1
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Parashar D, Mukherjee T, Gupta S, Kumar U, Das K. MicroRNAs in extracellular vesicles: A potential role in cancer progression. Cell Signal 2024; 121:111263. [PMID: 38897529 DOI: 10.1016/j.cellsig.2024.111263] [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: 04/30/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/21/2024]
Abstract
Intercellular communication, an essential biological process in multicellular organisms, is mediated by direct cell-to-cell contact and cell secretary molecules. Emerging evidence identifies a third mechanism of intercellular communication- the release of extracellular vesicles (EVs). EVs are membrane-enclosed nanosized bodies, released from cells into the extracellular environment, often found in all biofluids. The growing body of research indicates that EVs carry bioactive molecules in the form of proteins, DNA, RNAs, microRNAs (miRNAs), lipids, metabolites, etc., and upon transferring them, alter the phenotypes of the target recipient cells. Interestingly, the abundance of EVs is found to be significantly higher in different diseased conditions, most importantly cancer. In the past few decades, numerous studies have identified EV miRNAs as an important contributor in the pathogenesis of different types of cancer. However, the underlying mechanism behind EV miRNA-associated cancer progression and how it could be used as a targeted therapy remain ill-defined. The present review highlights how EV miRNAs influence essential processes in cancer, such as growth, proliferation, metastasis, angiogenesis, apoptosis, stemness, immune evasion, resistance to therapy, etc. A special emphasis has been given to the potential role of EV miRNAs as cancer biomarkers. The final section of the review delineates the ongoing clinical trials on the role of miRNAs in the progression of different types of cancer. Targeting EV miRNAs could be a potential therapeutic means in the treatment of different forms of cancer alongside conventional therapeutic approaches.
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Affiliation(s)
- Deepak Parashar
- Division of Hematology & Oncology, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
| | - Tanmoy Mukherjee
- Department of Cellular and Molecular Biology, The University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA.
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura 281406, Uttar Pradesh, India
| | - Umesh Kumar
- Department of Biosciences, Institute of Management Studies Ghaziabad (University Courses Campus), NH09, Adhyatmik Nagar, Ghaziabad 201015, Uttar Pradesh, India.
| | - Kaushik Das
- Biotechnology Research and Innovation Council-National Institute of Biomedical Genomics, Kalyani 741251, West Bengal, India.
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2
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Scheepbouwer C, Aparicio-Puerta E, Gómez-Martin C, van Eijndhoven MA, Drees EE, Bosch L, de Jong D, Wurdinger T, Zijlstra JM, Hackenberg M, Gerber A, Pegtel DM. Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.12.593148. [PMID: 38765958 PMCID: PMC11100784 DOI: 10.1101/2024.05.12.593148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Small extracellular vesicles (sEVs) are heterogenous lipid membrane particles typically less than 200 nm in size and secreted by most cell types either constitutively or upon activation signals. sEVs isolated from biofluids contain RNAs, including small non-coding RNAs (ncRNAs), that can be either encapsulated within the EV lumen or bound to the EV surface. EV-associated microRNAs (miRNAs) are, despite a relatively low abundance, extensively investigated for their selective incorporation and their role in cell-cell communication. In contrast, the sorting of highly-structured ncRNA species is understudied, mainly due to technical limitations of traditional small RNA sequencing protocols. Here, we adapted ALL-tRNAseq to profile the relative abundance of highly structured and potentially methylated small ncRNA species, including transfer RNAs (tRNAs), small nucleolar RNAs (snoRNAs), and Y RNAs in bulk EV preparations. We determined that full-length tRNAs, typically 75 to 90 nucleotides in length, were the dominant small ncRNA species (>60% of all reads in the 18-120 nucleotides size-range) in all cell culture-derived EVs, as well as in human plasma-derived EV samples, vastly outnumbering 21 nucleotides-long miRNAs. Nearly all EV-associated tRNAs were protected from external RNAse treatment, indicating a location within the EV lumen. Strikingly, the vast majority of luminal-sorted, full-length, nucleobase modification-containing EV-tRNA sequences, harbored a dysfunctional 3' CCA tail, 1 to 3 nucleotides truncated, rendering them incompetent for amino acid loading. In contrast, in non-EV associated extracellular particle fractions (NVEPs), tRNAs appeared almost exclusively fragmented or 'nicked' into tRNA-derived small RNAs (tsRNAs) with lengths between 18 to 35 nucleotides. We propose that in mammalian cells, tRNAs that lack a functional 3' CCA tail are selectively sorted into EVs and shuttled out of the producing cell, offering a new perspective into the physiological role of secreted EVs and luminal cargo-selection.
