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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.
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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
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2
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Szafron LA, Iwanicka-Nowicka R, Podgorska A, Bonna AM, Sobiczewski P, Kupryjanczyk J, Szafron LM. The Clinical Significance of CRNDE Gene Methylation, Polymorphisms, and CRNDEP Micropeptide Expression in Ovarian Tumors. Int J Mol Sci 2024; 25:7531. [PMID: 39062774 PMCID: PMC11277161 DOI: 10.3390/ijms25147531] [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: 04/28/2024] [Revised: 06/30/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
CRNDE is an oncogene expressed as a long non-coding RNA. However, our team previously reported that the CRNDE gene also encodes a micropeptide, CRNDEP. The amino acid sequence of CRNDEP has recently been revealed by other researchers, too. This study aimed to investigate genetic alterations within the CRNDEP-coding region of the CRNDE gene, methylation profiling of this gene, and CRNDEP expression analysis. All investigations were performed on clinical material from patients with ovarian tumors of diverse aggressiveness. We found that CRNDEP levels were significantly elevated in highly aggressive tumors compared to benign neoplasms. Consistently, a high level of this micropeptide was a negative, independent, prognostic, and predictive factor in high-grade ovarian cancer (hgOvCa) patients. The cancer-promoting role of CRNDE(P), shown in our recent study, was also supported by genetic and epigenetic results obtained herein, revealing no CRNDEP-disrupting mutations in any clinical sample. Moreover, in borderline ovarian tumors (BOTS), but not in ovarian cancers, the presence of a single nucleotide polymorphism in CRNDE, rs115515594, significantly increased the risk of recurrence. Consistently, in BOTS only, the same genetic variant was highly overrepresented compared to healthy individuals. We also discovered that hypomethylation of CRNDE is associated with increased aggressiveness of ovarian tumors. Accordingly, hypomethylation of this gene's promoter/first exon correlated with hgOvCa resistance to chemotherapy, but only in specimens with accumulation of the TP53 tumor suppressor protein. Taken together, these results contribute to a better understanding of the role of CRNDE(P) in tumorigenesis and potentially may lead to improvements in screening, diagnosis, and treatment of ovarian neoplasms.
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Affiliation(s)
| | - Roksana Iwanicka-Nowicka
- Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, 02-106 Warsaw, Poland
- Laboratory for Microarray Analysis, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 02-106 Warsaw, Poland
| | - Agnieszka Podgorska
- Cancer Molecular and Genetic Diagnostics Department, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | | | - Piotr Sobiczewski
- Department of Gynecological Oncology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
| | - Jolanta Kupryjanczyk
- Department of Cancer Pathomorphology, Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland;
| | - Lukasz Michal Szafron
- Maria Sklodowska-Curie National Research Institute of Oncology, 02-781 Warsaw, Poland
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3
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Kazemifard N, Farmani M, Baradaran Ghavami S, Kazemi M, Shahrokh S, Asadzadeh Aghdaei H, Zali M. A prediction of the CRNDE role by modulating NF-κB pathway in inflammatory bowel disease (IBD). Biochem Biophys Rep 2024; 38:101731. [PMID: 38766384 PMCID: PMC11101873 DOI: 10.1016/j.bbrep.2024.101731] [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: 03/06/2024] [Revised: 04/28/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate multiple pathways and cellular mechanisms. Recent research has emphasized their involvement in the pathogenesis of complex diseases, such as Inflammatory Bowel Disease (IBD) which is characterized by chronic inflammation of the intestines. The two most common types of IBD are ulcerative colitis and Crohn's disease. CRNDE lncRNA was initially detected in colorectal cancer (CRC) and found to be involved in the tumorigenesis pathways. Further studies revealed the role of CRNDE in activating inflammation and promoting the release of inflammatory cytokines. This study utilizes the RNA-seq data analysis and bioinformatics tools to clarify the role of CRNDE in the IBD pathogenesis and confirms its expression in inflamed HT-29 and Caco-2 cell lines and also colonic and blood samples of UC patients and controls ex vivo. Based on our results, CRNDE was significantly upregulated in IBD samples compared to controls in RNA-seq data analysis and Real-time PCR of inflamed HT-29 cell line and colonic biopsies from UC patients. Additionally, predicted that its expression is positively correlated with the pro-inflammatory cytokines production. CRNDE interactions was investigated with several inflammation-related miRNAs and regulatory proteins computationally. Thus, CRNDE upregulation in the colon of IBD patients could be involved in IBD pathogenesis by promoting inflammatory pathways and targeting anti-inflammatory miRNAs.
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Affiliation(s)
- Nesa Kazemifard
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Farmani
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shaghayegh Baradaran Ghavami
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Kazemi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Reproductive Sciences and Sexual Health Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Shabnam Shahrokh
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammadreza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Lin C, Jiang T, E C, Wang L, Chen T, Wang X, Xiang Y. LncRNA CRNDE promotes hepatoma cell proliferation by regulating the metabolic reprogramming of M2 macrophages via ERK pathway. Cancer Cell Int 2024; 24:193. [PMID: 38822362 PMCID: PMC11143606 DOI: 10.1186/s12935-024-03380-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 05/22/2024] [Indexed: 06/02/2024] Open
Abstract
BACKGROUND LncRNA colorectal neoplasia differentially expressed (CRNDE) was found to be an important regulator in many cancers. This project focuses on the function of CRNDE on macrophage metabolic reprogramming and Hepatocellular carcinoma (HCC). METHOD qRT-PCR and Immunofluorescence were used to analyze Arg-1, IL-10, CD163, CCL-18, CD206, and CRNDE expression in HCC tissues and macrophages. Western Blotting was used to analyze ERK and p-ERK expression. Edu assay, transwell assay and xenograft experiments were carried out to study cell viability, migrated and invasive capability. Immunohistochemical staining was used to evaluate Ki67 expression. A liquid chromatography-tandem mass spectrometry (LC-MS/MS) was performed for macrophages metabolites analysis. RESULTS Arg-1, IL-10, CD163, CD206, and CRNDE were significantly up-regulated in HCC tissues, M2 macrophage and M0 macrophage with CRNDE overexpressed (OV-CRNDE-M0), which downregulated in M0 macrophage with CRNDE knockdown (sh-CRNDE-M0). The conditioned medium (CM) of M2 cells and OV-CRNDE-M0 cells promoted cell viability, invasion, and migration of HCC cells, the effect was reversed by sh-CRNDE-M0 cells CM. OV-CRNDE-M0 cells promoted tumor growth, Ki67 and CD206 expression in xenograft model. 61 metabolites were detected, of which 18 metabolites changed significantly in OV-CRNDE-M0 group compared to M0 group, with 9 upregulated and 9 downregulated. KEGG analysis showed the enrichment pathways were biosynthesis, glyoxylate and dicarboxylate metabolism. SMPDB analysis showed the enrichment pathways were hypoacetylaspartia, canavan disease, and aspartate metabolism. CONCLUSION CRNDE regulated the metabolic reprogramming of M2 macrophage via ERK pathway, which thereby contributed to HCC proliferation, migration, and invasion.
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Affiliation(s)
- Chao Lin
- Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Tao Jiang
- Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Changyong E
- Hepatobiliary and Pancreatic Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Lun Wang
- Gastrointestinal Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Tong Chen
- Gastrointestinal Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Xia Wang
- General Surgery, China-Japan Union Hospital of Jilin University, Changchun, China
| | - Yien Xiang
- Hepatobiliary and Pancreatic Surgery, the Second Hospital of Jilin University, Changchun, China.
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Tahmasebi Dehkordi H, Khaledi F, Ghasemi S. Immunological processes of enhancers and suppressors of long non-coding RNAs associated with brain tumors and inflammation. Int Rev Immunol 2024; 43:178-196. [PMID: 37974420 DOI: 10.1080/08830185.2023.2280581] [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: 07/16/2022] [Accepted: 11/02/2023] [Indexed: 11/19/2023]
Abstract
Immunological processes, such as inflammation, can both cause tumor suppression and cancer progression. Moreover, deregulated levels of long non-coding RNA (lncRNA) expression in the brain may cause inflammation and lead to the growth of tumors. Like other biological processes, the immune system's role in cancer is complicated, varies, and can help or hurt the cancer's maintenance. According to research, inflammation and brain cancer are correlated via several signaling pathways. A variety of lncRNAs have recently been revealed to influence cancer by modulating inflammatory pathways. As a result, lncRNAs have the potential to influence carcinogenesis, tumor formation, or tumor suppression via an increase or decrease in inflammation functions. Although the study and targeting of lncRNAs have made great progress in the treatment of cancer, there are definitely limitations and challenges. Using new technologies like nanocarriers and cell-penetrating peptides (CPPs) to target treatments without hurting healthy body tissues has shown to be very effective. In this review article, we have collected significantly related lncRNAs and their inhibitory or stimulating roles in inflammation and brain cancer for the first time. However, there are limitations, such as side effects and damage to normal tissues. With the advancement of new targeting technologies, these lncRNAs may be candidates for the specific targeting therapy of brain cancers by limiting inflammation or stimulating the immune system against them in the future.
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Affiliation(s)
- Hossein Tahmasebi Dehkordi
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Fatemeh Khaledi
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Sorayya Ghasemi
- Cancer Research Center, Shahrekord University of Medical Sciences, Shahrekord, Iran
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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.
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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
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Pokorná M, Černá M, Boussios S, Ovsepian SV, O’Leary VB. lncRNA Biomarkers of Glioblastoma Multiforme. Biomedicines 2024; 12:932. [PMID: 38790894 PMCID: PMC11117901 DOI: 10.3390/biomedicines12050932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/26/2024] Open
Abstract
Long noncoding RNAs (lncRNAs) are RNA molecules of 200 nucleotides or more in length that are not translated into proteins. Their expression is tissue-specific, with the vast majority involved in the regulation of cellular processes and functions. Many human diseases, including cancer, have been shown to be associated with deregulated lncRNAs, rendering them potential therapeutic targets and biomarkers for differential diagnosis. The expression of lncRNAs in the nervous system varies in different cell types, implicated in mechanisms of neurons and glia, with effects on the development and functioning of the brain. Reports have also shown a link between changes in lncRNA molecules and the etiopathogenesis of brain neoplasia, including glioblastoma multiforme (GBM). GBM is an aggressive variant of brain cancer with an unfavourable prognosis and a median survival of 14-16 months. It is considered a brain-specific disease with the highly invasive malignant cells spreading throughout the neural tissue, impeding the complete resection, and leading to post-surgery recurrences, which are the prime cause of mortality. The early diagnosis of GBM could improve the treatment and extend survival, with the lncRNA profiling of biological fluids promising the detection of neoplastic changes at their initial stages and more effective therapeutic interventions. This review presents a systematic overview of GBM-associated deregulation of lncRNAs with a focus on lncRNA fingerprints in patients' blood.
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Affiliation(s)
- Markéta Pokorná
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
| | - Stergios Boussios
- Department of Medical Oncology, Medway NHS Foundation Trust, Gillingham ME7 5NY, UK;
- Faculty of Medicine, Health, and Social Care, Canterbury Christ Church University, Canterbury CT2 7PB, UK
- Faculty of Life Sciences & Medicine, School of Cancer & Pharmaceutical Sciences, King’s College London, Strand, London WC2R 2LS, UK
- Kent Medway Medical School, University of Kent, Canterbury CT2 7LX, UK
- AELIA Organization, 9th Km Thessaloniki-Thermi, 57001 Thessaloniki, Greece
| | - Saak V. Ovsepian
- Faculty of Engineering and Science, University of Greenwich London, Chatham Maritime, Kent ME4 4TB, UK;
- Faculty of Medicine, Tbilisi State University, Tbilisi 0177, Georgia
| | - Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Ruská 87, Vinohrady, 10000 Prague, Czech Republic; (M.Č.); (V.B.O.)
