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Stefanovic F, Brown LG, MacDonald J, Bammler T, Rinchai D, Nguyen S, Zeng Y, Shinkawa V, Adams K, Chaussabel D, Berthier E, Haack AJ, Theberge AB. Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood. Anal Chem 2025; 97:1635-1644. [PMID: 39818791 DOI: 10.1021/acs.analchem.4c04591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/19/2025]
Abstract
Remote research studies are an invaluable tool for reaching populations with limited access to large medical centers or universities. To expand the remote study toolkit, we previously developed homeRNA, which allows for at-home self-collection and stabilization of blood and demonstrated the feasibility of using homeRNA in high temperature climates. Here, we expand upon this work through a systematic study exploring the effects of high temperature on RNA integrity (represented as RNA Integrity Number, RIN) through in-lab and field experiments. Compared to the frozen controls (overall mean RIN of 8.2, n = 8), samples kept at 37 °C for 2, 4, and 8 days had mean RINs of 7.6, 5.9, and 5.2 (n = 3), respectively, indicating that typical shipping conditions (∼2 days) yield samples suitable for downstream RNA sequencing. Shorter time intervals (6 h) resulted in minimal RNA degradation (median RIN of 6.4, n = 3) even at higher temperatures (50 °C) compared to the frozen control (mean RIN of 7.8, n = 3). Additionally, we shipped homeRNA-stabilized blood from a single donor to 14 states and back during the summer with continuous temperature probes (7.1 median RIN, n = 42). Samples from all locations were analyzed with 3' mRNA-seq to assess differences in gene counts, with the data suggesting that there was no preferential degradation of transcripts as a result of different shipping times, temperatures, and regions. Overall, our data support that homeRNA can be used in elevated temperature conditions, enabling decentralized sample collection for telemedicine, global health, and clinical research.
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Affiliation(s)
- Filip Stefanovic
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lauren G Brown
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - James MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Theo Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Darawan Rinchai
- Department of Infectious Diseases, St Jude's Children Research Hospital, Tennessee, Memphis 38105, United States
| | - Serena Nguyen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Victoria Shinkawa
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Karen Adams
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Institute of Translational Health Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Damien Chaussabel
- Computer Sciences Department, The Jackson Laboratory, Farmington, Connecticut 06032, United States
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Amanda J Haack
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- School of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Ashleigh B Theberge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Urology, School of Medicine, University of Washington, Seattle, Washington 98195, United States
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Stefanovic F, Brown LG, MacDonald J, Bammler T, Rinchai D, Nguyen S, Zeng Y, Shinkawa V, Adams K, Chausabel D, Berthier E, Haack AJ, Theberge AB. Your Blood is Out for Delivery: Considerations of Shipping Time and Temperature on Degradation of RNA from Stabilized Whole Blood. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.24.609519. [PMID: 39229214 PMCID: PMC11370555 DOI: 10.1101/2024.08.24.609519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Academic Contribution Register] [Indexed: 09/05/2024]
Abstract
Remote research studies are an invaluable tool for reaching populations in geographical regions with limited access to large medical centers or universities. To expand the remote study toolkit, we have previously developed homeRNA, which allows for at-home self-collection and stabilization of blood and demonstrated the feasibility of using homeRNA in high temperature climates. Here, we expand upon this work through a systematic study exploring the effects of high temperature on RNA integrity through in-lab and field experiments. Compared to the frozen controls (overall mean RIN of 8.2, n = 8), samples kept at 37°C for 2, 4, and 8 days had mean RINs of 7.6, 5.9, and 5.2 (n = 3), respectively, indicating that typical shipping conditions (~2 days) yield samples suitable for downstream RNA sequencing. Shorter time intervals (6 hours) resulted in minimal RNA degradation (median RIN of 6.4, n = 3) even at higher temperatures (50°C) compared to the frozen control (mean RIN of 7.8, n = 3). Additionally, we shipped homeRNA-stabilized blood from a single donor to 14 different states and back during the summer with continuous temperature probes (7.1 median RIN, n = 42). Samples from all locations were analyzed with 3' mRNA-seq to assess differences in gene counts, with the transcriptomic data suggesting that there was no preferential degradation of transcripts as a result of different shipping times, temperatures, and regions. Overall, our data support that homeRNA can be used in elevated temperature conditions, enabling decentralized sample collection for telemedicine, global health, and clinical research.
