1
|
Zemek R, Albrecht LM, Johnston S, Leddy J, Ledoux AA, Reed N, Silverberg N, Yeates K, Lamoureux M, Anderson C, Barrowman N, Beauchamp MH, Chen K, Chintoh A, Cortel-LeBlanc A, Cortel-LeBlanc M, Corwin DJ, Cowle S, Dalton K, Dawson J, Dodd A, El Emam K, Emery C, Fox E, Fuselli P, Gagnon IJ, Giza C, Hicks S, Howell DR, Kutcher SA, Lalonde C, Mannix RC, Master CL, Mayer AR, Osmond MH, Robillard R, Schneider KJ, Tanuseputro P, Terekhov I, Webster R, Wellington CL. TRANSCENDENT (Transforming Research by Assessing Neuroinformatics across the Spectrum of Concussion by Embedding iNterdisciplinary Data-collection to Enable Novel Treatments): protocol for a prospective observational cohort study of concussion patients with embedded comparative effectiveness research within a network of learning health system concussion clinics in Canada. BMJ Open 2025; 15:e095292. [PMID: 40262965 PMCID: PMC12015710 DOI: 10.1136/bmjopen-2024-095292] [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: 10/18/2024] [Accepted: 04/10/2025] [Indexed: 04/24/2025] Open
Abstract
INTRODUCTION Concussion affects over 400 000 Canadians annually, with a range of causes and impacts on health-related quality of life. Research to date has disproportionately focused on athletes, military personnel and level I trauma centre patients, and may not be applicable to the broader community. The TRANSCENDENT Concussion Research Program aims to address patient- and clinician-identified research priorities, through the integration of clinical data from patients of all ages and injury mechanisms, patient-reported outcomes and objective biomarkers across factors of intersectionality. Seeking guidance from our Community Advisory Committee will ensure meaningful patient partnership and research findings that are relevant to the wider concussion community. METHODS AND ANALYSIS This prospective observational cohort study will recruit 5500 participants over 5 years from three 360 Concussion Care clinic locations across Ontario, Canada, with a subset of participants enrolling in specific objective assessments including testing of autonomic function, exercise tolerance, vision, advanced neuroimaging and fluid biomarkers. Analysis will be predicated on pre-specified research questions, and data shared with the Ontario Brain Institute's Brain-CODE database. This work will represent one of the largest concussion databases to date, and by sharing it, we will advance the field of concussion and prevent siloing within brain health research. ETHICS AND DISSEMINATION This study was approved by the Children's Hospital of Eastern Ontario Research Ethics Board and preregistered on OSF (25 June 2024); https://doi.org/10.17605/OSF.IO/HYDZC. Dissemination of findings will be multifaceted, including conference presentations, peer-reviewed publications and sharing of adapted materials (eg, videos, infographics, plain language summaries) with community groups and key knowledge users.
Collapse
Affiliation(s)
- Roger Zemek
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Lisa M Albrecht
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Sharon Johnston
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Institut du Savoir Montfort, Hôpital Montfort, Ottawa, Ontario, Canada
| | - John Leddy
- Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Andrée-Anne Ledoux
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Nick Reed
- Rehabilitation Sciences Institute, University of Toronto, Toronto, Ontario, Canada
| | - Noah Silverberg
- Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Keith Yeates
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Monica Lamoureux
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | | | - Nicholas Barrowman
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Miriam H Beauchamp
- Psychology, University of Montreal, Montreal, Quebec, Canada
- Azrieli Research Center, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Kitty Chen
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Araba Chintoh
- Psychiatry, University of Calgary, Calgary, Alberta, Canada
| | - Achelle Cortel-LeBlanc
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Institut du Savoir Montfort, Hôpital Montfort, Ottawa, Ontario, Canada
| | - Miguel Cortel-LeBlanc
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
- Institut du Savoir Montfort, Hôpital Montfort, Ottawa, Ontario, Canada
| | - Daniel J Corwin
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Kristine Dalton
- School of Optometry & Vision Science, University of Waterloo, Waterloo, Ontario, Canada
| | - Jennifer Dawson
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Andrew Dodd
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Khaled El Emam
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Carolyn Emery
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Erin Fox
- IKT/Patient Engagement, Ottawa, Ontario, Canada
| | | | - Isabelle J Gagnon
- School of Physical and Occupational Therapy, McGill University, Montreal, Quebec, Canada
- Child Health and Human Development Program, Research Institute of the McGill University Health Center, Montreal, Quebec, Canada
| | - Christopher Giza
- Pediatrics, Neurosurgery, UCLA Brain Injury Research Center, Los Angeles, California, USA
- Steve Tisch BrainSPORT Program, UCLA, Los Angeles, California, USA
| | - Steven Hicks
- Penn State College of Medicine, Hershey, Pennsylvania, USA
| | - David R Howell
- University of Colorado Denver School of Medicine, Aurora, Colorado, USA
- Sports Medicine Center, Children's Hospital Colorado, Aurora, Colorado, USA
| | | | - Carlos Lalonde
- Homewood Health, Guelph, Ontario, Canada
- Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, Ontario, Canada
| | - Rebekah C Mannix
- Pediatrics, Boston Children's Hospital, Boston, Massachusetts, USA
- Harvard Medical School, Boston, Massachusetts, USA
| | - Christina L Master
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Andrew R Mayer
- University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
- The Mind Research Network/Lovelace Biomedical and Environmental Research Institute, Albuquerque, New Mexico, USA
| | - Martin H Osmond
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
- Faculty of Medicine, University of Ottawa, Ottawa, Ontario, Canada
| | - Rebecca Robillard
- Sleep Research Unit, Institute for Mental Health Research, Ottawa, Ontario, Canada
- School of Psychology, University of Ottawa, Ottawa, Ontario, Canada
| | - Kathryn J Schneider
- Alberta Children's Hospital Research Institute, Calgary, Alberta, Canada
- Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | | | - Ivan Terekhov
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Richard Webster
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, Ontario, Canada
| | - Cheryl Lea Wellington
- Faculty of Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| |
Collapse
|
2
|
Tataranu LG. A Nexus of Biomolecular Complexities in Pituitary Neuroendocrine Tumors: Insights into Key Molecular Drivers. Biomedicines 2025; 13:968. [PMID: 40299639 PMCID: PMC12024600 DOI: 10.3390/biomedicines13040968] [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: 02/15/2025] [Revised: 03/10/2025] [Accepted: 03/17/2025] [Indexed: 05/01/2025] Open
Abstract
Approximately 90% of the lesions of hypophyseal origins are represented by pituitary neuroendocrine tumors, which further account for up to 22.5% of the intracranial tumors in the adult population. Although the intricacy of this pathology is yet to be fully understood on a biomolecular level, it is well known that these lesions develop within a microenvironment that supports their evolution and existence. The role of the tumoral microenvironment in pituitary lesions is pivotal, mainly due to this gland's distinct anatomical, histological, and physiological structure and function. Each component of the tumoral microenvironment is specifically involved in tumorigenesis, angiogenesis, tumoral growth, progression, and dissemination. By recognizing and understanding how these elements are involved in such processes, targeted treatments can emerge, and better future management of pituitary lesions can be provided. This article aims to summarize the role of each component of the tumoral microenvironment in pituitary lesions while assessing their association with biomolecular mechanisms.
Collapse
Affiliation(s)
- Ligia Gabriela Tataranu
- Department of Neurosurgery, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
- Department of Neurosurgery, Bagdasar-Arseni Emergency Clinical Hospital, 041915 Bucharest, Romania
| |
Collapse
|
3
|
Saha P, Skrodzki D, Aditya T, Moitra P, Alafeef M, Dighe K, Molinaro M, Hicks SD, Pan D. Tailored Anti-miR Decorated Covalent Organic Framework Enables Electrochemical Detection of Salivary miRNAs for Mild Traumatic Brain Injury. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2025; 21:e2412107. [PMID: 39961046 PMCID: PMC11983262 DOI: 10.1002/smll.202412107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2024] [Indexed: 04/11/2025]
Abstract
MicroRNAs (miRNAs) play pivotal role as biomarkers for various diseases, with salivary miRNAs offering a non-invasive diagnostic tool. For mild traumatic brain injury (mTBI), salivary miRNAs like miR-let7a, miR-21, and miR-30e show promise for early detection of subtle injuries lacking reliable indicators. To advance the detection of mTBI-related salivary miRNAs, this study integrates anti-miRNA and miRNA hybridization-based sensing with the development of a nanoscale covalent-organic framework (COF) platform. COFs, with their highly customizable structures, large surface area, and biocompatibility, serve as a versatile foundation for biosensing applications. Here, post-synthetic modification (PSM) of COFs is introduced for essential covalent conjugation of streptavidin for further immobilization of methylene blue-labeled and biotinylated Anti-miRNAs. Furthermore, the layer-by-layer assembly of conductive polymers enhanced the biosensor's electrical performance, enabling ultrasensitive and multiplexed detection of salivary miRNAs. Validated with samples from mixed martial arts participants and confirmed by polymerase chain reaction (PCR), this COF-based platform demonstrates robust accuracy and reliability. By combining COF functionalization with advanced electrode design, it offers a powerful, non-invasive solution for early mTBI detection and broader biomedical applications.
Collapse
Affiliation(s)
- Pranay Saha
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - David Skrodzki
- Department of Materials Science and EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Teresa Aditya
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Parikshit Moitra
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Present address:
Department of Chemical SciencesIISER BerhampurBerhampurOdisha760010India
| | - Maha Alafeef
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Biomedical Engineering DepartmentJordan University of Science and TechnologyIrbid22110Jordan
| | - Ketan Dighe
- Department of Biomedical EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Matthew Molinaro
- Department of Engineering Science and MechanicsThe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Steven D. Hicks
- Department of PediatricsPenn State Health Children's HospitalHersheyPA17033USA
| | - Dipanjan Pan
- Department of Nuclear EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Department of Materials Science and EngineeringThe Pennsylvania State UniversityUniversity ParkPA16802USA
- Huck Institutes of the Life Sciences101 Huck Life Sciences BuildingUniversity ParkPA16802USA
- Center for Infectious Disease DynamicsThe Pennsylvania State UniversityUniversity ParkPA16802USA
| |
Collapse
|
4
|
Hatzimanolis O, Sykes AM, Cristino AS. Circular RNAs in neurological conditions - computational identification, functional validation, and potential clinical applications. Mol Psychiatry 2025; 30:1652-1675. [PMID: 39966624 PMCID: PMC11919710 DOI: 10.1038/s41380-025-02925-1] [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: 07/19/2024] [Revised: 01/11/2025] [Accepted: 02/10/2025] [Indexed: 02/20/2025]
Abstract
Non-coding RNAs (ncRNAs) have gained significant attention in recent years due to advancements in biotechnology, particularly high-throughput total RNA sequencing. These developments have led to new understandings of non-coding biology, revealing that approximately 80% of non-coding regions in the genome possesses biochemical functionality. Among ncRNAs, circular RNAs (circRNAs), first identified in 1976, have emerged as a prominent research field. CircRNAs are abundant in most human cell types, evolutionary conserved, highly stable, and formed by back-splicing events which generate covalently closed ends. Notably, circRNAs exhibit high expression levels in neural tissue and perform diverse biochemical functions, including acting as molecular sponges for microRNAs, interacting with RNA-binding proteins to regulate their availability and activity, modulating transcription and splicing, and even translating into functional peptides in some cases. Recent advancements in computational and experimental methods have enhanced our ability to identify and validate circRNAs, providing valuable insights into their biological roles. This review focuses on recent developments in circRNA research as they related to neuropsychiatric and neurodegenerative conditions. We also explore their potential applications in clinical diagnostics, therapeutics, and future research directions. CircRNAs remain a relatively underexplored area of non-coding biology, particularly in the context of neurological disorders. However, emerging evidence supports their role as critical players in the etiology and molecular mechanisms of conditions such as schizophrenia, bipolar disorder, major depressive disorder, Alzheimer's disease, and Parkinson's disease. These findings suggest that circRNAs may provide a novel framework contributing to the molecular dysfunctions underpinning these complex neurological conditions.
Collapse
Affiliation(s)
- Oak Hatzimanolis
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Alex M Sykes
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, QLD, Australia
| | - Alexandre S Cristino
- Institute for Biomedicine and Glycomics, Griffith University, Brisbane, QLD, Australia.
| |
Collapse
|
5
|
Wang J, Zhang C, Zhang Y, Guo J, Xie C, Liu Y, Chen L, Ma L. Circular RNA in liver cancer research: biogenesis, functions, and roles. Front Oncol 2025; 15:1523061. [PMID: 40224186 PMCID: PMC11985449 DOI: 10.3389/fonc.2025.1523061] [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: 11/07/2024] [Accepted: 03/11/2025] [Indexed: 04/15/2025] Open
Abstract
Liver cancer, characterized by its insidious nature, aggressive invasiveness, and propensity for metastasis, has witnessed a sustained increase in both incidence and mortality rates in recent years, underscoring the urgent need for innovative diagnostic and therapeutic approaches. Emerging research indicates that CircRNAs (circular RNAs) are abundantly and stably present within cells, with their expression levels closely associated with the progression of various malignancies, including hepatocellular carcinoma. In the context of liver cancer progression, circRNAs exhibit promising potential as highly sensitive diagnostic biomarkers, offering novel avenues for early detection, and also function as pivotal regulatory factors within the carcinogenic process. This study endeavors to elucidate the biogenesis, functional roles, and underlying mechanisms of circRNAs in hepatocellular carcinoma, thereby providing a fresh perspective on the pathogenesis of liver cancer and laying a robust foundation for the development of more precise and effective early diagnostic tools and therapeutic strategies.
