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Pawar K, Kawamura T, Kirino Y. The tRNA Val half: A strong endogenous Toll-like receptor 7 ligand with a 5'-terminal universal sequence signature. Proc Natl Acad Sci U S A 2024; 121:e2319569121. [PMID: 38683985 PMCID: PMC11087793 DOI: 10.1073/pnas.2319569121] [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: 11/07/2023] [Accepted: 03/24/2024] [Indexed: 05/02/2024] Open
Abstract
Toll-like receptors (TLRs) are crucial components of the innate immune system. Endosomal TLR7 recognizes single-stranded RNAs, yet its endogenous ssRNA ligands are not fully understood. We previously showed that extracellular (ex-) 5'-half molecules of tRNAHisGUG (the 5'-tRNAHisGUG half) in extracellular vesicles (EVs) of human macrophages activate TLR7 when delivered into endosomes of recipient macrophages. Here, we fully explored immunostimulatory ex-5'-tRNA half molecules and identified the 5'-tRNAValCAC/AAC half, the most abundant tRNA-derived RNA in macrophage EVs, as another 5'-tRNA half molecule with strong TLR7 activation capacity. Levels of the ex-5'-tRNAValCAC/AAC half were highly up-regulated in macrophage EVs upon exposure to lipopolysaccharide and in the plasma of patients infected with Mycobacterium tuberculosis. The 5'-tRNAValCAC/AAC half-mediated activation of TLR7 effectively eradicated bacteria infected in macrophages. Mutation analyses of the 5'-tRNAValCAC/AAC half identified the terminal GUUU sequence as a determinant for TLR7 activation. We confirmed that GUUU is the optimal ratio of guanosine and uridine for TLR7 activation; microRNAs or other RNAs with the terminal GUUU motif can indeed stimulate TLR7, establishing the motif as a universal signature for TLR7 activation. These results advance our understanding of endogenous ssRNA ligands of TLR7 and offer insights into diverse TLR7-involved pathologies and their therapeutic strategies.
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Affiliation(s)
- Kamlesh Pawar
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
- Department of Life Sciences, School of Natural Science, Shiv Nadar Institution of Eminence Deemed to be University, Delhi National Capital Region, Greater Noida201314, India
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA19107
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Gumas J, Kawamura T, Shigematsu M, Kirino Y. Immunostimulatory short non-coding RNAs in the circulation of patients with tuberculosis infection. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102156. [PMID: 38481936 PMCID: PMC10933579 DOI: 10.1016/j.omtn.2024.102156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/14/2024] [Indexed: 03/20/2024]
Abstract
Mycobacterium tuberculosis (Mtb) infection is among the world's deadliest infectious diseases. Developing effective treatments and biomarkers for tuberculosis requires a deeper understanding of its pathobiology and host responses. Here, we report a comprehensive characterization of circulating short non-coding RNAs (sncRNAs) in plasma samples from Mtb-infected patients. We achieved this by pre-treating plasma RNAs with T4 polynucleotide kinase to convert all RNA ends to those compatible with sncRNA sequencing. We discovered a global and drastic upregulation of plasma sncRNAs in Mtb-infected patients, with tRNA-derived sncRNAs representing the most dramatically elevated class. Most of these tRNA-derived sncRNAs originated from a limited subset of tRNAs, specifically from three tRNA isoacceptors, and exhibited skewed patterns to 5'-derived fragments, such as 5' halves, 5' tRNA fragments (tRFs), and internal tRFs (i-tRFs) from the 5' regions. Further, Mtb-infected patients displayed markedly upregulated and distinct profiles of both rRNA- and mRNA-derived sncRNAs. Some of these sncRNAs, which are abundant and specific to Mtb-infected patients, robustly activated human macrophages via Toll-like receptor 7 and induced cytokine production. This drastic accumulation of circulating, immunostimulatory sncRNAs in the plasma of Mtb-infected patients offers insights into the sncRNA-driven aspects of host immune response against infectious diseases and suggests a pool of potential therapeutic targets and biomarkers.
