1
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Van Der Schueren C, Decruyenaere P, Avila Cobos F, Bult J, Deleu J, Dipalo LL, Helsmoortel HH, Hulstaert E, Morlion A, Ramos Varas E, Schoofs K, Trypsteen W, Vanden Eynde E, Van Droogenbroeck H, Verniers K, Vandesompele J, Decock A. Subpar reporting of pre-analytical variables in RNA-focused blood plasma studies. Mol Oncol 2024. [PMID: 38564603 DOI: 10.1002/1878-0261.13647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 02/13/2024] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
Extracellular RNA (cell-free RNA; exRNA) from blood-derived liquid biopsies is an appealing, minimally invasive source of disease biomarkers. As pre-analytical variables strongly influence exRNA measurements, their reporting is essential for meaningful interpretation and replication of results. The aim of this review was to chart to what extent pre-analytical variables are documented, to pinpoint shortcomings and to improve future reporting. In total, 200 blood plasma exRNA studies published in 2018 or 2023 were reviewed for annotation of 22 variables associated with blood collection, plasma preparation, and RNA purification. Our results show that pre-analytical variables are poorly documented, with only three out of 22 variables described in over half of the publications. The percentage of variables reported ranged from 4.6% to 54.6% (mean 24.84%) in 2023 and from 4.6% to 57.1% (mean 28.60%) in 2018. Recommendations and guidelines (i.e., BRISQ, ASCO-CAP, BloodPAC, PPMPT, and CEN standards) have currently not resulted in improved reporting. In conclusion, our results highlight the lack of reporting pre-analytical variables in exRNA studies and advocate for a consistent use of available standards, endorsed by funders and journals.
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Affiliation(s)
| | - Philippe Decruyenaere
- Department of Biomolecular Medicine, Ghent University, Belgium
- Department of Hematology, Ghent University Hospital, Belgium
| | - Francisco Avila Cobos
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Johanna Bult
- Department of Biomolecular Medicine, Ghent University, Belgium
- Department of Hematology, University Medical Center Groningen, The Netherlands
| | - Jill Deleu
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Laudonia Lidia Dipalo
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Hetty Hilde Helsmoortel
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- Department of Dermatology, AZ Sint-Blasius, Belgium
| | - Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Elena Ramos Varas
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Kathleen Schoofs
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- Translational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Belgium
- Center for Medical Biotechnology, VIB-UGent, Belgium
| | - Wim Trypsteen
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Eveline Vanden Eynde
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Hanne Van Droogenbroeck
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
- CellCarta, Belgium
| | - Anneleen Decock
- Department of Biomolecular Medicine, Ghent University, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Belgium
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2
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Vermeirssen V, Deleu J, Morlion A, Everaert C, De Wilde J, Anckaert J, Durinck K, Nuytens J, Rishfi M, Speleman F, Van Droogenbroeck H, Verniers K, Baietti M, Albersen M, Leucci E, Post E, Best M, Van Maerken T, De Wilde B, Vandesompele J, Decock A. Whole transcriptome profiling of liquid biopsies from tumour xenografted mouse models enables specific monitoring of tumour-derived extracellular RNA. NAR Cancer 2022; 4:zcac037. [DOI: 10.1093/narcan/zcac037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 09/23/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2022] Open
Abstract
Abstract
While cell-free DNA (cfDNA) is widely being investigated, free circulating RNA (extracellular RNA, exRNA) has the potential to improve cancer therapy response monitoring and detection due to its dynamic nature. However, it remains unclear in which blood subcompartment tumour-derived exRNAs primarily reside. We developed a host-xenograft deconvolution framework, exRNAxeno, with mapping strategies to either a combined human-mouse reference genome or both species genomes in parallel, applicable to exRNA sequencing data from liquid biopsies of human xenograft mouse models. The tool enables to distinguish (human) tumoural RNA from (murine) host RNA, to specifically analyse tumour-derived exRNA. We applied the combined pipeline to total exRNA sequencing data from 95 blood-derived liquid biopsy samples from 30 mice, xenografted with 11 different tumours. Tumoural exRNA concentrations are not determined by plasma platelet levels, while host exRNA concentrations increase with platelet content. Furthermore, a large variability in exRNA abundance and transcript content across individual mice is observed. The tumoural gene detectability in plasma is largely correlated with the RNA expression levels in the tumour tissue or cell line. These findings unravel new aspects of tumour-derived exRNA biology in xenograft models and open new avenues to further investigate the role of exRNA in cancer.
