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Alzahrani AK, Khan A, Singla N, Hai A, Alzahrani AR, Kamal M, Asdaq SMB, Alsalman AJ, Hawaj MAA, Al Odaini LH, Dzinamarira T, Imran M. From diagnosis to therapy: The critical role of lncRNAs in hepatoblastoma. Pathol Res Pract 2024; 260:155412. [PMID: 38889493 DOI: 10.1016/j.prp.2024.155412] [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: 03/31/2024] [Revised: 06/07/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
According to findings, long non-coding RNAs (lncRNAs) serves an integral part in growth and development of a variety of human malignancies, including Hepatoblastoma (HB). HB is a rare kind of carcinoma of the liver that mostly affects kids and babies under the age of three. Its manifestations include digestive swelling, abdominal discomfort, and losing weight. This thorough investigation digs into the many roles that lncRNAs serve in HB, giving views into their varied activities as well as possible therapeutic consequences. The function of lncRNAs in HB cell proliferation, apoptosis, migratory and penetrating capacities, epithelial-mesenchymal transition, and therapy tolerance is discussed. Various lncRNA regulatory roles are investigated in depth, yielding information on their effect on essential cell processes such as angiogenesis, apoptosis, immunity, and growth. Circulating lncRNAs are currently acknowledged as potential indications for the initial stages of identification of cancer, with the ability to diagnose as well as forecast. In addition to their diagnostic utility, lncRNAs provide curative opportunities as locations and actors, contributing to the expanding landscape of cancer research. Several HB-linked lncRNAs have been demonstrated to exhibit abnormal expression and are involved in tumor-like characteristics via DNA, RNA, or protein binding or encoding short peptides. As a result, a better knowledge of lncRNA instability might bring fresh perspectives into HB etiology as well as innovative strategies for HB early diagnosis and therapy. We describe the abnormalities of lncRNA expression in HB and their tumor-suppressive or carcinogenic activities during HB carcinogenesis in this study. Furthermore, we explore lncRNAs' diagnostic and therapeutic possibilities in HB.
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Affiliation(s)
- A Khuzaim Alzahrani
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar 91431, Saudi Arabia
| | - Abida Khan
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
| | - Neelam Singla
- School of Pharmacy, Suresh Gyan Vihar University, Jagatpura, Mahal Road, Jaipur 302017, India
| | - Abdul Hai
- Department of Medical Laboratory Technology, Faculty of Applied Medical Sciences, Northern Border University, Arar 91431, Saudi Arabia
| | - Abdullah R Alzahrani
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Al-Abidiyah, P.O. Box 13578, Makkah 21955, Saudi Arabia
| | - Mehnaz Kamal
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | | | | | - Maitham Abdullah Al Hawaj
- Department of Pharmacy Practice, College of Clinical Pharmacy, King Faisal University, Al Ahsa 31982, Saudi Arabia
| | - Lulu Homeed Al Odaini
- Department of Ambulatory Care Pharmacy, King Fahad Medical City, Riyadh 12242, Saudi Arabia
| | - Tafadzwa Dzinamarira
- School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, College of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia.
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2
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Almalki WH, Almujri SS. Circular RNAs and the JAK/STAT pathway: New frontiers in cancer therapeutics. Pathol Res Pract 2024; 260:155408. [PMID: 38909403 DOI: 10.1016/j.prp.2024.155408] [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: 05/01/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/25/2024]
Abstract
Circular RNAs, known as circRNAs, have drawn more attention to cancer biology in the last few years. Novel functions of circRNAs in cancer therapy open promising prospects for personalized medicine. This review focuses on the molecular properties and potential of circRNAs as biomarkers or therapeutic targets in cancer treatment. Unique properties of circular RNAs associated with a circular form provide stability and resilience to RNA exonuclease degradation. Circular RNAs' most important characteristic is that they are involved in the JAK/STAT pathway associated with oncogenesis. Notably, their deregulation has been reported in multiple carcinomas due to involvement in JAK/STAT signaling cascade modulation. Increased knowledge about circRNAs' interaction with the JAK/STAT pathway leads to the emergence of new possibilities for targeted cancer therapy. In addition, since circRNAs demonstrate tissue-relatedness of expression, they may be a reliable biomarker for predicting and diagnosing cancer. With the development of new technologies for targeting circRNAs, novel therapeutics can be produced that offer more personalized cancer treatment options based on the nature of the patient. The present review explores the exciting prospects of circRNAs for transforming cancer treatment into personalized medicine. It describes the current understanding of circRNA biology, its relationship to tumorigenesis, and possible targeting methods.
