1
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Coan M, Haefliger S, Ounzain S, Johnson R. Targeting and engineering long non-coding RNAs for cancer therapy. Nat Rev Genet 2024; 25:578-595. [PMID: 38424237 DOI: 10.1038/s41576-024-00693-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2024] [Indexed: 03/02/2024]
Abstract
RNA therapeutics (RNATx) aim to treat diseases, including cancer, by targeting or employing RNA molecules for therapeutic purposes. Amongst the most promising targets are long non-coding RNAs (lncRNAs), which regulate oncogenic molecular networks in a cell type-restricted manner. lncRNAs are distinct from protein-coding genes in important ways that increase their therapeutic potential yet also present hurdles to conventional clinical development. Advances in genome editing, oligonucleotide chemistry, multi-omics and RNA engineering are paving the way for efficient and cost-effective lncRNA-focused drug discovery pipelines. In this Review, we present the emerging field of lncRNA therapeutics for oncology, with emphasis on the unique strengths and challenges of lncRNAs within the broader RNATx framework. We outline the necessary steps for lncRNA therapeutics to deliver effective, durable, tolerable and personalized treatments for cancer.
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Affiliation(s)
- Michela Coan
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Simon Haefliger
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
- Department for BioMedical Research, University of Bern, Bern, Switzerland
| | | | - Rory Johnson
- School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Dublin, Ireland.
- Department of Medical Oncology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland.
- Department for BioMedical Research, University of Bern, Bern, Switzerland.
- FutureNeuro, SFI Research Centre for Chronic and Rare Neurological Diseases, Dublin, Ireland.
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2
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Sheikhnia F, Fazilat A, Rashidi V, Azizzadeh B, Mohammadi M, Maghsoudi H, Majidinia M. Exploring the therapeutic potential of quercetin in cancer treatment: Targeting long non-coding RNAs. Pathol Res Pract 2024; 260:155374. [PMID: 38889494 DOI: 10.1016/j.prp.2024.155374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 05/11/2024] [Accepted: 05/28/2024] [Indexed: 06/20/2024]
Abstract
The escalating global incidence of cancer, which results in millions of fatalities annually, underscores the pressing need for effective pharmacological interventions across diverse cancer types. Long noncoding RNAs (lncRNAs), a class of RNA molecules that lack protein-coding capacity but profoundly impact gene expression regulation, have emerged as pivotal players in key cellular processes, including proliferation, apoptosis, metastasis, cellular metabolism, and drug resistance. Among natural compounds, quercetin, a phenolic compound abundantly present in fruits and vegetables has garnered attention due to its significant anticancer properties. Quercetin demonstrates the ability to inhibit cancer cell growth and induce apoptosis-a process often impaired in malignant cells. In this comprehensive review, we delve into the therapeutic potential of quercetin in cancer treatment, with a specific focus on its intricate interactions with lncRNAs. We explore how quercetin modulates lncRNA expression and function to exert its anticancer effects. Notably, quercetin suppresses oncogenic lncRNAs that drive cancer development and progression while enhancing tumor-suppressive lncRNAs that impede cancer growth and dissemination. Additionally, we discuss quercetin's role as a chemopreventive agent, which plays a crucial role in mitigating cancer risk. We address research challenges and future directions, emphasizing the necessity for in-depth mechanistic studies and strategies to enhance quercetin's bioavailability and target specificity. By synthesizing existing knowledge, this review underscores quercetin's promising potential as a novel therapeutic strategy in the ongoing battle against cancer, offering fresh insights and avenues for further investigation in this critical field.
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Affiliation(s)
- Farhad Sheikhnia
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran; Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Ahmad Fazilat
- Motamed Cancer Institute, Breast Cancer Research Center, ACECR, Tehran, Iran
| | - Vahid Rashidi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran
| | - Bita Azizzadeh
- Department of Biochemistry, School of Medicine, Ilam University of Medical sciences, Ilam, Iran
| | - Mahya Mohammadi
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hossein Maghsoudi
- Student Research Committee, Urmia University of Medical Sciences, Urmia, Iran; Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Majidinia
- Solid Tumor Research Center, Cellular and Molecular Medicine Institute, Urmia University of Medical Sciences, Urmia, Iran.
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3
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Yousefnia S. A comprehensive review on lncRNA LOXL1-AS1: molecular mechanistic pathways of lncRNA LOXL1-AS1 in tumorigenicity of cancer cells. Front Oncol 2024; 14:1384342. [PMID: 39136001 PMCID: PMC11317273 DOI: 10.3389/fonc.2024.1384342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024] Open
Abstract
Long non-coding RNAs (lncRNAs) are versatile RNAs that regulate various cellular processes, such as gene regulation, by acting as signals, decoys, guides, and scaffolds. A novel recognized lncRNA, LOXL1-antisense RNA 1 (LOXL1-AS1), is dysregulated in some diseases, including cancer, and acts as an oncogenic lncRNA in many types of cancer cells. Upregulation of LOXL1-AS1 has been involved in proliferation, migration, metastasis, and EMT, as well as inhibiting apoptosis in cancer cells. Most importantly, the malignant promoting activity of LOXL1-AS1 can be mostly mediated by sequestering specific miRNAs and inhibiting their binding to the 3´UTR of their target mRNAs, thereby indirectly regulating gene expression. Additionally, LOXL1-AS1 can decoy transcription factors and proteins and prevent their binding to their regulatory regions, inhibiting their mechanistic activity on the regulation of gene expression and signaling pathways. This review presents the mechanistic pathways of the oncogenic role of LOXL1-AS1 by modulating its target miRNAs and proteins in various cancer cells. Having information about the molecular mechanisms regulated by LOXL1-AS1 in cancer cells can open ways to find out particular prognostic biomarkers, as well as discover novel therapeutic approaches for different types of cancer.
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Affiliation(s)
- Saghar Yousefnia
- Department of Cell and Molecular Biology, Semnan University, Semnan, Iran
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4
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Chen HF, Wu KJ. LncRNAs and asymmetric cell division: the epigenetic mechanisms. Biomed J 2024:100774. [PMID: 39059582 DOI: 10.1016/j.bj.2024.100774] [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: 04/23/2024] [Revised: 07/16/2024] [Accepted: 07/24/2024] [Indexed: 07/28/2024] Open
Abstract
Asymmetric cell division (ACD) plays a pivotal role in development, tissue homeostasis, and stem cell maintenance. Emerging evidence suggests that long non-coding RNAs (lncRNAs) are key regulators of ACD, orchestrating the intricate molecular machinery that governs cell fate determination. This review summarizes current literature to elucidate the diverse roles of lncRNAs in modulating ACD across various biological contexts. The regulatory mechanisms of asymmetric cell division mediated by lncRNAs, including their interactions with protein effectors, epigenetic regulation, and subcellular localization are explored. Additionally, we discuss the implications of dysregulated lncRNAs in mediating ACD that lead to tumorigenesis. By integrating findings from diverse experimental models and cell types, this review provides insights into the multifaceted roles of lncRNAs in governing asymmetric cell division, shedding light on fundamental biological processes. Further research in this area may lead to the development of novel therapies targeting dysregulated lncRNAs to restore proper cell division and function. The knowledge of lncRNAs regulating ACD could potentially revolutionize the field of regenerative medicine and cancer therapy by targeting specific lncRNAs involved in ACD. By unraveling the complex interactions between lncRNAs and cellular processes, the potential novel opportunities for precision medicine approaches may be uncovered.
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Affiliation(s)
- Hsiao-Fan Chen
- Graduate Institutes of Biomedical Sciences, China Medical University, Taichung 404, Taiwan; Graduate Institutes of Cell Biology, China Medical University, Taichung 404, Taiwan.
| | - Kou-Juey Wu
- Cancer Genome Research Center, Chang Gung Memorial Hospital at Linkou, Gueishan Dist., Taoyuan 333, Taiwan.
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5
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Çiftçi YC, Yurtsever Y, Akgül B. Long non-coding RNA-mediated modulation of endoplasmic reticulum stress under pathological conditions. J Cell Mol Med 2024; 28:e18561. [PMID: 39072992 DOI: 10.1111/jcmm.18561] [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: 03/23/2024] [Revised: 06/12/2024] [Accepted: 06/27/2024] [Indexed: 07/30/2024] Open
Abstract
Endoplasmic reticulum (ER) stress, which ensues from an overwhelming protein folding capacity, activates the unfolded protein response (UPR) in an effort to restore cellular homeostasis. As ER stress is associated with numerous diseases, it is highly important to delineate the molecular mechanisms governing the ER stress to gain insight into the disease pathology. Long non-coding RNAs, transcripts with a length of over 200 nucleotides that do not code for proteins, interact with proteins and nucleic acids, fine-tuning the UPR to restore ER homeostasis via various modes of actions. Dysregulation of specific lncRNAs is implicated in the progression of ER stress-related diseases, presenting these molecules as promising therapeutic targets. The comprehensive analysis underscores the importance of understanding the nuanced interplay between lncRNAs and ER stress for insights into disease mechanisms. Overall, this review consolidates current knowledge, identifies research gaps and offers a roadmap for future investigations into the multifaceted roles of lncRNAs in ER stress and associated diseases to shed light on their pivotal roles in the pathogenesis of related diseases.
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Affiliation(s)
- Yusuf Cem Çiftçi
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Yiğit Yurtsever
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - Bünyamin Akgül
- Noncoding RNA Laboratory, Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
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6
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Newsham I, Sendera M, Jammula SG, Samarajiwa SA. Early detection and diagnosis of cancer with interpretable machine learning to uncover cancer-specific DNA methylation patterns. Biol Methods Protoc 2024; 9:bpae028. [PMID: 38903861 PMCID: PMC11186673 DOI: 10.1093/biomethods/bpae028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/29/2024] [Indexed: 06/22/2024] Open
Abstract
Cancer, a collection of more than two hundred different diseases, remains a leading cause of morbidity and mortality worldwide. Usually detected at the advanced stages of disease, metastatic cancer accounts for 90% of cancer-associated deaths. Therefore, the early detection of cancer, combined with current therapies, would have a significant impact on survival and treatment of various cancer types. Epigenetic changes such as DNA methylation are some of the early events underlying carcinogenesis. Here, we report on an interpretable machine learning model that can classify 13 cancer types as well as non-cancer tissue samples using only DNA methylome data, with 98.2% accuracy. We utilize the features identified by this model to develop EMethylNET, a robust model consisting of an XGBoost model that provides information to a deep neural network that can generalize to independent data sets. We also demonstrate that the methylation-associated genomic loci detected by the classifier are associated with genes, pathways and networks involved in cancer, providing insights into the epigenomic regulation of carcinogenesis.
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Affiliation(s)
- Izzy Newsham
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- MRC Biostatistics Unit, University of Cambridge, Cambridge, CB2 0SR, United Kingdom
| | - Marcin Sendera
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- Jagiellonian University, Faculty of Mathematics and Computer Science, 30-348 Kraków, Poland
| | - Sri Ganesh Jammula
- CRUK Cambridge Institute, University of Cambridge, Cambridge, CB2 0RE, United Kingdom
- MedGenome labs, Bengaluru, 560099, India
| | - Shamith A Samarajiwa
- MRC Cancer Unit, University of Cambridge, Cambridge, CB2 0XZ, United Kingdom
- Imperial College London, Hammersmith Campus, London, W12 0NN, United Kingdom
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7
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Ledesma-Bazan S, Cascardo F, Bizzotto J, Olszevicki S, Vazquez E, Gueron G, Cotignola J. Predicting prostate cancer progression with a Multi-lncRNA expression-based risk score and nomogram integrating ISUP grading. Noncoding RNA Res 2024; 9:612-623. [PMID: 38576998 PMCID: PMC10993238 DOI: 10.1016/j.ncrna.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 01/11/2024] [Accepted: 01/23/2024] [Indexed: 04/06/2024] Open
Abstract
Prostate cancer is a highly heterogeneous disease; therefore, estimating patient prognosis accurately is challenging due to the lack of biomarkers with sufficient specificity and sensitivity. One of the current challenges lies in integrating genomic and transcriptomic data with clinico-pathological features and in incorporating their application in everyday clinical practice. Therefore, we aimed to model a risk score and nomogram containing long non-coding RNA (lncRNA) expression and clinico-pathological data to better predict the probability of prostate cancer progression. We performed bioinformatics analyses to identify lncRNAs differentially expressed across various prostate cancer stages and associated with progression-free survival. This information was further integrated into a prognostic risk score and nomogram containing transcriptomic and clinico-pathological features to estimate the risk of disease progression. We used RNA-seq data from 5 datasets from public repositories (total n = 178) comprising different stages of prostate cancer: pre-treatment primary prostate adenocarcinomas, post-treatment tumors and metastatic castration resistant prostate cancer. We found 30 lncRNAs with consistent differential expression in all comparisons made using two R-based packages. Multivariate progression-free survival analysis including the ISUP group as covariate, revealed that 7/30 lncRNAs were significantly associated with time-to-progression. Next, we combined the expression of these 7 lncRNAs into a multi-lncRNA score and dichotomized the patients into low- or high-score. Patients with a high-score showed a 4-fold risk of disease progression (HR = 4.30, 95 %CI = 2.66-6.97, p = 3.1e-9). Furthermore, we modelled a combined risk-score containing information on the multi-lncRNA score and ISUP group. We found that patients with a high-risk score had nearly 8-fold risk of progression (HR = 7.65, 95 %CI = 4.05-14.44, p = 3.4e-10). Finally, we created and validated a nomogram to help uro-oncologists to better predict patient's risk of progression at 3- and 5-years post-diagnosis. In conclusion, the integration of lncRNA expression data and clinico-pathological features of prostate tumors into predictive models might aid in tailored disease risk assessment and treatment for patients with prostate cancer.