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Affiliation(s)
- Chantal Scheepbouwer
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, Netherlands
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
| | - Ernesto Aparicio-Puerta
- Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY, USA
| | - Cristina Gómez-Martin
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Monique A.J. van Eijndhoven
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Esther E.E. Drees
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
| | - Leontien Bosch
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Daphne de Jong
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Thomas Wurdinger
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
| | - Josée M. Zijlstra
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
- Department of Hematology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
| | - Michael Hackenberg
- Bioinformatics Laboratory, Biomedical Research Centre (CIBM), Biotechnology Institute, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
- Genetics Department, Faculty of Science, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, Spain
- Instituto de Investigación Biosanitaria ibs. Granada, University Hospitals of Granada-University of Granada, Spain; Conocimiento s/n 18100, Granada. Spain
| | - Alan Gerber
- Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Cancer Biology, Amsterdam, Netherlands
| | - D. Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, Netherlands
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3
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Zhou M, He X, Zhang J, Mei C, Zhong B, Ou C. tRNA-derived small RNAs in human cancers: roles, mechanisms, and clinical application. Mol Cancer 2024; 23:76. [PMID: 38622694 PMCID: PMC11020452 DOI: 10.1186/s12943-024-01992-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 04/02/2024] [Indexed: 04/17/2024] Open
Abstract
Transfer RNA (tRNA)-derived small RNAs (tsRNAs) are a new type of non-coding RNAs (ncRNAs) produced by the specific cleavage of precursor or mature tRNAs. tsRNAs are involved in various basic biological processes such as epigenetic, transcriptional, post-transcriptional, and translation regulation, thereby affecting the occurrence and development of various human diseases, including cancers. Recent studies have shown that tsRNAs play an important role in tumorigenesis by regulating biological behaviors such as malignant proliferation, invasion and metastasis, angiogenesis, immune response, tumor resistance, and tumor metabolism reprogramming. These may be new potential targets for tumor treatment. Furthermore, tsRNAs can exist abundantly and stably in various bodily fluids (e.g., blood, serum, and urine) in the form of free or encapsulated extracellular vesicles, thereby affecting intercellular communication in the tumor microenvironment (TME). Meanwhile, their abnormal expression is closely related to the clinicopathological features of tumor patients, such as tumor staging, lymph node metastasis, and poor prognosis of tumor patients; thus, tsRNAs can be served as a novel type of liquid biopsy biomarker. This review summarizes the discovery, production, and expression of tsRNAs and analyzes their molecular mechanisms in tumor development and potential applications in tumor therapy, which may provide new strategies for early diagnosis and targeted therapy of tumors.
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Affiliation(s)
- Manli Zhou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Xiaoyun He
- Departments of Ultrasound Imaging, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Jing Zhang
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Cheng Mei
- Department of Blood Transfusion, Xiangya Hospital, Clinical Transfusion Research Center, Central South University, Changsha, Hunan, 410008, China.
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
| | - Chunlin Ou
- Department of Pathology, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China.
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4
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Cross T, Haug KBF, Brusletto BS, Ommundsen SK, Trøseid AMS, Aspelin T, Olstad OK, Aass HCD, Galtung HK, Utheim TP, Jensen JL, Øvstebø R. Non-Coding RNA in Salivary Extracellular Vesicles: A New Frontier in Sjögren's Syndrome Diagnostics? Int J Mol Sci 2023; 24:13409. [PMID: 37686214 PMCID: PMC10488010 DOI: 10.3390/ijms241713409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/23/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Sjögren's syndrome is an autoimmune rheumatic disease characterized by inflammation of the salivary and lacrimal glands, often manifesting as dry mouth and dry eyes. To simplify diagnostics of primary Sjögren's syndrome (pSS), a non-invasive marker is needed. The aim of the study was to compare the RNA content of salivary extracellular vesicles (EVs) between patients with pSS and healthy controls using microarray technology. Stimulated whole saliva was collected from 11 pSS patients and 11 age-matched controls. EV-RNA was isolated from the saliva samples using a Qiagen exoRNeasy Midi Kit and analyzed using Affymetrix Clariom D™ microarrays. A one-way ANOVA test was used to compare the mean signal values of each transcript between the two groups. A total of 9307 transcripts, coding and non-coding RNA, were detected in all samples. Of these transcripts, 1475 showed statistically significant differential abundance between the pSS and the control groups, generating two distinct EV-RNA patterns. In particular, tRNAs were downregulated in pSS patients, with the transcript tRNA-Ile-AAT-2-1 showing a 2-fold difference, and a promise as a potential biomarker candidate. This study therein demonstrates the potential for using salivary EV-RNA in pSS diagnostics.
