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Liu Z, Xu J, Que S, Geng L, Zhou L, Mardinoglu A, Zheng S. Recent Progress and Future Direction for the Application of Multiomics Data in Clinical Liver Transplantation. J Clin Transl Hepatol 2022; 10:363-373. [PMID: 35528975 PMCID: PMC9039708 DOI: 10.14218/jcth.2021.00219] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 08/14/2021] [Accepted: 10/07/2021] [Indexed: 12/04/2022] Open
Abstract
Omics data address key issues in liver transplantation (LT) as the most effective therapeutic means for end-stage liver disease. The purpose of this study was to review the current application and future direction for omics in LT. We reviewed the use of multiomics to elucidate the pathogenesis leading to LT and prognostication. Future directions with respect to the use of omics in LT are also described based on perspectives of surgeons with experience in omics. Significant molecules were identified and summarized based on omics, with a focus on post-transplant liver fibrosis, early allograft dysfunction, tumor recurrence, and graft failure. We emphasized the importance omics for clinicians who perform LTs and prioritized the directions that should be established. We also outlined the ideal workflow for omics in LT. In step with advances in technology, the quality of omics data can be guaranteed using an improved algorithm at a lower price. Concerns should be addressed on the translational value of omics for better therapeutic effects in patients undergoing LT.
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Affiliation(s)
- Zhengtao Liu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of the diagnosis and treatment of organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jun Xu
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuping Que
- DingXiang Clinics, Hangzhou, Zhejiang, China
| | - Lei Geng
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Lin Zhou
- NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of the diagnosis and treatment of organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Adil Mardinoglu
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King’s College London, London, UK
- Correspondence to: Adil Mardinoglu, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. ORCID: https://orcid.org/0000-0002-4254-6090. Tel: +46-31-772-3140, Fax: +46-31-772-3801, E-mail: ; Shusen Zheng, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China. ORCID: https://orcid.org/0000-0003-1459-8261. Tel/Fax: +86-571-87236570, E-mail:
| | - Shusen Zheng
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
- Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- NHC Key Laboratory of Combined Multi-organ Transplantation, Key Laboratory of the diagnosis and treatment of organ Transplantation, CAMS, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Organ Transplantation, Zhejiang Province, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Correspondence to: Adil Mardinoglu, Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden. ORCID: https://orcid.org/0000-0002-4254-6090. Tel: +46-31-772-3140, Fax: +46-31-772-3801, E-mail: ; Shusen Zheng, Division of Hepatobiliary and Pancreatic Surgery, Department of Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, China. ORCID: https://orcid.org/0000-0003-1459-8261. Tel/Fax: +86-571-87236570, E-mail:
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Neuber AC, Tostes CH, Ribeiro AG, Marczynski GT, Komoto TT, Rogeri CD, da Silva VD, Mauad EC, Reis RM, Marques MMC. The biobank of barretos cancer hospital: 14 years of experience in cancer research. Cell Tissue Bank 2021; 23:271-284. [PMID: 34216325 DOI: 10.1007/s10561-021-09941-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 06/20/2021] [Indexed: 01/15/2023]
Abstract
Despite the developments in cancer research over years, cancer is still one of the leading causes of death worldwide. In Brazil, the number of cancer cases for the several next years (2020-2022) is expected to increase up to 625,000. Thus, translational research has been vital to determine the potential risk, prognostic, and predictive biomarkers in cancer. Therefore, Barretos Cancer Hospital implemented a biobank (BB-BCH) in 2006, which is responsible for processing, storage, and provision of biological materials from cancer and non-cancer participants. Hence, this article aimed to describe BB-BCH's history, experiences, and outcomes and explore its impact on Brazilian translational oncology research scenario. BB-BCH has a multidisciplinary team who are responsible for guaranteeing the quality of all processes as recommended by international guidelines for biobanks. Furthermore, BB-BCH has ample equipment to ensure the quality of all material requested by researchers as genetic material (DNA and RNA) and/or entire biospecimens. From 2006 to 2019, BB-BCH contained 252,069 samples from 44,933 participants, the whole collection is represented by 15 different types of biospecimens collected from them. According to our data, the most collected and stored topography in men is head and neck (29%); in women is breast (28%); and in children is torso and limb (27%) samples. Finally, we supported national and international consortia and projects such as The Cancer Genome Atlas. BB-BCH is a vital knowledge source for scientific community, enabling the development of high-quality studies, with a wide variety of tumor categories and high national representativeness of Brazilian population.