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Affiliation(s)
- Sabrina Ledesma-Bazan
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
| | - Florencia Cascardo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
| | - Juan Bizzotto
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
- Universidad Argentina de la Empresa (UADE), Instituto de Tecnología (INTEC), Buenos Aires C1073AAO, Argentina
| | - Santiago Olszevicki
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
| | - Elba Vazquez
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
| | - Geraldine Gueron
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
| | - Javier Cotignola
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Química Biológica, Laboratorio de Inflamación y Cáncer, C1428EGA, CABA, Buenos Aires, Argentina
- CONICET - Universidad de Buenos Aires, Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales (IQUIBICEN), C1428EGA, CABA, Buenos Aires, Argentina
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Maharati A, Moghbeli M. Role of microRNA-505 during tumor progression and metastasis. Pathol Res Pract 2024; 258:155344. [PMID: 38744001 DOI: 10.1016/j.prp.2024.155344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/23/2024] [Accepted: 05/09/2024] [Indexed: 05/16/2024]
Abstract
Late diagnosis of cancer in advanced stages due to the lack of screening methods is considered as the main cause of poor prognosis and high mortality rate among these patients. Therefore, it is necessary to investigate the molecular tumor biology in order to introduce biomarkers that can be used in cancer screening programs and early diagnosis. MicroRNAs (miRNAs) have key roles in regulation of the cellular pathophysiological processes. Due to the high stability of miRNAs in body fluids, they are widely used as the non-invasive tumor markers. According to the numerous reports about miR-505 deregulation in a wide range of cancers, we investigated the role of miR-505 during tumor progression. It was shown that miR-505 mainly has the tumor suppressor functions through the regulation of signaling pathways, chromatin remodeling, and cellular metabolism. This review has an effective role in introducing miR-505 as a suitable marker for the early cancer diagnosis.
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Affiliation(s)
- Amirhosein Maharati
- Student Research Committee, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Meysam Moghbeli
- Department of Medical Genetics and Molecular Medicine, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Sharma S, Houfani AA, Foster LJ. Pivotal functions and impact of long con-coding RNAs on cellular processes and genome integrity. J Biomed Sci 2024; 31:52. [PMID: 38745221 PMCID: PMC11092263 DOI: 10.1186/s12929-024-01038-1] [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: 10/24/2023] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
Recent advances in uncovering the mysteries of the human genome suggest that long non-coding RNAs (lncRNAs) are important regulatory components. Although lncRNAs are known to affect gene transcription, their mechanisms and biological implications are still unclear. Experimental research has shown that lncRNA synthesis, subcellular localization, and interactions with macromolecules like DNA, other RNAs, or proteins can all have an impact on gene expression in various biological processes. In this review, we highlight and discuss the major mechanisms through which lncRNAs function as master regulators of the human genome. Specifically, the objective of our review is to examine how lncRNAs regulate different processes like cell division, cell cycle, and immune responses, and unravel their roles in maintaining genomic architecture and integrity.
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Affiliation(s)
- Siddhant Sharma
- Department of Chemical and Biological Engineering, University of British Columbia, Vancouver, BC, V6T 1Z3, Canada
| | - Aicha Asma Houfani
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Leonard J Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, 2185 E Mall, Vancouver, BC, V6T 1Z4, Canada.
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Liu Y, Xin Z, Zhang K, Jin X, Wang D. LncRNA NEAT1 promotes angiogenesis of retinoblastoma cells through regulation of the miR-106a/HIF-1α axis. Heliyon 2024; 10:e27653. [PMID: 38524558 PMCID: PMC10958356 DOI: 10.1016/j.heliyon.2024.e27653] [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: 09/17/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 03/26/2024] Open
Abstract
Objective To explore the role and mechanisms of lncRNA nuclear enriched abundant transcript 1 (NEAT1) in angiogenesis of retinoblastoma (RB) cells. Methods This study investigated the roles of NEAT1 in RB progression. The RNA expression levels of NEAT1, miR-106a, and hypoxia-inducible factor-1alpha (HIF-1α) examined by quantitative reverse transcription polymerase chain reaction (RT-qPCR) were compared between RB cells and normal retinal pigment epithelial (RPE) cells. The binding sites between NEAT1 and miR-106a, and between miR-106a and HIF-1α were predicted by the TargetScan database and verified using the dual-luciferase reporter assay. By transfection of overexpression plasmid or shRNA of NEAT1, and/or treatment of miR-106a inhibitor or mimics, proliferation, invasion, and angiogenesis of RB cells (measured by the MTT assay, the Transwell assay, and the tube formation assay, respectively) were compared between groups. Group comparisons were analyzed using one-way analysis of variance (ANOVA), and Tukey's post-hoc test was employed for further statistical assessment. P-value less than 0.05 was considered statistically significant. Results The RNA expression levels of NEAT1 and HIF-1α were upregulated in RB cells, whereas the expression level of miR-106a was downregulated compared with RPE cells. NEAT1 overexpression or miR-106a knockdown advanced proliferation, invasion, and tube formation of RB cells. As a target of NEAT1, miR-106a could sponge HIF-1α to downregulate HIF-1α expression level. Functional analyses indicated that miR-106a knockdown reversed the inhibitory effects of NEAT1 silencing on the proliferation, invasion, and tube formation of RB cells. Furthermore, miR-106a overexpression suppressed RB cell angiogenesis by downregulating HIF-1α expression level. Conclusion NEAT1 promoted proliferation, invasion, and angiogenesis of RB cells through upregulation of HIF-1α expression level by sponging miR-106a, demonstrating that NEAT1 may be a novel target for RB treatment.
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Affiliation(s)
- Ying Liu
- Department of Ophthalmology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, China
| | - Zhiyuan Xin
- Department of Ophthalmology, Senior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing 100144, China
| | - Kun Zhang
- Department of Ophthalmology, Beijing Rehabilitation Hospital, Capital Medical University, Beijing 100144, China
| | - Xin Jin
- Department of Ophthalmology, Senior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing 100144, China
| | - Dajiang Wang
- Department of Ophthalmology, Senior Department of Ophthalmology, The Third Medical Center of PLA General Hospital, Beijing 100144, China
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Ma RK, Tsai PY, Farghli AR, Shumway A, Kanke M, Gordan JD, Gujral TS, Vakili K, Nukaya M, Noetzli L, Ronnekleiv-Kelly S, Broom W, Barrow J, Sethupathy P. DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma. PLoS Genet 2024; 20:e1011216. [PMID: 38512964 PMCID: PMC11020935 DOI: 10.1371/journal.pgen.1011216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 04/16/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long noncoding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo disease models. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, which indicates mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.
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Affiliation(s)
- Rosanna K. Ma
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Pei-Yin Tsai
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Alaa R. Farghli
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Alexandria Shumway
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - Matt Kanke
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
| | - John D. Gordan
- Division of Hematology/Oncology, Helen Diller Family Comprehensive Cancer Center, UCSF, San Francisco, California, United States of America
| | - Taranjit S. Gujral
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Khashayar Vakili
- Department of Surgery, Boston Children’s Hospital, Boston, Massachusetts, United States of America
| | - Manabu Nukaya
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Leila Noetzli
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Sean Ronnekleiv-Kelly
- Department of Surgery, Division of Surgical Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, United States of America
| | - Wendy Broom
- Alnylam Pharmaceuticals, Cambridge, Massachusetts, United States of America
| | - Joeva Barrow
- Division of Nutritional Sciences, Cornell University, Ithaca, New York, United States of America
| | - Praveen Sethupathy
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York, United States of America
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Davodabadi F, Mirinejad S, Malik S, Dhasmana A, Ulucan-Karnak F, Sargazi S, Sargazi S, Fathi-Karkan S, Rahdar A. Nanotherapeutic approaches for delivery of long non-coding RNAs: an updated review with emphasis on cancer. NANOSCALE 2024; 16:3881-3914. [PMID: 38353296 DOI: 10.1039/d3nr05656b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
The long noncoding RNAs (lncRNAs) comprise a wide range of RNA species whose length exceeds 200 nucleotides, which regulate the expression of genes and cellular functions in a wide range of organisms. Several diseases, including malignancy, have been associated with lncRNA dysregulation. Due to their functions in cancer development and progression, lncRNAs have emerged as promising biomarkers and therapeutic targets in cancer diagnosis and treatment. Several studies have investigated the anti-cancer properties of lncRNAs; however, only a few lncRNAs have been found to exhibit tumor suppressor properties. Furthermore, their length and poor stability make them difficult to synthesize. Thus, to overcome the instability of lncRNAs, poor specificity, and their off-target effects, researchers have constructed nanocarriers that encapsulate lncRNAs. Recently, translational medicine research has focused on delivering lncRNAs into tumor cells, including cancer cells, through nano-drug delivery systems in vivo. The developed nanocarriers can protect, target, and release lncRNAs under controlled conditions without appreciable adverse effects. To deliver lncRNAs to cancer cells, various nanocarriers, such as exosomes, microbubbles, polymer nanoparticles, 1,2-dioleyl-3-trimethylammoniumpropane chloride nanocarriers, and virus-like particles, have been successfully developed. Despite this, every nanocarrier has its own advantages and disadvantages when it comes to delivering nucleic acids effectively and safely. This article examines the current status of nanocarriers for lncRNA delivery in cancer therapy, focusing on their potential to enhance cancer treatment.
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Affiliation(s)
- Fatemeh Davodabadi
- Department of Biology, Faculty of Basic Science, Payame Noor University, Tehran, Iran.
| | - Shekoufeh Mirinejad
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Sumira Malik
- Amity Institute of Biotechnology, Amity University Jharkhand, Ranchi-834002, India.
| | - Archna Dhasmana
- Himalayan School of Biosciences, Swami Rama Himalayan University, Jolly Grant, Dehradun, Uttarakhand, 248140, India.
| | - Fulden Ulucan-Karnak
- Department of Medical Biochemistry, Institute of Health Sciences, Ege University, İzmir 35100, Turkey.
| | - Sara Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
| | - Saman Sargazi
- Cellular and Molecular Research Center, Research Institute of Cellular and Molecular Sciences in Infectious Diseases, Zahedan University of Medical Sciences, Zahedan, Iran.
- Department of Clinical Biochemistry, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Sonia Fathi-Karkan
- Natural Products and Medicinal Plants Research Center, North Khorasan University of Medical Sciences, Bojnurd, 94531-55166, Iran
- Department of Advanced Sciences and Technologies in Medicine, School of Medicine, North Khorasan University of Medical Sciences, Bojnurd 9414974877, Iran.
| | - Abbas Rahdar
- Department of Physics, University of Zabol, Zabol, P. O. Box. 98613-35856, Iran.
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13
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Anilkumar AK, Vij P, Lopez S, Leslie SM, Doxtater K, Khan MM, Yallapu MM, Chauhan SC, Maestre GE, Tripathi MK. Long Non-Coding RNAs: New Insights in Neurodegenerative Diseases. Int J Mol Sci 2024; 25:2268. [PMID: 38396946 PMCID: PMC10889599 DOI: 10.3390/ijms25042268] [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: 01/03/2024] [Revised: 02/03/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Neurodegenerative diseases (NDDs), including Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS), are gradually becoming a burden to society. The adverse effects and mortality/morbidity rates associated with these NDDs are a cause of many healthcare concerns. The pathologic alterations of NDDs are related to mitochondrial dysfunction, oxidative stress, and inflammation, which further stimulate the progression of NDDs. Recently, long non-coding RNAs (lncRNAs) have attracted ample attention as critical mediators in the pathology of NDDs. However, there is a significant gap in understanding the biological function, molecular mechanisms, and potential importance of lncRNAs in NDDs. This review documents the current research on lncRNAs and their implications in NDDs. We further summarize the potential implication of lncRNAs to serve as novel therapeutic targets and biomarkers for patients with NDDs.