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Affiliation(s)
- Justin Gumas
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Takuya Kawamura
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA
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3
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Vachon A, Seo GE, Patel NH, Coffin CS, Marinier E, Eyras E, Osiowy C. Hepatitis B virus serum RNA transcript isoform composition and proportion in chronic hepatitis B patients by nanopore long-read sequencing. Front Microbiol 2023; 14:1233178. [PMID: 37645229 PMCID: PMC10461054 DOI: 10.3389/fmicb.2023.1233178] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 08/31/2023] Open
Abstract
Introduction Serum hepatitis B virus (HBV) RNA is a promising new biomarker to manage and predict clinical outcomes of chronic hepatitis B (CHB) infection. However, the HBV serum transcriptome within encapsidated particles, which is the biomarker analyte measured in serum, remains poorly characterized. This study aimed to evaluate serum HBV RNA transcript composition and proportionality by PCR-cDNA nanopore sequencing of samples from CHB patients having varied HBV genotype (gt, A to F) and HBeAg status. Methods Longitudinal specimens from 3 individuals during and following pregnancy (approximately 7 months between time points) were also investigated. HBV RNA extracted from 16 serum samples obtained from 13 patients (73.3% female, 84.6% Asian) was sequenced and serum HBV RNA isoform detection and quantification were performed using three bioinformatic workflows; FLAIR, RATTLE, and a GraphMap-based workflow within the Galaxy application. A spike-in RNA variant (SIRV) control mix was used to assess run quality and coverage. The proportionality of transcript isoforms was based on total HBV reads determined by each workflow. Results All chosen isoform detection workflows showed high agreement in transcript proportionality and composition for most samples. HBV pregenomic RNA (pgRNA) was the most frequently observed transcript isoform (93.8% of patient samples), while other detected transcripts included pgRNA spliced variants, 3' truncated variants and HBx mRNA, depending on the isoform detection method. Spliced variants of pgRNA were primarily observed in HBV gtB, C, E, or F-infected patients, with the Sp1 spliced variant detected most frequently. Twelve other pgRNA spliced variant transcripts were identified, including 3 previously unidentified transcripts, although spliced isoform identification was very dependent on the workflow used to analyze sequence data. Longitudinal sampling among pregnant and post-partum antiviral-treated individuals showed increasing proportions of 3' truncated pgRNA variants over time. Conclusions This study demonstrated long-read sequencing as a promising tool for the characterization of the serum HBV transcriptome. However, further studies are needed to better understand how serum HBV RNA isoform type and proportion are linked to CHB disease progression and antiviral treatment response.
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Affiliation(s)
- Alicia Vachon
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Grace E. Seo
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Nishi H. Patel
- Department of Medicine and Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Carla S. Coffin
- Department of Medicine and Department of Microbiology, Immunology, and Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Eric Marinier
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Eduardo Eyras
- EMBL Australia Partner Laboratory Network at the Australian National University, Canberra, ACT, Australia
- The John Curtin School of Medical Research, ANU College of Health and Medicine, Canberra, ACT, Australia
- Catalan Institution for Research and Advanced Studies, Barcelona, Spain
- Hospital del Mar Medical Research Institute, Barcelona, Spain
| | - Carla Osiowy
- Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Winnipeg, MB, Canada
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
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4
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Solaguren-Beascoa M, Gámez-Valero A, Escaramís G, Herrero-Lorenzo M, Ortiz AM, Minguet C, Gonzalo R, Bravo MI, Costa M, Martí E. Phospho-RNA-Seq Highlights Specific Small RNA Profiles in Plasma Extracellular Vesicles. Int J Mol Sci 2023; 24:11653. [PMID: 37511412 PMCID: PMC10380198 DOI: 10.3390/ijms241411653] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/04/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Small RNAs (sRNAs) are bioactive molecules that can be detected in biofluids, reflecting physiological and pathological states. In plasma, sRNAs are found within extracellular vesicles (EVs) and in extravesicular compartments, offering potential sources of highly sensitive biomarkers. Deep sequencing strategies to profile sRNAs favor the detection of microRNAs (miRNAs), the best-known class of sRNAs. Phospho-RNA-seq, through the enzymatic treatment of sRNAs with T4 polynucleotide kinase (T4-PNK), has been recently developed to increase the detection of thousands of previously inaccessible RNAs. In this study, we investigated the value of phospho-RNA-seq on both the EVs and extravesicular plasma subfractions. Phospho-RNA-seq increased the proportion of sRNAs used for alignment and highlighted the diversity of the sRNA transcriptome. Unsupervised clustering analysis using sRNA counts matrices correctly classified the EVs and extravesicular samples only in the T4-PNK treated samples, indicating that phospho-RNA-seq stresses the features of sRNAs in each plasma subfraction. Furthermore, T4-PNK treatment emphasized specific miRNA variants differing in the 5'-end (5'-isomiRs) and certain types of tRNA fragments in each plasma fraction. Phospho-RNA-seq increased the number of tissue-specific messenger RNA (mRNA) fragments in the EVs compared with the extravesicular fraction, suggesting that phospho-RNA-seq favors the discovery of tissue-specific sRNAs in EVs. Overall, the present data emphasizes the value of phospho-RNA-seq in uncovering RNA-based biomarkers in EVs.