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Shehata AMF, Gohar SF, Muharram NM, Soliman SS, Shalaby HM, Kamal Eldin SM, El-Bassal FI. LncRNA CRNDE is downregulated and associated with poor prognostic markers in chronic lymphocytic leukemia. Int J Lab Hematol 2024; 46:107-112. [PMID: 37814899 DOI: 10.1111/ijlh.14186] [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: 07/10/2023] [Accepted: 09/28/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Chronic lymphocytic leukemia (CLL) is characterized by a very heterogeneous clinical outcome. Thus, a plethora of prognostic factors and systems has been identified to place patients into different risk categories and to guide therapy decisions. The classic clinical staging models by Rai and Binet have been the cornerstone of patient management for several years. The greater insight into the molecular biology of CLL facilitated the advent of prognostic genetic biomarkers that are expected to impact clinical practice soon in the future. Therefore, we aimed to investigate the expression of long non-coding RNA (lncRNA) CRNDE in patients with CLL, and to analyze its relationship with the clinicopathological parameters of CLL. METHODS In this study, 40 untreated CLL patients and 30 age- and gender-matched controls were enrolled. The analysis of lncRNA CRNDE expression was determined using reverse transcription-quantitative polymerase chain reaction technique. RESULTS Our result confirmed the downregulated expression of LncRNA CRNDE in CLL patients compared to controls (p < 0.001). The low expression of CRNDE was significantly associated with poor prognostic markers including advanced stage of CLL, high levels of serum beta-2 microglobulin and lactic dehydrogenase, and the presence of del17p (p = 0.029, p = 0.013, p = 0.003, p = 0.028; respectively). CONCLUSION Our study demonstrated that LncRNA CRNDE is significantly downregulated and associated with poor prognostic markers in CLL. It provides a rationale to assess its biological and prognostic impact in CLL.
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Affiliation(s)
- Amira M F Shehata
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Suzy F Gohar
- Clinical Oncology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Nashwa M Muharram
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Shaimaa Sherif Soliman
- Public Health and Community Medicine Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Hadeel M Shalaby
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Samar M Kamal Eldin
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
| | - Fathia I El-Bassal
- Clinical Pathology Department, Faculty of Medicine, Menoufia University, Menoufia, Egypt
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Tao Y, Wei L, Shiba N, Tomizawa D, Hayashi Y, Ogawa S, Chen L, You H. Development and validation of a promising 5-gene prognostic model for pediatric acute myeloid leukemia. MOLECULAR BIOMEDICINE 2024; 5:1. [PMID: 38163849 PMCID: PMC10758381 DOI: 10.1186/s43556-023-00162-y] [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] [Accepted: 12/03/2023] [Indexed: 01/03/2024] Open
Abstract
Risk classification in pediatric acute myeloid leukemia (P-AML) is crucial for personalizing treatments. Thus, we aimed to establish a risk-stratification tool for P-AML patients and eventually guide individual treatment. A total of 256 P-AML patients with accredited mRNA-seq data from the TARGET database were divided into training and internal validation datasets. A gene-expression-based prognostic score was constructed for overall survival (OS), by using univariate Cox analysis, LASSO regression analysis, Kaplan-Meier (K-M) survival, and multivariate Cox analysis. A P-AML-5G prognostic score bioinformatically derived from expression levels of 5 genes (ZNF775, RNFT1, CRNDE, COL23A1, and TTC38), clustered P-AML patients in training dataset into high-risk group (above optimal cut-off) with shorter OS, and low-risk group (below optimal cut-off) with longer OS (p < 0.0001). Meanwhile, similar results were obtained in internal validation dataset (p = 0.005), combination dataset (p < 0.001), two treatment sub-groups (p < 0.05), intermediate-risk group defined with the Children's Oncology Group (COG) (p < 0.05) and an external Japanese P-AML dataset (p = 0.005). The model was further validated in the COG study AAML1031(p = 0.001), and based on transcriptomic analysis of 943 pediatric patients and 70 normal bone marrow samples from this dataset, two genes in the model demonstrated significant differential expression between the groups [all log2(foldchange) > 3, p < 0.001]. Independent of other prognostic factors, the P-AML-5G groups presented the highest concordance-index values in training dataset, chemo-therapy only treatment subgroups of the training and internal validation datasets, and whole genome-sequencing subgroup of the combined dataset, outperforming two Children's Oncology Group (COG) risk stratification systems, 2022 European LeukemiaNet (ELN) risk classification tool and two leukemic stem cell expression-based models. The 5-gene prognostic model generated by a single assay can further refine the current COG risk stratification system that relies on numerous tests and may have the potential for the risk judgment and identification of the high-risk pediatric AML patients receiving chemo-therapy only treatment.
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Affiliation(s)
- Yu Tao
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Pediatric Hematology and Oncology, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Li Wei
- NHC Key Laboratory of Birth Defects and Reproductive Health, Chongqing Population and Family Planning Science and Technology Research Institute, Chongqing, China
- Chongqing Hospital of Traditional Chinese Medicine, Chongqing, China
| | - Norio Shiba
- Department of Pediatrics, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Daisuke Tomizawa
- Division of Leukemia and Lymphoma, Children's Cancer Center, National Center for Child Health and Development, Tokyo, Japan
| | - Yasuhide Hayashi
- Department of Hematology/Oncology, Gunma and Institute of Physiology and Medicine, Gunma Children's Medical Center, Jobu University, Gunma, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Kyoto University, Kyoto, Japan
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto University, Kyoto, Japan
- Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska Institute, 17177, Stockholm, Sweden
| | - Li Chen
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Hua You
- Laboratory for Excellence in Systems Biomedicine of Pediatric Oncology, Department of Pediatric Hematology and Oncology, Chongqing Key Laboratory of Pediatrics, Ministry of Education Key Laboratory of Child Development and Disorders, China International Science and Technology Cooperation Base of Child Development and Critical Disorders, National Clinical Research Center for Child Health and Disorders, Children's Hospital of Chongqing Medical University, Chongqing, China.
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10
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Dang HX, Saha D, Jayasinghe R, Zhao S, Coonrod E, Mudd J, Goedegebuure S, Fields R, Ding L, Maher C. Single-cell transcriptomics reveals long noncoding RNAs associated with tumor biology and the microenvironment in pancreatic cancer. NAR Cancer 2023; 5:zcad055. [PMID: 38023733 PMCID: PMC10664695 DOI: 10.1093/narcan/zcad055] [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: 05/17/2023] [Revised: 10/31/2023] [Accepted: 11/09/2023] [Indexed: 12/01/2023] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is highly heterogeneous and lethal. Long noncoding RNAs (lncRNAs) are an important class of genes regulating tumorigenesis and progression. Prior bulk transcriptomic studies in PDAC have revealed the dysregulation of lncRNAs but lack single-cell resolution to distinguish lncRNAs in tumor-intrinsic biology and the tumor microenvironment (TME). We analyzed single-cell transcriptome data from 73 multiregion samples in 21 PDAC patients to evaluate lncRNAs associated with intratumoral heterogeneity and the TME in PDAC. We found 111 cell-specific lncRNAs that reflected tumor, immune and stromal cell contributions, associated with outcomes, and validated across orthogonal datasets. Single-cell analysis of tumor cells revealed lncRNAs associated with TP53 mutations and FOLFIRINOX treatment that were obscured in bulk tumor analysis. Lastly, tumor subcluster analysis revealed widespread intratumor heterogeneity and intratumoral lncRNAs associated with cancer hallmarks and tumor processes such as angiogenesis, epithelial-mesenchymal transition, metabolism and immune signaling. Intratumoral subclusters and lncRNAs were validated across six datasets and showed clinically relevant associations with patient outcomes. Our study provides the first comprehensive assessment of the lncRNA landscape in PDAC using single-cell transcriptomic data and can serve as a resource, PDACLncDB (accessible at https://www.maherlab.com/pdaclncdb-overview), to guide future functional studies.
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Affiliation(s)
- Ha X Dang
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO 63108, USA
| | - Debanjan Saha
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- MD–PhD Program, Washington University in St Louis, St Louis, MO 63110, USA
| | - Reyka Jayasinghe
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Sidi Zhao
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Emily Coonrod
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
| | - Jacqueline Mudd
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - S Peter Goedegebuure
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - Ryan Fields
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- Department of Surgery, Washington University in St Louis, St Louis, MO 63110, USA
| | - Li Ding
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
| | - Christopher A Maher
- Department of Internal Medicine, Washington University in St Louis, St Louis, MO 63110, USA
- Siteman Cancer Center, Washington University in St Louis, St Louis, MO 63110, USA
- McDonnell Genome Institute, Washington University in St Louis, St Louis, MO 63108, USA
- Department of Biomedical Engineering, Washington University in St Louis, St Louis, MO 63130, USA
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11
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Hor YZ, Salvamani S, Gunasekaran B, Yian KR. CRNDE: A Pivotal Oncogenic Long Non-Coding RNA in Cancers. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2023; 96:511-526. [PMID: 38161583 PMCID: PMC10751873 DOI: 10.59249/vhye2306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Colorectal Neoplasia Differentially Expressed (CRNDE), a long non-coding RNA that was initially identified as aberrantly expressed in colorectal cancer (CRC) has also been observed to exhibit elevated expression in various other human malignancies. Recent research has accumulated substantial evidence implicating CRNDE as an oncogenic player, exerting influence over critical cellular processes linked to cancer progression. Particularly, its regulatory interactions with microRNAs and proteins have been shown to modulate pathways that contribute to carcinogenesis and tumorigenesis. This review will comprehensively outline the roles of CRNDE in colorectal, liver, glioma, lung, cervical, gastric and prostate cancer, elucidating the mechanisms involved in modulating proliferation, apoptosis, migration, invasion, angiogenesis, and radio/chemoresistance. Furthermore, the review highlights CRNDE's potential as a multifaceted biomarker, owing to its presence in diverse biological samples and stable properties, thereby underscoring its diagnostic, therapeutic, and prognostic applications. This review aims to provide comprehensive insights of CRNDE-mediated oncogenesis and identify CRNDE as a promising target for future clinical interventions.
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Affiliation(s)
- Yi Zhen Hor
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Shamala Salvamani
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
| | - Baskaran Gunasekaran
- Department of Biotechnology, Faculty of Applied
Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Koh Rhun Yian
- Division of Applied Biomedical Sciences and
Biotechnology, School of Health Sciences, International Medical University,
Kuala Lumpur, Malaysia
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12
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Rahmani F, Mohammed Al-Asady A, Hanaie R, Zandigohar M, Faridnejad H, Payazdan M, Safavi P, Ryzhikov M, Hassanian SM. Interplay between lncRNA/miRNA and Wnt/ß-catenin signaling in brain cancer tumorigenesis. EXCLI JOURNAL 2023; 22:1211-1222. [PMID: 38204968 PMCID: PMC10776877 DOI: 10.17179/excli2023-6490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 11/20/2023] [Indexed: 01/12/2024]
Abstract
Brain cancers are among the most aggressive malignancies with high mortality and morbidity worldwide. The pathogenesis of brain cancers is a very complicated process involving various genetic mutations affecting several oncogenic signaling pathways like Wnt/β-catenin axis. Uncontrolled activation of this oncogenic signaling is associated with decreased survival rate and poor prognosis in cancer patients. Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) were shown to play important roles in regulating cell proliferation, differentiation, and apoptosis by regulating the expression of their target genes. Aberrant expression of these non-coding RNAs (ncRNAs) was reported in many human cancers, including glioblastoma, medulloblastoma, meningioma, and pituitary adenoma. Multiple lncRNAs were shown to participate in brain tumor pathogenesis by targeting Wnt signaling regulatory miRNAs. SNHG7/miR-5095, PCAT6/miR-139-3p, SNHG6/miR-944, SNHG1/ miR-556-5p, SNHG17/ miR-506-3p, LINC00702/miR-4652-3p, DLGAP1-AS1/miR-515-5p, HOTAIR/miR-1, HOTAIR/miR-206, CRNDE/miR-29c-3p, AGAP2-AS1/ miR-15a/b-5p, CLRN1-AS1/miR-217, MEG3/miR-23b-3p, and GAS5/miR-27a-5p are identified lncRNA/miRNA pairs that are involved in this process. Therefore, recognition of the expression profile and regulatory role of ncRNAs on the Wnt signaling may offer a novel approach to the diagnosis, prognosis, and treatment of human cancers. This review summarizes previous data on the modulatory role of lncRNAs/miRNAs on the Wnt/β-catenin pathway implicated in tumor growth, EMT, metastasis, and chemoresistance in brain cancers.