Collapse
Affiliation(s)
- Jiayi Wang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Congcong Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Yinghui Zhang
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Jiaojiao Guo
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Chenyu Xie
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Yulu Liu
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| | - Lidian Chen
- School of Rehabilitation Medicine, Henan University of Traditional Chinese Medicine, Zhengzhou, Henan, China
| | - Liangliang Ma
- The First Affiliated Hospital of Henan University of Chinese Medicine, Zhengzhou, Henan, China
| |
Collapse
|
6
|
Das S, Basak S, Sarkar S. Decoding Salivary ncRNAomes as Novel Biomarkers for Oral Cancer Detection and Prognosis. Noncoding RNA 2025; 11:28. [PMID: 40126352 PMCID: PMC11932315 DOI: 10.3390/ncrna11020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2024] [Revised: 01/16/2025] [Accepted: 03/07/2025] [Indexed: 03/25/2025] Open
Abstract
Oral cancer (OC) ranks among the most prevalent head and neck cancers, becoming the eleventh most common cancer worldwide with ~350,000 new cases and 177,000 fatalities annually. The rising trend in the occurrence of OC among young individuals and women who do not have tobacco habits is escalating rapidly. Surgical procedures, radiation therapy, and chemotherapy are among the most prevalent treatment options for oral cancer. To achieve better therapy and an early detection of the cancer, it is essential to understand the disease's etiology at the molecular level. Saliva, the most prevalent body fluid obtained non-invasively, holds a collection of distinct non-coding RNA pools (ncRNAomes) that can be assessed as biomarkers for identifying oral cancer. Non-coding signatures, which are transcripts lacking a protein-coding function, have been identified as significant in the progression of various cancers, including oral cancer. This review aims to examine the role of various salivary ncRNAs (microRNA, circular RNA, and lncRNA) associated with disease progression and to explore their functions as potential biomarkers for early disease identification to ensure better survival outcomes for oral cancer patients.
Collapse
Affiliation(s)
- Subhadeep Das
- Department of Biochemistry, Purdue University, BCHM A343, 175 S. University Street, West Lafayette, IN 47907-2063, USA
- Purdue University Institute for Cancer Research, Purdue University, Hansen Life Sciences Research Building, Room 141, 201 S. University Street, West Lafayette, IN 47907-2064, USA
| | - Sampad Basak
- Gujarat Biotechnology University, Gujarat International Finance Tec-City, Gandhinagar 382355, Gujarat, India;
| | - Soumyadev Sarkar
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Arizona State University, Tempe, AZ 85281, USA
| |
Collapse
|
7
|
Owecki W, Wojtowicz K, Nijakowski K. Salivary Extracellular Vesicles in Detection of Cancers Other than Head and Neck: A Systematic Review. Cells 2025; 14:411. [PMID: 40136660 PMCID: PMC11941535 DOI: 10.3390/cells14060411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2025] [Revised: 03/06/2025] [Accepted: 03/10/2025] [Indexed: 03/27/2025] Open
Abstract
Cancer is one of the leading causes of death worldwide. Evidence indicates that extracellular vesicles are involved in cancer development and may be used as promising biomarkers in cancer detection. Concomitantly, saliva constitutes a non-invasive and inexpensive source of biomarkers. This systematic review investigates the use of salivary extracellular vesicles in detecting cancers located outside of the head and neck. PubMed, Web of Science, Scopus, and Embase were thoroughly searched from database inception to 16 July 2024. Data from sixteen eligible studies were analyzed, including glioblastoma, lung, esophageal, gastric, prostate, hepatocellular, breast, and pancreatobiliary tract cancers. The findings highlight strong diagnostic potential for lung and esophageal cancers, where specific exosomal RNAs and proteins demonstrated high accuracy in distinguishing cancer patients from healthy individuals. Additionally, biomarkers in glioblastoma showed prognostic value, while those in hepatocellular and pancreatobiliary cancers exhibited potential for early detection. However, gastric and prostate cancer biomarkers showed limited reliability, and breast cancer biomarkers require further validation. In conclusion, salivary extracellular vesicles present potential in non-invasive detection across multiple cancer types; however, their diagnostic power needs further research, including standardization and large-scale validation.
Collapse
Affiliation(s)
- Wojciech Owecki
- Student’s Scientific Group in Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland;
- The Student Scientific Society, Poznan University of Medical Sciences, 60-806 Poznan, Poland
| | - Karolina Wojtowicz
- Department of Histology and Embryology, Poznan University of Medical Sciences, 60-781 Poznan, Poland;
| | - Kacper Nijakowski
- Department of Conservative Dentistry and Endodontics, Poznan University of Medical Sciences, 60-812 Poznan, Poland
| |
Collapse
|
8
|
Busato F, Ursuegui S, Deleuze JF, Tost J. Multiplex digital PCR for the simultaneous quantification of a miRNA panel. Anal Chim Acta 2025; 1335:343440. [PMID: 39643296 DOI: 10.1016/j.aca.2024.343440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2024] [Revised: 11/07/2024] [Accepted: 11/18/2024] [Indexed: 12/09/2024]
Abstract
BACKGROUND microRNAs (miRNAs) are small non-coding RNAs regulating gene expression. They have attracted significant interest as biomarkers for early diagnosis, prediction and monitoring of treatment response in many diseases. As individual miRNAs often lack the required sensitivity and specificity, miRNA signatures are developed for clinical applications. Digital PCR (dPCR) is a sensitive fluorescent-based quantification method, that can be used to detect the expression of miRNAs in patient samples. Our study presents the first proof-of-concept of a multiplexed dPCR assay for the simultaneous analysis and quantification of multiple miRNAs. RESULTS After reverse transcription (RT) using a pool of miRNA-specific stem-loop primers, dPCR was performed with a universal reverse primer and miRNA-specific forward primers along with fluorescently-labelled hydrolysis probes. Multiple experimental parameters were evaluated and strategies for modulating the observed signals were devised. The optimised assay was applied to the analysis of miRNAs from cell lines and biological samples. Although absolute quantification was lost, due to the reverse transcription step, quantification was linear for the dilution series and results were highly reproducible for independent dPCR and RT reactions. Our results confirmed the high sensitivity of dPCR for patient samples. CONCLUSIONS We demonstrate the feasibility and reliability of multiplexed detection and quantification of miRNAs by dPCR that can be applied in a clinical setting to evaluate miRNA signatures.
Collapse
Affiliation(s)
- Florence Busato
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | - Sylvain Ursuegui
- Stilla Technologies, Biopark 1, Mail du Professeur Georges Mathé, 94800, Villejuif, France
| | - Jean-François Deleuze
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France
| | - Jorg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie François Jacob, Université Paris-Saclay, Evry, France.
| |
Collapse
|
9
|
Fan Z, Yuan X, Yuan Y. Circular RNAs in coronary heart disease: From molecular mechanism to promising clinical application (Review). Int J Mol Med 2025; 55:11. [PMID: 39513584 PMCID: PMC11573316 DOI: 10.3892/ijmm.2024.5452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Accepted: 10/15/2024] [Indexed: 11/15/2024] Open
Abstract
Coronary heart disease (CHD) remains a leading cause of morbidity and mortality worldwide, posing a substantial public health burden. Despite advancements in treatment, the complex etiology of CHD necessitates ongoing exploration of novel diagnostic markers and therapeutic targets. Circular RNAs (circRNAs), a distinct class of non‑coding RNAs with a covalently closed loop structure, have emerged as significant regulators in various diseases, including CHD. Their high stability, tissue‑specific expression and evolutionary conservation underscore their potential as biomarkers and therapeutic agents in CHD. This review discusses the current knowledge on circRNAs in the context of CHD and explores the molecular mechanisms by which circRNAs influence the pathophysiology of CHD, including cardiomyocyte death, endothelial injury, vascular dysfunction and inflammation. It also summarizes the emerging evidence highlighting the differential expression of circRNAs in patients with CHD and their potential utilities as non‑invasive diagnostic and prognostic biomarkers and therapeutic targets for this disease.
Collapse
Affiliation(s)
- Zengguang Fan
- Department of Cardiology, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, Jiangxi 330006, P.R. China
| | - Xingxing Yuan
- Department of Gastroenterology, Heilongjiang Academy of Traditional Chinese Medicine, Harbin, Heilongjiang 150006, P.R. China
| | - Ye Yuan
- Department of Cardiology, Affiliated Hospital of Jiangxi University of Chinese Medicine, Nanchang, Jiangxi 330006, P.R. China
| |
Collapse
|
10
|
Amolegbe SM, Johnston NC, Ambrosi A, Ganguly A, Howcroft TK, Kuo LS, Labosky PA, Rudnicki DD, Satterlee JS, Tagle DA, Happel C. Extracellular RNA communication: A decade of NIH common fund support illuminates exRNA biology. J Extracell Vesicles 2025; 14:e70016. [PMID: 39815775 PMCID: PMC11735951 DOI: 10.1002/jev2.70016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2024] [Revised: 11/06/2024] [Accepted: 11/19/2024] [Indexed: 01/18/2025] Open
Abstract
The discovery that extracellular RNAs (exRNA) can act as endocrine signalling molecules established a novel paradigm in intercellular communication. ExRNAs can be transported, both locally and systemically in virtually all body fluids. In association with an array of carrier vehicles of varying complexity, exRNA can alter target cell phenotype. This highlights the important role secreted exRNAs have in regulating human health and disease. The NIH Common Fund exRNA Communication program was established in 2012 to accelerate and catalyze progress in the exRNA biology field. The program addressed both exRNA and exRNA carriers, and served to generate foundational knowledge for the field from basic exRNA biology to future potential clinical applications as biomarkers and therapeutics. To address scientific challenges, the exRNA Communication program developed novel tools and technologies to isolate exRNA carriers and analyze their cargo. Here, we discuss the outcomes of the NIH Common Fund exRNA Communication program, as well as the evolution of exRNA as a scientific field through the analysis of scientific publications and NIH funding. ExRNA and associated carriers have potential clinical use as biomarkers, diagnostics, and therapeutics. Recent translational applications include exRNA-related technologies repurposed as novel diagnostics in response to the COVID-19 pandemic, the clinical use of extracellular vesicle-based biomarker assays, and exRNA carriers as drug delivery platforms. This comprehensive landscape analysis illustrates how discoveries and innovations in exRNA biology are being translated both into the commercial market and the clinic. Analysis of program outcomes and NIH funding trends demonstrate the impact of this NIH Common Fund program.
Collapse
Affiliation(s)
- Sara M. Amolegbe
- Office of the DirectorNational Institutes of HealthBethesdaMarylandUSA
| | - Nicolas C. Johnston
- National Institute on Drug AbuseNational Institutes of HealthBethesdaMarylandUSA
| | - Angela Ambrosi
- Office of the DirectorNational Institutes of HealthBethesdaMarylandUSA
| | - Aniruddha Ganguly
- National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - T. Kevin Howcroft
- National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | - Lillian S. Kuo
- National Cancer InstituteNational Institutes of HealthBethesdaMarylandUSA
| | | | - Dobrila D. Rudnicki
- National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - John S. Satterlee
- National Institute on Drug AbuseNational Institutes of HealthBethesdaMarylandUSA
| | - Danilo A. Tagle
- National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| | - Christine Happel
- National Center for Advancing Translational SciencesNational Institutes of HealthBethesdaMarylandUSA
| |
Collapse
|
11
|
Boulestreau J, Molina L, Ouedraogo A, Laramy L, Grich I, Van TNN, Molina F, Kahli M. Salivary extracellular vesicles isolation methods impact the robustness of downstream biomarkers detection. Sci Rep 2024; 14:31233. [PMID: 39732788 DOI: 10.1038/s41598-024-82488-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 12/05/2024] [Indexed: 12/30/2024] Open
Abstract
Extracellular vesicles (EVs), crucial mediators in cell-to-cell communication, are implicated in both homeostatic and pathological processes. Their detectability in easily accessible peripheral fluids like saliva positions them as promising candidates for non-invasive biomarker discovery. However, the lack of standardized methods for salivary EVs isolation greatly limits our ability to study them. Therefore, we rigorously compared salivary EVs isolated using two scalable techniques-co-precipitation and immuno-affinity-against the long-established but labor-intensive ultracentrifugation method. Employing Cryo-Electron Microscopy (Cryo-EM), Nanoparticle Tracking Analysis, Western blots (WB), and proteomics, we identified significant method-dependent variances in the size, concentration, and protein content of EVs. Importantly, our study uniquely demonstrates the ability of EV isolation to detect specific biomarkers that remain undetected in whole saliva by WB. RT-qPCR analysis targeting six miRNAs confirmed a consistent enrichment of these miRNAs in EV-derived cargo across all three isolation methods. We also found that pre-filtering saliva samples with 0.22 or 0.45 µm pores adversely affects subsequent analyses. Our findings highlight the untapped potential of salivary EVs in diagnostics and advocate for the co-precipitation method as an efficient, cost-effective, and clinically relevant approach for small-volume saliva samples. This work not only sheds light on a neglected source of EVs but also paves the way for their application in routine clinical diagnostics.
Collapse
Affiliation(s)
- Jérémy Boulestreau
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France
- Department of Anatomy, Biochemistry, and Physiology John A. Burns School of Medicine, University of Hawaii at Manoa, 651 Ilalo St. BSB 211, Honolulu, HI, 96813, USA
| | - Laurence Molina
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France
| | - Alimata Ouedraogo
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France
| | - Louën Laramy
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France
| | - Ines Grich
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France
| | - Thi Nhu Ngoc Van
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France
- SkillCell, Montpellier, France
| | - Franck Molina
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France.
| | - Malik Kahli
- Sys2Diag, UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, 1682 Rue de la Valsière, CS 40182, 34184, Montpellier Cedex 4, France.
| |
Collapse
|
12
|
Van Der Hofstadt M, Cardinal A, Lepeltier M, Boulestreau J, Ouedraogo A, Kahli M, Champigneux P, Molina L, Molina F, Van TNN. Assessment of salivary microRNA by RT-qPCR: Facing challenges in data interpretation for clinical diagnosis. PLoS One 2024; 19:e0314733. [PMID: 39656703 PMCID: PMC11630609 DOI: 10.1371/journal.pone.0314733] [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: 07/04/2024] [Accepted: 11/14/2024] [Indexed: 12/17/2024] Open
Abstract
Salivary microRNAs (miRNAs) have been recently revealed as the next generation of non-invasive biomarkers for the diagnostics of diverse diseases. However, their short and highly homologous sequences make their quantification by RT-qPCR technique highly heterogeneous and study dependent, thus limiting their implementation for clinical applications. In this study, we evaluated the use of a widely used commercial RT-qPCR kit for quantification of salivary miRNAs for clinical diagnostics. Saliva from ten healthy volunteers were sampled four times within a three month time course and submitted for small RNA extraction followed by RT-qPCR analysed. Six miRNAs with different sequence homologies were analysed. Sensitivity and specificity of the tested miRNA assays were corroborated using synthetic miRNAs to evaluate the reliability of all tested assays. Significant variabilities in expression profiles of six miRNAs from ten healthy participants were revealed, yet the poor specificity of the assays offered insufficient performance to associate these differences to biological context. Indeed, as the limit of quantification (LOQ) concentrations are from 2-4 logs higher than that of the limit of detection (LOD) ones, the majority of the analysis for salivary miRNAs felt outside the quantification region. Most importantly, a remarkable number of crosstalk reactions exhibiting considerable OFF target signal intensities was detected, indicating their poor specificity and limited reliability. However, the spike-in of synthetic target miRNA increased the capacity to discriminate endogenous salivary miRNA at the LOQ concentrations from those that were significantly lower. Our results demonstrate that comparative analyses for salivary miRNA expression profiles by this commercial RT-qPCR kit are most likely associated to technical limitations rather than to biological differences. While further technological breakthroughs are still required to overcome discrepancies, standardization of rigorous sample handling and experimental design according to technical parameters of each assay plays a crucial role in reducing data inconsistencies across studies.