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Affiliation(s)
- Vanessa Vermeirssen
- Lab for Computational Biology, Integromics and Gene Regulation (CBIGR), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomedical Molecular Biology, Ghent University , 9000, Ghent , Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Jill Deleu
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Annelien Morlion
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Celine Everaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Jilke De Wilde
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Pathology, Ghent University Hospital , 9000, Ghent , Belgium
| | - Jasper Anckaert
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Kaat Durinck
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Justine Nuytens
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Muhammad Rishfi
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Frank Speleman
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Pediatric Precision Oncology Lab (PPOL), Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
| | - Hanne Van Droogenbroeck
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Kimberly Verniers
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Maria Francesca Baietti
- Laboratory for RNA Cancer Biology, Department of Oncology , KU Leuven, 3000, Leuven , Belgium
- TRACE, Leuven Cancer Institute , KU Leuven, 3000, Leuven, Belgium
| | - Maarten Albersen
- Department of Development and Regeneration, Laboratory of Experimental Urology, KU Leuven, Department of Urology, University Hospitals Leuven , 3000, Leuven , Belgium
| | - Eleonora Leucci
- Laboratory for RNA Cancer Biology, Department of Oncology , KU Leuven, 3000, Leuven , Belgium
- TRACE, Leuven Cancer Institute , KU Leuven, 3000, Leuven, Belgium
| | - Edward Post
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery , Boelelaan 1117, 1081 HV, Amsterdam , the Netherlands
- Cancer Center Amsterdam, Brain Tumor Center and Liquid Biopsy Center , 1081 HV, Amsterdam , the Netherlands
| | - Myron G Best
- Amsterdam UMC Location Vrije Universiteit Amsterdam, Department of Neurosurgery , Boelelaan 1117, 1081 HV, Amsterdam , the Netherlands
- Cancer Center Amsterdam, Brain Tumor Center and Liquid Biopsy Center , 1081 HV, Amsterdam , the Netherlands
| | - Tom Van Maerken
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Laboratory Medicine , AZ Groeninge, 8500, Kortrijk , Belgium
| | - Bram De Wilde
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
- Department of Paediatric Haematology Oncology and Stem Cell Transplantation, Ghent University Hospital , 9000, Ghent , Belgium
| | - Jo Vandesompele
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
| | - Anneleen Decock
- OncoRNALab, Cancer Research Institute Ghent (CRIG) , 9000, Ghent , Belgium
- Department of Biomolecular Medicine, Ghent University , 9000, Ghent , Belgium
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3
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Morlion A, Hulstaert E, Vromman M, Anckaert J, Everaert C, Vandesompele J, Mestdagh P. CiLiQuant: Quantification of RNA Junction Reads Based on Their Circular or Linear Transcript Origin. Front Bioinform 2022; 2:834034. [PMID: 36304262 PMCID: PMC9580843 DOI: 10.3389/fbinf.2022.834034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/07/2022] [Indexed: 11/17/2022] Open
Abstract
Distinguishing circular RNA reads from reads derived from the linear host transcript is a challenging task because of sequence overlap. We developed a computational approach, CiLiQuant, that determines the relative circular and linear abundance of transcripts and gene loci using back-splice and unambiguous forward-splice junction reads generated by existing mapping and circular RNA discovery tools.