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Affiliation(s)
| | | | - Adeylson Guimarães Ribeiro
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil
| | | | | | | | - Vinicius Duval da Silva
- Barretos Cancer Hospital Biobank, São Paulo, Brazil.,Department of Pathology, Barretos Cancer Hospital, São Paulo, Brazil
| | - Edmundo Carvalho Mauad
- Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil
| | - Rui Manuel Reis
- Barretos Cancer Hospital Biobank, São Paulo, Brazil.,Department of Prevention, Barretos Cancer Hospital, Barretos, Brazil.,Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Braga, Portugal.,ICVS/3B's-PT Government Associate Laboratory, Braga, Portugal
| | - Márcia M C Marques
- Barretos Cancer Hospital Biobank, São Paulo, Brazil. .,Molecular Oncology Research Center, Barretos Cancer Hospital, Rua Antenor Duarte Vilela, 1331, 14784-400, Barretos, SP, Brazil. .,Barretos School of Health Sciences, Barretos, SP, Brazil.
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3
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Esteva-Socias M, Artiga MJ, Bahamonde O, Belar O, Bermudo R, Castro E, Escámez T, Fraga M, Jauregui-Mosquera L, Novoa I, Peiró-Chova L, Rejón JD, Ruiz-Miró M, Vieiro-Balo P, Villar-Campo V, Zazo S, Rábano A, Villena C. In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network. J Transl Med 2019; 17:370. [PMID: 31718661 PMCID: PMC6852937 DOI: 10.1186/s12967-019-2124-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 11/01/2019] [Indexed: 01/10/2023] Open
Abstract
The purpose of the present work is to underline the importance of obtaining a standardized procedure to ensure and evaluate both clinical and research usability of human tissue samples. The study, which was carried out by the Biospecimen Science Working Group of the Spanish Biobank Network, is based on a general overview of the current situation about quality assurance in human tissue biospecimens. It was conducted an exhaustive review of the analytical techniques used to evaluate the quality of human tissue samples over the past 30 years, as well as their reference values if they were published, and classified them according to the biomolecules evaluated: (i) DNA, (ii) RNA, and (iii) soluble or/and fixed proteins for immunochemistry. More than 130 publications released between 1989 and 2019 were analysed, most of them reporting results focused on the analysis of tumour and biopsy samples. A quality assessment proposal with an algorithm has been developed for both frozen tissue samples and formalin-fixed paraffin-embedded (FFPE) samples, according to the expected quality of sample based on the available pre-analytical information and the experience of the participants in the Working Group. The high heterogeneity of human tissue samples and the wide number of pre-analytic factors associated to quality of samples makes it very difficult to harmonize the quality criteria. However, the proposed method to assess human tissue sample integrity and antigenicity will not only help to evaluate whether stored human tissue samples fit for the purpose of biomarker development, but will also allow to perform further studies, such as assessing the impact of different pre-analytical factors on very well characterized samples or evaluating the readjustment of tissue sample collection, processing and storing procedures. By ensuring the quality of the samples used on research, the reproducibility of scientific results will be guaranteed.
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Affiliation(s)
- Margalida Esteva-Socias
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain.,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain
| | | | | | - Oihana Belar
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Raquel Bermudo
- Hospital Clínic-IDIBAPS Biobank, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Erika Castro
- Basque Foundation for Health Innovation and Research, Basque Biobank, Barakaldo, Spain
| | - Teresa Escámez
- IMIB Biobank, Instituto Murciano de Investigación Biosanitaria, Murcia, Spain
| | - Máximo Fraga
- Depto. de Ciencias Forenses, Anatomía Patolóxica, Xinecología e Obstetricia, e Pediatría, Facultade de Medicina, Universidade de Santiago de Compostela (USC), Santiago, Spain.,Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Isabel Novoa
- Vall d'Hebron University Hospital Biobank, Vall d'Hebron Hospital Research Institute, Barcelona, Spain
| | | | - Juan-David Rejón
- Biobanco del Sistema Sanitario Público de Andalucía, Granada, Spain
| | - María Ruiz-Miró
- IRBLleida Biobank, Instituto de Investigaciones Biomédica de Lleida-Fundación Dr. Pifarre, Lérida, Spain
| | - Paula Vieiro-Balo
- Biobanco Complejo Hospitalario Universitario de Santiago de Compostela (CHUS), SERGAS, Santiago, Spain
| | | | - Sandra Zazo
- Department of Pathology, IIS-Fundación Jiménez Díaz, Madrid, Spain
| | - Alberto Rábano
- Banco de Tejidos, Fundación CIEN, Instituto de Salud Carlos III, Madrid, Spain
| | - Cristina Villena
- Centro de Investigación Biomédica en Red Respiratory Diseases (CIBERES), Plataforma Biobanco Pulmonar CIBERES, Hospital Universitari Son Espases, Palma, Spain. .,Grupo de Inflamación, reparación y cáncer en enfermedades respiratorias, Institut d'Investigació Sanitària de les Illes Balears (IdISBa), Hospital Universitari Son Espases, Palma, Spain.
