additionally, individualized immunotherapeutic strategies and candidate compounds were identified to guide clinical treatment. The experimental results demonstrated that CRNDE could increase the proliferation of SHG-44 cells. In conclusion, a large sample of human grade II-III glioma in The Cancer Genome Atlas database was used to construct a risk model using glycolysis-related lncRNAs to predict the prognosis of patients with grade II-III glioma.
Collapse
Affiliation(s)
- Tao Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300000, P.R. China
- Department of Neurosurgery, Heji Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Ruiguang Zhang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300000, P.R. China
| | - Zhenfen Cui
- Department of Neurosurgery, Heji Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi 046000, P.R. China
| | - Bowen Zheng
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300000, P.R. China
| | - Xiaowei Zhu
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300000, P.R. China
| | - Xinyu Yang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300000, P.R. China
| | - Qiang Huang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin 300000, P.R. China
| |
Collapse
|
5
|
Jasim SA, Al-Hawary SIS, Hjazi A, Ahmad I, Kaur I, Kadhum WR, Alkhafaji AT, Ghildiyal P, Jawad MA, Alsaadi SB. A comprehensive review of lncRNA CRNDE in cancer progression and pathology, with a specific glance at the epithelial-mesenchymal transition (EMT) process. Pathol Res Pract 2024; 256:155229. [PMID: 38484655 DOI: 10.1016/j.prp.2024.155229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/09/2024] [Accepted: 02/25/2024] [Indexed: 04/14/2024]
Abstract
It has been suggested that the long non-coding RNAs (lncRNAs), such as colorectal neoplasia differentially expressed (CRNDE), may contribute to the formation of human cancer. It is yet unknown, though, what therapeutic significance CRNDE expression has for different forms of cancer. CRNDE has recently been proposed as a possible diagnostic biomarker and prognostic pred for excellent specificity and sensitivity in cancer tissues and plasma. To provide the groundwork for potential future therapeutic uses of CRNDE, we briefly overview its biological action and related cancer-related pathways. Next, we mainly address the impact of CRNDE on the epithelial-mesenchymal transition (EMT). The epithelial-mesenchymal transition, or EMT, is an essential biological mechanism involved in the spread of cancer.
Collapse
Affiliation(s)
| | | | - Ahmed Hjazi
- Department of Medical Laboratory, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Irfan Ahmad
- Department of Clinical Laboratory Sciences, College of Applied Medical Science, King Khalid University, Abha, Saudi Arabia.
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Wesam R Kadhum
- Department of Pharmacy, Kut University College, Kut, Wasit 52001, Iraq; Advanced research center, Kut University College, Kut, Wasit 52001, Iraq
| | | | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Salim B Alsaadi
- Department of Pharmaceutics, Al-Hadi University College, Baghdad 10011, Iraq
| |
Collapse
|
6
|
Lobo-Alves SC, Oliveira LAD, Kretzschmar GC, Valengo AE, Rosati R. Long noncoding RNA expression in acute lymphoblastic leukemia: A systematic review. Crit Rev Oncol Hematol 2024; 196:104290. [PMID: 38341118 DOI: 10.1016/j.critrevonc.2024.104290] [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: 09/01/2023] [Revised: 01/03/2024] [Accepted: 02/05/2024] [Indexed: 02/12/2024] Open
Abstract
Long noncoding RNAs (lncRNAs), as gene expression modulators, are potential players in Acute Lymphoblastic Leukemia (ALL) pathogenesis. We systematically explored current literature on lncRNA expression in ALL to identify lncRNAs consistently reported as differentially expressed (DE) either in ALL versus controls or between ALL subtypes. By comparing articles that provided global expression data for DE lncRNAs in the ETV6::RUNX1-positive ALL subtype, we identified four DE lncRNAs in three independent studies (two versus other subtypes and one versus controls), showing concordant expression of LINC01013, CRNDE and lnc-KLF7-1. Additionally, LINC01503 was consistently downregulated on ALL versus controls. Within RT-qPCR studies, twelve lncRNA were DE in more than one source. Thus, several lncRNAs were supported as DE in ALL by multiple sources, highlighting their potential role as candidate biomarkers or therapeutic targets. Finally, as lncRNA annotation is rapidly expanding, standardization of reporting and nomenclature is urgently needed to improve data verifiability and compilation.