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Affiliation(s)
- Filip Stefanovic
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Lauren G. Brown
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - James MacDonald
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Theo Bammler
- Department of Environmental and Occupational Health Sciences, University of Washington, Seattle, Washington 98195, United States
| | - Darawan Rinchai
- Department of Infectious Diseases, St Jude’s Children Research Hospital, TN, Memphis 38105, United States
| | - Serena Nguyen
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Yuting Zeng
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Victoria Shinkawa
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Karen Adams
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Institute of Translational Health Sciences, School of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Damien Chausabel
- Computer Sciences Department, The Jackson Laboratory, Farmington, CT, 06032, United States
| | - Erwin Berthier
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Amanda J. Haack
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- School of Medicine, University of Washington, Seattle, Washington 98195, United States
| | - Ashleigh B. Theberge
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Department of Urology, School of Medicine, University of Washington, Seattle, Washington 98195, United States
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Obermayr E, Koppensteiner N, Heinzl N, Schuster E, Holzer B, Fabikan H, Weinlinger C, Illini O, Hochmair MJ, Zeillinger R. Effect of short-term storage of blood samples on gene expression in lung cancer patients. Clin Chem Lab Med 2023; 61:294-301. [PMID: 36395488 DOI: 10.1515/cclm-2022-0738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/29/2022] [Accepted: 11/07/2022] [Indexed: 11/18/2022]
Abstract
OBJECTIVES The stability of gene transcripts associated with the presence of circulating tumor cells (CTCs) has been predominantly studied in cultured cancer cell lines added to blood samples under artificial conditions. In the present study the effect of storage on CTC-related transcripts was assessed in blood samples taken from patients with non-small lung cancer (n=58). METHODS The blood samples were split in two equal parts to compare the gene expression with and without storage for 24 h at ambient temperature without preservative added. After enrichment using the microfluidic Parsortix® technology, the expression levels of selected genes were assessed using quantitative PCR following a gene-specific pre-amplification. The prognostic relevance of each gene in fresh and stored blood samples was evaluated using the R-package Survminer. RESULTS Some genes were either not affected (TWIST1, CDH5, CK19) or upregulated upon storage (NANOG, MET, UCHL1) but still associated with poor prognosis. In contrast, ERBB3, PTHLH, EpCAM, and TERT were no longer associated with the overall survival of the patients. CONCLUSIONS The study demonstrates the surprising stability of CTC-related transcripts, which makes overnight shipping of native blood samples possible. Careful verification is required when using model systems - such as normal blood spiked with tumor cells - or other CTC-related markers, as individual transcripts may respond differently to storage.
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Affiliation(s)
- Eva Obermayr
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Nina Koppensteiner
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Nicole Heinzl
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Eva Schuster
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Barbara Holzer
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
| | - Hannah Fabikan
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Christoph Weinlinger
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
| | - Oliver Illini
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Vienna, Austria
| | - Maximilian J Hochmair
- Karl Landsteiner Institute of Lung Research and Pulmonary Oncology, Klinik Floridsdorf, Vienna, Austria
- Department of Respiratory and Critical Care Medicine, Klinik Floridsdorf, Vienna Healthcare Group, Vienna, Austria
| | - Robert Zeillinger
- Department of Obstetrics and Gynecology, Molecular Oncology Group, Comprehensive Cancer Center, Medical University of Vienna, Vienna, Austria
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Martire S, Valentino P, Marnetto F, Mirabile L, Capobianco M, Bertolotto A. The impact of pre-freezing storage time and temperature on gene expression of blood collected in EDTA tubes. Mol Biol Rep 2022; 49:4709-4718. [PMID: 35279776 PMCID: PMC9262796 DOI: 10.1007/s11033-022-07320-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/25/2021] [Accepted: 03/02/2022] [Indexed: 12/03/2022]
Abstract
Background Blood is a common source of RNA for gene expression studies. However, it is known to be vulnerable to pre-analytical variables. Although RNA stabilization systems have been shown to reduce such influence, traditional EDTA tubes are still widely used since they are less expensive and enable to study specific leukocyte populations. This study aimed to assess the influence of storage time and temperature between blood sampling and handling on RNA from peripheral blood mononuclear cells (PBMCs). Methods and results Nine blood samples were collected in EDTA tubes from 10 healthy donors. One tube from each donor was immediately processed for PBMC isolation, while the others were first incubated at either 4 degrees Celsius (°C) or room temperature for 2, 4, 6 and 24 h. RNA yield and quality and the expression level of fourt housekeeping (B2M, CASC3, GAPDH, HPRT1) and 8 target genes (CD14, CD19, CD20, IL10, MxA, TNF, TNFAIP3, NR4A2) were compared between samples. RNA yield, quality and integrity did not vary significantly with time and temperature. B2M was the most stable housekeeping gene, while the others were increasingly influenced by storing time, especially at 4 °C. Even when normalized to B2M, the expression level of some target genes, particularly TNFAIP3 and NR4A2, was highly affected by delays in blood processing at either temperature, already from 2 h. Conclusion Pre-analytical processing has a great impact on transcript expression from blood collected in EDTA tubes, especially on genes related to inflammation. Standardized procedure of blood handling are needed to obtain reliable results. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07320-5.
