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Seyhan AA. Circulating Liquid Biopsy Biomarkers in Glioblastoma: Advances and Challenges. Int J Mol Sci 2024; 25:7974. [PMID: 39063215 PMCID: PMC11277426 DOI: 10.3390/ijms25147974] [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: 06/12/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Gliomas, particularly glioblastoma (GBM), represent the most prevalent and aggressive tumors of the central nervous system (CNS). Despite recent treatment advancements, patient survival rates remain low. The diagnosis of GBM traditionally relies on neuroimaging methods such as magnetic resonance imaging (MRI) or computed tomography (CT) scans and postoperative confirmation via histopathological and molecular analysis. Imaging techniques struggle to differentiate between tumor progression and treatment-related changes, leading to potential misinterpretation and treatment delays. Similarly, tissue biopsies, while informative, are invasive and not suitable for monitoring ongoing treatments. These challenges have led to the emergence of liquid biopsy, particularly through blood samples, as a promising alternative for GBM diagnosis and monitoring. Presently, blood and cerebrospinal fluid (CSF) sampling offers a minimally invasive means of obtaining tumor-related information to guide therapy. The idea that blood or any biofluid tests can be used to screen many cancer types has huge potential. Tumors release various components into the bloodstream or other biofluids, including cell-free nucleic acids such as microRNAs (miRNAs), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), proteins, extracellular vesicles (EVs) or exosomes, metabolites, and other factors. These factors have been shown to cross the blood-brain barrier (BBB), presenting an opportunity for the minimally invasive monitoring of GBM as well as for the real-time assessment of distinct genetic, epigenetic, transcriptomic, proteomic, and metabolomic changes associated with brain tumors. Despite their potential, the clinical utility of liquid biopsy-based circulating biomarkers is somewhat constrained by limitations such as the absence of standardized methodologies for blood or CSF collection, analyte extraction, analysis methods, and small cohort sizes. Additionally, tissue biopsies offer more precise insights into tumor morphology and the microenvironment. Therefore, the objective of a liquid biopsy should be to complement and enhance the diagnostic accuracy and monitoring of GBM patients by providing additional information alongside traditional tissue biopsies. Moreover, utilizing a combination of diverse biomarker types may enhance clinical effectiveness compared to solely relying on one biomarker category, potentially improving diagnostic sensitivity and specificity and addressing some of the existing limitations associated with liquid biomarkers for GBM. This review presents an overview of the latest research on circulating biomarkers found in GBM blood or CSF samples, discusses their potential as diagnostic, predictive, and prognostic indicators, and discusses associated challenges and future perspectives.
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Affiliation(s)
- Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA;
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Joint Program in Cancer Biology, Lifespan Health System and Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
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2
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Botwe G, Fang X, Mukhtar YM, Zhou Y, Tang H, Wang M, Zhang J, Fu M, Jiang P, Gu J, Zhang X. Circular RNAs as biomarkers and therapeutic targets for gastrointestinal cancers. J Gastroenterol Hepatol 2024; 39:1230-1246. [PMID: 38504413 DOI: 10.1111/jgh.16536] [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: 09/06/2023] [Revised: 02/03/2024] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
Circular RNAs are a class of noncoding RNAs with covalently linked 5' and 3' ends that arise from backsplicing events. The absence of a 5' cap and a 3' poly(A) tail makes circular RNAs relatively more stable than their linear counterparts. They are evolutionary conserved and tissue-specific, and some show disease-specific expression patterns. Although their biological functions remain largely unknown, circular RNAs have been shown to play regulatory roles by acting as microRNA sponges, regulators of RNA-binding proteins, alternative splicing, and parental gene expression, and they could even encode proteins. Over the past few decades, circular RNAs have attracted wide attention in oncology owing to their implications in various tumors. Many circular RNAs have been characterized as key players in gastrointestinal cancers and influence cancer growth, progression, metastasis, and therapeutic resistance. Accumulating evidence reveals that their unique characteristics, coupled with their critical roles in tumorigenesis, make circular RNAs promising non-invasive clinical biomarkers for gastrointestinal cancers. In the present review, we summarized the biological roles of the emerging circular RNAs and their potential as biomarkers and therapeutic targets, which may help better understand their clinical significance in the management of gastrointestinal cancers.
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Affiliation(s)
- Godwin Botwe
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xinjian Fang
- Department of Oncology, Gaochun Hospital Affiliated to Jiangsu University, Nanjing, Jiangsu, China
| | - Yusif Mohammed Mukhtar
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yue Zhou
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Haozhou Tang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Maoye Wang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jiahui Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Min Fu
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Pengcheng Jiang
- Institute of Digestive Diseases, The Affiliated People's Hospital of Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jianmei Gu
- Department of Clinical Laboratory Medicine, Nantong Tumor Hospital/Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xu Zhang
- Department of Laboratory Medicine, School of Medicine, Jiangsu University, Zhenjiang, Jiangsu, China
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3
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Mashayekhi V, Schomisch A, Rasheed S, Aparicio-Puerta E, Risch T, Yildiz D, Koch M, Both S, Ludwig N, Legroux TM, Keller A, Müller R, Fuhrmann G, Hoppstädter J, Kiemer AK. The RNA binding protein IGF2BP2/IMP2 alters the cargo of cancer cell-derived extracellular vesicles supporting tumor-associated macrophages. Cell Commun Signal 2024; 22:344. [PMID: 38937789 PMCID: PMC11212187 DOI: 10.1186/s12964-024-01701-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 06/05/2024] [Indexed: 06/29/2024] Open
Abstract
BACKGROUND Tumor cells release extracellular vesicles (EVs) that contribute to the polarization of macrophages towards tumor-associated macrophages (TAMs). High expression levels of the RNA binding protein IGF2BP2/IMP2 are correlated with increased tumor cell proliferation, invasion, and poor prognosis in the clinic. However, there is a lack of understanding of whether IMP2 affects the cargo of cancer cell-derived EVs, thereby modulating macrophage polarization. METHODS EVs were isolated from IMP2-expressing HCT116 parental cells (WT) and CRISPR/Cas9 IMP2 knockout (KO) cells. EVs were characterized according to MISEV guidelines, microRNA cargo was assessed by microRNA-Seq, and the protein cargo was analyzed by proteomics. Primary human monocyte-derived macrophages (HMDMs) were polarized by EVs, and the expression of genes and surface markers was assessed using qPCR and flow cytometry, respectively. Morphological changes of macrophages, as well as the migratory potential of cancer cells, were assessed by the Incucyte® system and macrophage matrix degradation potential by zymography. Changes in the metabolic activity of macrophages were quantified using a Seahorse® analyzer. For in vivo studies, EVs were injected into the yolk sac of zebrafish larvae, and macrophages were isolated by fluorescence-activated cell sorting. RESULTS EVs from WT and KO cells had a similar size and concentration and were positive for 25 vesicle markers. The expression of tumor-promoting genes was higher in macrophages polarized with WT EVs than KO EVs, while the expression of TNF and IL6 was reduced. A similar pattern was observed in macrophages from zebrafish larvae treated in vivo. WT EV-polarized macrophages showed a higher abundance of TAM-like surface markers, higher matrix degrading activity, as well as a higher promotion of cancer cell migration. MicroRNA-Seq revealed a significant difference in the microRNA composition of WT and KO EVs, particularly a high abundance of miR-181a-5p in WT EVs, which was absent in KO EVs. Inhibitors of macropinocytosis and phagocytosis antagonized the delivery of miR-181a-5p into macrophages and the downregulation of the miR-181a-5p target DUSP6. Proteomics data showed differences in protein cargo in KO vs. WT EVs, with the differentially abundant proteins mainly involved in metabolic pathways. WT EV-treated macrophages exhibited a higher basal oxygen consumption rate and a lower extracellular acidification rate than KO EV-treated cells. CONCLUSION Our results show that IMP2 determines the cargo of EVs released by cancer cells, thereby modulating the EVs' actions on macrophages. Expression of IMP2 is linked to the secretion of EVs that polarize macrophages towards a tumor-promoting phenotype.