Collapse
Affiliation(s)
- Sara Cristina Lobo-Alves
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Liana Alves de Oliveira
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Gabriela Canalli Kretzschmar
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| | - Andressa Eloisa Valengo
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil
| | - Roberto Rosati
- Instituto de Pesquisa Pelé Pequeno Príncipe, Av. Silva Jardim, 1632 - Água Verde, Curitiba, PR 80250-060, Brazil; Faculdades Pequeno Príncipe, Av Iguaçu, 333, Rebouças, Curitiba, PR 80230-020, Brazil; National Science and Technology Institute for Children's Cancer Biology and Pediatric Oncology - INCT BioOncoPed, Porto Alegre, RS 90035-003, Brazil.
| |
Collapse
|
7
|
Zabeti Touchaei A, Vahidi S, Samadani AA. Decoding the regulatory landscape of lncRNAs as potential diagnostic and prognostic biomarkers for gastric and colorectal cancers. Clin Exp Med 2024; 24:29. [PMID: 38294554 PMCID: PMC10830721 DOI: 10.1007/s10238-023-01260-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]
Abstract
Colorectal cancer (CRC) and gastric cancer (GC) are major contributors to cancer-related mortality worldwide. Despite advancements in understanding molecular mechanisms and improved drug treatments, the overall survival rate for patients remains unsatisfactory. Metastasis and drug resistance are major challenges contributing to the high mortality rate in both CRC and GC. Recent research has shed light on the role of long noncoding RNAs (lncRNAs) in the development and progression of these cancers. LncRNAs regulate gene expression through various mechanisms, including epigenetic modifications and interactions with microRNAs (miRNAs) and proteins. They can serve as miRNA precursors or pseudogenes, modulating gene expression at transcriptional and post-transcriptional levels. Additionally, circulating lncRNAs have emerged as non-invasive biomarkers for the diagnosis, prognosis, and prediction of drug therapy response in CRC and GC. This review explores the intricate relationship between lncRNAs and CRC/GC, encompassing their roles in cancer development, progression, and chemoresistance. Furthermore, it discusses the potential of lncRNAs as therapeutic targets in these malignancies. The interplay between lncRNAs, miRNAs, and tumor microenvironment is also highlighted, emphasizing their impact on the complexity of cancer biology. Understanding the regulatory landscape and molecular mechanisms governed by lncRNAs in CRC and GC is crucial for the development of effective diagnostic and prognostic biomarkers, as well as novel therapeutic strategies. This review provides a comprehensive overview of the current knowledge and paves the way for further exploration of lncRNAs as key players in the management of CRC and GC.
Collapse
Affiliation(s)
| | - Sogand Vahidi
- Medical Biology Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Ali Akbar Samadani
- Guilan Road Trauma Research Center, Trauma Institute, Guilan University of Medical Sciences, Rasht, Iran.
| |
Collapse
|
8
|
Modabber N, Mahboub SS, Khoshravesh S, Karimpour F, Karimi A, Goodarzi V. Evaluation of Long Non-coding RNA (LncRNA) in the Pathogenesis of Chemotherapy Resistance in Cervical Cancer: Diagnostic and Prognostic Approach. Mol Biotechnol 2023:10.1007/s12033-023-00909-6. [PMID: 37804407 DOI: 10.1007/s12033-023-00909-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 09/14/2023] [Indexed: 10/09/2023]
Abstract
Cervical cancer (CC), caused by human papillomavirus (HPV), is a leading cause of female malignancies worldwide. Therefore, understanding the underlying mechanisms of CC development and identifying novel therapeutic targets are significantly important. Cisplatin resistance is a significant challenge in the management of CC. Recent studies highlighted the critical role of long non-coding RNAs (lncRNAs) in modulation of cisplatin resistance. This comprehensive review aims to collect the current understanding roles of lncRNAs and their involvement in cisplatin resistance in CC by highlighting key processes of cancer progression, including apoptosis, proliferation, angiogenesis and epithelial-to-mesenchymal transition (EMT). We discussed the role of lncRNA in CC resistance to cisplatin through molecular pathways and examined gene expression changes. We also discussed treatment strategies and factors that reduce CC resistance to cisplatin by targeting them.
