1
|
Schmøkel SS, Nordentoft I, Lindskrog SV, Lamy P, Knudsen M, Jensen JB, Dyrskjøt L. Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies. Nucleus 2023; 14:2186686. [PMID: 36878883 PMCID: PMC10012951 DOI: 10.1080/19491034.2023.2186686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.
Collapse
Affiliation(s)
- Sofie S Schmøkel
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Iver Nordentoft
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Sia V Lindskrog
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Philippe Lamy
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Michael Knudsen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Jørgen Bjerggaard Jensen
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Urology, Aarhus University Hospital, Aarhus, Denmark
| | - Lars Dyrskjøt
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| |
Collapse
|
2
|
Bontoux C, Marcovich A, Goffinet S, Pesce F, Tanga V, Bohly D, Salah M, Washetine K, Messaoudi Z, Felix JM, Bonnetaud C, Wang L, Menon G, Berthet JP, Cohen C, Benzaquen J, Marquette CH, Lassalle S, Long-Mira E, Hofman V, Xerri L, Ilié M, Hofman P. The Need to Set up a Biobank Dedicated to Lymphoid Malignancies: Experience of a Single Center (Laboratory of Clinical and Experimental Pathology, University Côte d'Azur, Nice, France). J Pers Med 2023; 13:1076. [PMID: 37511690 PMCID: PMC10381579 DOI: 10.3390/jpm13071076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
Several therapies to improve the management of lymphoma are currently being investigated, necessitating the development of new biomarkers. However, this requires high-quality and clinically annotated biological material. Therefore, we established a lymphoma biobank including all available biological material (tissue specimens and matched biological resources) along with associated clinical data for lymphoma patients diagnosed, according to the WHO classification, between 2005 and 2022 in the Laboratory of Clinical and Experimental Pathology, Nice, France. We retrospectively included selected cases in a new collection at the Côte d'Azur Biobank, which contains 2150 samples from 363 cases (351 patients). The male/female ratio was 1.3, and the median age at diagnosis was 58 years. The most common lymphoma types were classical Hodgkin lymphoma, diffuse large B-cell lymphoma, and extra-nodal marginal zone lymphoma of MALT tissue. The main sites of lymphoma were the mediastinum, lymph node, Waldeyer's ring, and lung. The Côte d'Azur Biobank is ISO 9001 and ISO 20387 certified and aims to provide high quality and diverse biological material to support translational research projects into lymphoma. The clinico-pathological data generated by this collection should aid the development of new biomarkers to enhance the survival of patients with lymphoid malignancies.
Collapse
Affiliation(s)
- Christophe Bontoux
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Aubiège Marcovich
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Samantha Goffinet
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Florian Pesce
- Department of Biopathology and Tumor Immunology, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM U1068, Centre National de la Recherche Scientifique UMR 7258, Aix-Marseille University, UM105, CEDEX 9, 13273 Marseille, France
| | - Virginie Tanga
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Doriane Bohly
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Myriam Salah
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Kevin Washetine
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Zeineb Messaoudi
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
| | - Jean-Marc Felix
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Christelle Bonnetaud
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Lihui Wang
- Haemato-Oncology Diagnostic Service, Cheshire & Merseyside Cancer Network, Liverpool University Hospitals NHS Foundation Trust, CSSB Building Level 4, Vernon Street, Liverpool L7 8YE, UK
| | - Geetha Menon
- Haemato-Oncology Diagnostic Service, Cheshire & Merseyside Cancer Network, Liverpool University Hospitals NHS Foundation Trust, CSSB Building Level 4, Vernon Street, Liverpool L7 8YE, UK
| | - Jean-Philippe Berthet
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Thoracic Surgery, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Charlotte Cohen
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Thoracic Surgery, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Jonathan Benzaquen
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Pneumology, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Charles-Hugo Marquette
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Department of Pneumology, FHU OncoAge, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Veronique Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Luc Xerri
- Department of Biopathology and Tumor Immunology, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM U1068, Centre National de la Recherche Scientifique UMR 7258, Aix-Marseille University, UM105, CEDEX 9, 13273 Marseille, France
| | - Marius Ilié
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, CEDEX 2, 06107 Nice, France
- FHU OncoAge, Université Côte d'Azur, CEDEX 1, 06001 Nice, France
- Institut Hospitalo-Universitaire (IHU), RespirERA, Université Côte d'Azur, Hôpital Pasteur, CHU de Nice, CEDEX 1, 06001 Nice, France
| |
Collapse
|
3
|
Neuber AC, Komoto TT, da Silva ECA, Duval VDS, Scapulatempo-Neto C, Marques MMC. Quality Assessment of Cryopreserved Human Biological Samples from the Biobank of Barretos Cancer Hospital. Biopreserv Biobank 2023; 21:74-80. [PMID: 35613409 DOI: 10.1089/bio.2021.0131] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: Biobanks process, store, and supply biological materials for research. Preanalytical factors, especially storage time and temperature, must be controlled and standardized at all stages when handling biospecimen samples, especially because the literature reports highly contradictory optimal parameters. As large-sample studies are required to better understand the influence of time and temperature on cryopreserved samples' quality for genomic research, this study evaluated the integrity and quality of cryopreserved samples stored for up to 9 years at the biobank of Barretos Cancer Hospital, one of the largest biobanks in Latin America. Methods: We randomly selected 447 samples with tumor tissue paired with buffy coat or peripheral blood mononuclear cells (PBMCs) that were stored from 2008 to 2016. The genetic material quality was evaluated based on RNA integrity (RIN) and DNA integrity (DIN) ≥7, which indicated undegraded samples, and compared with storage time, which means that for DNA storage time, samples <8.1 and ≥8.1 years and for RNA <4.5 and ≥4.5 were used. Results: A total of 190 tumor tissues were eligible for DNA and RNA extraction. Those stored for 8 years had lower DIN (68%) than those stored for a shorter period (92%). A similar pattern, based on storage time (<8.1 and ≥8.1 years), was observed in the buffy coat (74% and 95%, respectively) and PBMCs (54% and 96%, respectively). For RNA extracted from tumor tissues, we observed lower RIN in samples stored for 4.5 years (17%) than in samples stored for a shorter period (45%). Buffy coat and PBMC samples stored at -30°C exhibited greater degradation (26%) than those stored at -80°C (1%). The DIN (p = 0.15) and RNA (p = 0.18) were unrelated to topography type. Conclusion: The temperature, particularly cryopreservation methodology, and storage time were the main factors that affected nucleic acid integrity, especially RNA, during cryopreservation of biospecimens.
Collapse
Affiliation(s)
| | | | | | - Vinicius da Silva Duval
- Barretos Cancer Hospital Biobank, Barretos, Brazil.,Department of Pathology, Barretos Cancer Hospital, Barretos, Brazil
| | | | - Márcia M C Marques
- Barretos Cancer Hospital Biobank, Barretos, Brazil.,Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil.,Barretos School of Health Sciences, Barretos, Brazil
| |
Collapse
|
4
|
Servais MD, Galtier F, Nouvel A, Rebuffat S, Laget J, Géan A, Provost N, Lorcy F, Rigau V, Couderc G, Géraud P, Nocca D, Builles N, De Préville N, Lajoix AD. Addressing the quality challenge of a human biospecimen biobank through the creation of a quality management system. PLoS One 2022; 17:e0278780. [PMID: 36584180 PMCID: PMC9803146 DOI: 10.1371/journal.pone.0278780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 11/22/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND The objective of the COMET (COllection of MEtabolic Tissues) biobank project is to create a high-quality collection of insulin-sensitive tissues (liver, muscle, adipose tissues, and epiploic artery) and blood sample derivatives (plasma, serum, DNA and RNA), collected from 270 grade 2-3 obese patients undergoing bariatric surgery. Relevant data on patient such as clinical/biological characteristics and sample handling are also collected. For this, our aim was to establish a Quality Management System (QMS) to meet the reliability and quality requirements necessary for its scientific exploitation. MATERIALS AND METHODS The COMET QMS includes: (1) Quality Assurance to standardize all stages of the biobanking process, (2) Quality Controls on samples from the first patients included in order to validate the sample management process and ensure reproducible quality; and 3) "in process" Quality Controls to ensure the reliability of the storage procedures and the stability of the samples over time. RESULTS For serum and plasma, several corrective actions, such as temperature handling and centrifugation conditions, were made to the protocol and led to improvement of the volume and quality of samples. Regarding DNA, all samples evaluated achieved a satisfactory level of purity and integrity and most of them yielded the required DNA quantity. All frozen tissue samples had RNAs of good purity. RNA quality was confirmed by RIN, achieving values in most cases over 7 and efficient amplification of housekeeping genes by RT-qPCR, with no significant differences among samples from the same tissue type. In the "in process" Quality Controls, DNA, RNA, and histological integrity of tissues showed no differences among samples after different preservation times. CONCLUSION Quality Control results have made it possible to validate the entire biobank process and confirm the utility of implementing QMS to guarantee the quality of a biospecimen collection.