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Affiliation(s)
- Serena Martire
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy.
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy.
| | - Paola Valentino
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy
| | - Fabiana Marnetto
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Department of Neuroscience "Rita Levi Montalcini", University of Turin, Via Cherasco 15, 10100, Turin, Italy
| | - Luca Mirabile
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
| | - Marco Capobianco
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- SCDO Neurologia and CRESM, University Hospital AOU San Luigi Gonzaga, Regione Gonzole 10, 10043, Orbassano, Italy
| | - Antonio Bertolotto
- Clinical Neurobiology Unit, Neuroscience Institute Cavalieri Ottolenghi (NICO), Regione Gonzole 10, 10043, Orbassano, Italy
- Koelliker Hospital, 10100, Turin, Italy
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5
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How long does the mRNA remains stable in untreated whole bovine blood? Mol Biol Rep 2021; 49:789-795. [PMID: 34655019 DOI: 10.1007/s11033-021-06808-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 08/02/2021] [Accepted: 10/05/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND High quality and quantity of messenger RNA (mRNA) are required for accuracy of gene expression studies and other RNA-based downstream applications. Since RNA is considered a labile macromolecular prone to degradation, which may result in falsely altered gene expression patterns, several commercial stabilizing reagents have been developed aiming to keep RNA stable for long period. However, for studies involving large number of experimental samples, the high costs related to these specific reagents may constitute a barrier. METHODS AND RESULTS In this context the present study was designed aiming to evaluate the stability of mRNA in whole bovine blood collected in EDTA tubes during storage at common fridge (4 °C). Whole blood samples were collected from six Holstein calves and submitted to RNA extraction in each different interval: immediately after blood sampling (< 2 h), at 1-day post-sampling (dps), 2 dps, 3 dps, 7 dps and 14dps intervals. RNA integrity and purity were evaluated, and RT-qPCR assays were run using seven different genes (B2M, ACTB, PPIA, GAPDH, YWHAZ, CD4 and IFN-γ) aiming to evaluate the presence of altered gene transcription during storage. All extracted RNA samples presented high purity, while optimal integrity and unaltered gene expression were observed in whole experimental group up to 3 days of storage. CONCLUSION Bovine blood RNA remained stable in K3EDTA tubes for 3 days stored at common fridge and can be successfully and accurately used for gene expression studies.
