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Shim SM, Lee M, Jeon JP. Assessment of the Impact of Preanalytical DNA Integrity on the Genome Data Quality. Biopreserv Biobank 2024. [PMID: 38563611 DOI: 10.1089/bio.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024] Open
Abstract
Many molecular approaches have been employed for the quality control (QC) of biobanked DNA samples. Since 2003, the National Biobank of Korea (NBK) has provided various studies with over half a million quality-controlled genomic DNA samples using conventional agarose gel electrophoresis and spectrophotometry. We assessed the postanalytical genomic data quality of DNA samples (n = 41) with a different range of the DNA quality index such as genomic quality number (GQN) for developing an evidence-based best practice for DNA quality criteria. We examined the quality indices of three different platforms, including single nucleotide polymorphism arrays, methylation arrays, and next-generation sequencing, using the same DNA samples (n = 41) of different quality, ranging from 4.0 to 10.0 values of the GQN. Our data analysis revealed that higher GQN value and/or double-stranded DNA concentration resulted in higher quality genomic data. In addition, all the analyzed DNA samples successfully generated good-quality genomic data. This study provides a guide for the QC of biobanked DNA samples for genomic analysis platforms.
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Affiliation(s)
- Sung-Mi Shim
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Meehee Lee
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
| | - Jae-Pil Jeon
- Division of Biobank, Department of Precision Medicine, Korea National Institute of Health, Cheongju-si, Republic of Korea
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2
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Shi X, Hu Z, Gan B, He Y, Zhang L, Chen M, Wang Y, Li X. Multivariate Evaluation of DNA Quality Differences in Different Preanalytical Procedures in Mouse Livers. Biopreserv Biobank 2023; 21:378-387. [PMID: 36067273 DOI: 10.1089/bio.2022.0027] [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: 11/13/2022] Open
Abstract
Successful histogenetic research relies on proper handling of tissue samples to maximize DNA quality. As the largest gland in the body, the liver is particularly sensitive to sample mishandling owing to its enzymatic and transcriptional activity. However, the impact of preanalytical procedures on the quality of extracted liver DNA remains poorly understood. In this study, we assessed the impact of extraction methods, duration of ex vivo liver ischemia, liver storage time, and temperature on extracted DNA quality. Comprehensive parameters such as DNA yields, purity, DNA integrity number, the percentage of double-stranded DNA (%dsDNA), and PCR amplification of the GAPDH gene fragment were assessed to identify the quality of extracted DNA. Our results revealed that these preanalytical processes had little effect on DIN values and PCR efficiency of GAPDH gene fragments for each sample, whereas the DNA yields, purity, and %dsDNAs varied widely across different processes. For liver DNA extraction, RNase is necessary to isolate "pure" DNA, and the presence of RNase could significantly increase the %dsDNA. In addition, significant increases in the yields, purity, and %dsDNA of extracted DNA were observed in the TissueLyser-processed livers compared with the mortar and pestle or shear cell disruption methods. Further investigation revealed that livers experiencing longer periods of ex vivo ischemia resulted in significantly compromised DNA yields, and to obtain sufficient DNA, the ex vivo liver ischemia should be limited to within 30 minutes. Moreover, compared with storage of livers at -80°C, storage of livers in the vapor phase of liquid nitrogen yielded a higher quality of the extracted DNA. Our findings exhibited significant implications for liver-derived DNA quality assessment and management.
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Affiliation(s)
- Xue Shi
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Zhenyue Hu
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Baoyu Gan
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yinlin He
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Linpei Zhang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Min Chen
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Yawen Wang
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
| | - Xiaojiao Li
- BioBank, The First Affiliated Hospital, Xi'an Jiaotong University, Shaanxi, China
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Kang S, Son Y, Shin IS, Moon C, Lee MY, Lim KS, Park SJ, Lee CG, Jo WS, Lee HJ, Kim JS. EFFECT OF ABDOMINAL IRRADIATION IN MICE MODEL OF INFLAMMATORY BOWEL DISEASE. RADIATION PROTECTION DOSIMETRY 2023; 199:564-571. [PMID: 36917812 DOI: 10.1093/rpd/ncad051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Inflammatory bowel diseases could be diagnosed in major measure by diagnostic imaging; however, radiation exposure in the intestine may also contribute to the progression of these pathologies. To better understand the impact of radiation in the presence of bowel disease, we administered dextran sodium sulfate (DSS) to C57BL/6 mice to induce colitis and exposed to radiation at abdominal area. We observed that abdominal irradiation (13 Gy) aggravates the DSS-induced decrease in survival rate (0%), body weight (74.54 ± 3.59%) and colon length (4.98 ± 0.14 cm). Additionally, abdominal irradiation markedly increased in colonic inflammation levels (3.16 ± 0.16) compared with that of DSS-induced sham mice. Furthermore, abdominal irradiation also increased the mRNA expression levels of inflammatory genes, such as cyclooxygenase-2 (13.10 folds), interleukin-6 (48.83 folds) and tumor necrosis factor-alpha (42.97 folds). We conclude that abdominal irradiation aggravates the detrimental effects of DSS-induced colitis in mice, which might be a useful guideline for inflammatory bowel disease patients.
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Affiliation(s)
- Sohi Kang
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, The Republic of Korea
| | - Yeonghoon Son
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, The Republic of Korea
| | - In-Sik Shin
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, The Republic of Korea
| | - Changjong Moon
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, The Republic of Korea
| | - Min Y Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Kyungpook National University, Daegu 41566, The Republic of Korea
| | - Kyung S Lim
- Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang 28116, Chungbuk, The Republic of Korea
| | - Su-Jin Park
- Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Ochang 28116, Chungbuk, The Republic of Korea
| | - Chang-Geun Lee
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan 46033, The Republic of Korea
| | - Wol S Jo
- Research Center, Dongnam Institute of Radiological & Medical Sciences, Busan 46033, The Republic of Korea
| | - Hae-June Lee
- Division of Radiation Biomedical Research, Korea Institute of Radiological & Medical Sciences, Seoul 01812, The Republic of Korea
| | - Joong S Kim
- College of Veterinary Medicine and BK21 FOUR Program, Chonnam National University, Gwangju 61186, The Republic of Korea
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Molecular characterization of low-grade serous ovarian carcinoma identifies genomic aberrations according to hormone receptor expression. NPJ Precis Oncol 2022; 6:47. [PMID: 35768582 PMCID: PMC9242985 DOI: 10.1038/s41698-022-00288-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 05/17/2022] [Indexed: 12/03/2022] Open
Abstract
Hormone receptor expression is a characteristic of low-grade serous ovarian carcinoma (LGSOC). Studies investigating estrogen receptor (ER) and progesterone receptor (PR) expression levels suggest its prognostic and predictive significance, although their associations with key molecular aberrations are not well understood. As such, we sought to describe the specific genomic profiles associated with different ER/PR expression patterns and survival outcomes in a cohort of patients with advanced disease. The study comprised fifty-five advanced-staged (III/IV) LGSOCs from the Canadian Ovarian Experimental Unified Resource (COEUR) for which targeted mutation sequencing, copy-number aberration, clinical and follow-up data were available. ER, PR, and p16 expression were assessed by immunohistochemistry. Tumors were divided into low and high ER/PR expression groups based on Allred scoring. Copy number analysis revealed that PR-low tumors (Allred score <2) had a higher fraction of the genome altered by copy number changes compared to PR-high tumors (p = 0.001), with cancer genes affected within specific loci linked to altered peptidyl-tyrosine kinase, MAP-kinase, and PI3-kinase signaling. Cox regression analysis showed that ER-high (p = 0.02), PR-high (p = 0.03), stage III disease (p = 0.02), low residual disease burden (p = 0.01) and normal p16 expression (p<0.001) were all significantly associated with improved overall survival. This study provides evidence that genomic aberrations are linked to ER/PR expression in primary LGSOC.