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Affiliation(s)
- Tanya Cross
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Kari Bente Foss Haug
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Berit Sletbakk Brusletto
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Stine Kamilla Ommundsen
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Anne-Marie Siebke Trøseid
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Trude Aspelin
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | - Ole Kristoffer Olstad
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
| | | | - Hilde Kanli Galtung
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
| | - Tor Paaske Utheim
- The Regenerative Medicine Unit, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
- Institute of Oral Biology, Faculty of Dentistry, University of Oslo, 0372 Oslo, Norway
- Department of Plastic and Reconstructive Surgery, Oslo University Hospital, 0372 Oslo, Norway
- Department of Ophthalmology, Oslo University Hospital, 0450 Oslo, Norway
- Department of Ophthalmology, Sørlandet Hospital Arendal, 4838 Arendal, Norway
- Department of Ophthalmology, Vestre Viken Hospital Trust, 3004 Drammen, Norway
- The Norwegian Dry Eye Clinic, 0369 Oslo, Norway
| | - Janicke Liaaen Jensen
- Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, University of Oslo, 0455 Oslo, Norway
| | - Reidun Øvstebø
- The Blood Cell Research Group, Department of Medical Biochemistry, Oslo University Hospital, Ullevål, 0450 Oslo, Norway
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5
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Maqueda JJ, Santos M, Ferreira M, Marinho S, Rocha S, Rocha M, Saraiva N, Bonito N, Carvalho J, Oliveira C. NGS Data Repurposing Allows Detection of tRNA Fragments as Gastric Cancer Biomarkers in Patient-Derived Extracellular Vesicles. Int J Mol Sci 2023; 24:ijms24108961. [PMID: 37240307 DOI: 10.3390/ijms24108961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Transfer RNA fragments (tRFs) have gene silencing effects similarly to miRNAs, can be sorted into extracellular vesicles (EVs) and are emerging as potential circulating biomarkers for cancer diagnoses. We aimed at analyzing the expression of tRFs in gastric cancer (GC) and understanding their potential as biomarkers. We explored miRNA datasets from gastric tumors and normal adjacent tissues (NATs) from TCGA repository, as well as proprietary 3D-cultured GC cell lines and corresponding EVs, in order to identify differentially represented tRFs using MINTmap and R/Bioconductor packages. Selected tRFs were validated in patient-derived EVs. We found 613 Differentially Expressed (DE)-tRFs in the TCGA dataset, of which 19 were concomitantly upregulated in TCGA gastric tumors and present in 3D cells and EVs, but barely expressed in NATs. Moreover, 20 tRFs were expressed in 3D cells and EVs and downregulated in TCGA gastric tumors. Of these 39 DE-tRFs, 9 tRFs were also detected in patient-derived EVs. Interestingly, the targets of these 9 tRFs affect neutrophil activation and degranulation, cadherin binding, focal adhesion and the cell-substrate junction, highlighting these pathways as major targets of EV-mediated crosstalk with the tumor microenvironment. Furthermore, as they are present in four distinct GC datasets and can be detected even in low quality patient-derived EV samples, they hold promise as GC biomarkers. By repurposing already available NGS data, we could identify and cross-validate a set of tRFs holding potential as GC diagnosis biomarkers.
