1
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Acharayothin O, Thiengtrong B, Juengwiwattanakitti P, Anekwiang P, Riansuwan W, Chinswangwatanakul V, Tanjak P. Impact of Washing Processes on RNA Quantity and Quality in Patient-Derived Colorectal Cancer Tissues. Biopreserv Biobank 2023; 21:31-37. [PMID: 35230139 DOI: 10.1089/bio.2021.0134] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: Colorectal cancer (CRC) is a common and lethal cancer worldwide. Extraction of high-quality RNA from CRC samples plays a key role in scientific research and translational medicine. Specimen collection and washing methods that do not compromise RNA quality or quantity are needed to ensure high quality specimens for gene expression analysis and other RNA-based downstream applications. We investigated the effect of tissue specimen collection and different preparation processes on the quality and quantity of RNA extracted from surgical CRC tissues. Materials and Methods: After surgical resection, tissues were harvested and prepared with various washing processes in a room adjacent to the operating room. One hundred fourteen tissues from 36 CRC patients were separately washed in either cold phosphate-buffered saline reagent (n = 34) or Dulbecco's modified Eagle's medium (DMEM; n = 34) for 2-3 minutes until the stool was removed, and unwashed specimens served as controls (n = 34). Six tissue specimens were washed and immersed in DMEM for up to 1 hour at 4°C. Before RNA extraction, all specimens were kept in the stabilizing reagent for 3 months at -80°C. RNA was extracted, and the concentration per milligram of tissue was measured. RNA quality was assessed using the RNA integrity number (RIN) value. Results: Different washing processes did not result in significant differences in RNA quantity or RIN values. In the six tissues that were washed and immersed in DMEM for 1 hour, RIN values significantly decreased. The quality of the extracted RNA from most specimens was excellent with the average RIN greater than 7. Conclusions: RNA is stable in specimens washed in different processes for short periods, but RIN values may decrease with prolonged wash times.
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Affiliation(s)
- Onchira Acharayothin
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Benjarat Thiengtrong
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panudeth Juengwiwattanakitti
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Panatna Anekwiang
- Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Woramin Riansuwan
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Vitoon Chinswangwatanakul
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Pariyada Tanjak
- Department of Surgery, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.,Siriraj Cancer Center, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
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2
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Test of an Improved DNA and RNA Purification Protocol—Importance of Proteinase K and Co-Purified Small RNAs. SEPARATIONS 2022. [DOI: 10.3390/separations9110324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Optimized and reliable DNA/RNA extraction protocols are a vital tool in clinical practice in the context of molecular testing. Here, we present our successful attempt to enhance the quantity of RNA isolated from clinical specimens, which we originally found challenging (breast and testis). We compared several purification methods with special focus on two AllPrep system-based protocols (QIAGEN). Our data suggest that addition of proteinase K may markedly increase RNA and, in some cases, also DNA yield. The extraction kit used, AllPrep DNA/RNA/miRNA universal kit, provides RNA amounts comparable with the phenol-chloroform extraction method; however, part of the final yield consisted of small RNAs, visible as a thick band in the bioanalyzer gel-like image (5S peak). The 5S peak, albeit in some cases dominating the bioanalyzer image, plays only a small role in RT-qPCR analysis, and Qubit or NanoDrop measurements can still be used as a reliable estimate of starting amounts of mRNA for downstream analyses. In conclusion, we showed that implementing a protocol containing a step of proteinase K digestion markedly increases RNA yield. The AllPrep DNA/RNA/miRNA Universal Kit can be successfully used for simultaneous extraction of DNA and total RNA, irrespective of the tissue of origin, and does not present inconveniences related to phenol-chloroform extraction.
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3
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Niedermair T, Bhatt M, Babel M, Feustel M, Mamilos A, Schweikl H, Ferstl G, Hofman P, Brochhausen C. Interim Storage of Biospecimen at Satellite Collection Centers: Dewar and Cryotube Choice Are Important for Temporary Storage in Liquid Nitrogen. Biopreserv Biobank 2022; 21:149-157. [PMID: 35704045 DOI: 10.1089/bio.2022.0002] [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: 11/12/2022] Open
Abstract
One major goal of biobanks is to provide the best possible biospecimen quality for research use. This can be achieved, notably in accredited structures, by using standardized procedures for collection, processing, and storage of biosamples and associated data. Since tissue samples of a clinical biobank are commonly collected at surgical theaters in satellite locations or hospitals in remote areas, adequate temporary storage of the biosample is mandatory to maintain optimal sample quality. In cases where immediate snap freezing of the collected material is possible, interim storage of the samples in portable dewars filled with liquid nitrogen (LN2) is a widely used method. Therefore, the ideal dewar size and maximum storage time need to be considered to maintain an optimal biospecimen quality. In addition, the nature of the cryotube material is an important aspect for keeping the biosample safe while storing it in LN2. The objective of this study was to test different dewar vessels with respect to LN2 volume and consumption and to analyze the impact of LN2 contact on cryotube material through scanning electron microscopy.
