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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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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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