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Affiliation(s)
- Farzad Rahmani
- Kashmar School of Medical Sciences, Mashhad University of Medical Sciences, Mashhad, Iran
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Abdulridha Mohammed Al-Asady
- Department of Medical Sciences, Faculty of Nursing, University of Warith Al-Anbiyaa, Iraq
- Department of Pharmacology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Reyhane Hanaie
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mehrdad Zandigohar
- Department of Biomedical Engineering, University of Illinois at Chicago, Chicago, IL, 60612, USA
| | | | - Mahya Payazdan
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Pegah Safavi
- Department of Medical Radiation, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mikhail Ryzhikov
- Saint Louis University, School of Medicine, Saint Louis, MO, USA
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
- Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
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13
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Lu Y, Zou R, Gu Q, Wang X, Zhang J, Ma R, Wang T, Wu J, Feng J, Zhang Y. CRNDE mediated hnRNPA2B1 stability facilitates nuclear export and translation of KRAS in colorectal cancer. Cell Death Dis 2023; 14:611. [PMID: 37716979 PMCID: PMC10505224 DOI: 10.1038/s41419-023-06137-9] [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: 02/11/2023] [Revised: 09/03/2023] [Accepted: 09/07/2023] [Indexed: 09/18/2023]
Abstract
Development of colorectal cancer (CRC) involves activation of Kirsten rat sarcoma viral oncogene homolog (KRAS) signaling. However, the post-transcriptional regulation of KRAS has yet to be fully characterized. Here, we found that the colorectal neoplasia differentially expressed (CRNDE)/heterogeneous nuclear ribonucleoprotein A2/B1 (hnRNPA2B1) axis was notably elevated in CRC and was strongly associated with poor prognosis of patients, while also significantly promoting CRC cell proliferation and metastasis both in vitro and in vivo. Furthermore, CRNDE maintained the stability of hnRNPA2B1 protein by inhibiting E3 ubiquitin ligase TRIM21 mediated K63 ubiquitination-dependent protein degradation. CRNDE/hnRNPA2B1 axis facilitated the nuclear export and translation of KRAS mRNA, which specifically activated the MAPK signaling pathway, eventually accelerating the malignant progression of CRC. Our findings provided insight into the regulatory network for stable hnRNPA2B1 protein expression, and the molecular mechanisms by which the CRNDE/hnRNPA2B1 axis mediated KRAS nucleocytoplasmic transport and translation, deeply underscoring the bright future of hnRNPA2B1 as a promising biomarker and therapeutic target for CRC. By hindering hnRNPA2B1 from binding to the E3 ubiquitin ligase TRIM21, whose mediated ubiquitin-dependent degradation was thereby inhibited, CRNDE protected the stability of hnRNPA2B1's high protein expression in CRC. Supported by the high level of the oncogenic molecule CRNDE, hnRNPA2B1 bound to KRAS mRNA and promoted KRAS mRNA nucleus export to enter the ribosomal translation program, subsequently activating the MAPK signaling pathway and ultimately accelerating the malignant progression of CRC.
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Affiliation(s)
- Ya Lu
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Renrui Zou
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Quan Gu
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Xinyue Wang
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Junying Zhang
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Research Center of Clinical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Ting Wang
- Department of Cell Biology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Research Center of Clinical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jifeng Feng
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.
| | - Yuan Zhang
- Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.
- Research Center of Clinical Oncology, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China.
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14
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Gabryelska MM, Conn SJ. The RNA interactome in the Hallmarks of Cancer. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1786. [PMID: 37042179 PMCID: PMC10909452 DOI: 10.1002/wrna.1786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/12/2023] [Accepted: 03/20/2023] [Indexed: 04/13/2023]
Abstract
Ribonucleic acid (RNA) molecules are indispensable for cellular homeostasis in healthy and malignant cells. However, the functions of RNA extend well beyond that of a protein-coding template. Rather, both coding and non-coding RNA molecules function through critical interactions with a plethora of cellular molecules, including other RNAs, DNA, and proteins. Deconvoluting this RNA interactome, including the interacting partners, the nature of the interaction, and dynamic changes of these interactions in malignancies has yielded fundamental advances in knowledge and are emerging as a novel therapeutic strategy in cancer. Here, we present an RNA-centric review of recent advances in the field of RNA-RNA, RNA-protein, and RNA-DNA interactomic network analysis and their impact across the Hallmarks of Cancer. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Marta M Gabryelska
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
| | - Simon J Conn
- Flinders Health and Medical Research Institute (FHMRI), College of Medicine and Public Health, Flinders University, Bedford Park, South Australia, Australia
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15
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Kim J, Kim Y, Lee B. Identification of Long Non-Coding RNA Profiles and Potential Therapeutic Agents for Fibrolamellar Carcinoma Based on RNA-Sequencing Data. Genes (Basel) 2023; 14:1709. [PMID: 37761849 PMCID: PMC10530820 DOI: 10.3390/genes14091709] [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: 08/01/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND Fibrolamellar carcinoma (FLC) is a rare type of liver cancer that primarily affects adolescents and young adults without prior liver disease or viral infections. Patients with FLC generally have non-specific symptoms, are often diagnosed at a later stage, and experience a higher frequency of metastases compared to patients with other liver cancers. A fusion transcript of DNAJB1 and PRKACA, which can lead to increased activity of PKA and cellular proliferation, has been identified in all FLC patients, but the exact mechanism through which FLC develops remains unclear. In this study, we investigated common lncRNA profiles in various FLC samples using bioinformatics analyses. METHODS We analyzed differentially expressed (DE) lncRNAs from three RNA sequencing datasets. Using lncRNAs and DE mRNAs, we predicted potential lncRNA target genes and performed Gene Ontology (GO) and KEGG analyses with the DE lncRNA target genes. Moreover, we screened for small-molecule compounds that could act as therapeutic targets for FLC. RESULTS We identified 308 DE lncRNAs from the RNA sequencing datasets. In addition, we performed a trans-target prediction analysis and identified 454 co-expressed pairs in FLC. The GO analysis showed that the lncRNA-related up-regulated mRNAs were enriched in the regulation of protein kinase C signaling and cAMP catabolic processes, while lncRNA-related down-regulated mRNAs were enriched in steroid, retinol, cholesterol, and xenobiotic metabolic processes. The analysis of small-molecule compounds for FLC treatment identified vitexin, chlorthalidone, triamterene, and amiloride, among other compounds. CONCLUSIONS We identified potential therapeutic targets for FLC, including lncRNA target genes as well as small-molecule compounds that could potentially be used as treatments. Our findings could contribute to furthering our understanding of FLC and providing potential avenues for diagnosis and treatment.
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Affiliation(s)
- Janghyun Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea (Y.K.)
| | - Young Kim
- Department of Oral Pathology, School of Dentistry, Chonnam National University, Gwangju 61186, Republic of Korea (Y.K.)
| | - Bora Lee
- Department of Biochemistry, Chonnam National University Medical School, Hwasun 58128, Republic of Korea
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16
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Shakhpazyan NK, Mikhaleva LM, Bedzhanyan AL, Sadykhov NK, Midiber KY, Konyukova AK, Kontorschikov AS, Maslenkina KS, Orekhov AN. Long Non-Coding RNAs in Colorectal Cancer: Navigating the Intersections of Immunity, Intercellular Communication, and Therapeutic Potential. Biomedicines 2023; 11:2411. [PMID: 37760852 PMCID: PMC10525929 DOI: 10.3390/biomedicines11092411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/29/2023] Open
Abstract
This comprehensive review elucidates the intricate roles of long non-coding RNAs (lncRNAs) within the colorectal cancer (CRC) microenvironment, intersecting the domains of immunity, intercellular communication, and therapeutic potential. lncRNAs, which are significantly involved in the pathogenesis of CRC, immune evasion, and the treatment response to CRC, have crucial implications in inflammation and serve as promising candidates for novel therapeutic strategies and biomarkers. This review scrutinizes the interaction of lncRNAs with the Consensus Molecular Subtypes (CMSs) of CRC, their complex interplay with the tumor stroma affecting immunity and inflammation, and their conveyance via extracellular vesicles, particularly exosomes. Furthermore, we delve into the intricate relationship between lncRNAs and other non-coding RNAs, including microRNAs and circular RNAs, in mediating cell-to-cell communication within the CRC microenvironment. Lastly, we propose potential strategies to manipulate lncRNAs to enhance anti-tumor immunity, thereby underlining the significance of lncRNAs in devising innovative therapeutic interventions in CRC.
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Affiliation(s)
- Nikolay K. Shakhpazyan
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Liudmila M. Mikhaleva
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Arcady L. Bedzhanyan
- Department of Abdominal Surgery and Oncology II (Coloproctology and Uro-Gynecology), Petrovsky National Research Center of Surgery, 119435 Moscow, Russia;
| | - Nikolay K. Sadykhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Konstantin Y. Midiber
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexandra K. Konyukova
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Andrey S. Kontorschikov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Ksenia S. Maslenkina
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
| | - Alexander N. Orekhov
- Avtsyn Research Institute of Human Morphology, Petrovsky National Research Center of Surgery, 119435 Moscow, Russia; (L.M.M.); (N.K.S.); (K.Y.M.); (A.K.K.); (A.S.K.); (K.S.M.); (A.N.O.)
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, 125315 Moscow, Russia
- Institute for Atherosclerosis Research, 121096 Moscow, Russia
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17
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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.
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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.
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18
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Ghafouri-Fard S, Safarzadeh A, Hussen BM, Taheri M, Mokhtari M. Contribution of CRNDE lncRNA in the development of cancer and the underlying mechanisms. Pathol Res Pract 2023; 244:154387. [PMID: 36893710 DOI: 10.1016/j.prp.2023.154387] [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: 01/25/2023] [Revised: 02/19/2023] [Accepted: 02/23/2023] [Indexed: 03/09/2023]
Abstract
Colorectal Neoplasia Differentially Expressed (CRNDE) is an lncRNA with crucial roles in cancer development. It is located on chromosome 16 on the opposite strand to the adjacent IRX5 gene, implying the presence of a shared bidirectional promoter for these two genes. Expression of CRNDE has been assessed in a diverse array of hematological malignancies and solid tumors, representing its potential as a therapeutic target in these conditions. This lncRNA has a regulatory effect on activity of several pathways and axes that are involved in the regulation of cell apoptosis, immune responses and tumorigenesis. The current review is an updated review about the role of CRNDE in the development of cancers.
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Affiliation(s)
- Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Arash Safarzadeh
- Phytochemistry Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Bashdar Mahmud Hussen
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
| | - Mohammad Taheri
- Institute of Human Genetics, Jena University Hospital, Jena, Germany; Urology and Nephrology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Majid Mokhtari
- Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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19
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Vosough P, Khatami SH, Hashemloo A, Tajbakhsh A, Karimi-Fard F, Taghvimi S, Taheri-Anganeh M, Soltani Fard E, Savardashtaki A, Movahedpour A. Exosomal lncRNAs in gastrointestinal cancer. Clin Chim Acta 2023; 540:117216. [PMID: 36592922 DOI: 10.1016/j.cca.2022.117216] [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: 08/24/2022] [Revised: 12/24/2022] [Accepted: 12/29/2022] [Indexed: 01/01/2023]
Abstract
Gastrointestinal cancer (GIC) remains a leading cause of morbidity and mortality worldwide. Unfortunately, these cancers are diagnosed in advanced metastatic stages due to lack of reliable biomarkers that are sufficiently specific and sensitive in early disease. There has been growing evidence that circulating exosomes can be used to diagnose cancer non-invasively with limited risks and side effects. Furthermore, exosomal long non-coding RNAs (lncRNAs) are emerging as a new class of promising biomarkers in cancer. This review provides an overview of the extraction and detection of exosomal lncRNAs with a focus on their potential role in GIC.