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East EG, Roberts E, Zhao L, Jorns JM. Repeat Biomarker Status in Breast Resection Specimens With Controlled Cold Ischemic Time. Am J Clin Pathol 2019; 152:766-774. [PMID: 31338514 DOI: 10.1093/ajcp/aqz105] [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: 11/14/2022] Open
Abstract
OBJECTIVES Current College of American Pathologists/American Society of Clinical Oncology guidelines recommend cold ischemic time (CIT) of 1 hour or less for breast specimens to preserve biomarker expression, although some publications support an acceptable CIT of 4 hours or less. We retrospectively evaluated changes in estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER2) from biopsy to resection specimens that were triaged to optimize CIT. METHODS We identified breast resection specimens collected after institutional implementation of a triage protocol. Clinicopathologic features were assessed. RESULTS In total, 295 excisions had a prior malignant diagnosis, with CIT of 4 hours or less and repeat ER, PR, and/or HER2; 230 (78%) had CIT of 1 hour or less, and 65 (22%) had CIT of more than 1 hour but 4 hours or less. Categorical change was seen in 10 (17.9%) of 56 with repeated ER/PR and 38 (13.3%) of 285 with repeated HER2 (of which five [1.8%] had meaningful change). CONCLUSIONS When CIT is optimized, a meaningful change in biomarker expression is infrequent. This study supports that when specimens are appropriately triaged, CIT of 4 hours or less may be acceptable.
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Affiliation(s)
- Ellen G East
- Department of Pathology, Michigan Medicine, Ann Arbor
| | - Emily Roberts
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor
| | - Lili Zhao
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor
| | - Julie M Jorns
- Department of Pathology, Medical College of Wisconsin, Milwaukee
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Vehniäinen ER, Ruusunen M, Vuorinen PJ, Keinänen M, Oikari AOJ, Kukkonen JVK. How to preserve and handle fish liver samples to conserve RNA integrity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2019; 26:17204-17213. [PMID: 31012072 PMCID: PMC6546660 DOI: 10.1007/s11356-019-05033-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 03/28/2019] [Indexed: 06/09/2023]
Abstract
As transcriptomic studies are becoming more and more common, it is important to ensure that the RNA used in the analyses is of good quality. The RNA integrity may be compromised by storage temperature or freeze-thaw cycles, but these have not been well studied in poikilothermic fishes. This work studied the effects of tissue storage time and temperature, and freeze-thaw cycles of tissue and extracted RNA on RNA integrity in brown trout (Salmo trutta L.) liver. The storage time and temperature had an effect on RNA integrity, but RNA suitable for quantitative reverse transcription PCR (RT-qPCR) (RIN > 7) was still obtained from samples preserved at - 20 °C for 6 months. Freeze-thaw cycles of tissue or RNA did not compromise the integrity of RNA. RNA degradation had an effect on RT-qPCR results, and the effect depended on gene. The RT-qPCR analysis of historical samples from a bleached kraft pulp mill effluent exposure in 1984 revealed no significant cyp1a induction. Recommendations are given for the preservation and handling procedures of samples designated for transcriptomic analyses.
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Affiliation(s)
- Eeva-Riikka Vehniäinen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylän yliopisto, Finland.
| | - Maiju Ruusunen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylän yliopisto, Finland
| | - Pekka J Vuorinen
- Natural Resources Institute Finland (Luke), P.O. Box 2, FI-00791, Helsinki, Finland
| | - Marja Keinänen
- Natural Resources Institute Finland (Luke), P.O. Box 2, FI-00791, Helsinki, Finland
| | - Aimo O J Oikari
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylän yliopisto, Finland
| | - Jussi V K Kukkonen
- Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, FI-40014, Jyväskylän yliopisto, Finland
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Jones W, Greytak S, Odeh H, Guan P, Powers J, Bavarva J, Moore HM. Deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles. Sci Rep 2019; 9:6980. [PMID: 31061401 PMCID: PMC6502812 DOI: 10.1038/s41598-019-43282-8] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 04/08/2019] [Indexed: 11/09/2022] Open
Abstract
The National Cancer Institute conducted the Biospecimen Pre-analytical Variables (BPV) study to determine the effects of formalin fixation and delay to fixation (DTF) on the analysis of nucleic acids. By performing whole transcriptome sequencing and small RNA profiling on matched snap-frozen and FFPE specimens exposed to different delays to fixation, this study aimed to determine acceptable delays to fixation and proper workflow for accurate and reliable Next-Generation Sequencing (NGS) analysis of FFPE specimens. In comparison to snap-freezing, formalin fixation changed the relative proportions of intronic/exonic/untranslated RNA captured by RNA-seq for most genes. The effects of DTF on NGS analysis were negligible. In 80% of specimens, a subset of RNAs was found to differ between snap-frozen and FFPE specimens in a consistent manner across tissue groups; this subset was unaffected in the remaining 20% of specimens. In contrast, miRNA expression was generally stable across various formalin fixation protocols, but displayed increased variability following a 12 h delay to fixation.