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Affiliation(s)
- Adithya K. Anilkumar
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Puneet Vij
- Department of Pharmaceutical Sciences, St. John’s University, Queens, NY 11439, USA
| | - Samantha Lopez
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Sophia M. Leslie
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Kyle Doxtater
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Mohammad Moshahid Khan
- Department of Neurology, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Murali M. Yallapu
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Subhash C. Chauhan
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
| | - Gladys E. Maestre
- Department of Neurosciences, University of Texas Rio Grande Valley School of Medicine, Brownsville, TX 78550, USA
- South Texas Alzheimer’s Disease Research Center, School of Medicine, University of Texas Rio Grande Valley, Harlingen, TX 78550, USA
| | - Manish K. Tripathi
- Medicine and Oncology, ISU, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
- South Texas Center of Excellence in Cancer Research, School of Medicine, University of Texas Rio Grande Valley, McAllen, TX 78504, USA
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14
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Amin HM, Abukhairan R, Szabo B, Jacksi M, Varady G, Lozsa R, Schad E, Tantos A. KMT2D preferentially binds mRNAs of the genes it regulates, suggesting a role in RNA processing. Protein Sci 2024; 33:e4847. [PMID: 38058280 PMCID: PMC10731558 DOI: 10.1002/pro.4847] [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: 04/19/2023] [Revised: 10/30/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Histone lysine methyltransferases (HKMTs) perform vital roles in cellular life by controlling gene expression programs through the posttranslational modification of histone tails. Since many of them are intimately involved in the development of different diseases, including several cancers, understanding the molecular mechanisms that control their target recognition and activity is vital for the treatment and prevention of such conditions. RNA binding has been shown to be an important regulatory factor in the function of several HKMTs, such as the yeast Set1 and the human Ezh2. Moreover, many HKMTs are capable of RNA binding in the absence of a canonical RNA binding domain. Here, we explored the RNA binding capacity of KMT2D, one of the major H3K4 monomethyl transferases in enhancers, using RNA immunoprecipitation followed by sequencing. We identified a broad range of coding and non-coding RNAs associated with KMT2D and confirmed their binding through RNA immunoprecipitation and quantitative PCR. We also showed that a separated RNA binding region within KMT2D is capable of binding a similar RNA pool, but differences in the binding specificity indicate the existence of other regulatory elements in the sequence of KMT2D. Analysis of the bound mRNAs revealed that KMT2D preferentially binds co-transcriptionally to the mRNAs of the genes under its control, while also interacting with super enhancer- and splicing-related non-coding RNAs. These observations, together with the nuclear colocalization of KMT2D with differentially phosphorylated forms of RNA Polymerase II suggest a so far unexplored role of KMT2D in the RNA processing of the nascent transcripts.
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Affiliation(s)
- Harem Muhamad Amin
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
- Doctoral School of Biology and Institute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
- Department of Biology, College of ScienceUniversity of SulaimaniSulaymaniyahIraq
| | - Rawan Abukhairan
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Beata Szabo
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Mevan Jacksi
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
- Doctoral School of Biology and Institute of Biology, ELTE Eötvös Loránd UniversityBudapestHungary
| | - Gyorgy Varady
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Rita Lozsa
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Eva Schad
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
| | - Agnes Tantos
- Institute of Enzymology, HUN‐REN Research Centre for Natural SciencesBudapestHungary
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Ismail NH, Mussa A, Al-Khreisat MJ, Mohamed Yusoff S, Husin A, Al-Jamal HAN, Johan MF, Islam MA. Dysregulation of Non-Coding RNAs: Roles of miRNAs and lncRNAs in the Pathogenesis of Multiple Myeloma. Noncoding RNA 2023; 9:68. [PMID: 37987364 PMCID: PMC10660696 DOI: 10.3390/ncrna9060068] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/27/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023] Open
Abstract
The dysregulation of non-coding RNAs (ncRNAs), specifically microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), leads to the development and advancement of multiple myeloma (MM). miRNAs, in particular, are paramount in post-transcriptional gene regulation, promoting mRNA degradation and translational inhibition. As a result, miRNAs can serve as oncogenes or tumor suppressors depending on the target genes. In MM, miRNA disruption could result in abnormal gene expression responsible for cell growth, apoptosis, and other biological processes pertinent to cancer development. The dysregulated miRNAs inhibit the activity of tumor suppressor genes, contributing to disease progression. Nonetheless, several miRNAs are downregulated in MM and have been identified as gene regulators implicated in extracellular matrix remodeling and cell adhesion. miRNA depletion potentially facilitates the tumor advancement and resistance of therapeutic drugs. Additionally, lncRNAs are key regulators of numerous cellular processes, such as gene expression, chromatin remodeling, protein trafficking, and recently linked MM development. The lncRNAs are uniquely expressed and influence gene expression that supports MM growth, in addition to facilitating cellular proliferation and viability via multiple molecular pathways. miRNA and lncRNA alterations potentially result in anomalous gene expression and interfere with the regular functioning of MM. Thus, this review aims to highlight the dysregulation of these ncRNAs, which engender novel therapeutic modalities for the treatment of MM.
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Affiliation(s)
- Nor Hayati Ismail
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Ali Mussa
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
- Department of Biology, Faculty of Education, Omdurman Islamic University, Omdurman 11111, Sudan
- Center for Global Health Research, Saveetha Medical College and Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, Tamil Nadu, India
| | - Mutaz Jamal Al-Khreisat
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Shafini Mohamed Yusoff
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Azlan Husin
- Department of Internal Medicine, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Hamid Ali Nagi Al-Jamal
- School of Biomedicine, Faculty of Health Sciences, Universiti Sultan Zainal Abidin (UniSZA), Kuala Nerus 21300, Terengganu, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, Kubang Kerian 16150, Kelantan, Malaysia
| | - Md Asiful Islam
- WHO Collaborating Centre for Global Women’s Health, Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, UK
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16
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Anber N, Tarabay MM, Elmougy R, Abdel-Dayem MA, Elbendary EY. Association of HOTAIR gene rs920778 (C > T) and rs4759314 (A > G) polymorphism with breast cancer in Egyptian women. Mol Biol Rep 2023; 50:9153-9163. [PMID: 37776415 PMCID: PMC10635973 DOI: 10.1007/s11033-023-08725-6] [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: 05/01/2023] [Accepted: 07/31/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Hox transcript antisense RNA (HOTAIR) is considered an oncogene associated with the initiation and progression of many malignancies. Previous studies have examined the connection between HOTAIR SNPs rs4759314 and rs920778 for breast cancer (BC), getting variable results in multiple ethnicities. Therefore, this study was designed to evaluate the connection between these two SNPs and disease vulnerability, clinic-laboratory, and hormonal parameters, featuring status associations with the BC risk in an Egyptian woman sample. METHODS AND RESULTS In this case-control study, DNA was taken from the blood of 100 BC patients and 100 unrelated healthy Egyptian females. The characterization of rs4759314 was genotyped using the T-ARMS-PCR method and rs920778 using the SNP-RFLP technique for all participants. The frequency of the rs4759314 A > G variation revealed a statistically significant increase in BC risk with dominant (p = 0.013, OR = 1.592, 95% Cl = 1.105-2.293), co-dominant (p = 0.006, OR = 2.314, 95%Cl = 1.278-4.191) and overdominant (p = 0.002, OR = 2.571, 95% Cl = 1.430-4.624) genetic models. On the other hand, the rs920778 C > T polymorphism was not significantly associated with BC. ER/PR positivity with HER2 negativity was significantly associated with the AA genotype compared to the AG genotype. Otherwise, no significant associations between the two SNPs and clinical stage or hormonal features could be found. In conclusion, the rs4759314 A > G SNP in the HOTAIR gene is strongly associated with BC, which might warrant its determination among affected families for prevention and early treatment.
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Affiliation(s)
- Nahla Anber
- Emergency Hospital, Faculty of Medicine, Mansoura University, Mansoura, Egypt.
| | | | - Rehab Elmougy
- Biochemistry Division, Chemistry Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Marwa Ahmed Abdel-Dayem
- Pharmacology and Toxicology Department, Faculty of Pharmacy, Horus University, New Damietta City, Egypt
| | - Ehab Yones Elbendary
- Clinical Nutrition Department, College of Applied Medical Sciences, Jazan University, Jazan, Kingdom of Saudi Arabia
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17
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Kyrgiafini MA, Giannoulis T, Chatziparasidou A, Christoforidis N, Mamuris Z. Unveiling the Genetic Complexity of Teratozoospermia: Integrated Genomic Analysis Reveals Novel Insights into lncRNAs' Role in Male Infertility. Int J Mol Sci 2023; 24:15002. [PMID: 37834450 PMCID: PMC10573971 DOI: 10.3390/ijms241915002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/15/2023] Open
Abstract
Male infertility is a global health issue, affecting over 20 million men worldwide. Genetic factors are crucial in various male infertility forms, including teratozoospermia. Nonetheless, the genetic causes of male infertility remain largely unexplored. In this study, we employed whole-genome sequencing and RNA expression analysis to detect differentially expressed (DE) long-noncoding RNAs (lncRNAs) in teratozoospermia, along with mutations that are exclusive to teratozoospermic individuals within these DE lncRNAs regions. Bioinformatic tools were used to assess variants' impact on lncRNA structure, function, and lncRNA-miRNA interactions. Our analysis identified 1166 unique mutations in teratozoospermic men within DE lncRNAs, distinguishing them from normozoospermic men. Among these, 64 variants in 23 lncRNAs showed potential regulatory roles, 7 variants affected 4 lncRNA structures, while 37 variants in 17 lncRNAs caused miRNA target loss or gain. Pathway Enrichment and Gene Ontology analyses of the genes targeted by the affected miRNAs revealed dysregulated pathways in teratozoospermia and a link between male infertility and cancer. This study lists novel variants and lncRNAs associated for the first time with teratozoospermia. These findings pave the way for future studies aiming to enhance diagnosis and therapy in the field of male infertility.
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Affiliation(s)
- Maria-Anna Kyrgiafini
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Sciences, University of Thessaly, Gaiopolis, 41336 Larissa, Greece
| | - Alexia Chatziparasidou
- Embryolab IVF Unit, St. 173-175 Ethnikis Antistaseos, Kalamaria, 55134 Thessaloniki, Greece
| | | | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece
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18
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Eldash S, Sanad EF, Nada D, Hamdy NM. The Intergenic Type LncRNA (LINC RNA) Faces in Cancer with In Silico Scope and a Directed Lens to LINC00511: A Step toward ncRNA Precision. Noncoding RNA 2023; 9:58. [PMID: 37888204 PMCID: PMC10610215 DOI: 10.3390/ncrna9050058] [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: 08/01/2023] [Revised: 09/09/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
BACKGROUND Long intergenic non-coding RNA, is one type of lncRNA, exerting various cellular activities, as does ncRNA, including the regulation of gene expression and chromatin remodeling. The abnormal expression of lincRNAs can induce or suppress carcinogenesis. MAIN BODY LincRNAs can regulate cancer progression through different mechanisms and are considered as potential drug targets. Genetic variations such as single nucleotide polymorphisms (SNPs) in lincRNAs may affect gene expression and messenger ribonucleic acid (mRNA) stability. SNPs in lincRNAs have been found to be associated with different types of cancer, as well. Specifically, LINC00511 has been known to promote the progression of multiple malignancies such as breast cancer, colorectal cancer, lung cancer, hepatocellular carcinoma, and others, making it a promising cancer prognostic molecular marker. CONCLUSION LincRNAs have been proved to be associated with different cancer types through various pathways. Herein, we performed a comprehensive literature and in silico databases search listing lncRNAs, lincRNAs including LINC00511, lncRNAs' SNPs, as well as LINC00511 SNPs in different cancer types, focusing on their role in various cancer types and mechanism(s) of action.
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Affiliation(s)
- Shorouk Eldash
- Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt (BUE), El Sherouk, Cairo 11837, Egypt; (S.E.)
| | - Eman F. Sanad
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Dina Nada
- Pharmacology and Biochemistry Department, Faculty of Pharmacy, The British University in Egypt (BUE), El Sherouk, Cairo 11837, Egypt; (S.E.)
| | - Nadia M. Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
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19
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Khan K, Irfan M, Sattar AA, Faiz MB, Rahman AU, Athar H, Calina D, Sharifi-Rad J, Cho WC. LncRNA SNHG6 role in clinicopathological parameters in cancers. Eur J Med Res 2023; 28:363. [PMID: 37735423 PMCID: PMC10515066 DOI: 10.1186/s40001-023-01358-2] [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: 01/14/2023] [Accepted: 09/10/2023] [Indexed: 09/23/2023] Open
Abstract
RNA sequencing has revealed that a substantial portion of the human genome undergoes transcription, yet a minimal fraction of these transcripts translates into proteins. LncRNAs, RNA molecules less than 200 nt in length, once deemed as transcriptional noise, have now emerged as crucial regulators of numerous cellular processes. This review focuses on the lncRNA SNHG6, aiming to elucidate its biogenesis, the pivotal roles it plays, and its mechanisms in facilitating the hallmarks of cancer. A comprehensive literature review and analysis were undertaken to delve into the biogenesis of SNHG6, its roles in cellular processes, and the mechanisms through which it contributes to the hallmarks of cancer. SNHG6 is a notable lncRNA, observed to be overexpressed in various cancer types; its perturbation has been linked to tumor progression, emphasizing its significance in oncogenesis. This lncRNA contributes to a range of cellular aberrations, influencing transcriptional, post-transcriptional, and epigenetic processes of mRNA, ultimately driving cancerous transformations. LncRNA SNHG6 serves as a potential biomarker and therapeutic target due to its association with tumorigenesis. Understanding its mechanism and role in cancer can pave the way for novel diagnostic and therapeutic strategies.
