1
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van der Wijngaart H, Jagga S, Dekker H, de Goeij R, Piersma SR, Pham TV, Knol JC, Zonderhuis BM, Holland HJ, Jiménez CR, Verheul HMW, Vanapalli S, Labots M. Advancing wide implementation of precision oncology: A liquid nitrogen-free snap freezer preserves molecular profiles of biological samples. Cancer Med 2023; 12:10979-10989. [PMID: 36916528 DOI: 10.1002/cam4.5781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/18/2023] [Accepted: 02/24/2023] [Indexed: 03/16/2023] Open
Abstract
PURPOSE In precision oncology, tumor molecular profiles guide selection of therapy. Standardized snap freezing of tissue biospecimens is necessary to ensure reproducible, high-quality samples that preserve tumor biology for adequate molecular profiling. Quenching in liquid nitrogen (LN2 ) is the golden standard method, but LN2 has several limitations. We developed a LN2 -independent snap freezer with adjustable cold sink temperature. To benchmark this device against the golden standard, we compared molecular profiles of biospecimens. METHODS Cancer cell lines and core needle normal tissue biopsies from five patients' liver resection specimens were used to compare mass spectrometry (MS)-based global phosphoproteomic and RNA sequencing profiles and RNA integrity obtained by both freezing methods. RESULTS Unsupervised cluster analysis of phosphoproteomic and transcriptomic profiles of snap freezer versus LN2 -frozen K562 samples and liver biopsies showed no separation based on freezing method (with Pearson's r 0.96 (range 0.92-0.98) and >0.99 for K562 profiles, respectively), while samples with +2 h bench-time formed a separate cluster. RNA integrity was also similar for both snap freezing methods. Molecular profiles of liver biopsies were clearly identified per individual patient regardless of the applied freezing method. Two to 25 s freezing time variations did not induce profiling differences in HCT116 samples. CONCLUSION The novel snap freezer preserves high-quality biospecimen and allows identification of individual patients' molecular profiles, while overcoming important limitations of the use of LN2 . This snap freezer may provide a useful tool in clinical cancer research and practice, enabling a wider implementation of (multi-)omics analyses for precision oncology.
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Affiliation(s)
- Hanneke van der Wijngaart
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Sahil Jagga
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Henk Dekker
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Richard de Goeij
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Babs M Zonderhuis
- Department of Surgery, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harry J Holland
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
| | - Henk M W Verheul
- Department of Medical Oncology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Srinivas Vanapalli
- Applied Thermal Sciences, Faculty of Science and Technology, University of Twente, Enschede, The Netherlands
| | - Mariette Labots
- Department of Medical Oncology, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Cancer Center Amsterdam, Imaging and Biomarkers, Amsterdam, The Netherlands
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2
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Ebner JN, Ritz D, von Fumetti S. Abiotic and past climatic conditions drive protein abundance variation among natural populations of the caddisfly Crunoecia irrorata. Sci Rep 2020; 10:15538. [PMID: 32968134 PMCID: PMC7512004 DOI: 10.1038/s41598-020-72569-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 09/02/2020] [Indexed: 01/05/2023] Open
Abstract
Deducing impacts of environmental change on species and the populations they form in nature is an important goal in contemporary ecology. Achieving this goal is hampered by our limited understanding of the influence of naturally occurring environmental variation on the molecular systems of ecologically relevant species, as the pathways underlying fitness-affecting plastic responses have primarily been studied in model organisms and under controlled laboratory conditions. Here, to test the hypothesis that proteome variation systematically relates to variation in abiotic conditions, we establish such relationships by profiling the proteomes of 24 natural populations of the spring-dwelling caddisfly Crunoecia irrorata. We identified protein networks whose abundances correlated with environmental (abiotic) gradients such as in situ pH, oxygen- and nitrate concentrations but also climatic data such as past thermal minima and temperature seasonality. Our analyses suggest that variations in abiotic conditions induce discrete proteome responses such as the differential abundance of proteins associated with cytoskeletal function, heat-shock proteins and proteins related to post-translational modification. Identifying these drivers of proteome divergence characterizes molecular "noise", and positions it as a background against which molecular signatures of species' adaptive responses to stressful conditions can be identified.