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Affiliation(s)
- Joaquín J Maqueda
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Bioinf2Bio LDA, 4200-150 Porto, Portugal
| | - Mafalda Santos
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Marta Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Sérgio Marinho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
| | - Sara Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Mafalda Rocha
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Nadine Saraiva
- Instituto Português de Oncologia de Coimbra Francisco Gentil, E.P.E. (IPOCFG, E.P.E.), 3000-075 Coimbra, Portugal
| | - Nuno Bonito
- Instituto Português de Oncologia de Coimbra Francisco Gentil, E.P.E. (IPOCFG, E.P.E.), 3000-075 Coimbra, Portugal
| | - Joana Carvalho
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
| | - Carla Oliveira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal
- Bioinf2Bio LDA, 4200-150 Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, 4200-135 Porto, Portugal
- Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
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6
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Gong M, Deng Y, Xiang Y, Ye D. The role and mechanism of action of tRNA-derived fragments in the diagnosis and treatment of malignant tumors. Cell Commun Signal 2023; 21:62. [PMID: 36964534 PMCID: PMC10036988 DOI: 10.1186/s12964-023-01079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 02/13/2023] [Indexed: 03/26/2023] Open
Abstract
Cancer is a leading cause of morbidity and death worldwide. While various factors are established as causing malignant tumors, the mechanisms underlying cancer development remain poorly understood. Early diagnosis and the development of effective treatments for cancer are important research topics. Transfer RNA (tRNA), the most abundant class of RNA molecules in the human transcriptome, participates in both protein synthesis and cellular metabolic processes. tRNA-derived fragments (tRFs) are produced by specific cleavage of pre-tRNA and mature tRNA molecules, which are highly conserved and occur widely in various organisms. tRFs were initially thought to be random products with no physiological function, but have been redefined as novel functional small non-coding RNA molecules that help to regulate RNA stability, modulate translation, and influence target gene expression, as well as other biological processes. There is increasing evidence supporting roles for tRFs in tumorigenesis and cancer development, including the regulation of tumor cell proliferation, invasion, migration, and drug resistance. Understanding the regulatory mechanisms by which tRFs impact these processes has potential to inform malignant tumor diagnosis and treatment. Further, tRFs are expected to become new biological markers for early diagnosis and prognosis prediction in patients with tumors, as well as a targets for precision cancer therapies. Video abstract.
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Affiliation(s)
- Mengdan Gong
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yongqin Deng
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Yizhen Xiang
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China
| | - Dong Ye
- Department of Otorhinolaryngology-Head and Neck Surgery, The Affiliated Lihuili Hospital, Ningbo University, Ningbo, 315040, Zhejiang, China.
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7
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Karvinen S, Korhonen T, Sievänen T, Karppinen JE, Juppi H, Jakoaho V, Kujala UM, Laukkanen JA, Lehti M, Laakkonen EK. Extracellular vesicles and high-density lipoproteins: Exercise and oestrogen-responsive small RNA carriers. J Extracell Vesicles 2023; 12:e12308. [PMID: 36739598 PMCID: PMC9899444 DOI: 10.1002/jev2.12308] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 12/22/2022] [Accepted: 01/22/2023] [Indexed: 02/06/2023] Open
Abstract
Decreased systemic oestrogen levels (i.e., menopause) affect metabolic health. However, the detailed mechanisms underlying this process remain unclear. Both oestrogens and exercise have been shown to improve metabolic health, which may be partly mediated by circulating microRNA (c-miR) signalling. In recent years, extracellular vesicles (EV) have increased interest in the field of tissue crosstalk. However, in many studies on EV-carried miRs, the co-isolation of high-density lipoprotein (HDL) particles with EVs has not been considered, potentially affecting the results. Here, we demonstrate that EV and HDL particles have distinct small RNA (sRNA) content, including both host and nonhost sRNAs. Exercise caused an acute increase in relative miR abundancy in EVs, whereas in HDL particles, it caused an increase in transfer RNA-derived sRNA. Furthermore, we demonstrate that oestrogen-based hormonal therapy (HT) allows the acute exercise-induced miR-response to occur in both EV and HDL particles in postmenopausal women, while the response was absent in nonusers.