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Cunningham JM, Winham SJ, Wang C, Weiglt B, Fu Z, Armasu SM, McCauley BM, Brand AH, Chiew YE, Elishaev E, Gourley C, Kennedy CJ, Laslavic A, Lester J, Piskorz A, Sekowska M, Brenton JD, Churchman M, DeFazio A, Drapkin R, Elias KM, Huntsman DG, Karlan BY, Köbel M, Konner J, Lawrenson K, Papaemmanuil E, Bolton KL, Modugno F, Goode EL. DNA Methylation Profiles of Ovarian Clear Cell Carcinoma. Cancer Epidemiol Biomarkers Prev 2022; 31:132-141. [PMID: 34697060 PMCID: PMC8755592 DOI: 10.1158/1055-9965.epi-21-0677] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/18/2021] [Accepted: 10/21/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Ovarian clear cell carcinoma (OCCC) is a rare ovarian cancer histotype that tends to be resistant to standard platinum-based chemotherapeutics. We sought to better understand the role of DNA methylation in clinical and biological subclassification of OCCC. METHODS We interrogated genome-wide methylation using DNA from fresh frozen tumors from 271 cases, applied nonsmooth nonnegative matrix factorization (nsNMF) clustering, and evaluated clinical associations and biological pathways. RESULTS Two approximately equally sized clusters that associated with several clinical features were identified. Compared with Cluster 2 (N = 137), Cluster 1 cases (N = 134) presented at a more advanced stage, were less likely to be of Asian ancestry, and tended to have poorer outcomes including macroscopic residual disease following primary debulking surgery (P < 0.10). Subset analyses of targeted tumor sequencing and IHC data revealed that Cluster 1 tumors showed TP53 mutation and abnormal p53 expression, and Cluster 2 tumors showed aneuploidy and ARID1A/PIK3CA mutation (P < 0.05). Cluster-defining CpGs included 1,388 CpGs residing within 200 bp of the transcription start sites of 977 genes; 38% of these genes (N = 369 genes) were differentially expressed across cluster in transcriptomic subset analysis (P < 10-4). Differentially expressed genes were enriched for six immune-related pathways, including IFNα and IFNγ responses (P < 10-6). CONCLUSIONS DNA methylation clusters in OCCC correlate with disease features and gene expression patterns among immune pathways. IMPACT This work serves as a foundation for integrative analyses that better understand the complex biology of OCCC in an effort to improve potential for development of targeted therapeutics.
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Affiliation(s)
- Julie M Cunningham
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Chen Wang
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Britta Weiglt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zhuxuan Fu
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
| | - Sebastian M Armasu
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Bryan M McCauley
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
| | - Alison H Brand
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
| | - Yoke-Eng Chiew
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Esther Elishaev
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Charlie Gourley
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Catherine J Kennedy
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Angela Laslavic
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Jenny Lester
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Anna Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Magdalena Sekowska
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Michael Churchman
- Nicola Murray Centre for Ovarian Cancer Research, Cancer Research UK Edinburgh Centre, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - Anna DeFazio
- Department of Gynaecological Oncology, Westmead Hospital, Sydney, New South Wales, Australia
- University of Sydney, Sydney, New South Wales, Australia
- Centre for Cancer Research, The Westmead Institute for Medical Research, Sydney, New South Wales, Australia
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, Department of Obstetrics and Gynecology, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | | | - David G Huntsman
- British Columbia's Ovarian Cancer Research (OVCARE) Program, BC Cancer, Vancouver General Hospital, and University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Molecular Oncology, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Beth Y Karlan
- David Geffen School of Medicine, Department of Obstetrics and Gynecology, University of California at Los Angeles, Los Angeles, California
| | - Martin Köbel
- Department of Laboratory and Pathology Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Jason Konner
- Weill Cornell Medical College of Cornell University, New York, New York
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Kate Lawrenson
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Women's Cancer Program at the Samuel Oschin Cancer Institute Cedars-Sinai Medical Center, Los Angeles, California
| | - Elli Papaemmanuil
- Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelly L Bolton
- Department of Medicine, Washington University, St. Louis, Missouri
| | - Francesmary Modugno
- Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania
- Womens Cancer Research Center, Magee-Womens Research Institute and Hillman Cancer Center, Pittsburgh, Pennsylvania
- Division of Gynecologic Oncology, Department of Obstetrics, Gynecology and Reproductive Sciences, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ellen L Goode
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota
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Bagchi A, Madaj Z, Engel KB, Guan P, Rohrer DC, Valley DR, Wolfrum E, Feenstra K, Roche N, Hostetter G, Moore HM, Jewell SD. Impact of Preanalytical Factors on the Measurement of Tumor Tissue Biomarkers Using Immunohistochemistry. J Histochem Cytochem 2021; 69:297-320. [PMID: 33641490 PMCID: PMC8091543 DOI: 10.1369/0022155421995600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 01/28/2021] [Indexed: 12/26/2022] Open
Abstract
Analysis of formalin-fixed paraffin-embedded (FFPE) tissue by immunohistochemistry (IHC) is commonplace in clinical and research laboratories. However, reports suggest that IHC results can be compromised by biospecimen preanalytical factors. The National Cancer Institute's Biospecimen Preanalytical Variables Program conducted a systematic study to examine the potential effects of delay to fixation (DTF) and time in fixative (TIF) on IHC using 24 cancer biomarkers. Differences in IHC staining, relative to controls with a DTF of 1 hr, were observed in FFPE kidney tumor specimens after a DTF of ≥2 hr. Reductions in H-score and/or staining intensity were observed for c-MET, p53, PAX2, PAX8, pAKT, and survivin, whereas increases were observed for RCC1, EGFR, and CD10. Prolonged TIF of 72 hr resulted in significantly reduced H-scores of CD44 and c-Met in kidney tumor specimens, compared with controls with 12-hr TIF. An elevated probability of altered staining intensity due to DTF was observed for nine antigens, whereas for prolonged TIF an elevated probability was observed for one antigen. Results reported here and elsewhere across tumor types and antigens support limiting DTF to ≤1 hr when possible and fixing tissues in formalin for 12-24 hr to avoid confounding effects of these preanalytical factors on IHC.
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Affiliation(s)
- Aditi Bagchi
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
- Spectrum Health Helen DeVos Children’s Hospital, Grand Rapids, Michigan
- St. Jude Children’s Research Hospital, Memphis, Tennessee
| | - Zachary Madaj
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | | | - Ping Guan
- Biorepositories and Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland
| | | | | | - Emily Wolfrum
- Bioinformatics and Biostatistics Core, Van Andel Institute, Grand Rapids, Michigan
| | - Kristin Feenstra
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Nancy Roche
- Leidos Biomedical Research, Inc., Frederick, Maryland
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
| | - Helen M. Moore
- Biorepositories and Biospecimen Research Branch, National Cancer Institute, Bethesda, Maryland
| | - Scott D. Jewell
- Pathology and Biorepository Core, Van Andel Institute, Grand Rapids, Michigan
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Morocco's First Biobank: Establishment, Ethical Issues, Biomedical Research Opportunities, and Challenges. BIOMED RESEARCH INTERNATIONAL 2020; 2020:8812609. [PMID: 33376744 PMCID: PMC7738781 DOI: 10.1155/2020/8812609] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/15/2020] [Accepted: 11/18/2020] [Indexed: 02/07/2023]
Abstract
Background Biobanks are highly organized infrastructures that allow the storage of human biological specimens associated with donors' personal and clinical data. These infrastructures play a key role in the development of translational medical research. In this context, we launched, in November 2015, the first biobank in Morocco (BRO Biobank) in order to promote biomedical research and provide opportunities to include Moroccan and North African ethnic groups in international biomedical studies. Here, we present the setup and the sample characteristics of BRO Biobank. Methods Patients were recruited at several departments of two major health-care centers in the city of Oujda. Healthy donors were enrolled during blood donation campaigns all over Eastern Morocco. From each participant, personal, clinical, and biomedical data were collected, and several biospecimens were stored. Standard operating procedures have been established in accordance with international guidelines on human biobanks. Results Between November 2015 and July 2020, 2446 participants were recruited into the BRO Biobank, of whom 2013 were healthy donors, and 433 were patients. For healthy donors, the median age was 35 years with a range between 18 and 65 years and the consanguinity rate was 28.96%. For patients, the median age was 11 years with a range between 1 day and 83 years. Among these patients, 55% had rare diseases (hemoglobinopathies, intellectual disabilities, disorders of sex differentiation, myopathies, etc.), 13% had lung cancer, 4% suffered from hematological neoplasms, 3% were from the kidney transplantation project, and 25% had unknown diagnoses. The BRO Biobank has collected 5092 biospecimens, including blood, white blood cells, plasma, serum, urine, frozen tissue, FFPE tissue, and nucleic acids. A sample quality control has been implemented and suggested that samples of the BRO Biobank are of high quality and therefore suitable for high-throughput nucleic acid analysis. Conclusions The BRO Biobank is the largest sample collection in Morocco, and it is ready to provide samples to national and international research projects. Therefore, the BRO Biobank is a valuable resource for advancing translational medical research.