Collapse
Affiliation(s)
| | - Anna Cardinal
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Morgane Lepeltier
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Jérémy Boulestreau
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Alimata Ouedraogo
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Malik Kahli
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Pierre Champigneux
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Laurence Molina
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Franck Molina
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| | - Thi Nhu Ngoc Van
- Sys2Diag UMR9005 CNRS/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
- SkillCell/ALCEN, Cap Gamma, Parc Euromédecine, Montpellier, France
| |
Collapse
|
13
|
Pu J, Yan X, Zhang H. The potential of circular RNAs as biomarkers and therapeutic targets for gastric cancer: A comprehensive review. J Adv Res 2024:S2090-1232(24)00551-4. [PMID: 39617262 DOI: 10.1016/j.jare.2024.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 11/22/2024] [Accepted: 11/26/2024] [Indexed: 12/08/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) is a global health concern, contributing significantly to cancer-related mortality rates. Early detection is vital for improving patient outcomes. Recently, circular RNAs (circRNAs) have emerged as crucial players in the development and progression of various cancers, including GC. AIM This comprehensive review underscores the promising potential of circRNAs as innovative biomarkers for the early diagnosis of GC, as well as their possible utility as therapeutic targets for this life-threatening disease. Specifically, the review focuses on recent findings, mechanistic insights, and clinical applications of circRNAs in GC. KEY SCIENTIFIC CONCEPTS OF REVIEW Dysregulation of circRNAs has been consistently observed in GC tissues, offering potential diagnostic value due to their stability in bodily fluids such as blood and urine. For instance, circPTPN22 and hsa_circ_000200. Furthermore, the expression levels of circRNAs such as circCUL2, hsa_circ_0000705 and circSHKBP1 have shown strong associations with critical clinical features of GC, including diagnosis, prognosis, tumor size, lymph node metastasis, tumor-node-metastasis (TNM) stage, and treatment response. Additionally, circRNAs such as circBGN, circLMO7, and circMAP7D1 have shown interactions with specific microRNAs (miRNAs), proteins, and other molecules that play key roles in development and progression of GC. This further highlighting their potential as therapeutic targets. Despite their potential, several challenges need to be addressed to effectively apply circRNAs as GC biomarkers. These include standardizing detection methods, establishing cutoff values for diagnostic accuracy, and validating findings in larger patient cohorts. Moreover, the functional mechanisms by which circRNAs contribute to GC pathogenesis and therapeutic resistance warrant further investigation. Advances in circRNAs research could provide valuable insights into the early detection and targeted treatment of GC, ultimately improving patient outcomes.
Collapse
Affiliation(s)
- Junlin Pu
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xiuli Yan
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai 200437, China.
| | - Hui Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China.
| |
Collapse
|
14
|
Prasad M, Sekar R, Priya MDL, Varma SR, Karobari MI. A new perspective on diagnostic strategies concerning the potential of saliva-based miRNA signatures in oral cancer. Diagn Pathol 2024; 19:147. [PMID: 39548527 PMCID: PMC11568613 DOI: 10.1186/s13000-024-01575-1] [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: 08/23/2024] [Accepted: 11/06/2024] [Indexed: 11/18/2024] Open
Abstract
Oral cancer, the most prevalent cancer worldwide, is far more likely to occur after the age of forty-five, according to the World Health Organization. Although many biomarkers have been discovered over the years using non-invasive saliva samples, biopsies, and human blood, these biomarkers have not been incorporated into standard clinical practice. Investigating the function of microRNAs (miRNAs) in the diagnosis, aetiology, prognosis, and treatment of oral cancer has drawn more attention in recent years. Though salivary microRNA can act as a window into the molecular environment of the tumour, there are challenges due to the heterogeneity of oral squamous cell carcinoma (OSCC), diversity in sample collection, processing techniques, and storage conditions. The up and downregulation of miRNAs has been found to have a profound role in OSCC as it regulates tumour stages by targeting many genes. As a result, the regulatory functions of miRNAs in OSCC underscore their significance in the field of cancer biology. Salivary miRNAs are useful diagnostic and prognostic indicators because their abnormal expression profiles shed light on tumour behaviour and patient prognosis. In addition to their diagnostic and prognostic value, miRNAs hold promise as therapeutic targets for oral cancer intervention. The current review sheds light on the challenges and potentials of microRNA studies that could lead to a better understanding of oral cancer prognosis, diagnosis, and therapeutic intervention. Furthermore, the clinical translation of OSCC biomarkers requires cooperation between investigators, physicians, regulatory bodies, and business partners. There is much potential for improving early identification, tracking therapy response, and forecasting outcomes in OSCC patients by including saliva-based miRNAs as biomarkers.
Collapse
Affiliation(s)
- Monisha Prasad
- Center for Global Health Research, Saveetha Institute of Medical and Technical Sciences, Saveetha Medical College and Hospitals, Saveetha University, Chennai, Tamil Nadu, 602105, India
| | - Ramya Sekar
- Department of Oral and Maxillofacial Pathology & Oral Microbiology, Meenakshi Ammal Dental College and Hospital, MAHER, Alapakkam Main Road, Maduravoyal, Chennai, Tamil Nadu, 600095, India
| | | | - Sudhir Rama Varma
- Department of Clinical Sciences, College of Dentistry, Center of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman University, Ajman - 346, Ajman, UAE
| | - Mohmed Isaqali Karobari
- Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu, 600077, India.
- Department of Restorative Dentistry & Endodontics, Faculty of Dentistry, University of Puthisastra, Phnom Penh, 12211, Cambodia.
| |
Collapse
|
15
|
Yuan P, Gao X, Xu M, Qiu L, Xiong Z, Shen J, Xing H, Yang R, Zhao L, Liu X, Gu J, Liu W. Novel miRNA markers and their mechanism of esophageal squamous cell carcinoma (ESCC) based on TCGA. Sci Rep 2024; 14:27261. [PMID: 39516222 PMCID: PMC11549395 DOI: 10.1038/s41598-024-76321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/14/2024] [Indexed: 11/16/2024] Open
Abstract
MicroRNAs(miRNAs) are promising biomarkers for early esophageal squamous cell carcinoma (ESCC) detection and prognostic prediction. This study aimed to explore the potential biomarkers and molecular pathogenesis in the early diagnosis of ESCC. Firstly, 48 differentially expressed miRNAs (DEMs) and 1319 differentially expressed genes (DEGs) were identified between 94 ESCC tissues and 13 normal esophageal tissues in TCGA. From miRNA-mRNA regulatory network, there are 6558 target genes of the 48 DEMs, where 400 target genes are also among 1319 DEGs. Then, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicate that the 400 DEGs significantly enriched in cell cycle, proteoglycans in cancer, p53 signaling pathway, protein digestion and absorption, transcriptional dysregulation in cancer, and oocyte meiosis. And there are 66 DEGs among these six biological pathways, which we called GO-DEGs. From miRNA-mRNA regulatory network, 32 DEMs regulated the 66 GO-DEGs, where 22 DEMs were verified by different types of experiments in ESCC tissues, cells, or serum from the literature. For the other novel 10 DEMs, single-factor Cox regression analysis show that only hsa-miR-34b-3p showed no significant correlation with the overall survival of ESCC patients. Finally, we obtained the novel 9 ESCC-related DEMs, where three are down-regulated, and six are up-regulated. We analyzed the expression trends of target genes for five miRNAs and identified three significantly different miRNAs (hsa-miR-205-3p, hsa-miR-452-3p, and hsa-miR-6499-3p) confirmed by qPCR. Moreover, the stage-specific miRNAs were also suggested. These three qPCR validated miRNAs are also specific to the early stages of ESCC: hsa-miR-452-3p is specific to Stage I, II and III; hsa-miR-205-3p is specific in Stage II and III; and hsa-miR-6499-3p is Stage II specific. They might be the potential biomarkers for ESCC stage diagnosis. This study identified three novel miRNA markers potentially related to the diagnosis of ESCC and participated in the occurrence and development of ESCC through cell cycle, proteoglycans in cancer, p53 signaling pathway, protein digestion and absorption, transcriptional dysregulation in cancer, and signaling pathway for oocyte meiosis.
Collapse
Affiliation(s)
- Ping Yuan
- Healthcare Big Data Center, School of Public Health, Hubei University of Medicine, 30 Chaoyang Middle Road, Shiyan, 442000, Hubei, People's Republic of China
- Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xiaoyan Gao
- Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Mingjun Xu
- Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Liangyu Qiu
- Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Zijun Xiong
- Healthcare Big Data Center, School of Public Health, Hubei University of Medicine, 30 Chaoyang Middle Road, Shiyan, 442000, Hubei, People's Republic of China
| | - Jun Shen
- Renmin Hospital, Hubei University of Medicine, Shiyan, Hubei, China
- Xinjiang Key Laboratory of Cardiac Electrophysiology and Remodeling, The First Affiliated Hospital of Xinjiang Medical University, Urumqi, China
| | - Huanhuan Xing
- Healthcare Big Data Center, School of Public Health, Hubei University of Medicine, 30 Chaoyang Middle Road, Shiyan, 442000, Hubei, People's Republic of China
| | - Ruofan Yang
- Healthcare Big Data Center, School of Public Health, Hubei University of Medicine, 30 Chaoyang Middle Road, Shiyan, 442000, Hubei, People's Republic of China
| | - Liang Zhao
- Precision Medicine Research Center, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China
| | - Xi Liu
- Healthcare Big Data Center, School of Public Health, Hubei University of Medicine, 30 Chaoyang Middle Road, Shiyan, 442000, Hubei, People's Republic of China
| | - Jiaowei Gu
- Hubei Provincial Clinical Research Center for Umbilical Cord Blood Hematopoietic Stem Cells, Taihe Hospital, Hubei University of Medicine, Shiyan, Hubei, China.
- Department of Pediatrics, Taihe Hospital, Hubei University of Medicine, 32 Renmin South Road, Shiyan, 442000, Hubei, People's Republic of China.
| | - Wenting Liu
- Healthcare Big Data Center, School of Public Health, Hubei University of Medicine, 30 Chaoyang Middle Road, Shiyan, 442000, Hubei, People's Republic of China.
| |
Collapse
|
16
|
Zhao X, Yang Y, Wang Y, Chen X, Yao Y, Yuan T, Li J, Li Y, Song X. Roles of noncoding RNA in allergic rhinitis. Int Forum Allergy Rhinol 2024; 14:1757-1775. [PMID: 39367803 DOI: 10.1002/alr.23461] [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: 05/30/2024] [Revised: 09/03/2024] [Accepted: 09/13/2024] [Indexed: 10/07/2024]
Abstract
BACKGROUND Allergic rhinitis (AR) is one of the most common respiratory noninfectious diseases and chronic inflammatory diseases, the incidence of which has been increasing in recent years. The main pathological characteristics of AR are repeated inflammation, airway hyperreactivity, mucus hypersecretion, and reversible airway obstruction due to inflammatory cell response. AR occurrence is associated with various factors, including those of genetic and environmental origins. Noncoding RNAs (ncRNAs) are a group of RNA molecules that cannot be converted into polypeptides. The three main categories of ncRNAs include microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs). NcRNAs play a crucial role in controlling gene expression and contribute to the development of numerous human diseases. METHODS Articles are selected based on Pubmed's literature review and the author's personal knowledge. The largest and highest quality studies were included. The search selection is not standardized. Several recent studies have indicated the relationship of ncRNAs with the development of respiratory allergic diseases. NcRNAs, including miRNAs, lncRNAs, and circRNAs, are important gene expression regulatory factors. We review the expression and function of ncRNAs in AR, their role as disease biomarkers, and their prospective applicability in future research and clinically. We also discuss interactions between ncRNAs and their influence on AR comprehensively, these interactions are essential for determining the underlying pathological mechanisms further and discovering new drug therapeutic targets. RESULTS NcRNAs can be used as biomarkers for early AR diagnosis, disease surveillance and prognosis assessment. Various categories of ncRNAs play distinct yet interconnected roles and actively contribute to intricate gene regulatory networks. They are also therapeutic targets and biomarkers in other allergic diseases. CONCLUSION This article demonstrates ncRNAs have a wide range of applications in AR treatment. The database covers three key areas: miRNAs, lncRNAs, and circRNAs. Additionally, potential avenues for future research to facilitate the practical application of ncRNAs as therapeutic targets and biomarkers will be explore. With further research and technological development, ncRNAs may provide additional innovative, effective solutions for AR treatment.