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Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
| | - Salem Salman Almujri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Aseer 61421, Saudi Arabia
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3
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Spagnolo CC, Pepe F, Ciappina G, Nucera F, Ruggeri P, Squeri A, Speranza D, Silvestris N, Malapelle U, Santarpia M. Circulating biomarkers as predictors of response to immune checkpoint inhibitors in NSCLC: Are we on the right path? Crit Rev Oncol Hematol 2024; 197:104332. [PMID: 38580184 DOI: 10.1016/j.critrevonc.2024.104332] [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: 02/14/2024] [Accepted: 03/25/2024] [Indexed: 04/07/2024] Open
Abstract
Immune checkpoints inhibitors (ICIs) have markedly improved the therapeutic management of advanced NSCLC and, more recently, they have demonstrated efficacy also in the early-stage disease. Despite better survival outcomes with ICIs compared to standard chemotherapy, a large proportion of patients can derive limited clinical benefit from these agents. So far, few predictive biomarkers, including the programmed death-ligand 1 (PD-L1), have been introduced in clinical practice. Therefore, there is an urgent need to identify novel biomarkers to select patients for immunotherapy, to improve efficacy and avoid unnecessary toxicity. A deeper understanding of the mechanisms involved in antitumor immunity and advances in the field of liquid biopsy have led to the identification of a wide range of circulating biomarkers that could potentially predict response to immunotherapy. Herein, we provide an updated overview of these circulating biomarkers, focusing on emerging data from clinical studies and describing modern technologies used for their detection.
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Affiliation(s)
- Calogera Claudia Spagnolo
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Francesco Pepe
- Department of Public Health, University of Naples Federico II, Via S. Pansini, Naples 80131, Italy
| | - Giuliana Ciappina
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Francesco Nucera
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina 98122, Italy
| | - Paolo Ruggeri
- Respiratory Medicine Unit, Department of Biomedical Sciences, Dentistry and Morphological and Functional Imaging (BIOMORF), University of Messina, Messina 98122, Italy
| | - Andrea Squeri
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Desirèe Speranza
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Nicola Silvestris
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy
| | - Umberto Malapelle
- Department of Public Health, University of Naples Federico II, Via S. Pansini, Naples 80131, Italy
| | - Mariacarmela Santarpia
- Medical Oncology Unit, Department of Human Pathology "G. Barresi", University of Messina, Messina 98122, Italy.
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Hussain MS, Moglad E, Bansal P, Kaur H, Deorari M, Almalki WH, Kazmi I, Alzarea SI, Singh M, Kukreti N. Exploring the oncogenic and tumor-suppressive roles of Circ-ADAM9 in cancer. Pathol Res Pract 2024; 256:155257. [PMID: 38537524 DOI: 10.1016/j.prp.2024.155257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/05/2024] [Accepted: 03/08/2024] [Indexed: 04/14/2024]
Abstract
Circular RNAs (circRNAs) constitute a recently identified category of closed continuous loop RNA transcripts, serving as a subset of competing endogenous RNAs (ceRNAs) with the capacity to modulate genes by acting as microRNA sponges. In the context of cancer growth, numerous investigations have explored the potential functions of circRNAs, revealing their diverse functions either as oncogenes, promoting cancer progression, or as tumor suppressors, mitigating disease development. Among these, circRNA ADAM9 (Circ-ADAM9) is now recognized as an important player in a variety of mechanisms, both physiological and pathological, especially in cancer. The aberrant expression of Circ-ADAM9 has been observed across multiple human malignancies, implying a significant involvement in tumorigenesis. This comprehensive review aims to synthesize recent findings elucidating the function of Circ-ADAM9 in many malignancies. Additionally, the review explores the possibility of Circ-ADAM9 as a valuable biomarker, offering insights into its prognostic, diagnostic, and therapeutic implications. By summarizing the latest discoveries in this field, the review contributes to our understanding of the multifaceted contribution of Circ-ADAM9 in tumor biology and its potential applications in clinical settings.
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Affiliation(s)
- Md Sadique Hussain
- School of Pharmaceutical Sciences, Jaipur National University, Jagatpura, Jaipur, Rajasthan 302017, India
| | - Ehssan Moglad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Prince Sattam Bin Abdulaziz University, Al Kharj 11942, Saudi Arabia
| | - Pooja Bansal
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bengaluru, Karnataka 560069, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan 303012, India
| | - Harpreet Kaur
- School of Basic & Applied Sciences, Shobhit University, Gangoh, Uttar Pradesh 247341, India; Department of Health & Allied Sciences, Arka Jain University, Jamshedpur, Jharkhand 831001, India
| | - Mahamedha Deorari
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | - Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, 21589, Jeddah, Saudi Arabia.