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Affiliation(s)
- Parisa Vosough
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Amir Tajbakhsh
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | | | - Sina Taghvimi
- Department of Biology, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Elahe Soltani Fard
- Department of Molecular Medicine, School of Advanced Technologies, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran; Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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20
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Bhal S, Kundu CN. Targeting crosstalk of signaling pathways in cancer stem cells: a promising approach for development of novel anti-cancer therapeutics. Med Oncol 2023; 40:82. [PMID: 36662310 DOI: 10.1007/s12032-022-01905-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 11/21/2022] [Indexed: 01/21/2023]
Abstract
Wnt, Hedgehog (Hh), and Notch signaling pathways are the evolutionarily conserved signaling pathways that regulate the embryonic development and also play crucial role in maintaining stemness properties of cancer stem cells (CSCs) and inducing epithelial-to-mesenchymal transition (EMT), metastasis, and angiogenesis. It has been highly challenging to inhibit the CSCs growth and proliferation as these are capable of evading chemotherapeutic drugs and cause cancer recurrence through multiple signaling pathways. Therefore, novel therapeutic strategies to target the key players involved in the crosstalk of these signaling pathways need to be developed. In this review, we have identified the interacting molecules of Wnt, Hh, and Notch pathways responsible for enhancing the malignant properties of CSCs. Analyzing the functions of these crosstalk molecules will help us to find an approach toward the development of new anti-cancer drugs for inhibition of CSCs growth and progression. Long non-coding RNAs (LncRNAs) play a significant role in various cellular processes, like chromatin remodeling, epigenetic modifications, transcriptional, and post-transcriptional regulations. Here, we have highlighted the research findings suggesting the involvement of LncRNAs in maintenance of the stemness properties of CSCs through modulation of the above-mentioned signaling pathways. We have also discussed about the different therapeutic approaches targeting those key players responsible for mediating the crosstalk between the pathways. Overall, this review article will surely help the cancer biologists to design novel anti-CSCs agents that will open up a new horizon in the field of anti-cancer therapeutics.
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Affiliation(s)
- Subhasmita Bhal
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India
| | - Chanakya Nath Kundu
- Cancer Biology Division, School of Biotechnology, Kalinga Institute of Industrial Technology (KIIT), Deemed to Be University, Campus-11, Patia, Bhubaneswar, Odisha, 751024, India.
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21
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Mao K, Tang R, Wu Y, Zhang Z, Gao Y, Huang H. Prognostic markers of ferroptosis-related long non-coding RNA in lung adenocarcinomas. Front Genet 2023; 14:1118273. [PMID: 36923797 PMCID: PMC10009162 DOI: 10.3389/fgene.2023.1118273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023] Open
Abstract
Ferroptosis is a recently established type of iron-dependent programmed cell death. Growing studies have focused on the function of ferroptosis in cancers, including lung adenocarcinoma (LUAD). However, the factors involved in the regulation of ferroptosis-related genes are not fully understood. In this study, we collected data from lung adenocarcinoma datasets of the Cancer Genome Atlas (TCGA-LUAD). The expression profiles of 60 ferroptosis-related genes were screened, and two differentially expressed ferroptosis subtypes were identified. We found the two ferroptosis subtypes can predict clinical outcomes and therapeutic responses in LUAD patients. Furthermore, key long non-coding RNAs (lncRNAs) were screened by single factor Cox and least absolute shrinkage and selection operator (LASSO) based on which co-expressed with the 60 ferroptosis-related genes. We then established a risk score model which included 13 LUAD ferroptosis-related lncRNAs with a multi-factor Cox regression. The risk score model showed a good performance in evaluating the outcome of LUAD. What's more, we divided TCGA-LUAD tumor samples into two groups with high- and low-risk scores and further explored the differences in clinical characteristics, tumor mutation burden, and tumor immune cell infiltration among different LUAD tumor risk score groups and evaluate the predictive ability of risk score for immunotherapy benefit. Our findings provide good support for immunotherapy in LUAD in the future.
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Affiliation(s)
- Kaimin Mao
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Ri Tang
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yali Wu
- Department of Respiratory and Critical Care Medicine, NHC Key Laboratory of Pulmonary Diseases, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhiyun Zhang
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Yuan Gao
- Department of Critical Care Medicine, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
| | - Huijing Huang
- Department of Rheumatology, Zhongshan Hospital, Fudan University, Shanghai, China
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22
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Sangeeth A, Malleswarapu M, Mishra A, Gutti RK. Long Non-Coding RNAs as Cellular Metabolism and Haematopoiesis Regulators. J Pharmacol Exp Ther 2023; 384:79-91. [PMID: 35667690 DOI: 10.1124/jpet.121.001120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 12/27/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a category of non-coding RNAs (ncRNAs) that are more than 200 bases long and play major regulatory roles in a wide range of biologic processes, including hematopoeisis and metabolism. Metabolism in cells is an immensely complex process that involves the interconnection and unification of numerous signaling pathways. A growing body of affirmation marks that lncRNAs do participate in metabolism, both directly and indirectly, via metabolic regulation of enzymes and signaling pathways, respectively. The complexities are disclosed by the latest studies demonstrating how lncRNAs could indeed alter tissue-specific metabolism. We have entered a new realm for discovery that is both intimidating and intriguing. Understanding the different functions of lncRNAs in various cellular pathways aids in the advancement of predictive and therapeutic capabilities for a wide variety of myelodysplastic and metabolic disorders. This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. We have focused on the pathway of action of several lncRNAs and have also delved into their prognostic value. Their use as biomarkers and possible therapeutic targets has also been discussed. SIGNIFICANCE STATEMENT: This review has tried to give an overview of the different ncRNAs and their effects on hematopoiesis and metabolism. The pathway of action of several lncRNAs and their prognostic value was discussed. Their use as biomarkers and possible therapeutic targets has also been elaborated.
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Affiliation(s)
- Anjali Sangeeth
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Mahesh Malleswarapu
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Amit Mishra
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
| | - Ravi Kumar Gutti
- Department of Biochemistry, School of Life Sciences, University of Hyderabad, (PO) Gachibowli, Hyderabad, India (A.S., M.M., R.K.G.) and Department of Bioscience & Bioengineering, Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, India (A.M.)
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23
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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.
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24
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Rahmani F, Safavi P, Fathollahpour A, Tanhaye Kalate Sabz F, Tajzadeh P, Arefnezhad M, Ferns GA, Hassanian SM, Avan A. The interplay between non-coding RNAs and Wnt/ß-catenin signaling pathway in urinary tract cancers: from tumorigenesis to metastasis. EXCLI JOURNAL 2022; 21:1273-1284. [PMID: 36483915 PMCID: PMC9727268 DOI: 10.17179/excli2022-5348] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/26/2022] [Indexed: 01/13/2023]
Abstract
Non-coding RNAs (ncRNAs) are emerging as important regulators in various pathological conditions including tumorigenesis, metastasis, and drug resistance in human cancers. Oncogenic or tumor suppressor ncRNAs exert prominent effects on cell proliferation, migration and invasion in cancer cells through modulating various signaling pathways including Wnt/β-catenin. Upregulation of the oncogenic Wnt/β-catenin pathway was reported to be implicated in multiple human cancers including breast, liver, colorectal, and urothelial cancers. Therefore, identifying interactions between ncRNAs and canonical Wnt signaling components may represent novel therapeutic targets for better treatment and management of cancer. In this review, we summarized the recent findings about miRNA/lncRNA-dependent mechanisms that regulate Wnt/β-catenin signaling involved in tumorigenesis and metastasis of urinary tract cancers.
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Affiliation(s)
- Farzad Rahmani
- Kashmar School of Nursing, Mashhad University of Medical Sciences, Mashhad, Iran,Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Pegah Safavi
- Department of Medical Radiation, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | | | - Parastoo Tajzadeh
- Kashmar School of Nursing, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Mohsen Arefnezhad
- Kashmar School of Nursing, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Gordon A. Ferns
- Brighton & Sussex Medical School, Division of Medical Education, Falmer, Brighton, Sussex, UK
| | - Seyed Mahdi Hassanian
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Amir Avan
- Metabolic Syndrome Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran,Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran,*To whom correspondence should be addressed: Amir Avan, Basic Medical Sciences Institute, Mashhad University of Medical Sciences, Mashhad, Iran, E-mail:
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25
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Zhang Q, Wu X, Sun Y, Yang L, Wang Z, Yang Y, Zhao X, Zhang X. Epithelial-mesenchymal transition-related lncRNAs associated with prognosis and immune cell infiltration in lung adenocarcinoma. Am J Transl Res 2022; 14:7308-7323. [PMID: 36398231 PMCID: PMC9641461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/11/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) remains the most common type of lung cancer and is associated with distant metastasis and poor prognosis. Epithelial-mesenchymal transition (EMT) plays crucial roles in carcinogenesis, embryogenesis, and wound healing. EMT-related molecules may be adopted for early diagnosis and prognosis of cancer and targeting them may constitute an attractive strategy for treatment. This study aims to identify the EMT-related long non-coding RNAs (lncRNAs) and develop a risk signature to accurately predict the prognosis of LUAD patients. METHODS The RNA-seq data and corresponding clinical profiles were obtained from LUAD cohort of The Cancer Genome Atlas (TCGA) database. EMT-related lncRNAs significantly associated with prognosis were identified by Pearson correlation analysis and univariate regression analysis. Subsequently, an EMT-related prognostic risk signature was developed through LASSO and multivariate regression analyses. Kaplan Meier and receiver operating characteristic curve analysis were implemented to assess the predictive performance of the signature. The nomogram was constructed to predict the 1-year, 3-year, and 5-year overall survival of LUAD patients. Additionally, enrichment analyses were carried out to identify probable biologic processes and cellular pathways involved in the signature. The correlation of immune cell infiltration and risk score was also evaluated by CIBERSORT algorithm. Finally, we constructed a ceRNA network to further study possible downstream targets and molecular mechanisms of EMT-related lncRNAs in LUAD. RESULTS Eight EMT-related lncRNAs were identified to develop a prognostic risk signature in LUAD. Patients with high-risk scores had worse survival outcomes than those with low-risk scores. The signature showed robust predictive potential, and was verified to be an independent prognostic factor. Moreover, the risk score based on the signature was significantly correlated with immune cell infiltration in LUAD. CONCLUSIONS We established and validated a prognostic signature that reflects the tumor microenvironment characteristics and predicts the outcomes for LUAD.
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Affiliation(s)
- Quncheng Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
| | - Xuan Wu
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
- Academy of Medical Science, Zhengzhou UniversityZhengzhou, China
| | - Ya Sun
- Xinxiang Medical UniversityXinxiang, China
| | - Li Yang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
- Academy of Medical Science, Zhengzhou UniversityZhengzhou, China
| | - Ziqi Wang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
- Academy of Medical Science, Zhengzhou UniversityZhengzhou, China
| | - Yuanjian Yang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
| | - Xingru Zhao
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
| | - Xiaoju Zhang
- Department of Respiratory and Critical Care Medicine, Zhengzhou University People’s HospitalChina
- Henan Provincial People’s HospitalZhengzhou, China
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26
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Zhao H, Li L, Zhao N, Lu A, Lu C, He X. The effect of long non-coding RNAs in joint destruction of rheumatoid arthritis. Front Cell Dev Biol 2022; 10:1011371. [PMID: 36263019 PMCID: PMC9574091 DOI: 10.3389/fcell.2022.1011371] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 09/12/2022] [Indexed: 11/18/2022] Open
Abstract
Rheumatoid arthritis (RA) is a systemic autoimmune disease accompanied with joint destruction. Serious joint destruction will eventually lead to disability and the decline of life quality in RA patients. At present, the therapeutic effect of drugs to alleviate joint destruction in RA is limited. Recently, accumulating evidences have shown that long non-coding RNAs (lncRNAs) play an important role in the pathogenesis of joint diseases. Therefore, this paper reviews the expression change and the action mechanism of lncRNAs in joint destruction of RA in recent years. A more comprehensive understanding of the role of lncRNAs in joint destruction will help the treatment of RA.