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Affiliation(s)
- Tanja Niedermair
- Institute of Pathology, University Regensburg, University of Regensburg, Regensburg, Germany
- Central Biobank Regensburg, University Clinic and University of Regensburg, Regensburg, Germany
| | - Meet Bhatt
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Nice Hospital Center, University Côte d'Azur, Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), University Cote D'Azur, Nice, France
| | - Maximilian Babel
- Institute of Pathology, University Regensburg, University of Regensburg, Regensburg, Germany
- Central Biobank Regensburg, University Clinic and University of Regensburg, Regensburg, Germany
| | - Moritz Feustel
- Institute of Pathology, University Regensburg, University of Regensburg, Regensburg, Germany
- Central Biobank Regensburg, University Clinic and University of Regensburg, Regensburg, Germany
| | - Andreas Mamilos
- Institute of Pathology, University Regensburg, University of Regensburg, Regensburg, Germany
| | - Helmut Schweikl
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Gerlinde Ferstl
- Department of Conservative Dentistry and Periodontology, University Hospital Regensburg, University of Regensburg, Regensburg, Germany
| | - Paul Hofman
- Laboratory of Clinical and Experimental Pathology, FHU OncoAge, Nice Hospital Center, University Côte d'Azur, Nice, France
- Hospital-Integrated Biobank (BB-0033-00025), University Cote D'Azur, Nice, France
| | - Christoph Brochhausen
- Institute of Pathology, University Regensburg, University of Regensburg, Regensburg, Germany
- Central Biobank Regensburg, University Clinic and University of Regensburg, Regensburg, Germany
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4
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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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5
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Flügge F, Figge L, Duhm-Harbeck P, Kammler R, Habermann JK. How clinical biobanks can support precision medicine: from standardized preprocessing to treatment guidance. EXPERT REVIEW OF PRECISION MEDICINE AND DRUG DEVELOPMENT 2019. [DOI: 10.1080/23808993.2019.1690395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Friedemann Flügge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | - Lena Figge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | | | - Rosita Kammler
- Translational Research Coordination for International Breast Cancer Study Group and European Thoracic Oncology Platform, Bern, Switzerland
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
| | - Jens K. Habermann
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein (UKSH), Lübeck, Germany
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6
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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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7
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Zheng H, Tao YP, Chen FQ, Li HF, Zhang ZD, Zhou XX, Yang Y, Zhou WP. Temporary Ischemia Time Before Snap Freezing Is Important for Maintaining High-Integrity RNA in Hepatocellular Carcinoma Tissues. Biopreserv Biobank 2019; 17:425-432. [PMID: 31025876 DOI: 10.1089/bio.2019.0003] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Hao Zheng
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Yuan-Ping Tao
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Feng-Qiu Chen
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
- Biobank of Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui-Fen Li
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Zhi-De Zhang
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Xue-Xun Zhou
- Shanghai Avantech Bioscience Co., Ltd., Shanghai, China
| | - Yuan Yang
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
| | - Wei-Ping Zhou
- National Liver Tissue Bank, Eastern Hepatobiliary Surgery Hospital, Second Military Medical University, Shanghai, China
- Key Laboratory of Signaling Regulation and Targeting Therapy of Liver Cancer (SMMU), Ministry of Education, Shanghai, China
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8
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Fan XJ, Huang Y, Wu PH, Yin XK, Yu XH, Fu XH, Feng LL, Wang YL, Yi HJ, Chen ZT, Yin JX, Zhang DL, Feng WX, Bai SM, Kim T, Mills GB, Lu YL, Wan XB, Wang L. Impact of Cold Ischemic Time and Freeze-Thaw Cycles on RNA, DNA and Protein Quality in Colorectal Cancer Tissues Biobanking. J Cancer 2019; 10:4978-4988. [PMID: 31598170 PMCID: PMC6775519 DOI: 10.7150/jca.29372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 06/23/2019] [Indexed: 12/20/2022] Open
Abstract
Tissue-derived RNA, DNA and protein samples become more and more crucial for molecular detection in clinical research, personalized and targeted cancer therapy. This study evaluated how to biobanking colorectal tissues through examining the influences of cold ischemic time and freeze-thaw cycles on RNA, DNA and protein integrity. Here, 144 pairs of tumor and normal colorectal tissues were used to investigate the impact of cold ischemic times (0-48h) on RNA, DNA and protein integrity at on ice or room temperature conditions. Additionally, 45 pairs of tissues experienced 0-9 freeze-thaw cycles, and then the RNA, DNA and protein quality were analyzed. On ice, RNA, DNA and protein from colorectal tumor and normal tissues were all stable up to 48h after surgery. At room temperature, RNA in colorectal tumor and normal tissues began to degrade at 8h and 24h, respectively. Meanwhile, the tumor tissues DNA degradation occurred at 24h after surgery at room temperature. Similarly, the protein expression level of tumor and normal tissues began to change at 24h after the surgery at room temperature. Interestingly, tissue RNA and DNA remained stable even after 9 freeze-thaw cycles, whereas the proteins levels were remarkably changed after 7 freeze-thaw cycles. This study provided a useful evidence on how to store human colorectal tissues for biobanking. Preserving the surgical colorectal tissue on ice was an effective way to prevent RNA, DNA and protein degradation. Importantly, more than 7 repeated freeze-thaw cycles were not recommended for colorectal tissues.