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Affiliation(s)
- Maria Solaguren-Beascoa
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
| | - Ana Gámez-Valero
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
| | - Georgia Escaramís
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
| | - Marina Herrero-Lorenzo
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
| | - Ana M Ortiz
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | - Carla Minguet
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | - Ricardo Gonzalo
- Grifols Scientific Innovation Office, 08022 Barcelona, Spain
| | | | | | - Eulàlia Martí
- Department de Biomedicina, Facultat de Medicina i Ciències de la Salut, Institut de Neurociències, Universitat de Barcelona, C/Casanova 143, 08036 Barcelona, Spain
- Centro de Investigación Biomédica en Red de Epidemiología y Salud Pública (CIBERESP), Ministerio de Ciencia Innovación y Universidades, 28029 Madrid, Spain
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5
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Maqueda JJ, Giovanazzi A, Rocha AM, Rocha S, Silva I, Saraiva N, Bonito N, Carvalho J, Maia L, Wauben MHM, Oliveira C. Adapter dimer contamination in sRNA-sequencing datasets predicts sequencing failure and batch effects and hampers extracellular vesicle-sRNA analysis. JOURNAL OF EXTRACELLULAR BIOLOGY 2023; 2:e91. [PMID: 38938917 PMCID: PMC11080836 DOI: 10.1002/jex2.91] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/21/2023] [Accepted: 05/10/2023] [Indexed: 06/29/2024]
Abstract
Small RNA (sRNA) profiling of Extracellular Vesicles (EVs) by Next-Generation Sequencing (NGS) often delivers poor outcomes, independently of reagents, platforms or pipelines used, which contributes to poor reproducibility of studies. Here we analysed pre/post-sequencing quality controls (QC) to predict issues potentially biasing biological sRNA-sequencing results from purified human milk EVs, human and mouse EV-enriched plasma and human paraffin-embedded tissues. Although different RNA isolation protocols and NGS platforms were used in these experiments, all datasets had samples characterized by a marked removal of reads after pre-processing. The extent of read loss between individual samples within a dataset did not correlate with isolated RNA quantity or sequenced base quality. Rather, cDNA electropherograms revealed the presence of a constant peak whose intensity correlated with the degree of read loss and, remarkably, with the percentage of adapter dimers, which were found to be overrepresented sequences in high read-loss samples. The analysis through a QC pipeline, which allowed us to monitor quality parameters in a step-by-step manner, provided compelling evidence that adapter dimer contamination was the main factor causing batch effects. We concluded this study by summarising peer-reviewed published workflows that perform consistently well in avoiding adapter dimer contamination towards a greater likelihood of sequencing success.