| | - Sami I Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, 72341, Sakaka, Aljouf, Saudi Arabia
| | - Mahaveer Singh
- School of Pharmacy and Technology Management, SVKMs, NMIMS University, Shirpur campus, Maharastra 425405, India
| | - Neelima Kukreti
- School of Pharmacy, Graphic Era Hill University, Dehradun 248007, India
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5
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Almalki WH. Unraveling the role of Xist RNA in cardiovascular pathogenesis. Pathol Res Pract 2024; 253:154944. [PMID: 38006839 DOI: 10.1016/j.prp.2023.154944] [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: 10/17/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/27/2023]
Abstract
Understanding the molecular pathways behind cardiovascular illnesses is crucial due to the enormous worldwide health burden they impose. New insights into the role played by Xist (X-inactive specific transcript) RNA in the onset and progression of cardiovascular diseases have emerged from recent studies. Since its discovery, Xist RNA has been known for its role in X chromosome inactivation during embryogenesis; however, new data suggest that its function extends well beyond the control of sex chromosomes. The regulatory roles of Xist RNA are extensive, encompassing epigenetic changes, gene expression, cellular identity, and sex chromosomal inactivation. There is potential for the involvement of this complex regulatory web in a wide range of illnesses, including cardiovascular problems. Atherosclerosis, hypertrophy, and cardiac fibrosis are all conditions linked to dysregulation of Xist RNA expression. Alterations in DNA methylation and histones are two examples of epigenetic changes that Xist RNA orchestrates, leading to modifications in gene expression patterns in different cardiovascular cells. Additionally, Xist RNA has been shown to contribute to the development of cardiovascular illnesses by modulating endothelial dysfunction, inflammation, and oxidative stress responses. New treatment approaches may become feasible with a thorough understanding of the complex function of Xist RNA in cardiovascular diseases. By focusing on Xist RNA and the regulatory network with which it interacts, we may be able to slow the progression of atherosclerosis, cardiac hypertrophy, and fibrosis, thereby opening novel therapeutic options for cardiovascular diseases amenable to precision medicine. This review summarizes the current state of knowledge concerning the impact of Xist RNA in cardiovascular disorders.
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Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
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Alharbi KS. Exploring GAS5's impact on prostate cancer: Recent discoveries and emerging paradigms. Pathol Res Pract 2023; 251:154851. [PMID: 37837861 DOI: 10.1016/j.prp.2023.154851] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/24/2023] [Accepted: 10/02/2023] [Indexed: 10/16/2023]
Abstract
Novel treatment targets must be discovered to improve the results for patients with prostate cancer, which continues to be a significant worldwide health problem. Growth Arrest-Specific 5 (GAS5) is a long non-coding RNA (lncRNA) that has emerged as a promising target. GAS5 is a non-coding RNA that is a tumour suppressor in many different cancers by reducing cell proliferation and increasing apoptosis. GAS5 influences cell cycle control and apoptosis via interactions with important signalling pathways and microRNAs, as has been shown by recent studies. Furthermore, GAS5 has attracted interest for its diagnostic and prognostic potential in prostate cancer. GAS5 expression is a promising biomarker for disease classification and individualized treatment approaches because of its association with clinicopathological characteristics such as tumour stage, Gleason score, and metastatic potential. Preclinical models have revealed encouraging anticancer benefits from experimental techniques employing GAS5 overexpression or synthetic analogues, indicating the possibility of translational treatments. Whether GAS5 can be used as a diagnostic biomarker and therapeutic target might lead to more effective and individualized ways to fight prostate cancer, improving patient outcomes and quality of life. To utilize its potential for therapy and establish it as a useful addition to the clinical arsenal against this pervasive malignancy, more investigation into the complex molecular pathways of GAS5 in prostate cancer is essential. This review highlights the recent advancements and insights into the role of GAS5 in prostate cancer pathogenesis and progression.
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Affiliation(s)
- Khalid Saad Alharbi
- Department of Pharmacology and Toxicology, Unaizah College of Pharmacy, Qassim University, Qassim 51452, Saudi Arabia.
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Georgoulis V, Koumpis E, Hatzimichael E. The Role of Non-Coding RNAs in Myelodysplastic Neoplasms. Cancers (Basel) 2023; 15:4810. [PMID: 37835504 PMCID: PMC10571949 DOI: 10.3390/cancers15194810] [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: 08/27/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Myelodysplastic syndromes or neoplasms (MDS) are a heterogeneous group of myeloid clonal disorders characterized by peripheral blood cytopenias, blood and marrow cell dysplasia, and increased risk of evolution to acute myeloid leukemia (AML). Non-coding RNAs, especially microRNAs and long non-coding RNAs, serve as regulators of normal and malignant hematopoiesis and have been implicated in carcinogenesis. This review presents a comprehensive summary of the biology and role of non-coding RNAs, including the less studied circRNA, siRNA, piRNA, and snoRNA as potential prognostic and/or predictive biomarkers or therapeutic targets in MDS.