Collapse
Affiliation(s)
- Xiangkun Zhao
- Department of Clinical Medicine, The Second School of Clinical Medicine of Binzhou Medical University, Yantai, China
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Yuteng Yang
- Department of Clinical Medicine, The Second School of Clinical Medicine of Binzhou Medical University, Yantai, China
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Yaqi Wang
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Xi Chen
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Yisong Yao
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Ting Yuan
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Jiaxuan Li
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Yumei Li
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| | - Xicheng Song
- Department of Clinical Medicine, The Second School of Clinical Medicine of Binzhou Medical University, Yantai, China
- Department of Otolaryngology, Head and Neck Surgery, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Shandong Provincial Clinical Research Center for Otorhinolaryngologic Diseases, Yantai Yuhuangding Hospital, Qingdao University, Yantai, China
- Yantai Key Laboratory of Otorhinolaryngologic Diseases, Yantai, China
| |
Collapse
|
17
|
Hejazian SM, Rahbar Saadat Y, Hosseiniyan Khatibi SM, Farnood F, Farzamikia N, Hejazian SS, Batoumchi S, Shoja MM, Zununi Vahed S, Ardalan M. Circular RNAs as novel biomarkers in glomerular diseases. Arch Physiol Biochem 2024; 130:568-580. [PMID: 37194131 DOI: 10.1080/13813455.2023.2212328] [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: 10/19/2022] [Revised: 05/03/2023] [Accepted: 05/03/2023] [Indexed: 05/18/2023]
Abstract
Circular RNAs (circRNAs) regulate gene expression and biological procedures by controlling target genes or downstream pathways by sponging their related miRNA (s). Three types of circRNAs have been identified; exonic circRNAs (ecircRNAs), intronic RNAs (ciRNAs), and exon-intron circRNAs (ElciRNAs). It is clarified that altered levels of circRNAs have dynamic pathological and physiological functions in kidney diseases. Evidence suggests that circRNAs can be considered novel diagnostic biomarkers and therapeutic targets for renal diseases. Glomerulonephritis (GN) is a general term used to refer to a wide range of glomerular diseases. GN is an important cause of chronic kidney diseases. Here, we review the biogenesis of circRNAs, and their molecular and physiological functions in the kidney. Moreover, the dysregulated expression of circRNAs and their biological functions are discussed in primary and secondary glomerulonephritis. Moreover, diagnostic and therapeutic values of circRNAs in distinguishing or treating different types of GN are highlighted.
Collapse
Affiliation(s)
| | | | | | - Farahnoosh Farnood
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Negin Farzamikia
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyyed Sina Hejazian
- Neurosciences Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Sepideh Batoumchi
- Kidney Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammadali M Shoja
- College of Allopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, USA
| | | | | |
Collapse
|
18
|
Chen R, Wang X, Li N, Golubnitschaja O, Zhan X. Body fluid multiomics in 3PM-guided ischemic stroke management: health risk assessment, targeted protection against health-to-disease transition, and cost-effective personalized approach are envisaged. EPMA J 2024; 15:415-452. [PMID: 39239108 PMCID: PMC11371995 DOI: 10.1007/s13167-024-00376-2] [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: 08/11/2024] [Accepted: 08/13/2024] [Indexed: 09/07/2024]
Abstract
Because of its rapid progression and frequently poor prognosis, stroke is the third major cause of death in Europe and the first one in China. Many independent studies demonstrated sufficient space for prevention interventions in the primary care of ischemic stroke defined as the most cost-effective protection of vulnerable subpopulations against health-to-disease transition. Although several studies identified molecular patterns specific for IS in body fluids, none of these approaches has yet been incorporated into IS treatment guidelines. The advantages and disadvantages of individual body fluids are thoroughly analyzed throughout the paper. For example, multiomics based on a minimally invasive approach utilizing blood and its components is recommended for real-time monitoring, due to the particularly high level of dynamics of the blood as a body system. On the other hand, tear fluid as a more stable system is recommended for a non-invasive and patient-friendly holistic approach appropriate for health risk assessment and innovative screening programs in cost-effective IS management. This article details aspects essential to promote the practical implementation of highlighted achievements in 3PM-guided IS management. Supplementary Information The online version contains supplementary material available at 10.1007/s13167-024-00376-2.
Collapse
Affiliation(s)
- Ruofei Chen
- Shandong Provincial Key Laboratory of Precision Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 P. R. China
| | - Xiaoyan Wang
- Shandong Provincial Key Laboratory of Precision Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 P. R. China
| | - Na Li
- Shandong Provincial Key Laboratory of Precision Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 P. R. China
| | - Olga Golubnitschaja
- Predictive, Preventive and Personalised (3P) Medicine, University Hospital Bonn, Venusberg Campus 1, Rheinische Friedrich-Wilhelms-University of Bonn, Bonn, 53127 Germany
| | - Xianquan Zhan
- Shandong Provincial Key Laboratory of Precision Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University & Shandong Academy of Medical Sciences, 440 Jiyan Road, Jinan, Shandong 250117 P. R. China
- Shandong Provincial Key Medical and Health Laboratory of Ovarian Cancer Multiomics, & Jinan Key Laboratory of Cancer Multiomics, Shandong First Medical University & Shandong Academy of Medical Sciences, 6699 Qingdao Road, Jinan, Shandong 250117 P. R. China
| |
Collapse
|
19
|
Wang Y, Zhang J, Yang Y, Liu Z, Sun S, Li R, Zhu H, Li T, Zheng J, Li J, Ma L. Circular RNAs in human diseases. MedComm (Beijing) 2024; 5:e699. [PMID: 39239069 PMCID: PMC11374765 DOI: 10.1002/mco2.699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/25/2024] [Accepted: 07/30/2024] [Indexed: 09/07/2024] Open
Abstract
Circular RNAs (circRNAs) are a unique class of RNA molecules formed through back-splicing rather than linear splicing. As an emerging field in molecular biology, circRNAs have garnered significant attention due to their distinct structure and potential functional implications. A comprehensive understanding of circRNAs' functions and potential clinical applications remains elusive despite accumulating evidence of their involvement in disease pathogenesis. Recent research highlights their significant roles in various human diseases, but comprehensive reviews on their functions and applications remain scarce. This review provides an in-depth examination of circRNAs, focusing first on their involvement in non-neoplastic diseases such as respiratory, endocrine, metabolic, musculoskeletal, cardiovascular, and renal disorders. We then explore their roles in tumors, with particular emphasis on exosomal circular RNAs, which are crucial for cancer initiation, progression, and resistance to treatment. By detailing their biogenesis, functions, and impact on disease mechanisms, this review underscores the potential of circRNAs as diagnostic biomarkers and therapeutic targets. The review not only enhances our understanding of circRNAs' roles in specific diseases and tumor types but also highlights their potential as novel diagnostic and therapeutic tools, thereby paving the way for future clinical investigations and potential therapeutic interventions.
Collapse
Affiliation(s)
- Yuanyong Wang
- Department of Thoracic SurgeryTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education)The First Department of Thoracic SurgeryPeking University Cancer Hospital and InstitutePeking University School of OncologyBeijingChina
| | - Jin Zhang
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Yuchen Yang
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Zhuofeng Liu
- Department of Traditional Chinese MedicineThe Third Affiliated Hospital of Xi'an Medical UniversityXi'anChina
| | - Sijia Sun
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Rui Li
- Department of EpidemiologySchool of Public HealthAir Force Medical UniversityXi'anChina
| | - Hui Zhu
- Department of AnatomyMedical College of Yan'an UniversityYan'anChina
- Institute of Medical ResearchNorthwestern Polytechnical UniversityXi'anChina
| | - Tian Li
- School of Basic MedicineFourth Military Medical UniversityXi'anChina
| | - Jin Zheng
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
| | - Jie Li
- Department of EndocrineXijing 986 HospitalAir Force Medical UniversityXi'anChina
| | - Litian Ma
- Department of Thoracic SurgeryTangdu HospitalAir Force Medical UniversityXi'anChina
- Department of Traditional Chinese MedicineTangdu HospitalAir Force Medical UniversityXi'anChina
- Key Laboratory of Integrated Traditional Chinese and Western Medicine Tumor Diagnosis and Treatment in Shaanxi ProvinceXi'anChina
- Department of GastroenterologyTangdu HospitalAir Force Medical UniversityXi'anChina
- School of MedicineNorthwest UniversityXi'anChina
| |
Collapse
|
20
|
Farhadi E, Khomeijani-Farahani M, Nikbakhsh R, Azizan A, Soltani S, Barekati H, Mahmoudi M. The potential role of circular RNAs in regulating p53 in different types of cancers. Pathol Res Pract 2024; 261:155488. [PMID: 39088876 DOI: 10.1016/j.prp.2024.155488] [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: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/03/2024]
Abstract
P53 tumor suppressor is a major regulator of various cellular processes and functions. It has been reported that mutation or inactivation of p53 plays a crucial role in tumorigenesis in different types of cancers. Circular RNAs (circRNAs) are single-stranded non-coding RNAs that have significant post-transcriptional effects on the regulation of gene expression in various ways. These molecules can alter the expression and function of multiple genes and proteins. In the present study, we aimed to review circRNAs that regulate the expression, function, and stability of p53 and the possible interactions between these molecules and p53. Considering the importance of p53 in cancer and the network between p53 and circRNAs, future clinical trials targeting these circRNAs as therapeutic agents deserve worthy of attention.
Collapse
Affiliation(s)
- Elham Farhadi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mohammadreza Khomeijani-Farahani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Students Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Rambod Nikbakhsh
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Department of Biology, Faculty of Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Amin Azizan
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Soltani
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Barekati
- School of Nursing & Midwifery, Tehran University of Medical Sciences, Tehran, Iran
| | - Mahdi Mahmoudi
- Rheumatology Research Center, Tehran University of Medical Sciences, Tehran, Iran; Research Center for Chronic Inflammatory Diseases, Tehran University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
21
|
Okholm TLH, Kamstrup AB, Nielsen MM, Hollensen AK, Graversgaard ML, Sørensen MH, Kristensen LS, Vang S, Park SS, Yeo E, Dyrskjøt L, Kjems J, Pedersen JS, Damgaard CK. circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA. eLife 2024; 13:RP91783. [PMID: 39041323 PMCID: PMC11265796 DOI: 10.7554/elife.91783] [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] [Indexed: 07/24/2024] Open
Abstract
Circular RNAs represent a class of endogenous RNAs that regulate gene expression and influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Using time-course depletion of circHIPK3 and specific candidate RNA-binding proteins, we identify several perturbed genes by RNA sequencing analyses. Expression-coupled motif analyses identify an 11-mer motif within circHIPK3, which also becomes enriched in genes that are downregulated upon circHIPK3 depletion. By mining eCLIP datasets and combined with RNA immunoprecipitation assays, we demonstrate that the 11-mer motif constitutes a strong binding site for IGF2BP2 in bladder cancer cell lines. Our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on the STAT3 mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2-STAT3 mRNA binding and, thereby, STAT3 mRNA levels. Surprisingly, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Our results support a model where a few cellular circHIPK3 molecules can induce IGF2BP2 condensation, thereby regulating key factors for cell proliferation.
Collapse
Affiliation(s)
- Trine Line Hauge Okholm
- Department of Molecular Medicine (MOMA), Aarhus University HospitalAarhusDenmark
- Departments of Otolaryngology-Head and Neck Surgery and Microbiology & Immunology, University of California, San FranciscoSan FranciscoUnited States
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
| | | | - Morten Muhlig Nielsen
- Department of Molecular Medicine (MOMA), Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
| | | | | | | | | | - Søren Vang
- Department of Molecular Medicine (MOMA), Aarhus University HospitalAarhusDenmark
| | - Samuel S Park
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Eugene Yeo
- Department of Cellular and Molecular Medicine, University of California, San DiegoSan DiegoUnited States
| | - Lars Dyrskjøt
- Department of Molecular Medicine (MOMA), Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
| | - Jørgen Kjems
- Department of Molecular Biology and Genetics, Aarhus UniversityAarhusDenmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus UniversityAarhusDenmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University HospitalAarhusDenmark
- Department of Clinical Medicine, Aarhus UniversityAarhusDenmark
- Bioinformatics Research Center (BiRC), Aarhus UniversityAarhusDenmark
| | | |
Collapse
|
22
|
Unlu I, Maguire S, Guan S, Sun Z. Induro-RT mediated circRNA-sequencing (IMCR-seq) enables comprehensive profiling of full-length and long circular RNAs from low input total RNA. Nucleic Acids Res 2024; 52:e55. [PMID: 38850158 PMCID: PMC11260445 DOI: 10.1093/nar/gkae465] [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: 12/11/2023] [Revised: 03/23/2024] [Accepted: 05/17/2024] [Indexed: 06/10/2024] Open
Abstract
Circular RNA (circRNA) has recently gained attention for its emerging biological activities, relevance to disease, potential as biomarkers, and promising an alternative modality for RNA vaccines. Nevertheless, sequencing circRNAs has presented challenges. In this context, we introduce a novel circRNA sequencing method called Induro-RT mediated circRNA-sequencing (IMCR-seq), which relies on a group II intron reverse transcriptase with robust rolling circle reverse transcription activity. The IMCR-seq protocol eliminates the need for conventional circRNA enrichment methods such as rRNA depletion and RNaseR digestion yet achieved the highest circRNA enrichment and detected 6-1000 times more circRNAs for the benchmarked human samples compared to other methods. IMCR-seq is applicable to any organism, capable of detecting circRNAs of longer than 7000 nucleotides, and is effective on samples as small as 10 ng of total RNA. These enhancements render IMCR-seq suitable for clinical samples, including disease tissues and liquid biopsies. We demonstrated the clinical relevance of IMCR-seq by detecting cancer-specific circRNAs as potential biomarkers from IMCR-seq results on lung tumor tissues together with blood plasma samples from both a healthy individual and a lung cancer patient. In summary, IMCR-seq presents an efficient and versatile circRNA sequencing method with high potential for research and clinical applications.
Collapse
Affiliation(s)
- Irem Unlu
- New England Biolabs Inc., Beverly, MA 01915, USA
| | - Sean Maguire
- New England Biolabs Inc., Beverly, MA 01915, USA
| | - Shengxi Guan
- New England Biolabs Inc., Beverly, MA 01915, USA
| | - Zhiyi Sun
- New England Biolabs Inc., Beverly, MA 01915, USA
| |
Collapse
|
23
|
Kong S, Xu YH, Zheng M, Ju SQ, Shi HC. Circ_0004592: An auxiliary diagnostic biomarker for gastric cancer. World J Gastrointest Oncol 2024; 16:2745-2756. [DOI: 10.4251/wjgo.v16.i6.2745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 04/12/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) has a high mortality rate, and robust diagnostic biomarkers are currently lacking. However, the clinical relevance of circular RNAs (circRNAs) as GC biomarkers remains largely unexplored.
AIM To evaluate the potential of novel circRNA circ_0004592 in the early screening and prognosis of GC.
METHODS High-throughput sequencing of circRNAs was performed to screen for potential target molecules. Circ_0004592 expression was examined in GC tissues, cells, and plasma. Plasma samples were collected from healthy subjects’ patients, as well as from patients with benign lesions, precancerous lesions, and GC, whereafter the diagnostic accuracy of circ_0004592 was evaluated. The correlation between circ_0004592 levels in plasma and clinicopathological data of patients with GC was further analyzed.
