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Nogueras Pérez R, Heredia-Nicolás N, de Lara-Peña L, López de Andrés J, Marchal JA, Jiménez G, Griñán-Lisón C. Unraveling the Potential of miRNAs from CSCs as an Emerging Clinical Tool for Breast Cancer Diagnosis and Prognosis. Int J Mol Sci 2023; 24:16010. [PMID: 37958993 PMCID: PMC10647353 DOI: 10.3390/ijms242116010] [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: 10/11/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Breast cancer (BC) is the most diagnosed cancer in women and the second most common cancer globally. Significant advances in BC research have led to improved early detection and effective therapies. One of the key challenges in BC is the presence of BC stem cells (BCSCs). This small subpopulation within the tumor possesses unique characteristics, including tumor-initiating capabilities, contributes to treatment resistance, and plays a role in cancer recurrence and metastasis. In recent years, microRNAs (miRNAs) have emerged as potential regulators of BCSCs, which can modulate gene expression and influence cellular processes like BCSCs' self-renewal, differentiation, and tumor-promoting pathways. Understanding the miRNA signatures of BCSCs holds great promise for improving BC diagnosis and prognosis. By targeting BCSCs and their associated miRNAs, researchers aim to develop more effective and personalized treatment strategies that may offer better outcomes for BC patients, minimizing tumor recurrence and metastasis. In conclusion, the investigation of miRNAs as regulators of BCSCs opens new directions for advancing BC research through the use of bioinformatics and the development of innovative therapeutic approaches. This review summarizes the most recent and innovative studies and clinical trials on the role of BCSCs miRNAs as potential tools for early diagnosis, prognosis, and resistance.
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Affiliation(s)
- Raquel Nogueras Pérez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
| | - Noelia Heredia-Nicolás
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
| | - Laura de Lara-Peña
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Julia López de Andrés
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Juan Antonio Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain; (R.N.P.); (N.H.-N.); (L.d.L.-P.); (J.L.d.A.); (J.A.M.)
- Biosanitary Research Institute of Granada (ibs. GRANADA), University Hospitals of Granada, University of Granada, 18012 Granada, Spain
- Excellence Research Unit “Modeling Nature” (MNat), University of Granada, 18016 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18071 Granada, Spain
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García-Ortega MB, Aparicio E, Griñán-Lisón C, Jiménez G, López-Ruiz E, Palacios JL, Ruiz-Alcalá G, Alba C, Martínez A, Boulaiz H, Perán M, Hackenberg M, Bragança J, Calado SM, Marchal JA, García MÁ. Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma. Cancers (Basel) 2023; 15:3666. [PMID: 37509327 PMCID: PMC10377490 DOI: 10.3390/cancers15143666] [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: 05/31/2023] [Revised: 07/06/2023] [Accepted: 07/15/2023] [Indexed: 07/30/2023] Open
Abstract
Malignant melanoma (MM) can spread to other organs and is resistant in part due to the presence of cancer stem cell subpopulations (CSCs). While a controversial high dose of interferon-alpha (IFN-α) has been used to treat non-metastatic high-risk melanoma, it comes with undesirable side effects. In this study, we evaluated the effect of low and high doses of IFN-α on CSCs by analyzing ALDH activity, side population and specific surface markers in established and patient-derived primary cell lines. We also assessed the clonogenicity, migration and tumor initiation capacities of IFN-α treated CSCs. Additionally, we investigated genomic modulations related to stemness properties using microRNA sequencing and microarrays. The effect of IFN-α on CSCs-derived exosomes was also analyzed using NanoSight and liquid chromatography (LC-HRMS)-based metabolomic analysis, among others. Our results showed that even low doses of IFN-α reduced CSC formation and stemness properties, and led to a significant decrease in the ability to form tumors in mice xenotransplants. IFN-α also modulated the expression of genes and microRNAs involved in several cancer processes and metabolomics of released exosomes. Our work suggests the utility of low doses of interferon, combined with the analysis of metabolic biomarkers, as a potential clinical approach against the aggressiveness of CSCs in melanoma.