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Chen M, Mithraprabhu S, Ramachandran M, Choi K, Khong T, Spencer A. Utility of Circulating Cell-Free RNA Analysis for the Characterization of Global Transcriptome Profiles of Multiple Myeloma Patients. Cancers (Basel) 2019; 11:cancers11060887. [PMID: 31242667 PMCID: PMC6628062 DOI: 10.3390/cancers11060887] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 05/09/2019] [Revised: 06/12/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
In this study, we evaluated the utility of extracellular RNA (exRNA) derived from the plasma of multiple myeloma (MM) patients for whole transcriptome characterization. exRNA from 10 healthy controls (HC), five newly diagnosed (NDMM), and 12 relapsed and refractory (RRMM) MM patients were analyzed and compared. We showed that ~45% of the exRNA genes were protein-coding genes and ~85% of the identified genes were covered >70%. Compared to HC, we identified 632 differentially expressed genes (DEGs) in MM patients, of which 26 were common to NDMM and RRMM. We further identified 54 and 191 genes specific to NDMM and RRMM, respectively, and these included potential biomarkers such as LINC00863, MIR6754, CHRNE, ITPKA, and RGS18 in NDMM, and LINC00462, PPBP, RPL5, IER3, and MIR425 in RRMM, that were subsequently validated using droplet digital PCR. Moreover, single nucleotide polymorphisms and small indels were identified in the exRNA, including mucin family genes that demonstrated different rates of mutations between NDMM and RRMM. This is the first whole transcriptome study of exRNA in hematological malignancy and has provided the basis for the utilization of exRNA to enhance our understanding of the MM biology and to identify potential biomarkers relevant to the diagnosis and prognosis of MM patients.
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Affiliation(s)
- Maoshan Chen
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
| | - Sridurga Mithraprabhu
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Malarmathy Ramachandran
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Kawa Choi
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Tiffany Khong
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
- Malignant Haematology and Stem Cell Transplantation, Alfred Hospital, Melbourne 3004, Australia.
| | - Andrew Spencer
- Myeloma Research Group, Australian Centre for Blood Diseases (ACBD), Clinical Central School, Monash University, Melbourne 3004, Australia.
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7
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Lianidou E, Pantel K. Liquid biopsies. Genes Chromosomes Cancer 2019; 58:219-232. [PMID: 30382599 DOI: 10.1002/gcc.22695] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/11/2018] [Revised: 08/28/2018] [Accepted: 10/01/2018] [Indexed: 02/06/2023] Open
Abstract
Liquid biopsy is based on minimally invasive blood tests and has a high potential to significantly change the therapeutic strategy in cancer patients, providing an extremely powerful and reliable noninvasive clinical tool for the individual molecular profiling of patients in real time. Liquid biopsy approaches include the analysis of circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), circulating miRNAs, and tumor-derived extracellular vesicles (EVs) that are shed from primary tumors and their metastatic sites into peripheral blood. The major advantage of liquid biopsy analysis is that it is minimally invasive, and can be serially repeated, thus allowing extracting information from the tumor in real time. Moreover, the identification of predictive biomarkers in peripheral blood that can monitor response to therapy in real time holds a very strong potential for novel approaches in the therapeutic management of cancer patients. In this review, we summarize recent knowledge on CTCs and ctDNA and discuss future trends in the field.
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Affiliation(s)
- Evi Lianidou
- Analysis of Circulating Tumor Cells Laboratory, Department of Chemistry, University of Athens, Athens, Greece
| | - Klaus Pantel
- Department of Tumor Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Ward Gahlawat A, Lenhardt J, Witte T, Keitel D, Kaufhold A, Maass KK, Pajtler KW, Sohn C, Schott S. Evaluation of Storage Tubes for Combined Analysis of Circulating Nucleic Acids in Liquid Biopsies. Int J Mol Sci 2019; 20:ijms20030704. [PMID: 30736351 PMCID: PMC6387045 DOI: 10.3390/ijms20030704] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/17/2019] [Revised: 01/29/2019] [Accepted: 01/30/2019] [Indexed: 02/06/2023] Open
Abstract
In the last decade, circulating nucleic acids such as microRNAs (miRNAs) and cell-free DNA (cfDNA) have become increasingly important in serving as potential novel biomarkers for a variety of human diseases. If cell-free nucleic acids are to become routinely used in diagnostics, the difference in plasma miRNA and cfDNA levels between healthy and diseased subjects must exceed pre-analytical and analytical variability. Until now, few studies have addressed the time limitations of pre-processing or explored the potential use of long-term blood storage tubes, which might need to be implemented in real-life diagnostics. In this study, we analyzed the stability of four breast cancer-associated miRNAs and two cancer-associated genes under various storage conditions, to test their limitations for potential application in clinical diagnostics. In two consecutive experiments, we tested the limits of conventional EDTA tubes, as well as long-term storage blood collection tubes (BCTs) from four different manufacturers. We found that circulating miRNAs are relatively stable when stored in EDTA monovettes for up to 12 h before processing. When stored in BCTs, circulating miRNAs and cfDNA are stable for up to 7 days, depending on the manufacturer. Norgen tubes were superior for cfDNA yield, while Streck tubes performed the worst in our study with hemolysis induction. In conclusion, plasma prepared from whole blood is suitable for the quantification of both cf-miRNAs and cfDNA simultaneously.