RESULTS Circ_0004592 was upregulated in both the tissue and plasma of patients with GC. Further, circ_0004592 expression was higher in patients with precancerous lesions than in healthy controls while being highest in patients with GC. In the same patient, the postoperative plasma level of circ_0004592 was lower than that in the preoperative period. Moreover, circ_0004592 level was significantly correlated with tumor differentiation, tumor depth, and lymph node metastasis. The area under the curve (AUC) of plasma circ_0004592 exhibited high sensitivity and specificity for differentiating patients with GC from healthy donors. Diagnosis based on circ_0004592, carcinoembryonic antigen, and cancer antigen 199 achieved a superior AUC and was highly sensitive.
CONCLUSION Plasma circ_0004592 may represent a potential non-invasive auxiliary diagnostic biomarker for patients with GC.
Collapse
Affiliation(s)
- Shan Kong
- Department of Laboratory Medicine, Jiangsu Province Official Hospital, Nanjing 210000, Jiangsu Province, China
| | - Yan-Hua Xu
- Department of Laboratory Medicine, Northern Jiangsu People’s Hospital, Yangzhou 225000, Jiangsu Province, China
| | - Ming Zheng
- Department of Laboratory Medicine, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Shao-Qing Ju
- Department of Laboratory Medicine, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Heng-Chuan Shi
- Department of Laboratory Medicine, Jiangsu Province Official Hospital, Nanjing 210000, Jiangsu Province, China
| |
Collapse
|
24
|
Kong S, Xu YH, Zheng M, Ju SQ, Shi HC. Circ_0004592: An auxiliary diagnostic biomarker for gastric cancer. World J Gastrointest Oncol 2024; 16:2757-2768. [PMID: 38994162 PMCID: PMC11236232 DOI: 10.4251/wjgo.v16.i6.2757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/12/2024] [Accepted: 04/12/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND Gastric cancer (GC) has a high mortality rate, and robust diagnostic biomarkers are currently lacking. However, the clinical relevance of circular RNAs (circRNAs) as GC biomarkers remains largely unexplored. AIM To evaluate the potential of novel circRNA circ_0004592 in the early screening and prognosis of GC. METHODS High-throughput sequencing of circRNAs was performed to screen for potential target molecules. Circ_0004592 expression was examined in GC tissues, cells, and plasma. Plasma samples were collected from healthy subjects' patients, as well as from patients with benign lesions, precancerous lesions, and GC, whereafter the diagnostic accuracy of circ_0004592 was evaluated. The correlation between circ_0004592 levels in plasma and clinicopathological data of patients with GC was further analyzed. RESULTS Circ_0004592 was upregulated in both the tissue and plasma of patients with GC. Further, circ_0004592 expression was higher in patients with precancerous lesions than in healthy controls while being highest in patients with GC. In the same patient, the postoperative plasma level of circ_0004592 was lower than that in the preoperative period. Moreover, circ_0004592 level was significantly correlated with tumor differentiation, tumor depth, and lymph node metastasis. The area under the curve (AUC) of plasma circ_0004592 exhibited high sensitivity and specificity for differentiating patients with GC from healthy donors. Diagnosis based on circ_0004592, carcinoembryonic antigen, and cancer antigen 199 achieved a superior AUC and was highly sensitive. CONCLUSION Plasma circ_0004592 may represent a potential non-invasive auxiliary diagnostic biomarker for patients with GC.
Collapse
Affiliation(s)
- Shan Kong
- Department of Laboratory Medicine, Jiangsu Province Official Hospital, Nanjing 210000, Jiangsu Province, China
| | - Yan-Hua Xu
- Department of Laboratory Medicine, Northern Jiangsu People’s Hospital, Yangzhou 225000, Jiangsu Province, China
| | - Ming Zheng
- Department of Laboratory Medicine, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Shao-Qing Ju
- Department of Laboratory Medicine, The Affiliated Hospital of Nantong University, Nantong 226001, Jiangsu Province, China
| | - Heng-Chuan Shi
- Department of Laboratory Medicine, Jiangsu Province Official Hospital, Nanjing 210000, Jiangsu Province, China
| |
Collapse
|
25
|
Amaya L, Abe B, Liu J, Zhao F, Zhang WL, Chen R, Li R, Wang S, Kamber RA, Tsai MC, Bassik MC, Majeti R, Chang HY. Pathways for macrophage uptake of cell-free circular RNAs. Mol Cell 2024; 84:2104-2118.e6. [PMID: 38761795 PMCID: PMC11218042 DOI: 10.1016/j.molcel.2024.04.022] [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: 08/17/2023] [Revised: 03/04/2024] [Accepted: 04/26/2024] [Indexed: 05/20/2024]
Abstract
Circular RNAs (circRNAs) are stable RNAs present in cell-free RNA, which may comprise cellular debris and pathogen genomes. Here, we investigate the phenomenon and mechanism of cellular uptake and intracellular fate of exogenous circRNAs. Human myeloid cells and B cells selectively internalize extracellular circRNAs. Macrophage uptake of circRNA is rapid, energy dependent, and saturable. CircRNA uptake can lead to translation of encoded sequences and antigen presentation. The route of internalization influences immune activation after circRNA uptake, with distinct gene expression programs depending on the route of RNA delivery. Genome-scale CRISPR screens and chemical inhibitor studies nominate macrophage scavenger receptor MSR1, Toll-like receptors, and mTOR signaling as key regulators of receptor-mediated phagocytosis of circRNAs, a dominant pathway to internalize circRNAs in parallel to macropinocytosis. These results suggest that cell-free circRNA serves as an "eat me" signal and danger-associated molecular pattern, indicating orderly pathways of recognition and disposal.
Collapse
Affiliation(s)
- Laura Amaya
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Brian Abe
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Division of Immunology and Rheumatology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jie Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Feifei Zhao
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Wenyan Lucy Zhang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Robert Chen
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Steven Wang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Roarke A Kamber
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Miao-Chih Tsai
- RNA Medicine Program, Stanford University, Stanford, CA 94305, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Medicine, Division of Hematology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA; RNA Medicine Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
26
|
Okholm TLH, Kamstrup AB, Nielsen MM, Hollensen AK, Graversgaard ML, Sørensen MH, Kristensen LS, Vang S, Park SS, Yeo GW, Dyrskjøt L, Kjems J, Pedersen JS, Damgaard CK. circHIPK3 nucleates IGF2BP2 and functions as a competing endogenous RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.14.557527. [PMID: 37745562 PMCID: PMC10515936 DOI: 10.1101/2023.09.14.557527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Circular RNAs (circRNAs) represent a class of widespread endogenous RNAs that regulate gene expression and thereby influence cell biological decisions with implications for the pathogenesis of several diseases. Here, we disclose a novel gene-regulatory role of circHIPK3 by combining analyses of large genomics datasets and mechanistic cell biological follow-up experiments. Specifically, we use temporal depletion of circHIPK3 or specific RNA binding proteins (RBPs) and identify several perturbed genes by RNA sequencing analyses. Using expression-coupled motif analyses of mRNA expression data from various knockdown experiments, we identify an 11-mer motif within circHIPK3, which is also enriched in genes that become downregulated upon circHIPK3 depletion. By mining eCLIP datasets, we find that the 11-mer motif constitutes a strong binding site for IGF2BP2 and validate this circHIPK3-IGF2BP2 interaction experimentally using RNA-immunoprecipitation and competition assays in bladder cancer cell lines. Our results suggest that circHIPK3 and IGF2BP2 mRNA targets compete for binding. Since the identified 11-mer motif found in circHIPK3 is enriched in upregulated genes following IGF2BP2 knockdown, and since IGF2BP2 depletion conversely globally antagonizes the effect of circHIPK3 knockdown on target genes, our results suggest that circHIPK3 can sequester IGF2BP2 as a competing endogenous RNA (ceRNA), leading to target mRNA stabilization. As an example of a circHIPK3-regulated gene, we focus on the STAT3 mRNA as a specific substrate of IGF2BP2 and validate that manipulation of circHIPK3 regulates IGF2BP2- STAT3 mRNA binding and thereby STAT3 mRNA levels. However, absolute copy number quantifications demonstrate that IGF2BP2 outnumbers circHIPK3 by orders of magnitude, which is inconsistent with a simple 1:1 ceRNA hypothesis. Instead, we show that circHIPK3 can nucleate multiple copies of IGF2BP2, potentially via phase separation, to produce IGF2BP2 condensates. Finally, we show that circHIPK3 expression correlates with overall survival of patients with bladder cancer. Our results are consistent with a model where relatively few cellular circHIPK3 molecules function as inducers of IGF2BP2 condensation thereby regulating STAT3 and other key factors for cell proliferation and potentially cancer progression.
Collapse
|
27
|
Shinde DB, Mahore JG, Giram PS, Singh SL, Sharda A, Choyan D, Musale S. Microbiota of Saliva: A Non-invasive Diagnostic Tool. Indian J Microbiol 2024; 64:328-342. [PMID: 39010986 PMCID: PMC11246313 DOI: 10.1007/s12088-024-01219-4] [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: 06/23/2023] [Accepted: 01/30/2024] [Indexed: 07/17/2024] Open
Abstract
Potential of salivary microbiota as a non-invasive diagnostic tool for various diseases are explained in the present review. Traditional diagnostic methods rely on blood, which has limitations in terms of collection and biomarker specificity. We discuss the concept of normal flora and how disruptions in oral microbiota can be indicative of diseases. Saliva, harboring a diverse microbial community, offers promise as a diagnostic biomarker source for oral and non-oral conditions. We delve into the role of microbial dysbiosis in disease pathogenesis and the prospects of using biological indicators like dysbiosis for diagnosis, prediction, and monitoring. This review also emphasizes the significance of saliva microbiota in advancing early disease detection and timely intervention. We addressed the following research question and objectives: Can the microbiota of saliva serve as a non-invasive diagnostic tool for the early detection and monitoring of both oral and non-oral diseases? To achieve this, we will explore the normal flora of microorganisms in the oral cavity, the impact of microbial dysbiosis, and the potential of using specific pathogenic microorganisms as biomarkers. Additionally, we will investigate the correlation between oral and non-oral diseases by analyzing total saliva or site-specific dental biofilms for signs of symbiosis or dysbiosis. This research seeks to contribute valuable insights into the development of a non-invasive diagnostic approach with broad applications in healthcare.
Collapse
Affiliation(s)
- Dasharath B Shinde
- Symbiosis School of Biological Sciences (SSBS), Symbiosis International (Deemed University), Pune, 412115 India
| | - Jayashri G Mahore
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
- Sinhgad College of Pharmacy, Vadgaon (Bk.), Pune, 411041 India
| | - Prabhanjan S Giram
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
- Department of Pharmaceutical Sciences, The State University of New York, Buffalo, NY 14214 USA
| | - Shaktikumar L Singh
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| | - Aditi Sharda
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| | - Divya Choyan
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| | - Shubham Musale
- Dr. D. Y. Patil Institute of Pharmaceutical Sciences and Research, Pimpri, Pune, 411018 India
| |
Collapse
|
28
|
Géli V, Nabet N. Saliva, a molecular reflection of the human body? Implications for diagnosis and treatment. Cell Stress 2024; 8:59-68. [PMID: 38826491 PMCID: PMC11144459 DOI: 10.15698/cst2024.05.297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/02/2024] [Accepted: 05/03/2024] [Indexed: 06/04/2024] Open
Abstract
For many diseases, and cancer in particular, early diagnosis allows a wider range of therapies and a better disease management. This has led to improvements in diagnostic procedures, most often based on tissue biopsies or blood samples. Other biological fluids have been used to diagnose disease, and among them saliva offers a number of advantages because it can be collected non-invasively from large populations at relatively low cost. To what extent might saliva content reveal the presence of a tumour located at a distance from the oral cavity and the molecular information obtained from saliva be used to establish a diagnosis are current questions. This review focuses primarily on the content of saliva and shows how it potentially offers a source of diagnosis, possibly at an early stage, for pathologies such as cancers or endometriosis.
Collapse
|
29
|
Romanò S, Nele V, Campani V, De Rosa G, Cinti S. A comprehensive guide to extract information from extracellular vesicles: a tutorial review towards novel analytical developments. Anal Chim Acta 2024; 1302:342473. [PMID: 38580402 DOI: 10.1016/j.aca.2024.342473] [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: 01/03/2024] [Revised: 03/11/2024] [Accepted: 03/12/2024] [Indexed: 04/07/2024]
Abstract
In the medical field, extracellular vesicles (EVs) are gaining importance as they act as cells mediators. These are phospholipid bilayer vesicles and contain crucial biochemical information about their mother cells being carrier of different biomolecules such as small molecules, proteins, lipids, and nucleic acids. After release into the extracellular matrix, they enter the systemic circulation and can be found in all human biofluids. Since EVs reflect the state of the cell of origin, there is exponential attention as potential source of new circulating biomarkers for liquid biopsy. The use of EVs in clinical practice faces several challenges that need to be addressed: these include the standardization of lysis protocols, the availability of low-cost reagents and the development of analytical tools capable of detecting biomarkers. The process of lysis is a crucial step that can impact all subsequent analyses, towards the development of novel analytical strategies. To aid researchers to support the evolution of measurement science technology, this tutorial review evaluates and discuss the most commonly protocols used to characterize the contents of EVs, including their advantages and disadvantages in terms of experimental procedures, time and equipment. The purpose of this tutorial review is to offer practical guide to researchers which are intended to develop novel analytical approaches. Some of the most significant applications are considered, highlighting their main characteristics divided per mechanism of action. Finally, comprehensive tables which provide an overview at a glance are provided to readers.