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Affiliation(s)
- María Belén García-Ortega
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Ernesto Aparicio
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18011 Granada, Spain
- GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government, 18016 Granada, Spain
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Elena López-Ruiz
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - José Luis Palacios
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
| | - Gloria Ruiz-Alcalá
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
| | - Cristina Alba
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Antonio Martínez
- Department of Dermatology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Houria Boulaiz
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Macarena Perán
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - Michael Hackenberg
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Sofia M Calado
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Juan A Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - María Ángel García
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit "Modelling Nature" (MNat), University of Granada, 18071 Granada, Spain
- Department of Molecular Biology and Biochemistry III and Immunology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
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García-Ortega MB, Aparicio E, Griñán-Lisón C, Jiménez G, López-Ruiz E, Palacios JL, Ruiz-Alcalá G, Alba C, Martínez A, Boulaiz H, Perán M, Hackenberg M, Bragança J, Calado SM, Marchal JA, García MÁ. Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma. Cancers (Basel) 2023; 15:3666. [DOI: https:/doi.org/10.3390/cancers15143666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Malignant melanoma (MM) can spread to other organs and is resistant in part due to the presence of cancer stem cell subpopulations (CSCs). While a controversial high dose of interferon-alpha (IFN-α) has been used to treat non-metastatic high-risk melanoma, it comes with undesirable side effects. In this study, we evaluated the effect of low and high doses of IFN-α on CSCs by analyzing ALDH activity, side population and specific surface markers in established and patient-derived primary cell lines. We also assessed the clonogenicity, migration and tumor initiation capacities of IFN-α treated CSCs. Additionally, we investigated genomic modulations related to stemness properties using microRNA sequencing and microarrays. The effect of IFN-α on CSCs-derived exosomes was also analyzed using NanoSight and liquid chromatography (LC-HRMS)-based metabolomic analysis, among others. Our results showed that even low doses of IFN-α reduced CSC formation and stemness properties, and led to a significant decrease in the ability to form tumors in mice xenotransplants. IFN-α also modulated the expression of genes and microRNAs involved in several cancer processes and metabolomics of released exosomes. Our work suggests the utility of low doses of interferon, combined with the analysis of metabolic biomarkers, as a potential clinical approach against the aggressiveness of CSCs in melanoma.
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Affiliation(s)
- María Belén García-Ortega
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Ernesto Aparicio
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - Carmen Griñán-Lisón
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, 18011 Granada, Spain
- GENYO-Centre for Genomics and Oncological Research-Pfizer/University of Granada/Andalusian Regional Government, 18016 Granada, Spain
| | - Gema Jiménez
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Elena López-Ruiz
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - José Luis Palacios
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - Gloria Ruiz-Alcalá
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - Cristina Alba
- Department of Oncology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Antonio Martínez
- Department of Dermatology, Virgen de las Nieves University Hospital, 18014 Granada, Spain
| | - Houria Boulaiz
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - Macarena Perán
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Health Sciences, University of Jaén, Campus de las Lagunillas SN, 23071 Jaén, Spain
| | - Michael Hackenberg
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Genetics, University of Granada, 18100 Granada, Spain
| | - José Bragança
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Sofia M. Calado
- Algarve Biomedical Center Research Institute (ABC-RI), Universidade do Algarve, 8005-139 Faro, Portugal
- Faculdade de Medicina e Ciências Biomédicas, Universidade do Algarve, 8005-139 Faro, Portugal
- Champalimaud Research Program, Champalimaud Center for the Unknown, 1400-038 Lisbon, Portugal
| | - Juan A. Marchal
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
| | - María Ángel García