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Affiliation(s)
- Xin-Juan Fan
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yan Huang
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pei-Huang Wu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Xin-Ke Yin
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Xi-Hu Yu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Gastrointestinal Surgery, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xin-Hui Fu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Li-Li Feng
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Yun-Long Wang
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Hong-Jun Yi
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhi-Ting Chen
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Jun-Xiang Yin
- China National Center for Biotechnology Development, Beijing, China
| | - Da-Lu Zhang
- China National Center for Biotechnology Development, Beijing, China
| | - Wei-Xing Feng
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Shao-Mei Bai
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Taewan Kim
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Gordon B Mills
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yi-Ling Lu
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiang-Bo Wan
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Radiation Oncology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Wang
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Gastrointestinal Surgery, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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9
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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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10
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Kelly R, Albert M, de Ladurantaye M, Moore M, Dokun O, Bartlett JMS. RNA and DNA Integrity Remain Stable in Frozen Tissue After Long-Term Storage at Cryogenic Temperatures: A Report from the Ontario Tumour Bank. Biopreserv Biobank 2019; 17:282-287. [PMID: 30762427 DOI: 10.1089/bio.2018.0095] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background: It is widely assumed that the integrity of tissue specimens remains stable indefinitely if preserved at cryogenic temperatures. With biobanking reaching a level of maturity where samples are increasingly stored for 10 years and beyond, this assumption of prolonged stability should be tested. Data from such an assessment are critical to verify if samples stored for extended durations remain "fit for purpose" or if there is need to reconsider the utility of samples stored beyond a certain timeframe. The Ontario Tumour Bank has been collecting samples since 2004, and assesses a random selection of frozen samples each year for RNA and DNA integrity as a part of ongoing quality control (QC) practices. This historical quality assessment data provide a unique opportunity to assess the impact of extended storage on nucleic acid integrity using replicate samples that remain in the bank in the present day as comparators. Methods: To examine the stability of fresh-frozen tumor tissue stored at cryogenic temperatures, RNA was extracted and analyzed from 87 cases over 14 disease sites stored long term in vapor-phase liquid nitrogen (LN2) (approximately -180°C). Historical QC data were compared against new data after re-extraction of replicate samples to determine the effect of extended storage on RNA quality. In addition, DNA was extracted from a subselection of samples (n = 20) to determine the effect of prolonged storage on DNA integrity. Results: No time-dependent decrease in tissue RNA or DNA quality, as measured by RNA integrity number (RIN) and DNA integrity number, was observed over an 11-year period. As a secondary observation, RNA integrity was not predictive of DNA integrity: DNA quality may still be very good, and as such RIN scores should not be used as a substitute indicator for evaluating DNA. Conclusions: Extended cryogenic storage beyond 2-11 years remains a viable option for maintaining the high quality of specimens in biobanks.
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Affiliation(s)
- Rachel Kelly
- 1Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Canada.,2Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Canada
| | - Monique Albert
- 1Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Canada
| | - Manon de Ladurantaye
- 3Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Canada
| | - Melissa Moore
- 4Ontario Health Study, Ontario Institute for Cancer Research, Toronto, Canada
| | - Olusola Dokun
- 5Health Services Research, Ontario Institute for Cancer Research, Toronto, Canada
| | - John M S Bartlett
- 1Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, Canada.,2Diagnostic Development, Ontario Institute for Cancer Research, Toronto, Canada
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11
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Zhang X, Han QY, Zhao ZS, Zhang JG, Zhou WJ, Lin A. Biobanking of Fresh-Frozen Gastric Cancer Tissues: Impact of Long-Term Storage and Clinicopathological Variables on RNA Quality. Biopreserv Biobank 2019; 17:58-63. [PMID: 30457887 DOI: 10.1089/bio.2018.0038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Xia Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Qiu-Yue Han
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Zhang-Sheng Zhao
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Jian-Gang Zhang
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Wen-Jun Zhou
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
| | - Aifen Lin
- Biological Resource Center, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Linhai, People's Republic of China
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12
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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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13
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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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14
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Vrentas CE, Boggiatto PM, Schaut RG, Olsen SC. Collection and Processing of Lymph Nodes from Large Animals for RNA Analysis: Preparing for Lymph Node Transcriptomic Studies of Large Animal Species. J Vis Exp 2018. [PMID: 29863658 DOI: 10.3791/57195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Large animals (both livestock and wildlife) serve as important reservoirs of zoonotic pathogens, including Brucella, Mycobacterium bovis, Salmonella, and E. coli, and are useful for the study of pathogenesis and/or spread of the bacteria in natural hosts. With the key function of lymph nodes in the host immune response, lymph node tissues serve as a potential source of RNA for downstream transcriptomic analyses, in order to assess the temporal changes in gene expression in cells over the course of an infection. This article presents an overview of the process of lymph node collection, tissue sampling, and downstream RNA processing in livestock, using cattle (Bos taurus) as a model, with additional examples provided from the American bison (Bison bison). The protocol includes information about the location, identification, and removal of lymph nodes from multiple key sites in the body. Additionally, a biopsy sampling methodology is presented that allows for a consistency of sampling across multiple animals. Several considerations for sample preservation are discussed, including the generation of RNA suitable for downstream methodologies like RNA-sequencing and RT-PCR. Due to the long delays inherent in large animal vs. mouse time course studies, representative results from bison and bovine lymph node tissues are presented to describe the time course of the degradation in this tissue type, in the context of a review of previous methodological work on RNA degradation in other tissues. Overall, this protocol will be useful to both veterinary researchers beginning transcriptome projects on large animal samples and to molecular biologists interested in learning techniques for in vivo tissue sampling and in vitro processing.