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8
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Cheasley D, Nigam A, Zethoven M, Hunter S, Etemadmoghadam D, Semple T, Allan P, Carey MS, Fernandez ML, Dawson A, Köbel M, Huntsman DG, Le Page C, Mes-Masson AM, Provencher D, Hacker N, Gao Y, Bowtell D, deFazio A, Gorringe KL, Campbell IG. Genomic analysis of low-grade serous ovarian carcinoma to identify key drivers and therapeutic vulnerabilities. J Pathol 2020; 253:41-54. [PMID: 32901952 DOI: 10.1002/path.5545] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 08/17/2020] [Accepted: 09/01/2020] [Indexed: 12/22/2022]
Abstract
Low-grade serous ovarian carcinoma (LGSOC) is associated with a poor response to existing chemotherapy, highlighting the need to perform comprehensive genomic analysis and identify new therapeutic vulnerabilities. The data presented here represent the largest genetic study of LGSOCs to date (n = 71), analysing 127 candidate genes derived from whole exome sequencing cohorts to generate mutation and copy-number variation data. Additionally, immunohistochemistry was performed on our LGSOC cohort assessing oestrogen receptor, progesterone receptor, TP53, and CDKN2A status. Targeted sequencing identified 47% of cases with mutations in key RAS/RAF pathway genes (KRAS, BRAF, and NRAS), as well as mutations in putative novel driver genes including USP9X (27%), MACF1 (11%), ARID1A (9%), NF2 (4%), DOT1L (6%), and ASH1L (4%). Immunohistochemistry evaluation revealed frequent oestrogen/progesterone receptor positivity (85%), along with CDKN2A protein loss (10%) and CDKN2A protein overexpression (6%), which were linked to shorter disease outcomes. Indeed, 90% of LGSOC samples harboured at least one potentially actionable alteration, which in 19/71 (27%) cases were predictive of clinical benefit from a standard treatment, either in another cancer's indication or in LGSOC specifically. In addition, we validated ubiquitin-specific protease 9X (USP9X), which is a chromosome X-linked substrate-specific deubiquitinase and tumour suppressor, as a relevant therapeutic target for LGSOC. Our comprehensive genomic study highlighted that there is an addiction to a limited number of unique 'driver' aberrations that could be translated into improved therapeutic paths. © 2020 The Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Dane Cheasley
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Abhimanyu Nigam
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Magnus Zethoven
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Bioinformatics Consulting Core, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sally Hunter
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Dariush Etemadmoghadam
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Timothy Semple
- Molecular Genomics Core, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Prue Allan
- Department of Clinical Pathology, Peter MacCallum Cancer Centre, and University of Melbourne, Melbourne, VIC, Australia
| | - Mark S Carey
- Department of Obstetrics & Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Marta L Fernandez
- Department of Obstetrics & Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Amy Dawson
- Department of Obstetrics & Gynaecology, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Cécile Le Page
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Diane Provencher
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, QC, Canada
| | - Neville Hacker
- Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Yunkai Gao
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - David Bowtell
- Cancer Genetics and Genomics Program, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Anna deFazio
- Centre for Cancer Research, The Westmead Institute for Medical Research, The University of Sydney and the Department of Gynaecological Oncology, Westmead Hospital, Sydney, NSW, Australia
| | - Kylie L Gorringe
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
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Chronic lymphocytic leukemia with TP53 gene alterations: a detailed clinicopathologic analysis. Mod Pathol 2020; 33:344-353. [PMID: 31477813 DOI: 10.1038/s41379-019-0356-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022]
Abstract
TP53 alteration in chronic lymphocytic leukemia indicates a high-risk disease that is usually refractory to chemotherapy. It may be caused by deletion of 17p involving the loss of TP53 gene, which occurs in low percentage of patients at diagnosis but can be acquired as the disease progresses. Since patients may harbor TP53 mutation without chromosome 17p deletion, consensus recommendations call for both cytogenetic and PCR mutation analysis of TP53 in chronic lymphocytic leukemia. We conducted a single-institution retrospective study to investigate the clinicopathologic features of chronic lymphocytic leukemia with TP53 alterations as well as the utility of different diagnostic modalities to identify p53 alterations. Forty percent of chronic lymphocytic leukemia patients with TP53 alterations demonstrated atypical lymphocytes with cleaved/irregularly shaped nuclei and/or large atypical lymphoid cells with abundant cytoplasm in the peripheral blood. Progression was also observed in lymph node and bone marrow samples (21% with Richter transformation; 33% with findings suggestive of "accelerated phase" of chronic lymphocytic leukemia including prominent proliferation centers and/or increased numbers of prolymphocytes). However, the presence of the morphologic features suggestive of "accelerated phase" had no effect on overall survival within the chronic lymphocytic leukemia group with TP53 abnormalities (p > 0.05). As previously reported by others, a subset of patients with TP53 alterations were only identified by either PCR mutation analysis (12%) or cytogenetic studies (14%). p53 immunostain positivity was only identified in approximately half of the patients with TP53 alterations identified by either method, and it failed to identify any additional patients with p53 abnormalities. In summary, chronic lymphocytic leukemia patients with TP53 alterations frequently show atypical morphologic features. Use of multiple modalities to identify p53 abnormalities is recommended to ensure optimal sensitivity and specificity.
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10
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Llaurado Fernandez M, Dawson A, Kim H, Lam N, Russell H, Bruce M, Bittner M, Hoenisch J, Scott SA, Talhouk A, Chiu D, Provencher D, Nourmoussavi M, DiMattia G, Lee CH, Gilks CB, Köbel M, Carey MS. Hormone receptor expression and outcomes in low-grade serous ovarian carcinoma. Gynecol Oncol 2020; 157:12-20. [PMID: 31954537 DOI: 10.1016/j.ygyno.2019.11.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 11/15/2019] [Accepted: 11/19/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Low-grade serous ovarian carcinomas (LGSC) are frequently ER/PR positive, though the mechanisms by which ER/PR regulate prognosis or anti-estrogen treatment efficacy are poorly understood. We studied ER/PR expression in LGSC tumors and cell lines to evaluate patient outcomes and cellular treatment responses. METHODS LGSC tumors and patient-derived cell lines were studied from patients with advanced-stage (III/IV) disease. Tumor samples and clinical data were obtained from the Canadian Ovarian Experimental Unified Resource (COEUR-tissue microarray) and the Ovarian Cancer Research (OvCaRe) tissue bank. ER/PR expression was assessed by both Western blot and immunohistochemistry (IHC). Two different IHC scoring systems (simple and Allred) were used. Cox regression was used to identify factors (age, disease residuum, ER/PR status, etc.) associated with progression-free (PFS) and overall survival (OS). Estradiol and tamoxifen proliferation and viability experiments were performed in LGSC cell lines. RESULTS In 55 LGSC cases studied, median follow-up was 56 months (range 1-227). Fifty-three (96%) cases strongly expressed ER whereas 37 (67%) expressed PR. Cox-regression analysis showed that residuum (p < 0.001) was significantly associated with PFS, whereas both ER Allred score (p = 0.005) and residuum (p = 0.004) were significant for OS. None of the LGSC cell lines expressed PR. Loss of PR and ER expression over time was detected in LGSC tumors and cell lines respectively. Estrogen and tamoxifen treatment did not alter LGSC cell proliferation or viability in-vitro. CONCLUSIONS In patients with advanced LGSC, higher ER Allred scores were significantly associated with better overall survival. ER/PR expression changed over time in both LGSC tumors and cell lines. Better translational research models are needed to elucidate the molecular mechanisms of ER/PR signalling in LGSC.
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Affiliation(s)
- Marta Llaurado Fernandez
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Amy Dawson
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Hannah Kim
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Nicole Lam
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Holly Russell
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Maegan Bruce
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Madison Bittner
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joshua Hoenisch
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Stephanie A Scott
- Department of Obstetrics and Gynecology, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Aline Talhouk
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Derek Chiu
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Diane Provencher
- Division of Gynecologic-Oncology, Centre Hospitalier de l'Université de Montréal (CHUM) and Centre de Recherche du CHUM, Montreal, Quebec, Canada.
| | - Melica Nourmoussavi
- Division of Gynecologic-Oncology, Centre Hospitalier de l'Université de Montréal (CHUM) and Centre de Recherche du CHUM, Montreal, Quebec, Canada
| | - Gabriel DiMattia
- Department of Oncology, University of Western Ontario, London, Ontario, Canada.
| | - Cheng-Han Lee
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - C Blake Gilks
- Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Alberta Public Lab, Calgary, Alberta, Canada.
| | - Mark S Carey
- Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, British Columbia, Canada.