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Affiliation(s)
- Aoife Ward Gahlawat
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Judith Lenhardt
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Tania Witte
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Denise Keitel
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Anna Kaufhold
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Kendra K Maass
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
| | - Kristian W Pajtler
- Division of Pediatric Neuro-oncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
- Department of Pediatric Oncology, Hematology and Immunology, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Christof Sohn
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
| | - Sarah Schott
- Department of Gynecology and Obstetrics, University Hospital of Heidelberg, 69120 Heidelberg, Germany.
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Kofanova O, Bellora C, Quesada RA, Bulla A, Panadero-Fajardo S, Keipes M, Shea K, Stone M, Lescuyer P, Betsou F. IL8 and EDEM3 gene expression ratio indicates peripheral blood mononuclear cell (PBMC) quality. J Immunol Methods 2019; 465:13-19. [DOI: 10.1016/j.jim.2018.11.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/27/2018] [Revised: 11/19/2018] [Accepted: 11/19/2018] [Indexed: 10/27/2022]
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10
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Nishizuka SS, Sato KA, Hachiya T. A Pipeline for ctDNA Detection Following Primary Tumor Profiling Using a Cancer-Related Gene Sequencing Panel. Methods Mol Biol 2019; 1908:229-241. [PMID: 30649732 DOI: 10.1007/978-1-4939-9004-7_16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/23/2022]
Abstract
Circulating tumor DNA (ctDNA) is emerging as a promising biomarker for cancer diagnosis. However, the system to detect gene mutations with very low frequencies from plasma remains to be established in terms of technical aspects of sequencing technologies and cost for universal use. One strategy is to employ a cancer sequencing panel to detect mutations in a primary tumor in a time- and cost-effective manner, and subsequently assess these mutations with a digital PCR technology from plasma ctDNA. This strategy enables the accurate detection of low frequency mutations (i.e., less than 1% allele frequency) from ctDNA, since both comprehensive coverage of genes and quantitative mutation detection with very low frequencies are required for cancer diagnosis from plasma samples. Here, we present a pipeline can be used to detect mutations from plasma ctDNA with very low allele frequencies using a next-generation sequencing technology for comprehensive coverage of primary tumors and droplet digital PCR for sensitive detection from plasma ctDNA.
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Affiliation(s)
- Satoshi S Nishizuka
- Division of Biomedical Research and Development, Institute of Biomedical Sciences, Iwate Medical University, Morioka, Iwate, Japan.
| | - Kei A Sato
- Department of Surgery, Iwate Medical University School of Medicine, Morioka, Iwate, Japan
| | - Tsuyoshi Hachiya
- Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Yahaba, Shiwa, Iwate, Japan
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11
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Rodríguez-Lee M, Kolatkar A, McCormick M, Dago AD, Kendall J, Carlsson NA, Bethel K, Greenspan EJ, Hwang SE, Waitman KR, Nieva JJ, Hicks J, Kuhn P. Effect of Blood Collection Tube Type and Time to Processing on the Enumeration and High-Content Characterization of Circulating Tumor Cells Using the High-Definition Single-Cell Assay. Arch Pathol Lab Med 2018; 142:198-207. [PMID: 29144792 PMCID: PMC7679174 DOI: 10.5858/arpa.2016-0483-oa] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/06/2022]
Abstract
CONTEXT - As circulating tumor cell (CTC) assays gain clinical relevance, it is essential to address preanalytic variability and to develop standard operating procedures for sample handling in order to successfully implement genomically informed, precision health care. OBJECTIVE - To evaluate the effects of blood collection tube (BCT) type and time-to-assay (TTA) on the enumeration and high-content characterization of CTCs by using the high-definition single-cell assay (HD-SCA). DESIGN - Blood samples of patients with early- and advanced-stage breast cancer were collected into cell-free DNA (CfDNA), EDTA, acid-citrate-dextrose solution, and heparin BCTs. Time-to-assay was evaluated at 24 and 72 hours, representing the fastest possible and more routine domestic shipping intervals, respectively. RESULTS - We detected the highest CTC levels and the lowest levels of negative events in CfDNA BCT at 24 hours. At 72 hours in this BCT, all CTC subpopulations were decreased with the larger effect observed in high-definition CTCs and cytokeratin-positive cells smaller than white blood cells. Overall cell retention was also optimal in CfDNA BCT at 24 hours. Whole-genome copy number variation profiles were generated from single cells isolated from all BCT types and TTAs. Cells from CfDNA BCT at 24-hour TTA exhibited the least noise. CONCLUSIONS - Circulating tumor cells can be identified and characterized under a variety of collection, handling, and processing conditions, but the highest quality can be achieved with optimized conditions. We quantified performance differences of the HD-SCA for specific preanalytic variables that may be used as a guide to develop best practices for implementation into patient care and/or research biorepository processes.