Collapse
Affiliation(s)
| | - Florence Galtier
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
- Department of Endocrinology, Lapeyronie Hospital, University Hospital of Montpellier, Montpellier, France
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Agathe Nouvel
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Sandra Rebuffat
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | - Jonas Laget
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
| | | | | | - Frédéric Lorcy
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Valérie Rigau
- Biological Resources Center, Anatomy and Cytology Laboratory, University Hospital of Montpellier, Montpellier, France
| | - Guilhem Couderc
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | - Philippe Géraud
- INSERM, Clinical Investigation Center 1411, St Eloi Hospital, University Hospital of Montpellier, Montpellier, France
| | - David Nocca
- Department of Digestive Surgery, University Hospital of Montpellier, Montpellier, France
| | - Nicolas Builles
- Biological Resources Center, Tissue Bank, University Hospital of Montpellier, Montpellier, France
| | | | - Anne-Dominique Lajoix
- Biocommunication in Cardio-Metabolism (BC2M), University of Montpellier, Montpellier, France
- * E-mail:
| |
Collapse
|
5
|
Maclean A, Adishesh M, Button L, Richards L, Alnafakh R, Newton E, Drury J, Hapangama DK. The effect of pre-analytical variables on downstream application and data analysis of human endometrial biopsies. Hum Reprod Open 2022; 2022:hoac026. [PMID: 35775066 PMCID: PMC9240853 DOI: 10.1093/hropen/hoac026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 05/27/2022] [Indexed: 11/14/2022] Open
Abstract
STUDY QUESTION What are the effects of pre-analytical variables on the downstream analysis of patient-derived endometrial biopsies? SUMMARY ANSWER There are distinct differences in the protein levels of the master regulator of oxygen homeostasis, hypoxia-inducible factor-1-alpha (HIF1α), and the protein and mRNA levels of three related genes, carbonic anhydrase 9 (CA9), vascular endothelial growth factor A (VEGFA) and progesterone receptor (PR) in human endometrial biopsies, depending on the pre-analytical variables: disease status (cancer vs benign), timing of biopsy (pre- vs post-hysterectomy) and type of biopsy (pipelle vs full-thickness). WHAT IS KNOWN ALREADY Patient-derived biopsies are vital to endometrial research, but pre-analytical variables relating to their collection may affect downstream analysis, as is evident in other tissues. STUDY DESIGN SIZE DURATION A prospective observational study including patients undergoing hysterectomy for endometrial cancer (EC) or benign indications was conducted at a large tertiary gynaecological unit in the UK. Endometrial biopsies were obtained at different time points (pre- or post-hysterectomy) using either a pipelle endometrial sampler or as a full-thickness wedge biopsy. PARTICIPANTS/MATERIALS SETTING METHODS The changes in HIF1α, CA9, VEGFA and PR protein levels were measured by semi-quantitative analysis of immunostaining, and the expression levels of three genes (CA9, VEGFA and PR) were investigated by quantitative real-time PCR, in endometrial biopsies from 43 patients undergoing hysterectomy for EC (n = 22) or benign gynaecological indications (n = 21). MAIN RESULTS AND THE ROLE OF CHANCE An increase in HIF1α immunostaining was observed in EC versus benign endometrium (functionalis glands) obtained pre-hysterectomy (P < 0.001). An increase in CA9 immunostaining was observed in EC versus benign endometrial functionalis glands at both pre- and post-hysterectomy time points (P = 0.03 and P = 0.003, respectively). Compared with benign endometrial pipelle samples, EC samples demonstrated increased mRNA expression of CA9 (pre-hysterectomy P < 0.001, post-hysterectomy P = 0.008) and VEGFA (pre-hysterectomy P = 0.004, post-hysterectomy P = 0.002). In benign uteri, HIF1α immunoscores (functionalis glands, P = 0.03 and stroma, P = 0.009), VEGFA immunoscores (functionalis glands, P = 0.03 and stroma, P = 0.01) and VEGFA mRNA levels (P = 0.008) were increased in matched post-hysterectomy versus pre-hysterectomy samples. Similarly, in EC, an increase in VEGFA immunoscores (epithelial and stromal) and VEGFA mRNA expression was observed in the matched post-hysterectomy versus pre-hysterectomy biopsies (P = 0.008, P = 0.004 and P = 0.018, respectively). Full-thickness benign post-hysterectomy endometrial biopsies displayed increased VEGFA (P = 0.011) and PR (P = 0.006) mRNA expression compared with time-matched pipelle biopsies. LARGE SCALE DATA N/A. LIMITATIONS REASONS FOR CAUTION This descriptive study explores the effect of pre-analytical variables on the expression of four proteins and three hypoxia-related genes in a limited number of endometrial biopsies from patients with EC and benign controls. Due to the small number, it was not possible to investigate other potential variables such as menstrual cycle phase, region-specific differences within the endometrium, grade and stage of cancer, and surgical technicalities. WIDER IMPLICATIONS OF THE FINDINGS Careful consideration of the effects of these pre-analytical variables is essential when interpreting data relating to human endometrial biopsies. A standardized approach to endometrial tissue collection is essential to ensure accurate and clinically transferrable data. STUDY FUNDING/COMPETING INTERESTS The authors have no conflicts of interest to declare. The work included in this manuscript was funded by Wellbeing of Women project grants RG1073 and RG2137 (D.K.H.), Wellbeing of Women Entry-Level Scholarship ELS706 and Medical Research Council MR/V007238/1 (A.M./D.K.H.), Liverpool Women's Hospital Cancer Charity (M.A.) and University of Liverpool (L.B., L.R. and E.N.).
Collapse
Affiliation(s)
- A Maclean
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - M Adishesh
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - L Button
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - L Richards
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - R Alnafakh
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - E Newton
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - J Drury
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| | - D K Hapangama
- Department of Women's and Children's Health, Institute of Life Course and Medical Sciences, University of Liverpool, Liverpool, UK
| |
Collapse
|
6
|
Liu N, Luo Y, Zhu Y, Peng H, Zou C, Zhou Z, Chen W, Wang H, Liu H, Hu Y, Zhang S, Qian K. Effects of Warm Ischemia Time, Cryopreservation, and Grinding Methods on RNA Quality of Mouse Kidney Tissues. Biopreserv Biobank 2021; 19:306-311. [PMID: 33577406 DOI: 10.1089/bio.2020.0129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: High-quality RNA extraction from tissue samples is of key importance for scientific research and translational medicine. Tissue collection and preparation may affect RNA quality. In this study, we investigated effects of warm ischemia time, cryopreservation, and grinding methods on RNA quality. Methods: Total RNA was extracted from mouse kidney tissues with warm ischemia times of 0, 30, 60, 90, and 120 minutes. Half of the tissues were used to extract RNA immediately, while the others were cryopreserved in the vapor phase of liquid nitrogen for 6 months before RNA extraction. A mortar, homogenizer, and tissue lyser were used to grind tissues. RNA was extracted by TRIzol, and RNA integrity was assessed by the RNA integrity number (RIN) value. Results: For fresh tissues and frozen tissues with warm ischemia time within 60 minutes, RIN values were above 7.0 and remained above 6.0 with warm ischemia time within 120 minutes. For the same warm ischemia time, RIN values of frozen tissues were slightly lower than those of fresh tissues. No significant RIN value alterations were observed among grinding methods, but for RNA extraction efficiency, a mortar was much less efficient than the homogenizer or tissue lyser. For frozen tissues, RNA tended to degrade within 8 minutes at room temperature. Conclusions: Mouse kidney tissues with a warm ischemia time within 120 minutes are suitable for general RNA-related research. For tissues with a warm ischemia time within 60 minutes, cryopreservation may not affect RNA quality. The duration of frozen tissues held at room temperature before grinding affects the integrity of RNA, while grinding methods do not affect RNA integrity.