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Affiliation(s)
- Vasileios Georgoulis
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
| | - Epameinondas Koumpis
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
| | - Eleftheria Hatzimichael
- Department of Haematology, University Hospital of Ioannina, Faculty of Medicine, University of Ioannina, 45 500 Ioannina, Greece; (V.G.); (E.K.)
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19 107, USA
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Zepeda-Enríquez P, Silva-Cázares MB, López-Camarillo C. Novel Insights into Circular RNAs in Metastasis in Breast Cancer: An Update. Noncoding RNA 2023; 9:55. [PMID: 37736901 PMCID: PMC10514845 DOI: 10.3390/ncrna9050055] [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: 07/23/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/23/2023] Open
Abstract
Circular RNAs (circRNAs) are single-stranded closed non-coding RNA molecules that are aberrantly expressed and produce tumor-specific gene signatures in human cancers. They exert biological functions by acting as transcriptional regulators, microRNA sponges, and protein scaffolds, regulating the formation of protein-RNA complexes and, ultimately, regulating gene expression. Triple-negative breast cancer (TNBC) is one of the most aggressive cancers of the mammary gland and has a poor prognosis. Studies of circRNAs in TNBC are limited but have demonstrated these molecules' pivotal roles in cell proliferation, invasion, metastasis, and resistance to chemo/radiotherapy, suggesting that they could be potential prognostic biomarkers and novel therapeutic targets. Here, we reviewed the status of actual knowledge about circRNA biogenesis and functions and summarized novel findings regarding their roles in TNBC development and progression. In addition, we discussed recent data about the importance of exosomes in the transport and export of circRNAs in TNBC. Deep knowledge of circRNA functions in metastasis and therapy responses could be an invaluable guide in the identification of novel therapeutic targets for advancing the treatment of TNBC.
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Affiliation(s)
- Paola Zepeda-Enríquez
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX 03100, Mexico;
| | - Macrina B. Silva-Cázares
- Coordinación Academica Región Altiplano, Universidad Autónoma de San Luis Potosí, Matehuala 78700, Mexico;
| | - César López-Camarillo
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, CDMX 03100, Mexico;
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Almalki WH. LncRNAs and PTEN/PI3K signaling: A symphony of regulation in cancer biology. Pathol Res Pract 2023; 249:154764. [PMID: 37643526 DOI: 10.1016/j.prp.2023.154764] [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: 07/21/2023] [Revised: 08/11/2023] [Accepted: 08/12/2023] [Indexed: 08/31/2023]
Abstract
The Emergence of Long Non-coding RNAs (lncRNAs) as Key Regulators in Diverse Biological Processes: A Paradigm Shift in Understanding Gene Expression and its Impact on Cancer. The PTEN/PI3K pathway, a pivotal signaling cascade involved in cancer progression, orchestrates critical cellular functions such as survival, proliferation, and growth. In light of these advances, our investigation delves into the intricate and multifaceted interplay between lncRNAs and the PTEN/PI3K signaling pathway, unearthing previously undisclosed mechanisms that underpin cancer growth and advancement. These elusive lncRNAs exert their influence through direct targeting of the PTEN/PI3K pathway or by skillfully regulating the expression and activity of specific lncRNAs. This comprehensive review underscores the paramount significance of the interaction between lncRNAs and the PTEN/PI3K signaling pathway in cancer biology, unveiling an auspicious avenue for novel diagnostic tools and targeted therapeutic interventions. In this review, we navigate through the functional roles of specific lncRNAs in modulating PTEN/PI3K expression and activity. Additionally, we scrutinize their consequential effects on downstream components of the PTEN/PI3K pathway, unraveling the intricacies of their mutual regulation. By advancing our understanding of this complex regulatory network, this study holds the potential to revolutionize the landscape of cancer research, paving the way for tailored and efficacious treatments to combat this devastating disease.
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Affiliation(s)
- Waleed Hassan Almalki
- Department of Pharmacology, College of Pharmacy, Umm Al-Qura University, Makkah, Saudi Arabia.