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research, University of Granada, 18016 Granada, Spain
- Instituto de Investigación Biosanitaria de Granada (ibs. GRANADA), 18012 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
- Department of Molecular Biology and Biochemistry III and Immunology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
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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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Gómez-Martín C, Aparicio-Puerta E, van Eijndhoven MA, Medina JM, Hackenberg M, Pegtel DM. Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing. CELL REPORTS METHODS 2023; 3:100480. [PMID: 37323569 PMCID: PMC10261927 DOI: 10.1016/j.crmeth.2023.100480] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 03/07/2023] [Accepted: 04/21/2023] [Indexed: 06/17/2023]
Abstract
IsomiRs, sequence variants of mature microRNAs, are usually detected and quantified using high-throughput sequencing. Many examples of their biological relevance have been reported, but sequencing artifacts identified as artificial variants might bias biological inference and therefore need to be ideally avoided. We conducted a comprehensive evaluation of 10 different small RNA sequencing protocols, exploring both a theoretically isomiR-free pool of synthetic miRNAs and HEK293T cells. We calculated that, with the exception of two protocols, less than 5% of miRNA reads can be attributed to library preparation artifacts. Randomized-end adapter protocols showed superior accuracy, with 40% of true biological isomiRs. Nevertheless, we demonstrate concordance across protocols for selected miRNAs in non-templated uridyl additions. Notably, NTA-U calling and isomiR target prediction can be inaccurate when using protocols with poor single-nucleotide resolution. Our results highlight the relevance of protocol choice for biological isomiRs detection and annotation, which has key potential implications for biomedical applications.
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Affiliation(s)
- Cristina Gómez-Martín
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | | | - Monique A.J. van Eijndhoven
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
| | - José M. Medina
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
| | - Michael Hackenberg
- Department of Genetics, Faculty of Science, University of Granada, 18071 Granada, Spain
- Bioinformatics Laboratory, Biotechnology Institute, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, University of Granada, 18071 Granada, Spain
- Excellence Research Unit “Modelling Nature” (MNat), University of Granada, 18071 Granada, Spain
| | - D. Michiel Pegtel
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Pathology, De Boelelaan, 1117 Amsterdam, the Netherlands
- Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, the Netherlands
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6
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Cherchi R, Cusano R, Orrù S, Ferrari PA, Massidda M, Fotia G, De Matteis S, Cocco P. Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study. Epigenet Insights 2023; 16:25168657231160985. [PMID: 37025420 PMCID: PMC10070752 DOI: 10.1177/25168657231160985] [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: 12/19/2022] [Accepted: 02/14/2023] [Indexed: 04/05/2023] Open
Abstract
Introduction: Exhaled breath condensate (EBC) sampling has been suggested as a less-invasive and cost-effective method to detect biological macromolecules, including miRNA. To explore the feasibility of its use as a biomarker of early effects of asbestos exposure, we conducted a preliminary test on male volunteers by comparing the miRNA profile in the EBC and the plasma using 2 different sequencing platforms. Methods: Six male volunteers, all retired and unexposed to dust or fumes, participated in the test. RNA was extracted from 200 μL EBC samples and same-size plasma samples. Sample aliquots were processed in 2 laboratories using 2 different sequencing platforms: a MiSeq Illumina® platform and a more performing HiSeq Illumina® platform. Results: The HiSeq3000® sequencing platform identified twice as many unique molecular indexes (UMI)-validated miRNA as the MiSeq® platform. The Spearman’s correlation coefficient between EBC counts and plasma counts was significant in 5/6 subjects with either platform (MiSeq® = 0.128-0.508, P = .026-<.001; HiSeq® = 0.156-0.412, P = .001-<.001). The intraclass correlation coefficient confirmed the consistency of the miRNA profile over the 6 participants with both biospecimens. Exploring the agreement between the EBC and plasma samples with Bland-Altman plots showed that using the HiSeq3000® platform substantially improved the EBC miRNA detection rate. Conclusion: Our preliminary study confirms that, when using the HiSeq® sequencing platform, EBC sampling is a suitable, non-invasive method to detect the miRNA profile in healthy subjects.