Collapse
Affiliation(s)
- Nan Liu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yi Luo
- Department of Urology, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yuan Zhu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
| | - Hongwei Peng
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Cong Zou
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Zongning Zhou
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen Chen
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hui Wang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Huiqin Liu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Ying Hu
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Shanshan Zhang
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Kaiyu Qian
- Department of Biological Repositories, Zhongnan Hospital of Wuhan University, Wuhan, China.,Human Genetic Resources Preservation Center of Hubei Province, Wuhan, China
| |
Collapse
|
7
|
Pre-analytics and tumor heterogeneity. N Biotechnol 2020; 55:30-35. [DOI: 10.1016/j.nbt.2019.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 09/19/2019] [Accepted: 09/29/2019] [Indexed: 12/11/2022]
|
8
|
Lu M. An embedded method for gene identification problems involving unwanted data heterogeneity. Hum Genomics 2019; 13:45. [PMID: 31639059 PMCID: PMC6805328 DOI: 10.1186/s40246-019-0228-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Modern applications such as bioinformatics collecting data in various ways can easily result in heterogeneous data. Traditional variable selection methods assume samples are independent and identically distributed, which however is not suitable for these applications. Some existing statistical models capable of taking care of unwanted variation were developed for gene identification involving heterogeneous data, but they lack model predictability and suffer from variable redundancy. RESULTS By accounting for the unwanted heterogeneity effectively, our method have shown its superiority over several state-of-the art methods, which is validated by the experimental results in both unsupervised and supervised gene identification problems. Moreover, we also applied our method to a pan-cancer study where our method can identify the most discriminative genes best distinguishing different cancer types. CONCLUSIONS This article provides an alternative gene identification method that can accounting for unwanted data heterogeneity. It is a promising method to provide new insights into the complex cancer biology and clues for understanding tumorigenesis and tumor progression.
Collapse
Affiliation(s)
- Meng Lu
- Department of Information Management,Tianjin University, Tianjin, China.
| |
Collapse
|
9
|
Kumar A, Singh M, Bhatia P, Singh A. Audit of Quality and Quantity of Nucleic Acid Yield from Pediatric Acute Leukemia Cases Following a Bio-banking Initiative. Indian J Hematol Blood Transfus 2019; 35:77-82. [PMID: 30828152 DOI: 10.1007/s12288-018-0975-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 06/15/2018] [Indexed: 10/28/2022] Open
Abstract
Information which can be harvested from a biological sample has greatly improved with advancements in diagnostic technologies. However, in developing countries, the awareness about usefulness of bio-banking concept is lacking and centres which do offer it, depend mainly on - 20 or - 80 °C for sample storage due to lack of sophisticated infrastructure like vapour phase nitrogen storage preservation. Hence in these resource constraint settings, timely audit of quality of nucleic acids extractable from samples stored is of utmost importance. In this study, we explore the effect of - 20 °C storage over nucleic acids (DNA/RNA) isolated from blood samples of 180 patients with various leukaemia's following a bio-banking initiative. We observed that the integrity and quality of both DNA and RNA were maintained in 70 and 80% samples respectively over time as reflected by their concentration measurements and inherent uniform expression of housekeeping gene GAPDH. Only 3.7% of the RNA samples and 4.2% of the DNA samples yielded very low concentrations despite minimizing processing and technical loss. In nutshell, audit of our biobank sample yield highlights that storage of blood samples at - 20 °C does not compromise the fidelity of nucleic acids for future diagnostic and research work in a resource constraint setting.
Collapse
Affiliation(s)
- A Kumar
- 1University of Pittsburgh School of Medicine, Pittsburgh, USA.,2Pediatric Hematology - Oncology Unit, Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - M Singh
- 2Pediatric Hematology - Oncology Unit, Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - P Bhatia
- 2Pediatric Hematology - Oncology Unit, Department of Pediatrics, APC, PGIMER, Chandigarh, India
| | - A Singh
- 1University of Pittsburgh School of Medicine, Pittsburgh, USA
| |
Collapse
|
10
|
Zheng XH, Zhang SD, Zhang PF, Li XZ, Hu YZ, Tian T, Zhu L, Wang RZ, Jia WH. Tumor Cell Content and RNA Integrity of Surgical Tissues from Different Types of Tumors and Its Correlation with Ex Vivo and In Vivo Ischemia. Ann Surg Oncol 2018; 25:3764-3770. [PMID: 30225832 DOI: 10.1245/s10434-018-6697-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Indexed: 12/18/2022]
Abstract
BACKGROUND Tissues from tumor patients are important resources for promoting cancer research, and therefore many biobanks have been established to collect tumor tissues; however, the quality of tumor tissues after surgical resection has not been well documented. METHODS A total of 896 cases of tissues from 12 types of tumors were chosen for this study. First, histopathological examination was conducted to evaluate the tumor cell content; second, microchip electrophoresis was used to determine the RNA integrity number (RIN) in 466 cases of tissues with a tumor cell content ≥ 75%; and, finally, a correlation test was used to analyze the effect of ischemia on RNA integrity in 384 cases of tissues with a recorded ischemia time. RESULTS Tumor tissues from 12 different organs had different tumor cell contents and RNA integrity. The liver had the highest percentage (69.7%) of tissue samples with a tumor cell content ≥ 75%, and the highest percentage (96%) of samples with an RIN ≥ 7. RNA integrity was not correlated with limited ex vivo ischemia time (5-60 min) in any of the 12 types of tumors. In contrast, a significant correlation with in vivo ischemia time was observed in several types of tumors. CONCLUSIONS Not every sample of excised tumor tissue has a sufficient amount of tumor cells and enough RNA integrity. In vivo ischemia has a more significant influence on RNA integrity, and tumor tissues have different tolerances to pre-analytical variables. Those conducting translational research should pay attention to pre-analytical variables when collecting and utilizing tumor tissues.
Collapse
Affiliation(s)
- Xiao-Hui Zheng
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China.,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Shao-Dan Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Pei-Fen Zhang
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Xi-Zhao Li
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Ye-Zhu Hu
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Tian Tian
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China
| | - Lin Zhu
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China
| | - Ruo-Zheng Wang
- Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| | - Wei-Hua Jia
- Tumor Biobank, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong, People's Republic of China. .,Affiliated Tumor Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, People's Republic of China.
| |
Collapse
|
11
|
Neumeister VM, Juhl H. Tumor Pre-Analytics in Molecular Pathology: Impact on Protein Expression and Analysis. CURRENT PATHOBIOLOGY REPORTS 2018; 6:265-274. [PMID: 30595971 PMCID: PMC6290693 DOI: 10.1007/s40139-018-0179-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Purpose of Review Precision medicine promises patient tailored, individualized diagnosis and treatment of diseases and relies on clinical specimen integrity and accuracy of companion diagnostic testing. Therefore, pre-analytics, which are defined as the collection, processing, and storage of clinical specimens, are critically important to enable optimal diagnostics, molecular profiling, and clinical decision-making around harvested specimens. This review article discusses the impact of tumor pre-analytics on molecular pathology focusing on biospecimen protein expression and analysis. Recent Findings Due to busy clinical schedules and workflows that have been established for many years and to lack of standardization and limited assessment tools to quantify variability in pre-analytical processing, the effects of pre-analytics on biospecimen integrity are often overlooked. Several studies have recently emphasized an emerging crisis in science and reproducibility of results. Summary Biomarker instability due to pre-analytical variables affects comprehensive analysis and molecular phenotyping of patients’ tissue. This problematic emphasizes the critical need for standardized protocols and technologies to be applied in the clinical and research setting.