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Affiliation(s)
- Sira Karvinen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Tia‐Marje Korhonen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Tero Sievänen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Jari E. Karppinen
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Hanna‐Kaarina Juppi
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Veera Jakoaho
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Urho M. Kujala
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Jari A. Laukkanen
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland,Institute of Clinical MedicineUniversity of Eastern FinlandKuopioFinland
| | - Maarit Lehti
- Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
| | - Eija K. Laakkonen
- Gerontology Research Center and Faculty of Sport and Health SciencesUniversity of JyväskyläJyväskyläFinland
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8
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Needhamsen M, Khoonsari PE, Zheleznyakova GY, Piket E, Hagemann-Jensen M, Han Y, Gierlich J, Ekman D, Jagodic M. Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis. Front Genet 2022; 13:1042483. [DOI: 10.3389/fgene.2022.1042483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 10/21/2022] [Indexed: 11/18/2022] Open
Abstract
Multiple Sclerosis (MS) is an autoimmune, neurological disease, commonly presenting with a relapsing-remitting form, that later converts to a secondary progressive stage, referred to as RRMS and SPMS, respectively. Early treatment slows disease progression, hence, accurate and early diagnosis is crucial. Recent advances in large-scale data processing and analysis have progressed molecular biomarker development. Here, we focus on small RNA data derived from cell-free cerebrospinal fluid (CSF), cerebrospinal fluid cells, plasma and peripheral blood mononuclear cells as well as CSF cell methylome data, from people with RRMS (n = 20), clinically/radiologically isolated syndrome (CIS/RIS, n = 2) and neurological disease controls (n = 14). We applied multiple co-inertia analysis (MCIA), an unsupervised and thereby unbiased, multivariate method for simultaneous data integration and found that the top latent variable classifies RRMS status with an Area Under the Receiver Operating Characteristics (AUROC) score of 0.82. Variable selection based on Lasso regression reduced features to 44, derived from the small RNAs from plasma (20), CSF cells (8) and cell-free CSF (16), with a marginal reduction in AUROC to 0.79. Samples from SPMS patients (n = 6) were subsequently projected on the latent space and differed significantly from RRMS and controls. On contrary, we found no differences between relapse and remission or between inflammatory and non-inflammatory disease controls, suggesting that the latent variable is not prone to inflammatory signals alone, but could be MS-specific. Hence, we here showcase that integration of small RNAs from plasma and CSF can be utilized to distinguish RRMS from SPMS and neurological disease controls.
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9
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Strassler SE, Bowles IE, Dey D, Jackman JE, Conn GL. Tied up in knots: Untangling substrate recognition by the SPOUT methyltransferases. J Biol Chem 2022; 298:102393. [PMID: 35988649 PMCID: PMC9508554 DOI: 10.1016/j.jbc.2022.102393] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 10/25/2022] Open
Abstract
The SpoU-TrmD (SPOUT) methyltransferase superfamily was designated when structural similarity was identified between the transfer RNA-modifying enzymes TrmH (SpoU) and TrmD. SPOUT methyltransferases are found in all domains of life and predominantly modify transfer RNA or ribosomal RNA substrates, though one instance of an enzyme with a protein substrate has been reported. Modifications placed by SPOUT methyltransferases play diverse roles in regulating cellular processes such as ensuring translational fidelity, altering RNA stability, and conferring bacterial resistance to antibiotics. This large collection of S-adenosyl-L-methionine-dependent methyltransferases is defined by a unique α/β fold with a deep trefoil knot in their catalytic (SPOUT) domain. Herein, we describe current knowledge of SPOUT enzyme structure, domain architecture, and key elements of catalytic function, including S-adenosyl-L-methionine co-substrate binding, beginning with a new sequence alignment that divides the SPOUT methyltransferase superfamily into four major clades. Finally, a major focus of this review will be on our growing understanding of how these diverse enzymes accomplish the molecular feat of specific substrate recognition and modification, as highlighted by recent advances in our knowledge of protein-RNA complex structures and the discovery of the dependence of one SPOUT methyltransferase on metal ion binding for catalysis. Considering the broad biological roles of RNA modifications, developing a deeper understanding of the process of substrate recognition by the SPOUT enzymes will be critical for defining many facets of fundamental RNA biology with implications for human disease.
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Affiliation(s)
- Sarah E Strassler
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA
| | - Isobel E Bowles
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA
| | - Debayan Dey
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Jane E Jackman
- Department of Chemistry and Biochemistry, Center for RNA Biology and Ohio State Biochemistry Program, Columbus, Ohio, USA.
| | - Graeme L Conn
- Department of Biochemistry, Emory University School of Medicine, Atlanta, Georgia, USA; Graduate Program in Biochemistry, Cell and Developmental Biology, Graduate Division of Biological and Biomedical Sciences, Emory University, Atlanta, Georgia, USA.