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Affiliation(s)
- Joaquín J. Maqueda
- BIOINF2BIO, LDAPortoPortugal
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- Ipatimup – Institute of Molecular Pathology and Immunology of the University of PortoPortoPortugal
| | - Alberta Giovanazzi
- Department of Biomolecular Health SciencesFaculty of Veterinary Medicine Utrecht UniversityUtrechtThe Netherlands
| | - Ana Mafalda Rocha
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- Ipatimup – Institute of Molecular Pathology and Immunology of the University of PortoPortoPortugal
| | - Sara Rocha
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- Ipatimup – Institute of Molecular Pathology and Immunology of the University of PortoPortoPortugal
| | - Isabel Silva
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- IBMC ‐ Instituto de Biologia Molecular e CelularUniversity of PortoPortoPortugal
| | - Nadine Saraiva
- IPOC – Instituto Português de Oncologia Francisco GentilCoimbraPortugal
| | - Nuno Bonito
- IPOC – Instituto Português de Oncologia Francisco GentilCoimbraPortugal
| | - Joana Carvalho
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- Ipatimup – Institute of Molecular Pathology and Immunology of the University of PortoPortoPortugal
| | - Luis Maia
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- ICBAS‐UP ‐ Instituto de Ciências Biomédicas Abel SalazarUniversity of PortoPortoPortugal
- CHUPorto – Department of NeurologyCentro Hospitalar Universitário do PortoPortoPortugal
| | - Marca H. M. Wauben
- Department of Biomolecular Health SciencesFaculty of Veterinary Medicine Utrecht UniversityUtrechtThe Netherlands
| | - Carla Oliveira
- BIOINF2BIO, LDAPortoPortugal
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- Ipatimup – Institute of Molecular Pathology and Immunology of the University of PortoPortoPortugal
- FMUP – Faculty of MedicineUniversity of PortoPortoPortugal
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6
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Vermeirssen V, Deleu J, Morlion A, Everaert C, De Wilde J, Anckaert J, Durinck K, Nuytens J, Rishfi M, Speleman F, Van Droogenbroeck H, Verniers K, Baietti M, Albersen M, Leucci E, Post E, Best M, Van Maerken T, De Wilde B, Vandesompele J, Decock A. Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA. NAR Cancer 2022; 4:zcac037. [DOI: 10.1093/narcan/zcac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 09/23/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
While cell-free DNA (cfDNA) is widely being investigated, free circulating RNA (extracellular RNA, exRNA) has the potential to improve cancer therapy response monitoring and detection due to its dynamic nature. However, it remains unclear in which blood subcompartment tumour-derived exRNAs primarily reside. We developed a host-xenograft deconvolution framework, exRNAxeno, with mapping strategies to either a combined human-mouse reference genome or both species genomes in parallel, applicable to exRNA sequencing data from liquid biopsies of human xenograft mouse models. The tool enables to distinguish (human) tumoural RNA from (murine) host RNA, to specifically analyse tumour-derived exRNA. We applied the combined pipeline to total exRNA sequencing data from 95 blood-derived liquid biopsy samples from 30 mice, xenografted with 11 different tumours. Tumoural exRNA concentrations are not determined by plasma platelet levels, while host exRNA concentrations increase with platelet content. Furthermore, a large variability in exRNA abundance and transcript content across individual mice is observed. The tumoural gene detectability in plasma is largely correlated with the RNA expression levels in the tumour tissue or cell line. These findings unravel new aspects of tumour-derived exRNA biology in xenograft models and open new avenues to further investigate the role of exRNA in cancer.
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Affiliation(s)
- Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomedical Molecular Biology, Ghent University , 9000, Ghent , Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Jill Deleu
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Annelien Morlion
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Celine Everaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Pathology, Ghent University Hospital , 9000, Ghent , Belgium
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Justine Nuytens
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Muhammad Rishfi
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Hanne Van Droogenbroeck
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Kimberly Verniers
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Maria Francesca Baietti
- Laboratory for RNA Cancer Biology, Department of Oncology , KU Leuven, 3000, Leuven , Belgium
- TRACE, Leuven Cancer Institute , KU Leuven, 3000, Leuven, Belgium
| | - Maarten Albersen
- Department of Development and Regeneration, Laboratory of Experimental Urology, KU Leuven, Department of Urology, University Hospitals Leuven , 3000, Leuven , Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology , KU Leuven, 3000, Leuven , Belgium
- TRACE, Leuven Cancer Institute , KU Leuven, 3000, Leuven, Belgium
| | - Edward Post
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery , Boelelaan 1117, 1081 HV, Amsterdam , the Netherlands
- Cancer Center Amsterdam, Brain Tumor Center and Liquid Biopsy Center , 1081 HV, Amsterdam , the Netherlands
| | - Myron G Best
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery , Boelelaan 1117, 1081 HV, Amsterdam , the Netherlands
- Cancer Center Amsterdam, Brain Tumor Center and Liquid Biopsy Center , 1081 HV, Amsterdam , the Netherlands
| | - Tom Van Maerken
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Laboratory Medicine , AZ Groeninge, 8500, Kortrijk , Belgium
| | - Bram De Wilde