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Affiliation(s)
- Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- *Correspondence: Annelien Morlion, ; Pieter Mestdagh,
| | - Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Marieke Vromman
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jasper Anckaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Celine Everaert
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Translational Oncogenomics and Bioinformatics Lab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- OncoRNALab, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- *Correspondence: Annelien Morlion, ; Pieter Mestdagh,
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4
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Hulstaert E, Levanon K, Morlion A, Van Aelst S, Christidis AA, Zamar R, Anckaert J, Verniers K, Bahar-Shany K, Sapoznik S, Vandesompele J, Mestdagh P. RNA biomarkers from proximal liquid biopsy for diagnosis of ovarian cancer. Neoplasia 2022; 24:155-164. [PMID: 34998206 PMCID: PMC8740458 DOI: 10.1016/j.neo.2021.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/20/2021] [Indexed: 10/29/2022]
Abstract
BACKGROUND Most ovarian cancer patients are diagnosed at an advanced stage and have a high mortality rate. Current screening strategies fail to improve prognosis because markers that are sensitive for early stage disease are lacking. This medical need justifies the search for novel approaches using utero-tubal lavage as a proximal liquid biopsy. METHODS In this study, we explore the extracellular transcriptome of utero-tubal lavage fluid obtained from 26 ovarian cancer patients and 48 controls using messenger RNA (mRNA) capture and small RNA sequencing. RESULTS We observed an enrichment of ovarian and fallopian tube specific messenger RNAs in utero-tubal lavage fluid compared to other human biofluids. Over 300 mRNAs and 41 miRNAs were upregulated in ovarian cancer samples compared with controls. Upregulated genes were enriched for genes involved in cell cycle activation and proliferation, hinting at a tumor-derived signal. CONCLUSION This is a proof-of-principle that mRNA capture sequencing of utero-tubal lavage fluid is technically feasible, and that the extracellular transcriptome of utero-tubal lavage should be further explored in larger cohorts to assess the diagnostic value of the biomarkers identified in this study. IMPACT Proximal liquid biopsy from the gynecologic tract is a promising source for mRNA and miRNA biomarkers for diagnosis of early-stage ovarian cancer.
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Affiliation(s)
- Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium; Department of Dermatology, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel; Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | | | | | - Ruben Zamar
- Department of Statistics, University of British Columbia, Vancouver, Canada
| | - Jasper Anckaert
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Kimberly Verniers
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Keren Bahar-Shany
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Stav Sapoznik
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan, Israel
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, 9000 Ghent, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, 9000 Ghent, Belgium.
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5
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Morlion A, Everaert C, Nuytens J, Hulstaert E, Vandesompele J, Mestdagh P. Custom long non-coding RNA capture enhances detection sensitivity in different human sample types. RNA Biol 2021; 18:215-222. [PMID: 34470578 PMCID: PMC8682977 DOI: 10.1080/15476286.2021.1971438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are a heterogeneous group of transcripts that lack protein coding potential and display regulatory functions in various cellular processes. As a result of their cell- and cancer-specific expression patterns, lncRNAs have emerged as potential diagnostic and therapeutic targets. The accurate characterization of lncRNAs in bulk transcriptome data remains challenging due to their low abundance compared to protein coding genes. To tackle this issue, we describe a unique short-read custom lncRNA capture sequencing approach that relies on a comprehensive set of 565,878 capture probes for 49,372 human lncRNA genes. This custom lncRNA capture approach was evaluated on various sample types ranging from artificial high-quality RNA mixtures to more challenging formalin-fixed paraffin-embedded tissue and biofluid material. The custom enrichment approach allows the detection of a more diverse repertoire of lncRNAs, with better reproducibility and higher coverage compared to classic total RNA-sequencing.