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Affiliation(s)
- Roberto Cherchi
- Operative Unit of Thoracic Surgery, Hospital G. Brotzu, Cagliari, Italy
| | - Roberto Cusano
- CRS4-NGS Core, POLARIS Research Park, Pula—Cagliari, Italy
| | - Sandro Orrù
- Operative Unit of Medical Genetics, Health Agency of Sardinia, Hospital Binaghi, Cagliari, Italy
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato—Cagliari, Italy
- Orrù S, Unit of Medical Genetics, Health Agency of Sardinia, Hospital Binaghi, Via Is Guadazzonis 3, Cagliari 09126, Italy.
| | - Paolo A Ferrari
- Operative Unit of Thoracic Surgery, Hospital G. Brotzu, Cagliari, Italy
| | | | - Giorgio Fotia
- CRS4-NGS Core, POLARIS Research Park, Pula—Cagliari, Italy
| | - Sara De Matteis
- Department of Medical Sciences and Public Health, University of Cagliari, Monserrato—Cagliari, Italy
| | - Pierluigi Cocco
- Centre for Occupational and Environmental Health, Division of Population Health, Health Services Research & Primary Care, University of Manchester, Manchester, UK
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7
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Smith MD, Leemaqz SY, Jankovic-Karasoulos T, McCullough D, McAninch D, Arthurs AL, Breen J, Roberts CT, Pillman KA. DraculR: A Web-Based Application for In Silico Haemolysis Detection in High-Throughput microRNA Sequencing Data. Genes (Basel) 2023; 14:448. [PMID: 36833375 PMCID: PMC9957079 DOI: 10.3390/genes14020448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/19/2023] [Accepted: 02/01/2023] [Indexed: 02/12/2023] Open
Abstract
The search for novel microRNA (miRNA) biomarkers in plasma is hampered by haemolysis, the lysis and subsequent release of red blood cell contents, including miRNAs, into surrounding fluid. The biomarker potential of miRNAs comes in part from their multicompartment origin and the long-lived nature of miRNA transcripts in plasma, giving researchers a functional window for tissues that are otherwise difficult or disadvantageous to sample. The inclusion of red-blood-cell-derived miRNA transcripts in downstream analysis introduces a source of error that is difficult to identify posthoc and may lead to spurious results. Where access to a physical specimen is not possible, our tool will provide an in silico approach to haemolysis prediction. We present DraculR, an interactive Shiny/R application that enables a user to upload miRNA expression data from a short-read sequencing of human plasma as a raw read counts table and interactively calculate a metric that indicates the degree of haemolysis contamination. The code, DraculR web tool and its tutorial are freely available as detailed herein.
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Affiliation(s)
- Melanie D. Smith
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Shalem Y. Leemaqz
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Tanja Jankovic-Karasoulos
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Dylan McCullough
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - Dale McAninch
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Anya L. Arthurs
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
| | - James Breen
- Indigenous Genomics, Telethon Kids Institute, Adelaide, SA 5000, Australia
- College of Health & Medicine, Australian National University, Canberra, ACT 2600, Australia
| | - Claire T. Roberts
- Flinders Health and Medical Research Institute, Flinders University, Bedford Park, SA 5042, Australia
- Adelaide Medical School, University of Adelaide, Adelaide, SA 5005, Australia
| | - Katherine A. Pillman
- Centre for Cancer Biology, an Alliance between SA Pathology and the University of South Australia, Adelaide, SA 5000, Australia
- School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
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8
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Huang L, Zhang L, Chen X. Updated review of advances in microRNAs and complex diseases: experimental results, databases, webservers and data fusion. Brief Bioinform 2022; 23:6696143. [PMID: 36094095 DOI: 10.1093/bib/bbac397] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/19/2022] [Accepted: 08/15/2022] [Indexed: 12/14/2022] Open
Abstract
MicroRNAs (miRNAs) are gene regulators involved in the pathogenesis of complex diseases such as cancers, and thus serve as potential diagnostic markers and therapeutic targets. The prerequisite for designing effective miRNA therapies is accurate discovery of miRNA-disease associations (MDAs), which has attracted substantial research interests during the last 15 years, as reflected by more than 55 000 related entries available on PubMed. Abundant experimental data gathered from the wealth of literature could effectively support the development of computational models for predicting novel associations. In 2017, Chen et al. published the first-ever comprehensive review on MDA prediction, presenting various relevant databases, 20 representative computational models, and suggestions for building more powerful ones. In the current review, as the continuation of the previous study, we revisit miRNA biogenesis, detection techniques and functions; summarize recent experimental findings related to common miRNA-associated diseases; introduce recent updates of miRNA-relevant databases and novel database releases since 2017, present mainstream webservers and new webserver releases since 2017 and finally elaborate on how fusion of diverse data sources has contributed to accurate MDA prediction.