Collapse
Affiliation(s)
- Sabrina Romanò
- Department of Pharmacy, University of Naples Federico II, Italy.
| | - Valeria Nele
- Department of Pharmacy, University of Naples Federico II, Italy
| | | | | | - Stefano Cinti
- Department of Pharmacy, University of Naples Federico II, Italy.
| |
Collapse
|
30
|
Chen D, Zeng S, Qiu H, Yang M, Lin X, Lv X, Li P, Weng S, Kou S, Luo K, Liu Z, Yi Y, Liu H. Circ-FOXO3 inhibits triple-negative breast cancer growth and metastasis via regulating WHSC1-H3K36me2-Zeb2 axis. Cell Signal 2024; 117:111079. [PMID: 38341124 DOI: 10.1016/j.cellsig.2024.111079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Circular RNAs (circRNAs), a subclass of non-coding RNAs characterized by covalently closed continuous loops, play a key role in tumorigenesis and aggressiveness. However, the potential molecular mechanism of circRNAs in triple-negative breast cancer (TNBC) remains largely unknown. Exploring their roles and mechanisms in TNBC progression may help identify new diagnostic markers and therapeutic targets. In this study, we found that circ-FOXO3 was dramatically downregulated in TNBC tissues and blood samples from patients with TNBC. Notably, low circ-FOXO3 expression in TNBC tissues and bloods was associated with lymph node metastasis and unfavorable outcomes in patients with TNBC. Overexpression of circ-FOXO3 significantly inhibited the growth, invasion, and metastasis of TNBC cells both in vitro and in vivo. Moreover, we demonstrated that circ-FOXO3 was predominantly expressed in the cytoplasm and directly interacted with Wolf-Hirschhorn syndrome candidate 1 (WHSC1), thereby inhibiting WHSC1 nuclear localization and activity, resulting in the inhibition of H3K36me2 modifications at the Zeb2 promoter, ultimately inhibiting Zeb2 expression and halting TNBC growth and metastasis. Taken together, these results reveal the tumor-suppressive functions of circ-FOXO3 in inhibiting WHSC1-mediated H3K36me2 modification of Zeb2, suggesting that circ-FOXO3 could serve as a potential novel predictive prognostic biomarker and therapeutic target for TNBC.
Collapse
Affiliation(s)
- Danyang Chen
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Shanshan Zeng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Huisi Qiu
- The Sixth Affiliated Hospital of Guangzhou Medical University, Qingyuan People's Hospital, Qingyuan, Guangdong, China
| | - Mingqiang Yang
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Xin Lin
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Xinwu Lv
- School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang, Guangdong, China
| | - Pan Li
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Shaojuan Weng
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Siyue Kou
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Kai Luo
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China
| | - Zongcai Liu
- Laboratory of Endocrinology and Metabolism, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Yanmei Yi
- School of Basic Medical Sciences, Guangdong Medical University, Zhanjiang, Guangdong, China.
| | - Hao Liu
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Key Laboratory of "Translational Medicine on Malignant Tumor Treatment", Guangzhou, Guangdong, China.
| |
Collapse
|
31
|
Jiao LL, Dong HL, Liu MM, Wu PL, Cao Y, Zhang Y, Gao FG, Zhu HY. The potential roles of salivary biomarkers in neurodegenerative diseases. Neurobiol Dis 2024; 193:106442. [PMID: 38382884 DOI: 10.1016/j.nbd.2024.106442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 02/01/2024] [Accepted: 02/18/2024] [Indexed: 02/23/2024] Open
Abstract
Current research efforts on neurodegenerative diseases are focused on identifying novel and reliable biomarkers for early diagnosis and insight into disease progression. Salivary analysis is gaining increasing interest as a promising source of biomarkers and matrices for measuring neurodegenerative diseases. Saliva collection offers multiple advantages over the currently detected biofluids as it is easily accessible, non-invasive, and repeatable, allowing early diagnosis and timely treatment of the diseases. Here, we review the existing findings on salivary biomarkers and address the potential value in diagnosing neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, Huntington's disease and Amyotrophic lateral sclerosis. Based on the available research, β-amyloid, tau protein, α-synuclein, DJ-1, Huntington protein in saliva profiles display reliability and validity as the biomarkers of neurodegenerative diseases.
Collapse
Affiliation(s)
- Ling-Ling Jiao
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Hui-Lin Dong
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China
| | - Meng-Meng Liu
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China
| | - Peng-Lin Wu
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China
| | - Yi Cao
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China
| | - Yuan Zhang
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China
| | - Fu-Gao Gao
- Xuzhou Cigarette Factory, China Tobacco Jiangsu Industrial Co Ltd, Xuzhou 221005, China.
| | - Huai-Yuan Zhu
- China Tobacco Jiangsu Industrial Co Ltd, Nanjing 210019, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China.
| |
Collapse
|
32
|
Karamali N, Daraei A, Rostamlou A, Mahdavi R, Akbari Jonoush Z, Ghadiri N, Mahmoudi Z, Mardi A, Javidan M, Sohrabi S, Baradaran B. Decoding contextual crosstalk: revealing distinct interactions between non-coding RNAs and unfolded protein response in breast cancer. Cancer Cell Int 2024; 24:104. [PMID: 38468244 PMCID: PMC10926595 DOI: 10.1186/s12935-024-03296-3] [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: 10/29/2023] [Accepted: 03/06/2024] [Indexed: 03/13/2024] Open
Abstract
Breast cancer is significantly influenced by endoplasmic reticulum (ER) stress, impacting both its initiation and progression. When cells experience an accumulation of misfolded or unfolded proteins, they activate the unfolded protein response (UPR) to restore cellular balance. In breast cancer, the UPR is frequently triggered due to challenging conditions within tumors. The UPR has a dual impact on breast cancer. On one hand, it can contribute to tumor growth by enhancing cell survival and resistance to programmed cell death in unfavorable environments. On the other hand, prolonged and severe ER stress can trigger cell death mechanisms, limiting tumor progression. Furthermore, ER stress has been linked to the regulation of non-coding RNAs (ncRNAs) in breast cancer cells. These ncRNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), play essential roles in cancer development by influencing gene expression and cellular processes. An improved understanding of how ER stress and ncRNAs interact in breast cancer can potentially lead to new treatment approaches. Modifying specific ncRNAs involved in the ER stress response might interfere with cancer cell survival and induce cell death. Additionally, focusing on UPR-associated proteins that interact with ncRNAs could offer novel therapeutic possibilities. Therefore, this review provides a concise overview of the interconnection between ER stress and ncRNAs in breast cancer, elucidating the nuanced effects of the UPR on cell fate and emphasizing the regulatory roles of ncRNAs in breast cancer progression.
Collapse
Affiliation(s)
- Negin Karamali
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Arshia Daraei
- Department of Immunology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Arman Rostamlou
- Department of Medical Biology, School of Medicine, University of EGE, Bornova, Izmir, Turkey
| | - Roya Mahdavi
- Student Research Committee, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Akbari Jonoush
- Student Research Committee, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Nooshin Ghadiri
- Student Research Committee, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Zahra Mahmoudi
- Department of Immunology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Amirhossein Mardi
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Moslem Javidan
- Student Research Committee, Ahvaz Jundishapur University of Medical Science, Ahvaz, Iran
- Department of Immunology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Sepideh Sohrabi
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Behzad Baradaran
- Department of Immunology, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| |
Collapse
|
33
|
Yaghoobi Z, Seyed Bagher Nazeri SS, Asadi A, Derafsh E, Talebi Taheri A, Tamtaji Z, Dadgostar E, Rahmati-Dehkordi F, Aschner M, Mirzaei H, Tamtaji OR, Nabavizadeh F. Non-coding RNAs and Aquaporin 4: Their Role in the Pathogenesis of Neurological Disorders. Neurochem Res 2024; 49:583-596. [PMID: 38114727 DOI: 10.1007/s11064-023-04067-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 11/10/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023]
Abstract
Neurological disorders are a major group of non-communicable diseases affecting quality of life. Non-Coding RNAs (ncRNAs) have an important role in the etiology of neurological disorders. In studies on the genesis of neurological diseases, aquaporin 4 (AQP4) expression and activity have both been linked to ncRNAs. The upregulation or downregulation of several ncRNAs leads to neurological disorder progression by targeting AQP4. The role of ncRNAs and AQP4 in neurological disorders is discussed in this review.
Collapse
Affiliation(s)
- Zahra Yaghoobi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran
| | | | - Amir Asadi
- Psychiatry and Behavioral Sciences Research Center, School of Medicine, Addiction Institute, and Department of Psychiatry, Mazandaran University of Medical Sciences, Sari, Iran
| | - Ehsan Derafsh
- Windsor University School of Medicine, Cayon, St Kitts and Nevis
| | - Abdolkarim Talebi Taheri
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zeinab Tamtaji
- Student Research Committee, Kashan University of Medical Sciences, Kashan, I.R. of Iran
| | - Ehsan Dadgostar
- Behavioral Sciences Research Center, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
- Student Research Committee, Isfahan University of Medical Sciences, Isfahan, I.R. of Iran
| | - Fatemeh Rahmati-Dehkordi
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran
| | - Michael Aschner
- Department of Molecular Pharmacology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Hamed Mirzaei
- Research Center for Biochemistry and Nutrition in Metabolic Diseases, Kashan University of Medical Sciences, Kashan, I.R. of Iran.
| | - Omid Reza Tamtaji
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| | - Fatemeh Nabavizadeh
- Electrophysiology Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
- Department of Physiology, School of Medicine, Tehran University of Medical Sciences, Tehran, I.R. of Iran.
| |
Collapse
|
34
|
Lv H, Chen K, Zhang D. Exploring the diagnostic value of blood circular RNA in atherosclerotic cardiovascular diseases by integrating bioinformatics and evidence-based medicine meta-analysis. Int J Biol Macromol 2024; 261:129386. [PMID: 38218302 DOI: 10.1016/j.ijbiomac.2024.129386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/21/2023] [Accepted: 12/29/2023] [Indexed: 01/15/2024]
Abstract
This meta-analysis aimed to investigate the diagnostic value of blood circular RNA (circRNA) in atherosclerotic cardiovascular diseases (AS). Using bioinformatics and evidence-based medicine, we identified circ_0001900 as a potential biomarker for diagnosing AS-related cardiovascular diseases. Bioinformatics analysis indicated that circ_0001900 may participate in AS progression by regulating lipid and atherosclerosis-related genes on the MAPK1/3, SRC, TRAF6, and STAT3 signaling pathways. In vivo results showed that circ_0001900 was significantly up-regulated in AS mouse and AS patients' peripheral blood (PB), serum, serum serum extracellular vesicles (EVs), and peripheral blood mononuclear cells (PBMCs), with good diagnostic efficacy as evaluated by ROC curve analysis. Circ_0001900 knockout inhibited AS progression, which may be related to the regulation of these signaling pathways. These findings suggest that circ_0001900 may serve as a potential diagnostic and therapeutic target for AS-related cardiovascular diseases.
Collapse
Affiliation(s)
- Huina Lv
- Department of Ultrasound, Shengjing Hospital of China Medical University, Shenyang 110004, China
| | - Keyan Chen
- Laboratory Animal Science of China Medical University, Shenyang, Liaoning 110122, China.
| | - Di Zhang
- Department of Cardiology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China.
| |
Collapse
|
35
|
Saleem A, Khan MU, Zahid T, Khurram I, Ghani MU, Ullah I, Munir R, Calina D, Sharifi-Rad J. Biological role and regulation of circular RNA as an emerging biomarker and potential therapeutic target for cancer. Mol Biol Rep 2024; 51:296. [PMID: 38340202 DOI: 10.1007/s11033-024-09211-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 01/04/2024] [Indexed: 02/12/2024]
Abstract
Circular RNAs (circRNAs) are a unique family of endogenous RNAs devoid of 3' poly-A tails and 5' end caps. These single-stranded circRNAs, found in the cytoplasm, are synthesized via back-splicing mechanisms, merging introns, exons, or both, resulting in covalently closed circular loops. They are profusely expressed across the eukaryotic transcriptome and offer heightened stability against exonuclease RNase R compared to linear RNA counterparts. This review endeavors to provide a comprehensive overview of circRNAs' characteristics, biogenesis, and mechanisms of action. Furthermore, aimed to shed light on the potential of circRNAs as significant biomarkers in various cancer types. It has been performed an exhaustive literature review, drawing on recent studies and findings related to circRNA characteristics, synthesis, function, evaluation techniques, and their associations with oncogenesis. CircRNAs are intricately associated with tumor progression and development. Their multifaceted roles encompass gene regulation through the sponging of proteins and microRNAs, controlling transcription and splicing, interacting with RNA binding proteins (RBPs), and facilitating gene translation. Due to these varied roles, circRNAs have become a focal point in tumor pathology investigations, given their promising potential as both biomarkers and therapeutic agents. CircRNAs, due to their unique biogenesis and multifunctionality, hold immense promise in the realm of oncology. Their stability, widespread expression, and intricate involvement in gene regulation underscore their prospective utility as reliable biomarkers and therapeutic targets in cancer. As our understanding of circRNAs deepens, advanced techniques for their detection, evaluation, and manipulation will likely emerge. These advancements might catalyze the translation of circRNA-based diagnostics and therapeutics into clinical practice, potentially revolutionizing cancer care and prognosis.
Collapse
Affiliation(s)
- Ayman Saleem
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Muhammad Umer Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan.
| | - Tazeen Zahid
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Iqra Khurram
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Muhammad Usman Ghani
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
| | - Rakhtasha Munir
- Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Daniela Calina
- Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, 200349, Craiova, Romania.
| | | |
Collapse
|
36
|
Meccariello R, Bellenchi GC, Pulcrano S, D’Addario SL, Tafuri D, Mercuri NB, Guatteo E. Neuronal dysfunction and gene modulation by non-coding RNA in Parkinson's disease and synucleinopathies. Front Cell Neurosci 2024; 17:1328269. [PMID: 38249528 PMCID: PMC10796818 DOI: 10.3389/fncel.2023.1328269] [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: 10/26/2023] [Accepted: 12/07/2023] [Indexed: 01/23/2024] Open
Abstract
Over the last few decades, emerging evidence suggests that non-coding RNAs (ncRNAs) including long-non-coding RNA (lncRNA), microRNA (miRNA) and circular-RNA (circRNA) contribute to the molecular events underlying progressive neuronal degeneration, and a plethora of ncRNAs have been identified significantly misregulated in many neurodegenerative diseases, including Parkinson's disease and synucleinopathy. Although a direct link between neuropathology and causative candidates has not been clearly established in many cases, the contribution of ncRNAs to the molecular processes leading to cellular dysfunction observed in neurodegenerative diseases has been addressed, suggesting that they may play a role in the pathophysiology of these diseases. Aim of the present Review is to overview and discuss recent literature focused on the role of RNA-based mechanisms involved in different aspects of neuronal pathology in Parkinson's disease and synucleinopathy models.