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Affiliation(s)
- Catherine E Vrentas
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture;
| | - Paola M Boggiatto
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture
| | - Robert G Schaut
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture
| | - Steven C Olsen
- National Animal Disease Center, Agricultural Research Service, U.S. Department of Agriculture
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15
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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.
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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.
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16
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Ostrom QT, Devine K, Fulop J, Wolinsky Y, Liao P, Stetson L, Couce M, Sloan AE, Barnholtz-Sloan JS. Brain tumor biobanking in the precision medicine era: building a high-quality resource for translational research in neuro-oncology. Neurooncol Pract 2017; 4:220-228. [PMID: 29692920 PMCID: PMC5909804 DOI: 10.1093/nop/npw029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The growth of precision medicine has made access to biobanks with high-quality, well-annotated neuro-oncology biospecimens critical. Developing and maintaining neuro-oncology biobanks is best accomplished through multidisciplinary collaboration between clinicians and researchers. Balancing the needs and leveraging the skills of all stakeholders in this multidisciplinary effort is of utmost importance. Collaboration with a multidisciplinary team of clinicians, health care team members, and institutions, as well as patients and their families, is essential for access to participants in order to obtain informed consent, collect samples under strict standard operating procedures, and accurate and relevant clinical annotation. Once a neuro-oncology biobank is established, development and implementation of policies related to governance and distribution of biospecimens (both within and outside the institution) is of critical importance for sustainability. Proper implementation of a governance process helps to ensure that the biospecimens and data can be utilized in research with the largest potential benefit. New NIH and peer-reviewed journal policies related to public sharing of 'omic' data generated from stored biospecimens create new ethical challenges that must be addressed in developing informed consents, protocols, and standard operating procedures. In addition, diversification of sources of funding for the biobanks is needed for long-term sustainability.
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Affiliation(s)
- Quinn T Ostrom
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Karen Devine
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Jordonna Fulop
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Yingli Wolinsky
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Peter Liao
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Lindsay Stetson
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Marta Couce
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Andrew E Sloan
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Wearn 152, Case Western Reserve University School of Medicine, 11100 Euclid Avenue, Cleveland, Ohio 44106 (Q.T.O., K.D., J.F., P.L., L.S., A.E.S., J.S.B.S.); Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, 2103 Cornell Rd, WRB 2-532, Cleveland, Ohio 44106-7295 (Y.W.); Department of Pathology, University Hospitals Case Medical Center, Cleveland, Ohio 44106 (M.C.); Brain Tumor and Neuro-oncology Center, Department of Neurosurgery, University Hospitals Case Medical Center, Case Western Reserve School of Medicine, 11100 Euclid Ave, Cleveland, Ohio 44106 (A.E.S., J.S.B.S.)
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17
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Song SY, Jun J, Park M, Park SK, Choi W, Park K, Jang KT, Lee M. Biobanking of Fresh-Frozen Cancer Tissue: RNA Is Stable Independent of Tissue Type with Less Than 1 Hour of Cold Ischemia. Biopreserv Biobank 2017; 16:28-35. [PMID: 29148824 DOI: 10.1089/bio.2017.0062] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND The effects of preanalytical variables in tissue processing and storage periods on RNA quality of tissues have been well documented in each type of cancer. However, few studies have been performed on a comparative assessment of the impacts across different cancer tissues, even though it is well known that RNase activity is highly variable in various tissue types and RNase-rich tissues have been found to yield low-quality RNA. METHODS We investigated the impacts of cold ischemia times and long-term storage on RNA integrity in various types of cancer tissue, which had been fresh-frozen and collected at the Samsung Medical Center Biobank. RNA quality was also evaluated with regard to histopathological variables. We analyzed RNA integrity number (RIN) data, which had been obtained from our quality control (QC) processes over the last 7 years. Approximately 2% of samples were randomly selected and processed to measure RIN quarterly and after 6 years of storage for QC purposes. RESULTS Fresh-frozen tumor tissues yielded high-quality RNA regardless of tumor type and histopathological features. Up to 1-hour cold ischemia times and up to 6-year storage times did not adversely influence RNA integrity. Only 3 samples showed RIN of <7 out of a total of 396 analyzed tumor tissues. CONCLUSIONS Tissue quality was not adversely affected by long-term storage or limited variations of cold ischemia times. The low-quality samples could be correlated with the structural composition or intratumoral heterogeneity of tissues. The strict application of standardized protocols for tissue collection is the key for high-quality biobanking.