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11
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Le Page C, Rahimi K, Rodrigues M, Heinzelmann-Schwarz V, Recio N, Tommasi S, Bataillon G, Portelance L, Golmard L, Meunier L, Tonin PN, Gotlieb W, Yasmeen A, Ray-Coquard I, Labidi-Galy SI, Provencher D, Mes-Masson AM. Clinicopathological features of women with epithelial ovarian cancer and double heterozygosity for BRCA1 and BRCA2: A systematic review and case report analysis. Gynecol Oncol 2019; 156:377-386. [PMID: 31753525 DOI: 10.1016/j.ygyno.2019.11.019] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/08/2019] [Accepted: 11/11/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND Carriers of pathogenic variants in both BRCA1 and BRCA2 genes as a double mutation (BRCA1/2 DM) have been rarely reported in women with epithelial ovarian cancer (EOC). METHODS We reviewed the English literature and interrogated three repositories reporting EOC patients carrying BRCA1/2 DM. The clinicopathological parameters of 36 EOC patients carrying germline BRCA1/2 DM were compared to high-grade serous EOC women of the COEUR cohort with known germline BRCA1/BRCA2 mutation carrier status (n = 376 non-carriers, n = 65 BRCA1 and n = 38 BRCA2). Clinicopathological parameters evaluated were age at diagnosis, stage of disease, loss of heterozygosity, type of mutation, immunohistochemistry profile, progression occurrence and survival. RESULTS Median age at diagnosis of BRCA1/2 DM patients was 51.9 years, similar to BRCA1 mutation carriers (49.7 years, p = .58) and younger than BRCA2 mutation carriers (58.1 years, p = .02). Most patients were diagnosed at advanced stage (III-IV; 82%) and were carriers of founder/frequent mutations (69%). Tissue immunostainings revealed no progesterone receptor expression and low intraepithelial inflammation. The 5-year survival rate (60%) was significantly lower than that of BRCA2 mutation carriers (76%, p = .03) but not of BRCA1 mutation carriers (51%, p = .37). CONCLUSIONS Our data suggests some co-dominant effect of both mutations but the outcome of these patients more closely resembled that of BRCA1 mutation carriers with poor prognosis factors.
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Affiliation(s)
- Cécile Le Page
- Centre de recherche du Centre hospitalier de l'Université de Montreal (CRCHUM), and Institut du cancer de Montréal, Montreal, QC, Canada.
| | - Kurosh Rahimi
- Centre de recherche du Centre hospitalier de l'Université de Montreal (CRCHUM), and Institut du cancer de Montréal, Montreal, QC, Canada; Department of Pathology, Centre hospitalier de l'Université de Montreal (CHUM), Montreal, QC, Canada
| | - Manuel Rodrigues
- Institut Curie, PSL Research University, Paris, France; Department of Medical Oncology, INSERM U830 "Cancer, heterogeneity, instability and plasticity", Paris, France
| | - Viola Heinzelmann-Schwarz
- Gynecological Cancer Centre and Ovarian Cancer Research Group, University Hospital Basel and Department of Biomedicine, Basel, Switzerland
| | - Neil Recio
- Departments of Human Genetics, McGill University; Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | - Guillaume Bataillon
- Institut Curie, PSL Research University, Paris, France; Department of Biopathology, Paris, France
| | - Lise Portelance
- Centre de recherche du Centre hospitalier de l'Université de Montreal (CRCHUM), and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Lisa Golmard
- Institut Curie, PSL Research University, Paris, France; Department of Genetics, Paris, France
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montreal (CRCHUM), and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Patricia N Tonin
- Departments of Human Genetics, McGill University; Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada; Department of Medicine, McGill University, Montreal, QC, Canada
| | - Walter Gotlieb
- Segal Cancer Center, Lady Davis Institute of Medical research, McGill University, Montreal, QC, Canada
| | - Amber Yasmeen
- Segal Cancer Center, Lady Davis Institute of Medical research, McGill University, Montreal, QC, Canada
| | | | - S Intidhar Labidi-Galy
- Department of Oncology, Hôpitaux Universitaires de Genève and Department of Medicine, Faculty of Medicine, Geneva, Switzerland
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montreal (CRCHUM), and Institut du cancer de Montréal, Montreal, QC, Canada; Division of Gynecology-Oncology, CHUM, QC, Canada; Department of Obstetrics and Gynecology, University of Montreal, Montreal, QC, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montreal (CRCHUM), and Institut du cancer de Montréal, Montreal, QC, Canada; Department of Medicine, University of Montreal, Montreal, QC, Canada.
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12
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Tang R, She Q, Lu Y, Yin R, Zhu P, Zhu L, Zhou M, Zheng C. Quality Control of RNA Extracted from PAXgene Blood RNA Tubes After Different Storage Periods. Biopreserv Biobank 2019; 17:477-482. [PMID: 31343263 DOI: 10.1089/bio.2019.0029] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Rong Tang
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Qinying She
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Yinghui Lu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ru Yin
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ping Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Ling Zhu
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Minlin Zhou
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
| | - Chunxia Zheng
- National Clinical Research Center of Kidney Diseases, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
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13
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Le Page C, Köbel M, Meunier L, Provencher DM, Mes-Masson AM, Rahimi K. A COEUR cohort study of SATB2 expression and its prognostic value in ovarian endometrioid carcinoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2019; 5:177-188. [PMID: 30924313 PMCID: PMC6648975 DOI: 10.1002/cjp2.131] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/08/2019] [Accepted: 03/25/2019] [Indexed: 12/16/2022]
Abstract
The aim of this study was to describe the expression of special AT-rich sequence-binding protein 2 (SATB2) in ovarian endometrioid carcinoma (EC). SATB2 is a nuclear matrix-associated transcription factor that is associated with abnormal expression in certain cancers but has not been reported for ovarian carcinoma. SATB2 mRNA and protein expression was first assessed in a pilot cohort of 26 samples by Affymetrix microarray and by routine immunohistochemistry on a small tissue microarray. A large multicenter validation cohort representing the well-characterized cases of 235 ovarian EC from the Canadian Ovarian Experimental Unified Resource (COEUR) was then used to validate this result and to assess the prognostic impact of SATB2 expression. SATB2 staining was scored as negative, weak, moderate, and strong intensity, and by percentage of stained cells. No SATB2 expression was observed in clear cell carcinomas but 10% (n = 3) of the ECs in the pilot cohort showed SATB2 expression. In the validation cohort, strong expression was observed in 11% of ECs, while weak or moderate expression levels were detected in 12% of cases. Evaluation of SATB2 expression with clinicopathological parameters revealed an association with patient age and Federation International of Gynecology and Obstetrics grade but not with disease stage or postoperative residual disease. Any expression of SATB2, independent of intensity, was also associated with longer survival and improved progression-free survival with hazard ratio (HR) = 0.14 (95% CI 0.03-0.56) and HR = 0.16 (95% CI 0.02-1.24) respectively. A greater beneficial effect was observed in patients with stage III/IV disease compared to patients with stage I/II disease. Furthermore, direct comparison of SATB2 with other reported prognostic biomarkers such as progesterone receptor, CDX2 and β-catenin within this cohort showed that SATB2 had the strongest association with survival. Given the current lack of accurate prognostic factors for these patients, SATB2 has promising clinical utility and warrants further study.
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Affiliation(s)
- Cécile Le Page
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, Canada
| | - Liliane Meunier
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, Canada
| | - Diane M Provencher
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, Canada.,Division of Gynecologic-Oncology, CHUM, Montreal, Canada
| | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, Canada.,Department of Medicine, Université de Montréal, Montreal, Canada
| | - Kurosh Rahimi
- Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM) and Institut du Cancer de Montréal, Montreal, Canada.,Department of Pathology, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Canada
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14
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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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15
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Richards J, Unger ER, Rajeevan MS. Simultaneous extraction of mRNA and microRNA from whole blood stabilized in tempus tubes. BMC Res Notes 2019; 12:39. [PMID: 30658701 PMCID: PMC6339331 DOI: 10.1186/s13104-019-4087-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 01/14/2019] [Indexed: 11/22/2022] Open
Abstract
Objective Studies of mRNA and miRNA expression profiling increasingly use stabilized whole blood. Commercial RNA extraction kits do not provide information about the simultaneous recovery of both mRNA and miRNA. This study evaluated yield, quality, integrity and representation of mRNA and miRNA from whole blood stabilized in Tempus tubes using three RNA extraction kits; two filter-based (Tempus and Norgen) and one bead-based (MagMax; manual vs. semi-automated, and with and without DNase treatment). Results All RNA extraction kits and methods resulted in similar yields of mRNA (total RNA yield, quality, integrity and representation) whereas there were differences in yields of miRNA. MagMax, either manual or semi-automated, with or without DNase treatment, yielded 1.6–2.2-fold more miRNA than Tempus and Norgen kits. In addition, MagMax and Norgen methods gave greater than 12-fold more and 3.3-fold less enrichment of specific miRNA targets, respectively, in comparison to Tempus extraction reagents. This study identified MagMax kit for simultaneous recovery of both mRNA and miRNA from whole blood collected in Tempus tubes.