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10
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Li G, Manning AC, Bagi A, Yang X, Gokulnath P, Spanos M, Howard J, Chan PP, Sweeney T, Kitchen R, Li H, Laurent BD, Aranki SF, Kontaridis MI, Laurent LC, Van Keuren‐Jensen K, Muehlschlegel J, Lowe TM, Das S. Distinct Stress-Dependent Signatures of Cellular and Extracellular tRNA-Derived Small RNAs. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2200829. [PMID: 35373532 PMCID: PMC9189662 DOI: 10.1002/advs.202200829] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Indexed: 05/11/2023]
Abstract
The cellular response to stress is an important determinant of disease pathogenesis. Uncovering the molecular fingerprints of distinct stress responses may identify novel biomarkers and key signaling pathways for different diseases. Emerging evidence shows that transfer RNA-derived small RNAs (tDRs) play pivotal roles in stress responses. However, RNA modifications present on tDRs are barriers to accurately quantifying tDRs using traditional small RNA sequencing. Here, AlkB-facilitated methylation sequencing is used to generate a comprehensive landscape of cellular and extracellular tDR abundances in various cell types during different stress responses. Extracellular tDRs are found to have distinct fragmentation signatures from intracellular tDRs and these tDR signatures are better indicators of different stress responses than miRNAs. These distinct extracellular tDR fragmentation patterns and signatures are also observed in plasma from patients on cardiopulmonary bypass. It is additionally demonstrated that angiogenin and RNASE1 are themselves regulated by stressors and contribute to the stress-modulated abundance of sub-populations of cellular and extracellular tDRs. Finally, a sub-population of extracellular tDRs is identified for which AGO2 appears to be required for their expression. Together, these findings provide a detailed profile of stress-responsive tDRs and provide insight about tDR biogenesis and stability in response to cellular stressors.
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Affiliation(s)
- Guoping Li
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Aidan C. Manning
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Alex Bagi
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Xinyu Yang
- Fangshan Hospital of BeijingUniversity of Traditional Chinese MedicineBeijing102499China
| | - Priyanka Gokulnath
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Michail Spanos
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Jonathan Howard
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Patricia P. Chan
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Thadryan Sweeney
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Robert Kitchen
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Haobo Li
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Brice D. Laurent
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
| | - Sary F. Aranki
- Division of Cardiac SurgeryDepartment of SurgeryBrigham and Women's HospitalHarvard Medical SchoolBostonMA02115USA
| | - Maria I. Kontaridis
- Department of Biomedical Research and Translational MedicineMasonic Medical Research InstituteUticaNY13501USA
- Department of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA02115USA
- Department of MedicineDivision of CardiologyBeth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMA02215USA
| | - Louise C. Laurent
- Department of Obstetrics, Gynecology, and Reproductive SciencesUniversity of CaliforniaSan DiegoLa JollaCA92093USA
| | | | - Jochen Muehlschlegel
- Department of Anesthesiology, Perioperative and Pain MedicineBrigham and Women's Hospital and Harvard Medical SchoolBostonMA02115USA
| | - Todd M. Lowe
- Department of Biomolecular EngineeringBaskin School of EngineeringUniversity of CaliforniaSanta CruzSanta CruzCA95064USA
| | - Saumya Das
- Cardiovascular Research CenterMassachusetts General Hospital and Harvard Medical SchoolBostonMA02114USA
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11
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Boldrin F, Cioetto Mazzabò L, Lanéelle MA, Rindi L, Segafreddo G, Lemassu A, Etienne G, Conflitti M, Daffé M, Garzino Demo A, Manganelli R, Marrakchi H, Provvedi R. LysX2 is a Mycobacterium tuberculosis membrane protein with an extracytoplasmic MprF-like domain. BMC Microbiol 2022; 22:85. [PMID: 35365094 PMCID: PMC8974105 DOI: 10.1186/s12866-022-02493-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 03/11/2022] [Indexed: 11/17/2022] Open
Abstract