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Affiliation(s)
- Sang Yong Song
- 1 Biobank, Samsung Medical Center , Seoul, Korea.,2 Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul, Korea
| | - Jonghyun Jun
- 1 Biobank, Samsung Medical Center , Seoul, Korea
| | - Miyeon Park
- 1 Biobank, Samsung Medical Center , Seoul, Korea
| | - Seo Kyu Park
- 1 Biobank, Samsung Medical Center , Seoul, Korea
| | - Wonju Choi
- 1 Biobank, Samsung Medical Center , Seoul, Korea
| | - Kyunghee Park
- 3 Samsung Genome Institute , Samsung Medical Center, Seoul, Korea
| | - Kee-Taek Jang
- 1 Biobank, Samsung Medical Center , Seoul, Korea.,2 Department of Pathology and Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine , Seoul, Korea
| | - Myoyong Lee
- 1 Biobank, Samsung Medical Center , Seoul, Korea
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18
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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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19
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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.
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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:
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20
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Stiekema J, Cats A, Boot H, Langers AMJ, Balague Ponz O, van Velthuysen MLF, Braaf LM, Nieuwland M, van Sandick JW. Biobanking of fresh-frozen endoscopic biopsy specimens from esophageal adenocarcinoma. Dis Esophagus 2016; 29:1100-1106. [PMID: 26541751 DOI: 10.1111/dote.12430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The process of preparing endoscopic esophageal adenocarcinoma samples for next-generation DNA/RNA sequencing is poorly described. Therefore, we assessed the feasibility and pitfalls of preparing esophageal adenocarcinoma endoscopic biopsies toward DNA/RNA samples suitable for next-generation sequencing. In this prospective study, four tumor biopsy samples were collected from consecutive esophageal cancer patients during esophagogastroduodenoscopy and fresh-frozen in liquid nitrogen. DNA and RNA were isolated from samples with a tumor percentage of at least 50%. For next-generation sequencing, double-stranded DNA (dsDNA) is required and high-quality RNA preferred. The quantity dsDNA and RNA quantity and quality were assessed with the Nanodrop 2000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA) and Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA). Biopsy samples of 69 consecutive patients with esophageal adenocarcinoma were included. In five patients (7%), the tumor percentage was less than 50% in all four biopsies. Using a protocol allowing simultaneous DNA and RNA isolation, the median dsDNA yield was 2.4 μg (range 0.1-12.0 μg) and the median RNA yield was 0.5 μg (range 0.01-2.05 μg). The median RNA integrity number of samples that were fresh-frozen within 30 minutes after sampling was 6.7 (range 4.2-8.9) compared with 2.5 (1.8-4.5) for samples that were fresh-frozen after 2 hours. The results from this study show that obtaining dsDNA and RNA for next-generation sequencing from endoscopic esophageal adenocarcinoma samples is feasible. Tumor percentage and dsDNA/RNA yield and quality emphasize the need for sampling multiple biopsies and minimizing the delay before fresh-freezing.
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Affiliation(s)
- J Stiekema
- Department of Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A Cats
- Department of Gastroenterology and Hepatology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - H Boot
- Department of Gastroenterology and Hepatology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - A M J Langers
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - O Balague Ponz
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M L F van Velthuysen
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - L M Braaf
- Core Facility Molecular Pathology and Biobanking, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - M Nieuwland
- Deep Sequencing Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - J W van Sandick
- Department of Surgery, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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21
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Prasad G, Seers C, Reynolds E, McCullough MJ. The assessment of the robustness of microRNAs from oral cytological scrapings. J Oral Pathol Med 2016; 46:359-364. [PMID: 27560550 DOI: 10.1111/jop.12489] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/01/2016] [Indexed: 11/28/2022]
Abstract
BACKGROUND Sampling of suspect oral lesions in the general dental clinic may increase early carcinoma detection thus oral cancer survival rates. One means of lesion sampling that is an alternative to incisional biopsy is cytological scraping. MicroRNA alterations are also being explored as a means of diagnosing carcinoma as an alternative to histopathology. METHODS We obtained cytological scrapings using 10 strokes ('light') or 40 strokes ('heavy') from the buccal mucosa of one healthy subject using a dermatological curette. MicroRNA was isolated from oral cytological scrapings immediately, or the scrapings were stored in buffer or RNA later, at 4°C, room temperature or 36°C, from 1 to 7 days prior to RNA isolation. All scrape comparisons and test conditions were conducted in triplicate. MicroRNAs were measured using qRT-PCR. RESULTS MicroRNAs can be obtained from cytological scrapings independent of the number of strokes and can be measured using qRT-PCR after storage under all conditions tested. CONCLUSION MicroRNAs are robust to a wide range of storage conditions that bodes well for use of cytological scrapings to be of use in a clinical setting as a chair side sampling method for suspect oral lesions.