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Affiliation(s)
- Vida Mashayekhi
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Annika Schomisch
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Sari Rasheed
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Brunswick, Germany
| | - Ernesto Aparicio-Puerta
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | - Timo Risch
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Brunswick, Germany
| | - Daniela Yildiz
- Institute of Experimental and Clinical Pharmacology and Toxicology, PZMS, ZHMB, Saarland University, Homburg, Germany
| | - Marcus Koch
- INM - Leibniz Institute for New Materials, Saarbrücken, Germany
| | - Simon Both
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Nicole Ludwig
- Department of Human Genetics, Saarland University, Homburg, Germany
| | - Thierry M Legroux
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, University Hospital, Saarbrücken, Germany
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) - Helmholtz Centre for Infection Research (HZI), and Department of Pharmacy, Saarland University, Saarbrücken, Germany
- German Centre for Infection Research (DZIF), Brunswick, Germany
- Department of Pharmacy, Saarland University, Saarbrücken, Germany
| | - Gregor Fuhrmann
- Department of Pharmaceutical Biology, Friedrich-Alexander-Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Jessica Hoppstädter
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany
| | - Alexandra K Kiemer
- Department of Pharmacy, Pharmaceutical Biology, Saarland University, 66123, Saarbrücken, Germany.
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Boros LG, Kyriakopoulos AM, Brogna C, Piscopo M, McCullough PA, Seneff S. Long-lasting, biochemically modified mRNA, and its frameshifted recombinant spike proteins in human tissues and circulation after COVID-19 vaccination. Pharmacol Res Perspect 2024; 12:e1218. [PMID: 38867495 PMCID: PMC11169277 DOI: 10.1002/prp2.1218] [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: 12/28/2023] [Accepted: 04/20/2024] [Indexed: 06/14/2024] Open
Abstract
According to the CDC, both Pfizer and Moderna COVID-19 vaccines contain nucleoside-modified messenger RNA (mRNA) encoding the viral spike glycoprotein of severe acute respiratory syndrome caused by corona virus (SARS-CoV-2), administered via intramuscular injections. Despite their worldwide use, very little is known about how nucleoside modifications in mRNA sequences affect their breakdown, transcription and protein synthesis. It was hoped that resident and circulating immune cells attracted to the injection site make copies of the spike protein while the injected mRNA degrades within a few days. It was also originally estimated that recombinant spike proteins generated by mRNA vaccines would persist in the body for a few weeks. In reality, clinical studies now report that modified SARS-CoV-2 mRNA routinely persist up to a month from injection and can be detected in cardiac and skeletal muscle at sites of inflammation and fibrosis, while the recombinant spike protein may persist a little over half a year in blood. Vaccination with 1-methylΨ (pseudouridine enriched) mRNA can elicit cellular immunity to peptide antigens produced by +1 ribosomal frameshifting in major histocompatibility complex-diverse people. The translation of 1-methylΨ mRNA using liquid chromatography tandem mass spectrometry identified nine peptides derived from the mRNA +1 frame. These products impact on off-target host T cell immunity that include increased production of new B cell antigens with far reaching clinical consequences. As an example, a highly significant increase in heart muscle 18-flourodeoxyglucose uptake was detected in vaccinated patients up to half a year (180 days). This review article focuses on medical biochemistry, proteomics and deutenomics principles that explain the persisting spike phenomenon in circulation with organ-related functional damage even in asymptomatic individuals. Proline and hydroxyproline residues emerge as prominent deuterium (heavy hydrogen) binding sites in structural proteins with robust isotopic stability that resists not only enzymatic breakdown, but virtually all (non)-enzymatic cleavage mechanisms known in chemistry.
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Affiliation(s)
- László G. Boros
- Sub‐Molecular Medical Sciences Deutenomics CoreVrije University AmsterdamAmsterdamThe Netherlands
| | | | - Carlo Brogna
- Department of ResearchCraniomed Group Facility SrlItaly
| | - Marina Piscopo
- Department of BiologyUniversity of Naples Federico IINaplesItaly
| | | | - Stephanie Seneff
- Computer Science and Artificial Intelligence LaboratoryMassachusetts Institute of TechnologyCambridgeMassachusettsUSA
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5
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular tau RNAs. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167036. [PMID: 38286213 DOI: 10.1016/j.bbadis.2024.167036] [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: 09/20/2023] [Revised: 12/21/2023] [Accepted: 01/21/2024] [Indexed: 01/31/2024]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occurs through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations.
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Affiliation(s)
- Giorgi Margvelani
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Justin R Welden
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA; Sanders-Brown Center on Aging, University of Kentucky, Lexington, KY, USA
| | - Andrea Arizaca Maquera
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | | | | | - Sandra C Miranda Sardon
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA
| | - Stefan Stamm
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY, USA.