Collapse
Affiliation(s)
| | - Hartmut Juhl
- Indivumed, GmbH, Falkenried 88, D-20251 Hamburg, Germany
| |
Collapse
|
12
|
Washetine K, Heeke S, Bonnetaud C, Kara-Borni M, Ilié M, Lassalle S, Butori C, Long-Mira E, Marquette CH, Cohen C, Mouroux J, Selva E, Tanga V, Bence C, Félix JM, Gazoppi L, Skhiri T, Gormally E, Boucher P, Clément B, Dagher G, Hofman V, Hofman P. Establishing a Dedicated Lung Cancer Biobank at the University Center Hospital of Nice (France). Why and How? Cancers (Basel) 2018; 10:cancers10070220. [PMID: 29966305 PMCID: PMC6070810 DOI: 10.3390/cancers10070220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Revised: 06/20/2018] [Accepted: 06/28/2018] [Indexed: 12/11/2022] Open
Abstract
Lung cancer is the major cause of death from cancer in the world and its incidence is increasing in women. Despite the progress made in developing immunotherapies and therapies targeting genomic alterations, improvement in the survival rate of advanced stages or metastatic patients remains low. Thus, urgent development of effective therapeutic molecules is needed. The discovery of novel therapeutic targets and their validation requires high quality biological material and associated clinical data. With this aim, we established a biobank dedicated to lung cancers. We describe here our strategy and the indicators used and, through an overall assessment, present the strengths, weaknesses, opportunities and associated risks of this biobank.
Collapse
Affiliation(s)
- Kevin Washetine
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Simon Heeke
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
| | - Christelle Bonnetaud
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Mehdi Kara-Borni
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Marius Ilié
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Sandra Lassalle
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Catherine Butori
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Elodie Long-Mira
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Charles Hugo Marquette
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Pulmonary Medicine and Oncology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Charlotte Cohen
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Jérôme Mouroux
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
- Department of Thoracic Surgery, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Eric Selva
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Virginie Tanga
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Coraline Bence
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
| | - Jean-Marc Félix
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Loic Gazoppi
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
| | - Taycir Skhiri
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | | | - Pascal Boucher
- French National Cancer Institut, 92513 Boulogne Billancourt CEDEX, France.
| | - Bruno Clément
- INSERM, INRA, University of Rennes, NuMeCan, CRB Santé, CHU Rennes, 35042 Rennes, France.
| | | | - Véronique Hofman
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| | - Paul Hofman
- Hospital-Integrated Biobank (BB-0033-00025), Université Côte d'Azur, CHU de Nice, 06001 Nice CEDEX 1, France.
- Laboratory of Clinical and Experimental Pathology, Université Côte d'Azur, CHU de Nice, University Hospital Federation OncoAge, 06001 Nice CEDEX 1, France.
- Team 4, Institute of Research on Cancer and Aging of Nice (IRCAN), Inserm U1081, CNRS UMR7284, Université Côte d'Azur, CHU de Nice, 06107 Nice CEDEX 2, France.
- FHU OncoAge, University of Nice Sophia Antipolis, 06001 Nice CEDEX 1, France.
| |
Collapse
|
13
|
Jun E, Oh J, Lee S, Jun HR, Seo EH, Jang JY, Kim SC. Method Optimization for Extracting High-Quality RNA From the Human Pancreas Tissue. Transl Oncol 2018; 11:800-807. [PMID: 29705629 PMCID: PMC6060079 DOI: 10.1016/j.tranon.2018.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 11/29/2022] Open
Abstract
Nucleic acid sequencing is frequently used to determine the molecular basis of diseases. Therefore, proper storage of biological specimens is essential to inhibit nucleic acid degradation. RNA isolated from the human pancreas is generally of poor quality because of its high concentration of endogenous RNase. In this study, we optimized the method for extracting high quality RNA from paired tumor and normal pancreatic tissues obtained from eight pancreatic cancer patients post-surgery. RNA integrity number (RIN) was checked to evaluate the integrity of RNA, we tried to extract the RNA with an RIN value of 8 or higher that allows for the latest genetic analysis. The effect of several parameters, including the method used for tissue lysis, RNAlater treatment, tissue weight at storage, and the time to storage after surgical resection, on the quantity and quality of RNA extracted was examined. Data showed that the highest quantity of RNA was isolated using a combination of manual and mechanical methods of tissue lysis. Additionally, sectioning the tissues into small pieces (<100 mg) and treating them with RNAlater solution prior to storage increased RNA stability. Following these guidelines, high quality RNA was obtained from 100% (8/8) of tumor tissues and 75% (6/8) of normal tissues. High-quality RNA was still stable under repeated freezing and thawing. The application of these results during sample handling and storage in clinical settings will facilitate the genetic diagnosis of diseases and their subsequent treatment.
Collapse
Affiliation(s)
- Eunsung Jun
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea; Department of Convergence Medicine, Asan Institute for Life Sciences, University of Ulsan, College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea
| | - Juyun Oh
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea
| | - Song Lee
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea
| | - Hye-Ryeong Jun
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea
| | - Eun Hye Seo
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea
| | - Jin-Young Jang
- Department of Surgery, Seoul National University College of Medicine, Seoul, South Korea
| | - Song Cheol Kim
- Division of Hepato-Biliary and Pancreatic Surgery, Department of Surgery, University of Ulsan College of Medicine and Asan Medical Center, 388-1 Pungnap-2 Dong, Songpa-gu, Seoul, South Korea.
| |
Collapse
|
14
|
Cummings M, Mappa G, Orsi NM. Laser Capture Microdissection and Isolation of High-Quality RNA from Frozen Endometrial Tissue. Methods Mol Biol 2018; 1723:155-166. [PMID: 29344859 DOI: 10.1007/978-1-4939-7558-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023]
Abstract
Laser capture microdissection (LCM) allows expression profiling of specific cell populations within tissues. However, isolation of high-quality RNA from laser capture microdissected frozen tissue is beset by problems arising from intrinsic tissue RNase activity. Herein, we describe an optimized staining/LCM/RNA extraction protocol developed for the isolation of epithelial RNA from frozen tissue sections using human endometrial cancer as a model tissue. This method combines excellent, reproducible visualization of tissue morphology with the isolation of high-integrity RNA suitable for downstream applications such as expression microarray analysis. We present quantitative and qualitative RNA data obtained from >200 endometrial epithelial samples (normal, hyperplastic, and cancerous), where 92% of samples had RIN values of 7 and above and highlight common pitfalls faced by investigators. This method should also be broadly applicable to a range of other tissue types.
Collapse
Affiliation(s)
- Michele Cummings
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Georgia Mappa
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK
| | - Nicolas M Orsi
- Leeds Institute of Cancer and Pathology, St. James's University Hospital, Leeds, UK.
| |
Collapse
|
15
|
Dickerson C, Hsu Y, Mendoza S, Osman I, Ogilvie J, Patel K, Moreira AL. Quality Assurance After a Natural Disaster: Lessons from Hurricane Sandy. Biopreserv Biobank 2018; 16:92-96. [PMID: 29298082 DOI: 10.1089/bio.2017.0104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Biospecimen quality can vary depending on many pre- and post-collection variables. In this study, we consider a natural disaster as a post-collection variable that may have compromised the quality of frozen tissue specimens. To investigate this possible link, we compared the quality of nucleic acids, the level of antigenicity, and the preservation of histology from frozen specimens collected before and after the power outage caused by Hurricane Sandy. To analyze nucleic acid quality, we extracted both DNA and RNA and performed capillary electrophoresis to compare the quality and concentrations of the nucleic acids. To compare antigenicity, frozen sections were cut and immunostained for thyroid transcription factor 1 (TTF-1), a nuclear transcription protein commonly used as a diagnostic biomarker for multiple cancer types, including thyroid and lung cancers. Positive expression of TTF-1, as noted by homogenous nuclear staining, would demonstrate that the TTF-1 proteins could still bind antibodies and, therefore, that these proteins were not significantly degraded. Furthermore, representative frozen sections stained with hematoxylin and eosin were also assessed qualitatively by a trained pathologist to examine any possible histologic aberrations. Due to the similar quality of the tissue samples collected before and after the storm, Hurricane Sandy had no discernable effect on the quality of frozen specimens, and these specimens exposed to the natural disaster are still valuable research tools.