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Affiliation(s)
- Gareema Prasad
- Melbourne Dental School, The University of Melbourne, Melbourne, VIC, Australia.,Oral Health Cooperative Research Centre, The University of Melbourne, Melbourne, VIC, Australia
| | - Christine Seers
- Melbourne Dental School, The University of Melbourne, Melbourne, VIC, Australia.,Oral Health Cooperative Research Centre, The University of Melbourne, Melbourne, VIC, Australia
| | - Eric Reynolds
- Melbourne Dental School, The University of Melbourne, Melbourne, VIC, Australia.,Oral Health Cooperative Research Centre, The University of Melbourne, Melbourne, VIC, Australia
| | - Michael J McCullough
- Melbourne Dental School, The University of Melbourne, Melbourne, VIC, Australia.,Oral Health Cooperative Research Centre, The University of Melbourne, Melbourne, VIC, Australia
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22
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Grizzle WE, Otali D, Sexton KC, Atherton DS. Effects of Cold Ischemia on Gene Expression: A Review and Commentary. Biopreserv Biobank 2016; 14:548-558. [PMID: 27551929 DOI: 10.1089/bio.2016.0013] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Frequently investigators request that tissues be collected and processed in less than one hour following removal from a patient. Some biorepositories expend significant personnel time and other resources in trying to meet such goals; however, it is unclear whether the perceived benefits of relatively short cold ischemia times warrant these added costs. The literature of human surgical tissues prospectively exposed to cold ischemia at several time points was reviewed to compare the changes in transcripts/genes and microRNA with time of cold ischemia. Also, reports of protein changes in response to cold ischemia were correlated to changes in genes. The literature is limited; however, for most tissues, only a small proportion of transcripts/genes (<1%) changes up to 3 hours following surgery and most transcripts increase rather than decrease in less than 2 hours of cold ischemia. Biorepositories and investigators must consider the literature for evidence of significant changes in molecular results from tissues before spending significant resources on relatively rapid collection of tissues to meet cold ischemia times of less than 3 hours. Instead, those using human tissues in research must consider if the cold ischemia times affect their use in specific research; hence are these tissues "fit for purpose?"
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Affiliation(s)
- William E Grizzle
- Department of Pathology and the Comprehensive Cancer Center, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Dennis Otali
- Department of Pathology and the Comprehensive Cancer Center, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Katherine C Sexton
- Department of Pathology and the Comprehensive Cancer Center, The University of Alabama at Birmingham , Birmingham, Alabama
| | - Daniel S Atherton
- Department of Pathology and the Comprehensive Cancer Center, The University of Alabama at Birmingham , Birmingham, Alabama
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23
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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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24
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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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25
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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]
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26
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Wang Y, Zheng H, Chen J, Zhong X, Wang Y, Wang Z, Wang Y. The Impact of Different Preservation Conditions and Freezing-Thawing Cycles on Quality of RNA, DNA, and Proteins in Cancer Tissue. Biopreserv Biobank 2015; 13:335-47. [PMID: 26484573 DOI: 10.1089/bio.2015.0029] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Yaogeng Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
| | - Hong Zheng
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Jie Chen
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaorong Zhong
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Zhu Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
| | - Yanping Wang
- Laboratory of Molecular Diagnosis of Cancer, West China Hospital, Sichuan University, Chengdu, China
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu, China
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27
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Lee SML, Schelcher C, Thasler R, Schiergens TS, Thasler WE. Pre-Analytical Determination of the Effect of Extended Warm or Cold Ischaemia on RNA Stability in the Human Ileum Mucosa. PLoS One 2015; 10:e0138214. [PMID: 26371767 PMCID: PMC4570714 DOI: 10.1371/journal.pone.0138214] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 08/26/2015] [Indexed: 01/15/2023] Open
Abstract
The use of banked human tissue, obtained with informed consent after elective surgical procedures, represents a powerful model for understanding underlying mechanisms of diseases or therapeutic interventions and for establishing prognostic markers. However, donated tissues typically have varying times of warm ischaemia in situ due to blood arrest or cold ischaemia due to procurement and transportation. Hence, before using these tissues, it is important to carry out pre-analytical studies to ensure that they are representative of the in vivo state. In particular, tissues of the gastrointestinal tract have been thought to have low RNA stability. Therefore, this study aimed to determine if extended warm or cold ischaemia times and snap-freezing or banking in RNA stabilization solution affects RNA integrity or gene expression in human ileum mucosa. In short, ileum mucosa was collected for up to 1.5 h and 6 h of simulated warm or cold ischaemia respectively. Subsequently, RNA integrity and gene expressions were determined. It was found that RNA integrity remained high over the course of warm and cold ischaemia examined and there were in general no significant differences between snap-freezing and banking in RNA stabilization solution. Following the same trend, there were in general no significant changes in gene expressions measured (MYC, HIF1α, CDX, HMOX1 and IL1β). In conclusion, RNA in the ileum mucosa is maintained at a high integrity and has stable gene expression over the examined time course of warm or cold ischaemia when banked in RNA stabilization solution or snap-frozen in liquid nitrogen. As the average warm and cold ischaemia times imposed by surgery and the process of tissue banking are shorter than the time period examined in this study, human ileum mucosa samples collected after surgeries could be used for gene expression studies.
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Affiliation(s)
- Serene M. L. Lee
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Hospital of the University of Munich, Munich, Germany
| | - Celine Schelcher
- Biobank under the administration of the Human Tissue and Cell Research (HTCR) Foundation, Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Hospital of the University of Munich, Munich, Germany
| | - Reinhard Thasler
- Biobank under the administration of the Human Tissue and Cell Research (HTCR) Foundation, Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Hospital of the University of Munich, Munich, Germany
| | - Tobias S. Schiergens
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Hospital of the University of Munich, Munich, Germany
| | - Wolfgang E. Thasler
- Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Hospital of the University of Munich, Munich, Germany
- Biobank under the administration of the Human Tissue and Cell Research (HTCR) Foundation, Department of General, Visceral, Transplantation, Vascular and Thoracic Surgery, Hospital of the University of Munich, Munich, Germany
- * E-mail:
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28
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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.