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Affiliation(s)
- Hanxiao Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- The Second Clinical College of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Li Li
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Ning Zhao
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
- Shanghai GuangHua Hospital of Integrated Traditional Chinese and Western Medicine, Institute of Arthritis Research, Shanghai Academy of Chinese Medical Sciences, Shanghai, China
- *Correspondence: Aiping Lu, ; Cheng Lu, ; Xiaojuan He,
| | - Cheng Lu
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Aiping Lu, ; Cheng Lu, ; Xiaojuan He,
| | - Xiaojuan He
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing, China
- *Correspondence: Aiping Lu, ; Cheng Lu, ; Xiaojuan He,
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27
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Small Extracellular Vesicles and Their Involvement in Cancer Resistance: An Up-to-Date Review. Cells 2022; 11:cells11182913. [PMID: 36139487 PMCID: PMC9496799 DOI: 10.3390/cells11182913] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/25/2022] [Accepted: 09/15/2022] [Indexed: 12/11/2022] Open
Abstract
In recent years, tremendous progress has been made in understanding the roles of extracellular vesicles (EVs) in cancer. Thanks to advancements in molecular biology, it has been found that the fraction of EVs called exosomes or small EVs (sEVs) modulates the sensitivity of cancer cells to chemotherapeutic agents by delivering molecularly active non-coding RNAs (ncRNAs). An in-depth analysis shows that two main molecular mechanisms are involved in exosomal modified chemoresistance: (1) translational repression of anti-oncogenes by exosomal microRNAs (miRs) and (2) lack of translational repression of oncogenes by sponging of miRs through long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs). At the cellular level, these processes increase the proliferation and survival of cancer cells and improve their ability to metastasize and resist apoptosis. In addition, studies in animal models have shown enhancing tumor size under the influence of exosomal ncRNAs. Ultimately, exosomal ncRNAs are responsible for clinically significant chemotherapy failures in patients with different types of cancer. Preliminary data have also revealed that exosomal ncRNAs can overcome chemotherapeutic agent resistance, but the results are thoroughly fragmented. This review presents how exosomes modulate the response of cancer cells to chemotherapeutic agents. Understanding how exosomes interfere with chemoresistance may become a milestone in developing new therapeutic options, but more data are still required.
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The Insulin-like Growth Factor System and Colorectal Cancer. LIFE (BASEL, SWITZERLAND) 2022; 12:life12081274. [PMID: 36013453 PMCID: PMC9410426 DOI: 10.3390/life12081274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 11/29/2022]
Abstract
Insulin-like growth factors (IGFs) are peptides which exert mitogenic, endocrine and cytokine activities. Together with their receptors, binding proteins and associated molecules, they participate in numerous pathophysiological processes, including cancer development. Colorectal cancer (CRC) is a disease with high incidence and mortality rates worldwide, whose etiology usually represents a combination of the environmental and genetic factors. IGFs are most often increased in CRC, enabling excessive autocrine/paracrine stimulation of the cell growth. Overexpression or increased activation/accessibility of IGF receptors is a coinciding step which transmits IGF-related signals. A number of molecules and biochemical mechanisms exert modulatory effects shaping the final outcome of the IGF-stimulated processes, frequently leading to neoplastic transformation in the case of irreparable disbalance. The IGF system and related molecules and pathways which participate in the development of CRC are the focus of this review.
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29
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Castro-Oropeza R, Piña-Sánchez P. Epigenetic and Transcriptomic Regulation Landscape in HPV+ Cancers: Biological and Clinical Implications. Front Genet 2022; 13:886613. [PMID: 35774512 PMCID: PMC9237502 DOI: 10.3389/fgene.2022.886613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 05/24/2022] [Indexed: 11/13/2022] Open
Abstract
Human Papillomavirus (HPV) is an oncogenic virus that causes the highest number of viral-associated cancer cases and deaths worldwide, with more than 690,000 new cases per year and 342,000 deaths only for cervical cancer (CC). Although the incidence and mortality rates for CC are declining in countries where screening and vaccination programs have been implemented, other types of cancer in which HPV is involved, such as oropharyngeal cancer, are increasing, particularly in men. Mutational and transcriptional profiles of various HPV-associated neoplasms have been described, and accumulated evidence has shown the oncogenic capacity of E6, E7, and E5 genes of high-risk HPV. Interestingly, transcriptomic analysis has revealed that although a vast majority of the human genome is transcribed into RNAs, only 2% of transcripts are translated into proteins. The remaining transcripts lacking protein-coding potential are called non-coding RNAs. In addition to the transfer and ribosomal RNAs, there are regulatory non-coding RNAs classified according to size and structure in long non-coding RNAs (lncRNAs), circular RNAs (circRNAs), and small RNAs; such as microRNAs (miRNAs), piwi-associated RNAs (piRNAs), small nucleolar RNAs (snoRNAs) and endogenous short-interfering RNAs. Recent evidence has shown that lncRNAs, miRNAs, and circRNAs are aberrantly expressed under pathological conditions such as cancer. In addition, those transcripts are dysregulated in HPV-related neoplasms, and their expression correlates with tumor progression, metastasis, poor prognosis, and recurrence. Nuclear lncRNAs are epigenetic regulators involved in controlling gene expression at the transcriptional level through chromatin modification and remodeling. Moreover, disruption of the expression profiles of those lncRNAs affects multiple biological processes such as cell proliferation, apoptosis, and migration. This review highlights the epigenetic alterations induced by HPV, from infection to neoplastic transformation. We condense the epigenetic role of non-coding RNA alterations and their potential as biomarkers in transformation's early stages and clinical applications. We also summarize the molecular mechanisms of action of nuclear lncRNAs to understand better their role in the epigenetic control of gene expression and how they can drive the malignant phenotype of HPV-related neoplasia. Finally, we review several chemical and epigenetic therapy options to prevent and treat HPV-associated neoplasms.
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Affiliation(s)
| | - Patricia Piña-Sánchez
- Molecular Oncology Laboratory, Oncology Research Unit, Oncology Hospital, IMSS National Medical Center, Mexico City, Mexico
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30
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CRNDE: A valuable long noncoding RNA for diagnosis and therapy of solid and hematological malignancies. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 28:190-201. [PMID: 35402077 PMCID: PMC8961077 DOI: 10.1016/j.omtn.2022.03.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Colorectal neoplasia differentially expressed (CRNDE) is an oncogenic long noncoding RNA (lncRNA). Increased CRNDE expression was initially discovered in colorectal cancer and then in a variety of solid tumors and hematological malignancies. CRNDE participates in multiple biological processes, such as cell proliferation, differentiation, migration, and apoptosis. CRNDE has been shown to modulate target gene expression through multiple mechanisms, including transcriptional regulation, post-transcriptional regulation, and competition for microRNA (miRNA) binding. In this review, we summarize the evidence that supports CRNDE in the diagnosis and prognosis predicting of cancers. The functional roles and molecular mechanisms of CRNDE are further described for major types of solid tumors and hematological malignancies. The therapeutic potential of CRNDE as a target for research and development is also discussed.
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Du L, Zhao Q, Li J, Wang M, Qiao H. Expression of colorectal neoplasia differentially expressed in anaplastic thyroid carcinoma and its effect on cancer cell proliferation. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:473. [PMID: 35571426 PMCID: PMC9096416 DOI: 10.21037/atm-22-945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/08/2022] [Indexed: 11/07/2022]
Abstract
Background The incidence of anaplastic thyroid cancer (ATC) is high among human cancers. Colorectal neoplasia differentially expressed (CRNDE) is highly expressed in common tumors, and is therefore a potential molecular target for anti-tumor therapy. However, the function of CRNDE in ATC remains elusive. Methods The Gene Expression Omnibus (GEO) database was used to screen the differential expression of long-noncoding RNA (lncRNA) in ATC tissues. The Cancer Genome Atlas (TCGA) database was used to analyze the expression of CRNDE in thyroid cancer (THCA) tissues and its impact on patient prognosis. Quantitative real-time PCR (qRT-PCR) was used to determine the expression level of CRNDE in tumor and control tissues. The biological function of CRNDE in THCA was explored using TCGA RNA sequencing (RNA-seq) data analysis. ATC cell lines with low and high CRNDE expression were selected for CRNDE siRNA transfection, and the proliferation of cells was detected in each group. Results The GEO and TCGA databases analysis results showed that CRNDE was highly expressed in ATC tissues, which is related to the poor prognosis of THCA patients. Also, the expression of CRNDE in the ATC cell line, ARO (human thyroid cancer cell line), was relatively high, while the expression in sw579 is relatively low. Therefore, ARO and sw579 were chosen for CRNDE small interfering RNA (siRNA) transfection. Compared with negative control (si-NC), the expression of CRNDE in si-CRNDE-1, si-CRNDE-2, and si-CRNDE-3 was reduced, indicating that the inhibitory effect was significantly enhanced and the cell proliferation ability was reduced, and the cell cycle is arrested in the G0/G1 phase. Finally, it was found that the wnt3a, β-catenin, and cyclinD1 protein expressions of si-CRNDE-1 and si-CRNDE-2 were significantly reduced. Conclusions The high expression of CRNDE in ATC tissues may promote the proliferation of ATC cells by regulating the Wnt/β-catenin signaling pathway. CRNDE may be a potential molecular target for the treatment of ATC.
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Affiliation(s)
- Lili Du
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Qingsong Zhao
- Department of Endocrinology and Metabolism, The Fourth Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jingjing Li
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Mingli Wang
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hong Qiao
- Department of Endocrinology and Metabolism, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Chen Y, Guo Y, Li S, Xu J, Wang X, Ning W, Ma L, Qu Y, Zhang M, Zhang H. Identification of N6-Methyladenosine-Related lncRNAs as a Prognostic Signature in Glioma. Front Oncol 2022; 12:789283. [PMID: 35311131 PMCID: PMC8927984 DOI: 10.3389/fonc.2022.789283] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/09/2022] [Indexed: 12/17/2022] Open
Abstract
N6-methyladenosine (m6A) modification is the most abundant modification in long noncoding RNAs (lncRNAs). Current studies have shown that the abnormal expression of m6A-related genes is closely associated with the tumorigenesis and progression of glioma. However, the role of m6A-related lncRNAs in glioma development is still unclear. Herein, we screened 566 m6A-related lncRNAs in glioma from The Cancer Genome Atlas (TCGA) database. The expression pattern of these lncRNAs could cluster samples into two groups, in which various classical tumor-related functions and the tumor immune microenvironment were significantly different. Subsequently, a nine-factor m6A-related lncRNA prognostic signature (MLPS) was constructed by using a LASSO regression analysis in the training set and was validated in the test set and independent datasets. The AUC values of the MLPS were 0.881, 0.918 and 0.887 for 1-, 3- and 5-year survival in the training set, respectively, and 0.856, 0.916 and 0.909 for 1-, 3-, and 5-year survival in the test set, respectively. Stratification analyses of the MLPS illustrated its prognostic performance in gliomas with different characteristics. Correlation analyses showed that the infiltrations of monocytes and tumor-associated macrophages (TAMs) were significantly relevant to the risk score in the MLPS. Moreover, we detected the expression of four MLPS factors with defined sequences in glioma and normal cells by using RT-PCR. Afterwards, we investigated the functions of LNCTAM34A (one of the MLPS factors) in glioma cells, which have rarely been reported. Via in vitro experiments, LNCTAM34A was demonstrated to promote the proliferation, migration and epithelial-mesenchymal transition (EMT) of glioma cells. Overall, our study revealed the critical role of m6A-related lncRNAs in glioma and elucidated that LNCTAM34A could promote glioma proliferation, migration and EMT.