Collapse
Affiliation(s)
- Noushin Modabber
- Shahid Akbar-Abadi Clinical Research Development Unit (SHACRDU), School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Sarah Sadat Mahboub
- Shahid Akbar-Abadi Clinical Research Development Unit (SHACRDU), School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | | | - Fatemeh Karimpour
- Cancer Reserch Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Anita Karimi
- Shahid Beheshti University of Medical Science, Tehran, Iran
| | - Vahid Goodarzi
- Department of Anesthesiology, Rasoul-Akram Medical Center, Iran University of Medical Sciences (IUMS), Tehran, Iran.
| |
Collapse
|
9
|
Bashiri H, Moazam-Jazi M, Karimzadeh MR, Jafarinejad-Farsangi S, Moslemizadeh A, Lotfian M, Karam ZM, Kheirandish R, Farazi MM. Autophagy in combination therapy of temozolomide and IFN-γ in C6-induced glioblastoma: role of non-coding RNAs. Immunotherapy 2023; 15:1157-1169. [PMID: 37584216 DOI: 10.2217/imt-2022-0212] [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] [Indexed: 08/17/2023] Open
Abstract
Aim: We predicted the modulation of autophagy and apoptosis in response to temozolomide (TMZ) and IFN-γ based on changes in the expression of non-coding RNAs in C6-induced glioblastoma (GBM). Materials & methods: Each rat received an intraperitoneal injection of TMZ (7.5 mg/kg) and/or IFN-γ (50,000 IU). Results: The reduced expression of H19 and colorectal neoplasia differentially expressed (CRNDE) was associated with a reduction in autophagy in response to TMZ, IFN-γ and TMZ + IFN-γ therapy, whereas the decreased level of miR-29a (proapoptotic miRNA) was associated with an increase in apoptosis. Conclusion: It appears that H19 promotes switching from autophagy to apoptosis in response to combination therapy of TMZ and IFN-γ through the miR-29a/autophagy-related protein 9A (ATG9A) pathway in C6-induced GBM.
Collapse
Affiliation(s)
- Hamideh Bashiri
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, 76198-13159, Iran
| | - Maryam Moazam-Jazi
- Cellular & Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, 19857-17413, Iran
| | - Mohammad Reza Karimzadeh
- Department of Medical Genetics, School of Medicine, Bam University of Medical Sciences, Bam, 76198-13159, Iran
| | | | | | - Marziyeh Lotfian
- Endocrinology & Metabolism Research Center, Institute of Basic & Clinical Physiology Sciences, Kerman University of Medical Sciences Kerman, 76198-13159, Iran
| | - Zahra Miri Karam
- Cardiovascular Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, 76198-13159, Iran
| | - Reza Kheirandish
- Department of Pathobiology, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, 76198-13159, Iran
| | - Mohammad Mojtaba Farazi
- Physiology Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, 76198-13159, Iran
| |
Collapse
|
10
|
Shi Z, Wu Y, Zhuo Q, Zuo Y, Lin J, Shi H, Zhou H, Xu Z. Comprehensive analysis of oxidative stress-related lncRNA signatures in glioma reveals the discrepancy of prognostic and immune infiltration. Sci Rep 2023; 13:7731. [PMID: 37173373 PMCID: PMC10182081 DOI: 10.1038/s41598-023-34909-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 05/09/2023] [Indexed: 05/15/2023] Open
Abstract
Oxidative stress refers to the process of reactive oxide species (ROS) increase in human body due to various factors, which leads to oxidative damage in human tissues. Current studies have confirmed that sustained oxidative stress is one of the distinctive features throughout the development of tumors. Numerous reports have shown that lncRNAs can regulate the process of oxidative stress through multiple pathways. However, the relationship between glioma-associated oxidative stress and lncRNAs is not clearly investigated. RNA sequencing data of GBM (glioblastoma) and LGG (low grade glioma) and corresponding clinical data were retrieved from the TCGA database. Oxidative stress related lncRNAs (ORLs) were identified by Pearson correlation analysis. Prognostic models for 6-ORLs were structured in the training cohort by univariate Cox regression analysis, multivariate Cox regression analysis and LASSO regression analysis. We constructed the nomogram and verified its predictive efficacy by Calibration curves and DCA decision curves. The biological functions and pathways of 6-ORLs-related mRNAs were inferred by Gene Set Enrichment Analysis. Immune cell abundance and immune function associated with risk score (RS) were estimated by ssGSEA, CIBERSORT and MCPcounter synthetically. External validation of the signature was completed using the CGGA-325 and CGGA-693 datasets. 6-ORLs signature-AC083864.2, AC107294.1, AL035446.1, CRNDE, LINC02600, and SNAI3-AS1-were identified through our analysis as being predictive of glioma prognosis. Kaplan-Meier and ROC curves indicated that the signature has a dependable predictive efficacy in the TCGA training cohort, validation cohort and CGGA-325/CGGA-693 test cohort. The 6-ORLs signature were verified to be independent prognostic predictors by multivariate cox regression and stratified survival analysis. Nomogram built with risk scores had strong predictive efficacy for patients' overall survival (OS). The outcomes of the functional enrichment analysis revealing potential molecular regulatory mechanisms for the 6-ORLs. Patients in the high-risk subgroup presented a significant immune microenvironment of macrophage M0 and cancer-associated fibroblast infiltration which was associated with a poorer prognosis. Finally, the expression levels of 6-ORLs in U87/U251/T98/U138 and HA1800 cell lines were verified by RT-qPCR. The nomogram in this study has been made available as a web version for clinicians. This 6-ORLs risk signature has the capabilities to predict the prognosis of glioma patients, assist in evaluating immune infiltration, and assess the efficacy of various anti-tumor systemic therapy regimens.