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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)
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29
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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
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Sun H, Sun R, Hao M, Wang Y, Zhang X, Liu Y, Cong X. Effect of Duration of Ex Vivo Ischemia Time and Storage Period on RNA Quality in Biobanked Human Renal Cell Carcinoma Tissue. Ann Surg Oncol 2015; 23:297-304. [DOI: 10.1245/s10434-014-4327-9] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Indexed: 01/01/2023]
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Samadani AA, Nikbakhsh N, Fattahi S, Pourbagher R, Aghajanpour Mir SM, Mousavi Kani N, Abedian Z, Akhavan-Niaki H. RNA Extraction from Animal and Human's Cancerous Tissues: Does Tissue Matter? INTERNATIONAL JOURNAL OF MOLECULAR AND CELLULAR MEDICINE 2015; 4:54-9. [PMID: 25815283 PMCID: PMC4359706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Revised: 01/28/2015] [Accepted: 02/02/2015] [Indexed: 11/01/2022]
Abstract
The reliability of gene expression profiling, based technologies and methods to find transcriptional differences representative of the original samples is influenced by the quality of the extracted RNA. Hence, RNA extraction is the first step to investigate the gene expression and its function. Consequently, the quality of extracted RNA is really significant. Correspondingly, this research was accomplished to optimize the RNA extraction methods and compare the amounts of tissue or quality of tissue. Relatively, the cancerous tissue of human stomach in fresh and frozen conditions and also the mouse fresh tissue were studied. Some factors like the amount of samples, efficacy differences of diverse extraction buffers (TriPure, Trizol) and also the efficacy of b-mercaptoethanol were compared and investigated. The results indicated that the less amount (1-2 mg) compared to other amounts (2-5 mg, 5-15 mg) yielded the best quality and the RNA bands (5S, 18S, 28S) were observed perfectly. Relatively, comparing and measuring some kinds of buffers (Trizol, TriPure) indicated no difference in RNA extraction quality. The last investigated factor was the effect of b- mercaptoethanol which was used along with TriPure to remove the RNAse. Conclusively, no effective impression was observed.
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Affiliation(s)
- Ali Akbar Samadani
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.
| | - Novin Nikbakhsh
- Department of Surgery, Babol University of Medical Sciences, Babol, Iran.
| | - Sadegh Fattahi
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.
| | - Roghayeh Pourbagher
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.
| | | | - Narges Mousavi Kani
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.
| | - Zeinab Abedian
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.
| | - Haleh Akhavan-Niaki
- Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran.,Corresponding author: Cellular and Molecular Biology Research Center, Babol University of Medical Sciences, Babol, Iran. E-mail:
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Gallego Romero I, Pai AA, Tung J, Gilad Y. RNA-seq: impact of RNA degradation on transcript quantification. BMC Biol 2014; 12:42. [PMID: 24885439 PMCID: PMC4071332 DOI: 10.1186/1741-7007-12-42] [Citation(s) in RCA: 290] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 05/27/2014] [Indexed: 12/03/2022] Open
Abstract
Background The use of low quality RNA samples in whole-genome gene expression profiling remains controversial. It is unclear if transcript degradation in low quality RNA samples occurs uniformly, in which case the effects of degradation can be corrected via data normalization, or whether different transcripts are degraded at different rates, potentially biasing measurements of expression levels. This concern has rendered the use of low quality RNA samples in whole-genome expression profiling problematic. Yet, low quality samples (for example, samples collected in the course of fieldwork) are at times the sole means of addressing specific questions. Results We sought to quantify the impact of variation in RNA quality on estimates of gene expression levels based on RNA-seq data. To do so, we collected expression data from tissue samples that were allowed to decay for varying amounts of time prior to RNA extraction. The RNA samples we collected spanned the entire range of RNA Integrity Number (RIN) values (a metric commonly used to assess RNA quality). We observed widespread effects of RNA quality on measurements of gene expression levels, as well as a slight but significant loss of library complexity in more degraded samples. Conclusions While standard normalizations failed to account for the effects of degradation, we found that by explicitly controlling for the effects of RIN using a linear model framework we can correct for the majority of these effects. We conclude that in instances in which RIN and the effect of interest are not associated, this approach can help recover biologically meaningful signals in data from degraded RNA samples.
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Affiliation(s)
| | | | | | - Yoav Gilad
- Department of Human Genetics, University of Chicago, 920 E 58th St, CLSC 317, Chicago, IL 60637, USA.
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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.
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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.