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Affiliation(s)
- Yujia Chen
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yuduo Guo
- CAS Key Laboratory of Infection and Immunity, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Shenglun Li
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Jiacheng Xu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Xiang Wang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Weihai Ning
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Lixin Ma
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yanming Qu
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Mingshan Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Hongwei Zhang
- Department of Neurosurgery, Sanbo Brain Hospital, Capital Medical University, Beijing, China
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Lift the curtain on long non-coding RNAs in hematological malignancies: Pathogenic elements and potential targets. Cancer Lett 2022; 536:215645. [DOI: 10.1016/j.canlet.2022.215645] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 03/01/2022] [Accepted: 03/12/2022] [Indexed: 12/19/2022]
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Shen J, Yan D, Bai L, Geng R, Zhao X, Li H, Dong Y, Cao J, Tang Z, Liu SB. An 11-Gene Signature Based on Treatment Responsiveness Predicts Radiation Therapy Survival Benefit Among Breast Cancer Patients. Front Oncol 2022; 11:816053. [PMID: 35071020 PMCID: PMC8770413 DOI: 10.3389/fonc.2021.816053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Purpose We developed a strategy of building prognosis gene signature based on clinical treatment responsiveness to predict radiotherapy survival benefit in breast cancer patients. Methods and Materials Analyzed data came from the public database. PFS was used as an indicator of clinical treatment responsiveness. WGCNA was used to identify the most relevant modules to radiotherapy response. Based on the module genes, Cox regression model was used to build survival prognosis signature to distinguish the benefit group of radiotherapy. An external validation was also performed. Results In the developed dataset, MEbrown module with 534 genes was identified by WGCNA, which was most correlated to the radiotherapy response of patients. A number of 11 hub genes were selected to build the survival prognosis signature. Patients that were divided into radio-sensitivity group and radio-resistant group based on the signature risk score had varied survival benefit. In developed dataset, the 3-, 5-, and 10-year AUC of the signature were 0.814 (CI95%: 0.742–0.905), 0.781 (CI95%: 0.682–0.880), and 0.762 (CI95%: 0.626–0.897), respectively. In validation dataset, the 3- and 5-year AUC of the signature were 0.706 (CI95%: 0.523–0.889) and 0.743 (CI95%: 0.595–0.891). The signature had higher predictive power than clinical factors alone and had more clinical prognosis efficiency. Functional enrichment analysis revealed that the identified genes were mainly enriched in immune-related processes. Further immune estimated analysis showed the difference in distribution of immune micro-environment between radio-sensitivity group and radio-resistant group. Conclusions The 11-gene signature may reflect differences in tumor immune micro-environment that underlie the differential response to radiation therapy and could guide clinical-decision making related to radiation in breast cancer patients.
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Affiliation(s)
- Junjie Shen
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China
| | - Derui Yan
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Lu Bai
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Ruirui Geng
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Xulun Zhao
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Huijun Li
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Yongfei Dong
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Jianping Cao
- School of Radiation Medicine and Protection and Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou, China
| | - Zaixiang Tang
- Department of Biostatistics, School of Public Health, Medical College of Soochow University, Suzhou, China.,Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Medical College of Soochow University, Suzhou, China
| | - Song-Bai Liu
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
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Ge S, Jiang C, Li M, Cheng Z, Feng X. Long non-coding RNA CRNDE exacerbates NPC advancement mediated by the miR-545-5p/CCND2 axis. Cancer Cell Int 2021; 21:650. [PMID: 34863152 PMCID: PMC8645150 DOI: 10.1186/s12935-021-02348-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous studies indicated CRNDE to have a pivotal part within tumorigenesis. Notwithstanding, precise details on CRNDE activities within NPC are still uncertain. The investigation described in this article served to focus in greater depth on the mechanistics regarding CRNDE, together with all associated regulatory networks, on nasopharyngeal carcinoma (NPC) and its treatment possibilities. METHODS Quantitative real-time polymerase chain reaction (RT-qPCR) analyzed CRNDE, miR-545-5p and CCND2 expression within NPCs and representative cell lineages. CCK-8 cell counting-, EdU-, wound-healing-/transwell-assays analyzed cellular proliferation, migrative, together with invasive properties. Apoptosis/cell cycle progression were scrutinized through flow cytometry. Dual-luciferase reporter assays validated CRNDE/miR-545-5p/CCND2 interplay. Proteomic expression of apoptosis-related protein, EMT-related protein and CCND2 protein were evaluated through Western blotting. In addition, Ki67 expression was evaluated through immunohistochemical staining. The effect of CRNDE in vivo was assessed by nude murine xenograft model studies. RESULTS This study demonstrated up-regulated expression of CRNDE and CCND2 within NPC tissues/cell lines. Meanwhile, miR-545-5p was down-regulated. CRNDE knock-down or miR-545-5p over-expression drastically reduced NPC proliferative, migrative and invasive properties, promoted apoptosis/altered cell cycle, and inhibited CCND2 expression. However, miR-545-5p down-regulation had opposing effects. All inhibiting functions generated by CRNDE down-regulation upon NPC progression could be counterbalanced or synergistically exacerbated, depending on miR-545-5p down-regulation or up-regulation, respectively. Multiple-level investigations revealed CRNDE to serve as a sponge for miR-545-5p, and can target CCND2 within NPCs. CONCLUSIONS CRNDE increases CCND2 expression by competitive binding with miR-545-5p, thus accelerating the development of NPC. This provides potential therapeutic targets and prognostic markers against NPC.
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Affiliation(s)
- Sichen Ge
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Chengyi Jiang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China.
| | - Min Li
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Zhongqiang Cheng
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
| | - Xiaojia Feng
- Department of Surgical Oncology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233000, Anhui, China
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Xiong G, Pan S, Jin J, Wang X, He R, Peng F, Li X, Wang M, Zheng J, Zhu F, Qin R. Long Noncoding Competing Endogenous RNA Networks in Pancreatic Cancer. Front Oncol 2021; 11:765216. [PMID: 34760707 PMCID: PMC8573238 DOI: 10.3389/fonc.2021.765216] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022] Open
Abstract
Pancreatic cancer (PC) is a highly malignant disease characterized by insidious onset, rapid progress, and poor therapeutic effects. The molecular mechanisms associated with PC initiation and progression are largely insufficient, hampering the exploitation of novel diagnostic biomarkers and development of efficient therapeutic strategies. Emerging evidence recently reveals that noncoding RNAs (ncRNAs), including long ncRNAs (lncRNAs) and microRNAs (miRNAs), extensively participate in PC pathogenesis. Specifically, lncRNAs can function as competing endogenous RNAs (ceRNAs), competitively sequestering miRNAs, therefore modulating the expression levels of their downstream target genes. Such complex lncRNA/miRNA/mRNA networks, namely, ceRNA networks, play crucial roles in the biological processes of PC by regulating cell growth and survival, epithelial-mesenchymal transition and metastasis, cancer stem cell maintenance, metabolism, autophagy, chemoresistance, and angiogenesis. In this review, the emerging knowledge on the lncRNA-associated ceRNA networks involved in PC initiation and progression will be summarized, and the potentials of the competitive crosstalk as diagnostic, prognostic, and therapeutic targets will be comprehensively discussed.
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Affiliation(s)
- Guangbing Xiong
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Shutao Pan
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jikuan Jin
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaoxiang Wang
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ruizhi He
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Peng
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xu Li
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Min Wang
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jianwei Zheng
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Feng Zhu
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Renyi Qin
- Department of Biliary-Pancreatic Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Li Q, Yao L, Lin Z, Li F, Xie D, Li C, Zhan W, Lin W, Huang L, Wu S, Zhou H. Identification of Prognostic Model Based on Immune-Related LncRNAs in Stage I-III Non-Small Cell Lung Cancer. Front Oncol 2021; 11:706616. [PMID: 34745939 PMCID: PMC8564147 DOI: 10.3389/fonc.2021.706616] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/24/2021] [Indexed: 12/13/2022] Open
Abstract
Background Long non-coding RNAs (lncRNAs) participate in the regulation of immune response and carcinogenesis, shaping tumor immune microenvironment, which could be utilized in the construction of prognostic signatures for non-small cell lung cancer (NSCLC) as supplements. Methods Data of patients with stage I-III NSCLC was downloaded from online databases. The least absolute shrinkage and selection operator was used to construct a lncRNA-based prognostic model. Differences in tumor immune microenvironments and pathways were explored for high-risk and low-risk groups, stratified by the model. We explored the potential association between the model and immunotherapy by the tumor immune dysfunction and exclusion algorithm. Results Our study extracted 15 immune-related lncRNAs to construct a prognostic model. Survival analysis suggested better survival probability in low-risk group in training and validation cohorts. The combination of tumor, node, and metastasis staging systems with immune-related lncRNA signatures presented higher prognostic efficacy than tumor, node, and metastasis staging systems. Single sample gene set enrichment analysis showed higher infiltration abundance in the low-risk group, including B cells (p<0.001), activated CD8+ T cells (p<0.01), CD4+ T cells (p<0.001), activated dendritic cells (p<0.01), and CD56+ Natural killer cells (p<0.01). Low-risk patients had significantly higher immune scores and estimated scores from the ESTIMATE algorithm. The predicted proportion of responders to immunotherapy was higher in the low-risk group. Critical pathways in the model were enriched in immune response and cytoskeleton. Conclusions Our immune-related lncRNA model could describe the immune contexture of tumor microenvironments and facilitate clinical therapeutic strategies by improving the prognostic efficacy of traditional tumor staging systems.
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Affiliation(s)
- Qiaxuan Li
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,College of Medicine, Shantou University, Shantou, China
| | - Lintong Yao
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,College of Medicine, Shantou University, Shantou, China
| | - Zenan Lin
- Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fasheng Li
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Daipeng Xie
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China
| | - Congsen Li
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,College of Medicine, Shantou University, Shantou, China
| | - Weijie Zhan
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Weihuan Lin
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Luyu Huang
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,College of Medicine, Shantou University, Shantou, China
| | - Shaowei Wu
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,College of Medicine, Shantou University, Shantou, China
| | - Haiyu Zhou
- Department of Thoracic Surgery, Guangdong Provincial People's Hospital & Guangdong Academy of Medical Sciences, School of Medicine, South China University of Technology, Southern Medical University, Guangzhou, China.,College of Medicine, Shantou University, Shantou, China.,The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China.,Department of Thoracic Surgery, Jiangxi Cancer Hospital, Nanchang, China
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Chu Q, Gu X, Zheng Q, Guo Z, Shan D, Wang J, Zhu H. Long noncoding RNA SNHG4: a novel target in human diseases. Cancer Cell Int 2021; 21:583. [PMID: 34717631 PMCID: PMC8557547 DOI: 10.1186/s12935-021-02292-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/21/2021] [Indexed: 12/21/2022] Open
Abstract
Recently, long noncoding RNAs (lncRNAs) have attracted great attention from researchers. LncRNAs are non-protein-coding RNAs of more than 200 nucleotides in length. Multiple studies have been published on the relationship between lncRNA expression and the progression of human diseases. LncRNA small nucleolar RNA host gene 4 (SNHG4), a member of the lncRNA SNHG family, is abnormally expressed in a variety of human diseases, including gastric cancer, renal cell carcinoma, glioblastoma, neuroblastoma, prostate cancer, colorectal cancer, osteosarcoma, cervical cancer, liver cancer, lung cancer, non-small-cell lung cancer, neonatal pneumonia, diabetic retinopathy, neuropathic pain, acute cerebral infarction, acute myeloid leukaemia, and endometriosis. In this paper, the structure of SNHG4 is first introduced, and then studies in humans, animal models and cells are summarized to highlight the expression and function of SNHG4 in the above diseases. In addition, the specific mechanism of SNHG4 as a competing endogenous RNA (ceRNA) is discussed. The findings indicate that SNHG4 can be used as a biomarker for disease prognosis evaluation and as a potential target for disease diagnosis and treatment.