Background Aminoacyl-phosphatidylglycerol (aaPG) synthases are bacterial enzymes that usually catalyze transfer of aminoacyl residues to the plasma membrane phospholipid phosphatidylglycerol (PG). The result is introduction of positive charges onto the cytoplasmic membrane, yielding reduced affinity towards cationic antimicrobial peptides, and increased resistance to acidic environments. Therefore, these enzymes represent an important defense mechanism for many pathogens, including Staphylococcus aureus and Mycobacterium tuberculosis (Mtb), which are known to encode for lysyl-(Lys)-PG synthase MprF and LysX, respectively. Here, we used a combination of bioinformatic, genetic and bacteriological methods to characterize a protein encoded by the Mtb genome, Rv1619, carrying a domain with high similarity to MprF-like domains, suggesting that this protein could be a new aaPG synthase family member. However, unlike homologous domains of MprF and LysX that are positioned in the cytoplasm, we predicted that the MprF-like domain in LysX2 is in the extracytoplasmic region. Results Using genetic fusions to the Escherichia coli proteins PhoA and LacZ of LysX2, we confirmed this unique membrane topology, as well as LysX and MprF as benchmarks. Expression of lysX2 in Mycobacterium smegmatis increased cell resistance to human β-defensin 2 and sodium nitrite, enhanced cell viability and delayed biofilm formation in acidic pH environment. Remarkably, MtLysX2 significantly reduced the negative charge on the bacterial surface upon exposure to an acidic environment. Additionally, we found LysX2 orthologues in major human pathogens and in rapid-growing mycobacteria frequently associated with human infections, but not in environmental and non-pathogenic mycobacteria. Conclusions Overall, our data suggest that LysX2 is a prototype of a new class within the MprF-like protein family that likely enhances survival of the pathogenic species through its catalytic domain which is exposed to the extracytoplasmic side of the cell membrane and is required to decrease the negative charge on the bacterial surface through a yet uncharacterized mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-022-02493-2.
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Affiliation(s)
| | | | - Marie-Antoinette Lanéelle
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Laura Rindi
- Department of Translational Research, University of Pisa, Pisa, Italy
| | - Greta Segafreddo
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Anne Lemassu
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Gilles Etienne
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Marta Conflitti
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Mamadou Daffé
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Alfredo Garzino Demo
- Department of Molecular Medicine, University of Padua, Padua, Italy.,Department of Microbiology and Immunology, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | | | - Hedia Marrakchi
- Institut de Pharmacologie et de Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
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12
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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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13
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Weng Q, Wang Y, Xie Y, Yu X, Zhang S, Ge J, Li Z, Ye G, Guo J. Extracellular vesicles-associated tRNA-derived fragments (tRFs): biogenesis, biological functions, and their role as potential biomarkers in human diseases. J Mol Med (Berl) 2022; 100:679-695. [PMID: 35322869 PMCID: PMC9110440 DOI: 10.1007/s00109-022-02189-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 02/10/2022] [Accepted: 03/09/2022] [Indexed: 02/06/2023]
Abstract
Traditionally, transfer RNAs (tRNAs) specifically decoded messenger RNA (mRNA) and participated in protein translation. tRNA-derived fragments (tRFs), also known as tRNA-derived small RNAs (tsRNAs), are generated by the specific cleavage of pre- and mature tRNAs and are a class of newly defined functional small non-coding RNAs (sncRNAs). Following the different cleavage positions of precursor or mature tRNA, tRFs are classified into seven types, 5′-tRNA half, 3′-tRNA half, tRF-1, 5′U-tRF, 3′-tRF, 5′-tRF, and i-tRF. It has been demonstrated that tRFs have a diverse range of biological functions in cellular processes, which include inhibiting protein translation, modulating stress response, regulating gene expression, and involvement in cell cycles and epigenetic inheritance. Emerging evidences have indicated that tRFs in extracellular vesicles (EVs) seem to act as regulatory molecules in various cellular processes and play essential roles in cell-to-cell communication. Furthermore, the dysregulation of EV-associated tRFs has been associated with the occurrence and progression of a variety of cancers and they can serve as novel potential biomarkers for cancer diagnosis. In this review, the biogenesis and classification of tRFs are summarized, and the biological functions of EV-associated tRFs and their roles as potential biomarkers in human diseases are discussed.
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Affiliation(s)
- Qiuyan Weng
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Yao Wang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Yaoyao Xie
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Xiuchong Yu
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Shuangshuang Zhang
- Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China
| | - Jiaxin Ge
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Zhe Li
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China
| | - Guoliang Ye
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
| | - Junming Guo
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, 315020, China. .,Department of Biochemistry and Molecular Biology and Zhejiang Key Laboratory of Pathophysiology, Ningbo University School of Medicine, Ningbo, 315211, China. .,Institute of Digestive Diseases of Ningbo University, Ningbo, 315020, China.