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Han C, Wang J, Chen YL, Guan CP, Zhang YA, Wang MS. The role of Bacillus Calmette-Guérin administration on the risk of dementia in bladder cancer patients: a systematic review and meta-analysis. Front Aging Neurosci 2023; 15:1243588. [PMID: 37693645 PMCID: PMC10484104 DOI: 10.3389/fnagi.2023.1243588] [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: 06/21/2023] [Accepted: 07/28/2023] [Indexed: 09/12/2023] Open
Abstract
Background Previous cohort studies have found an association between Bacillus Calmette-Guérin (BCG) administration and incident dementia. In the systematic review and meta-analysis, we aimed to summarize the current evidence of the effect of BCG use on the risk of developing dementia. Methods We searched six databases until 20 May 2023 for studies investigating the risk of dementia and BCG administration. Hazard ratios (HRs) and 95% confidence intervals (95% CIs) were pooled in the meta-analysis. Meta-regression, subgroup, and sensitivity analysis were conducted as well. Results Of the 4,043 records initially evaluated, five articles were included for final analysis, with a total of 45,407 bladder cancer (BC) patients. All five studies were evaluated and rated as with high quality, and a low possibility of publication bias was indicated. A significant association between BCG and the incidence of dementia in BC patients was found in all five studies. Although a high heterogeneity (I2 = 84.5%, p < 0.001) was observed, the pooled HR was 0.55 (0.42-0.73), indicating that BCG exposure or treatment reduced the risk of incident dementia by 45%. Moreover, the sensitivity analysis showed good robustness of the overall effect with no serious publication bias. Conclusion BCG administration is associated with a significantly lower risk of developing dementia. However, an epidemiological cohort is needed to establish a relationship between BCG use and incident dementia in the normal population. Once the relationship is confirmed, more people may benefit from the association. Systematic review registration identifier: CRD42023428317.
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Affiliation(s)
- Chao Han
- Department of Outpatient, Shandong Mental Health Center, Jinan, China
| | - Juan Wang
- Department of Geriatrics, Shandong Mental Health Center, Jinan, China
| | - Ya-Li Chen
- Department of Lab Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, China
| | - Cui-Ping Guan
- Department of Lab Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, China
| | - Yan-An Zhang
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, China
- Department of Cardiovascular Surgery, Shandong Public Health Clinical Center, Shandong University, Jinan, China
| | - Mao-Shui Wang
- Department of Lab Medicine, Shandong Public Health Clinical Center, Shandong University, Jinan, China
- Shandong Key Laboratory of Infectious Respiratory Disease, Jinan, China
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Li G, Zhu X, Wang Y, Ma H, Wang Y, Wu H, Li X, Wang Y, Gao J, Chen X, Huang X, Yao Y, Hu X. Transcription-wide impact by RESCUE-induced off-target single-nucleotide variants in mammalian cells. J Mol Cell Biol 2023; 15:mjad011. [PMID: 36822625 PMCID: PMC10485882 DOI: 10.1093/jmcb/mjad011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 02/19/2023] [Accepted: 02/22/2023] [Indexed: 02/25/2023] Open
Abstract
RNA base editing is a promising tool in precise molecular therapy. Currently, there are two widely used RNA base editors, REPAIR and RESCUE. REPAIR only facilitates A-to-I conversions, while RESCUE performs both A-to-I and C-to-U conversions. Thus, RESCUE can generate twice the number of mutations compared to REPAIR. However, transcription-wide impact due to RESCUE-induced off-target single-nucleotide variants (SNVs) is not fully appreciated. Therefore, to determine the off-target effects of RESCUE-mediated editing, we employed transcription-wide sequencing on cells edited by RESCUE. The SNVs showed different off-target effects on mRNA, circRNA, lncRNA, and miRNA expression patterns and their interacting networks. Our results illustrate the transcription-wide impact of RESCUE-induced off-target SNVs and highlight the need for careful characterization of the off-target impact by this editing platform.
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Affiliation(s)
- Guo Li
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoning Zhu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yihan Wang
- National Research Institute for Family Planning, Beijing 100081, China
| | - Hongru Ma
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Yuzhe Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hanyu Wu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yiling Wang
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Jianen Gao
- National Research Institute for Family Planning, Beijing 100081, China
| | - Xuexin Chen
- Institute of Insect Sciences, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | | | - Yuan Yao
- College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou 311200, China
| | - Xiaoxiang Hu
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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12
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Usability evaluation of circRNA identification tools: Development of a heuristic-based framework and analysis. Comput Biol Med 2022; 147:105785. [PMID: 35780604 DOI: 10.1016/j.compbiomed.2022.105785] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/23/2022] [Accepted: 06/26/2022] [Indexed: 11/21/2022]
Abstract
BACKGROUND AND OBJECTIVE Circular RNAs (circRNAs) are endogenous molecules of non-coding RNA that form a covalently closed loop at the 3' and 5' ends. Recently, the role of these molecules in the regulation of gene expression and their involvement in several human pathologies has gained notoriety. The identification of circRNAs is highly dependent on computational methods for analyzing RNA sequencing data. However, bioinformatics software is known to be problematic in terms of usability. Evidence points out that tools for identifying circRNAs can have such problems, negatively impacting researchers in this field. Here we present a heuristic-based framework for evaluating the usability of command-line circRNA identification software. METHODS We used heuristics evaluation to comprehensively identify the usability issues in a sample of circRNA identification tools. RESULTS We identified 46 usability issues presented individually in four tools. Most of the issues had cosmetic or minor severity. These are unlikely to challenge experienced users but may cause inconvenience for novice users. We also identified severe issues with the potential to harm users regardless of their experience. The areas most affected were the documentation and the installability of the tools. CONCLUSIONS With the proposed framework, we formally describe, for the first time, the usability problems that can affect users in this area of circRNA research. We hope that our framework can help researchers evaluate their software's usability during development.