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Affiliation(s)
- Annelien Morlion
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Celine Everaert
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Justine Nuytens
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Eva Hulstaert
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, Ghent, Belgium
| | - Jo Vandesompele
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Pieter Mestdagh
- OncoRNALab, Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, B-9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Hulstaert E, Decock A, Morlion A, Everaert C, Verniers K, Nuytens J, Nijs N, Schroth GP, Kuersten S, Gross SM, Mestdagh P, Vandesompele J. Messenger RNA capture sequencing of extracellular RNA from human biofluids using a comprehensive set of spike-in controls. STAR Protoc 2021; 2:100475. [PMID: 33937877 PMCID: PMC8076706 DOI: 10.1016/j.xpro.2021.100475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Comprehensive transcriptome analysis of extracellular RNA (exRNA) purified from human biofluids is challenging because of the low RNA concentration and compromised RNA integrity. Here, we describe an optimized workflow to (1) isolate exRNA from different types of biofluids and (2) to prepare messenger RNA (mRNA)-enriched sequencing libraries using complementary hybridization probes. Importantly, the workflow includes 2 sets of synthetic spike-in RNA molecules as processing controls for RNA purification and sequencing library preparation and as an alternative data normalization strategy. For complete details on the use and execution of this protocol, please refer to Hulstaert et al. (2020). Extracellular RNA from biofluids has a low concentration and a compromised integrity An optimized workflow for mRNA capture sequencing of human biofluids is provided Synthetic spike-in RNA molecules serve as processing controls Spike-in RNAs allow for data normalization and calculation of mRNA concentration
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Affiliation(s)
- Eva Hulstaert
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Department of Dermatology, Ghent University Hospital, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Anneleen Decock
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Annelien Morlion
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Celine Everaert
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Kimberly Verniers
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Justine Nuytens
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium
| | - Nele Nijs
- Biogazelle, Technologiepark 82, 9052 Zwijnaarde, Belgium
| | | | | | | | - Pieter Mestdagh
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Biogazelle, Technologiepark 82, 9052 Zwijnaarde, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics, Department of Biomolecular Medicine, OncoRNALab, Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Cancer Research Institute Ghent (CRIG), Ghent University, C. Heymanslaan 10, 9000 Ghent, Belgium.,Biogazelle, Technologiepark 82, 9052 Zwijnaarde, Belgium
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7
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Hulstaert E, Morlion A, Levanon K, Vandesompele J, Mestdagh P. Candidate RNA biomarkers in biofluids for early diagnosis of ovarian cancer: A systematic review. Gynecol Oncol 2020; 160:633-642. [PMID: 33257015 DOI: 10.1016/j.ygyno.2020.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 11/14/2020] [Indexed: 12/27/2022]
Abstract
Ovarian cancer is often diagnosed in an advanced stage and is associated with a high mortality rate. It is assumed that early detection of ovarian cancer could improve patient outcomes. Unfortunately, effective screening methods for early diagnosis of ovarian cancer are still lacking. Extracellular RNAs circulating in human biofluids can reliably be measured and are emerging as potential biomarkers in cancer. In this systematic review, we present 75 RNA biomarkers detectable in human biofluids that have been studied for early diagnosis of ovarian cancer. The majority of these markers are microRNAs identified using RT-qPCR or microarrays in blood-based fluids. A handful of studies used RNA-sequencing and explored alternative fluids, such as urine and ascites. Candidate RNA biomarkers that were more abundant in biofluids of ovarian cancer patients compared to controls in at least two independent studies include miR-21, the miR-200 family, miR-205, miR-10a and miR-346. Amongst the markers confirmed to be lower in at least two studies are miR-122, miR-193a, miR-223, miR-126 and miR-106b. While these biomarkers show promising diagnostic potential, further validation is required before implementation in routine clinical care. Challenges related to biomarker validation and reflections on future perspectives to accelerate progress in this field are discussed.
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Affiliation(s)
- Eva Hulstaert
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent 9000, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, Ghent 9000, Belgium; Department of Dermatology, Ghent University Hospital, Corneel Heymanslaan 10, Ghent 9000, Belgium.
| | - Annelien Morlion
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent 9000, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, Ghent 9000, Belgium.
| | - Keren Levanon
- Sheba Cancer Research Center, Chaim Sheba Medical Center, Ramat Gan 52621, Israel; Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel.