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Affiliation(s)
- Khushbukhat Khan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000 Pakistan
| | - Muhammad Irfan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000 Pakistan
| | - Areej Abdul Sattar
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000 Pakistan
| | - Manal Bint Faiz
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000 Pakistan
| | - Anees ur Rahman
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000 Pakistan
| | - Hafsa Athar
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad, 44000 Pakistan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349 Craiova, Romania
| | | | - William C. Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong
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20
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Hussain MS, Afzal O, Gupta G, Altamimi ASA, Almalki WH, Alzarea SI, Kazmi I, Fuloria NK, Sekar M, Meenakshi DU, Thangavelu L, Sharma A. Long non-coding RNAs in lung cancer: Unraveling the molecular modulators of MAPK signaling. Pathol Res Pract 2023; 249:154738. [PMID: 37595448 DOI: 10.1016/j.prp.2023.154738] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/20/2023]
Abstract
Lung cancer (LC) continues to pose a significant global medical burden, necessitating a comprehensive understanding of its molecular foundations to establish effective treatment strategies. The mitogen-activated protein kinase (MAPK) signaling system has been scientifically associated with LC growth; however, the intricate regulatory mechanisms governing this system remain unknown. Long non-coding RNAs (lncRNAs) are emerging as crucial regulators of diverse cellular activities, including cancer growth. LncRNAs have been implicated in LC, which can function as oncogenes or tumor suppressors, and their dysregulation has been linked to cancer cell death, metastasis, spread, and proliferation. Due to their involvement in critical pathophysiological processes, lncRNAs are gaining attention as potential candidates for anti-cancer treatments. This article aims to elucidate the regulatory role of lncRNAs in MAPK signaling in LC. We provide a comprehensive review of the key components of the MAPK pathway and their relevance in LC, focusing on aberrant signaling processes associated with disease progression. By examining recent research and experimental findings, this article examines the molecular mechanisms through which lncRNAs influence MAPK signaling in lung cancer, ultimately contributing to tumor development.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, 302017 Jaipur, Rajasthan, India
| | - Obaid Afzal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Gaurav Gupta
- School of Pharmacy, Suresh Gyan Vihar University, Mahal Road, Jagatpura, Jaipur, India; Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India; School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
| | | | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Al-Jouf, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Mahendran Sekar
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Subang Jaya 47500, Selangor, Malaysia
| | | | - Lakshmi Thangavelu
- Center for Global Health Research , Saveetha Medical College , Saveetha Institute of Medical and Technical Sciences, Saveetha University, India
| | - Ajay Sharma
- Delhi Pharmaceutical Science and Research University, Pushp Vihar Sector-3, MB Road, New Delhi 110017, India.
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21
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Singh D, Desai N, Shah V, Datta B. In Silico Identification of Potential Quadruplex Forming Sequences in LncRNAs of Cervical Cancer. Int J Mol Sci 2023; 24:12658. [PMID: 37628839 PMCID: PMC10454738 DOI: 10.3390/ijms241612658] [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: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) have emerged as auxiliary regulators of gene expression influencing tumor microenvironment, metastasis and radio-resistance in cancer. The presence of lncRNA in extracellular fluids makes them promising diagnostic markers. LncRNAs deploy higher-order structures to facilitate a complex range of functions. Among such structures, G-quadruplexes (G4s) can be detected or targeted by small molecular probes to drive theranostic applications. The in vitro identification of G4 formation in lncRNAs can be a tedious and expensive proposition. Bioinformatics-driven strategies can provide comprehensive and economic alternatives in conjunction with suitable experimental validation. We propose a pipeline to identify G4-forming sequences, protein partners and biological functions associated with dysregulated lncRNAs in cervical cancer. We identified 17 lncRNA clusters which possess transcripts that can fold into a G4 structure. We confirmed in vitro G4 formation in the four biologically active isoforms of SNHG20, MEG3, CRNDE and LINP1 by Circular Dichroism spectroscopy and Thioflavin-T-assisted fluorescence spectroscopy and reverse-transcriptase stop assay. Gene expression data demonstrated that these four lncRNAs can be potential prognostic biomarkers of cervical cancer. Two approaches were employed for identifying G4 specific protein partners for these lncRNAs and FMR2 was a potential interacting partner for all four clusters. We report a detailed investigation of G4 formation in lncRNAs that are dysregulated in cervical cancer. LncRNAs MEG3, CRNDE, LINP1 and SNHG20 are shown to influence cervical cancer progression and we report G4 specific protein partners for these lncRNAs. The protein partners and G4s predicted in lncRNAs can be exploited for theranostic objectives.
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Affiliation(s)
- Deepshikha Singh
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Nakshi Desai
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Viraj Shah
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
| | - Bhaskar Datta
- Department of Biological Engineering, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India; (D.S.); (N.D.); (V.S.)
- Department of Chemistry, Indian Institute of Technology Gandhinagar, Gandhinagar 382355, India
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22
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Ahmad M, Weiswald LB, Poulain L, Denoyelle C, Meryet-Figuiere M. Involvement of lncRNAs in cancer cells migration, invasion and metastasis: cytoskeleton and ECM crosstalk. J Exp Clin Cancer Res 2023; 42:173. [PMID: 37464436 PMCID: PMC10353155 DOI: 10.1186/s13046-023-02741-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/26/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer is the main cause of death worldwide and metastasis is a major cause of poor prognosis and cancer-associated mortality. Metastatic conversion of cancer cells is a multiplex process, including EMT through cytoskeleton remodeling and interaction with TME. Tens of thousands of putative lncRNAs have been identified, but the biological functions of most are still to be identified. However, lncRNAs have already emerged as key regulators of gene expression at transcriptional and post-transcriptional level to control gene expression in a spatio-temporal fashion. LncRNA-dependent mechanisms can control cell fates during development and their perturbed expression is associated with the onset and progression of many diseases including cancer. LncRNAs have been involved in each step of cancer cells metastasis through different modes of action. The investigation of lncRNAs different roles in cancer metastasis could possibly lead to the identification of new biomarkers and innovative cancer therapeutic options.
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Affiliation(s)
- Mohammad Ahmad
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
- Biochemistry Division, Chemistry Department, Faculty of Science, Damanhour University, Damanhour, 14000, Egypt
| | - Louis-Bastien Weiswald
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Laurent Poulain
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Christophe Denoyelle
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France
| | - Matthieu Meryet-Figuiere
- (Interdisciplinary Research Unit for Cancer Prevention and Treatment), Baclesse Cancer Centre, Université de Caen Normandie Inserm Anticipe UMR 1086, Normandie Univ, Research Building, F-14000 François 3 Avenue Général Harris, BP 45026, 14 076, cedex 05, Caen, France.
- Comprehensive Cancer Center François Baclesse, UNICANCER, Caen, France.
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23
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Al-Imam MJ, Hussein UAR, Sead FF, Faqri AMA, Mekkey SM, Khazel AJ, Almashhadani HA. The interactions between DNA methylation machinery and long non-coding RNAs in tumor progression and drug resistance. DNA Repair (Amst) 2023; 128:103526. [PMID: 37406581 DOI: 10.1016/j.dnarep.2023.103526] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/13/2023] [Accepted: 06/14/2023] [Indexed: 07/07/2023]
Abstract
DNA methylation is one of the main epigenetic mechanisms in cancer development and progression. Aberrant DNA methylation of CpG islands within promoter regions contributes to the dysregulation of various tumor suppressors and oncogenes; this leads to the appearance of malignant features, including rapid proliferation, metastasis, stemness, and drug resistance. The discovery of two important protein families, DNA methyltransferases (DNMTs) and Ten-eleven translocation (TET) dioxygenases, respectively, which are responsible for deregulated transcription of genes that play pivotal roles in tumorigenesis, led to further understanding of DNA methylation-related pathways. But how these enzymes can target specific genes in different malignancies; recent studies have highlighted the considerable role of Long Non-coding RNAs (LncRNAs). LncRNAs recruit these enzymes to promoter regions of genes and mediate their functions, showing great potential as therapeutic agents targeting the epigenetic regulation of various genes. Considering the importance of combining the current treatment methods, especially chemotherapies, with DNA methylation inhibitors in improving patients' outcomes, this review aimed to summarize the recent findings about the interaction between DNA methylation machinery and LncRNAs in regulating genes involved in tumorigenesis and drug resistance. So, these studies could provide insights toward developing novel strategies for cancer-targeted therapy.
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Affiliation(s)
- Mokhtar Jawad Al-Imam
- Department of Experimental Therapy, Iraqi Center for Cancer and Medical Genetics Research, Almustansiriyah University, Baghdad, Iraq
| | | | | | | | - Shereen M Mekkey
- Pharmacy Department, Al-Mustaqbal University College, 51001 Hilla, Babylon, Iraq
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24
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Spirito L, Maturi R, Credendino SC, Manfredi C, Arcaniolo D, De Martino M, Esposito F, Napolitano L, Di Bello F, Fusco A, Pallante P, De Sio M, De Vita G. Differential Expression of LncRNA in Bladder Cancer Development. Diagnostics (Basel) 2023; 13:diagnostics13101745. [PMID: 37238229 DOI: 10.3390/diagnostics13101745] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/05/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Bladder cancer (BC) is the tenth most common cancer, with urothelial carcinoma representing about 90% of all BC, including neoplasms and carcinomas of different grades of malignancy. Urinary cytology has a significant role in BC screening and surveillance, although it has a low detection rate and high dependence on the pathologist's experience. The currently available biomarkers are not implemented into routine clinical practice due to high costs or low sensitivity. In recent years, the role of lncRNAs in BC has emerged, even though it is still poorly explored. We have previously shown that the lncRNAs Metallophosphoesterase Domain-Containing 2 Antisense RNA 1 (MPPED2-AS1), Rhabdomyosarcoma-2 Associated Transcript (RMST), Kelch-like protein 14 antisense (Klhl14AS) and Prader Willi/Angelman region RNA 5 (PAR5) are involved in the progression of different types of cancers. Here, we investigated the expression of these molecules in BC, first by interrogating the GEPIA database and observing a different distribution of expression levels between normal and cancer specimens. We then measured them in a cohort of neoplastic bladder lesions, either benign or malignant, from patients with suspicion of BC undergoing transurethral resection of bladder tumor (TURBT). The total RNA from biopsies was analyzed using qRT-PCR for the expression of the four lncRNA genes, showing differential expression of the investigated lncRNAs between normal tissue, benign lesions and cancers. In conclusion, the data reported here highlight the involvement of novel lncRNAs in BC development, whose altered expression could potentially affect the regulatory circuits in which these molecules are involved. Our study paves the way for testing lncRNA genes as markers for BC diagnosis and/or follow-up.
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Affiliation(s)
- Lorenzo Spirito
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Rufina Maturi
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Sara Carmela Credendino
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Celeste Manfredi
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Davide Arcaniolo
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Marco De Martino
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
- Department of Precision Medicine, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Napoli, Italy
| | - Francesco Esposito
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
| | - Luigi Napolitano
- Urology Unit, Department of Neurosciences, Reproductive Sciences, and Odontostomatology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Francesco Di Bello
- Urology Unit, Department of Neurosciences, Reproductive Sciences, and Odontostomatology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
| | - Alfredo Fusco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
| | - Pierlorenzo Pallante
- Institute of Experimental Endocrinology and Oncology "G. Salvatore", National Research Council (CNR), Via Pansini, 5, 80131 Naples, Italy
| | - Marco De Sio
- Urology Unit, Department of Woman Child and General and Specialized Surgery, University of Campania "Luigi Vanvitelli", Via De Crecchio 7, 80138 Naples, Italy
| | - Gabriella De Vita
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via Pansini 5, 80131 Naples, Italy
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25
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Raju GSR, Pavitra E, Bandaru SS, Varaprasad GL, Nagaraju GP, Malla RR, Huh YS, Han YK. HOTAIR: a potential metastatic, drug-resistant and prognostic regulator of breast cancer. Mol Cancer 2023; 22:65. [PMID: 36997931 PMCID: PMC10061914 DOI: 10.1186/s12943-023-01765-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 03/14/2023] [Indexed: 04/01/2023] Open
Abstract
HOX transcript antisense intergenic RNA (HOTAIR) is an oncogenic non-coding RNA whose expression is strongly correlated with the tumor grade and prognosis of a variety of carcinomas including breast cancer (BC). HOTAIR regulates various target genes via sponging and epigenetic mechanisms and controls various oncogenic cellular and signaling mechanisms including metastasis and drug resistance. In BC cells, HOTAIR expression is regulated by a variety of transcriptional and epigenetic mechanisms. In this review, we describe the regulatory mechanisms that govern HOTAIR expression during cancer development and explore how HOTAIR drives BC development, metastasis, and drug resistance. In the final section of this review, we focus on the role of HOTAIR in BC management, therapeutic treatment, and prognosis, highlighting its potential therapeutic applications.