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Affiliation(s)
| | | | - Hana Odeh
- National Cancer Institute, Bethesda, MD, USA
| | - Ping Guan
- National Cancer Institute, Bethesda, MD, USA
| | - Jason Powers
- Q2 Solutions - EA Genomics, Morrisville, NC, USA
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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.
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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
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Liu Y, Gao H, Hu Y, Ding J, Ge M, Ye Q. Quality Control System in an Obstetrics and Gynecology Disease Biobank. Biopreserv Biobank 2018; 17:27-38. [PMID: 30299984 DOI: 10.1089/bio.2018.0056] [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] [Indexed: 01/21/2023] Open
Abstract
AIM To ensure that sample quality meets the requirements of experimental research, the gynecology and obstetrics biobank of the Nanjing Drum Tower hospital designed different quality control methods for relevant types of samples. A range of quality control procedures has been formulated. METHODS The sample types were frozen tissue, paraffin-embedded tissue, optimal cutting temperature (OCT)-embedded tissue, plasma, buffy coat, serum, blood clots, and urine. Different categories of samples from a random selection of 1% of cases were analyzed for quality control experiments: (i) frozen tissue, buffy coat, and blood clots: RNA and DNA were extracted and the concentration, purity, and integrity were determined; (ii) paraffin-embedded tissue: morphological observations were made after hematoxylin-eosin staining and immunohistochemical detection of β-actin or CD10; (iii) OCT-embedded tissue: hematoxylin-eosin staining and immunofluorescence detection of β-actin; and (iv) frozen tissue samples derived from different organs of 18 fetal autopsy specimens with different cold ischemia times (CITs), 0-12 hours, 12-18 hours, 18-24 hours, and 24-48 hours, were chosen to study RNA quality. There is no universally recognized quality control index for plasma, serum, and urine, so the quality of samples was evaluated from feedback from the research projects in which the samples were used. RESULTS Currently, there are ∼2000 cases and 360,000 sample vials in the biobank. According to the experiments, (i) the concentration and purity of all nucleic acids of selected samples were qualified; (ii) for frozen tissues with a CIT ≤1 hour, using a qualified standard RNA quality number (RQN) ≥7, the qualification rate was 90%; (iii) frozen tissues with CIT between 1 and 18 hours, using a qualified standard RQN ≥5, the qualification rate was 61.1%; (iv) all of the paraffin-embedded tissues qualified for morphological observation; (v) the qualification rate of OCT-embedded tissue was 89%; and (vi) CIT had a great influence on the integrity of frozen tissue RNA. As the tissue CIT lengthened, the integrity of the RNA decreased. The RNA integrity parameters of different tissue types in the same specimen were significantly different. CONCLUSIONS A quality control system was constructed in an obstetrics and gynecology disease biobank with various types of diseases and abundant samples. Using specific quality control experiments for different types of samples was a reliable operating strategy that can be beneficial for providing qualified research resources. For birth defect autopsy specimens, the samples used for RNA research should have a CIT of at least <12 hours.
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Affiliation(s)
- Yanhong Liu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Hong Gao
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Yue Hu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Jie Ding
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Meiling Ge
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Qing Ye
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
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Gao H, Liu Y, Ding J, Yang J, Zhang B, Hu Y, Ge M, Ye Q. A Nucleic Acid Quality Control Strategy for Frozen Tissues from a Biobank of High-Risk Pregnancy. Biopreserv Biobank 2018; 17:18-26. [PMID: 30256683 DOI: 10.1089/bio.2018.0041] [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: 12/17/2022] Open
Abstract
BACKGROUND The preservation of placental and fetal tissues will contribute to studying the pathogenesis of high-risk pregnancy diseases. However, few studies have focused on the effects of different preservation methods and cold ischemia time (CIT) on the quality of nucleic acids. An available quality control (QC) strategy will be beneficial to evaluate these effects for high-risk pregnancy biobanks. METHODS We established an evaluation strategy of nucleic acid QC by analyzing total RNA and genomic DNA (gDNA). Through this strategy, the effects of CIT, cryoprotectants (CPAs), and freeze/thaw cycles on the yield and integrity of placental RNA were analyzed. In addition, the effects of CIT on the yield and integrity of fetal DNA were determined. RESULTS For placental samples, there was no significant difference in RNA integrity (CIT <2 hours). After several freeze/thaw cycles, the RNA quality number values of placental samples in the CPA-free group and in the RNasin (TRIzol) group were decreased. For fetal samples, the DNA integrity of different organs (CIT <24 hours) was completely satisfactory, but it declined with the extension of CIT. Furthermore, different organs had different tolerances to cold ischemia, and the rank was as follows: skin, heart, liver, and placenta. In addition, the content of medium-length (600 bp) and long (1310 bp) fragments of gDNA were mainly reduced with the extension of CIT. CONCLUSION The RNA integrity of placental tissue was affected by CIT significantly. It is recommended that placenta should be cryopreserved within 2 hours (4°C) from isolation. To ensure DNA quality of fetal tissues, the samples are suggested to be frozen within 24 hours (4°C) from isolation. On the contrary, if samples have a long CIT, skin is superior to other organs in the aspect of biobanking donor's genetic information.