Collapse
Affiliation(s)
- Rosaria Meccariello
- Department of Medical and Movement Sciences and Wellness, University of Naples Parthenope, Naples, Italy
| | - Gian Carlo Bellenchi
- Institute of Genetics and Biophysics, CNR, Naples, Italy
- Experimental Neurology Laboratory, Santa Lucia Foundation IRCCS, Rome, Italy
| | | | - Sebastian Luca D’Addario
- Experimental Neurology Laboratory, Santa Lucia Foundation IRCCS, Rome, Italy
- Computational and Translational Neuroscience Laboratory, Institute of Cognitive Sciences and Technologies, CNR, Rome, Italy
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| | - Domenico Tafuri
- Department of Medical and Movement Sciences and Wellness, University of Naples Parthenope, Naples, Italy
| | - Nicola B. Mercuri
- Experimental Neurology Laboratory, Santa Lucia Foundation IRCCS, Rome, Italy
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
- Department of Systems Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Ezia Guatteo
- Department of Medical and Movement Sciences and Wellness, University of Naples Parthenope, Naples, Italy
- Experimental Neurology Laboratory, Santa Lucia Foundation IRCCS, Rome, Italy
- Aligning Science Across Parkinson’s (ASAP) Collaborative Research Network, Chevy Chase, MD, United States
| |
Collapse
|
37
|
Lun J, Guo J, Yu M, Zhang H, Fang J. Circular RNAs in inflammatory bowel disease. Front Immunol 2023; 14:1307985. [PMID: 38187401 PMCID: PMC10771839 DOI: 10.3389/fimmu.2023.1307985] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 12/07/2023] [Indexed: 01/09/2024] Open
Abstract
Inflammatory bowel disease (IBD) is a term encompassing a few chronic inflammatory disorders that leads to damage of the intestinal tract. Although much progress has been made in understanding the pathology of IBD, the precise pathogenesis is not completely understood. Circular RNAs (circRNAs) are single-stranded, covalently closed, endogenous molecules in eukaryotes with a variety of biological functions. CircRNAs have been shown to have regulatory effects in many diseases, such as cancer, cardiovascular disease, and neurological disorders. CircRNAs have also been found to play important roles in IBD, and although they are not sufficiently investigated in the context of IBD, a few circRNAs have been identified as potential biomarkers for the diagnosis and prognosis of IBD and as potential therapeutic targets for IBD. Herein, we survey recent progress in understanding the functions and roles of circRNAs in IBD and discuss their potential clinical applications.
Collapse
Affiliation(s)
- Jie Lun
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Jing Guo
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao, China
| | - Mengchao Yu
- Central Laboratories, Qingdao Municipal Hospital, Qingdao, China
| | - Hongwei Zhang
- Shandong Provincial Maternal and Child Health Care Hospital Affiliated to Qingdao University, Jinan, China
| | - Jing Fang
- Department of Oncology, The Affiliated Hospital of Qingdao University, Qingdao Cancer Institute, Qingdao, China
| |
Collapse
|
38
|
Xie G, Wu T, Ji G, Wu H, Lai Y, Wei B, Huang W. Circular RNA and intervertebral disc degeneration: unravelling mechanisms and implications. Front Mol Biosci 2023; 10:1302017. [PMID: 38192334 PMCID: PMC10773835 DOI: 10.3389/fmolb.2023.1302017] [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: 09/25/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
Low back pain (LBP) is a major public health problem worldwide and a significant health and economic burden. Intervertebral disc degeneration (IDD) is the reason for LBP. However, we have not identified effective therapeutic strategies to address this challenge. With accumulating knowledge on the role of circular RNAs in the pathogenesis of IDD, we realised that circular RNAs (circRNAs) may have tremendous therapeutic potential and clinical application prospects in this field. This review presents an overview of the current understanding of characteristics, classification, biogenesis, and function of circRNAs and summarises the protective and detrimental circRNAs involved in the intervertebral disc that have been studied thus far. This review is aimed to help researchers better understand the regulatory role of circRNAs in the progression of IDD, reveal their clinical therapeutic potential, and provide a theoretical basis for the prevention and targeted treatment of IDD.
Collapse
Affiliation(s)
- Guohao Xie
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Tingrui Wu
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Guangju Ji
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Hang Wu
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Yue Lai
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Bo Wei
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
| | - Wenhua Huang
- Orthopaedic Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, China
- Guangdong Engineering Research Center for Translation of Medical 3D Printing Application, Guangdong Provincial Key Laboratory of Medical Biomechanics, National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Guangdong Medical Innovation Platform for Translation of 3D Printing Application, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| |
Collapse
|
39
|
Li G, Zeng F, Luo J, Liang C, Xiao Q. MNCLCDA: predicting circRNA-drug sensitivity associations by using mixed neighbourhood information and contrastive learning. BMC Med Inform Decis Mak 2023; 23:291. [PMID: 38110886 PMCID: PMC10729363 DOI: 10.1186/s12911-023-02384-0] [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: 07/12/2023] [Accepted: 12/01/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND circRNAs play an important role in drug resistance and cancer development. Recently, many studies have shown that the expressions of circRNAs in human cells can affect the sensitivity of cells to therapeutic drugs, thus significantly influencing the therapeutic effects of these drugs. Traditional biomedical experiments required to verify this sensitivity relationship are not only time-consuming but also expensive. Hence, the development of an efficient computational approach that can accurately predict the novel associations between drug sensitivities and circRNAs is a crucial and pressing need. METHODS In this research, we present a novel computational framework called MNCLCDA, which aims to predict the potential associations between drug sensitivities and circRNAs to assist with medical research. First, MNCLCDA quantifies the similarity between the given drug and circRNA using drug structure information, circRNA gene sequence information, and GIP kernel information. Due to the existence of noise in similarity information, we employ a preprocessing approach based on random walk with restart for similarity networks to efficiently capture the useful features of circRNAs and drugs. Second, we use a mixed neighbourhood graph convolutional network to obtain the neighbourhood information of nodes. Then, a graph-based contrastive learning method is used to enhance the robustness of the model, and finally, a double Laplace-regularized least-squares method is used to predict potential circRNA-drug associations through the kernel matrices in the circRNA and drug spaces. RESULTS Numerous experimental results show that MNCLCDA outperforms six other advanced methods. In addition, the excellent performance of our proposed model in case studies illustrates that MNCLCDA also has the ability to predict the associations between drug sensitivity and circRNA in practical situations. CONCLUSIONS After a large number of experiments, it is illustrated that MNCLCDA is an efficient tool for predicting the potential associations between drug sensitivities and circRNAs, thereby can provide some guidance for clinical trials.
Collapse
Affiliation(s)
- Guanghui Li
- School of Information Engineering, East China Jiaotong University, Nanchang, China.
| | - Feifan Zeng
- School of Information Engineering, East China Jiaotong University, Nanchang, China
| | - Jiawei Luo
- College of Computer Science and Electronic Engineering, Hunan University, Changsha, China.
| | - Cheng Liang
- School of Information Science and Engineering, Shandong Normal University, Jinan, China
| | - Qiu Xiao
- College of Information Science and Engineering, Hunan Normal University, Changsha, China
| |
Collapse
|
40
|
Khalilian S, Tabari MAK, Omrani MA, Ghafouri-Fard S. Emerging functions and significance of circCDYL in human disorders. Mol Biol Rep 2023; 51:7. [PMID: 38085365 DOI: 10.1007/s11033-023-08993-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/13/2023] [Indexed: 12/18/2023]
Abstract
Circular RNAs (circRNAs) are a group of non-coding transcripts in which a loop structure is shaped via a back splicing procedure. They have central roles in the regulation of gene expression. hsa_circ_0008285, alternatively named as circCDYL, is a circular RNA originated from the exon 4 of CDYL gene. It is produced by a back-splice incident and is mainly located in the cytoplasm. It has no internal ribosome entry site, open reading frame and intronic sequences. CircCDYL dysregulation has been reported in the malignant conditions including multiple myeloma, mantle cell lymphoma, breast cancer, non-small cell lung cancer, Wilms tumor, bladder cancer, colon cancer, and hepatocellular carcinoma. It also has an emerging role in the pathophysiology of non-malignant conditions including myocardial infarction, gestational diabetes mellitus, membranous nephropathy, and abdominal aortic aneurysm. In the current study, we summarize the emerging roles of circCDYL in malignant and non-malignant conditions.
Collapse
Affiliation(s)
- Sheyda Khalilian
- Student Research Committee, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- USERN Office, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Amin Khazeei Tabari
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
- USERN Office, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| |
Collapse
|
41
|
Zhu W, Huang Y, Yu C. The emerging role of circRNAs on skeletal muscle development in economical animals. Anim Biotechnol 2023; 34:2778-2792. [PMID: 36052979 DOI: 10.1080/10495398.2022.2118130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
CircRNAs are a novel type of closed circular molecules formed through a covalent bond lacking a 5'cap and 3' end tail, which mainly arise from mRNA precursor. They are widely distributed in plants and animals and are characterized by stable structure, high conservativeness in cells or tissues, and showed the expression specificity at different stages of development in different tissues. CircRNAs have been gradually attracted wide attention with the development of RNA sequencing, which become a new research hotspot in the field of RNA. CircRNAs play an important role in gene expression regulation. Presently, the related circRNAs research in the regulation of animal muscle development is still at the initial stage. In this review, the formation, properties, biological functions of circRNAs were summarized. The recent research progresses of circRNAs in skeletal muscle growth and development from economic animals including livestock, poultry and fishes were introduced. Finally, we proposed a prospective for further studies of circRNAs in muscle development, and we hope our research could provide new ideas, some theoretical supports and helps for new molecular genetic markers exploitation and animal genetic breeding in future.
Collapse
Affiliation(s)
- Wenwen Zhu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| | - Yong Huang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Chuan Yu
- Animal Diseases and Public Health Engineering Research Center of Henan Province, Luoyang Polytechnic, Luoyang, China
| |
Collapse
|
42
|
Xu T, Hu Y, Zhao Y, Qi Y, Zhang S, Li P. Hsa_circ_0046534 accelerates esophageal squamous cell carcinoma proliferation and metastasis via regulating MMP2 expression by sponging miR-339-5p. Cell Signal 2023; 112:110906. [PMID: 37748540 DOI: 10.1016/j.cellsig.2023.110906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 09/27/2023]
Abstract
Esophageal cancer is one of the most malignant gastrointestinal malignancies. Esophageal squamous cell carcinoma (ESCC) is the most common type of esophageal cancer in China. In recent years, with developments in basic medicine, it has been demonstrated that the abnormal expression of circular RNA (circRNA) plays an important role in the progression and prognosis of ESCC. This study explored the role and downstream molecular mechanisms of circ_0046534 in ESCC. We identified circ_0046534, which was found to be highly expressed in ESCC tissues and cells. Moreover, the downregulation of circ_0046534 inhibited the proliferation, migration and invasion of ESCC cells and the growth and metastasis of ESCC tumours in vivo. Dual-luciferase reporter assays showed that circ_0046534 sponged miR-339-5p and inhibited the expression of miR-339-5p. Furthermore, MMP2 was identified to be a direct target of miR-339-5p through bioinformatics analysis. In addition, the knockdown of circ_0046534 inhibited the expression of the downstream target gene matrix metalloproteinase 2 (MMP2) by releasing the adsorption of miR-339-5p. Taken together, this study demonstrated that silencing circ_0046534 inhibited the growth and metastasis of ESCC through the miR-339-5p/MMP2 pathway. Circ_0046534 is expected to serve as a new biomarker and target for ESCC and provide a new direction for its diagnosis and treatment.
Collapse
Affiliation(s)
- Tingting Xu
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; Department of Pathology, Henan Provincial People's Hospital, Zhengzhou 450001, China
| | - Yanglin Hu
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanyan Zhao
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yanan Qi
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shanfeng Zhang
- Department of Basic Medical Experimental Center, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Pei Li
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; Department of Basic Medical Experimental Center, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| |
Collapse
|
43
|
Yang T, Qiu L, Jiang Y, Bai H, Bi Y, Wang Z, Chen G, Chang G. Identification, biogenesis, and function prediction of a novel circRNA_3238 of chicken. Anim Biotechnol 2023; 34:2527-2536. [PMID: 35875943 DOI: 10.1080/10495398.2022.2102504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
With the development of high-throughput sequencing, circular RNA has come into people's vision and attracted more and more attention. Many studies have found that circular RNA plays an important role in a variety of biological processes and the occurrence and development of diseases. According to the previous sequencing results, circRNA_3238 was differentially expressed in ALV-J infected group and the non-infected group was selected for subsequent verification and analysis. We found that circRNA_3238 is a stable, circular transcript, which mainly exists in the cytoplasm. And it is widely expressed in various tissues of chickens, and highly expressed in lung, lymph, and bursa of fabricius. Bioinformatics results show that circRNA_3238 and the predicted target genes enriched MAPK signaling pathway, Notch signaling pathway, and other pathways related to disease or immune, revealing circRNA_3238 may indirectly regulate the process of ALV-J infection by regulating target genes.
Collapse
Affiliation(s)
- Ting Yang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lingling Qiu
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Bai
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Yulin Bi
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| |
Collapse
|
44
|
Yuan L, Duan J, Zhou H. Perspectives of circular RNAs in diabetic complications from biological markers to potential therapeutic targets (Review). Mol Med Rep 2023; 28:194. [PMID: 37681455 PMCID: PMC10502942 DOI: 10.3892/mmr.2023.13081] [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: 02/13/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023] Open
Abstract
Chronic complications of diabetes increase mortality and disability of patients. It is crucial to find potential early biomarkers and provide novel therapeutic strategies for diabetic complications. Circular RNAs (circRNAs), covalently closed RNA molecules in eukaryotes, have high stability. Recent studies have confirmed that differentially expressed circRNAs have a vital role in diabetic complications. Certain circRNAs, such as circRNA ankyrin repeat domain 36, circRNA homeodomain‑interacting protein kinase 3 (circHIPK3) and circRNA WD repeat domain 77, are associated with inflammation, endothelial cell apoptosis and smooth muscle cell proliferation, leading to vascular endothelial dysfunction and atherosclerosis. CircRNA LDL receptor related protein 6, circRNA actin related protein 2, circ_0000064, circ‑0101383, circ_0123996, hsa_circ_0003928 and circ_0000285 mediate inflammation, apoptosis and autophagy of podocytes, mesangial cell hypertrophy and proliferation, as well as tubulointerstitial fibrosis, in diabetic nephropathy by regulating the expression of microRNAs and proteins. Circ_0005015, circRNA PWWP domain containing 2A, circRNA zinc finger protein 532, circRNA zinc finger protein 609, circRNA DNA methyltransferase 3β, circRNA collagen type I α2 chain and circHIPK3 widely affect multiple biological processes of diabetic retinopathy. Furthermore, circ_000203, circ_010567, circHIPK3, hsa_circ_0076631 and circRNA cerebellar degeneration‑related protein 1 antisense are involved in the pathology of diabetic cardiomyopathy. CircHIPK3 is the most well‑studied circRNA in the field of diabetic complications and is most likely to become a biological marker and therapeutic target for diabetic complications. The applications of circRNAs may be a promising treatment strategy for human diseases at the molecular level. The relationship between circRNAs and diabetic complications is summarized in the present study. Of note, circRNA‑targeted therapy and the role of circRNAs as biomarkers may potentially be used in diabetic complications in the future.