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Affiliation(s)
- Jendai Richards
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Elizabeth R Unger
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA
| | - Mangalathu S Rajeevan
- Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, 1600 Clifton Road, Atlanta, GA, 30329, USA.
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16
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Liu Y, Gao H, Hu Y, Ding J, Ge M, Ye Q. Quality Control System in an Obstetrics and Gynecology Disease Biobank. Biopreserv Biobank 2018; 17:27-38. [PMID: 30299984 DOI: 10.1089/bio.2018.0056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
AIM To ensure that sample quality meets the requirements of experimental research, the gynecology and obstetrics biobank of the Nanjing Drum Tower hospital designed different quality control methods for relevant types of samples. A range of quality control procedures has been formulated. METHODS The sample types were frozen tissue, paraffin-embedded tissue, optimal cutting temperature (OCT)-embedded tissue, plasma, buffy coat, serum, blood clots, and urine. Different categories of samples from a random selection of 1% of cases were analyzed for quality control experiments: (i) frozen tissue, buffy coat, and blood clots: RNA and DNA were extracted and the concentration, purity, and integrity were determined; (ii) paraffin-embedded tissue: morphological observations were made after hematoxylin-eosin staining and immunohistochemical detection of β-actin or CD10; (iii) OCT-embedded tissue: hematoxylin-eosin staining and immunofluorescence detection of β-actin; and (iv) frozen tissue samples derived from different organs of 18 fetal autopsy specimens with different cold ischemia times (CITs), 0-12 hours, 12-18 hours, 18-24 hours, and 24-48 hours, were chosen to study RNA quality. There is no universally recognized quality control index for plasma, serum, and urine, so the quality of samples was evaluated from feedback from the research projects in which the samples were used. RESULTS Currently, there are ∼2000 cases and 360,000 sample vials in the biobank. According to the experiments, (i) the concentration and purity of all nucleic acids of selected samples were qualified; (ii) for frozen tissues with a CIT ≤1 hour, using a qualified standard RNA quality number (RQN) ≥7, the qualification rate was 90%; (iii) frozen tissues with CIT between 1 and 18 hours, using a qualified standard RQN ≥5, the qualification rate was 61.1%; (iv) all of the paraffin-embedded tissues qualified for morphological observation; (v) the qualification rate of OCT-embedded tissue was 89%; and (vi) CIT had a great influence on the integrity of frozen tissue RNA. As the tissue CIT lengthened, the integrity of the RNA decreased. The RNA integrity parameters of different tissue types in the same specimen were significantly different. CONCLUSIONS A quality control system was constructed in an obstetrics and gynecology disease biobank with various types of diseases and abundant samples. Using specific quality control experiments for different types of samples was a reliable operating strategy that can be beneficial for providing qualified research resources. For birth defect autopsy specimens, the samples used for RNA research should have a CIT of at least <12 hours.
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Affiliation(s)
- Yanhong Liu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Hong Gao
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Yue Hu
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Jie Ding
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Meiling Ge
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
| | - Qing Ye
- 1 Department of Pathology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,2 Biobank of Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing, China.,3 Jiangsu Biobank of Clinical Resources, Biobank of Obstetrics and Gynecology Disease, Nanjing, China.,4 Nanjing Multi-Center Biobank, Nanjing Health and Family Planning Commission, Nanjing, China
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17
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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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Le Page C, Rahimi K, Köbel M, Tonin PN, Meunier L, Portelance L, Bernard M, Nelson BH, Bernardini MQ, Bartlett JMS, Bachvarov D, Gotlieb WH, Gilks B, McAlpine JN, Nachtigal MW, Piché A, Watson PH, Vanderhyden B, Huntsman DG, Provencher DM, Mes-Masson AM. Characteristics and outcome of the COEUR Canadian validation cohort for ovarian cancer biomarkers. BMC Cancer 2018. [PMID: 29587661 DOI: 10.1186/s12885-018-4242-8] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023] Open
Abstract
BACKGROUND Ovarian carcinoma is the most lethal gynecological malignancy due to early dissemination and acquired resistance to platinum-based chemotherapy. Reliable markers that are independent and complementary to clinical parameters are needed to improve the management of patients with this disease. The Canadian Ovarian Experimental Unified Resource (COEUR) provides researchers with biological material and associated clinical data to conduct biomarker validation studies. Using standards defined by the Canadian Tissue Repository Network (CTRNet), we have previously demonstrated the quality of the biological material from this resource. Here we describe the clinical characteristics of the COEUR cohort. METHODS With support from 12 Canadian ovarian cancer biobanks in Canada, we created a central retrospective cohort comprised of more than 2000 patient tissue samples with associated clinical data, including 1246 high-grade serous, 102 low-grade serous, 295 endometrioid, 259 clear cell and 89 mucinous carcinoma histotypes. A two-step reclassification process was applied to assure contemporary histological classification (histotyping). For each histotypes individually, we evaluated the association between the known clinico-pathological parameters (stage, cytoreduction, chemotherapy treatment, BRCA1 and BRCA2 mutation) and patient outcome by using Kaplan-Meier and Cox proportional hazard regression analyses. RESULTS The median follow-up time of the cohort was 45 months and the 5-year survival rate for patients with high-grade serous carcinomas was 34%, in contrast to endometrioid carcinomas with 80% at 5 years. Survival profiles differed by histotype when stratified by stage or cytoreduction. Women with mucinous or clear cell carcinomas at advanced stage or with non-optimally debulked disease had the worst outcomes. In high-grade serous carcinoma, we observed significant association with longer survival in women harboring BRCA1 or BRCA2 mutation as compared to patients without detectable mutation. CONCLUSIONS Our results show the expected survival rates, as compared with current literature, in each histotype suggesting that the cohort is an unbiased representation of the five major histotypes. COEUR, a one stop comprehensive biorepository, has collected mature outcome data and relevant clinical data in a comprehensive manner allowing stratified analysis.
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Affiliation(s)
- Cécile Le Page
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Kurosh Rahimi
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada.,Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory of Medicine, University of Calgary, Calgary, AB, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University; Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Lise Portelance
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Monique Bernard
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Brad H Nelson
- Tumour Tissue Repository, Trev and Joyce Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada
| | - Marcus Q Bernardini
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - John M S Bartlett
- Diagnostic Development and Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Walter H Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Blake Gilks
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
| | - Jessica N McAlpine
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Mark W Nachtigal
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Alain Piché
- Centre de Recherche du CHUS. Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Canada
| | - Peter H Watson
- Tumour Tissue Repository, Trev and Joyce Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada
| | - Barbara Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - David G Huntsman
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
| | - Diane M Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada. .,Department of Medicine, Université de Montréal, Montreal, Canada. .,, 900 rue Saint Denis, Tour R, Montreal, H2X2A0, Canada.
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19
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Le Page C, Rahimi K, Köbel M, Tonin PN, Meunier L, Portelance L, Bernard M, Nelson BH, Bernardini MQ, Bartlett JMS, Bachvarov D, Gotlieb WH, Gilks B, McAlpine JN, Nachtigal MW, Piché A, Watson PH, Vanderhyden B, Huntsman DG, Provencher DM, Mes-Masson AM. Characteristics and outcome of the COEUR Canadian validation cohort for ovarian cancer biomarkers. BMC Cancer 2018; 18:347. [PMID: 29587661 PMCID: PMC5872529 DOI: 10.1186/s12885-018-4242-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 03/16/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Ovarian carcinoma is the most lethal gynecological malignancy due to early dissemination and acquired resistance to platinum-based chemotherapy. Reliable markers that are independent and complementary to clinical parameters are needed to improve the management of patients with this disease. The Canadian Ovarian Experimental Unified Resource (COEUR) provides researchers with biological material and associated clinical data to conduct biomarker validation studies. Using standards defined by the Canadian Tissue Repository Network (CTRNet), we have previously demonstrated the quality of the biological material from this resource. Here we describe the clinical characteristics of the COEUR cohort. METHODS With support from 12 Canadian ovarian cancer biobanks in Canada, we created a central retrospective cohort comprised of more than 2000 patient tissue samples with associated clinical data, including 1246 high-grade serous, 102 low-grade serous, 295 endometrioid, 259 clear cell and 89 mucinous carcinoma histotypes. A two-step reclassification process was applied to assure contemporary histological classification (histotyping). For each histotypes individually, we evaluated the association between the known clinico-pathological parameters (stage, cytoreduction, chemotherapy treatment, BRCA1 and BRCA2 mutation) and patient outcome by using Kaplan-Meier and Cox proportional hazard regression analyses. RESULTS The median follow-up time of the cohort was 45 months and the 5-year survival rate for patients with high-grade serous carcinomas was 34%, in contrast to endometrioid carcinomas with 80% at 5 years. Survival profiles differed by histotype when stratified by stage or cytoreduction. Women with mucinous or clear cell carcinomas at advanced stage or with non-optimally debulked disease had the worst outcomes. In high-grade serous carcinoma, we observed significant association with longer survival in women harboring BRCA1 or BRCA2 mutation as compared to patients without detectable mutation. CONCLUSIONS Our results show the expected survival rates, as compared with current literature, in each histotype suggesting that the cohort is an unbiased representation of the five major histotypes. COEUR, a one stop comprehensive biorepository, has collected mature outcome data and relevant clinical data in a comprehensive manner allowing stratified analysis.