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Circ_0001955 Acts as a miR-646 Sponge to Promote the Proliferation, Metastasis and Angiogenesis of Hepatocellular Carcinoma. Dig Dis Sci 2022; 67:2257-2268. [PMID: 34021822 DOI: 10.1007/s10620-021-07053-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/11/2021] [Indexed: 01/10/2023]
Abstract
BACKGROUND Circular RNA (circRNA) exerts a crucial role in the progression of many cancers, including hepatocellular carcinoma (HCC). However, the function of circ_0001955 in HCC progression has been poorly studied. AIMS Elucidating the role and molecular mechanism of circ_0001955 in HCC progression. METHODS Quantitative real-time PCR was employed to detect the expression of circ_0001955 and miR-646. Cell counting kit 8 assay, Ethynyl-2-deoxyuridine assay, flow cytometry, transwell assay, and tube formation assay were conducted to measure cell proliferation, metastasis, angiogenesis and apoptosis. Dual-luciferase reporter assay and biotin-labeled RNA pull-down assay were performed to analyze the interactions among circ_0001955, miR-646 and frizzled class receptor 4 (FZD4). Moreover, animal experiments were performed to examine the influence of circ_0001955 on HCC tumor growth in vivo. RESULTS Circ_0001955 was a highly expressed circRNA in HCC tissues and cells. Circ_0001955 knockdown inhibited the proliferation, metastasis, angiogenesis, and enhanced the apoptosis of HCC cells. Meanwhile, miR-646 could be sponged by circ_0001955, and its inhibitor could reverse the negative regulation of circ_0001955 knockdown on HCC progression. Further, FZD4 was a target of miR-646, and its overexpression could invert the inhibition effect of miR-646 mimic on HCC progression. Besides, our results also indicated that circ_0001955 promoted FZD4 expression by sponging miR-646. Animal experiment results showed that circ_0001955 silencing restrained HCC tumor growth in vivo. CONCLUSION Our findings suggested that circ_0001955 might play a positive role in HCC progression via regulating the miR-646/FZD4 axis, indicating that circ_0001955 might be a potential therapeutic target for HCC.
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Wen Y, Chun Y, Lian ZQ, Yong ZW, Lan YM, Huan L, Xi CY, Juan LS, Qing ZW, Jia C, Ji ZH. circRNA‑0006896‑miR1264‑DNMT1 axis plays an important role in carotid plaque destabilization by regulating the behavior of endothelial cells in atherosclerosis. Mol Med Rep 2021; 23:311. [PMID: 33649864 PMCID: PMC7974330 DOI: 10.3892/mmr.2021.11950] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/27/2020] [Indexed: 12/14/2022] Open
Abstract
Atherosclerosis (AS) is a chronic inflammatory disease of the vascular wall with multiple causes. AS is the primary pathological basis of cardiovascular disease and stroke. Moreover, carotid plaque rupture and thrombus formation are the main causes of ischemic stroke. Therefore, understanding the formation of carotid plaques may help improve the prediction and prevention of cardiovascular and cerebrovascular events. Endothelial cell dysfunction results in re‑endothelialization and angiogenesis in atherosclerotic plaques, thus promoting plaque destabilization. The aim of the present study was to evaluate the effect of circular RNA (circRNA) molecules in serum exosomes (serum‑Exos) from patients with stable plaque atherosclerosis (SA) and unstable/vulnerable plaque atherosclerosis (UA). Specifically, the effect of circRNA on human umbilical vein endothelial cell (HUVEC) behavior and the mechanisms underlying plaque destabilization in AS were evaluated. Serum‑Exos were isolated, then identified using transmission electron microscopy, nanoparticle tracking analysis and western blotting. The serum‑Exo‑circRNA expression profile of patients with SA or UA was investigated using a circRNA array. The relationship between circRNA‑006896 in serum‑Exos and biochemical parameters of patients with SA and UA were analyzed using Spearman's correlation. In addition, HUVECs were incubated with serum‑Exos for in vitro functional assays. The present study demonstrated that circRNAs expression profiles in SA and UA serum‑Exos were significantly different, indicating a potential role for circRNAs in carotid plaque destabilization. The expression of circRNA‑0006896 was positively correlated with triglyceride, low‑density lipoprotein cholesterol (LDL‑C) and C‑reactive protein levels, and negatively correlated with albumin levels in patients with UA. However, circRNA‑0006896 expression was positively correlated with LDL‑C in patients with SA. Using bioinformatic analysis, a competing endogenous RNA (ceRNA) network was selected to study the regulatory roles of circRNA‑0006896 in serum‑Exos. Additionally, in HUVECs treated with serum‑Exos derived from patients with UA, the expression of circRNA‑0006896 in HUVECs was upregulated. This was accompanied by decreased expression of microRNA‑1264 and SOCS3, increased levels of DNMT1 and phosphorylated STAT3. HUVEC proliferation and migration were significantly increased in the UA group, compared with the mock and SA groups. This finding indicates that the circRNA‑0006896‑miR-1264‑DNMT1 axis plays an important role in carotid plaque destabilization by regulating the behavior of endothelial cells. Moreover, it suggests that circRNA‑0006896 may represent a therapeutic target for controlling JNK/STAT3 signaling in HUVECs. Thus, this study may provide insight on potential interventions against vulnerable plaque formation in patients with AS.