Collapse
Affiliation(s)
- Collin Dickerson
- 1 Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Yanshen Hsu
- 1 Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Sandra Mendoza
- 1 Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Iman Osman
- 2 Department of Medicine, Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| | - Jennifer Ogilvie
- 3 Department of Surgery, New York University Langone Health , New York, New York
| | - Kepal Patel
- 3 Department of Surgery, New York University Langone Health , New York, New York
| | - Andre L Moreira
- 4 Department of Pathology, Center for Biospecimen Research and Development, New York University Langone Health , New York, New York
| |
Collapse
|
16
|
Ji X, Wang M, Li L, Chen F, Zhang Y, Li Q, Zhou J. The Impact of Repeated Freeze–Thaw Cycles on the Quality of Biomolecules in Four Different Tissues. Biopreserv Biobank 2017; 15:475-483. [PMID: 28930488 DOI: 10.1089/bio.2017.0064] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Xiaoli Ji
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Min Wang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Lingling Li
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Fang Chen
- Department of Urology, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Yanyang Zhang
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Li
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Junmei Zhou
- Department of Central Laboratory, Shanghai Children's Hospital, Shanghai Jiao Tong University, Shanghai, China
| |
Collapse
|
17
|
Reiman M, Laan M, Rull K, Sõber S. Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples. FASEB J 2017; 31:3298-3308. [PMID: 28446590 DOI: 10.1096/fj.201601031rr] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 04/05/2017] [Indexed: 01/10/2023]
Abstract
RNA degradation is a ubiquitous process that occurs in living and dead cells, as well as during handling and storage of extracted RNA. Reduced RNA quality caused by degradation is an established source of uncertainty for all RNA-based gene expression quantification techniques. RNA sequencing is an increasingly preferred method for transcriptome analyses, and dependence of its results on input RNA integrity is of significant practical importance. This study aimed to characterize the effects of varying input RNA integrity [estimated as RNA integrity number (RIN)] on transcript level estimates and delineate the characteristic differences between transcripts that differ in degradation rate. The study used ribodepleted total RNA sequencing data from a real-life clinically collected set (n = 32) of human solid tissue (placenta) samples. RIN-dependent alterations in gene expression profiles were quantified by using DESeq2 software. Our results indicate that small differences in RNA integrity affect gene expression quantification by introducing a moderate and pervasive bias in expression level estimates that significantly affected 8.1% of studied genes. The rapidly degrading transcript pool was enriched in pseudogenes, short noncoding RNAs, and transcripts with extended 3' untranslated regions. Typical slowly degrading transcripts (median length, 2389 nt) represented protein coding genes with 4-10 exons and high guanine-cytosine content.-Reiman, M., Laan, M., Rull, K., Sõber, S. Effects of RNA integrity on transcript quantification by total RNA sequencing of clinically collected human placental samples.
Collapse
Affiliation(s)
- Mario Reiman
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maris Laan
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kristiina Rull
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Women's Clinic of Tartu University Hospital, Tartu, Estonia
| | - Siim Sõber
- Human Molecular Genetics Research Group, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; .,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| |
Collapse
|
18
|
|
19
|
Choi S, Ray HE, Lai SH, Alwood JS, Globus RK. Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments. PLoS One 2016; 11:e0167391. [PMID: 27907194 PMCID: PMC5132293 DOI: 10.1371/journal.pone.0167391] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/10/2016] [Indexed: 12/27/2022] Open
Abstract
Background Even with recent scientific advancements, challenges posed by limited resources and capabilities at the time of sample dissection continue to limit the collection of high quality tissues from experiments that can be conducted only infrequently and at high cost, such as in space. The resources and time it takes to harvest tissues post-euthanasia, and the methods and duration of long duration storage, potentially have negative impacts on sample quantity and quality, thereby limiting the scientific outcome that can be achieved. Objectives The goals of this study were to optimize methods for both sample recovery and science return from rodent experiments, with possible relevance to both ground based and spaceflight studies. The first objective was to determine the impacts of tissue harvest time post-euthanasia, preservation methods, and storage duration, focusing on RNA quality and enzyme activities in liver and spleen as indices of sample quality. The second objective was to develop methods that will maximize science return by dissecting multiple tissues after long duration storage in situ at -80°C. Methods Tissues of C57Bl/6J mice were dissected and preserved at various time points post-euthanasia and stored at -80°C for up to 11 months. In some experiments, tissues were recovered from frozen carcasses which had been stored at -80°C up to 7 months. RNA quantity and quality was assessed by measuring RNA Integrity Number (RIN) values using an Agilent Bioanalyzer. Additionally, the quality of tissues was assessed by measuring activities of hepatic enzymes (catalase, glutathione reductase and GAPDH). Results Fresh tissues were collected up to one hour post-euthanasia, and stored up to 11 months at -80°C, with minimal adverse effects on the RNA quality of either livers or RNAlater-preserved spleens. Liver enzyme activities were similar to those of positive controls, with no significant effect observed at any time point. Tissues dissected from frozen carcasses that had been stored for up to 7 months at -80°C had variable results, depending on the specific tissue analyzed. RNA quality of liver, heart, and kidneys were minimally affected after 6–7 months of storage at -80°C, whereas RNA degradation was evident in tissues such as small intestine, bone, and bone marrow when they were collected from the carcasses frozen for 2.5 months. Conclusion These results demonstrate that 1) the protocols developed for spaceflight experiments with on-orbit dissections support the retrieval of high quality samples for RNA expression and some protein analyses, despite delayed preservation post-euthanasia or prolonged storage, and 2) many additional tissues for gene expression analysis can be obtained by dissection even following prolonged storage of the tissue in situ at -80°C. These findings have relevance both to high value, ground-based experiments when sample collection capability is severely constrained, and to spaceflight experiments that entail on-orbit sample recovery by astronauts.
Collapse
Affiliation(s)
- Sungshin Choi
- KBRwyle, Moffett Field, California, United States of America
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - Hami E. Ray
- ASRC Federal Space and Defense, Inc., Moffett Field, California, United States of America
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - San-Huei Lai
- KBRwyle, Moffett Field, California, United States of America
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - Joshua S. Alwood
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
| | - Ruth K. Globus
- Space Biosciences Division, NASA-Ames Research Center, Moffett Field, California, United States of America
- * E-mail:
| |
Collapse
|
20
|
Korenkova V, Slyskova J, Novosadova V, Pizzamiglio S, Langerova L, Bjorkman J, Vycital O, Liska V, Levy M, Veskrna K, Vodicka P, Vodickova L, Kubista M, Verderio P. The focus on sample quality: Influence of colon tissue collection on reliability of qPCR data. Sci Rep 2016; 6:29023. [PMID: 27383461 PMCID: PMC4935944 DOI: 10.1038/srep29023] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 06/14/2016] [Indexed: 01/12/2023] Open
Abstract
Successful molecular analyses of human solid tissues require intact biological material with well-preserved nucleic acids, proteins, and other cell structures. Pre-analytical handling, comprising of the collection of material at the operating theatre, is among the first critical steps that influence sample quality. The aim of this study was to compare the experimental outcomes obtained from samples collected and stored by the conventional means of snap freezing and by PAXgene Tissue System (Qiagen). These approaches were evaluated by measuring rRNA and mRNA integrity of the samples (RNA Quality Indicator and Differential Amplification Method) and by gene expression profiling. The collection procedures of the biological material were implemented in two hospitals during colon cancer surgery in order to identify the impact of the collection method on the experimental outcome. Our study shows that the pre-analytical sample handling has a significant effect on the quality of RNA and on the variability of qPCR data. PAXgene collection mode proved to be more easily implemented in the operating room and moreover the quality of RNA obtained from human colon tissues by this method is superior to the one obtained by snap freezing.