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Affiliation(s)
- Hong Gao
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yanhong Liu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Jie Ding
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Jun Yang
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Biao Zhang
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Yue Hu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Meiling Ge
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
| | - Qing Ye
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, People's Republic of China
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10
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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.
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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.
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11
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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.
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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
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12
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Wang TH, Chen CC, Liang KH, Chen CY, Chuang WY, Ueng SH, Chu PH, Huang CG, Chen TC, Hsueh C. A Multivariate Evaluation of Factors Affecting the Quality of Freshly Frozen Tissue Specimens. Biopreserv Biobank 2017; 15:344-349. [DOI: 10.1089/bio.2016.0104] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Tong-Hong Wang
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Liver Research Center, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chin-Chuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Graduate Institute of Natural Products, Chang Gung University, Taoyuan, Taiwan
| | - Kung-Hao Liang
- Liver Research Center, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chi-Yuan Chen
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Research Center for Industry of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
| | - Wen-Yu Chuang
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Shir-Hwa Ueng
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Pao-Hsien Chu
- Healthcare Center, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chung-Guei Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital, Linko, Taiwan
- Department of Medical Biotechnology and Laboratory Science, Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Tse-Ching Chen
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
| | - Chuen Hsueh
- Tissue Bank, Chang Gung Memorial Hospital, Linko, Taiwan
- Department of Anatomic Pathology, Chang Gung Memorial Hospital, Linko, Taiwan
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13
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Multicenter fresh frozen tissue sampling in colorectal cancer: does the quality meet the standards for state of the art biomarker research? Cell Tissue Bank 2017; 18:425-431. [PMID: 28258397 PMCID: PMC5587614 DOI: 10.1007/s10561-017-9613-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 02/23/2017] [Indexed: 02/07/2023]
Abstract
The growing interest in the molecular subclassification of colorectal cancers is increasingly facilitated by large multicenter biobanking initiatives. The quality of tissue sampling is pivotal for successful translational research. This study shows the quality of fresh frozen tissue sampling within a multicenter cohort study for colorectal cancer (CRC) patients. Each of the seven participating hospitals randomly contributed ten tissue samples, which were collected following Standard Operating Procedures (SOP) using established techniques. To indicate if the amount of intact RNA is sufficient for molecular discovery research and prove SOP compliance, the RNA integrity number (RIN) was determined. Samples with a RIN < 6 were measured a second time and when consistently low a third time. The highest RIN was used for further analysis. 91% of the tissue samples had a RIN ≥ 6 (91%). The remaining six samples had a RIN between 5 and 6 (4.5%) or lower than 5 (4.5%). The median overall RIN was 7.3 (range 2.9-9.0). The median RIN of samples in the university hospital homing the biobank was 7.7 and the median RIN for the teaching hospitals was 7.3, ranging from 6.5 to 7.8. No differences were found in the outcome of different hospitals (p = 0.39). This study shows that the collection of high quality fresh frozen samples of colorectal cancers is feasible in a multicenter design with complete SOP adherence. Thus, using basic sampling techniques large patient cohorts can be organized for predictive and prognostic (bio)marker research for CRC.
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14
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Bordinhão ALR, Evangelista AF, Oliveira RJS, Macedo T, Silveira HC, Reis RM, Marques MM. MicroRNA profiling in human breast cancer cell lines exposed to the anti-neoplastic drug cediranib. Oncol Rep 2016; 36:3197-3206. [PMID: 27748845 DOI: 10.3892/or.2016.5153] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 03/15/2016] [Indexed: 11/06/2022] Open
Abstract
Cediranib, a pan-tyrosine kinase inhibitor is showing promising results for the treatment of several solid tumours. In breast cancer, its effects remain unclear, and there are no predictive biomarkers. Several studies have examined the expression profiles of microRNAs (miRNAs) in response to different chemotherapy treatments and found that the expression patterns may be associated with the treatment response. Therefore, our aim was to evaluate the cellular behaviour and differential expression profiles of miRNAs in breast cancer cell lines exposed to cediranib. The biological effect of this drug was measured by viability, migration, invasion and cell death in in vitro assays. Signaling pathways were assessed using a human phospho-receptor tyrosine kinase array. Furthermore, using a miRNA array and quantitative real-time PCR (qRT‑PCR), we assessed the relative expression of miRNAs following cediranib treatment. The breast cancer cell lines exhibited a distinct cytotoxic response to cediranib treatment. Cediranib exposure resulted in a decrease in the cell migration and invasion of all the breast cancer cell lines. Treatment with cediranib appeared to be able to modulate the activation of several RTKs that are targets of cediranib such as EGFR and a new potential target ROR2. Furthermore, this drug was able to modulate the expression profile of different microRNAs such as miR-494, miR-923, miR-449a, miR-449b and miR-886-3 in breast cancer cell lines. These miRNAs are reported to regulate genes involved in important molecular processes, according to bioinformatics prediction tools.