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Affiliation(s)
- Joshua Niklas Ebner
- Geoecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland.
| | - Danilo Ritz
- Proteomics Core Facility, University of Basel, Biozentrum Basel, Switzerland
| | - Stefanie von Fumetti
- Geoecology Research Group, Department of Environmental Sciences, University of Basel, Basel, Switzerland
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3
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Fan XJ, Huang Y, Wu PH, Yin XK, Yu XH, Fu XH, Feng LL, Wang YL, Yi HJ, Chen ZT, Yin JX, Zhang DL, Feng WX, Bai SM, Kim T, Mills GB, Lu YL, Wan XB, Wang L. Impact of Cold Ischemic Time and Freeze-Thaw Cycles on RNA, DNA and Protein Quality in Colorectal Cancer Tissues Biobanking. J Cancer 2019; 10:4978-4988. [PMID: 31598170 PMCID: PMC6775519 DOI: 10.7150/jca.29372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 06/23/2019] [Indexed: 12/20/2022] Open
Abstract
Tissue-derived RNA, DNA and protein samples become more and more crucial for molecular detection in clinical research, personalized and targeted cancer therapy. This study evaluated how to biobanking colorectal tissues through examining the influences of cold ischemic time and freeze-thaw cycles on RNA, DNA and protein integrity. Here, 144 pairs of tumor and normal colorectal tissues were used to investigate the impact of cold ischemic times (0-48h) on RNA, DNA and protein integrity at on ice or room temperature conditions. Additionally, 45 pairs of tissues experienced 0-9 freeze-thaw cycles, and then the RNA, DNA and protein quality were analyzed. On ice, RNA, DNA and protein from colorectal tumor and normal tissues were all stable up to 48h after surgery. At room temperature, RNA in colorectal tumor and normal tissues began to degrade at 8h and 24h, respectively. Meanwhile, the tumor tissues DNA degradation occurred at 24h after surgery at room temperature. Similarly, the protein expression level of tumor and normal tissues began to change at 24h after the surgery at room temperature. Interestingly, tissue RNA and DNA remained stable even after 9 freeze-thaw cycles, whereas the proteins levels were remarkably changed after 7 freeze-thaw cycles. This study provided a useful evidence on how to store human colorectal tissues for biobanking. Preserving the surgical colorectal tissue on ice was an effective way to prevent RNA, DNA and protein degradation. Importantly, more than 7 repeated freeze-thaw cycles were not recommended for colorectal tissues.
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Affiliation(s)
- Xin-Juan Fan
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Yan Huang
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Pei-Huang Wu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Xin-Ke Yin
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Xi-Hu Yu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Gastrointestinal Surgery, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Xin-Hui Fu
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Li-Li Feng
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Yun-Long Wang
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Hong-Jun Yi
- Department of Pathology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Zhi-Ting Chen
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Jun-Xiang Yin
- China National Center for Biotechnology Development, Beijing, China
| | - Da-Lu Zhang
- China National Center for Biotechnology Development, Beijing, China
| | - Wei-Xing Feng
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Shao-Mei Bai
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China
| | - Taewan Kim
- The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Gordon B Mills
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yi-Ling Lu
- Department of Systems Biology, Division of Basic Science Research, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xiang-Bo Wan
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Radiation Oncology, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Lei Wang
- Guangdong Institute of Gastrointestinal, Guangzhou, Guangdong, China.,Department of Gastrointestinal Surgery, the Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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4
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Yu K, Xing J, Zhang J, Zhao R, Zhang Y, Zhao L. Effect of multiple cycles of freeze-thawing on the RNA quality of lung cancer tissues. Cell Tissue Bank 2017; 18:433-440. [PMID: 28573389 DOI: 10.1007/s10561-016-9600-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 11/07/2016] [Indexed: 11/25/2022]