Collapse
Affiliation(s)
- Vlasta Korenkova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Jana Slyskova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Vendula Novosadova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | - Sara Pizzamiglio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| | - Lucie Langerova
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic
| | | | - Ondrej Vycital
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Vaclav Liska
- Deparment of Surgery, Teaching Hospital and Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic
| | - Miroslav Levy
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Karel Veskrna
- Surgical Department, Thomayer Hospital, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Pavel Vodicka
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Ludmila Vodickova
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic.,Biomedical Centre, Medical School Pilsen, Charles University in Prague, Pilsen, Czech Republic.,Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Mikael Kubista
- Institute of Biotechnology, BIOCEV Centre, Czech Academy of Sciences, Průmyslová 595, 252 42, Vestec u Prahy, Czech Republic.,TATAA Biocenter AB, Göteborg, Sweden
| | - Paolo Verderio
- Unit of Medical Statistics, Biometry and Bioinformatics, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Istituto Nazionale dei Tumori, Milan, Italy
| |
Collapse
|
21
|
Kap M, Sieuwerts AM, Kubista M, Oomen M, Arshad S, Riegman P. The influence of tissue procurement procedures on RNA integrity, gene expression, and morphology in porcine and human liver tissue. Biopreserv Biobank 2016; 13:200-6. [PMID: 26035010 DOI: 10.1089/bio.2014.0076] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The advent of molecular characterization of tissues has brought an increasing emphasis on the quality of biospecimens, starting with the tissue procurement process. RNA levels are particularly affected by factors in the collection process, but the influence of different pre-analytical factors is not well understood. Here we present the influence of tissue specimen size, as well as the transport and freezing protocols, on RNA quality. Large, medium, and smaller porcine liver samples were stored either dry, on moist gauze, or in salt solution for various times, and then frozen in either liquid nitrogen or in pre-cooled isopentane. Large and small human liver samples were frozen in pre-cooled isopentane either immediately or after one hour at room temperature. The small samples were stored dry, on moist gauze, or in salt solution. RNA was isolated and RIN values were measured. The RNA for six standard reference genes from human liver was analyzed by RT-qPCR, and tissue morphology was assessed for artifacts of freezing. Experiments using porcine liver samples showed that RNA derived from smaller samples was more degraded after one hour of cold ischemia, and that cooled transport is preferable. Human liver samples showed significant RNA degradation after 1 h of cold ischemia, which was more pronounced in smaller samples. RNA integrity was not significantly influenced by the transport or freezing method, but changes in gene expression were observed in samples either transported on gauze or in salt solution. Based on observations in liver samples, smaller samples are more subject to gene expression variability introduced by post-excision sample handling than are larger samples. Small biopsies should be transported on ice and snap frozen as soon as possible after acquisition from the patient.
Collapse
Affiliation(s)
- Marcel Kap
- 1Erasmus MC Tissuebank and Tissue Research Support Unit, Department of Pathology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Anieta M Sieuwerts
- 2Department of Medical Oncology, Erasmus MC Cancer Institute, Cancer Genomics Netherlands, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | | | - Monique Oomen
- 1Erasmus MC Tissuebank and Tissue Research Support Unit, Department of Pathology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Shazia Arshad
- 1Erasmus MC Tissuebank and Tissue Research Support Unit, Department of Pathology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| | - Peter Riegman
- 1Erasmus MC Tissuebank and Tissue Research Support Unit, Department of Pathology, Erasmus University Medical Centre, Rotterdam, The Netherlands
| |
Collapse
|
22
|
Caixeiro NJ, Lai K, Lee CS. Quality assessment and preservation of RNA from biobank tissue specimens: a systematic review. J Clin Pathol 2015; 69:260-5. [DOI: 10.1136/jclinpath-2015-203384] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 10/27/2015] [Indexed: 11/04/2022]
|
23
|
Rifatbegovic F, Abbasi MR, Taschner-Mandl S, Kauer M, Weinhäusel A, Handgretinger R, Ambros PF. Enriched Bone Marrow Derived Disseminated Neuroblastoma Cells Can Be a Reliable Source for Gene Expression Studies-A Validation Study. PLoS One 2015; 10:e0137995. [PMID: 26360775 PMCID: PMC4567134 DOI: 10.1371/journal.pone.0137995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Metastases in the bone marrow (BM) in form of disseminated tumor cells (DTCs) are frequent events at diagnosis and also at relapse in high-risk neuroblastoma patients. The frequently highly diluted occurrence of DTCs requires adequate enrichment strategies to enable their detailed characterization. However, to avoid methodical artifacts we tested whether pre-analytical processing steps-including transport duration, temperature and, importantly, tumor cell enrichment techniques-are confounding factors for gene expression analysis in DTCs. METHODS LAN-1 neuroblastoma cells were spiked into tumor free BM and/or peripheral blood and: i) kept at room temperature or at 4°C for 24, 48 and 72 hours; ii) frozen down at -80°C and thawed; iii) enriched via magnetic beads. The effect on the gene expression signature of LAN-1 cells was analyzed by qPCR arrays and gene expression microarrays. RESULTS Neither storage at -80°C in DMSO and subsequent thawing nor enrichment of spiked-in neuroblastoma cells changed the expression of the analyzed genes significantly. Whereas storage at 4°C altered the expression of analyzed genes (14.3%) only at the 72h-timepoint in comparison to the 0h-timepoint, storage at room temperature had a much more profound effect on gene expression by affecting 20% at 24h, 26% at 48h and 43% at 72h of the analyzed genes. CONCLUSION Using neuroblastoma as a model, we show that tumor cell enrichment by magnetic bead separation has virtually no effect on gene expression in DTCs. However, transport time and temperature can influence the expression profile remarkably. Thus, the expression profile of routinely collected BM samples can be analyzed without concern as long as the transport conditions are monitored.
Collapse
Affiliation(s)
- Fikret Rifatbegovic
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- * E-mail: (FR); (PFA)
| | - M. Reza Abbasi
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Sabine Taschner-Mandl
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Maximilian Kauer
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
| | - Andreas Weinhäusel
- Molecular Diagnostics, Health & Environment Department, AIT Austrian Institute of Technology GmbH, Vienna, Austria
| | | | - Peter F. Ambros
- CCRI, Children’s Cancer Research Institute, St. Anna Kinderkrebsforschung, Vienna, Austria
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
- * E-mail: (FR); (PFA)
| |
Collapse
|
24
|
Olsen J, Kirkeby LT, Eiholm S, Jess P, Troelsen JT, Gögenür I, Olsen J. Impact of in Vivo Ischemic Time on RNA Quality—Experiences from a Colon Cancer Biobank. Biopreserv Biobank 2015; 13:255-62. [DOI: 10.1089/bio.2015.0009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Jesper Olsen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
| | - Lene T. Kirkeby
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
| | - Susanne Eiholm
- Department of Pathology, Roskilde University, Roskilde, Denmark
| | - Per Jess
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
| | - Jesper T. Troelsen
- Department of Science, Systems and Models, Roskilde University, Roskilde, Denmark
| | - Ismail Gögenür
- Department of Surgery, Koege-Roskilde University Hospital, Roskilde, Denmark
- Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| | - Jorgen Olsen
- Faculty of Health and Medical Sciences, Copenhagen University, Copenhagen, Denmark
| |
Collapse
|
25
|
Hofman V, Ilie M, Long E, Washetine K, Chabannon C, Figarella-Branger D, Clément B, Mabile L, Cambon-Thomsen A, Boucher P, Dagher G, Hewitt R, Parodi B, Hofman P. Measuring the contribution of tumor biobanks to research in oncology: surrogate indicators and bibliographic output. Biopreserv Biobank 2015; 11:235-44. [PMID: 24845591 DOI: 10.1089/bio.2013.0015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The number of biobanks, in particular hospital-integrated tumor biobanks (HITB), is increasing all around the world. This is the consequence of an increase in the need for human biological resources for scientific projects and more specifically, for translational and clinical research. The robustness and reproducibility of the results obtained depend greatly on the quality of the biospecimens and the associated clinical data. They also depend on the number of patients studied and on the expertise of the biobank that supplied the biospecimens. The quality of a research biobank is undoubtedly reflected in the number and overall quality of the research projects conducted with biospecimens provided by the biobank. Since the quality of a research project can be measured from the impact factor of resulting publications, this also provides some indication of the quality of a research biobank. It is necessary for the biobank community to define "surrogate" quality indicators, and to establish systems of evaluation in relation to current and future resource requirements. These indicators will help in the realistic assessment of biobanks by institutions and funding bodies, and they will help biobanks demonstrate their value, raise their quality standards, and compete for funding. Given that biobanks are expensive structures to maintain, funding issues are particularly important, especially in the current economic climate. Use of performance indicators may also contribute to the development of a biobank impact factor or "bioresource research impact factor" (BRIF). Here we review four major categories of indicators that appear to be useful for the evaluation of a(m) HITB (quality, activity, scientific productivity, and "visibility"). In addition, we propose a scoring system to measure the chosen indicators.