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Affiliation(s)
- Cécile Le Page
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Kurosh Rahimi
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada.,Department of Pathology du Centre hospitalier de l'Université de Montréal, Montreal, QC, Canada
| | - Martin Köbel
- Department of Pathology and Laboratory of Medicine, University of Calgary, Calgary, AB, Canada
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University; Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Lise Portelance
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Monique Bernard
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada
| | - Brad H Nelson
- Tumour Tissue Repository, Trev and Joyce Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada
| | - Marcus Q Bernardini
- Department of Obstetrics and Gynaecology, University of Toronto, Toronto, ON, Canada
| | - John M S Bartlett
- Diagnostic Development and Ontario Tumour Bank, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | | | - Walter H Gotlieb
- Laboratory of Gynecologic Oncology, Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Blake Gilks
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
| | - Jessica N McAlpine
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada
| | - Mark W Nachtigal
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB, Canada
| | - Alain Piché
- Centre de Recherche du CHUS. Département de Microbiologie et Infectiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Canada
| | - Peter H Watson
- Tumour Tissue Repository, Trev and Joyce Deeley Research Centre, BC Cancer Agency, Victoria, BC, Canada
| | - Barbara Vanderhyden
- Cancer Therapeutics Program, Ottawa Hospital Research Institute, Ottawa, Canada.,Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, Canada
| | - David G Huntsman
- Department of Pathology, Vancouver General Hospital and University of British Columbia, Vancouver, BC, Canada.,Department of Obstetrics and Gynaecology, University of British Columbia, Vancouver, BC, Canada
| | - Diane M Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM) and Institut du cancer de Montréal, Montreal, QC, Canada. .,Department of Medicine, Université de Montréal, Montreal, Canada. .,, 900 rue Saint Denis, Tour R, Montreal, H2X2A0, Canada.
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Characteristics and outcome of the COEUR Canadian validation cohort for ovarian cancer biomarkers. BMC Cancer 2018. [PMID: 29587661 DOI: 10.1186/s12885-018-4242-8]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Ovarian carcinoma is the most lethal gynecological malignancy due to early dissemination and acquired resistance to platinum-based chemotherapy. Reliable markers that are independent and complementary to clinical parameters are needed to improve the management of patients with this disease. The Canadian Ovarian Experimental Unified Resource (COEUR) provides researchers with biological material and associated clinical data to conduct biomarker validation studies. Using standards defined by the Canadian Tissue Repository Network (CTRNet), we have previously demonstrated the quality of the biological material from this resource. Here we describe the clinical characteristics of the COEUR cohort. METHODS With support from 12 Canadian ovarian cancer biobanks in Canada, we created a central retrospective cohort comprised of more than 2000 patient tissue samples with associated clinical data, including 1246 high-grade serous, 102 low-grade serous, 295 endometrioid, 259 clear cell and 89 mucinous carcinoma histotypes. A two-step reclassification process was applied to assure contemporary histological classification (histotyping). For each histotypes individually, we evaluated the association between the known clinico-pathological parameters (stage, cytoreduction, chemotherapy treatment, BRCA1 and BRCA2 mutation) and patient outcome by using Kaplan-Meier and Cox proportional hazard regression analyses. RESULTS The median follow-up time of the cohort was 45 months and the 5-year survival rate for patients with high-grade serous carcinomas was 34%, in contrast to endometrioid carcinomas with 80% at 5 years. Survival profiles differed by histotype when stratified by stage or cytoreduction. Women with mucinous or clear cell carcinomas at advanced stage or with non-optimally debulked disease had the worst outcomes. In high-grade serous carcinoma, we observed significant association with longer survival in women harboring BRCA1 or BRCA2 mutation as compared to patients without detectable mutation. CONCLUSIONS Our results show the expected survival rates, as compared with current literature, in each histotype suggesting that the cohort is an unbiased representation of the five major histotypes. COEUR, a one stop comprehensive biorepository, has collected mature outcome data and relevant clinical data in a comprehensive manner allowing stratified analysis.
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21
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Application of ribonucleoside vanadyl complex (RVC) for developing a multifunctional tissue preservative solution. PLoS One 2018. [PMID: 29538436 PMCID: PMC5851642 DOI: 10.1371/journal.pone.0194393] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The quality of biological samples greatly affects the accuracy of scientific results. However, RNA in cryopreserved tissues gradually degrades during storage, leading to errors in the results of subsequent experiments. A suitable sample preservative solution can prolong storage and enhance the research value of samples. Here, we developed a sample preservative solution using the properties of the ribonucleoside vanadyl complex (RVC) and compared its effects on RNA and DNA quality, protein activity, and tissue morphology with the commercially available and widely used RNAlater® Stabilization Solution. The results showed that both the RVC-based preservative solution and RNAlater can effectively delay RNA degradation in tissue samples stored at 4°C or −80°C compared with samples stored without any preservative solution. In contrast to RNAlater, the RVC-based preservative solution did not result in damage to the tissue morphology or a loss of protein activity. Additionally, the RVC-based preservative solution did not affect the RNA and genomic DNA contents of the tissue samples or the results of subsequent experimental analyses. An RVC-based reagent can be used as a multifunctional yet relatively inexpensive tissue preservative solution to provide a comprehensive and cost-effective method for preserving samples for tissue banks.
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Kong F, Zhang W, Qiao L, Li Q, Li H, Cao J, He W, Dong C, He Y, He L, Liu L, Fu W, Liu L, Li Z, Wang Y. Establishment and quality evaluation of a glioma biobank in Beijing Tiantan Hospital. PeerJ 2018; 6:e4450. [PMID: 29576945 PMCID: PMC5855883 DOI: 10.7717/peerj.4450] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/13/2018] [Indexed: 01/01/2023] Open
Abstract
Background We established a glioma biobank at Beijing Tiantan Hospital in November, 2010. Specialized residents have been trained to collect, store and manage the biobank in accordance with standard operating procedures. Methods One hundred samples were selected to evaluate the quality of glioma samples stored in the liquid nitrogen tank during different periods (from 2011 to 2015) by morphological examination, RNA integrity determination, DNA integrity determination and housekeeping gene expression determination. Results The majority of samples (95%) had high RNA quality for further analysis with RIN ≥6. Quality of DNA of all samples were stable without significant degradation. Conclusion Storage conditions of our biobank are suitable for long-term (at least five years) sample preservation with high molecular quality.
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Affiliation(s)
- Fanhong Kong
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenli Zhang
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lin Qiao
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Qi Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Haowen Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jingli Cao
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wenyan He
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Chengya Dong
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yanjiao He
- Neuropathological department, Beijing Neurosugical Institute, Capital Medical University, Beijing, China
| | - Lu He
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Li Liu
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Weilun Fu
- Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Lijun Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zirui Li
- Clinical Medical Research Laboratory, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yajie Wang
- Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
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Calibration and Optimization of p53, WT1, and Napsin A Immunohistochemistry Ancillary Tests for Histotyping of Ovarian Carcinoma: Canadian Immunohistochemistry Quality Control (CIQC) Experience. Int J Gynecol Pathol 2017; 35:209-21. [PMID: 26598982 DOI: 10.1097/pgp.0000000000000251] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The Canadian Immunohistochemistry Quality Control provides proficiency testing for immunohistochemistry in Canadian laboratories. Canadian Immunohistochemistry Quality Control Run 42 assessed WT1, Napsin A, and p53; commonly used markers for histotyping ovarian carcinomas. A 42-core tissue microarray, which included the 5 major histotypes of ovarian carcinomas with a subset having known TP53 mutational status, was used for this Canadian Immunohistochemistry Quality Control challenge. Participants included 43 laboratories for p53, 29 for WT1, and 26 for Napsin A. p53 was scored as aberrant if the staining was strong and diffuse or absent. Napsin A and WT1 were scored positive if any tumor cells stained. The reference p53 expression pattern was inferred by TP53 mutation type when available. For WT1, Napsin A, and cases lacking mutational data, the reference staining pattern was based on the majority staining result. The error rate for p53 was 8.8%. Most errors (84%) were due to weak staining. The sensitivity and specificity of aberrant p53 expression for an underlying TP53 mutation was 91.6% and 87.9%, respectively. The error rate for WT1 was 0.76% with all errors occurring in laboratories using the 6F-h2 clone. The average errors for laboratories using 6F-h2 were 2.4 compared with 0 for WT-49. The error rate for Napsin A was 4%. The average errors for laboratories using polyclonal Napsin A were 3 compared with 1.1 for monoclonal Napsin A. Weak p53 staining increases interpretative errors, primarily due to absence of staining in tumors with wild-type TP53. p53 immunohistochemistry correlates strongly with TP53 mutational status. Polyclonal Napsin A and 6F-h2 may lack specificity in comparison to monoclonal Napsin A and WT-49.