Collapse
Affiliation(s)
- Lingling Yuan
- Department of Endocrinology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Jinsheng Duan
- Department of Cardiology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| | - Hong Zhou
- Department of Endocrinology, The Second Hospital of Hebei Medical University, Shijiazhuang, Hebei 050000, P.R. China
| |
Collapse
|
45
|
Ning J, Luo Y, Chen L, Xiao G, Tanzhu G, Zhou R. CircRNAs and lung cancer: Insight into their roles in metastasis. Biomed Pharmacother 2023; 166:115260. [PMID: 37633056 DOI: 10.1016/j.biopha.2023.115260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/28/2023] [Accepted: 07/30/2023] [Indexed: 08/28/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related mortality worldwide. A major contributing factor to the poor survival rates in lung cancer is the high prevalence of metastasis at the time of diagnosis. To address this critical issue, it is imperative to investigate the mechanisms underlying lung cancer metastasis. Circular RNAs (circRNAs), a distinct type of ribonucleic acid characterized by their unique circular structure, have been implicated in the progression of various diseases. Recent studies have highlighted the close association between circRNAs and the occurrence and development of lung cancer, particularly in relation to metastasis. In this review, we provide a concise overview of the expression patterns and prognostic significance of circRNAs in lung cancer. Additionally, we summarized the current understanding of the clinical relevance of circRNAs in lung cancer metastasis. Furthermore, we systematically focused on the roles of circRNAs in each step of lung cancer metastasis, reflecting the sequential progression of this process. Notably, circRNAs exhibit dual functionality in lung cancer metastasis, acting both as facilitators and inhibitors of metastatic processes. Given their potential, circRNAs hold promise as novel biomarkers and therapeutic targets for lung cancer metastasis, warranting further investigation.
Collapse
Affiliation(s)
- Jiaoyang Ning
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Yi Luo
- Department of Geriatric Medicine, Center of Coronary Circulation, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha 410008, China
| | - Liu Chen
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Gang Xiao
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China
| | - Guilong Tanzhu
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China.
| | - Rongrong Zhou
- Department of Oncology, Xiangya Hospital, Central South University, Changsha 410008, China; Xiangya Lung Cancer Center, Xiangya Hospital, Central South University, Changsha 410008, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China.
| |
Collapse
|
46
|
Zhu SY, Wang XY, Xie H, Liu LZ. Comprehensive analysis of circular RNAs in nasopharyngeal cancer. Genes Genomics 2023; 45:1339-1346. [PMID: 37651065 DOI: 10.1007/s13258-023-01438-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/07/2023] [Indexed: 09/01/2023]
Abstract
BACKGROUND Nasopharyngeal cancer (NPC) is a type of epithelial malignancy that is positive for Epstein-Barr virus (EBV) and affects several populations worldwide. Due to the high rates of relapse and metastasis following primary treatment, there is an urgent need to identify new candidates for NPC therapy. Recently, circular RNA (circRNA) has emerged as a promising target for cancer diagnosis and prevention. OBJECTIVE This study aimed to study the circRNAs enriched in NPC patients, and further analyze potential signaling pathways involved. METHODS A new bioinformatic tool named psirc was used to analyze RNA-sequencing datasets from NPC patients and normal specimens to study the NPC-enriched circRNAs. RESULTS We identified and quantified the full-length circRNA in these samples and found the top 10 enriched circRNAs in NPC patients compared to control samples. Furthermore, we selected the most enriched circRNA, circEEF1A1_E8B1, and studied its protein coding ability, microRNA and RNA-binding protein (RBP) binding capacity. We also constructed a protein-protein interaction (PPI) network for its binding proteins and extracted hub genes. Finally, we conducted survival analysis for these hub genes in head and neck cancer patients. CONCLUSIONS In summary, our study has revealed the presence of previously unidentified circRNAs that are enriched in NPC patients. Through an analysis of their molecular functions, we have advanced our understanding of the potential role of circRNAs in NPC development.
Collapse
Affiliation(s)
- Si-Yu Zhu
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China
| | - Xiao-Yi Wang
- Department of Radiology, Hainan General Hospital (Hainan Affiliated Hospital of Hainan Medical University), Haikou, China
| | - Hui Xie
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China.
| | - Li-Zhi Liu
- Department of Radiology, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, 651 Dongfeng Road East, 510060, Guangzhou, Guangdong, People's Republic of China.
| |
Collapse
|
47
|
Eun JW, Cheong JY, Jeong JY, Kim HS. A New Understanding of Long Non-Coding RNA in Hepatocellular Carcinoma-From m 6A Modification to Blood Biomarkers. Cells 2023; 12:2272. [PMID: 37759495 PMCID: PMC10528438 DOI: 10.3390/cells12182272] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
With recent advancements in biological research, long non-coding RNAs (lncRNAs) with lengths exceeding 200 nucleotides have emerged as pivotal regulators of gene expression and cellular phenotypic modulation. Despite initial skepticism due to their low sequence conservation and expression levels, their significance in various biological processes has become increasingly apparent. We provided an overview of lncRNAs and discussed their defining features and modes of operation. We then explored their crucial function in the hepatocarcinogenesis process, elucidating their complex involvement in hepatocellular carcinoma (HCC). The influential role of lncRNAs within the HCC tumor microenvironment is emphasized, illustrating their potential as key modulators of disease dynamics. We also investigated the significant influence of N6-methyladenosine (m6A) modification on lncRNA function in HCC, enhancing our understanding of both their roles and their upstream regulators. Additionally, the potential of lncRNAs as promising biomarkers was discussed in liver cancer diagnosis, suggesting a novel avenue for future research and clinical application. Finally, our work underscored the dual potential of lncRNAs as both contributors to HCC pathogenesis and innovative tools for its diagnosis. Existing challenges and prospective trajectories in lncRNA research are also discussed, emphasizing their potential in advancing liver cancer research.
Collapse
Affiliation(s)
- Jung Woo Eun
- Department of Gastroenterology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; (J.W.E.); (J.Y.C.)
| | - Jae Youn Cheong
- Department of Gastroenterology, Ajou University School of Medicine, 164 World cup-ro, Yeongtong-gu, Suwon 16499, Republic of Korea; (J.W.E.); (J.Y.C.)
| | - Jee-Yeong Jeong
- Department of Biochemistry, College of Medicine, Kosin University, Seo-gu, Busan 49267, Republic of Korea;
- Institute for Medical Science, College of Medicine, Kosin University, Seo-gu, Busan 49267, Republic of Korea
| | - Hyung Seok Kim
- Department of Biochemistry, College of Medicine, Kosin University, Seo-gu, Busan 49267, Republic of Korea;
| |
Collapse
|
48
|
Pisignano G, Michael DC, Visal TH, Pirlog R, Ladomery M, Calin GA. Going circular: history, present, and future of circRNAs in cancer. Oncogene 2023; 42:2783-2800. [PMID: 37587333 PMCID: PMC10504067 DOI: 10.1038/s41388-023-02780-w] [Citation(s) in RCA: 98] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 07/04/2023] [Accepted: 07/10/2023] [Indexed: 08/18/2023]
Abstract
To date, thousands of highly abundant and conserved single-stranded RNA molecules shaped into ring structures (circRNAs) have been identified. CircRNAs are multifunctional molecules that have been shown to regulate gene expression transcriptionally and post-transcriptionally and exhibit distinct tissue- and development-specific expression patterns associated with a variety of normal and disease conditions, including cancer pathogenesis. Over the past years, due to their intrinsic stability and resistance to ribonucleases, particular attention has been drawn to their use as reliable diagnostic and prognostic biomarkers in cancer diagnosis, treatment, and prevention. However, there are some critical caveats to their utility in the clinic. Their circular shape limits their annotation and a complete functional elucidation is lacking. This makes their detection and biomedical application still challenging. Herein, we review the current knowledge of circRNA biogenesis and function, and of their involvement in tumorigenesis and potential utility in cancer-targeted therapy.
Collapse
Affiliation(s)
- Giuseppina Pisignano
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK.
| | - David C Michael
- Department of Life Sciences, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Tanvi H Visal
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Radu Pirlog
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Michael Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol, BS16 1QY, UK
| | - George A Calin
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|
49
|
Maarouf M, Wang L, Wang Y, Rai KR, Chen Y, Fang M, Chen JL. Functional Involvement of circRNAs in the Innate Immune Responses to Viral Infection. Viruses 2023; 15:1697. [PMID: 37632040 PMCID: PMC10458642 DOI: 10.3390/v15081697] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
Effective viral clearance requires fine-tuned immune responses to minimize undesirable inflammatory responses. Circular RNAs (circRNAs) are a class of non-coding RNAs that are abundant and highly stable, formed by backsplicing pre-mRNAs, and expressed ubiquitously in eukaryotic cells, emerging as critical regulators of a plethora of signaling pathways. Recent progress in high-throughput sequencing has enabled a better understanding of the physiological and pathophysiological functions of circRNAs, overcoming the obstacle of the sequence overlap between circRNAs and their linear cognate mRNAs. Some viruses also encode circRNAs implicated in viral replication or disease progression. There is increasing evidence that viral infections dysregulate circRNA expression and that the altered expression of circRNAs is critical in regulating viral infection and replication. circRNAs were shown to regulate gene expression via microRNA and protein sponging or via encoding small polypeptides. Recent studies have also highlighted the potential role of circRNAs as promising diagnostic and prognostic biomarkers, RNA vaccines and antiviral therapy candidates due to their higher stability and lower immunogenicity. This review presents an up-to-date summary of the mechanistic involvement of circRNAs in innate immunity against viral infections, the current understanding of their regulatory roles, and the suggested applications.
Collapse
Affiliation(s)
- Mohamed Maarouf
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Lulu Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yiming Wang
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Kul Raj Rai
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Microbiology, ShiGan International College of Science and Technology/ShiGan Health Foundation, Narayangopal Chowk, Kathmandu 44600, Nepal
| | - Yuhai Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Min Fang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences (CAS), Beijing 100101, China;
| | - Ji-Long Chen
- Key Laboratory of Animal Pathogen Infection and Immunology of Fujian Province, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (M.M.); (L.W.); (Y.W.); (K.R.R.); (Y.C.)
- Fujian Province Joint Laboratory of Animal Pathogen Prevention and Control of the “Belt and Road”, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| |
Collapse
|
50
|
Santini D, Botticelli A, Galvano A, Iuliani M, Incorvaia L, Gristina V, Taffon C, Foderaro S, Paccagnella E, Simonetti S, Fazio F, Scagnoli S, Pomati G, Pantano F, Perrone G, De Falco E, Russo A, Spinelli GP. Network approach in liquidomics landscape. J Exp Clin Cancer Res 2023; 42:193. [PMID: 37542343 PMCID: PMC10401883 DOI: 10.1186/s13046-023-02743-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 06/27/2023] [Indexed: 08/06/2023] Open
Abstract
Tissue-based biopsy is the present main tool to explore the molecular landscape of cancer, but it also has many limits to be frequently executed, being too invasive with the risk of side effects. These limits and the ability of cancer to constantly evolve its genomic profile, have recently led to the need of a less invasive and more accurate alternative, such as liquid biopsy. By searching Circulating Tumor Cells and residues of their nucleic acids or other tumor products in body fluids, especially in blood, but also in urine, stools and saliva, liquid biopsy is becoming the future of clinical oncology. Despite the current lack of a standardization for its workflows, that makes it hard to be reproduced, liquid biopsy has already obtained promising results for cancer screening, diagnosis, prognosis, and risk of recurrence.Through a more accessible molecular profiling of tumors, it could become easier to identify biomarkers predictive of response to treatment, such as EGFR mutations in non-small cell lung cancer and KRAS mutations in colorectal cancer, or Microsatellite Instability and Mismatch Repair as predictive markers of pembrolizumab response.By monitoring circulating tumor DNA in longitudinal repeated sampling of blood we could also predict Minimal Residual Disease and the risk of recurrence in already radically resected patients.In this review we will discuss about the current knowledge of limitations and strengths of the different forms of liquid biopsies for its inclusion in normal cancer management, with a brief nod to their newest biomarkers and its future implications.
Collapse
Affiliation(s)
- Daniele Santini
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Andrea Botticelli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | - Antonio Galvano
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Michele Iuliani
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Lorena Incorvaia
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Valerio Gristina
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Chiara Taffon
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Simone Foderaro
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Elisa Paccagnella
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
| | - Sonia Simonetti
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Federico Fazio
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy.
| | - Simone Scagnoli
- Oncologia Medica A, Policlinico Umberto 1, La Sapienza Università Di Roma, Rome, Italy
| | | | - Francesco Pantano
- Medical Oncology, Fondazione Policlinico Universitario Campus Bio-Medico, Department of Medicine and Surgery, Università Campus Bio-Medico Di Roma, Selcetta, Italy
| | - Giuseppe Perrone
- Anatomical Pathology Operative Research Unit, Fondazione Policlinico Universitario Campus Bio-Medico, Rome, Italy
- Department of Medicine and Surgery, Research Unit of Anatomical Pathology, Università Campus Bio-Medico Di Roma, Rome, Italy
| | - Elena De Falco
- Department of Medical Surgical Sciences and Biotechnologies, Sapienza University of Rome, C.So Della Repubblica 79, 04100, Latina, Italy
- Mediterranea Cardiocentro, 80122, Naples, Italy
| | - Antonio Russo
- Section of Medical Oncology, Department of Surgical, Oncological and Oral Sciences, University of Palermo, Palermo, Italy
| | - Gian Paolo Spinelli
- UOC Oncologia Territoriale, Polo Pontino, La Sapienza Università Di Roma, Latina, Italy
| |
Collapse
|