Collapse
Affiliation(s)
- Véronique Hofman
- 1 Hospital-Integrated Biobank, Pasteur Hospital, University of Nice Sophia Antipolis , Nice, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Andreasson A, Kiss NB, Juhlin CC, Höög A. Long-term storage of endocrine tissues at - 80°C does not adversely affect RNA quality or overall histomorphology. Biopreserv Biobank 2015; 11:366-70. [PMID: 24475321 DOI: 10.1089/bio.2013.0038] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Today, no consensus exists regarding how human tissues are best preserved for long-term storage. Very low temperature storage in liquid nitrogen is often advocated as the superlative method for extended periods, but storage in -80 degrees Celsius (-80°C) freezers, while sometimes debated, is a possible alternative. RNA is the most easily degradable component of a biological sample in a molecular biology context and the quality can reliably be measured. AIM To investigate to what extent long-term storage of tissues in -80°C affects the RNA quality and overall histomorphology. The tissue storage period represents nearly three decades (1986-2013). METHODS RNA extraction from 153 tissue samples with different storage periods was performed with the mirVana kit (Invitrogen). RNA integrity was assessed using an Agilent bioanalyzer to obtain RNA integrity numbers (RIN). Further, tissue representative testing using light microscopy was performed by two pathologists to assess tissue composition and morphology. RESULTS RIN values were measured in all samples, showing a variability that did not correlate with the storage time of the tissues. Microscopically, all samples displayed acceptable tissue morphology regardless of storage time. CONCLUSION Long-term storage in -80°C does not adversely affect the quality of the RNA extracted from the stored tissues, and the tissue morphology is maintained to a good standard.
Collapse
|
27
|
Ma Y, Kang XN, Ding WB, Yang HZ, Wang Y, Zhang J, Huang YR, Dai HL. Renal tissue thawed for 30 minutes is still suitable for gene expression analysis. PLoS One 2014; 9:e93175. [PMID: 24687048 PMCID: PMC3970958 DOI: 10.1371/journal.pone.0093175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 03/03/2014] [Indexed: 11/19/2022] Open
Abstract
Some biosamples obtained from biobanks may go through thawing before processing. We aim to evaluate the effects of thawing at room temperature for different time periods on gene expression analysis. A time course study with four time points was conducted to investigate the expression profiling on 10 thawed normal mice renal tissue samples through Affymetrix GeneChip mouse gene 2.0 st array. Microarray results were validated by quantitative real time polymerase chain reactions (qPCR) on 6 candidate reference genes and 11 target genes. Additionally, we used geNorm plus and NormFinder to identify the most stably expressed reference genes over time. The results showed RNA degraded more after longer incubation at room temperature. However, microarray results showed only 240 genes (0.91%) altered significantly in response to thawing at room temperature. The signal of majority altered probe sets decreased with thawing time, and the crossing point (Cp) values of all candidate reference genes correlated positively with the thawing time (p<0.05). The combination of B2M, ACTB and PPIA was identified as the best choice for qPCR normalization. We found most target genes were stable by using this normalization method. However, serious gene quantification errors were resulted from improper reference genes. In conclusion, thirty minutes of thawing at room temperature has a limited impact on microarray and qPCR analysis, gene expression variations due to RNA degradation in early period after thawing can be largely reduced by proper normalization.
Collapse
Affiliation(s)
- Yi Ma
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- Department of Urology, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Xiao-Nan Kang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Wen-Bin Ding
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Hao-Zheng Yang
- Department of Central Laboratory, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Ye Wang
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Jin Zhang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
| | - Yi-Ran Huang
- Department of Urology, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- * E-mail: (YRH); (HLD)
| | - Hui-Li Dai
- Department of Biobank, Renji Hospital, School of Medicine, Shanghai JiaoTong University, Shanghai, China
- * E-mail: (YRH); (HLD)
| |
Collapse
|
28
|
Yamagishi A, Matsumoto S, Watanabe A, Mizuguchi Y, Hara K, Kan H, Yamada T, Koizumi M, Shinji S, Matsuda A, Sasaki J, Shimada T, Uchida E. Gene profiling and bioinformatics analyses reveal time course differential gene expression in surgically resected colorectal tissues. Oncol Rep 2014; 31:1531-8. [PMID: 24573535 PMCID: PMC3975991 DOI: 10.3892/or.2014.3053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Accepted: 12/03/2013] [Indexed: 12/20/2022] Open
Abstract
It has previously been reported that gene profiles in surgically-resected colorectal cancer tissues are altered over time possibly due to the different tissue-acquisition methods and sample extraction timing that were used. However, the changes that occur are still not clearly understood. In the present study, time-dependent changes in gene expression profiling in colorectal surgical specimens were analyzed. Normal and tumor tissues at several time-points (0, 30, 60 and 120 min) were extracted, and RNA quality, microarray experiments, quantitative PCR and bioinformatics clustering were performed. Although RNA integrity was preserved 2 h after resection, inherent increased/decreased gene expression was observed from 30–120 min in approximately 10% of genes. Bioinformatics clustering could not distinguish case-by-case, probably due to gene profiling changes. Irregular changes in gene expression after surgical resection were found, which could be a crucial confounding factor for quantitative analyses.
Collapse
Affiliation(s)
- Aya Yamagishi
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Satoshi Matsumoto
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Atsushi Watanabe
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8603, Japan
| | - Yoshiaki Mizuguchi
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Keisuke Hara
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Hayato Kan
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Takeshi Yamada
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Michihiro Koizumi
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Seiichi Shinji
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Akihisa Matsuda
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Junpei Sasaki
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| | - Takashi Shimada
- Department of Biochemistry and Molecular Biology, Nippon Medical School, Tokyo 113-8603, Japan
| | - Eiji Uchida
- Surgery for Organ Function and Biological Regulation, Graduate School of Medicine, Nippon Medical School, Tokyo 113-8603, Japan
| |
Collapse
|
29
|
Cole KD, He HJ, Wang L. Breast cancer biomarker measurements and standards. Proteomics Clin Appl 2014; 7:17-29. [PMID: 23341234 DOI: 10.1002/prca.201200075] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 11/09/2012] [Accepted: 11/13/2012] [Indexed: 12/23/2022]
Abstract
Cancer is a heterogeneous disease characterized by changes in the levels and activities of important cellular proteins, including oncogenes and tumor suppressors. Genetic mutations cause changes in protein activity and protein expression levels that result in the altered metabolism, proliferation, and metastasis seen in cancer cells. The identification of the critical biochemical changes in cancer has led to advances in its detection and treatment. An important example of this is the measurement of human epidermal growth factor receptor 2 (HER2), where increased expression occurs in approximately 20-30% of breast cancer tumors. HER2 is a member of the epidermal growth factor receptor family and is an important biomarker expressed on the cell surface. Measurement of the HER2 levels in tumor cells provides diagnostic, prognostic, and treatment information, because a targeted therapeutic is available. The most common methods to measure HER2 levels are immunohistochemistry and in situ hybridization assays. The accurate and reliable measurements of the specific changes in protein biomarkers for detection and treatment of cancer are important challenges. This review is focused on efforts to improve the quantitation and reliability of cancer biomarkers by using standards and reference materials.
Collapse
Affiliation(s)
- Kenneth D Cole
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
| | | | | |
Collapse
|
30
|
The procurement, storage, and quality assurance of frozen blood and tissue biospecimens in pathology, biorepository, and biobank settings. Clin Biochem 2014; 47:258-66. [PMID: 24424103 DOI: 10.1016/j.clinbiochem.2014.01.002] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 01/04/2014] [Accepted: 01/04/2014] [Indexed: 01/19/2023]
Abstract
Well preserved frozen biospecimens are ideal for evaluating the genome, transcriptome, and proteome. While papers reviewing individual aspects of frozen biospecimens are available, we present a current overview of experimental data regarding procurement, storage, and quality assurance that can inform the handling of frozen biospecimens. Frozen biospecimen degradation can be influenced by factors independent of the collection methodology including tissue type, premortem agonal changes, and warm ischemia time during surgery. Rapid stabilization of tissues by snap freezing immediately can mitigate artifactually altered gene expression and, less appreciated, protein phosphorylation profiles. Collection protocols may be adjusted for specific tissue types as cellular ischemia tolerance varies widely. If data is not available for a particular tissue type, a practical goal is snap freezing within 20min. Tolerance for freeze-thaw events is also tissue type dependent. Tissue storage at -80°C can preserve DNA and protein for years but RNA can show degradation at 5years. For -80°C freezers, aliquots frozen in RNAlater or similar RNA stabilizing solutions are a consideration. It remains unresolved as to whether storage at -150°C provides significant advantages relative to that at -80°C. Histologic quality assurance of tissue biospecimens is typically performed at the time of surgery but should also be conducted on the aliquot to be distributed because of tissue heterogeneity. Biobanking protocols for blood and its components are highly dependent on intended use and multiple collection tube types may be needed. Additional quality assurance testing should be dictated by the anticipated downstream applications.