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6
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YADOLLAHVANDMIANDOAB REZA, JALALIZADEH MEHRSA, DIONATO FRANCIELEAPARECIDAVECHIA, BUOSI KEINI, LEME PATRÍCIAAF, COL LUCIANASBDAL, GIACOMELLI CRISTIANEF, ASSIS ALEXDIAS, BASHIRICHELKASARI NASIM, REIS LEONARDOOLIVEIRA. Clinical implications of single cell sequencing for bladder cancer. Oncol Res 2024; 32:597-605. [PMID: 38560564 PMCID: PMC10972735 DOI: 10.32604/or.2024.045442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Accepted: 01/08/2024] [Indexed: 04/04/2024] Open
Abstract
Bladder cancer (BC) is the 10th most common cancer worldwide, with about 0.5 million reported new cases and about 0.2 million deaths per year. In this scoping review, we summarize the current evidence regarding the clinical implications of single-cell sequencing for bladder cancer based on PRISMA guidelines. We searched PubMed, CENTRAL, Embase, and supplemented with manual searches through the Scopus, and Web of Science for published studies until February 2023. We included original studies that used at least one single-cell technology to study bladder cancer. Forty-one publications were included in the review. Twenty-nine studies showed that this technology can identify cell subtypes in the tumor microenvironment that may predict prognosis or response to immune checkpoint inhibition therapy. Two studies were able to diagnose BC by identifying neoplastic cells through single-cell sequencing urine samples. The remaining studies were mainly a preclinical exploration of tumor microenvironment at single cell level. Single-cell sequencing technology can discriminate heterogeneity in bladder tumor cells and determine the key molecular properties that can lead to the discovery of novel perspectives on cancer management. This nascent tool can advance the early diagnosis, prognosis judgment, and targeted therapy of bladder cancer.
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Affiliation(s)
- REZA YADOLLAHVANDMIANDOAB
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - MEHRSA JALALIZADEH
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | | | - KEINI BUOSI
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - PATRÍCIA A. F. LEME
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - LUCIANA S. B. DAL COL
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - CRISTIANE F. GIACOMELLI
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - ALEX DIAS ASSIS
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - NASIM BASHIRICHELKASARI
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
| | - LEONARDO OLIVEIRA REIS
- UroScience, School of Medical Sciences, University of Campinas, UNICAMP, Campinas, Sao Paulo, 13083-872, Brazil
- ImmunOncology, Pontifical Catholic University of Campinas, PUC-Campinas, Campinas, Sao Paulo, 13087-571, Brazil
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7
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Dremel SE, Tagawa T, Koparde VN, Hernandez-Perez C, Arbuckle JH, Kristie TM, Krug LT, Ziegelbauer JM. Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection. EMBO Rep 2024; 25:1541-1569. [PMID: 38263330 PMCID: PMC10933408 DOI: 10.1038/s44319-023-00051-z] [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: 11/09/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/25/2024] Open
Abstract
To globally profile circRNAs, we employ RNA-Sequencing paired with chimeric junction analysis for alpha-, beta-, and gamma-herpesvirus infection. We find circRNAs are, as a population, resistant to host shutoff. We validate this observation using ectopic expression assays of human and murine herpesvirus endoribonucleases. During lytic infection, four circRNAs are commonly induced across all subfamilies of human herpesviruses, suggesting a shared mechanism of regulation. We test one such mechanism, namely how interferon-stimulation influences circRNA expression. 67 circRNAs are upregulated by either interferon-β or -γ treatment, with half of these also upregulated during lytic infection. Using gain and loss of function studies we find an interferon-stimulated circRNA, circRELL1, inhibits lytic Herpes Simplex Virus-1 infection. We previously reported circRELL1 inhibits lytic Kaposi sarcoma-associated herpesvirus infection, suggesting a pan-herpesvirus antiviral activity. We propose a two-pronged model in which interferon-stimulated genes may encode both mRNA and circRNA with antiviral activity. This is critical in cases of host shutoff, such as alpha- and gamma-herpesvirus infection, where the mRNA products are degraded but circRNAs escape.
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Affiliation(s)
- Sarah E Dremel
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA
| | - Takanobu Tagawa
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA
| | - Vishal N Koparde
- CCR Collaborative Bioinformatics Resource, National Cancer Institute, Bethesda, 20892, USA
- Frederick National Laboratory for Cancer Research Advanced Biomedical Computational Sciences, Leidos Biomedical Research, Inc., Frederick, 21701, USA
| | | | - Jesse H Arbuckle
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, 20892, USA
| | - Thomas M Kristie
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, 20892, USA
| | - Laurie T Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA
| | - Joseph M Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, 20892, USA.
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8
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Patel SK, Billingsley MM, Mukalel AJ, Thatte AS, Hamilton AG, Gong N, El-Mayta R, Safford HC, Merolle M, Mitchell MJ. Bile acid-containing lipid nanoparticles enhance extrahepatic mRNA delivery. Theranostics 2024; 14:1-16. [PMID: 38164140 PMCID: PMC10750194 DOI: 10.7150/thno.89913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/10/2023] [Indexed: 01/03/2024] Open
Abstract
Lipid nanoparticles (LNPs) have emerged as a viable, clinically-validated platform for the delivery of mRNA therapeutics. LNPs have been utilized as mRNA delivery systems for applications including vaccines, gene therapy, and cancer immunotherapy. However, LNPs, which are typically composed of ionizable lipids, cholesterol, helper lipids, and lipid-anchored polyethylene glycol, often traffic to the liver which limits the therapeutic potential of the platform. Several approaches have been proposed to resolve this tropism such as post-synthesis surface modification or the addition of synthetic cationic lipids. Methods: Here, we present a strategy for achieving extrahepatic delivery of mRNA involving the incorporation of bile acids, a naturally-occurring class of cholesterol analogs, during LNP synthesis. We synthesized a series of bile acid-containing C14-4 LNPs by replacing cholesterol with bile acids (cholic acid, chenodeoxycholic acid, deoxycholic acid, or lithocholic acid) at various ratios. Results: Bile acid-containing LNPs (BA-LNPs) were able to reduce delivery to liver cells in vitro and improve delivery in a variety of other cell types, including T cells, B cells, and epithelial cells. Our subsequent in vivo screening of selected LNP candidates injected intraperitoneally or intravenously identified a highly spleen tropic BA-LNP: CA-100, a four-component LNP containing cholic acid and no cholesterol. These screens also identified BA-LNP candidates demonstrating promise for other mRNA therapeutic applications such as for gastrointestinal or immune cell delivery. We further found that the substitution of cholic acid for cholesterol in an LNP formulation utilizing a different ionizable lipid, C12-200, also shifted mRNA delivery from the liver to the spleen, suggesting that this cholic acid replacement strategy may be generalizable. Conclusion: These results demonstrate the potential of a four-component BA-LNP formulation, CA-100, for extrahepatic mRNA delivery that could potentially be utilized for a range of therapeutic and vaccine applications.