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Paediatric Haematology Oncology and Stem Cell Transplantation, Ghent University Hospital , 9000, Ghent , Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Anneleen Decock
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
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7
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Goh TX, Tan SL, Roebuck MM, Teo SH, Kamarul T. A systematic review of EV-piRNA in human body fluid and its role in disease progression. Tissue Eng Part C Methods 2022; 28:511-528. [PMID: 35959742 DOI: 10.1089/ten.tec.2022.0092] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The state of host cells is reflected in the cargo carried by their extracellular vesicles (EVs). This makes EV a potential source of biomarkers for human diseases. Piwi-interacting RNA (piRNA) regulates gene expression through epigenetic regulation and post-transcriptional gene silencing. Thus, piRNA profiles in EVs derived from human clinical samples could identify markers that characterize disease stages, and unveil their roles in disease pathology. This review aimed to report the expression profiles of EV-derived piRNA (EV-piRNA) in various human samples, as well as their role in each pathology. A systematic review was conducted to collate the findings of human EV-piRNA from original research articles published in indexed scientific journals up to 16th Feb 2022. Article searches were performed in PubMed, Web of Science, and Scopus databases, using a combination of keywords including 'EV' and 'piRNA'. A total of 775 non-redundant original articles were identified. After subjecting articles to inclusion and exclusion criteria, 34 articles were accepted for this review. The piRNA expression levels among the small RNA profiles of human-derived EVs range from 0.09% to 43.84%, with the lowest expression level reported in urine-derived EVs and the highest percentage in plasma-derived EVs. Differentially expressed EV-piRNAs have been identified in patients with specific disease conditions compared to their counterparts (healthy control), suggesting an association between piRNA and progression in various diseases. Seven articles identified piRNA putative target genes and/or the pathway enrichment of piRNA target genes, and one study demonstrated a direct tole of piRNA candidates in disease pathology. In conclusion, EV-piRNA has been isolated successfully from various human body fluids. EV-piRNA is a new research niche in human disease pathology. The expression profiles of EV-piRNA in various tissue types and disease conditions remain largely unexplored. Furthermore, there is currently a lack of guidelines on piRNA bioinformatics analysis, which could lead to inconsistent results and thus hinder the progression of piRNA discoveries. Lastly, the lack of published scientific evidence on the role of EV-piRNA supports the need for future research to focus on the functional analysis of EV-piRNA as part of the route in piRNA discoveries.
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Affiliation(s)
- Tuan Xin Goh
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Malaysia;
| | - Sik Loo Tan
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Malaysia;
| | - Margaret M Roebuck
- University of Liverpool Faculty of Health and Life Sciences, Department of Musculoskeletal & Ageing Science Institute of Life Course & Medical Sciences (ILCaMS) Faculty of Health & Life Sciences William Henry Duncan Building University of Liverpool, Liverpool, 6 West Derby Street Liverpool L7 8TX, United Kingdom of Great Britain and Northern Ireland;
| | - Seow-Hui Teo
- Division of Sports Injuries and Arthroscopic Surgery, National Orthopaedic Center of Excellence for Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, MALAYSIA., Division of Sports Injuries and Arthroscopic Surgery, National Orthopaedic Center of Excellence for Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Faculty of Medicine, University of Malaya, Federal Territory, Kuala Lumpur, Malaysia;
| | - Tunku Kamarul
- University of Malaya Faculty of Medicine, Tissue Engineering Group (TEG), National Orthopaedic Center of Excellent Research & Learning (NOCERAL), Department of Orthopaedic Surgery, Kuala Lumpur, Wilayah Persekutuan, Malaysia;
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8
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Liu DSK, Yang QZC, Asim M, Krell J, Frampton AE. The Clinical Significance of Transfer RNAs Present in Extracellular Vesicles. Int J Mol Sci 2022; 23:ijms23073692. [PMID: 35409051 PMCID: PMC8998272 DOI: 10.3390/ijms23073692] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/22/2022] [Accepted: 03/23/2022] [Indexed: 12/19/2022] Open
Abstract
Extracellular vesicles (EVs) are important for intercellular signalling in multi-cellular organisms. However, the role of mature transfer RNAs (tRNAs) and tRNA fragments in EVs has yet to be characterised. This systematic review aimed to identify up-to-date literature on tRNAs present within human EVs and explores their potential clinical significance in health and disease. A comprehensive and systematic literature search was performed, and the study was conducted in accordance with PRISMA guidelines. Electronic databases MEDLINE and EMBASE were searched up until 1 January 2022. From 685 papers, 60 studies were identified for analysis. The majority of papers reviewed focussed on the role of EV tRNAs in cancers (31.7%), with numerous other conditions represented. Blood and cell lines were the most common EV sources, representing 85.9% of protocols used. EV isolation methods included most known methods, precipitation being the most common (49.3%). The proportion of EV tRNAs was highly variable, ranging between 0.04% to >95% depending on tissue source. EV tRNAs are present in a multitude of sources and show promise as disease markers in breast cancer, gastrointestinal cancers, and other diseases. EV tRNA research is an emerging field, with increasing numbers of papers highlighting novel methodologies for tRNA and tRNA fragment discovery.