Collapse
Affiliation(s)
- Zhenyi Shi
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Yingying Wu
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Qingchan Zhuo
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Yufang Zuo
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Jiong Lin
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China
| | - Huadi Shi
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China.
| | - Hechao Zhou
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China.
| | - Zumin Xu
- Cancer Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524000, Guangdong, People's Republic of China.
| |
Collapse
|
11
|
Qin J, Ke B, Liu T, Kong C, Li A, Fu H, Jin C. Aberrantly expressed long noncoding RNAs as potential prognostic biomarkers in newly diagnosed multiple myeloma: A systemic review and meta-analysis. Cancer Med 2023; 12:2199-2218. [PMID: 36057947 PMCID: PMC9939128 DOI: 10.1002/cam4.5135] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Revised: 05/17/2022] [Accepted: 08/02/2022] [Indexed: 11/08/2022] Open
Abstract
BACKGROUND Numerous studies have manifested long noncoding RNAs (lncRNAs) as biomarkers to determine the prognosis of multiple myeloma (MM) patients. Nevertheless, the prognostic role of lncRNAs in MM is still ambiguous. Herein, we performed a meta-analysis to evaluate the predictive value of aberrantly expressed lncRNAs in MM. METHODS A systemic literature search was performed in PubMed, EMBASE, Cochrane, and Web of Science databases until October 9, 2021, and the protocol was registered in the PROSPERO database (CRD42021284364). Our study extracted the hazard ratios (HRs) and 95% confidence intervals (CIs) of overall survival (OS), progression-free survival (PFS), or event-free survival (EFS). Begg's and Egger's tests were employed to correct publication bias. RESULT Twenty-six individual studies containing 3501 MM patients were enrolled in this study. The results showed that aberrant expression of lncRNAs was associated with poor OS and PFS of MM patients. The pooled HRs for univariate OS and PFS were 1.48 (95% CI = 1.17-1.88, p < 0.001) and 1.30 (95% CI = 1.18-1.43, p < 0.001), respectively, whereas the pooled HRs for multivariate OS and PFS were 1.50 (95% CI = 1.16-1.95, p < 0.001) and 1.59 (95% CI = 1.22-2.07, p < 0.001), respectively. Subgroup analysis suggested that MALAT1, TCF7, NEAT1, and PVT1 upregulation were associated with poor OS (p < 0.05), PVT1, and TCF7 upregulation were implicated with worse PFS (p < 0.05), while only TCF7 overexpression was correlated with reduced EFS (p < 0.05). Moreover, the contour-enhanced funnel plot demonstrated the reliability of our current conclusion, which was not affected by publication bias. CONCLUSION Aberrantly expressed particular lncRNAs are critical prognostic indicators in long-term survival as well as promising biomarkers in progression-free status. However, different cutoff values and dissimilar methods to assess lncRNA expression among studies may lead to heterogeneity.