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Affiliation(s)
- Savan K. Patel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Alvin J. Mukalel
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ajay S. Thatte
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Alex G. Hamilton
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rakan El-Mayta
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hannah C. Safford
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Maria Merolle
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael J. Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Penn Institute for RNA Innovation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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9
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Hoque P, Romero B, Akins RE, Batish M. Exploring the Multifaceted Biologically Relevant Roles of circRNAs: From Regulation, Translation to Biomarkers. Cells 2023; 12:2813. [PMID: 38132133 PMCID: PMC10741722 DOI: 10.3390/cells12242813] [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: 11/15/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
CircRNAs are a category of regulatory RNAs that have garnered significant attention in the field of regulatory RNA research due to their structural stability and tissue-specific expression. Their circular configuration, formed via back-splicing, results in a covalently closed structure that exhibits greater resistance to exonucleases compared to linear RNAs. The distinctive regulation of circRNAs is closely associated with several physiological processes, as well as the advancement of pathophysiological processes in several human diseases. Despite a good understanding of the biogenesis of circular RNA, details of their biological roles are still being explored. With the steady rise in the number of investigations being carried out regarding the involvement of circRNAs in various regulatory pathways, understanding the biological and clinical relevance of circRNA-mediated regulation has become challenging. Given the vast landscape of circRNA research in the development of the heart and vasculature, we evaluated cardiovascular system research as a model to critically review the state-of-the-art understanding of the biologically relevant functions of circRNAs. We conclude the review with a discussion of the limitations of current functional studies and provide potential solutions by which these limitations can be addressed to identify and validate the meaningful and impactful functions of circRNAs in different physiological processes and diseases.
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Affiliation(s)
- Parsa Hoque
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Brigette Romero
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
| | - Robert E Akins
- Nemours Children’s Research, Nemours Children’s Health System, Wilmington, DE 19803, USA;
| | - Mona Batish
- Department of Biological Sciences, University of Delaware, Newark, DE 19716, USA;
- Department of Medical and Molecular Sciences, University of Delaware, Newark, DE 19716, USA;
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Liu C, Yu C, Song G, Fan X, Peng S, Zhang S, Zhou X, Zhang C, Geng X, Wang T, Cheng W, Zhu W. Comprehensive analysis of miRNA-mRNA regulatory pairs associated with colorectal cancer and the role in tumor immunity. BMC Genomics 2023; 24:724. [PMID: 38036953 PMCID: PMC10688136 DOI: 10.1186/s12864-023-09635-4] [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: 06/20/2023] [Accepted: 08/29/2023] [Indexed: 12/02/2023] Open
Abstract
BACKGROUND MicroRNA (miRNA) which can act as post-transcriptional regulators of mRNAs via base-pairing with complementary sequences within mRNAs is involved in processes of the complex interaction between immune system and tumors. In this research, we elucidated the profiles of miRNAs and target mRNAs expression and their associations with the phenotypic hallmarks of colorectal cancers (CRC) by integrating transcriptomic, immunophenotype, methylation, mutation and survival data. RESULTS We conducted the analysis of differential miRNA/mRNA expression profile by GEO, TCGA and GTEx databases and the correlation between miRNA and targeted mRNA by miRTarBase and TarBase. Then we detected using qRT-PCR and validated the diagnostic value of miRNA-mRNA regulator pairs by the ROC, calibration curve and DCA. Phenotypic hallmarks of regulatory pairs including tumor-infiltrating lymphocytes, tumor microenvironment, tumor mutation burden, global methylation and gene mutation were also described. The expression levels of miRNAs and target mRNAs were detected in 80 paired colon tissue samples. Ultimately, we picked up two pivotal regulatory pairs (miR-139-5p/ STC1 and miR-20a-5p/ FGL2) and verified the diagnostic value of the complex model which is the combination of 4 signatures above-mentioned in 3 testing GEO datasets and an external validation cohort. CONCLUSIONS We found that 2 miRNAs by targeting 2 metastasis-related mRNAs were correlated with tumor-infiltrating macrophages, HRAS, and BRAF gene mutation status. Our results established the diagnostic model containing 2 miRNAs and their respective targeted mRNAs to distinguish CRCs and normal controls and displayed their complex roles in CRC pathogenesis especially tumor immunity.
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Affiliation(s)
- Cheng Liu
- Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Chun Yu
- Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China
| | - Guoxin Song
- Department of Pathology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China, Jiangsu
| | - Xingchen Fan
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China, Jiangsu
| | - Shuang Peng
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China, Jiangsu
| | - Shiyu Zhang
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China, Jiangsu
| | - Xin Zhou
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China, Jiangsu
| | - Cheng Zhang
- Department of Science and Technology, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China, Jiangsu
| | - Xiangnan Geng
- Department of Clinical Engineer, the First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China, Jiangsu
| | - Tongshan Wang
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China, Jiangsu
| | - Wenfang Cheng
- Department of Gastroenterology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, Jiangsu, China.
| | - Wei Zhu
- Department of Oncology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, 210029, China, Jiangsu.