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Affiliation(s)
- Li Huang
- Academy of Arts and Design, Tsinghua University, Beijing, 10084, China.,The Future Laboratory, Tsinghua University, Beijing, 10084, China
| | - Li Zhang
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China
| | - Xing Chen
- School of Information and Control Engineering, China University of Mining and Technology, Xuzhou, 221116, China.,Artificial Intelligence Research Institute, China University of Mining and Technology, Xuzhou, 221116, China
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9
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Aparicio-Puerta E, Hirsch P, Schmartz GP, Fehlmann T, Keller V, Engel A, Kern F, Hackenberg M, Keller A. isomiRdb: microRNA expression at isoform resolution. Nucleic Acids Res 2022; 51:D179-D185. [PMID: 36243964 PMCID: PMC9825445 DOI: 10.1093/nar/gkac884] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 09/19/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023] Open
Abstract
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.
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Affiliation(s)
| | | | - Georges P Schmartz
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Tobias Fehlmann
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Rejuvenome, Astera Institute, Berkeley, CA 94705, USA
| | - Verena Keller
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Department for Internal Medicine II, Saarland University Hospital, 66421 Homburg, Germany
| | - Annika Engel
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Fabian Kern
- Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS)–Helmholtz Centre for Infection Research (HZI), Saarland University Campus, 66123 Saarbrücken, Germany
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, Universidad de Granada, 18071 Granada, Spain
| | - Andreas Keller
- To whom correspondence should be addressed. Tel: +49 681 30268611; Fax: +49 681 30268610;
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10
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Blanco-Domínguez R, Sánchez-Díaz R, Martín P. A Novel Circulating MicroRNA for the Detection of Acute Myocarditis. Reply. N Engl J Med 2022; 387:1240-1241. [PMID: 36170511 DOI: 10.1056/nejmc2115639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
| | | | - Pilar Martín
- Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
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11
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Céspedes PF, Jainarayanan A, Fernández-Messina L, Valvo S, Saliba DG, Kurz E, Kvalvaag A, Chen L, Ganskow C, Colin-York H, Fritzsche M, Peng Y, Dong T, Johnson E, Siller-Farfán JA, Dushek O, Sezgin E, Peacock B, Law A, Aubert D, Engledow S, Attar M, Hester S, Fischer R, Sánchez-Madrid F, Dustin ML. T-cell trans-synaptic vesicles are distinct and carry greater effector content than constitutive extracellular vesicles. Nat Commun 2022; 13:3460. [PMID: 35710644 PMCID: PMC9203538 DOI: 10.1038/s41467-022-31160-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 06/07/2022] [Indexed: 12/19/2022] Open
Abstract
The immunological synapse is a molecular hub that facilitates the delivery of three activation signals, namely antigen, costimulation/corepression and cytokines, from antigen-presenting cells (APC) to T cells. T cells release a fourth class of signaling entities, trans-synaptic vesicles (tSV), to mediate bidirectional communication. Here we present bead-supported lipid bilayers (BSLB) as versatile synthetic APCs to capture, characterize and advance the understanding of tSV biogenesis. Specifically, the integration of juxtacrine signals, such as CD40 and antigen, results in the adaptive tailoring and release of tSV, which differ in size, yields and immune receptor cargo compared with steadily released extracellular vesicles (EVs). Focusing on CD40L+ tSV as model effectors, we show that PD-L1 trans-presentation together with TSG101, ADAM10 and CD81 are key in determining CD40L vesicular release. Lastly, we find greater RNA-binding protein and microRNA content in tSV compared with EVs, supporting the specialized role of tSV as intercellular messengers.