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Affiliation(s)
- Ganji Seeta Rama Raju
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul, 04620, Republic of Korea
| | - Eluri Pavitra
- NanoBio High-Tech Materials Research Center, Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | | | - Ganji Lakshmi Varaprasad
- NanoBio High-Tech Materials Research Center, Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea
| | | | - Rama Rao Malla
- Cancer Biology Laboratory, Department of Biochemistry and Bioinformatics, GIS, GITAM (Deemed to be University), Visakhapatnam, Andhra Pradesh, 530045, India.
| | - Yun Suk Huh
- NanoBio High-Tech Materials Research Center, Biological Sciences and Bioengineering, Inha University, Incheon, 22212, Republic of Korea.
| | - Young-Kyu Han
- Department of Energy and Materials Engineering, Dongguk University-Seoul, Seoul, 04620, Republic of Korea.
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26
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Chen H, Xu S, Zhang Y, Chen P. Systematic analysis of lncRNA gene characteristics based on PD-1 immune related pathway for the prediction of non-small cell lung cancer prognosis. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2023; 20:9818-9838. [PMID: 37322912 DOI: 10.3934/mbe.2023430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
BACKGROUND Non-small cell lung cancer (NSCLC) is heterogeneous. Molecular subtyping based on the gene expression profiles is an effective technique for diagnosing and determining the prognosis of NSCLC patients. METHODS Here, we downloaded the NSCLC expression profiles from The Cancer Genome Atlas and the Gene Expression Omnibus databases. ConsensusClusterPlus was used to derive the molecular subtypes based on long-chain noncoding RNA (lncRNA) associated with the PD-1-related pathway. The LIMMA package and least absolute shrinkage and selection operator (LASSO)-Cox analysis were used to construct the prognostic risk model. The nomogram was constructed to predict the clinical outcomes, followed by decision curve analysis (DCA) to validate the reliability of this nomogram. RESULTS We discovered that PD-1 was strongly and positively linked to the T-cell receptor signaling pathway. Furthermore, we identified two NSCLC molecular subtypes yielding a significantly distinctive prognosis. Subsequently, we developed and validated the 13-lncRNA-based prognostic risk model in the four datasets with high AUC values. Patients with low-risk showed a better survival rate and were more sensitive to PD-1 treatment. Nomogram construction combined with DCA revealed that the risk score model could accurately predict the prognosis of NSCLC patients. CONCLUSIONS This study demonstrated that lncRNAs engaged in the T-cell receptor signaling pathway played a significant role in the onset and development of NSCLC, and that they could influence the sensitivity to PD-1 treatment. In addition, the 13 lncRNA model was effective in assisting clinical treatment decision-making and prognosis evaluation.
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Affiliation(s)
- Hejian Chen
- Department of Respiratory and Critical Care Medicine, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
| | - Shuiyu Xu
- Department of Oncology, HaploX Biotechnology, Shenzhen 518035, China
| | - Yuhong Zhang
- Department of Oncology, HaploX Biotechnology, Shenzhen 518035, China
| | - Peifeng Chen
- Department of Respiratory and Critical Care Medicine, Zhuji People's Hospital of Zhejiang Province, Zhuji 311800, China
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27
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Huang HH, You GR, Tang SJ, Chang JT, Cheng AJ. Molecular Signature of Long Non-Coding RNA Associated with Areca Nut-Induced Head and Neck Cancer. Cells 2023; 12:cells12060873. [PMID: 36980216 PMCID: PMC10047708 DOI: 10.3390/cells12060873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Revised: 02/26/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
The areca nut is a high-risk carcinogen for head and neck cancer (HNC) patients in Southeast Asia. The underlying molecular mechanism of areca nut-induced HNC remains unclear, especially regarding the role of long non-coding RNA (lncRNA). This study employed a systemic strategy to identify lncRNA signatures related to areca nut-induced HNC. In total, 84 cancer-related lncRNAs were identified. Using a PCR array method, 28 lncRNAs were identified as being dysregulated in HNC cells treated with areca nut (17 upregulated and 11 downregulated). Using bioinformatics analysis of The Cancer Genome Atlas Head-Neck Squamous Cell Carcinoma (TCGA-HNSC) dataset, 45 lncRNAs were differentially expressed in tumor tissues from HNC patients (39 over- and 6 under-expressions). The integrated evaluation showed 10 lncRNAs dysregulated by the areca nut and altered expression in patients, suggesting that these panel molecules participate in areca nut-induced HNC. Five oncogenic (LUCAT1, MIR31HG, UCA1, HIF1A-AS2, and SUMO1P3) and tumor-suppressive (LINC00312) lncRNAs were independently validated, and three key molecules were further examined. Pathway prediction revealed that LUCAT1, UCA1, and MIR31HG modulate multiple oncogenic mechanisms, including stress response and cellular motility. Clinical assessment showed that these lncRNAs exhibited biomarker potentials in diagnosis (area under the curve = 0.815 for LUCAT1) and a worse prognosis (both p < 0.05, survival analysis). Cellular studies further demonstrated that MIR31HG facilitates areca nut-induced cancer progression, as silencing this molecule attenuated arecoline-induced invasion ability in HNC cells. This study identified lncRNA signatures that play a role in areca nut-induced HNC. These molecules may be further applied in risk assessment, diagnosis, prognosis, and therapeutics for areca nut-associated malignancies.
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Affiliation(s)
- Hung-Han Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Guo-Rung You
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Shang-Ju Tang
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
| | - Joseph T. Chang
- Department of Radiation Oncology and Proton Therapy Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
- School of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Correspondence: (J.T.C.); (A.-J.C.); Tel.: +886-3-328-1200 (J.T.C.); +886-3-2118-800 (A.-J.C.)
| | - Ann-Joy Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan 33302, Taiwan
- Department of Radiation Oncology and Proton Therapy Center, Linkou Chang Gung Memorial Hospital, Taoyuan 333423, Taiwan
- Correspondence: (J.T.C.); (A.-J.C.); Tel.: +886-3-328-1200 (J.T.C.); +886-3-2118-800 (A.-J.C.)
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28
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Gholami M, Klashami ZN, Ebrahimi P, Mahboobipour AA, Farid AS, Vahidi A, Zoughi M, Asadi M, Amoli MM. Metformin and long non-coding RNAs in breast cancer. J Transl Med 2023; 21:155. [PMID: 36849958 PMCID: PMC9969691 DOI: 10.1186/s12967-023-03909-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 01/21/2023] [Indexed: 03/01/2023] Open
Abstract
Breast cancer (BC) is the second most common cancer and cause of death in women. In recent years many studies investigated the association of long non-coding RNAs (lncRNAs), as novel genetic factors, on BC risk, survival, clinical and pathological features. Recent studies also investigated the roles of metformin treatment as the firstline treatment for type 2 diabetes (T2D) played in lncRNAs expression/regulation or BC incidence, outcome, mortality and survival, separately. This comprehensive study aimed to review lncRNAs associated with BC features and identify metformin-regulated lncRNAs and their mechanisms of action on BC or other types of cancers. Finally, metformin affects BC by regulating five BC-associated lncRNAs including GAS5, HOTAIR, MALAT1, and H19, by several molecular mechanisms have been described in this review. In addition, metformin action on other types of cancers by regulating ten lncRNAs including AC006160.1, Loc100506691, lncRNA-AF085935, SNHG7, HULC, UCA1, H19, MALAT1, AFAP1-AS1, AC026904.1 is described.
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Affiliation(s)
- Morteza Gholami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.,Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Zeynab Nickhah Klashami
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Pirooz Ebrahimi
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Arcavacata, Italy
| | | | - Amir Salehi Farid
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Aida Vahidi
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Marziyeh Zoughi
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mojgan Asadi
- Metabolomics and Genomics Research Center Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahsa M Amoli
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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29
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Koffler-Brill T, Noy Y, Avraham KB. The long and short: Non-coding RNAs in the mammalian inner ear. Hear Res 2023; 428:108666. [PMID: 36566643 PMCID: PMC9883734 DOI: 10.1016/j.heares.2022.108666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Revised: 10/21/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
Non-coding RNAs (ncRNAs) play a critical role in the entire body, and their mis-regulation is often associated with disease. In parallel with the advances in high-throughput sequencing technologies, there is a great deal of focus on this broad class of RNAs. Although these molecules are not translated into proteins, they are now well established as significant regulatory components in many biological pathways and pathological conditions. ncRNAs can be roughly divided into two main sub-groups based on the length of the transcript, with both the small and long non-coding RNAs having diverse regulatory functions. The smaller length group includes ribosomal RNAs (rRNA), transfer RNAs (tRNA), small nuclear RNAs (snRNA), small nucleolar RNAs (snoRNA), microRNAs (miRNA), small interfering RNAs (siRNA), and PIWI-associated RNAs (piRNA). The longer length group includes linear long non-coding RNAs (lncRNA) and circular RNAs (circRNA). This review is designed to present the different classes of small and long ncRNA molecules and describe some of their known roles in physiological and pathological conditions, as well as methods used to assess the validity and function of miRNAs and lncRNAs, with a focus on their role and functions in the inner ear, hearing and deafness.
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Affiliation(s)
- Tal Koffler-Brill
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yael Noy
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Karen B Avraham
- Department of Human Molecular Genetics and Biochemistry, Faculty of Medicine and Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel.
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30
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Asadi MR, Abed S, Kouchakali G, Fattahi F, Sabaie H, Moslehian MS, Sharifi-Bonab M, Hussen BM, Taheri M, Ghafouri-Fard S, Rezazadeh M. Competing endogenous RNA (ceRNA) networks in Parkinson's disease: A systematic review. Front Cell Neurosci 2023; 17:1044634. [PMID: 36761351 PMCID: PMC9902725 DOI: 10.3389/fncel.2023.1044634] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 01/06/2023] [Indexed: 01/25/2023] Open
Abstract
Parkinson's disease (PD) is a distinctive clinical syndrome with several causes and clinical manifestations. Aside from an infectious cause, PD is a rapidly developing neurological disorder with a global rise in frequency. Notably, improved knowledge of molecular pathways and the developing novel diagnostic methods may result in better therapy for PD patients. In this regard, the amount of research on ceRNA axes is rising, highlighting the importance of these axes in PD. CeRNAs are transcripts that cross-regulate one another via competition for shared microRNAs (miRNAs). These transcripts may be either coding RNAs (mRNAs) or non-coding RNAs (ncRNAs). This research used a systematic review to assess validated loops of ceRNA in PD. The Prisma guideline was used to conduct this systematic review, which entailed systematically examining the articles of seven databases. Out of 309 entries, forty articles met all criteria for inclusion and were summarized in the appropriate table. CeRNA axes have been described through one of the shared vital components of the axes, including lncRNAs such as NEAT1, SNHG family, HOTAIR, MALAT1, XIST, circRNAs, and lincRNAs. Understanding the multiple aspects of this regulatory structure may aid in elucidating the unknown causal causes of PD and providing innovative molecular therapeutic targets and medical fields.