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14
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Peña N, Zhang W, Watkins C, Halucha M, Alshammary H, Hernandez MM, Liu WC, Albrecht RA, Garcia-Sastre A, Simon V, Katanski C, Pan T. Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. Front Cell Dev Biol 2022; 10:768356. [PMID: 35186917 PMCID: PMC8851031 DOI: 10.3389/fcell.2022.768356] [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: 08/31/2021] [Accepted: 01/18/2022] [Indexed: 11/24/2022] Open
Abstract
Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.
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Affiliation(s)
- Noah Peña
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Christopher Watkins
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Mateusz Halucha
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Hala Alshammary
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Matthew M. Hernandez
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Adolfo Garcia-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Viviana Simon
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Department of Pathology, Molecular and Cell Based Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- The Global Health and Emerging Pathogen Institute, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Division of Infectious Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Christopher Katanski
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
| | - Tao Pan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, United States
- Committee on Microbiology, University of Chicago, Chicago, IL, United States
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15
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Bian M, Huang S, Yu D, Zhou Z. tRNA Metabolism and Lung Cancer: Beyond Translation. Front Mol Biosci 2021; 8:659388. [PMID: 34660690 PMCID: PMC8516113 DOI: 10.3389/fmolb.2021.659388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 08/25/2021] [Indexed: 12/15/2022] Open
Abstract
Lung cancer, one of the most malignant tumors, has extremely high morbidity and mortality, posing a serious threat to global health. It is an urgent need to fully understand the pathogenesis of lung cancer and provide new ideas for its treatment. Interestingly, accumulating evidence has identified that transfer RNAs (tRNAs) and tRNA metabolism–associated enzymes not only participate in the protein translation but also play an important role in the occurrence and development of lung cancer. In this review, we summarize the different aspects of tRNA metabolism in lung cancer, such as tRNA transcription and mutation, tRNA molecules and derivatives, tRNA-modifying enzymes, and aminoacyl-tRNA synthetases (ARSs), aiming at a better understanding of the pathogenesis of lung cancer and providing new therapeutic strategies for it.
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Affiliation(s)
- Meng Bian
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Shiqiong Huang
- Department of Pharmacy, The First Hospital of Changsha, Changsha, China
| | - Dongsheng Yu
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zheng Zhou
- Department of Chinese Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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16
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Kuscu C, Kiran M, Mohammed A, Kuscu C, Satpathy S, Wolen A, Bardhi E, Bajwa A, Eason JD, Maluf D, Mas V, Akalin E. Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy. Int J Mol Sci 2021; 22:ijms22126218. [PMID: 34207555 PMCID: PMC8226568 DOI: 10.3390/ijms22126218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transplant glomerulopathy develops through multiple mechanisms, including donor-specific antibodies, T cells and innate immunity. This study investigates circulating small RNA profiles in serum samples of kidney transplant recipients with biopsy-proven transplant glomerulopathy. Among total small RNA population, miRNAs were the most abundant species in the serum of kidney transplant patients. In addition, fragments arising from mature tRNA and rRNA were detected. Most of the tRNA fragments were generated from 5′ ends of mature tRNA and mainly from two parental tRNAs: tRNA-Gly and tRNA-Glu. Moreover, transplant patients with transplant glomerulopathy displayed a novel tRNA fragments signature. Gene expression analysis from allograft tissues demonstrated changes in canonical pathways related to immune activation such as iCos-iCosL signaling pathway in T helper cells, Th1 and Th2 activation pathway, and dendritic cell maturation. mRNA targets of down-regulated miRNAs such as miR-1224-5p, miR-4508, miR-320, miR-378a from serum were globally upregulated in tissue. Integration of serum miRNA profiles with tissue gene expression showed that changes in serum miRNAs support the role of T-cell mediated mechanisms in ongoing allograft injury.
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Affiliation(s)
- Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
- Correspondence: ; Tel.: +1-901-448-3162
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Akram Mohammed
- Center for Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Sarthak Satpathy
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Aaron Wolen
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Elissa Bardhi
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - James D. Eason
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Daniel Maluf
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Valeria Mas
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Enver Akalin
- Montefiore Medical Center, Abdominal Transplant Program, Albert Einstein College of Medicine, Bronx, NY 10467, USA;
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