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Affiliation(s)
- A L R Bordinhão
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - A F Evangelista
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - R J S Oliveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - T Macedo
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - H C Silveira
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - R M Reis
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
| | - M M Marques
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, São Paulo, Brazil
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15
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Liang W, Zhou X, Yao L, Liu B. Cryopreservation-Altered Expression of RNA and Protein Markers in Biological Specimens. Biopreserv Biobank 2016; 15:176-181. [PMID: 27618161 DOI: 10.1089/bio.2015.0114] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The preservation of DNA, RNA, and protein markers in biological specimens is essential for initial diagnosis, subsequent verification, and comparison, as well as for archival retention of pathological materials in modern molecular diagnostics and precision medicine. Considerable attention has been paid to the methods of collection, handling, and preparation of specimens for initial testing, but insufficient attention to the long-term specimen preservation for later verification, comparison, and archival retention. In the present study, we have investigated the changes of expressions of RNAs and proteins in Hep-G2 cell specimens after cryopreservation at -80°C and in liquid nitrogen. Storage temperature and different cryoprotective agent (CPA) solutions not only affect cell viability but also more importantly the retention of various molecular markers after storage as detected by western blot and real-time fluorescent quantitative polymerase chain reaction. While the presence of CPAs increased the survival rates of cells after cryopreservation as expected, there was no consistent trend observed with regard to the RNA expression measurements. The data have significant implications with regard to the accuracy and interpretation of acquired data from specimens that have been cryopreserved without RNA and protein stabilization and point to the need for rethinking the assumptions, strategies, and criteria of optimizing biological specimen cryopreservation in molecular diagnostics.
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Affiliation(s)
- Wei Liang
- Institute of Biothermal Science, University of Shanghai for Science and Technology , Shanghai, China
| | - Xuexun Zhou
- Institute of Biothermal Science, University of Shanghai for Science and Technology , Shanghai, China
| | - Lan Yao
- Institute of Biothermal Science, University of Shanghai for Science and Technology , Shanghai, China
| | - Baolin Liu
- Institute of Biothermal Science, University of Shanghai for Science and Technology , Shanghai, China
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16
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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.
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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
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17
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Pop LA, Pileczki V, Cojocneanu-Petric RM, Petrut B, Braicu C, Jurj AM, Buiga R, Achimas-Cadariu P, Berindan-Neagoe I. Normalization of gene expression measurement of tissue samples obtained by transurethral resection of bladder tumors. Onco Targets Ther 2016; 9:3369-80. [PMID: 27330317 PMCID: PMC4898429 DOI: 10.2147/ott.s97519] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Background Sample processing is a crucial step for all types of genomic studies. A major challenge for researchers is to understand and predict how RNA quality affects the identification of transcriptional differences (by introducing either false-positive or false-negative errors). Nanotechnologies help improve the quality and quantity control for gene expression studies. Patients and methods The study was performed on 14 tumor and matched normal pairs of tissue from patients with bladder urothelial carcinomas. We assessed the RNA quantity by using the NanoDrop spectrophotometer and the quality by nano-microfluidic capillary electrophoresis technology provided by Agilent 2100 Bioanalyzer. We evaluated the amplification status of three housekeeping genes and one small nuclear RNA gene using the ViiA 7 platform, with specific primers. Results Every step of the sample handling protocol, which begins with sample harvest and ends with the data analysis, is of utmost importance due to the fact that it is time consuming, labor intensive, and highly expensive. High temperature of the surgical procedure does not affect the small nucleic acid sequences in comparison with the mRNA. Conclusion Gene expression is clearly affected by the RNA quality, but less affected in the case of small nuclear RNAs. We proved that the high-temperature, highly invasive transurethral resection of bladder tumor procedure damages the tissue and affects the integrity of the RNA from biological specimens.