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Affiliation(s)
- Mohammad Reza Asadi
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Samin Abed
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ghazal Kouchakali
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Fateme Fattahi
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hani Sabaie
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Marziyeh Sadat Moslehian
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mirmohsen Sharifi-Bonab
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Bashdar Mahmud Hussen
- Department of Biomedical Sciences, Cihan University-Erbil, Erbil, Iraq
- Department of Pharmacognosy, College of Pharmacy, Hawler Medical University, Erbil, Iraq
| | - Mohammad Taheri
- Urology and Nephrology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Institute of Human Genetics, Jena University Hospital, Jena, Germany
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Clinical Research Development Unit of Tabriz Valiasr Hospital, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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31
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Lv N, Shen S, Chen Q, Tong J. Long noncoding RNAs: glycolysis regulators in gynaecologic cancers. Cancer Cell Int 2023; 23:4. [PMID: 36639695 PMCID: PMC9838043 DOI: 10.1186/s12935-023-02849-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Accepted: 01/05/2023] [Indexed: 01/15/2023] Open
Abstract
The three most common gynaecologic cancers that seriously threaten female lives and health are ovarian cancer, cervical cancer, and endometrial cancer. Glycolysis plays a vital role in gynaecologic cancers. Several long noncoding RNAs (lncRNAs) are known to function as oncogenic molecules. LncRNAs impact downstream target genes by acting as ceRNAs, guides, scaffolds, decoys, or signalling molecules. However, the role of glycolysis-related lncRNAs in regulating gynaecologic cancers remains poorly understood. In this review, we emphasize the functional roles of many lncRNAs that have been found to promote glycolysis in gynaecologic cancers and discuss reasonable strategies for future research.
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Affiliation(s)
- Nengyuan Lv
- grid.268505.c0000 0000 8744 8924Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang Province People’s Republic of China ,grid.13402.340000 0004 1759 700XDepartment of Obstetrics and Gynecology, Affiliated Hangzhou First People’s Hospital, Zhejiang University of Medicine, Hangzhou, 310006 Zhejiang Province People’s Republic of China
| | - Siyi Shen
- grid.268505.c0000 0000 8744 8924Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang Province People’s Republic of China ,grid.13402.340000 0004 1759 700XDepartment of Obstetrics and Gynecology, Affiliated Hangzhou First People’s Hospital, Zhejiang University of Medicine, Hangzhou, 310006 Zhejiang Province People’s Republic of China
| | - Qianying Chen
- grid.268505.c0000 0000 8744 8924Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang Province People’s Republic of China ,grid.13402.340000 0004 1759 700XDepartment of Obstetrics and Gynecology, Affiliated Hangzhou First People’s Hospital, Zhejiang University of Medicine, Hangzhou, 310006 Zhejiang Province People’s Republic of China
| | - Jinyi Tong
- grid.268505.c0000 0000 8744 8924Department of the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, 310053 Zhejiang Province People’s Republic of China ,grid.13402.340000 0004 1759 700XDepartment of Obstetrics and Gynecology, Affiliated Hangzhou First People’s Hospital, Zhejiang University of Medicine, Hangzhou, 310006 Zhejiang Province People’s Republic of China
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Ghazimoradi MH, Karimpour-Fard N, Babashah S. The Promising Role of Non-Coding RNAs as Biomarkers and Therapeutic Targets for Leukemia. Genes (Basel) 2023; 14:131. [PMID: 36672872 PMCID: PMC9859176 DOI: 10.3390/genes14010131] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/02/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Early-stage leukemia identification is crucial for effective disease management and leads to an improvement in the survival of leukemia patients. Approaches based on cutting-edge biomarkers with excellent accuracy in body liquids provide patients with the possibility of early diagnosis with high sensitivity and specificity. Non-coding RNAs have recently received a great deal of interest as possible biomarkers in leukemia due to their participation in crucial oncogenic processes such as proliferation, differentiation, invasion, apoptosis, and their availability in body fluids. Recent studies have revealed a strong correlation between leukemia and the deregulated non-coding RNAs. On this basis, these RNAs are also great therapeutic targets. Based on these advantages, we tried to review the role of non-coding RNAs in leukemia. Here, the significance of several non-coding RNA types in leukemia is highlighted, and their potential roles as diagnostic, prognostic, and therapeutic targets are covered.
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Affiliation(s)
- Mohammad H. Ghazimoradi
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
| | - Naeim Karimpour-Fard
- Department of Pharmacoeconomics and Pharmaceutical Administration, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran 1417614411, Iran
| | - Sadegh Babashah
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 1411713116, Iran
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Siri G, Yazdani O, Esbati R, Akhavanfar R, Asadi F, Adili A, Ebrahimzadeh F, Hosseini SME. A comprehensive review of the role of lncRNAs in gastric cancer (GC) pathogenesis, immune regulation, and their clinical applications. Pathol Res Pract 2023; 241:154221. [PMID: 36563559 DOI: 10.1016/j.prp.2022.154221] [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: 10/01/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
Abstract
Gastric cancer (GC) is the fifth most common malignant tumor and the third leading cause of cancer-related deaths worldwide. Although numerous studies have been conducted on advanced GC, the molecular mechanisms behind it remain obscure. Long non-coding RNAs (lncRNAs) are a family of RNA transcripts capable of regulating target genes at transcriptional, post-transcriptional, and translational stages. They do this by modifying mRNAs, miRNAs, and proteins. These RNAs are critical regulators of many biological processes, including gene epigenetics, transcription, and post-transcriptional levels. This article highlights recent results on lncRNAs involved in drug resistance, proliferation, migration, angiogenesis, apoptosis, autophagy, and immune response in GC. The potential clinical implications of lncRNAs as biomarkers and therapeutic targets in GC are also discussed.
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Affiliation(s)
- Goli Siri
- Department of Internal Medicine, Amir Alam Hospital, Tehran University of Medical Sciences, Tehran, Iran
| | - Omid Yazdani
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Romina Esbati
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Roozbeh Akhavanfar
- School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Fatemeh Asadi
- Department of Genetics, Marvdasht Branch, Islamic Azad University, Marvdasht, Iran
| | - Ali Adili
- Senior Adult Oncology Department, Moffitt Cancer Center, University of South Florida, Tampa, FL, USA; Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
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Rastad H, Samimisedeh P, Alan MS, Afshar EJ, Ghalami J, Hashemnejad M, Alan MS. The role of lncRNA CERS6-AS1 in cancer and its molecular mechanisms: A systematic review and meta-analysis. Pathol Res Pract 2023; 241:154245. [PMID: 36580796 DOI: 10.1016/j.prp.2022.154245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND LncRNAs have the potential to play a regulatory role in different processes of cancer development and progression. We conducted a systematic review and meta-analysis of evidence on the clinical significance and prognostic value of lncRNA CERS6-AS1 in cancer. METHODS This systematic review was conducted following PRISMA guidelines. Medline and Embase databases were searched using the relevant key terms covering lncRNA CERS6-AS1 and cancer. We pooled the estimated effect sizes and their 95 % confidence interval (CI) using random-effects models in STATA 16.0 (StataCorp, College Station, TX, USA). RESULTS Eleven articles on pancreatic, colorectal, gastric, papillary thyroid, breast, and hepatocellular cancers fulfilled our eligibility criteria. Studies consistently found that lncRNA CERS6-AS1 expression is upregulated in all assessed cancers. Based on our meta-analysis, its aberrant expression was directly associated with unfavorable clinical outcomes, including higher stage (pooled Odds ratios (95 % CI): 3.15 (2.01-4.93; I2 = 0.0 %), tumor size (1.97 (1.27-3.05; I2 = 37.8 %), lymph node metastasis (6.48 (4.01-10.45; I2 = 0.40 %), and poor survival (Pooled log-rank test P-value < 0.001) in patients. Regarding potential mechanisms, functional studies revealed that LncRNA CERS6-AS1 is involved in cancer growth mainly by sponging miRNAs and regulating their downstream targets. CONCLUSION Available evidence suggests that LncRNA CERS6-AS1 is upregulated in different cancers and has an oncogenic role. LncRNA CERS6-AS1 expression level might predict cancer prognosis, highlighting its potential application as a prognostic biomarker for cancer.
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Affiliation(s)
- Hadith Rastad
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Parham Samimisedeh
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahin Seifi Alan
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Elmira Jafari Afshar
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Jamileh Ghalami
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran; The Clinical Research Development units of Kamali Hospital, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Hashemnejad
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Mahnaz Seifi Alan
- Cardiovascular Research Center, Alborz University of Medical Sciences, Karaj, Iran.
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35
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Arunima A, van Schaik EJ, Samuel JE. The emerging roles of long non-coding RNA in host immune response and intracellular bacterial infections. Front Cell Infect Microbiol 2023; 13:1160198. [PMID: 37153158 PMCID: PMC10160451 DOI: 10.3389/fcimb.2023.1160198] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 04/07/2023] [Indexed: 05/09/2023] Open
Abstract
The long non-coding RNAs (lncRNAs) are evolutionarily conserved classes of non-coding regulatory transcripts of > 200 nucleotides in length. They modulate several transcriptional and post-transcriptional events in the organism. Depending on their cellular localization and interactions, they regulate chromatin function and assembly; and alter the stability and translation of cytoplasmic mRNAs. Although their proposed range of functionality remains controversial, there is increasing research evidence that lncRNAs play a regulatory role in the activation, differentiation and development of immune signaling cascades; microbiome development; and in diseases such as neuronal and cardiovascular disorders; cancer; and pathogenic infections. This review discusses the functional roles of different lncRNAs in regulation of host immune responses, signaling pathways during host-microbe interaction and infection caused by obligate intracellular bacterial pathogens. The study of lncRNAs is assuming significance as it could be exploited for development of alternative therapeutic strategies for the treatment of severe and chronic pathogenic infections caused by Mycobacterium, Chlamydia and Rickettsia infections, as well as commensal colonization. Finally, this review summarizes the translational potential of lncRNA research in development of diagnostic and prognostic tools for human diseases.
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Roshani M, Baniebrahimi G, Mousavi M, Zare N, Sadeghi R, Salarinia R, Sheida A, Molavizadeh D, Sadeghi S, Moammer F, Zolfaghari MR, Mirzaei H. Exosomal long non-coding RNAs: novel molecules in gastrointestinal cancers' progression and diagnosis. Front Oncol 2022; 12:1014949. [PMID: 36591473 PMCID: PMC9795196 DOI: 10.3389/fonc.2022.1014949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 11/10/2022] [Indexed: 12/15/2022] Open
Abstract
Gastrointestinal (GI) cancers arise in the GI tract and accessory organs, including the mouth, esophagus, stomach, liver, biliary tract, pancreas, small intestine, large intestine, and rectum. GI cancers are a major cause of cancer-related morbidity and mortality worldwide. Exosomes act as mediators of cell-to-cell communication, with pleiotropic activity in the regulation of homeostasis, and can be markers for diseases. Non-coding RNAs (ncRNAs), such as long non-coding RNAs (lncRNAs), can be transported by exosomes derived from tumor cells or non-tumor cells. They can be taken by recipient cells to alter their function or remodel the tumor microenvironment. Moreover, due to their uniquely low immunogenicity and excellent stability, exosomes can be used as natural carriers for therapeutic ncRNAs in vivo. Exosomal lncRNAs have a crucial role in regulating several cancer processes, including angiogenesis, proliferation, drug resistance, metastasis, and immunomodulation. Exosomal lncRNA levels frequently alter according to the onset and progression of cancer. Exosomal lncRNAs can therefore be employed as biomarkers for the diagnosis and prognosis of cancer. Exosomal lncRNAs can also monitor the patient's response to chemotherapy while also serving as potential targets for cancer treatment. Here, we discuss the role of exosomal lncRNAs in the biology and possible future treatment of GI cancer.
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Affiliation(s)
- Mohammad Roshani
- Internal Medicine and Gastroenterology, Colorectal Research Center, Iran University of Medical Sciences, Tehran, Iran
| | - Ghazaleh Baniebrahimi
- Department of Pediatric Dentistry, School of Dentistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahboubeh Mousavi
- Department of Anatomy, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Noushid Zare
- Faculty of Pharmacy, Tehran University of Medical Science, Tehran, Iran
| | - Reza Sadeghi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Salarinia
- Department of Advanced Technologies, School of Medicine, North Khorasan University of Sciences, Bojnurd, Iran
| | - Amirhossein Sheida
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran,Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Danial Molavizadeh
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran,Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Sara Sadeghi
- School of Medicine, Kashan University of Medical Sciences, Kashan, Iran,Research Committee, Kashan University of Medical Sciences, Kashan, Iran
| | - Farzaneh Moammer
- Research Committee, School of Medicine, Guilan University of Medical Sciences, Rasht, Iran,*Correspondence: Farzaneh Moammer, ; Mohammad Reza Zolfaghari, ; Hamed Mirzaei, ;
| | - Mohammad Reza Zolfaghari
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran,*Correspondence: Farzaneh Moammer, ; Mohammad Reza Zolfaghari, ; Hamed Mirzaei, ;
| | - Hamed Mirzaei
- Center for Biochemistry and Nutrition in Metabolic Diseases, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran,*Correspondence: Farzaneh Moammer, ; Mohammad Reza Zolfaghari, ; Hamed Mirzaei, ;
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El-Sheikh NM, Abulsoud AI, Wasfey EF, Hamdy NM. Insights on the potential oncogenic impact of long non-coding RNA nicotinamide nucleotide transhydrogenase antisense RNA 1 in different cancer types; integrating pathway(s) and clinical outcome(s) association. Pathol Res Pract 2022; 240:154183. [PMID: 36327824 DOI: 10.1016/j.prp.2022.154183] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 11/05/2022]
Abstract
Long non-coding RNAs (lncRNAs) are becoming more prevalent in the cancer field arena, with functional roles in both oncogenic and onco-suppressive pathways. Despite their widespread aberrant expression in a range of human malignancies, the biological activities of the ncRNAs majority are unknown. All showed the involvement of the lncRNA nicotinamide nucleotide transhydrogenase antisense RNA 1 (NNT-AS1). Since NNT-AS1 influences cellular proliferation, invasion, migration, apoptosis, and metastasis, this lncRNA appears to be linked to deregulating the normal cellular processes driving malignancy. This was observed in breast cancer (BC), gastric cancer (GC), colorectal cancer (CRC), epithelial ovarian cancer (EOC), and hepatocellular carcinoma (HCC). The current narrative non-systematic review will discuss "the significance of lncRNAs in cancer", as well as "lncRNAs future potential application(s) as diagnostic or predictive biomarkers", therefore, comprising an opportunity as treatment target(s). The review will have a special emphasis on lncRNA NNT-AS1.