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent 9000, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, Ghent 9000, Belgium.
| | - Pieter Mestdagh
- Department of Biomolecular Medicine, Ghent University, Corneel Heymanslaan 10, Ghent 9000, Belgium; OncoRNALab, Cancer Research Institute Ghent (CRIG), Corneel Heymanslaan 10, Ghent 9000, Belgium.
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Van Paemel R, De Koker A, Caggiano C, Morlion A, Mestdagh P, De Wilde B, Vandesompele J, De Preter K. Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome. Epigenetics 2020; 16:797-807. [PMID: 33074045 PMCID: PMC8216177 DOI: 10.1080/15592294.2020.1827714] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulphite-based cfDNA methylation profiling. Fifteen tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulphite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics. All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes. The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.
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Affiliation(s)
- Ruben Van Paemel
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Andries De Koker
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, Belgium
| | - Christa Caggiano
- Departments of Neurology and Computational Medicine, University of California, Los Angeles, CA, USA
| | - Annelien Morlion
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Biogazelle NV, Ghent, Belgium
| | - Bram De Wilde
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Internal Medicine and Pediatrics, Ghent University Hospital, Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Jo Vandesompele
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.,Biogazelle NV, Ghent, Belgium
| | - Katleen De Preter
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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Decock A, Anckaert J, Everaert C, Nuytens J, Kuersten S, Hendrix A, Vandesompele J, Mestdagh P, Dhondt B, Van Paemel R, Verniers K, Schroth G, Fierro C, Yigit N, Schoofs K, Morlion A, Deleu J, Hulstaert E, Cobos FA, Nijs N, Eynde EV, Helsmoortel HH, De Wever O, Philippron A. Abstract B49: Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control study—important considerations for liquid biopsies. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-b49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer biomarker studies require procedures that provide accurate and precise test results with high analytical sensitivity. Consequently, the growing use of extracellular RNA from human biofluids as clinically relevant biomarker requires the implementation of benchmarked methods for sample collection, processing, and profiling. While several small-scale studies have pointed at the impact of individual preanalytical factors, no comprehensive study has addressed the many preanalytical variables affecting downstream sequencing of blood-derived exRNAs. In the Extracellular RNA Quality Control study, we have systematically evaluated the type of blood collection tube (n=10, including 5 so-called preservation tubes), the time between blood draw and plasma preparation (n=3), different plasma types (n=3, i.e., platelet-free, -poor, and -rich plasma), and RNA purification methods using the supplier-specified minimum and maximum plasma input volumes (n=15). The impact of these preanalytical factors is assessed by deep transcriptome profiling of all small and messenger RNAs from healthy donors’ plasma, using TruSeq Small RNA sequencing and TruSeq RNA Exome sequencing, respectively. All experiments are conducted in triplicate (for a total of 270 transcriptomes) using 191 synthetic RNA spike-in molecules as processing controls over a relevant dynamic range. When comparing blood collection tubes, serum mRNA seems very similar to EDTA plasma mRNA, but serum-derived small RNAs are markedly different in biotype composition compared to their plasma counterparts. Furthermore, several plasma tubes with preservation reagents do not stabilize RNA very well, as is reflected by increasing RNA concentrations and number of detected genes over time. Also, their reproducibility is generally compromised. In addition, we demonstrate large differences in RNA purification kit performance in terms of reproducibility, sensitivity, and observed transcriptome complexity. Among others, we note a 50-fold difference in mRNA yield and a 5-fold difference in the number of detected mRNAs. We summarized the results in 12 performance parameters that enable an informed selection of the most optimal sample processing workflow. In conclusion, using a systematic approach, we put forward robust quality control metrics for exRNA quantification methods with validated SOPs for sample collection, processing, and profiling. Our results are crucially important for all future RNA-based liquid biopsy-guided precision oncology applications. Authors in random order; abstract submitted on behalf of the exRNAQC Consortium.