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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,
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Mathot L, Wallin M, Sjöblom T. Automated serial extraction of DNA and RNA from biobanked tissue specimens. BMC Biotechnol 2013; 13:66. [PMID: 23957867 PMCID: PMC3751724 DOI: 10.1186/1472-6750-13-66] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2012] [Accepted: 08/15/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With increasing biobanking of biological samples, methods for large scale extraction of nucleic acids are in demand. The lack of such techniques designed for extraction from tissues results in a bottleneck in downstream genetic analyses, particularly in the field of cancer research. We have developed an automated procedure for tissue homogenization and extraction of DNA and RNA into separate fractions from the same frozen tissue specimen. A purpose developed magnetic bead based technology to serially extract both DNA and RNA from tissues was automated on a Tecan Freedom Evo robotic workstation. RESULTS 864 fresh-frozen human normal and tumor tissue samples from breast and colon were serially extracted in batches of 96 samples. Yields and quality of DNA and RNA were determined. The DNA was evaluated in several downstream analyses, and the stability of RNA was determined after 9 months of storage. The extracted DNA performed consistently well in processes including PCR-based STR analysis, HaloPlex selection and deep sequencing on an Illumina platform, and gene copy number analysis using microarrays. The RNA has performed well in RT-PCR analyses and maintains integrity upon storage. CONCLUSIONS The technology described here enables the processing of many tissue samples simultaneously with a high quality product and a time and cost reduction for the user. This reduces the sample preparation bottleneck in cancer research. The open automation format also enables integration with upstream and downstream devices for automated sample quantitation or storage.
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Affiliation(s)
- Lucy Mathot
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, SE-751 85, Uppsala, Sweden
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Barteneva NS, Ketman K, Fasler-Kan E, Potashnikova D, Vorobjev IA. Cell sorting in cancer research--diminishing degree of cell heterogeneity. Biochim Biophys Acta Rev Cancer 2013; 1836:105-22. [PMID: 23481260 DOI: 10.1016/j.bbcan.2013.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 12/18/2022]
Abstract
Increasing evidence of intratumor heterogeneity and its augmentation due to selective pressure of microenvironment and recent achievements in cancer therapeutics lead to the need to investigate and track the tumor subclonal structure. Cell sorting of heterogeneous subpopulations of tumor and tumor-associated cells has been a long established strategy in cancer research. Advancement in lasers, computer technology and optics has led to a new generation of flow cytometers and cell sorters capable of high-speed processing of single cell suspensions. Over the last several years cell sorting was used in combination with molecular biological methods, imaging and proteomics to characterize primary and metastatic cancer cell populations, minimal residual disease and single tumor cells. It was the principal method for identification and characterization of cancer stem cells. Analysis of single cancer cells may improve early detection of tumors, monitoring of circulating tumor cells, evaluation of intratumor heterogeneity and chemotherapeutic treatments. The aim of this review is to provide an overview of major cell sorting applications and approaches with new prospective developments such as microfluidics and microchip technologies.
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Affiliation(s)
- Natasha S Barteneva
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA.
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Bao WG, Zhang X, Zhang JG, Zhou WJ, Bi TN, Wang JC, Yan WH, Lin A. Biobanking of fresh-frozen human colon tissues: impact of tissue ex-vivo ischemia times and storage periods on RNA quality. Ann Surg Oncol 2012; 20:1737-44. [PMID: 22711177 DOI: 10.1245/s10434-012-2440-1] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 11/18/2022]
Abstract
BACKGROUND Biobanking plays an important role in translational cancer research. The impact of tissue ex-vivo ischemia time and storage period on RNA integrity is not well documented. METHODS Fresh-frozen colon tissues were collected in Taizhou Hospital of Zhejiang Province in China since 2004. Fifty-one colon cancer tissues with tumor cell content higher than 70 % and matched normal tissues during four storage periods (less than 15 months, 16-20 months, 21-25 months, and 26-40 months) were chosen to detect RNA quality. Fresh colon cancer tissues from 5 patients were cut into pieces and kept at room temperature or on ice for 0.5, 1, 2, and 4 h before snap freezing. RNA integrity was determined by microcapillary electrophoresis by the RNA integrity number (RIN) algorithm. RESULTS Sixty-seven percent of normal colon tissues and 94 % of colon cancer specimens yielded RNA with a RIN of ≥7. Matched colon cancer and normal tissues showed significant difference in RNA quality. RNA remained stable in colon cancer tissues kept at room temperature and on ice for up to 4 h, and long-term storage of banked colon specimens did not negatively influence RNA quality (RNA with RIN of ≥7 banked less than 15 months, 83 %; 16-20 months, 78 %; 21-25 months, 77 %; 26-40 months, 90 %). CONCLUSIONS Frozen colon tissues yield high-quality RNA in approximately 80 % of specimens. Ex-vivo ischemia times and storage periods did not adversely affect RNA quality. This study showed that standard operation protocols and the maintenance of high-quality tissue repositories were the keys to translational medicine research.
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Affiliation(s)
- Wei-Guang Bao
- Human Tissue Bank, Taizhou Hospital of Zhejiang Province, Wenzhou Medical College, Zhejiang, China
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Ma Y, Dai H, Kong X. Impact of warm ischemia on gene expression analysis in surgically removed biosamples. Anal Biochem 2012; 423:229-35. [DOI: 10.1016/j.ab.2012.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/15/2012] [Accepted: 02/03/2012] [Indexed: 02/01/2023]
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