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Affiliation(s)
- Daniel S. K. Liu
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
| | - Qi Zhi Clayton Yang
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
| | - Mohammad Asim
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7WG, UK;
| | - Jonathan Krell
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
| | - Adam E. Frampton
- Division of Cancer, Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0HS, UK; (D.S.K.L.); (Q.Z.C.Y.); (J.K.)
- Department of Clinical and Experimental Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey GU2 7WG, UK;
- HPB Surgical Unit, Royal Surrey County Hospital NHS Foundation Trust, Guildford, Surrey GU2 7XX, UK
- Correspondence: or
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Kalimuthu K, Keerthana CK, Mohan M, Arivalagan J, Christyraj JRSS, Firer MA, Choudry MHA, Anto RJ, Lee YJ. The emerging role of selenium metabolic pathways in cancer: New therapeutic targets for cancer. J Cell Biochem 2022; 123:532-542. [PMID: 34935169 PMCID: PMC8940641 DOI: 10.1002/jcb.30196] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/11/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023]
Abstract
Selenium (Se) is incorporated into the body via the selenocysteine (Sec) biosynthesis pathway, which is critical in the synthesis of selenoproteins, such as glutathione peroxidases and thioredoxin reductases. Selenoproteins, which play a key role in several biological processes, including ferroptosis, drug resistance, endoplasmic reticulum stress, and epigenetic processes, are guided by Se uptake. In this review, we critically analyze the molecular mechanisms of Se metabolism and its potential as a therapeutic target for cancer. Sec insertion sequence binding protein 2 (SECISBP2), which is a positive regulator for the expression of selenoproteins, would be a novel prognostic predictor and an alternate target for cancer. We highlight strategies that attempt to develop a novel Se metabolism-based approach to uncover a new metabolic drug target for cancer therapy. Moreover, we expect extensive clinical use of SECISBP2 as a specific biomarker in cancer therapy in the near future. Of note, scientists face additional challenges in conducting successful research, including investigations on anticancer peptides to target SECISBP2 intracellular protein.
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Affiliation(s)
- Kalishwaralal Kalimuthu
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India
| | | | - Manikandan Mohan
- College of Pharmacy, University of Georgia, Athens, GA, USA.,VAXIGEN International Research Center Private Limited, INDIA
| | - Jaison Arivalagan
- Department of Chemistry, Molecular Biosciences and Proteomics Center of Excellence, Northwestern University, Evanston, IL, 60208, USA
| | - Johnson Retnaraj Samuel Selvan Christyraj
- Regeneration and Stem Cell Biology Lab, Centre for Molecular and Nanomedical Sciences, International Research Centre, Sathyabama Institute of Science and Technology, Chennai, 600119, Tamilnadu, India
| | - Michael A Firer
- Dept. Chemical Engineering, Ariel University, 40700, Ariel, Israel.,Adelson School of Medicine, Ariel University, Ariel, 40700, Israel,Ariel Center for Applied Cancer Research, Ariel University, Ariel 40700, Israel
| | - M. Haroon A Choudry
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Ruby John Anto
- Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India.,Correspondence: All correspondence should be addressed to Dr. Yong J. Lee, Department of Surgery, University of Pittsburgh, Hillman Cancer Center, 5117 Centre Ave. Room 1.46C, Pittsburgh, PA 15213,U.S.A., Tel: (412) 623-3268, Fax: (412) 623-7709, ., Dr. Ruby John Anto, Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India.
| | - Yong J Lee
- Department of Surgery, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Correspondence: All correspondence should be addressed to Dr. Yong J. Lee, Department of Surgery, University of Pittsburgh, Hillman Cancer Center, 5117 Centre Ave. Room 1.46C, Pittsburgh, PA 15213,U.S.A., Tel: (412) 623-3268, Fax: (412) 623-7709, ., Dr. Ruby John Anto, Division of Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, 695014, Kerala, India.
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