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Affiliation(s)
- Yan Wen
- General Practice Department, The Eighth Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Yao Chun
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Zhong Qing Lian
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Zhang Wei Yong
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Yang Mei Lan
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Liao Huan
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Chen Yi Xi
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Li Shu Juan
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Zhong Wen Qing
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Cheng Jia
- Office of Scientific Research and Development, Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
| | - Zhang Huan Ji
- Cardiovascular Department, The Eighth Affiliated Hospital of Sun Yat-Sen University, Shenzhen, Guangdong 518000, P.R. China
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Jiao K, Walsh LJ, Ivanovski S, Han P. The Emerging Regulatory Role of Circular RNAs in Periodontal Tissues and Cells. Int J Mol Sci 2021; 22:ijms22094636. [PMID: 33924932 PMCID: PMC8124626 DOI: 10.3390/ijms22094636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/24/2021] [Accepted: 04/24/2021] [Indexed: 02/07/2023] Open
Abstract
Periodontitis is a chronic complex inflammatory disease associated with a destructive host immune response to microbial dysbiosis, leading to irreversible loss of tooth-supporting tissues. Regeneration of functional periodontal soft (periodontal ligament and gingiva) and hard tissue components (cementum and alveolar bone) to replace lost tissues is the ultimate goal of periodontal treatment, but clinically predictable treatments are lacking. Similarly, the identification of biomarkers that can be used to accurately diagnose periodontitis activity is lacking. A relatively novel category of molecules found in oral tissue, circular RNAs (circRNAs) are single-stranded endogenous, long, non-coding RNA molecules, with covalently circular-closed structures without a 5' cap and a 3' tail via non-classic backsplicing. Emerging research indicates that circRNAs are tissue and disease-specific expressed and have crucial regulatory functions in various diseases. CircRNAs can function as microRNA or RNA binding sites or can regulate mRNA. In this review, we explore the biogenesis and function of circRNAs in the context of the emerging role of circRNAs in periodontitis pathogenesis and the differentiation of periodontal cells. CircMAP3K11, circCDK8, circCDR1as, circ_0062491, and circ_0095812 are associated with pathological periodontitis tissues. Furthermore, circRNAs are expressed in periodontal cells in a cell-specific manner. They can function as microRNA sponges and can form circRNA-miRNA-mRNA networks during osteogenic differentiation for periodontal-tissue (or dental pulp)-derived progenitor cells.
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Affiliation(s)
- Kexin Jiao
- Epigenetics Nanodiagnostic and Therapeutic Group, Center for Oral-Facial Regeneration, Rehabilitation and Reconstruction (COR3), School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia;
| | - Laurence J. Walsh
- School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia;
| | - Sašo Ivanovski
- Epigenetics Nanodiagnostic and Therapeutic Group, Center for Oral-Facial Regeneration, Rehabilitation and Reconstruction (COR3), School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia;
- School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia;
- Correspondence: (S.I.); (P.H.)
| | - Pingping Han
- Epigenetics Nanodiagnostic and Therapeutic Group, Center for Oral-Facial Regeneration, Rehabilitation and Reconstruction (COR3), School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia;
- School of Dentistry, Faculty of Health and Behavioural Sciences, The University of Queensland, Brisbane, QLD 4006, Australia;
- Correspondence: (S.I.); (P.H.)