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Affiliation(s)
- Qingfei Chu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Xinyu Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Qiuxian Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Zixuan Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Dandan Shan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Jing Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China
| | - Haihong Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, NO. 79 Qingchun Road, Hangzhou, 310003, Zhejiang, China.
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Tsai WL, Wang CY, Lee YC, Tang WC, Anuraga G, Ta HDK, Wu YF, Lee KH. A New Light on Potential Therapeutic Targets for Colorectal Cancer Treatment. Biomedicines 2021; 9:1438. [PMID: 34680556 PMCID: PMC8533612 DOI: 10.3390/biomedicines9101438] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/21/2021] [Accepted: 09/29/2021] [Indexed: 12/25/2022] Open
Abstract
The development and progression of colorectal cancer (CRC) involve changes in genetic and epigenetic levels of oncogenes and/or tumor suppressors. In spite of advances in understanding of the molecular mechanisms involved in CRC, the overall survival rate of CRC still remains relatively low. Thus, more research is needed to discover and investigate effective biomarkers and targets for diagnosing and treating CRC. The roles of long non-coding RNAs (lncRNAs) participating in various aspects of cell biology have been investigated and potentially contribute to tumor development. Our recent study also showed that CRNDE was among the top 20 upregulated genes in CRC clinical tissues compared to normal colorectal tissues by analyzing a Gene Expression Omnibus (GEO) dataset (GSE21815). Although CRNDE is widely reported to be associated with different types of cancer, most studies of CRNDE were limited to examining regulation of its transcription levels, and in-depth mechanistic research is lacking. In the present study, CRNDE was found to be significantly upregulated in CRC patients at an advanced TNM stage, and its high expression was correlated with poor outcomes of CRC patients. In addition, we found that knocking down CRNDE could reduce lipid accumulation through the miR-29b-3p/ANGPTL4 axis and consequently induce autophagy of CRC cells.
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Affiliation(s)
- Wei-Lun Tsai
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (W.-L.T.); (G.A.); (H.D.K.T.)
| | - Chih-Yang Wang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (C.-Y.W.); (W.-C.T.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yu-Cheng Lee
- Graduate Institute of Medical Sciences, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan;
| | - Wan-Chun Tang
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (C.-Y.W.); (W.-C.T.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Gangga Anuraga
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (W.-L.T.); (G.A.); (H.D.K.T.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Department of Statistics, Faculty of Science and Technology, Universitas PGRI Adi Buana, Surabaya 60234, East Java, Indonesia
| | - Hoang Dang Khoa Ta
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University and Academia Sinica, Taipei 11031, Taiwan; (W.-L.T.); (G.A.); (H.D.K.T.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
| | - Yung-Fu Wu
- National Defense Medical Center, Department of Medical Research, School of Medicine, Tri-Service General Hospital, Taipei 11490, Taiwan;
| | - Kuen-Haur Lee
- PhD Program for Cancer Molecular Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan; (C.-Y.W.); (W.-C.T.)
- Graduate Institute of Cancer Biology and Drug Discovery, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan
- Cancer Center, Wan Fang Hospital, Taipei Medical University, Taipei 11031, Taiwan
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Zhang Q, Zhu D, Li Q. LncRNA CRNDE exacerbates neuropathic pain in chronic constriction injury-induced(CCI) rats through regulating miR-146a-5p/WNT5A pathway. Bioengineered 2021; 12:7348-7359. [PMID: 34612146 PMCID: PMC8806618 DOI: 10.1080/21655979.2021.1972901] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Neuropathic pain (NP) originating from a dysfunction in the nervous system is often intractable and chronic. Many studies have implicated long noncoding RNAs (lncRNAs) in the physiological and pathological development of NP. The lncRNA colorectal neoplasia differentially expressed gene (CRNDE) has been shown to mediate NP progression. However, further investigations are needed to gain deeper understanding of the specific mechanisms governing CRNDE in NP etiopathology. In this study, we successfully used chronic constrictive injury (CCI)-induced rats to establish an NP model with intrathecal injection, and confirmed the upregulation of CRNDE in CCI-induced rats. Moreover, silencing of CRNDE relieved mechanical allodynia, thermal hyperalgesia, and neuroinflammation in the NP model. Bioinformatics analysis predicted that miR-146a-5p binds to CRNDE. Our findings validated that miR-146a-5p was a target of CRNDE and that the expression of miR-146a-5p was decreased in CCI rats. Furthermore, miR-151A-3p was found to exert a negative regulatory effect on WNT5A. In addition, knockdown of WNT5A alleviated the pain-related behavior and inflammatory response of NP in vivo. Finally, we demonstrated that CRNDE contributed to the progression of CCI-induced NP via competitive binding to miR-146a-5p to upregulate WNT5A. The present study offers novel insights that may be translated into improved therapies for NP.
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Affiliation(s)
- Qiangze Zhang
- Department of Pain, Ji'nan People's Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong China
| | - Dongxia Zhu
- Department of Traditional Chinese Medicine, Ji'nan People's Hospital Affiliated to Shandong First Medical University, Ji'nan, Shandong China
| | - Qiang Li
- Department of Infectious Diseases Division, Laiwu People's Hospital, Ji'nan, Shandong China
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Zheng L, Guan Z, Xue M. A crucial role for the long non-coding RNA CASC11 in the pathogenesis of human cancers. Am J Transl Res 2021; 13:10922-10932. [PMID: 34650773 PMCID: PMC8507062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 08/16/2021] [Indexed: 06/13/2023]
Abstract
Long non-coding RNAs (lncRNAs) are non-coding RNAs more than 200 nucleotides in length. Although they do not encode proteins, lncRNAs can regulate gene expression at the transcriptional, post-transcriptional, and epigenetic levels. Emerging data show that lncRNAs are important for tumorigenesis and cancer progression. Cancer susceptibility candidate 11 (CASC11) is a prominent lncRNA that is upregulated in various types of cancers. Moreover, its overexpression correlates with larger tumor size, more advanced cancer stages, cancer metastasis, and poor overall survival for most types of cancer. Functionally, the knockdown of CASC11 can inhibit cell proliferation, invasion, and migration, while enhancing apoptosis through its regulation of gene expression and signaling pathways and its interactions with functional proteins. Here, we discuss the identification, expression, and function of CASC11. Additionally, we discuss the potential roles of CASC11 as a diagnostic biomarker, prognostic biomarker, and therapeutic target in various cancers.
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Affiliation(s)
- Lian Zheng
- Department of Oral and Maxillofacial Surgery, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Zhenjie Guan
- Department of Stomatology, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
| | - Miaomiao Xue
- Department of General Dentistry, The First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052, Henan, P. R. China
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Chang YC, Chan MH, Li CH, Fang CY, Hsiao M, Chen CL. Exosomal Components and Modulators in Colorectal Cancer: Novel Diagnosis and Prognosis Biomarkers. Biomedicines 2021; 9:biomedicines9080931. [PMID: 34440135 PMCID: PMC8391321 DOI: 10.3390/biomedicines9080931] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 07/23/2021] [Accepted: 07/29/2021] [Indexed: 02/07/2023] Open
Abstract
The relatively high incidence and mortality rates for colorectal carcinoma (CRC) make it a formidable malignant tumor. Comprehensive strategies have been applied to predict patient survival and diagnosis. Various clinical regimens have also been developed to improve the therapeutic outcome. Extracellular vesicles (EVs) are recently proposed cellular structures that can be produced by natural or artificial methods and have been extensively studied. In addition to their innate functions, EVs can be manipulated to be drug carriers and exert many biological functions. The composition of EVs, their intravesicular components, and the surrounding tumor microenvironment are closely related to the development of colorectal cancer. Determining the expression profiles of exocytosis samples and using them as indicators for selecting effective combination therapy is an indispensable direction for EV study and should be regarded as a novel prediction platform in addition to cancer stage, prognosis, and other clinical assessments. In this review, we summarize the function, regulation, and application of EVs in the colon cancer research field. We provide an update on and discuss potential values for clinical applications of EVs. Moreover, we illustrate the specific markers, mediators, and genetic alterations of EVs in colorectal carcinogenesis. Furthermore, we outline the vital markers present in the EVs and discuss their plausible uses in colon cancer patient therapy in combination with the currently used clinical strategies. The development and application of these EVs will significantly improve the accuracy of diagnosis, lead to more precise prognoses, and may lead to the improved treatment of colorectal cancer.
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Affiliation(s)
- Yu-Chan Chang
- Department of Biomedical Imaging and Radiological Science, National Yang-Ming University, Taipei 112, Taiwan;
- Department of Biomedical Imaging and Radiological Science, National Yang Ming Chiao Tung University, Taipei 112, Taiwan
| | - Ming-Hsien Chan
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (M.-H.C.); (C.-H.L.)
| | - Chien-Hsiu Li
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (M.-H.C.); (C.-H.L.)
| | - Chih-Yeu Fang
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Miaoli 350, Taiwan;
| | - Michael Hsiao
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan; (M.-H.C.); (C.-H.L.)
- Department of Biochemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Correspondence: (M.H.); (C.-L.C.); Tel.: +886-2-2787-1243 (M.H.); +886-2-2736-1661 (ext. 3139) (C.-L.C.); Fax: +886-2-2789-9931 (M.H.)
| | - Chi-Long Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei 110, Taiwan
- Department of Pathology, Taipei Medical University Hospital, Taipei 110, Taiwan
- Correspondence: (M.H.); (C.-L.C.); Tel.: +886-2-2787-1243 (M.H.); +886-2-2736-1661 (ext. 3139) (C.-L.C.); Fax: +886-2-2789-9931 (M.H.)
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Li W, Wang X, Sun S, An H. LncRNA CRNDE correlates negatively with miR-33a and miR-495 and positively with inflammatory cytokines in asthmatic children. CLINICAL RESPIRATORY JOURNAL 2021; 15:1175-1184. [PMID: 34288494 PMCID: PMC9291623 DOI: 10.1111/crj.13424] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/05/2021] [Accepted: 07/15/2021] [Indexed: 12/02/2022]
Abstract
Objectives It is reported that long non‐coding RNA (lncRNA) colorectal neoplasia differentially expressed (CRNDE) targets microRNA (miR)‐33a, miR‐181a and miR‐495 to regulate inflammation process, while few studies report their clinical application for paediatric asthma management. Therefore, this study aimed to explore the interaction of lncRNA CRNDE with miR‐33a, miR‐181a and miR‐495, as well as their correlation with inflammation, exacerbation risk and severity in paediatric patients with asthma. Methods Asthmatic exacerbation children (N = 65), asthmatic controlled children (N = 65) and controls (N = 65) were recruited. LncRNA CRNDE, miR‐33a, miR‐181a and miR‐495 expressions in peripheral blood mononuclear cells were detected by RT‐qPCR. Besides, serum inflammatory cytokines (including TNF‐α, IL‐1β, IL‐6 and IL‐17) were determined by enzyme‐linked immunosorbent assay (ELISA). Results LncRNA CRNDE, miR‐33a and miR‐495 expressions were different, while miR‐181a expression was similar among asthmatic exacerbation children, asthmatic controlled children and controls. Moreover, lncRNA CRNDE negatively correlated with miR‐33a and miR‐495 in asthmatic exacerbation children and asthmatic controlled children, but not in controls. Further analyses showed that lncRNA CRNDE positively correlated with TNF‐α, IL‐1β, IL‐17 and exacerbation severity, while it negatively correlated with FEV1/FVC in asthmatic exacerbation children. Meanwhile, miR‐33a, miR‐181a and miR‐495 all negatively correlated with some individual inflammatory cytokines, while only miR‐33a negatively correlated with exacerbation severity in asthmatic exacerbation children. Conclusion LncRNA CRNDE correlates negatively with miR‐33a and miR‐495 and positively with inflammatory cytokines in asthmatic children.