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Liao Y, Qiu X, Liu J, Zhang Z, Liu B, Jin C. The role of m6A-modified CircEPHB4 in glioma pathogenesis: Insights into cancer stemness metastasis. Ann Clin Transl Neurol 2023; 10:1749-1767. [PMID: 37614011 PMCID: PMC10578901 DOI: 10.1002/acn3.51864] [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: 03/08/2023] [Revised: 06/27/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023] Open
Abstract
OBJECTIVE While existing literature has provided insights into involvement of circEPHB4, SOX2 in glioma, their precise molecular mechanisms and synergistic implications in glioma pathogenesis still dim. This study aims to investigate significance and underlying mechanism of m6A-modified circEPHB4 in regulating SOX2/PHLDB2 axis in gliomas. METHODS The mRNA and protein expression were tested by qRT-PCR and Western blot, respectively. ChIP assay was performed to detect SOX2 enrichment on the PHLDB2 promoter. Cell sphere-forming assay to detect self-renewal ability, flow cytometry to determine positivity of CD133 expressions, Malignant behavior of glioma cells were detected by CCK-8, plate colony formation, scratch, and transwell assays. Glioma xenograft models were constructed to investigate effects of CircEPHB4 in tumor development in vivo. RESULTS Methyltransferase MELLT3 upregulated m6A modification of CircEPHB4, and YTHDC1 promoted cytoplasmic localization of m6A-modified CircEPHB4. Overexpression of wild-type CircEPHB4 enhanced glioma cells' stemness, metastasis, and proliferation. Cytoplasmic CircEPHB4 increased SOX2 mRNA stability by binding to IGF2BP2, and the effects observed by SOX2 knockdown were reversed by CircEPHB4 in glioma cells. SOX2 promoted transcriptional expression of PHLDB2 by enriching the PHLDB2 promoter region. SOX2 reversed the inhibition of PHLDB2 knockdown on stemness of glioma, cell proliferation, and metastasis. In vivo experiments also revealed that CircEPHB4 upregulated PHLDB2 expression by stabilizing SOX2 mRNA, which promoted in vivo tumor growth and accelerated stemness of glioma cells and metastasis. CONCLUSION This study reveals functional interaction and molecular mechanisms of m6A-modified circEPHB4 in regulating SOX2/PHLDB2 axis, highlighting their importance in glioma pathogenesis and potential as therapeutic targets.
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Affiliation(s)
- Yuxiang Liao
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Xiaohui Qiu
- Department of Plastic Surgery, The Third Xiangya HospitalCentral South UniversityChangsha410013HunanP.R. China
| | - Jingping Liu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Zhiping Zhang
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Bo Liu
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
| | - Chen Jin
- Department of Neurosurgery, Xiangya HospitalCentral South UniversityChangsha410008HunanP.R. China
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Margvelani G, Welden JR, Maquera AA, Van Eyk JE, Murray C, Miranda Sardon SC, Stamm S. Influence of FTDP-17 mutants on circular Tau RNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.08.556913. [PMID: 37786725 PMCID: PMC10541600 DOI: 10.1101/2023.09.08.556913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
At least 53 mutations in the microtubule associated protein tau gene (MAPT) have been identified that cause frontotemporal dementia. 47 of these mutations are localized between exons 7 and 13. They could thus affect the formation of circular RNAs (circRNAs) from the MAPT gene that occur through backsplicing from exon 12 to either exon 10 or exon 7. We analyzed representative mutants and found that five FTDP-17 mutations increase the formation of 12➔7 circRNA and three different mutations increase the amount of 12➔10 circRNA. CircRNAs are translated after undergoing adenosine to inosine RNA editing, catalyzed by ADAR enzymes. We found that the interferon induced ADAR1-p150 isoform has the strongest effect on circTau RNA translation. ADAR1-p150 activity had a stronger effect on circTau RNA expression and strongly decreased 12➔7 circRNA, but unexpectedly increased 12➔10 circRNA. In both cases, ADAR-activity strongly promoted translation of circTau RNAs. Unexpectedly, we found that the 12➔7 circTau protein interacts with eukaryotic initiation factor 4B (eIF4B), which is reduced by four FTDP-17 mutations located in the second microtubule domain. These are the first studies of the effect of human mutations on circular RNA formation and translation. They show that point mutations influence circRNA expression levels, likely through changes in the secondary pre-mRNA structures. The effect of the mutations is surpassed by editing of the circular RNAs, leading to their translation. Thus, circular RNAs and their editing status should be considered when analyzing FTDP-17 mutations. Highlights 47/53 known FTDP-17 mutations are located in regions that could influence generation of circular RNAs from the MAPT geneCircular Tau RNAs are translated after adenosine to inosine RNA editing, most effectively caused by ADAR1-p150FTDP-17 mutations influence both circTau RNA and circTau protein expression levelsCircTau protein expression levels do not correlate with circTau RNA expression levelsCircTau proteins bind to eukaryotic initiation factor 4B, which is antagonized by FTDP-17 mutations in exon 10. Graphic Abstract
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13
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Morgunova A, Ibrahim P, Chen GG, Coury SM, Turecki G, Meaney MJ, Gifuni A, Gotlib IH, Nagy C, Ho TC, Flores C. Preparation and processing of dried blood spots for microRNA sequencing. Biol Methods Protoc 2023; 8:bpad020. [PMID: 37901452 PMCID: PMC10603595 DOI: 10.1093/biomethods/bpad020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 10/31/2023] Open
Abstract
Dried blood spots (DBS) are biological samples commonly collected from newborns and in geographic areas distanced from laboratory settings for the purposes of disease testing and identification. MicroRNAs (miRNAs)-small non-coding RNAs that regulate gene activity at the post-transcriptional level-are emerging as critical markers and mediators of disease, including cancer, infectious diseases, and mental disorders. This protocol describes optimized procedural steps for utilizing DBS as a reliable source of biological material for obtaining peripheral miRNA expression profiles. We outline key practices, such as the method of DBS rehydration that maximizes RNA extraction yield, and the use of degenerate oligonucleotide adapters to mitigate ligase-dependent biases that are associated with small RNA sequencing. The standardization of miRNA readout from DBS offers numerous benefits: cost-effectiveness in sample collection and processing, enhanced reliability and consistency of miRNA profiling, and minimal invasiveness that facilitates repeated testing and retention of participants. The use of DBS-based miRNA sequencing is a promising method to investigate disease mechanisms and to advance personalized medicine.