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Zhang Z, Sui Y, Luan L, Li B, Qin C. Retracted: A Novel CircRNA Circ_0095424 Regulates Proliferation, Metastasis, and Apoptosis of Osteosarcoma Cells Via the PI3K/AKT Signaling Pathway Through Targeting the miR-1238/ HMGB1 Axis. Cancer Biother Radiopharm 2020; 35:e802-e813. [PMID: 32822247 DOI: 10.1089/cbr.2020.3563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Cancer Biotherapy and Radiopharmaceuticals is officially retracting the article entitled, A Novel CircRNA Circ_0095424 Regulates Proliferation, Metastasis, and Apoptosis of Osteosarcoma Cells Via the PI3K/AKT Signaling Pathway Through Targeting the miR-1238/HMGB1 Axis by Zhang et al., (Cancer Biother Radiopharm epub 19 Aug 2020; DOI: 10.1089/cbr.2020.3563), due to manipulated images appearing in the published paper. The Editor of the journal received an email on August 31, 2020 from the corresponding author of the article, Dr. Chuan Qin, indicating that, ''due to our negligence in organizing the pictures, the protein pictures are repeatedly placed in Figure 7G PI3K. For this, we express our sincerest apologies. We need to [issue] an [erratum] on this issue. We have replaced the protein picture of Figure 7G with the correct picture.'' However, one of the attachments submitted with the request appeared to be the original version of Figure 7 from the accepted manuscript. A second attachment appeared to be the data from three replicates to be used (by the journal) to construct a revised version of Figure 7. The Editor, in turn, informed the authors that it was not at the journal's discretion to create a new image for them, and asked the authors to create the revised figure and supply it to the publisher. Below is the response from Dr. Qin, dated September 2, 2020. "In fact, our team's Western blot experiment commissioned a third-party company for testing. At present, some peers have found that the company has forged experimental reports. We believe that the authenticity of the data provided by the company is problematic. After contacting the company, they were unable to provide the original images. In view of the problems in this manuscript, all the authors discussed and agreed to withdraw the manuscript." As the entirety of the situation is unacceptable, the Editor officially retracts the article based on the "forged experimental reports" and the questionable validity of the data provided. The Editor and Publisher of Cancer Biotherapy and Radiopharmaceuticals is dedicated to preserving the integrity of the scientific literature and the community it serves.
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Affiliation(s)
- Zhiguo Zhang
- Department of Orthopedics, Rizhao City Traditional Chinese Medicine Hospital, Rizhao, China
| | - Yutong Sui
- State Key Laboratory for Molecular Biology of Special Economic Animals, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Liyi Luan
- Department of Orthopedic, The People's Hospital of Gaotang, Liaocheng, China
| | - Bo Li
- Department of Joint Surgery, No. 1 Hospital of Jilin University, Changchun, China
| | - Chuan Qin
- Department of Orthopedics, The No. 4 Hospital of Jinan, Jinan, China
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Zhang G, Deng Y, Liu Q, Ye B, Dai Z, Chen Y, Dai X. Identifying Circular RNA and Predicting Its Regulatory Interactions by Machine Learning. Front Genet 2020; 11:655. [PMID: 32849764 PMCID: PMC7396586 DOI: 10.3389/fgene.2020.00655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 05/29/2020] [Indexed: 12/11/2022] Open
Abstract
Circular RNA (circRNA) is a closed long non-coding RNA (lncRNA) formed by covalently closed loops through back-splicing. Emerging evidence indicates that circRNA can influence cellular physiology through various molecular mechanisms. Thus, accurate circRNA identification and prediction of its regulatory information are critical for understanding its biogenesis. Although several computational tools based on machine learning have been proposed for circRNA identification, the prediction accuracy remains to be improved. Here, first we present circLGB, a machine learning-based framework to discriminate circRNA from other lncRNAs. circLGB integrates commonly used sequence-derived features and three new features containing adenosine to inosine (A-to-I) deamination, A-to-I density and the internal ribosome entry site. circLGB categorizes circRNAs by utilizing a LightGBM classifier with feature selection. Second, we introduce circMRT, an ensemble machine learning framework to systematically predict the regulatory information for circRNA, including their interactions with microRNA, the RNA binding protein, and transcriptional regulation. Feature sets including sequence-based features, graph features, genome context, and regulatory information features were modeled in circMRT. Experiments on public and our constructed datasets show that the proposed algorithms outperform the available state-of-the-art methods. circLGB is available at http://www.circlgb.com. Source codes are available at https://github.com/Peppags/circLGB-circMRT.
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Affiliation(s)
- Guishan Zhang
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Yiyun Deng
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Qingyu Liu
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China
| | - Bingxu Ye
- Key Laboratory of Digital Signal and Image Processing of Guangdong Provincial, College of Engineering, Shantou University, Shantou, China
| | - Zhiming Dai
- School of Data and Computer Science, Sun Yat-sen University, Guangzhou, China.,Guangdong Province Key Laboratory of Big Data Analysis and Processing, Sun Yat-sen University, Guangzhou, China
| | - Yaowen Chen
- Key Laboratory of Digital Signal and Image Processing of Guangdong Provincial, College of Engineering, Shantou University, Shantou, China
| | - Xianhua Dai
- School of Electronics and Information Technology, Sun Yat-sen University, Guangzhou, China.,Southern Marine Science and Engineering Guangdong Laboratory, Zhuhai, China
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