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Affiliation(s)
- Pablo F Céspedes
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK.
| | - Ashwin Jainarayanan
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Lola Fernández-Messina
- Immunology Service, Hospital de la Princesa, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Madrid, Spain
- Intercellular communication in the inflammatory response. Vascular Physiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Salvatore Valvo
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - David G Saliba
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Elke Kurz
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Audun Kvalvaag
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Lina Chen
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Charity Ganskow
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
| | - Huw Colin-York
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Marco Fritzsche
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
| | - Yanchun Peng
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Tao Dong
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, The University of Oxford, Oxford, UK
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Errin Johnson
- Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK
| | | | - Omer Dushek
- Sir William Dunn School of Pathology, The University of Oxford, Oxford, UK
| | - Erdinc Sezgin
- Science for Life Laboratory, Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | | | | | | | - Simon Engledow
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, The University of Oxford, Oxford, UK
| | - Moustafa Attar
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK
- Oxford Genomics Centre, Wellcome Centre for Human Genetics, The University of Oxford, Oxford, UK
| | - Svenja Hester
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, The University of Oxford, Oxford, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, The University of Oxford, Oxford, UK
| | - Francisco Sánchez-Madrid
- Immunology Service, Hospital de la Princesa, Instituto Investigación Sanitaria Princesa, Universidad Autónoma de Madrid, Madrid, Spain
- Intercellular communication in the inflammatory response. Vascular Physiology Area, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Michael L Dustin
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, The University of Oxford, Oxford, UK.
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12
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Aparicio-Puerta E, Gómez-Martín C, Giannoukakos S, Medina JM, Scheepbouwer C, García-Moreno A, Carmona-Saez P, Fromm B, Pegtel M, Keller A, Marchal JA, Hackenberg M. sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms. Nucleic Acids Res 2022; 50:W710-W717. [PMID: 35556129 PMCID: PMC9252802 DOI: 10.1093/nar/gkac363] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/13/2022] [Accepted: 04/28/2022] [Indexed: 12/13/2022] Open
Abstract
The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.
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Affiliation(s)
| | - Cristina Gómez-Martín
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam 1081HV, Netherlands
| | - Stavros Giannoukakos
- Genetics Department, Faculty of Science, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Bioinformatics Laboratory, Biomedical Research Centre (CIBM), PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain.,Excellence Research Unit "Modeling Nature" (MNat), University of Granada, Spain
| | - José María Medina
- Genetics Department, Faculty of Science, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Bioinformatics Laboratory, Biomedical Research Centre (CIBM), PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain.,Excellence Research Unit "Modeling Nature" (MNat), University of Granada, Spain
| | - Chantal Scheepbouwer
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam 1081HV, Netherlands.,Department of Neurosurgery, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam 1081HV, Netherlands
| | - Adrián García-Moreno
- Centre for Genomics and Oncological Research. GENYO. Pfizer / University of Granada,18016 Granada, Spain
| | - Pedro Carmona-Saez
- Centre for Genomics and Oncological Research. GENYO. Pfizer / University of Granada,18016 Granada, Spain
| | - Bastian Fromm
- The Arctic University Museum of Norway, 9006 Tromso, Norway
| | - Michiel Pegtel
- Department of Pathology, Cancer Center Amsterdam, Amsterdam UMC, VU University, Amsterdam 1081HV, Netherlands
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, 66123 Saarbrücken, Germany
| | - Juan Antonio Marchal