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Affiliation(s)
- Alice Morgunova
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Pascal Ibrahim
- Integrated Program in Neuroscience, McGill University, Montreal, Quebec H3A 1A1, Canada
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Gary Gang Chen
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
| | - Saché M Coury
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Gustavo Turecki
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Michael J Meaney
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
- Singapore Institute for Clinical Sciences, Agency for Science, Technology and Research (A*STAR), Brenner Centre for Molecular Medicine, Singapore City 138632, Singapore
| | - Anthony Gifuni
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Ian H Gotlib
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
| | - Corina Nagy
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Verdun, Quebec H4H 1R3, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
| | - Tiffany C Ho
- Department of Psychology, Stanford University, Stanford, CA 94305, United States
- Department of Psychology, University of California, Los Angeles, CA 90095, United States
| | - Cecilia Flores
- Douglas Mental Health University Institute, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Psychiatry, McGill University, Montreal, Quebec H3A 0G4, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, Quebec H3A 1A1, Canada
- Ludmer Centre for Neuroinformatics and Mental Health, McGill University, Montreal, Quebec H3A 2B4, Canada
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Dremel SE, Tagawa T, Koparde VN, Arbuckle JH, Kristie TM, Krug LT, Ziegelbauer JM. Interferon induced circRNAs escape herpesvirus host shutoff and suppress lytic infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.07.556698. [PMID: 37886542 PMCID: PMC10602050 DOI: 10.1101/2023.09.07.556698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
A first line of defense during infection is expression of interferon (IFN)-stimulated gene products which suppress viral lytic infection. To combat this, herpesviruses express endoribonucleases to deplete host RNAs. Here we demonstrate that IFN-induced circular RNAs (circRNAs) can escape viral-mediated degradation. We performed comparative circRNA expression profiling for representative alpha- (Herpes simplex virus-1, HSV-1), beta- (human cytomegalovirus, HCMV), and gamma-herpesviruses (Kaposi sarcoma herpesvirus, KSHV; murine gamma-herpesvirus 68, MHV68). Strikingly, we found that circRNAs are, as a population, resistant to host shutoff. This observation was confirmed by ectopic expression assays of human and murine herpesvirus endoribonucleases. During primary lytic infection, ten circRNAs were commonly regulated across all subfamilies of human herpesviruses, suggesting a common mechanism of regulation. We tested one such mechanism, namely how interferon-stimulation influences circRNA expression. 67 circRNAs were upregulated by either IFN-β or -γ treatment, with half of these also upregulated during lytic infection. Using gain and loss of function studies we found an interferon-stimulated circRNA, circRELL1, inhibited lytic HSV-1 infection. We have previously reported circRELL1 inhibits lytic KSHV infection, suggesting a pan-herpesvirus antiviral activity. We propose a two-pronged model in which interferon-stimulated genes may encode both mRNA and circRNA with antiviral activity. This is critical in cases of host shutoff, such as alpha- and gamma-herpesvirus infection, where the mRNA products are degraded but circRNAs escape.
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Affiliation(s)
- Sarah E. Dremel
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
| | - Takanobu Tagawa
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
| | - Vishal N. Koparde
- CCR Collaborative Bioinformatics Resource, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
- Advanced Biomedical Computational Sciences, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc., Frederick, MD, United States
| | - Jesse H. Arbuckle
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Thomas M. Kristie
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Laurie T. Krug
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
| | - Joseph M. Ziegelbauer
- HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD, United States
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15
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Webster J, Mai H, Ly A, Maher C. INTEGRATE-Circ and INTEGRATE-Vis: unbiased detection and visualization of fusion-derived circular RNA. Bioinformatics 2023; 39:btad569. [PMID: 37707537 PMCID: PMC10516643 DOI: 10.1093/bioinformatics/btad569] [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: 05/26/2023] [Revised: 09/06/2023] [Accepted: 09/12/2023] [Indexed: 09/15/2023] Open
Abstract
MOTIVATION Backsplicing of RNA results in circularized rather than linear transcripts, known as circular RNA (circRNA). A recently discovered and poorly understood subset of circRNAs that are composed of multiple genes, termed fusion-derived circular RNAs (fcircRNAs), represent a class of potential biomarkers shown to have oncogenic potential. Detection of fcircRNAs eludes existing analytical tools, making it difficult to more comprehensively assess their prevalence and function. Improved detection methods may lead to additional biological and clinical insights related to fcircRNAs. RESULTS We developed the first unbiased tool for detecting fcircRNAs (INTEGRATE-Circ) and visualizing fcircRNAs (INTEGRATE-Vis) from RNA-Seq data. We found that INTEGRATE-Circ was more sensitive, precise and accurate than other tools based on our analysis of simulated RNA-Seq data and our tool was able to outperform other tools in an analysis of public lymphoblast cell line data. Finally, we were able to validate in vitro three novel fcircRNAs detected by INTEGRATE-Circ in a well-characterized breast cancer cell line. AVAILABILITY AND IMPLEMENTATION Open source code for INTEGRATE-Circ and INTEGRATE-Vis is available at https://www.github.com/ChrisMaherLab/INTEGRATE-CIRC and https://www.github.com/ChrisMaherLab/INTEGRATE-Vis.
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Affiliation(s)
- Jace Webster
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Hung Mai
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Amy Ly
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, United States
| | - Christopher Maher
- Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO 63110, United States
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, United States
- Department of Biomedical Engineering, Washington University School of Medicine, St. Louis, MO 63130, United States
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Szymanowska A, Rodriguez-Aguayo C, Lopez-Berestein G, Amero P. Non-Coding RNAs: Foes or Friends for Targeting Tumor Microenvironment. Noncoding RNA 2023; 9:52. [PMID: 37736898 PMCID: PMC10514839 DOI: 10.3390/ncrna9050052] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/17/2023] [Accepted: 08/22/2023] [Indexed: 09/23/2023] Open
Abstract
Non-coding RNAs (ncRNAs) are a group of molecules critical for cell development and growth regulation. They are key regulators of important cellular pathways in the tumor microenvironment. To analyze ncRNAs in the tumor microenvironment, the use of RNA sequencing technology has revolutionized the field. The advancement of this technique has broadened our understanding of the molecular biology of cancer, presenting abundant possibilities for the exploration of novel biomarkers for cancer treatment. In this review, we will summarize recent achievements in understanding the complex role of ncRNA in the tumor microenvironment, we will report the latest studies on the tumor microenvironment using RNA sequencing, and we will discuss the potential use of ncRNAs as therapeutics for the treatment of cancer.
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Affiliation(s)
- Anna Szymanowska
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
- Center for RNA Interference and Non-Coding RNA, Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA; (A.S.); (C.R.-A.); (G.L.-B.)
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Lam YT, Lee BSL, Hung J, Michael P, Santos M, Tan RP, Liu R, Wise SG. Delivery of Therapeutic miRNA via Plasma-Polymerised Nanoparticles Rescues Diabetes-Impaired Endothelial Function. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2360. [PMID: 37630945 PMCID: PMC10459051 DOI: 10.3390/nano13162360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/16/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
MicroRNAs (miRNAs) are increasingly recognised as key regulators of the development and progression of many diseases due to their ability to modulate gene expression post-translationally. While this makes them an attractive therapeutic target, clinical application of miRNA therapy remains at an early stage and in part is limited by the lack of effective delivery modalities. Here, we determined the feasibility of delivering miRNA using a new class of plasma-polymerised nanoparticles (PPNs), which we have recently isolated and characterised. We showed that PPN-miRNAs have no significant effect on endothelial cell viability in vitro in either normal media or in the presence of high-glucose conditions. Delivery of a miRNA inhibitor targeting miR-503 suppressed glucose-induced miR-503 upregulation and restored the downstream mRNA expression of CCNE1 and CDC25a in endothelial cells. Subsequently, PPN delivery of miR-503 inhibitors enhanced endothelial angiogenesis, including tubulogenesis and migration, in culture conditions that mimic diabetic ischemia. An intramuscular injection of a PPN-miR-503 inhibitor promoted blood-perfusion recovery in the hindlimb of diabetic mice following surgically induced ischemia, linked with an increase in new blood vessel formation. Together, this study demonstrates the effective use of PPN to deliver therapeutic miRNAs in the context of diabetes.