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Abstract
There are 5 major histotypes of ovarian carcinomas. Diagnostic typing criteria have evolved over time, and past cohorts may be misclassified by current standards. Our objective was to reclassify the recently assembled Canadian Ovarian Experimental Unified Resource and the Alberta Ovarian Tumor Type cohorts using immunohistochemical (IHC) biomarkers and to develop an IHC algorithm for ovarian carcinoma histotyping. A total of 1626 ovarian carcinoma samples from the Canadian Ovarian Experimental Unified Resource and the Alberta Ovarian Tumor Type were subjected to a reclassification by comparing the original with the predicted histotype. Histotype prediction was derived from a nominal logistic regression modeling using a previously reclassified cohort (N=784) with the binary input of 8 IHC markers. Cases with discordant original or predicted histotypes were subjected to arbitration. After reclassification, 1762 cases from all cohorts were subjected to prediction models (χ Automatic Interaction Detection, recursive partitioning, and nominal logistic regression) with a variable IHC marker input. The histologic type was confirmed in 1521/1626 (93.5%) cases of the Canadian Ovarian Experimental Unified Resource and the Alberta Ovarian Tumor Type cohorts. The highest misclassification occurred in the endometrioid type, where most of the changes involved reclassification from endometrioid to high-grade serous carcinoma, which was additionally supported by mutational data and outcome. Using the reclassified histotype as the endpoint, a 4-marker prediction model correctly classified 88%, a 6-marker 91%, and an 8-marker 93% of the 1762 cases. This study provides statistically validated, inexpensive IHC algorithms, which have versatile applications in research, clinical practice, and clinical trials.
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Barnes RO, Shea KE, Watson PH. The Canadian Tissue Repository Network Biobank Certification and the College of American Pathologists Biorepository Accreditation Programs: Two Strategies for Knowledge Dissemination in Biobanking. Biopreserv Biobank 2017; 15:9-16. [DOI: 10.1089/bio.2016.0021] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Rebecca O. Barnes
- Canadian Tissue Repository Network, Vancouver, British Columbia, Canada
| | - Katheryn E. Shea
- Global Operations, BioStorage Technologies, Indianapolis, Indiana
| | - Peter H. Watson
- Canadian Tissue Repository Network, Vancouver, British Columbia, Canada
- Tumour Tissue Repository BC Cancer Agency, Victoria, British Columbia, Canada
- Office of Biobank Education and Research, Department of Pathology, University of British Columbia, Vancouver, British Columbia, Canada
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Köbel M, Piskorz AM, Lee S, Lui S, LePage C, Marass F, Rosenfeld N, Mes Masson AM, Brenton JD. Optimized p53 immunohistochemistry is an accurate predictor of TP53 mutation in ovarian carcinoma. JOURNAL OF PATHOLOGY CLINICAL RESEARCH 2016. [PMID: 27840695 DOI: 10.1002/cjp2.53] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
TP53 mutations are ubiquitous in high-grade serous ovarian carcinomas (HGSOC), and the presence of TP53 mutation discriminates between high and low-grade serous carcinomas and is now an important biomarker for clinical trials targeting mutant p53. p53 immunohistochemistry (IHC) is widely used as a surrogate for TP53 mutation but its accuracy has not been established. The objective of this study was to test whether improved methods for p53 IHC could reliably predict TP53 mutations independently identified by next generation sequencing (NGS). Four clinical p53 IHC assays and tagged-amplicon NGS for TP53 were performed on 171 HGSOC and 80 endometrioid carcinomas (EC). p53 expression was scored as overexpression (OE), complete absence (CA), cytoplasmic (CY) or wild type (WT). p53 IHC was evaluated as a binary classifier where any abnormal staining predicted deleterious TP53 mutation and as a ternary classifier where OE, CA or WT staining predicted gain-of-function (GOF or nonsynonymous), loss-of-function (LOF including stopgain, indel, splicing) or no detectable TP53 mutations (NDM), respectively. Deleterious TP53 mutations were detected in 169/171 (99%) HGSOC and 7/80 (8.8%) EC. The overall accuracy for the best performing IHC assay for binary and ternary prediction was 0.94 and 0.91 respectively, which improved to 0.97 (sensitivity 0.96, specificity 1.00) and 0.95 after secondary analysis of discordant cases. The sensitivity for predicting LOF mutations was lower at 0.76 because p53 IHC detected mutant p53 protein in 13 HGSOC with LOF mutations. CY staining associated with LOF was seen in 4 (2.3%) of HGSOC. Optimized p53 IHC can approach 100% specificity for the presence of TP53 mutation and its high negative predictive value is clinically useful as it can exclude the possibility of a low-grade serous tumour. 4.1% of HGSOC cases have detectable WT staining while harboring a TP53 LOF mutation, which limits sensitivity for binary prediction of mutation to 96%.
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Affiliation(s)
- Martin Köbel
- Department of Pathology and Laboratory Medicine University of Calgary Calgary AB Canada
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre Cambridge CB2 0RE UK
| | - Sandra Lee
- Department of Pathology and Laboratory Medicine University of Calgary Calgary AB Canada
| | - Shuhong Lui
- Department of Pathology and Laboratory Medicine University of Calgary Calgary AB Canada
| | - Cecile LePage
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM)MontrealQCCanada; Institut du cancer de Montréal, MontrealQCCanada
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre Cambridge CB2 0RE UK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre Cambridge CB2 0RE UK
| | - Anne-Marie Mes Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM)MontrealQCCanada; Institut du cancer de Montréal, MontrealQCCanada
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre Cambridge CB2 0RE UK
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Köbel M, Piskorz AM, Lee S, Lui S, LePage C, Marass F, Rosenfeld N, Mes Masson A, Brenton JD. Optimized p53 immunohistochemistry is an accurate predictor of TP53 mutation in ovarian carcinoma. J Pathol Clin Res 2016; 2:247-258. [PMID: 27840695 PMCID: PMC5091634 DOI: 10.1002/cjp2.53] [Citation(s) in RCA: 262] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 06/02/2016] [Indexed: 12/21/2022]
Abstract
TP53 mutations are ubiquitous in high-grade serous ovarian carcinomas (HGSOC), and the presence of TP53 mutation discriminates between high and low-grade serous carcinomas and is now an important biomarker for clinical trials targeting mutant p53. p53 immunohistochemistry (IHC) is widely used as a surrogate for TP53 mutation but its accuracy has not been established. The objective of this study was to test whether improved methods for p53 IHC could reliably predict TP53 mutations independently identified by next generation sequencing (NGS). Four clinical p53 IHC assays and tagged-amplicon NGS for TP53 were performed on 171 HGSOC and 80 endometrioid carcinomas (EC). p53 expression was scored as overexpression (OE), complete absence (CA), cytoplasmic (CY) or wild type (WT). p53 IHC was evaluated as a binary classifier where any abnormal staining predicted deleterious TP53 mutation and as a ternary classifier where OE, CA or WT staining predicted gain-of-function (GOF or nonsynonymous), loss-of-function (LOF including stopgain, indel, splicing) or no detectable TP53 mutations (NDM), respectively. Deleterious TP53 mutations were detected in 169/171 (99%) HGSOC and 7/80 (8.8%) EC. The overall accuracy for the best performing IHC assay for binary and ternary prediction was 0.94 and 0.91 respectively, which improved to 0.97 (sensitivity 0.96, specificity 1.00) and 0.95 after secondary analysis of discordant cases. The sensitivity for predicting LOF mutations was lower at 0.76 because p53 IHC detected mutant p53 protein in 13 HGSOC with LOF mutations. CY staining associated with LOF was seen in 4 (2.3%) of HGSOC. Optimized p53 IHC can approach 100% specificity for the presence of TP53 mutation and its high negative predictive value is clinically useful as it can exclude the possibility of a low-grade serous tumour. 4.1% of HGSOC cases have detectable WT staining while harboring a TP53 LOF mutation, which limits sensitivity for binary prediction of mutation to 96%.