Collapse
Affiliation(s)
- Jiading Qin
- Medical College of Nanchang UniversityNanchangJiangxi330006China
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
| | - Bo Ke
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
- National Clinical Research Center for Hematologic DiseasesThe First Affiliated Hospital of Soochow UniversitySoochowJiangsu215006China
| | - Tingting Liu
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
| | - Chunfang Kong
- Medical College of Nanchang UniversityNanchangJiangxi330006China
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
| | - Anna Li
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
| | - Huan Fu
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
| | - Chenghao Jin
- Medical College of Nanchang UniversityNanchangJiangxi330006China
- Department of HematologyJiangxi Provincial People's HospitalNanchangJiangxi330006China
- National Clinical Research Center for Hematologic DiseasesThe First Affiliated Hospital of Soochow UniversitySoochowJiangsu215006China
| |
Collapse
|
12
|
Liu Z, Bian M, Pang L. LncRNA CRNDE binds hnRNPA1 to facilitate carbon monoxide poisoning-induced delayed encephalopathy via inhibiting UCHL5-mediated SMO deubiquitination. Metab Brain Dis 2023; 38:1097-1113. [PMID: 36648699 DOI: 10.1007/s11011-022-01157-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Delayed encephalopathy after acute carbon monoxide poisoning (DEACMP) is one of the most common complications following carbon monoxide intoxication. Long noncoding RNAs (lncRNAs) exert critical functions in numerous neurological disorders. We intended to investigate the role of CRNDE in DEACMP. The DEACMP model in rats and the oxygen-glucose deprivation/reoxygenation (OGD/R) model in PC-12 cells were established. Brain and cell injuries were assessed with H&E staining, Nissl staining, TUNEL and CCK8 assays, respectively. Related proteins and RNAs were quantified with western blot and qRT-PCR. The N6-methyladenosine (m6A) level was determined using MeRIP-qPCR and immunofluorescence. Loss and gain function studies were performed to investigate the biological function of CRNDE. The potential mechanisms between each factor were explored using RNA immunoprecipitation, RNA-pull down and co-immunoprecipitation. CRNDE was increased in the hippocampal tissues of DEACMP rats and in OGD/R-treated PC-12 cells, which was positively correlated to m6A modification. Knockdown of CRNDE reduced cell damage and elevated UCHL5 and SMO expressions in OGD/R-treated PC-12 cells. hnRNPA1 was upregulated in DEACMP. In addition, inhibiting hnRNPA1 prevented apoptosis in PC-12 cells subjected to OGD/R. hnRNPA1 bound to CRNDE and remained in the nucleus, which inhibited UCHL5 expression through the formation of CRNDE-hnRNPA1-mRNA complex. UCHL5 could inhibit SMO ubiquitination and suppress PC-12 cell apoptosis during OGD/R. CRNDE silencing blocked brain injury in DEACMP, while knocking down UCHL5 reversed these effects. CRNDE interacted with hnRNPA1 to facilitate DEACMP via inhibition of UCHL5-mediated SMO deubiquitination. CRNDE might be a latent therapeutic target for treating DEACMP.
Collapse
Affiliation(s)
- Zuolong Liu
- Department of Emergency, the First Hospital of Jilin University, No. 1 Xinmin Road, Changchun, 130021, Jilin Province, People's Republic of China
| | - Miao Bian
- Department of Respiratory, Qianwei Hospital of Jilin Province, Changchun, 130012, Jilin Province, People's Republic of China
| | - Li Pang
- Department of Emergency, the First Hospital of Jilin University, No. 1 Xinmin Road, Changchun, 130021, Jilin Province, People's Republic of China.
| |
Collapse
|
13
|
Comprehensive Analysis of the Prognostic Value and Molecular Function of CRNDE in Glioma at Bulk and Single-Cell Levels. Cells 2022; 11:cells11223669. [PMID: 36429098 PMCID: PMC9688829 DOI: 10.3390/cells11223669] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/13/2022] [Indexed: 11/22/2022] Open
Abstract
Colorectal neoplasia differentially expressed (CRNDE) is an oncogenic long noncoding RNA (lncRNA) overexpressed in diverse malignancies. Here, we comprehensively analyze the prognostic value and molecular function of CRNDE in glioma. Bulk RNA-sequencing data from The Cancer Genome Atlas (TCGA) and Chinese Glioma Genome Atlas (CGGA), and single-cell RNA-sequencing data from the Tumor Immune Single-Cell Hub (TISCH) were analyzed. Kaplan-Meier survival analysis was applied to verify the prognostic value of CRNDE. Then, a nomogram based on multivariate Cox regression was established for individualized survival prediction. Subsequently, the expression characteristic and biological function of CRNDE were analyzed at the single-cell level. Lastly, the effects of CRNDE on the proliferation and invasion of glioma cell were explored in vitro. We discovered that CRNDE was a powerful marker for risk stratification of glioma patients. Regardless of the status of IDH and 1p/19q, CRNDE could effectively stratify patients' prognosis. The nomogram that incorporated the CRNDE expression was proved to be a reliable tool for survival prediction. In addition, epithelial-mesenchymal transition may be the most important biological process regulated by CRNDE, which was identified at both the bulk and single-cell levels. Moreover, CRNDE knockdown significantly inhibited the proliferation and invasion of glioma cell. Overall, CRNDE is a vital oncogene and may be a valuable supplement to improve the clinical stratification of glioma.
Collapse
|