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Affiliation(s)
- Weina Li
- Second Department of Pediatrics, Xingtai People's Hospital, Xingtai, Hebei, China
| | - Xiaoxue Wang
- Second Department of Pediatrics, Xingtai People's Hospital, Xingtai, Hebei, China
| | - Shixin Sun
- Second Department of Pediatrics, Xingtai People's Hospital, Xingtai, Hebei, China
| | - Hong An
- Second Department of Pediatrics, Xingtai People's Hospital, Xingtai, Hebei, China
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Sorokin M, Raevskiy M, Zottel A, Šamec N, Skoblar Vidmar M, Matjašič A, Zupan A, Mlakar J, Suntsova M, Kuzmin DV, Buzdin A, Jovčevska I. Large-Scale Transcriptomics-Driven Approach Revealed Overexpression of CRNDE as a Poor Survival Prognosis Biomarker in Glioblastoma. Cancers (Basel) 2021; 13:3419. [PMID: 34298634 PMCID: PMC8303503 DOI: 10.3390/cancers13143419] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/16/2022] Open
Abstract
Glioblastoma is the most common and malignant brain malignancy worldwide, with a 10-year survival of only 0.7%. Aggressive multimodal treatment is not enough to increase life expectancy and provide good quality of life for glioblastoma patients. In addition, despite decades of research, there are no established biomarkers for early disease diagnosis and monitoring of patient response to treatment. High throughput sequencing technologies allow for the identification of unique molecules from large clinically annotated datasets. Thus, the aim of our study was to identify significant molecular changes between short- and long-term glioblastoma survivors by transcriptome RNA sequencing profiling, followed by differential pathway-activation-level analysis. We used data from the publicly available repositories The Cancer Genome Atlas (TCGA; number of annotated cases = 135) and Chinese Glioma Genome Atlas (CGGA; number of annotated cases = 218), and experimental clinically annotated glioblastoma tissue samples from the Institute of Pathology, Faculty of Medicine in Ljubljana corresponding to 2-58 months overall survival (n = 16). We found one differential gene for long noncoding RNA CRNDE whose overexpression showed correlation to poor patient OS. Moreover, we identified overlapping sets of congruently regulated differential genes involved in cell growth, division, and migration, structure and dynamics of extracellular matrix, DNA methylation, and regulation through noncoding RNAs. Gene ontology analysis can provide additional information about the function of protein- and nonprotein-coding genes of interest and the processes in which they are involved. In the future, this can shape the design of more targeted therapeutic approaches.
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Affiliation(s)
- Maxim Sorokin
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1000 Brussels, Belgium;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Mikhail Raevskiy
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Alja Zottel
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
| | - Neja Šamec
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
| | | | - Alenka Matjašič
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Andrej Zupan
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Jernej Mlakar
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.M.); (A.Z.); (J.M.)
| | - Maria Suntsova
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Denis V. Kuzmin
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
| | - Anton Buzdin
- European Organization for Research and Treatment of Cancer (EORTC), Biostatistics and Bioinformatics Subgroup, 1000 Brussels, Belgium;
- World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Moscow Institute of Physics and Technology, National Research University, 141700 Moscow, Russia; (M.R.); (D.V.K.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- OmicsWay Corp., Walnut, CA 91789, USA
| | - Ivana Jovčevska
- Medical Centre for Molecular Biology, Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, 1000 Ljubljana, Slovenia; (A.Z.); (N.Š.)
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Shiu TY, Lin HH, Shih YL, Feng AC, Huang HH, Huang TY, Hsieh CB, Chang WK, Hsieh TY. CRNDE-h transcript/miR-136-5p axis regulates interleukin enhancer binding factor 2 expression to promote hepatocellular carcinoma cell proliferation. Life Sci 2021; 284:119708. [PMID: 34153299 DOI: 10.1016/j.lfs.2021.119708] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/27/2021] [Accepted: 06/02/2021] [Indexed: 12/12/2022]
Abstract
AIMS Hepatocellular carcinoma (HCC) is a primary malignancy of the hepatocyte. Interleukin enhancer binding factor 2 (ILF2) plays a role in the development of HCC. However, the regulatory mechanisms of ILF2 expression in HCC remain unclear. In this study, we aimed to identify ILF2-targeting microRNAs (miRNAs) and to explore how they affect ILF2 expression in HCC. MAIN METHODS The tissue specimens were collected from 25 HCC patients. The underlying regulatory mechanism of ILF2 expression in HCC progression was determined using luciferase reporter assay, quantitative real-time PCR, Western blotting, and BrdU incorporation assay. KEY FINDINGS Of predicted miRNA candidates (miR-122-5p, miR-425-5p, miR-136-5p, miR-7-5p, miR-421 and miR-543), a statistically significant inverse correlation by linear correlation analysis was observed between miR-136-5p and ILF2 mRNA expressions in patients with HCC (r = -0.627, P < 0.001). Further analysis demonstrated that ILF2 was directly regulated by miR-136-5p. In addition, we showed that long noncoding RNA colorectal neoplasia differentially expressed-h (lncRNA CRNDE-h) transcript expression was significantly up-regulated in HCC, and a miR-136-5p binding site was newly found in the lncRNA CRNDE-h transcript sequence using IntaRNA tool. In terms of mechanism, highly-expressed lncRNA CRNDE-h transcript can sponge miR-136-5p, thereby preventing it from interacting with target ILF2 mRNA while promoting the proliferation of HCC cells. SIGNIFICANCE The lncRNA CRNDE-h/miR-136-5p/ILF2 axis plays a significant regulatory role in HCC progression, which may partly explain the pathogenic mechanisms of HCC and may provide promising potential targets for the diagnosis, treatment, and prognosis of HCC.
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Affiliation(s)
- Tzu-Yue Shiu
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsuan-Hwai Lin
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC.
| | - Yu-Lueng Shih
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - An-Chieh Feng
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Hsin-Hung Huang
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Tien-Yu Huang
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Chung-Bao Hsieh
- Division of General Surgery, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Wei-Kuo Chang
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC
| | - Tsai-Yuan Hsieh
- Division of Gastroenterology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan, ROC.
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Luo X, Tu T, Zhong Y, Xu S, Chen X, Chen L, Yang F. ceRNA Network Analysis Shows That lncRNA CRNDE Promotes Progression of Glioblastoma Through Sponge mir-9-5p. Front Genet 2021; 12:617350. [PMID: 33767729 PMCID: PMC7985093 DOI: 10.3389/fgene.2021.617350] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Glioblastoma accounts for 45.2% of central nervous system tumors. Despite the availability of multiple treatments (e.g., surgery, radiotherapy, chemotherapy, biological therapy, immunotherapy, and electric field therapy), glioblastoma has a poor prognosis, with a 5-year survival rate of approximately 5%. The pathogenesis and prognostic markers of this cancer are currently unclear. To this end, this study aimed to explore the pathogenesis of glioblastoma and identify potential prognostic markers. We used data from the GEO and TCGA databases and identified five genes (ITGA5, MMP9, PTPRN, PTX3, and STX1A) that could affect the survival rate of glioblastoma patients and that were differentially expressed between glioblastoma patients and non-tumors groups. Based on a variety of bioinformatics tools for reverse prediction of target genes associated with the prognosis of GBM, a ceRNA network of messenger RNA (STX1A, PTX3, MMP9)-microRNA (miR-9-5p)-long non-coding RNA (CRNDE) was constructed. Finally, we identified five potential therapeutic drugs (bacitracin, hecogenin, clemizole, chrysin, and gibberellic acid) that may be effective treatments for glioblastoma.
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Affiliation(s)
- Xiaobin Luo
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Tianqi Tu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Yali Zhong
- Graduate School of Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Shangyi Xu
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Xiangzhou Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Ligang Chen
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Laboratory of Neurological Diseases and Brain Function, The Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Fubing Yang
- Department of Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Sichuan Clinical Research Center for Neurosurgery, The Affiliated Hospital of Southwest Medical University, Luzhou, China.,Academician (Expert) Workstation of Sichuan Province, The Affiliated Hospital of Southwest Medical University, Luzhou, China
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Chaudhary R. Potential of long non-coding RNAs as a therapeutic target and molecular markers in glioblastoma pathogenesis. Heliyon 2021; 7:e06502. [PMID: 33786397 PMCID: PMC7988331 DOI: 10.1016/j.heliyon.2021.e06502] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 09/20/2020] [Accepted: 03/09/2021] [Indexed: 12/14/2022] Open
Abstract
Glioblastoma (GB) is by far the most hostile type of malignant tumor that primarily affects the brain and spine, derived from star-shaped glial cells that are astrocytes and oligodendrocytes. Despite of significant efforts in recent years in glioblastoma research, the clinical efficacy of existing medical intervention is still limited and very few potential diagnostic markers are available. Long non-coding RNAs (lncRNAs) that lacks protein-coding capabilities were previously thought to be "junk sequences" in mammalian genomes are quite indispensible epigenetic regulators that can positively or negatively regulate gene expression and nuclear architecture, with significant roles in the initiation and development of tumors. Nevertheless, the precise mechanism of these distortedly expressed lncRNAs in glioblastoma pathogenesis is not yet fully understood. Since the advent of high-throughput sequencing technologies, more and more research have elucidated that lncRNAs are one of the most promising prognostic biomarkers and therapeutic targets for glioblastoma. In this paper, I briefly outlined the existing findings of lncRNAs. And also summarizes the profiles of different lncRNAs that have been broadly classified in glioblastoma research, with emphasis on both their prognostic and therapeutic values.
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Affiliation(s)
- Rishabh Chaudhary
- Department of Pharmaceutical Sciences, Babasaheb Bhimrao Ambedkar University, Vidya Vihar, Raebareli Road, Lucknow 226025, U.P., India
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Zhang F, Wang H, Yu J, Yao X, Yang S, Li W, Xu L, Zhao L. LncRNA CRNDE attenuates chemoresistance in gastric cancer via SRSF6-regulated alternative splicing of PICALM. Mol Cancer 2021; 20:6. [PMID: 33397371 PMCID: PMC7780690 DOI: 10.1186/s12943-020-01299-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
De novo and acquired resistance, which are mainly mediated by genetic alterations, are barriers to effective routine chemotherapy. However, the mechanisms underlying gastric cancer (GC) resistance to chemotherapy are still unclear. We showed that the long noncoding RNA CRNDE was related to the chemosensitivity of GC in clinical samples and a PDX model. CRNDE was decreased and inhibited autophagy flux in chemoresistant GC cells. CRNDE directly bound to splicing protein SRSF6 to reduce its protein stability and thus regulate alternative splicing (AS) events. We determined that SRSF6 regulated the PICALM exon 14 skip splice variant and triggered a significant S-to-L isoform switch, which contributed to the expression of the long isoform of PICALM (encoding PICALML). Collectively, our findings reveal the key role of CRNDE in autophagy regulation, highlighting the significance of CRNDE as a potential prognostic marker and therapeutic target against chemoresistance in GC.
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Affiliation(s)
- Feifei Zhang
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Hui Wang
- Department of Medical Oncology, Affiliated Tumour Hospital of Guangzhou Medical University, Guangzhou, China
| | - Jiang Yu
- Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangdong Provincial Engineering Technology Research Center of Minimally Invasive Surgery, Guangzhou, China
| | - Xueqing Yao
- Department of General Surgery, Guangdong General Hospital, Guangdong Academy of Medical Science, Guangzhou, China
| | - Shibin Yang
- Gastrointestinal Surgical Center, The First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Weidong Li
- Department of Medical Oncology, Affiliated Tumour Hospital of Guangzhou Medical University, Guangzhou, China
| | - Lijun Xu
- Department of Pathology, Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Liang Zhao
- Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, China. .,Department of Pathology, Guangdong Provincial Key Laboratory of Molecular Oncologic Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
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