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Affiliation(s)
- Martin Köbel
- Department of Pathology and Laboratory MedicineUniversity of CalgaryCalgaryABCanada
| | - Anna M Piskorz
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeCB2 0REUK
| | - Sandra Lee
- Department of Pathology and Laboratory MedicineUniversity of CalgaryCalgaryABCanada
| | - Shuhong Lui
- Department of Pathology and Laboratory MedicineUniversity of CalgaryCalgaryABCanada
| | - Cecile LePage
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM)MontrealQCCanada
- Institut du cancer de Montréal, MontrealQCCanada
| | - Francesco Marass
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeCB2 0REUK
| | - Nitzan Rosenfeld
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeCB2 0REUK
| | - Anne‐Marie Mes Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal (CRCHUM)MontrealQCCanada
- Institut du cancer de Montréal, MontrealQCCanada
| | - James D Brenton
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing CentreCambridgeCB2 0REUK
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Simeon-Dubach D, Zeisberger SM, Hoerstrup SP. Quality Assurance in Biobanking for Pre-Clinical Research. Transfus Med Hemother 2016; 43:353-357. [PMID: 27781023 DOI: 10.1159/000448254] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/04/2016] [Indexed: 12/29/2022] Open
Abstract
It is estimated that not less than USD 28 billion are spent each year in the USA alone on irreproducible pre-clinical research, which is not only a fundamental loss of investment and resources but also a strong inhibitor of efficiency for upstream processes regarding the translation towards clinical applications and therapies. The issues and cost of irreproducibility has mainly been published on pre-clinical research. In contrast to pre-clinical research, test material is often being transferred into humans in clinical research. To protect treated human subjects and guarantee a defined quality standard in the field of clinical research, the manufacturing and processing infrastructures have to strictly follow and adhere to certain (inter-)national quality standards. It is assumed and suggested by the authors that by an implementation of certain quality standards within the area of pre-clinical research, billions of USD might be saved and the translation phase of promising pre-clinical results towards clinical applications may substantially be improved. In this review, we discuss how an implementation of a quality assurance (QA) management system might positively improve sample quality and sustainability within pre-clinically focused biobank infrastructures. Biobanks are frequently positioned at the very beginning of the biomedical research value chain, and, since almost every research material has been stored in a biobank during the investigated life cycle, biobanking seems to be of substantial importance from this perspective. The role model of a QA-regulated biobank structure can be found in biobanks within the context of clinical research organizations such as in regenerative medicine clusters.
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Affiliation(s)
| | - Steffen M Zeisberger
- Wyss Translational Center Zurich, Regenerative Medicine Technologies Platform, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Simon P Hoerstrup
- Wyss Translational Center Zurich, University of Zurich and ETH Zurich, and Institute of Regenerative Medicine, University of Zurich, Zurich, Switzerland
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Calleros-Basilio L, Cortés MA, García-Jerez A, Luengo-Rodríguez A, Orozco-Agudo A, Valdivielso JM, Rodríguez-Puyol D, Rodríguez-Puyol M. Quality Assurance of Samples and Processes in the Spanish Renal Research Network (REDinREN) Biobank. Biopreserv Biobank 2016; 14:499-510. [PMID: 27541936 DOI: 10.1089/bio.2015.0095] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Biobanks are useful platforms to build bridges between basic, translational, and clinical research and clinical care. They are repositories of high-quality human biological samples ideal for evaluating their histological characteristics and also their genome, transcriptome, and proteome. The Spanish Renal Research Network Biobank contains more than 76,500 well-preserved frozen samples of a wide variety of kidney diseases, collected from 5450 patients seen by over 70 nephrology services throughout the Spanish territory. OBJECTIVE To determine and to report the results of the quality control of samples and processes conducted in our biobank, implemented in accordance with the requirements of the ISO 9001:2008 international standard. STUDY DESIGN Two types of quality controls were performed: (1) systematic, that is, measurement of viable peripheral blood mononuclear cells (PBMCs) obtained and purity of nucleic acids and (2) ad-hoc, that is, viability of thawed PBMC, DNA extraction process reproducibility, and the integrity and functionality of nucleic acids, implemented on a routine basis. METHODS AND RESULTS PBMC isolation by Ficoll yielded reproducible results and its cryopreserved viability was >90%. Acceptable A260/A280 ratios were obtained for the vast majority of the DNA (n = 2328) and RNA (n = 78) samples analyzed. DNA integrity was demonstrated by agarose gels and by β-globulin gene polymerase chain reaction (PCR) amplification of 1327 and 989 bp fragments. DNA of acceptable quality had at least three bands of β-globulin amplified obtained (n = 26/30). RNA integrity number (RIN) determinations obtained RIN numbers ≥7 (n = 87/96). The amplifiability of nucleic acids was confirmed by qPCR and RT-qPCR of β-actin and GAPDH genes. Long storage or delayed processing time did not affect the quality of the samples analyzed. The processes of DNA extraction also yielded reproducible results. CONCLUSIONS These results clearly indicate that our PBMC, DNA, and RNA stored samples meet the required quality standards to be used for biomedical research, ensuring their long-term preservation.
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Affiliation(s)
- Laura Calleros-Basilio
- 1 Physiology Unit, Department of Systems Biology, Medicine School, Alcala University , Madrid, Spain .,2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain
| | - María Alicia Cortés
- 3 CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Medicine School, Universidad Nacional del Nordeste , Corrientes, Argentina
| | - Andrea García-Jerez
- 1 Physiology Unit, Department of Systems Biology, Medicine School, Alcala University , Madrid, Spain .,2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain
| | - Alicia Luengo-Rodríguez
- 1 Physiology Unit, Department of Systems Biology, Medicine School, Alcala University , Madrid, Spain .,2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain
| | - Ana Orozco-Agudo
- 1 Physiology Unit, Department of Systems Biology, Medicine School, Alcala University , Madrid, Spain .,2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain
| | - José Manuel Valdivielso
- 2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain .,4 Department of Experimental Nephrology, Institut de Recerca Biomédica de Lleida, Universitat de Lleida , Lleida, Spain
| | - Diego Rodríguez-Puyol
- 2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain .,5 Nephrology Section and Research Unit, Hospital Universitario Príncipe de Asturias , Alcalá de Henares, Madrid, Spain
| | - Manuel Rodríguez-Puyol
- 1 Physiology Unit, Department of Systems Biology, Medicine School, Alcala University , Madrid, Spain .,2 IRSIN and REDinREN (Instituto de Salud Carlos III), Madrid, Spain
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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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Liu X, Li Q, Wang X, Zhou X, Liao Q, He X, Zhang J, Sun J, Wu J, Cheng L, Zhang Y. Comparison of six different pretreatment methods for blood RNA extraction. Biopreserv Biobank 2015; 13:56-60. [PMID: 25686049 DOI: 10.1089/bio.2014.0090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Human blood specimens serve as important research materials in the field of translational medicine research. The RNA extracted from blood, for example, represents the gene expression profiles of individuals or groups, and can be indicative of the pathological basis for human diseases. Meanwhile, the RNA quality may have severe impacts on the results of RNA studies. RNA is susceptible to many factors, such as the time of sample collection, transportation conditions, protectants, pretreatments, and extraction methods. In this study, six different pretreatment methods are evaluated for their effects on blood RNA extraction including the RNA yields and quality. Results show that most of these methods meet the basic requirements for RNA studies. While considering the simplicity of the procedure, the cost factor, and how to make full use of the samples, the proper method should be employed by researchers who have specific requirements for their research.
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Affiliation(s)
- Xiaopan Liu
- 1 China National Genebank, BGI-Shenzhen , Shenzhen, China
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Kaye PV. p53 Immunohistochemistry as a biomarker of dysplasia and neoplastic progression in Barrett's oesophagus. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.mpdhp.2015.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Li H, Guo Y, Sun B, Chen K. Histological Assessment of Tumor Tissue Samples via the Mirror Image Method. Biopreserv Biobank 2015; 13:25-30. [PMID: 25686044 DOI: 10.1089/bio.2014.0093] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Haixin Li
- Cancer Biobank, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Yan Guo
- Cancer Biobank, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Baocun Sun
- Department of Pathology, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy of Tianjin, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China
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