Abstract
RNA degradation is a major problem in tissue banking. We explored the effect of thawing flash-frozen biospecimens on the quality and integrity of RNA for genetic testing as well as for other cancer research studies. The histological quality of the frozen tumor sections was evaluated by using hematoxylin and eosin staining. RNA extraction from 60 lung cancer tissue samples subjected to various freeze/thaw cycles was performed using the RNeasy Plus isolation kit. RNA integrity was assessed by using an Agilent bioanalyzer to obtain RNA integrity numbers (RIN). Furthermore, RNA from different groups was used for fluorescence Reverse transcription-polymerase chain reaction (RT-PCR) analysis of the echinoderm microtubule-associated protein-like 4 and anaplastic lymphoma kinase (EML4-ALK) fusion gene mutation to verify whether it can be used for research or clinical testing. Highly variable RIN values were observed among the samples, which showed no correlation with the number of freeze/thaw cycles conducted. However, after 3 freeze/thaw cycles (each thaw event lasted for 10 min), an increasing number of changes in peak intensity in RINs were observed. After 5 freeze/thaw cycles, RNA integrity decreased to approximately 35%. After 3 freeze/thaw cycles, the RNA could still be used for RT-PCR analysis of EML4-ALK fusion gene mutations; whereas those subjected to 5 freeze/thaw cycles could not. Limited (<3) freeze/thaw cycles did not adversely affect the quality of RNA extracted from tumor tissues and subsequent RT-PCR analysis. Our data could be utilized in the establishment of a standardized procedure for tissue biospecimen collection and storage.
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Affiliation(s)
- Keke Yu
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University, West Huaihai Road, No. 241, Building 2, Room 4B, Shanghai, 230000, China
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, 230000, China
| | - Jie Xing
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University, West Huaihai Road, No. 241, Building 2, Room 4B, Shanghai, 230000, China
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, 230000, China
| | - Jie Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University, West Huaihai Road, No. 241, Building 2, Room 4B, Shanghai, 230000, China.
| | - Ruiying Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University, West Huaihai Road, No. 241, Building 2, Room 4B, Shanghai, 230000, China
| | - Ye Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University, West Huaihai Road, No. 241, Building 2, Room 4B, Shanghai, 230000, China
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University, Shanghai, 230000, China
| | - Lanxiang Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University, West Huaihai Road, No. 241, Building 2, Room 4B, Shanghai, 230000, China
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5
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Abstract
CONTEXT Genomic medicine requires the identification of biomarkers and therapeutic targets, which in turn, requires high-quality biospecimens. Achieving high-quality biospecimens requires implementing standard operating procedures to control the variations of preanalytic variables in biobanking. Currently, most biobanks do not control the variations of preanalytic variables when collecting, processing, and storing their biospecimens. However, those variations have been shown to affect the quality of biospecimens and gene expression profiling. OBJECTIVE To identify evidence-based preanalytic parameters that can be applied and those parameters that need further study. DATA SOURCES We searched the Biospecimen Research and PubMed databases using defined key words. We retrieved and reviewed 212 articles obtained through those searches. We included 58 articles (27%) according to our inclusion and exclusion criteria for this review. CONCLUSION -Preanalytic variables in biobanking can degrade the quality of biospecimens and alter gene expression profiling. Variables that require further study include the effect of surgical manipulation; the effect of warm ischemia; the allowable duration of delayed specimen processing; the optimal type, duration, and temperature of preservation and fixation; and the optimal storage duration of formalin-fixed, paraffin embedded specimens in a fit-for-purpose approach.