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Affiliation(s)
- Yuen Ting Lam
- Chronic Diseases Theme, School of Medical Science, University of Sydney, Sydney 2006, Australia
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia
| | - Bob S. L. Lee
- Victor Chang Cardiac Research Institute, Darlinghurst 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Darlinghurst 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney 2050, Australia
| | - Juichien Hung
- Chronic Diseases Theme, School of Medical Science, University of Sydney, Sydney 2006, Australia
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia
| | - Praveesuda Michael
- Chronic Diseases Theme, School of Medical Science, University of Sydney, Sydney 2006, Australia
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia
| | - Miguel Santos
- Chronic Diseases Theme, School of Medical Science, University of Sydney, Sydney 2006, Australia
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia
| | - Richard P. Tan
- Chronic Diseases Theme, School of Medical Science, University of Sydney, Sydney 2006, Australia
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia
| | - Renjing Liu
- Victor Chang Cardiac Research Institute, Darlinghurst 2010, Australia
- St. Vincent’s Clinical School, University of New South Wales, Darlinghurst 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, University of New South Wales, Sydney 2050, Australia
| | - Steven G. Wise
- Chronic Diseases Theme, School of Medical Science, University of Sydney, Sydney 2006, Australia
- Charles Perkins Centre, University of Sydney, Sydney 2006, Australia
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Kabzinski J, Kucharska-Lusina A, Majsterek I. RNA-Based Liquid Biopsy in Head and Neck Cancer. Cells 2023; 12:1916. [PMID: 37508579 PMCID: PMC10377854 DOI: 10.3390/cells12141916] [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: 06/26/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Head and neck cancer (HNC) is a prevalent and diverse group of malignancies with substantial morbidity and mortality rates. Early detection and monitoring of HNC are crucial for improving patient outcomes. Liquid biopsy, a non-invasive diagnostic approach, has emerged as a promising tool for cancer detection and monitoring. In this article, we review the application of RNA-based liquid biopsy in HNC. Various types of RNA, including messenger RNA (mRNA), microRNA (miRNA), long non-coding RNA (lncRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), circular RNA (circRNA) and PIWI-interacting RNA (piRNA), are explored as potential biomarkers in HNC liquid-based diagnostics. The roles of RNAs in HNC diagnosis, metastasis, tumor resistance to radio and chemotherapy, and overall prognosis are discussed. RNA-based liquid biopsy holds great promise for the early detection, prognosis, and personalized treatment of HNC. Further research and validation are necessary to translate these findings into clinical practice and improve patient outcomes.
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Affiliation(s)
- Jacek Kabzinski
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Aleksandra Kucharska-Lusina
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Medical University of Lodz, MolecoLAB A6, Mazowiecka 5, 92-215 Lodz, Poland
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Liu C, Shi Q, Huang X, Koo S, Kong N, Tao W. mRNA-based cancer therapeutics. Nat Rev Cancer 2023:10.1038/s41568-023-00586-2. [PMID: 37311817 DOI: 10.1038/s41568-023-00586-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 69.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/15/2023]
Abstract
Due to the fact that mRNA technology allows the production of diverse vaccines and treatments in a shorter time frame and with reduced expense compared to conventional approaches, there has been a surge in the use of mRNA-based therapeutics in recent years. With the aim of encoding tumour antigens for cancer vaccines, cytokines for immunotherapy, tumour suppressors to inhibit tumour development, chimeric antigen receptors for engineered T cell therapy or genome-editing proteins for gene therapy, many of these therapeutics have shown promising efficacy in preclinical studies, and some have even entered clinical trials. Given the evidence supporting the effectiveness and safety of clinically approved mRNA vaccines, coupled with growing interest in mRNA-based therapeutics, mRNA technology is poised to become one of the major pillars in cancer drug development. In this Review, we present in vitro transcribed mRNA-based therapeutics for cancer treatment, including the characteristics of the various types of synthetic mRNA, the packaging systems for efficient mRNA delivery, preclinical and clinical studies, current challenges and future prospects in the field. We anticipate the translation of promising mRNA-based treatments into clinical applications, to ultimately benefit patients.
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Affiliation(s)
- Chuang Liu
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Qiangqiang Shi
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China
| | - Xiangang Huang
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Seyoung Koo
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Na Kong
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, China.
| | - Wei Tao
- Center for Nanomedicine and Department of Anaesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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20
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Aryankalayil M, Bylicky MA, Chopra S, Dalo J, Scott K, Ueda Y, Coleman CN. Biomarkers for Biodosimetry and Their Role in Predicting Radiation Injury. Cytogenet Genome Res 2023; 163:103-109. [PMID: 37285811 PMCID: PMC10946629 DOI: 10.1159/000531444] [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: 03/11/2023] [Accepted: 06/06/2023] [Indexed: 06/09/2023] Open
Abstract
Radiation-related normal tissue injury sustained during cancer radiotherapy or in a radiological or mass casualty nuclear incident is a major health concern. Reducing the risk and mitigating consequences of radiation injury could have a broad impact on cancer patients and citizens. Efforts to discover biomarkers that can determine radiation dose, predict tissue damage, and aid medical triage are underway. Exposure to ionizing radiation causes changes in gene, protein, and metabolite expression that needs to be understood to provide a holistic picture for treating acute and chronic radiation-induced toxicities. We present evidence that both RNA (mRNA, microRNA, long noncoding RNA) and metabolomic assays may provide useful biomarkers of radiation injury. RNA markers may provide information on early pathway alterations after radiation injury that can predict damage and implicate downstream targets for mitigation. In contrast, metabolomics is impacted by changes in epigenetics, genetics, and proteomics and can be considered a downstream marker that incorporates all these changes to provide an assessment of what is currently happening within an organ. We highlight research from the past 10 years to understand how biomarkers may be used to improve personalized medicine in cancer therapy and medical decision-making in mass casualty scenarios.