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Luk AWS, Ma Y, Ding PN, Young FP, Chua W, Balakrishnar B, Dransfield DT, Souza PD, Becker TM. CTC-mRNA (AR-V7) Analysis from Blood Samples-Impact of Blood Collection Tube and Storage Time. Int J Mol Sci 2017; 18:ijms18051047. [PMID: 28498319 PMCID: PMC5454959 DOI: 10.3390/ijms18051047] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/31/2017] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 12/29/2022] Open
Abstract
Circulating tumour cells (CTCs) are an emerging resource for monitoring cancer biomarkers. New technologies for CTC isolation and biomarker detection are increasingly sensitive, however, the ideal blood storage conditions to preserve CTC-specific mRNA biomarkers remains undetermined. Here we tested the preservation of tumour cells and CTC-mRNA over time in common anticoagulant ethylene-diamine-tetra-acetic acid (EDTA) and acid citrate dextrose solution B (Citrate) blood tubes compared to preservative-containing blood tubes. Blood samples spiked with prostate cancer cells were processed after 0, 24, 30, and 48 h storage at room temperature. The tumour cell isolation efficiency and the mRNA levels of the prostate cancer biomarkers androgen receptor variant 7 (AR-V7) and total AR, as well as epithelial cell adhesion molecule (EpCAM) were measured. Spiked cells were recovered across all storage tube types and times. Surprisingly, tumour mRNA biomarkers were readily detectable after 48 h storage in EDTA and Citrate tubes, but not in preservative-containing tubes. Notably, AR-V7 expression was detected in prostate cancer patient blood samples after 48 h storage in EDTA tubes at room temperature. This important finding presents opportunities for measuring AR-V7 expression from clinical trial patient samples processed within 48 h-a much more feasible timeframe compared to previous recommendations.
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Affiliation(s)
- Alison W S Luk
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St., Liverpool, NSW 2170, Australia.
| | - Yafeng Ma
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St., Liverpool, NSW 2170, Australia.
| | - Pei N Ding
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St., Liverpool, NSW 2170, Australia.
- Department of Medical Oncology, Liverpool Hospital, Elizabeth St & Goulburn St, Liverpool, NSW 2170, Australia.
- Western Sydney University Clinical School, Elizabeth St, Liverpool, NSW 2170, Australia.
| | - Francis P Young
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St., Liverpool, NSW 2170, Australia.
- South Western Clinical School, University of New South Wales, Goulburn St., Liverpool, NSW 2170, Australia.
| | - Wei Chua
- Department of Medical Oncology, Liverpool Hospital, Elizabeth St & Goulburn St, Liverpool, NSW 2170, Australia.
| | - Bavanthi Balakrishnar
- Department of Medical Oncology, Liverpool Hospital, Elizabeth St & Goulburn St, Liverpool, NSW 2170, Australia.
| | - Daniel T Dransfield
- Tokai Pharmaceuticals, Inc., 255 State Street, 6th Floor, Boston, MA 0210, USA.
| | - Paul de Souza
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St., Liverpool, NSW 2170, Australia.