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Affiliation(s)
- Laura A Pop
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Valentina Pileczki
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Analytical Chemistry, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Roxana M Cojocneanu-Petric
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Bogdan Petrut
- Department of Surgery II - Urology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Urology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Cornelia Braicu
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ancuta M Jurj
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Rares Buiga
- Department of Pathology, The Oncology Institute "Prof. Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
| | - Patriciu Achimas-Cadariu
- Department of Surgery, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania; Department of Surgical Oncology and Gynecological Oncology, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania
| | - Ioana Berindan-Neagoe
- The Research Center for Functional Genomics, Biomedicine and Translational Medicine, Iuliu Haţieganu University of Medicine and Pharmacy, Cluj-Napoca, Cluj, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof Dr Ion Chiricuţă", Cluj-Napoca, Cluj, Romania
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18
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Galissier T, Schneider C, Nasri S, Kanagaratnam L, Fichel C, Coquelet C, Diebold MD, Kianmanesh R, Bellon G, Dedieu S, Marchal Bressenot A, Boulagnon-Rombi C. Biobanking of Fresh-Frozen Human Adenocarcinomatous and Normal Colon Tissues: Which Parameters Influence RNA Quality? PLoS One 2016; 11:e0154326. [PMID: 27124490 PMCID: PMC4849710 DOI: 10.1371/journal.pone.0154326] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/12/2016] [Indexed: 12/01/2022] Open
Abstract
Medical research projects become increasingly dependent on biobanked tissue of high quality because the reliability of gene expression is affected by the quality of extracted RNA. Hence, the present study aimed to determine if clinical, surgical, histological, and molecular parameters influence RNA quality of normal and tumoral frozen colonic tissues. RNA Quality Index (RQI) was evaluated on 241 adenocarcinomas and 115 matched normal frozen colon tissues collected between October 2006 and December 2012. RQI results were compared to patients’ age and sex, tumor site, kind of surgery, anastomosis failure, adenocarcinoma type and grade, tumor cell percentage, necrosis extent, HIF-1α and cleaved caspase-3 immunohistochemistry, and BRAF, KRAS and microsatellites status. The RQI was significantly higher in colon cancer tissue than in matched normal tissue. RQI from left-sided colonic cancers was significantly higher than RQI from right-sided cancers. The RNA quality was not affected by ischemia and storage duration. According to histological control, 7.9% of the samples were unsatisfactory because of inadequate sampling. Biobanked tumoral tissues with RQI ≥5 had lower malignant cells to stromal cells ratio than samples with RQI <5 (p <0.05). Cellularity, necrosis extent and mucinous component did not influence RQI results. Cleaved caspase-3 and HIF-1α immunolabelling were not correlated to RQI. BRAF, KRAS and microsatellites molecular status did not influence RNA quality. Multivariate analysis revealed that the tumor location, the surgical approach (laparoscopy versus open colectomy) and the occurrence of anastomotic leakage were the only parameters influencing significantly RQI results of tumor samples. We failed to identify parameter influencing RQI of normal colon samples. These data suggest that RNA quality of colonic adenocarcinoma biospecimens is determined by clinical and surgical parameters. More attention should be paid during the biobanking procedure of right-sided colon cancer or laparoscopic colectomy specimen. Histological quality control remains essential to control sampling accuracy.
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Affiliation(s)
- Thibaut Galissier
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
| | - Christophe Schneider
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Saviz Nasri
- Tumorothèque de Champagne Ardenne, Reims, France
| | - Lukshe Kanagaratnam
- Unité d’Aide Méthodologique, Centre Hospitalier Universitaire, Reims, France
| | - Caroline Fichel
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | | | - Marie-Danièle Diebold
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Tumorothèque de Champagne Ardenne, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Reza Kianmanesh
- Service de Chirurgie Digestive, Centre Hospitalier Universitaire, Reims, France
| | - Georges Bellon
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire de Biochimie, Centre Hospitalier Universitaire, Reims, France
| | - Stéphane Dedieu
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire SiRMa, Université de Reims Champagne-Ardenne, UFR Sciences Exactes et Naturelles, Reims, France
| | - Aude Marchal Bressenot
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
| | - Camille Boulagnon-Rombi
- Laboratoire d’Anatomie Pathologique, Centre Hospitalier Universitaire, Reims, France
- CNRS UMR 7369, Matrice Extracellulaire et Dynamique Cellulaire, MEDyC, Reims, France
- Laboratoire d’Anatomie Pathologique, Université de Reims Champagne-Ardenne, UFR Médecine, Reims, France
- * E-mail:
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Milley KM, Nimmo JS, Bacci B, Ryan SD, Richardson SJ, Danks JA. DogMATIC--A Remote Biospecimen Collection Kit for Biobanking. Biopreserv Biobank 2015; 13:247-54. [PMID: 26186583 DOI: 10.1089/bio.2014.0085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Canine tumors are valuable comparative oncology models. This research was designed to create a sustainable biobank of canine mammary tumors for breast cancer research. The aim was to provide a well-characterized sample cohort for specimen sharing, data mining, and long-term research aims. Canine mammary tumors are most frequently managed at a local veterinary clinic or hospital. We adopted a biobank framework based on a large number of participating veterinary hospitals and clinics acting as collection centers that were serviced by a centralized storage facility. Recruitment was targeted at rural veterinary clinics. A tailored, stable collection kit (DogMATIC) was designed that was used by veterinarians in remote or rural locations to collect both fresh and fixed tissue for submission to the biobank. To validate this methodology the kit design, collection rate, and sample quality were analyzed. The Australian Veterinary Cancer Biobank was established as a network of 47 veterinary clinics and three veterinary pathology laboratories spanning over 200,000 km(2). In the first 12 months, 30 canine mammary tumor cases were submitted via the DogMATIC kit. Pure intact RNA was isolated in over 80% of samples with an average yield of 14.49 μg. A large network biobank, utilizing off-site collection with the DogMATIC kit, was successfully coordinated. The creation of the Australian Veterinary Cancer Biobank has established a long-term, sustainable, comparative oncology research resource in Australia. There are broader implications for biobanking with this very different form of collection and banking.