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Affiliation(s)
- Nada M El-Sheikh
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, Cairo 11785, Egypt
| | - Ahmed I Abulsoud
- Biochemistry Department, Faculty of Pharmacy, Heliopolis University, El Salam City, Cairo 11785, Egypt; Biochemistry Department, Faculty of Pharmacy (Boy's branch), Al-Azhar University, Nasr City, Cairo 11884, Egypt
| | - Eman F Wasfey
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt
| | - Nadia M Hamdy
- Biochemistry Department, Faculty of Pharmacy, Ain Shams University, Abassia, Cairo 11566, Egypt.
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38
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Porman AM, Roberts JT, Duncan ED, Chrupcala ML, Levine AA, Kennedy MA, Williams MM, Richer JK, Johnson AM. A single N6-methyladenosine site regulates lncRNA HOTAIR function in breast cancer cells. PLoS Biol 2022; 20:e3001885. [PMID: 36441764 PMCID: PMC9731500 DOI: 10.1371/journal.pbio.3001885] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 12/08/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022] Open
Abstract
N6-methyladenosine (m6A) modification of RNA regulates normal and cancer biology, but knowledge of its function on long noncoding RNAs (lncRNAs) remains limited. Here, we reveal that m6A regulates the breast cancer-associated human lncRNA HOTAIR. Mapping m6A in breast cancer cell lines, we identify multiple m6A sites on HOTAIR, with 1 single consistently methylated site (A783) that is critical for HOTAIR-driven proliferation and invasion of triple-negative breast cancer (TNBC) cells. Methylated A783 interacts with the m6A "reader" YTHDC1, promoting chromatin association of HOTAIR, proliferation and invasion of TNBC cells, and gene repression. A783U mutant HOTAIR induces a unique antitumor gene expression profile and displays loss-of-function and antimorph behaviors by impairing and, in some cases, causing opposite gene expression changes induced by wild-type (WT) HOTAIR. Our work demonstrates how modification of 1 base in an lncRNA can elicit a distinct gene regulation mechanism and drive cancer-associated phenotypes.
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Affiliation(s)
- Allison M. Porman
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
| | - Justin T. Roberts
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, Aurora, Colorado, United States of America
| | - Emily D. Duncan
- University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, Cell and Developmental Biology Department, Aurora, Colorado, United States of America
| | - Madeline L. Chrupcala
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, RNA Bioscience Initiative, Aurora, Colorado, United States of America
| | - Ariel A. Levine
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, RNA Bioscience Initiative, Aurora, Colorado, United States of America
| | - Michelle A. Kennedy
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
| | - Michelle M. Williams
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Jennifer K. Richer
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Aaron M. Johnson
- University of Colorado Anschutz Medical Campus, Biochemistry and Molecular Genetics Department, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, Molecular Biology Graduate Program, Aurora, Colorado, United States of America
- University of Colorado Anschutz Medical Campus, RNA Bioscience Initiative, Aurora, Colorado, United States of America
- * E-mail:
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Meta-Analysis of RNA-Seq Datasets Identifies Novel Players in Glioblastoma. Cancers (Basel) 2022; 14:cancers14235788. [PMID: 36497269 PMCID: PMC9737249 DOI: 10.3390/cancers14235788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/18/2022] [Accepted: 11/21/2022] [Indexed: 11/27/2022] Open
Abstract
Glioblastoma is a devastating grade IV glioma with poor prognosis. Identification of predictive molecular biomarkers of disease progression would substantially contribute to better disease management. In the current study, we performed a meta-analysis of different RNA-seq datasets to identify differentially expressed protein-coding genes (PCGs) and long non-coding RNAs (lncRNAs). This meta-analysis aimed to improve power and reproducibility of the individual studies while identifying overlapping disease-relevant pathways. We supplemented the meta-analysis with small RNA-seq on glioblastoma tissue samples to provide an overall transcriptomic view of glioblastoma. Co-expression correlation of filtered differentially expressed PCGs and lncRNAs identified a functionally relevant sub-cluster containing DANCR and SNHG6, with two novel lncRNAs and two novel PCGs. Small RNA-seq of glioblastoma tissues identified five differentially expressed microRNAs of which three interacted with the functionally relevant sub-cluster. Pathway analysis of this sub-cluster identified several glioblastoma-linked pathways, which were also previously associated with the novel cell death pathway, ferroptosis. In conclusion, the current meta-analysis strengthens evidence of an overarching involvement of ferroptosis in glioblastoma pathogenesis and also suggests some candidates for further analyses.
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40
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Kerachian MA, Azghandi M. Identification of long non-coding RNA using single nucleotide epimutation analysis: a novel gene discovery approach. Cancer Cell Int 2022; 22:337. [PMID: 36333783 PMCID: PMC9636742 DOI: 10.1186/s12935-022-02752-2] [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: 10/05/2021] [Accepted: 10/12/2022] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Long non-coding RNAs (lncRNAs) are involved in a variety of mechanisms related to tumorigenesis by functioning as oncogenes or tumor-suppressors or even harboring oncogenic and tumor-suppressing effects; representing a new class of cancer biomarkers and therapeutic targets. It is predicted that more than 35,000 ncRNA especially lncRNA are positioned at the intergenic regions of the human genome. Emerging research indicates that one of the key pathways controlling lncRNA expression and tissue specificity is epigenetic regulation. METHODS In the current article, a novel approach for lncRNA discovery based on the intergenic position of most lncRNAs and a single CpG site methylation level representing epigenetic characteristics has been suggested. RESULTS Using this method, a novel antisense lncRNA named LINC02892 presenting three transcripts without the capacity of coding a protein was found exhibiting nuclear, cytoplasmic, and exosome distributions. CONCLUSION The current discovery strategy could be applied to identify novel non-coding RNAs influenced by methylation aberrations.
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Affiliation(s)
- Mohammad Amin Kerachian
- Medical Genetics Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Medical Genetics, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran.
- Department of Chemistry and Biology, Toronto Metropolitan University, Toronto, ON, Canada.
| | - Marjan Azghandi
- Cancer Genetics Research Unit, Reza Radiotherapy and Oncology Center, Mashhad, Iran
- Department of Animal Science, Faculty of Agriculture, Ferdowsi University of Mashhad, Mashhad, Iran
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41
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Wang T, Mao P, Zhang Y, Cui B, Wang MD, Li Y, Gao K. LncRNA MYMLR promotes pituitary adenoma development by upregulating carbonyl reductase 1 via sponging miR-197-3p. Anticancer Drugs 2022; 33:1058-1068. [DOI: 10.1097/cad.0000000000001385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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Moradi F, Mohajerani F, Sadeghizadeh M. CCAT2 knockdown inhibits cell growth, and migration and promotes apoptosis through regulating the hsa-mir-145-5p/AKT3/mTOR axis in tamoxifen-resistant MCF7 cells. Life Sci 2022; 311:121183. [DOI: 10.1016/j.lfs.2022.121183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/31/2022] [Accepted: 11/08/2022] [Indexed: 11/15/2022]
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43
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Ruffo P, De Amicis F, Giardina E, Conforti FL. Long-noncoding RNAs as epigenetic regulators in neurodegenerative diseases. Neural Regen Res 2022; 18:1243-1248. [PMID: 36453400 PMCID: PMC9838156 DOI: 10.4103/1673-5374.358615] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
The growing and rapid development of high-throughput sequencing technologies have allowed a greater understanding of the mechanisms underlying gene expression regulation. Editing the epigenome and epitranscriptome directs the fate of the transcript influencing the functional outcome of each mRNA. In this context, non-coding RNAs play a decisive role in addressing the expression regulation at the gene and chromosomal levels. Long-noncoding RNAs, consisting of more than 200 nucleotides, have been shown to act as epigenetic regulators in several key molecular processes involving neurodegenerative disorders, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Long-noncoding RNAs are abundantly expressed in the central nervous system, suggesting that their deregulation could trigger neuronal degeneration through RNA modifications. The evaluation of their diagnostic significance and therapeutic potential could lead to new treatments for these diseases for which there is no cure.
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Affiliation(s)
- Paola Ruffo
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Francesca De Amicis
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Emiliano Giardina
- Genomic Medicine Laboratory UILDM, IRCCS Fondazione Santa Lucia, Rome, Italy,Department of Biomedicine & Prevention, Tor Vergata University of Rome, Rome, Italy
| | - Francesca Luisa Conforti
- Medical Genetics Laboratory, Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy,Correspondence to: Francesca Luisa Conforti, .
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44
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Qiao Y, Wang B, Yan Y, Niu L. Long noncoding RNA ST8SIA6-AS1 promotes cell proliferation and metastasis in triple-negative breast cancer by targeting miR-145-5p/CDCA3 to inactivate the p53/p21 signaling pathway. ENVIRONMENTAL TOXICOLOGY 2022; 37:2398-2411. [PMID: 35730485 DOI: 10.1002/tox.23605] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 05/08/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Triple-negative breast cancer (TNBC), the most aggressive subtype of breast cancer, always exhibits a poor prognosis due to high risk of early recurrence and distant metastasis. Long noncoding RNAs (lncRNAs) have been reported as crucial regulators in breast cancer. However, the functions and action mechanisms of lncRNA ST8SIA6-AS1 in TNBC are largely unknown. METHODS Quantitative real-time PCR and western blot assays were used to measure the expression levels of different genes and proteins. Cell proliferation ability was monitored by CCK-8, colony forming and flow cytometry assays. Wound healing and transwell assays were performed to evaluate cell migration and invasion. The regulatory mechanisms of ST8SIA6-AS1 in TNBC were confirmed by dual luciferase reporter and RIP assays. A mouse xenograft model was established to investigate the role of ST8SIA6-AS1 in TNBC tumor growth. RESULTS ST8SIA6-AS1 displayed a higher expression in TNBC cells. Silencing ST8SIA6-AS1 impaired cell proliferation, cell cycle progression, migration, and invasion in vitro, and slowed tumor growth in vivo. Mechanistically, ST8SIA6-AS1 could facilitate the expression of its target CDCA3 (cell division cycle associated protein 3) and inactivate the p53/p21 signaling by inhibiting miR-145-5p. Moreover, miR-145-5p exerted a tumor-suppressive activity by targeting CDCA3. The tumor-suppressive effects induced by ST8SIA6-AS1 knockdown were abated by the down-regulation of miR-145-5p or the up-regulation of CDCA3. CONCLUSION ST8SIA6-AS1 exerts an oncogenic role in TNBC by interacting with miR-145-5p to up-regulate CDCA3 expression and inactivate the p53/p21 signaling, highlighting ST8SIA6-AS1 as a promising molecular target to combat TNBC.
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Affiliation(s)
- Yan Qiao
- Department of Breast Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Bin Wang
- Department of Breast Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yu Yan
- Department of Breast Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ligang Niu
- Department of Breast Surgery, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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Gimbel AT, Koziarek S, Theodorou K, Schulz JF, Stanicek L, Kremer V, Ali T, Günther S, Kumar S, Jo H, Hübner N, Maegdefessel L, Dimmeler S, van Heesch S, Boon RA. Aging-regulated TUG1 is dispensable for endothelial cell function. PLoS One 2022; 17:e0265160. [PMID: 36173935 PMCID: PMC9522302 DOI: 10.1371/journal.pone.0265160] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/12/2022] [Indexed: 11/29/2022] Open
Abstract
The evolutionary conserved Taurine Upregulated Gene 1 (TUG1) is a ubiquitously expressed gene that is one of the highest expressed genes in human and rodent endothelial cells (ECs). We here show that TUG1 expression decreases significantly in aging mouse carotid artery ECs and human ECs in vitro, indicating a potential role in the aging endothelial vasculature system. We therefore investigated if, and how, TUG1 might function in aging ECs, but despite extensive phenotyping found no alterations in basal EC proliferation, apoptosis, barrier function, migration, mitochondrial function, or monocyte adhesion upon TUG1 silencing in vitro. TUG1 knockdown did slightly and significantly decrease cumulative sprout length upon vascular endothelial growth factor A stimulation in human umbilical vein endothelial cells (HUVECs), though TUG1-silenced HUVECs displayed no transcriptome-wide mRNA expression changes explaining this effect. Further, ectopic expression of the highly conserved and recently discovered 153 amino acid protein translated from certain TUG1 transcript isoforms did not alter angiogenic sprouting in vitro. Our data show that, despite a high expression and strong evolutionary conservation of both the TUG1 locus and the protein sequence it encodes, TUG1 does not seem to play a major role in basic endothelial cell function.