Citation Format: Anneleen Decock, Jasper Anckaert, Celine Everaert, Justine Nuytens, Scott Kuersten, An Hendrix, Jo Vandesompele, Pieter Mestdagh, Bert Dhondt, Ruben Van Paemel, Kimberly Verniers, Gary Schroth, Carolina Fierro, Nurten Yigit, Kathleen Schoofs, Annelien Morlion, Jill Deleu, Eva Hulstaert, Francisco Avila Cobos, Nele Nijs, Eveline Vanden Eynde, Hetty Hilde Helsmoortel, Olivier De Wever, Annouck Philippron. Substantial performance differences among RNA purification kits and blood collection tubes in the Extracellular RNA Quality Control study—important considerations for liquid biopsies [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr B49.
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Affiliation(s)
- Anneleen Decock
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Jasper Anckaert
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Celine Everaert
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Justine Nuytens
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | | | - An Hendrix
- 3Laboratory of Experimental Cancer Research, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Jo Vandesompele
- 4Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Biogazelle, Ghent, Belgium,
| | - Pieter Mestdagh
- 4Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Biogazelle, Ghent, Belgium,
| | - Bert Dhondt
- 5Laboratory of Experimental Cancer Research, Ghent University, Department of Urology, Ghent University Hospital, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Ruben Van Paemel
- 6Center for Medical Genetics, Ghent University, Department of Pediatrics, Ghent University Hospital, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Kimberly Verniers
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | | | | | - Nurten Yigit
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Kathleen Schoofs
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Annelien Morlion
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Jill Deleu
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Eva Hulstaert
- 8Center for Medical Genetics, Ghent University, Department of Dermatology, Ghent University Hospital, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Francisco Avila Cobos
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | | | - Eveline Vanden Eynde
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Hetty Hilde Helsmoortel
- 1Center for Medical Genetics, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Olivier De Wever
- 3Laboratory of Experimental Cancer Research, Ghent University, Cancer Research Institute Ghent (CRIG), Ghent, Belgium,
| | - Annouck Philippron
- 9Lab for Experimental Surgery, Ghent University, Department of Gastrointestinal Surgery, Ghent University Hospital, Cancer Research Institute Ghent (CRIG), Ghent, Belgium
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Everaert C, Volders PJ, Morlion A, Thas O, Mestdagh P. SPECS: a non-parametric method to identify tissue-specific molecular features for unbalanced sample groups. BMC Bioinformatics 2020; 21:58. [PMID: 32066370 PMCID: PMC7026976 DOI: 10.1186/s12859-020-3407-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 02/11/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND To understand biology and differences among various tissues or cell types, one typically searches for molecular features that display characteristic abundance patterns. Several specificity metrics have been introduced to identify tissue-specific molecular features, but these either require an equal number of replicates per tissue or they can't handle replicates at all. RESULTS We describe a non-parametric specificity score that is compatible with unequal sample group sizes. To demonstrate its usefulness, the specificity score was calculated on all GTEx samples, detecting known and novel tissue-specific genes. A webtool was developed to browse these results for genes or tissues of interest. An example python implementation of SPECS is available at https://github.com/celineeveraert/SPECS. The precalculated SPECS results on the GTEx data are available through a user-friendly browser at specs.cmgg.be. CONCLUSIONS SPECS is a non-parametric method that identifies known and novel specific-expressed genes. In addition, SPECS could be adopted for other features and applications.
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Affiliation(s)
- Celine Everaert
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- Cancer Research Institute Ghent, Ghent, Belgium.
| | - Pieter-Jan Volders
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
- Flemish Institute for Biotechnology, Ghent, Belgium
| | - Annelien Morlion
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
| | - Olivier Thas
- I-Biostat, Data Science Institute, Hasselt University, Hasselt, Belgium
- National Institute for Applied Statistics Australia (NIASRA), University of Wollongong, Wollongong, Australia
- Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Pieter Mestdagh
- Center for Medical Genetics, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent, Ghent, Belgium
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