- Department of Medical Oncology, Liverpool Hospital, Elizabeth St & Goulburn St, Liverpool, NSW 2170, Australia.
- Western Sydney University Clinical School, Elizabeth St, Liverpool, NSW 2170, Australia.
- South Western Clinical School, University of New South Wales, Goulburn St., Liverpool, NSW 2170, Australia.
| | - Therese M Becker
- Centre for Circulating Tumour Cell Diagnostics and Research, Ingham Institute for Applied Medical Research, 1 Campbell St., Liverpool, NSW 2170, Australia.
- Western Sydney University Clinical School, Elizabeth St, Liverpool, NSW 2170, Australia.
- South Western Clinical School, University of New South Wales, Goulburn St., Liverpool, NSW 2170, Australia.
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Mithraprabhu S, Khong T, Ramachandran M, Chow A, Klarica D, Mai L, Walsh S, Broemeling D, Marziali A, Wiggin M, Hocking J, Kalff A, Durie B, Spencer A. Circulating tumour DNA analysis demonstrates spatial mutational heterogeneity that coincides with disease relapse in myeloma. Leukemia 2016; 31:1695-1705. [DOI: 10.1038/leu.2016.366] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/01/2016] [Revised: 11/05/2016] [Accepted: 11/18/2016] [Indexed: 02/06/2023]
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Hrebien S, O’Leary B, Beaney M, Schiavon G, Fribbens C, Bhambra A, Johnson R, Garcia-Murillas I, Turner N. Reproducibility of Digital PCR Assays for Circulating Tumor DNA Analysis in Advanced Breast Cancer. PLoS One 2016; 11:e0165023. [PMID: 27760227 PMCID: PMC5070760 DOI: 10.1371/journal.pone.0165023] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 05/13/2016] [Accepted: 10/05/2016] [Indexed: 02/05/2023] Open
Abstract
Circulating tumor DNA (ctDNA) analysis has the potential to allow non-invasive analysis of tumor mutations in advanced cancer. In this study we assessed the reproducibility of digital PCR (dPCR) assays of circulating tumor DNA in a cohort of patients with advanced breast cancer and assessed delayed plasma processing using cell free DNA preservative tubes. We recruited a cohort of 96 paired samples from 71 women with advanced breast cancer who had paired blood samples processed either immediately or delayed in preservative tubes with processing 48–72 hours after collection. Plasma DNA was analysed with multiplex digital PCR (mdPCR) assays for hotspot mutations in PIK3CA, ESR1 and ERBB2, and for AKT1 E17K. There was 94.8% (91/96) agreement in mutation calling between immediate and delayed processed tubes, kappa 0.88 95% CI 0.77–0.98). Discordance in mutation calling resulted from low allele frequency and likely stochastic effects. In concordant samples there was high correlation in mutant copies per ml plasma (r2 = 0.98; p<0.0001). There was elevation of total cell free plasma DNA concentrations in 10.3% of delayed processed tubes, although overall quantification of total cell free plasma DNA had similar prognostic effects in immediate (HR 3.6) and delayed (HR 3.0) tubes. There was moderate agreement in changes in allele fraction between sequential samples in quantitative mutation tracking (r = 0.84, p = 0.0002). Delayed processing of samples using preservative tubes allows for centralized ctDNA digital PCR mutation screening in advanced breast cancer. The potential of preservative tubes in quantitative mutation tracking requires further research.
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Affiliation(s)
- Sarah Hrebien
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Ben O’Leary
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
- Breast Unit, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, United Kingdom
| | - Matthew Beaney
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Gaia Schiavon
- Translational Science, Oncology iMed, AstraZeneca, Cambridge, CB4 0WG, United Kingdom
| | - Charlotte Fribbens
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
- Breast Unit, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, United Kingdom
| | - Amarjit Bhambra
- Breast Unit, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, United Kingdom
| | - Richard Johnson
- Breast Unit, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, United Kingdom
| | - Isaac Garcia-Murillas
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
| | - Nicholas Turner
- The Breast Cancer Now Research Centre, The Institute of Cancer Research, London, SW3 6JB, United Kingdom
- Breast Unit, Royal Marsden Hospital, Fulham Road, London, SW3 6JJ, United Kingdom
- * E-mail:
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