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Affiliation(s)
- Kristi M Milley
- 1 School of Medical Sciences, RMIT University , Bundoora, Australia .,2 Australian Veterinary Cancer Biobank , Bundoora, Australia
| | - Judith S Nimmo
- 3 Australian Specialized Animal Pathology Laboratories , Mulgrave, Australia
| | - Barbara Bacci
- 2 Australian Veterinary Cancer Biobank , Bundoora, Australia .,4 Faculty of Veterinary Science, The University of Melbourne , Werribee, Australia
| | - Stewart D Ryan
- 2 Australian Veterinary Cancer Biobank , Bundoora, Australia .,4 Faculty of Veterinary Science, The University of Melbourne , Werribee, Australia
| | | | - Janine A Danks
- 1 School of Medical Sciences, RMIT University , Bundoora, Australia .,2 Australian Veterinary Cancer Biobank , Bundoora, Australia .,5 Department of Medicine, The University of Melbourne , Austin Health, Heidelberg, Australia
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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.
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Zeugner S, Mayr T, Zietz C, Aust DE, Baretton GB. RNA quality in fresh-frozen gastrointestinal tumor specimens-experiences from the tumor and healthy tissue bank TU Dresden. Recent Results Cancer Res 2015; 199:85-93. [PMID: 25636432 DOI: 10.1007/978-3-319-13957-9_9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The term "pre-analytics" summarizes all procedures concerned with specimen collection or processing as well as logistical aspects like transport or storage of tissue specimens. All or these variables as well as tissue-specific characteristics affect sample quality. While certain parameters like warm ischemia or tissue-specific characteristics cannot be changed, other parameters can be assessed and optimized. The aim of this study was to determine RNA quality by assessing the RIN values of specimens from different organs and to assess the influence of vacuum preservation. Samples from the GI tract, in general, appear to have lower RNA quality when compared to samples from other organ sites. This may be due to the digestive enzymes or bacterial colonization. Processing time in pathology does not significantly influence RNA quality. Tissue preservation with a vacuum sealer leads to preserved RNA quality over an extended period of time and offers a feasible alternative to minimize the influence of transport time into pathology.
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Affiliation(s)
- Silke Zeugner
- Institute of Pathology, University Hospital Carl Gustav Carus, Technische Universität Dresden, Fetscherstr. 74, 01307, Dresden, Germany
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Liu H, McDowell TL, Hanson NE, Tang X, Fujimoto J, Rodriguez-Canales J. Laser capture microdissection for the investigative pathologist. Vet Pathol 2013; 51:257-69. [PMID: 24227008 DOI: 10.1177/0300985813510533] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
An important step in translational research is the validation of molecular findings from in vitro experiments using tissue specimens. However, tissue specimens are complex and contain a multitude of diverse cell populations that interfere with the molecular profiling data of a specific cell type. Laser capture microdissection (LCM) alleviates this issue by providing a valuable tool for the enrichment of a specific cell type within complex tissue samples. However, LCM and molecular analysis from tissue specimens can be complex and challenging due to numerous issues related with the tissue processing and its impact on the integrity of biomolecules in the specimen. The intricate nature of this application highlights the essential role a pathologist plays in translational research by contributing an expertise in histopathology, tissue handling, tissue analysis techniques, and clinical correlation of biological findings. The present review examines key practical aspects in tissue handling, specimen selection, quality control, and sample preparation for LCM and downstream molecular analyses that are a primary objective of the investigative pathologist.
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Affiliation(s)
- H Liu
- Department of Translational Molecular Pathology, UT-MD Anderson Cancer Center, 1515 Holcombe Blvd, Unit 0432, Houston, TX 77030, USA.
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