- Excellence Research Unit "Modeling Nature" (MNat), University of Granada, Spain.,Department of Human Anatomy and Embryology, Institute of Biopathology and Regenerative Medicine, University of Granada, 18011 Granada, Spain.,Instituto de Investigación Biosanitaria ibs.GRANADA, University Hospitals of Granada-University of Granada, Spain; Conocimiento s/n 18100, Granada. Spain
| | - Michael Hackenberg
- Genetics Department, Faculty of Science, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain.,Bioinformatics Laboratory, Biomedical Research Centre (CIBM), PTS, Avda. del Conocimiento s/n, 18100 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
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13
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Sempere LF, Azmi AS, Moore A. microRNA-based diagnostic and therapeutic applications in cancer medicine. WILEY INTERDISCIPLINARY REVIEWS. RNA 2021; 12:e1662. [PMID: 33998154 PMCID: PMC8519065 DOI: 10.1002/wrna.1662] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 01/18/2023]
Abstract
It has been almost two decades since the first link between microRNAs and cancer was established. In the ensuing years, this abundant class of short noncoding regulatory RNAs has been studied in virtually all cancer types. This tremendously large body of research has generated innovative technological advances for detection of microRNAs in tissue and bodily fluids, identified the diagnostic, prognostic, and/or predictive value of individual microRNAs or microRNA signatures as potential biomarkers for patient management, shed light on regulatory mechanisms of RNA-RNA interactions that modulate gene expression, uncovered cell-autonomous and cell-to-cell communication roles of specific microRNAs, and developed a battery of viral and nonviral delivery approaches for therapeutic intervention. Despite these intense and prolific research efforts in preclinical and clinical settings, there are a limited number of microRNA-based applications that have been incorporated into clinical practice. We review recent literature and ongoing clinical trials that highlight most promising approaches and standing challenges to translate these findings into viable microRNA-based clinical tools for cancer medicine. This article is categorized under: RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Lorenzo F. Sempere
- Department of Radiology, Precision Health ProgramMichigan State UniversityEast LansingMichiganUSA
| | - Asfar S. Azmi
- Department of OncologyWayne State University School of MedicineDetroitMichiganUSA
- Karmanos Cancer InstituteDetroitMichiganUSA
| | - Anna Moore
- Departments of Radiology and Physiology, Precision Health ProgramMichigan State UniversityEast LansingMichiganUSA
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14
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Li QS, Cai D. Integrated miRNA-Seq and mRNA-Seq Study to Identify miRNAs Associated With Alzheimer's Disease Using Post-mortem Brain Tissue Samples. Front Neurosci 2021; 15:620899. [PMID: 33833661 PMCID: PMC8021900 DOI: 10.3389/fnins.2021.620899] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/23/2021] [Indexed: 01/06/2023] Open
Abstract
Alzheimer's disease (AD), the leading form of dementia, is associated with abnormal tau and β-amyloid accumulation in the brain. We conducted a miRNA-seq study to identify miRNAs associated with AD in the post-mortem brain from the inferior frontal gyrus (IFG, n = 69) and superior temporal gyrus (STG, n = 81). Four and 64 miRNAs were differentially expressed (adjusted p-value < 0.05) in AD compared to cognitively normal controls in the IFG and STG, respectively. We observed down-regulation of several miRNAs that have previously been implicated in AD, including hsa-miR-212-5p and hsa-miR-132-5p, in AD samples across both brain regions, and up-regulation of hsa-miR-146a-5p, hsa-miR-501-3p, hsa-miR-34a-5p, and hsa-miR-454-3p in the STG. The differentially expressed miRNAs were previously implicated in the formation of amyloid-β plaques, the dysregulation of tau, and inflammation. We have also observed differential expressions for dozens of other miRNAs in the STG, including hsa-miR-4446-3p, that have not been described previously. Putative targets of these miRNAs (adjusted p-value < 0.1) were found to be involved in Wnt signaling pathway, MAPK family signaling cascades, sphingosine 1-phosphate (S1P) pathway, adaptive immune system, innate immune system, and neurogenesis. Our results support the finding of dysregulated miRNAs previously implicated in AD and propose additional miRNAs that appear to be dysregulated in AD for experimental follow-up.
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Affiliation(s)
- Qingqin S. Li
- Neuroscience, Janssen Research & Development, LLC, Titusville, NJ, United States
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