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Affiliation(s)
- Jane H Zhou
- From the Departments of Pathology (Drs Zhou and Sahin) and Head and Neck Surgery (Dr Myers), University of Texas MD Anderson Cancer Center, Houston. Dr Zhou is now with Human Genome Sequencing Center, Baylor College of Medicine, Houston
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6
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Torlakovic EE, Brynes RK, Hyjek E, Lee SH, Kreipe H, Kremer M, McKenna R, Sadahira Y, Tzankov A, Reis M, Porwit A. ICSH guidelines for the standardization of bone marrow immunohistochemistry. Int J Lab Hematol 2015; 37:431-49. [DOI: 10.1111/ijlh.12365] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/02/2015] [Indexed: 12/25/2022]
Affiliation(s)
- E. E. Torlakovic
- Department of Laboratory Hematology; University Health Network; University of Toronto; Toronto ON Canada
| | - R. K. Brynes
- Department of Pathology; Keck School of Medicine; University of Southern California; Los Angeles CA USA
| | - E. Hyjek
- Department of Pathology; University of Chicago; Chicago IL USA
| | - S.-H. Lee
- Department of Haematology; St George Hospital; SEALS Central; Sydney NSW Australia
| | - H. Kreipe
- Department of Pathology; Hannover Medical School; Hannover Germany
| | - M. Kremer
- Munich Municipal Hospital; Institute of Pathology; Munich Germany
| | - R. McKenna
- Special Hematology; Department of Laboratory Medicine and Pathology; University of Minnesota; Minneapolis MN USA
| | - Y. Sadahira
- Department of Pathology; Kawasaki Medical School; Kurashiki Japan
| | - A. Tzankov
- Institute of Pathology; University Hospital Basel; Basel Switzerland
| | - M. Reis
- Department of Clinical Pathology; Sunnybrook Health Sciences Centre; Toronto ON Canada
| | - A. Porwit
- Department of Laboratory Hematology; University Health Network; University of Toronto; Toronto ON Canada
- Department of Pathology; Karolinska Institute; Stockholm Sweden
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7
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Yu K, Zhang J, Li X, Xu L, Zhang Y, Xing J, Shao J, Zhu L, Liu J, Zhao L, Han B. Establishment and management of a lung cancer biobank in Eastern China. Thorac Cancer 2015; 6:58-63. [PMID: 26273336 PMCID: PMC4448472 DOI: 10.1111/1759-7714.12144] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/20/2014] [Indexed: 12/02/2022] Open
Abstract
Background The prevalence of lung cancer, a highly complex neoplasm, increases annually. Thus, a lung cancer biobank, which stores lung cancer tissue and blood matched according to standard methods, is needed to advance lung cancer research and develop promising therapies. Methods To accomplish this aim, we implemented standardized procedures for tissue samples and patient information acquired from consenting donors. The banked tissue includes blood, pleural effusions, and surgical resection samples. An independent information management system was used to match samples and collect data, including clinical cancer manifestation, laboratory tests, and de-identified data about cancer patients. Results From 2009 to 2013, more than 2000 lung cancer cases were collected. At this time, we have more than 10 000 biological samples stored in our biobank. DNA, ribonucleic acid (RNA), and protein quality were confirmed to be appropriate for clinical and basic research. Conclusion Our standardized, large-scale lung cancer biobank offers high quality cancer research samples for China and the world.
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Affiliation(s)
- Keke Yu
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jie Zhang
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Xin Li
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Lei Xu
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Ye Zhang
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jie Xing
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jinchen Shao
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Lei Zhu
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Jinguo Liu
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Lanxiang Zhao
- Department of Pathology, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
| | - Baohui Han
- Department of Biaobank, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China ; Department of Pulmonary Medcine, Shanghai Chest Hospital, Shanghai JiaoTong University Shanghai, China
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8
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Andreasson A, Kiss NB, Juhlin CC, Höög A. Long-term storage of endocrine tissues at - 80°C does not adversely affect RNA quality or overall histomorphology. Biopreserv Biobank 2015; 11:366-70. [PMID: 24475321 DOI: 10.1089/bio.2013.0038] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Today, no consensus exists regarding how human tissues are best preserved for long-term storage. Very low temperature storage in liquid nitrogen is often advocated as the superlative method for extended periods, but storage in -80 degrees Celsius (-80°C) freezers, while sometimes debated, is a possible alternative. RNA is the most easily degradable component of a biological sample in a molecular biology context and the quality can reliably be measured. AIM To investigate to what extent long-term storage of tissues in -80°C affects the RNA quality and overall histomorphology. The tissue storage period represents nearly three decades (1986-2013). METHODS RNA extraction from 153 tissue samples with different storage periods was performed with the mirVana kit (Invitrogen). RNA integrity was assessed using an Agilent bioanalyzer to obtain RNA integrity numbers (RIN). Further, tissue representative testing using light microscopy was performed by two pathologists to assess tissue composition and morphology. RESULTS RIN values were measured in all samples, showing a variability that did not correlate with the storage time of the tissues. Microscopically, all samples displayed acceptable tissue morphology regardless of storage time. CONCLUSION Long-term storage in -80°C does not adversely affect the quality of the RNA extracted from the stored tissues, and the tissue morphology is maintained to a good standard.