Collapse
|
31
|
Abstract
Powerful technologies critical to personalized medicine and targeted therapeutics require the analysis of carefully validated, procured, stored, and managed biospecimens. Reflecting advancements in biospecimen science, the National Cancer Institute and the International Society for Biological and Environmental Repositories are periodically publishing best practices that can guide the biobanker. The modern biobank will operate more like a clinical laboratory with formal accreditation, standard operating procedures, and quality assurance protocols. This chapter highlights practical issues of consent, procurement, storage, quality assurance, disbursement, funding, and space. Common topics of concern are discussed including the differences between clinical and research biospecimens, stabilization of biospecimens during procurement, optimal storage temperatures, and technical validation of biospecimen content and quality. With quickly expanding biospecimen needs and limited healthcare budgets, biobanks may need to be selective as to what is stored. Furthermore, a shift to room-temperature storage modalities where possible can reduce long-term space and fiscal requirements.
Collapse
Affiliation(s)
- William H Yong
- Translational Pathology Core Laboratory, Brain Tumor Translational Resource, Department of Pathology and Laboratory Medicine, Center for Health Sciences, David Geffen School of Medicine at UCLA, 10833 Le Conte Ave, 18-161 CHS, Los Angeles, CA, 90095, USA,
| | | | | |
Collapse
|
32
|
Hofman P, Bréchot C, Zatloukal K, Dagher G, Clément B. Public-private relationships in biobanking: a still underestimated key component of open innovation. Virchows Arch 2013; 464:3-9. [PMID: 24337181 DOI: 10.1007/s00428-013-1524-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/19/2013] [Accepted: 11/28/2013] [Indexed: 02/05/2023]
Abstract
Access to human bioresources is essential to the understanding of human diseases and to the discovery of new biomarkers aimed at improving the diagnosis, prognosis, and the predictive response of patients to treatments. The use of biospecimens is strictly controlled by ethical assessment, which complies with the laws of the country. These laws regulate the partnerships between the biobanks and industrial actors. However, private-public partnerships (PPP) can be limiting for several reasons, which can hamper the discovery of new biological tests and new active molecules targeted to human diseases. The bottlenecks and roadblocks in establishing these partnerships include: poor organization of the biobank in setting up PPP, evaluation of the cost of human samples, the absence of experience on the public side in setting up contracts with industry, and the fact that public and private partners may not share the same objectives. However, it is critical, in particular for academic biobanks, to establish strong PPP to accelerate translational research for the benefits of patients, and to allow the sustainability of the biobank. The purpose of this review is to discuss the main bottlenecks and roadblocks that can hamper the establishment of PPP based on solid and trusting relationships.
Collapse
Affiliation(s)
- Paul Hofman
- Hospital-Integrated Tumor Biobank, Pasteur Hospital, Nice, France,
| | | | | | | | | |
Collapse
|
33
|
Caboux E, Paciencia M, Durand G, Robinot N, Wozniak MB, Galateau-Salle F, Byrnes G, Hainaut P, Le Calvez-Kelm F. Impact of delay to cryopreservation on RNA integrity and genome-wide expression profiles in resected tumor samples. PLoS One 2013; 8:e79826. [PMID: 24278187 PMCID: PMC3835918 DOI: 10.1371/journal.pone.0079826] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 10/03/2013] [Indexed: 12/31/2022] Open
Abstract
The quality of tissue samples and extracted mRNA is a major source of variability in tumor transcriptome analysis using genome-wide expression microarrays. During and immediately after surgical tumor resection, tissues are exposed to metabolic, biochemical and physical stresses characterized as “warm ischemia”. Current practice advocates cryopreservation of biosamples within 30 minutes of resection, but this recommendation has not been systematically validated by measurements of mRNA decay over time. Using Illumina HumanHT-12 v3 Expression BeadChips, providing a genome-wide coverage of over 24,000 genes, we have analyzed gene expression variation in samples of 3 hepatocellular carcinomas (HCC) and 3 lung carcinomas (LC) cryopreserved at times up to 2 hours after resection. RNA Integrity Numbers (RIN) revealed no significant deterioration of mRNA up to 2 hours after resection. Genome-wide transcriptome analysis detected non-significant gene expression variations of −3.5%/hr (95% CI: −7.0%/hr to 0.1%/hr; p = 0.054). In LC, no consistent gene expression pattern was detected in relation with warm ischemia. In HCC, a signature of 6 up-regulated genes (CYP2E1, IGLL1, CABYR, CLDN2, NQO1, SCL13A5) and 6 down-regulated genes (MT1G, MT1H, MT1E, MT1F, HABP2, SPINK1) was identified (FDR <0.05). Overall, our observations support current recommendation of time to cryopreservation of up to 30 minutes and emphasize the need for identifying tissue-specific genes deregulated following resection to avoid misinterpreting expression changes induced by warm ischemia as pathologically significant changes.
Collapse
Affiliation(s)
- Elodie Caboux
- Laboratory Services and Biobank, International Agency for Research on Cancer, Lyon, France
| | - Maria Paciencia
- Department of Pathology, Centre Hospitalier Universitaire de Caen, Caen, France
| | - Geoffroy Durand
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Nivonirina Robinot
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
| | - Magdalena B. Wozniak
- Genetic Epidemiology Group, International Agency for Research on Cancer, Lyon, France
| | | | - Graham Byrnes
- Biostatistics Group, International Agency for Research on Cancer, Lyon, France
| | - Pierre Hainaut
- International Agency for Research on Cancer, Lyon, France
- International Prevention Research Institute, Lyon, France
| | - Florence Le Calvez-Kelm
- Genetic Cancer Susceptibility Group, International Agency for Research on Cancer, Lyon, France
- * E-mail:
| |
Collapse
|
34
|
Peiró-Chova L, Peña-Chilet M, López-Guerrero JA, García-Giménez JL, Alonso-Yuste E, Burgues O, Lluch A, Ferrer-Lozano J, Ribas G. High stability of microRNAs in tissue samples of compromised quality. Virchows Arch 2013; 463:765-74. [PMID: 24197449 DOI: 10.1007/s00428-013-1485-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 09/13/2013] [Accepted: 09/17/2013] [Indexed: 12/24/2022]
Abstract
Degradation of tissue samples limits performing RNA-based molecular studies, but little is known about the potential usefulness of samples of compromised quality for studies focused on miRNAs. In this work we analyze a series of cryopreserved tissue samples (n = 14), frozen samples that underwent a severe thawing process (n = 10), and their paired formalin-fixed paraffin-embedded (FFPE) tissue samples (n = 24) from patients with breast cancer obtained during primary surgical resection and collected in 2011. Quality and integrity analyses of the total and small fraction of RNA were carried out. Recovery of specific RNA molecules (miRNAs hsa-miR-21, hsa-miR-125b, and hsa-miR-191; snoRNA RNU6B; and mRNAs GAPDH and HPRT1) was also analyzed by quantitative RT-PCR. Our results suggest that visualisation of the small RNA electrophoretic profiles obtained using the Agilent 2100 bioanalyzer makes it possible to differentiate between the three groups of samples (optimally frozen, thawed, and FFPE). We demonstrate that specific miRNA molecules can be similarly recovered from different tissue sample sources, which supports their high degree of stability. We conclude that miRNAs are robustly detected irrespective of the quality of the tissue sample. In this regard, a word of caution should be raised before degraded samples are discarded: although prior quality assessment of the biological material to be analyzed is recommended, our work demonstrates that degraded tissue samples are also suitable for miRNA studies.
Collapse
Affiliation(s)
- Lorena Peiró-Chova
- Biobank, INCLIVA Biomedical Research Institute, Avenida Blasco Ibáñez, 17, 46010, Valencia, Spain
| | | | | | | | | | | | | | | | | |
Collapse
|