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Affiliation(s)
- Anna Theresa Gimbel
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
| | - Susanne Koziarek
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Kosta Theodorou
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Jana Felicitas Schulz
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
| | - Laura Stanicek
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
| | - Veerle Kremer
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
| | - Tamer Ali
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
| | - Stefan Günther
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
- Max Planck Institute for Heart and Lung Research, Bioinformatics and Deep Sequencing Platform, Bad Nauheim, Germany
| | - Sandeep Kumar
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Division of Cardiology, Emory University, Atlanta, Georgia, United States of America
| | - Hanjoong Jo
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia, United States of America
- Division of Cardiology, Emory University, Atlanta, Georgia, United States of America
| | - Norbert Hübner
- Cardiovascular and Metabolic Sciences, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Berlin, Berlin, Germany
- Charité-Universitätsmedizin, Berlin, Germany
| | - Lars Maegdefessel
- Department of Vascular and Endovascular Surgery, Technical University Munich, Munich, Germany
- German Center for Cardiovascular Research DZHK, Partner Site Munich, Munich, Germany
- Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Stefanie Dimmeler
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
| | | | - Reinier A. Boon
- Centre of Molecular Medicine, Institute of Cardiovascular Regeneration, Goethe-University, Frankfurt am Main, Germany
- DZHK (German Centre for Cardiovascular Research), Partner Site Rhine-Main, Frankfurt, Germany
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Centre, Amsterdam, Netherlands
- * E-mail:
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Interactome battling of lncRNA CCDC144NL-AS1: Its role in the emergence and ferocity of cancer and beyond. Int J Biol Macromol 2022; 222:1676-1687. [PMID: 36179873 DOI: 10.1016/j.ijbiomac.2022.09.209] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/23/2022] [Indexed: 11/05/2022]
Abstract
Long non-coding RNAs (lncRNAs) were, once, viewed as "noise" for transcription. Recently, many lncRNAs are functionally linked to several human disorders, including cancer. Coiled-Coil Domain Containing 144 N-Terminal-Like antisense1 (CCDC144NL-AS1) is a newly discovered cytosolic lncRNA. Aberrant CCDC144NL-AS1 expression was discovered in hepatocellular carcinoma (HCC), ovarian cancer (OC), gastric cancer (GC), non-small cell lung cancer (NSCLC), and osteosarcoma. CCDC144NL-AS1 could be a promising prognostic biological marker and therapeutic target for cancer. In this review, we will collect and highlight the available information about CCDC144NL-AS1 role in various cancers. Moreover, we will discuss the diagnostic and prognostic utility of CCDC144NL-AS1 as a new molecular biomarker for several human malignancies, besides its potential therapeutic importance.
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Changizian M, Nourisanami F, Hajpoor V, Parvaresh M, Bahri Z, Motovali-Bashi M. LINC00467: A key oncogenic long non-coding RNA. Clin Chim Acta 2022; 536:112-125. [PMID: 36122666 DOI: 10.1016/j.cca.2022.09.013] [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: 06/23/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 11/03/2022]
Abstract
The significance of long non-coding RNAs (lncRNAs) in the development and progression of human cancers has attracted increasing attention in recent years of investigations. Having versatile interactions and diverse functions, lncRNAs can act as oncogenes or tumor-suppressors to actively regulate cell proliferation, survival, stemness, drug resistance, invasion and metastasis. LINC00467, an oncogenic member of long intergenic non-coding RNAs, is upregulated in numerous malignancies and its high expression is often related to poor clinicopathological features. LINC00467 facilitates the progression of cancer via sponging tumor-suppressive microRNAs, inhibiting cell death cascade, modulating cell cycle controllers, and regulating signalling pathways including AKT, STAT3, NF-κB and Wnt/β-catenin. A growing number of studies have revealed that LINC00467 may serve as a novel prognostic biomarker and its inhibitory targeting has a valuable therapeutic potential to suppress the malignant phenotypes of cancer cells. In the present review, we discuss the importance of LINC00467 and provide a comprehensive collection of its functions and molecular mechanisms in a variety of cancer types.
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Affiliation(s)
- Mohammad Changizian
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJarib Street, Isfahan 81746-73441, Iran
| | - Farahdokht Nourisanami
- Department of Cell Biology, Faculty of Science, Charles University, Prague 12800, Czech Republic
| | - Vida Hajpoor
- Department of Medical Genetics, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrak-e Pajoohesh, km 15, Tehran - Karaj Highway, Tehran 14965/161, Iran
| | - Maryam Parvaresh
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJarib Street, Isfahan 81746-73441, Iran
| | - Zahra Bahri
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJarib Street, Isfahan 81746-73441, Iran
| | - Majid Motovali-Bashi
- Division of Genetics, Department of Cell and Molecular Biology and Microbiology, Faculty of Biological Science and Technology, University of Isfahan, HezarJarib Street, Isfahan 81746-73441, Iran.
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Doke M, McLaughlin JP, Cai JJ, Pendyala G, Kashanchi F, Khan MA, Samikkannu T. HIV-1 Tat and cocaine impact astrocytic energy reservoirs and epigenetic regulation by influencing the LINC01133-hsa-miR-4726-5p-NDUFA9 axis. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 29:243-258. [PMID: 35892093 PMCID: PMC9307901 DOI: 10.1016/j.omtn.2022.07.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Clinical research has proven that HIV-positive (HIV+) individuals with cocaine abuse show behavioral and neurocognitive disorders. Noncoding RNAs (ncRNAs), such as long ncRNAs (lncRNAs) and microRNAs (miRNAs), are known to regulate gene expression in the contexts of HIV infection and drug abuse. However, there are no specific lncRNA or miRNA biomarkers associated with HIV-1 Transactivator of transcription protein (Tat) and cocaine coexposure. In the central nervous system (CNS), astrocytes are the primary regulators of energy metabolism, and impairment of the astrocytic energy supply can trigger neurodegeneration. The aim of this study was to uncover the roles of lncRNAs and miRNAs in the regulation of messenger RNA (mRNA) targets affected by HIV infection and cocaine abuse. Integrative bioinformatics analysis revealed altered expression of 10 lncRNAs, 10 miRNAs, and 4 mRNA/gene targets in human primary astrocytes treated with cocaine and HIV-1 Tat. We assessed the alterations in the expression of two miRNAs, hsa-miR-2355 and hsa-miR-4726-5p; four lncRNAs, LINC01133, H19, HHIP-AS1, and NOP14-AS1; and four genes, NDUFA9, KYNU, HKDC1, and LIPG. The results revealed interactions in the LINC01133-hsa-miR-4726-5p-NDUFA9 axis that may eventually help us understand cocaine- and HIV-1 Tat-induced astrocyte dysfunction that may ultimately result in neurodegeneration.
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Affiliation(s)
- Mayur Doke
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, TX 78363, USA
| | - Jay P. McLaughlin
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, Gainesville, FL 32611, USA
| | - James J. Cai
- Veterinary Integrative Biosciences, Texas A&M University, TAMU 4458, College Station, TX 77845, USA
| | - Gurudutt Pendyala
- Department of Anesthesiology, University of Nebraska Medical Center (UNMC), Omaha, NE 68198, USA
| | - Fatah Kashanchi
- National Center for Biodefense and Infectious Disease, Laboratory of Molecular Virology, George Mason University, Manassas, VA 20110, USA
| | - Mansoor A. Khan
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, TX 78363, USA
| | - Thangavel Samikkannu
- Department of Pharmaceutical Sciences, Irma Lerma Rangel College of Pharmacy, Texas A&M University, TX 78363, USA
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49
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Hewitt SC, Wu SP, Wang T, Ray M, Brolinson M, Young SL, Spencer TE, DeCherney A, DeMayo FJ. The Estrogen Receptor α Cistrome in Human Endometrium and Epithelial Organoids. Endocrinology 2022; 163:bqac116. [PMID: 35895287 PMCID: PMC9368022 DOI: 10.1210/endocr/bqac116] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Indexed: 11/19/2022]
Abstract
Endometrial health is affected by molecular processes that underlie estrogen responses. We assessed estrogen regulation of endometrial function by integrating the estrogen receptor α (ESR1) cistromes and transcriptomes of endometrial biopsies taken from the proliferative and mid-secretory phases of the menstrual cycle together with hormonally stimulated endometrial epithelial organoids. The cycle stage-specific ESR1 binding sites were determined by chromatin immunoprecipitation and next-generation sequencing and then integrated with changes in gene expression from RNA sequencing data to infer candidate ESR1 targets in normal endometrium. Genes with ESR1 binding in whole endometrium were enriched for chromatin modification and regulation of cell proliferation. The distribution of ESR1 binding sites in organoids was more distal from gene promoters when compared to primary endometrium and was more similar to the proliferative than the mid-secretory phase ESR1 cistrome. Inferred organoid estrogen/ESR1 candidate target genes affected formation of cellular protrusions and chromatin modification. Comparison of signaling effected by candidate ESR1 target genes in endometrium vs organoids reveals enrichment of both overlapping and distinct responses. Our analysis of the ESR1 cistromes and transcriptomes from endometrium and organoids provides important resources for understanding how estrogen affects endometrial health and function.
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Affiliation(s)
- Sylvia C Hewitt
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - San-pin Wu
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Tianyuan Wang
- Integrative Bioinformatics Support Group, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Madhumita Ray
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
| | - Marja Brolinson
- Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, Maryland 20847, USA
| | - Steven L Young
- Department of Obstetrics and Gynecology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Thomas E Spencer
- Department of Obstetrics, Gynecology and Women’s Health, University of Missouri, Columbia, Missouri 65211, USA
| | - Alan DeCherney
- Program in Reproductive and Adult Endocrinology, NICHD, Bethesda, Maryland 20847, USA
| | - Francesco J DeMayo
- Pregnancy & Female Reproduction, RDBL, NIEHS, Research Triangle Park, North Carolina 27709, USA
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50
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Goenka A, Tiek DM, Song X, Iglesia RP, Lu M, Hu B, Cheng SY. The Role of Non-Coding RNAs in Glioma. Biomedicines 2022; 10:2031. [PMID: 36009578 PMCID: PMC9405925 DOI: 10.3390/biomedicines10082031] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/14/2022] [Accepted: 08/16/2022] [Indexed: 12/14/2022] Open
Abstract
For decades, research in cancer biology has been focused on the protein-coding fraction of the human genome. However, with the discovery of non-coding RNAs (ncRNAs), it has become known that these entities not only function in numerous fundamental life processes such as growth, differentiation, and development, but also play critical roles in a wide spectrum of human diseases, including cancer. Dysregulated ncRNA expression is found to affect cancer initiation, progression, and therapy resistance, through transcriptional, post-transcriptional, or epigenetic processes in the cell. In this review, we focus on the recent development and advances in ncRNA biology that are pertinent to their role in glioma tumorigenesis and therapy response. Gliomas are common, and are the most aggressive type of primary tumors, which account for ~30% of central nervous system (CNS) tumors. Of these, glioblastoma (GBM), which are grade IV tumors, are the most lethal brain tumors. Only 5% of GBM patients survive beyond five years upon diagnosis. Hence, a deeper understanding of the cellular non-coding transcriptome might help identify biomarkers and therapeutic agents for a better treatment of glioma. Here, we delve into the functional roles of microRNA (miRNA), long non-coding RNA (lncRNA), and circular RNA (circRNA) in glioma tumorigenesis, discuss the function of their extracellular counterparts, and highlight their potential as biomarkers and therapeutic agents in glioma.
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Affiliation(s)
- Anshika Goenka
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Deanna Marie Tiek
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Xiao Song
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rebeca Piatniczka Iglesia
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Minghui Lu
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Master of Biotechnology Program, Northwestern University, Evanston, IL 60208, USA
| | - Bo Hu
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Shi-Yuan Cheng
- The Ken & Ruth Davee Department of Neurology, Lou & Jean Malnati Brain Tumor Institute at Northwestern Medicine, The Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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