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9
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de Gramont A, Watson S, Ellis LM, Rodón J, Tabernero J, de Gramont A, Hamilton SR. Pragmatic issues in biomarker evaluation for targeted therapies in cancer. Nat Rev Clin Oncol 2014; 12:197-212. [PMID: 25421275 DOI: 10.1038/nrclinonc.2014.202] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Predictive biomarkers are becoming increasingly important tools in drug development and clinical research. The importance of using both guidelines for specimen acquisition and analytical methods for biomarker measurements that are standardized has become recognized widely as an important issue, which must be addressed in order to provide high-quality, validated assays. Herein, we review the major challenges in biomarker validation processes, including pre-analytical (sample-related), analytical, and post-analytical (data-related) aspects of assay development. Recommendations for improving biomarker assay development and method validation are proposed to facilitate the use of predictive biomarkers in clinical trials and the practice of oncology.
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Affiliation(s)
- Armand de Gramont
- New Drug Evaluation Laboratory, Centre of Experimental Therapeutics, Department of Oncology, Centre Hospitalier Universitaire Vaudois (CHUV), 1011 Lausanne, Switzerland
| | - Sarah Watson
- INSERM U830, Genetics and Biology of Paediatric Tumours Group, Institut Curie, France
| | - Lee M Ellis
- Departments of Surgical Oncology, and Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, USA
| | - Jordi Rodón
- Medical Oncology, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona (UAB), Spain
| | - Josep Tabernero
- Medical Oncology, Vall d'Hebron University Hospital, Vall d'Hebron Institute of Oncology (VHIO) and Universitat Autonoma de Barcelona (UAB), Spain
| | - Aimery de Gramont
- Medical Oncology Department, Institut Hospitalier Franco-Britannique, France
| | - Stanley R Hamilton
- Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, USA
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10
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Wolf C, Jarutat T, Vega Harring S, Haupt K, Babitzki G, Bader S, David K, Juhl H, Arbogast S. Determination of phosphorylated proteins in tissue specimens requires high-quality samples collected under stringent conditions. Histopathology 2013; 64:431-44. [PMID: 24266863 DOI: 10.1111/his.12268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2013] [Accepted: 08/26/2013] [Indexed: 01/10/2023]
Abstract
AIMS For selection of patients who will benefit from targeted therapies, identification of biomarkers predictive of treatment response is desirable. Activation of the targeted pathway becomes apparent by protein phosphorylation. Determination of this phenomenon is therefore considered a promising biomarker approach. To date, however, it is unclear whether routinely collected tissue specimens allow determination of in-vivo phosphorylation states. METHODS AND RESULTS To investigate whether routinely collected tissue specimens retain the true phosphorylation states of a tumour's proteins, we compared protein phosphorylation states between matched tumour samples that were subjected to different ischaemic times by immunohistochemistry. The influence of formalin fixation and paraffin-embedding on phosphorylation states was investigated by comparison of matched fresh frozen and formalin-fixed paraffin-embedded surgical specimens as well as small biopsies. We show that ischaemia influences protein phosphorylation in a tumour-specific, unpredictable manner. Formalin fixation and paraffin-embedding lead to a decrease in detectable protein phosphorylation in larger surgical specimens, but not in small biopsies. CONCLUSIONS Determination of protein phosphorylation using routinely collected surgical specimens results in artefacts which do not reflect a tumour's true states of pathway activation. Valid measurement of phosphorylated biomarkers requires that tissue collection procedures are tightly controlled, avoiding ischaemia and large-specimen fixation.