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Affiliation(s)
- Molykutty Aryankalayil
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Michelle A Bylicky
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA,
| | - Sunita Chopra
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Juan Dalo
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Kevin Scott
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yuki Ueda
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - C Norman Coleman
- Radiation Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
- Radiation Research Program, National Cancer Institute, National Institutes of Health, Rockville, Maryland, USA
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21
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Guang Y, Hui L. Determining half-life of SARS-CoV-2 antigen in respiratory secretion. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:69697-69702. [PMID: 37129805 PMCID: PMC10151215 DOI: 10.1007/s11356-023-27326-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 04/26/2023] [Indexed: 05/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is primarily transmitted from person to person through respiratory droplets and aerosols. It is also possible for the virus to be transmitted indirectly through environmental contamination. The likelihood of environmental transmission depends on several factors, including the survival time of the virus in respiratory secretions. However, the stability of SARS-CoV-2 in respiratory secretions has not been investigated. In this study, we compared the half-life of the SARS-CoV-2 antigen in respiratory secretion under different conditions. We applied respiratory secretion (5 µL) to glass slides, air-dried the slides for 1 h, and kept them at 24 °C or 4 °C for 10 days. Respiratory secretions were also placed in test tubes (sealed to preserve moisture) and in normal saline for 10 days. The concentration of SARS-CoV-2 antigen in all samples was simultaneously measured using colloidal gold immunochromatography, and the half-life of the antigen was calculated. The half-life of the antigen in the wet (sealed tube) and saline samples at room temperature was 5.0 and 2.92 days, respectively. The half-life of the antigen in the air-dried sample at room temperature and at 4 °C was 2.93 and 11.4 days, respectively. The half-life was longer in respiratory secretions than that in normal saline. The half-life was also longer in respiratory secretions, at a lower temperature, and under wet conditions. Therefore, environmental transmission can also play a significant role in the spread of the virus. Robust prevention and control strategies could be developed based on the half-life of the antigen in respiratory secretions.
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Affiliation(s)
- Yang Guang
- Department of Laboratory and Quarantine, Dalian Medical University, Dalian, 116044, China
| | - Liu Hui
- Department of Laboratory and Quarantine, Dalian Medical University, Dalian, 116044, China.
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22
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Yuan Q, Sun Y, Yang F, Yan D, Shen M, Jin Z, Zhan L, Liu G, Yang L, Zhou Q, Yu Z, Zhou X, Yu Y, Xu Y, Wu Q, Luo J, Hu X, Zhang C. CircRNA DICAR as a novel endogenous regulator for diabetic cardiomyopathy and diabetic pyroptosis of cardiomyocytes. Signal Transduct Target Ther 2023; 8:99. [PMID: 36882410 PMCID: PMC9992392 DOI: 10.1038/s41392-022-01306-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 10/29/2022] [Accepted: 12/18/2022] [Indexed: 03/09/2023] Open
Abstract
In this study, we identified that a conserved circular RNA (circRNA) DICAR, which was downregulated in diabetic mouse hearts. DICAR had an inhibitory effect on diabetic cardiomyopathy (DCM), as the spontaneous cardiac dysfunction, cardiac cell hypertrophy, and cardiac fibrosis occurred in DICAR deficiency (DICAR+/-) mice, whereas the DCM was alleviated in DICAR-overexpressed DICARTg mice. At the cellular level, we found that overexpression of DICAR inhibited, but knockdown of DICAR enhanced the diabetic cardiomyocyte pyroptosis. At the molecular level, we identified that DICAR-VCP-Med12 degradation could be the underlying molecular mechanism in DICAR-mediated effects. The synthesized DICAR junction part (DICAR-JP) exhibited a similar effect to the entire DICAR. In addition, the expression of DICAR in circulating blood cells and plasma from diabetic patients was lower than that from health controls, which was consistent with the decreased DICAR expression in diabetic hearts. DICAR and the synthesized DICAR-JP may be drug candidates for DCM.
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Affiliation(s)
- Qiong Yuan
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University and Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research and Institute of Metabolic Diseases, Southwest Medical University, Luzhou, 646000, China
| | - Yunwei Sun
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Fan Yang
- Department of Emergency and Critical Care Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, 510080, China
| | - Dan Yan
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Meihua Shen
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Zhigang Jin
- China Resource & WISCO General Hospital, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Lin Zhan
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Guangqi Liu
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Ling Yang
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Qianyi Zhou
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Zhijun Yu
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Xiangyu Zhou
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University and Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research and Institute of Metabolic Diseases, Southwest Medical University, Luzhou, 646000, China
| | - Yang Yu
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University and Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research and Institute of Metabolic Diseases, Southwest Medical University, Luzhou, 646000, China
| | - Yong Xu
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University and Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research and Institute of Metabolic Diseases, Southwest Medical University, Luzhou, 646000, China
| | - Qingming Wu
- College of Medicine, Wuhan University of Science and Technology, Wuhan, 430065, China
| | - Jianfang Luo
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial Key Laboratory of Coronary Heart Disease Prevention, Guangdong General Hospital, Guangzhou, China
| | - Xiamin Hu
- College of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 210000, China.
| | - Chunxiang Zhang
- Department of Cardiology, the Affiliated Hospital of Southwest Medical University and Key Laboratory of Medical Electrophysiology, Ministry of Education, Institute of Cardiovascular Research and Institute of Metabolic Diseases, Southwest Medical University, Luzhou, 646000, China.
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23
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Demystifying Extrachromosomal DNA Circles: Categories, Biogenesis, and Cancer Therapeutics. Comput Struct Biotechnol J 2022; 20:6011-6022. [PMID: 36382182 PMCID: PMC9647416 DOI: 10.1016/j.csbj.2022.10.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 10/21/2022] [Accepted: 10/21/2022] [Indexed: 12/01/2022] Open
Abstract
Since the advent of sequencing technologies in the 1990s, researchers have focused on the association between aberrations in chromosomal DNA and disease. However, not all forms of the DNA are linear and chromosomal. Extrachromosomal circular DNAs (eccDNAs) are double-stranded, closed-circled DNA constructs free from the chromosome that reside in the nuclei. Although widely overlooked, the eccDNAs have recently gained attention for their potential roles in physiological response, intratumoral heterogeneity and cancer therapeutics. In this review, we summarize the history, classifications, biogenesis, and highlight recent progresses on the emerging topic of eccDNAs and comment on their potential application as biomarkers in clinical settings.
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