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Affiliation(s)
- Corinna Wolf
- Department for Tissue Biomarkers and Pathology, Roche Diagnostics GmbH, Penzberg, Germany
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11
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Abstract
Arterial hypertension is a major cardiovascular risk factor that affects between 10 and 40% of the population in industrialized countries. Primary aldosteronism (PA) is the most common form of secondary hypertension with an estimated prevalence of around 10% in referral centers and 4% in a primary care setting. Despite its high prevalence until recently, the underlying genetic and molecular basis of this common disease had remained largely obscure. Over the past decade, a number of insights have been achieved that have relied on in vitro cellular systems, wild-type and genetically modified in vivo models, as well as clinical studies in well-characterized patient populations. This progress has been made possible by a number of independent technical developments including that of specific hormone assays that allow measurement in small sample volumes as well as genetic techniques that enable high-throughput sequencing of a large number of samples. Furthermore, animal models have provided important insights into the physiology of aldosterone regulation that have served as a starting point for investigation of mechanisms involved in autonomous aldosterone secretion. Finally, national and international networks that have built up registries and biobanks have been instrumental in fostering translational research endeavors in PA. Therefore, it is to be expected that in the near future, further pathophysiological mechanisms that result in autonomous aldosterone secretion will be unraveled.
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Affiliation(s)
- Felix Beuschlein
- Endocrine Research Unit, Medizinische Klinik und Poliklinik IV, Klinikum der Universität München, Ziemssenstrasse 1, D-80336 Munich, Germany.
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12
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Ma Y, Dai H, Kong X. Impact of warm ischemia on gene expression analysis in surgically removed biosamples. Anal Biochem 2012; 423:229-35. [DOI: 10.1016/j.ab.2012.02.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 01/15/2012] [Accepted: 02/03/2012] [Indexed: 02/01/2023]
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13
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Abbaraju NV, Cai Y, Rees BB. Protein recovery and identification from the gulf killifish, Fundulus grandis: comparing snap-frozen and RNAlater® preserved tissues. Proteomics 2011; 11:4257-61. [PMID: 21898826 DOI: 10.1002/pmic.201100328] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2011] [Revised: 07/20/2011] [Accepted: 08/04/2011] [Indexed: 11/12/2022]
Abstract
Reliable proteomic analysis of biological tissues requires sampling approaches that preserve proteins as close to their in vivo state as possible. In the current study, the patterns of protein abundance in one-dimensional (1-D) gels were assessed for five tissues of the gulf killifish, Fundulus grandis, following snap-freezing tissues in liquid nitrogen or immersion of fresh tissues in RNAlater(®). In liver and heart, the protein profiles in 1-D gels were better preserved by snap-freezing, while in gill, the 1-D protein profile was better preserved by immersion in RNAlater(®). In skeletal muscle and brain, the two approaches yielded similar patterns of protein abundance. LC-MS/MS analyses and database searching resulted in the identification of 17 proteins in liver and 12 proteins in gill. Identified proteins include enzymes of energy metabolism, structural proteins, and proteins serving other biological functions. These protein identifications for a species without a sequenced genome demonstrate the utility of F. grandis as a model organism for environmental proteomic studies in vertebrates.
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Affiliation(s)
- Naga V Abbaraju
- Department of Chemistry, University of New Orleans, New Orleans, LA 70148, USA
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14
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Shaw PM, Patterson SD. The Value of Banked Samples for Oncology Drug Discovery and Development. J Natl Cancer Inst Monogr 2011; 2011:46-9. [DOI: 10.1093/jncimonographs/lgr004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Elger BS, Biller-Andorno N. Biobanks and Research: Scientific Potential and Regulatory Challenge. THE INTERNATIONAL LIBRARY OF ETHICS, LAW AND TECHNOLOGY 2011. [DOI: 10.1007/978-94-007-1673-5_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2022]
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