Expert Opinion on Drug Discovery
ISSN: 1746-0441 (Print) 1746-045X (Online) Journal homepage: http://www.tandfonline.com/loi/iedc20
Using molecular profiled human tissue to accelerate drug discovery Katherine A Tarvin MPH & George E Sandusky DVM PhD To cite this article: Katherine A Tarvin MPH & George E Sandusky DVM PhD (2014) Using molecular profiled human tissue to accelerate drug discovery, Expert Opinion on Drug Discovery, 9:12, 1383-1387 To link to this article: http://dx.doi.org/10.1517/17460441.2014.959926
Published online: 12 Sep 2014.
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Date: 11 September 2015, At: 22:02
Editorial
Using molecular profiled human tissue to accelerate drug discovery Katherine A Tarvin & George E Sandusky† †
1.
Introduction
2.
Biobanks and biospecimen quality
3.
Molecular tissue profiling for research and drug development
Downloaded by [University of Nebraska, Lincoln] at 22:02 11 September 2015
4.
Large scale tissue profiling efforts
5.
Tissue profiling, data acquisition and integration
6.
Future directions
7.
Expert opinion
Indiana University School of Medicine, Department of Pathology & Laboratory Medicine, Indianapolis, IN, USA
The value of molecular profiled human tissue lies in its potential to improve the efficiency of drug discovery and development. The sequencing and profiling of human biospecimens across multiple omics dimensions provides layers of molecular information that can be used to enhance our knowledge of disease mechanisms to identify and prioritize novel drug targets and provide supportive biological evidence to support a therapeutic hypothesis. It is critical to control pre-analytical variables because the reproducibility and accuracy of molecular data generated by high-throughput technologies is dependent upon biospecimen quality. The scientific knowledge and technology developments gained in tissue banking research are transforming biospecimen collection and biostorage practices. These tissue banking advancements will improve specimen quality and utilization and, at the same time, reduce biobanking costs. Furthermore, well-annotated, high quality biospecimens will provide reliable, consistent gene expression data for target validation for drug discovery. Challenges in understanding the molecular signatures of biospecimens follow the challenges of human tissue acquisition. Sequencing and profiling high-throughput technologies generate heterogeneous, complex data sets that require sophisticated informatics tools for data storage and analysis. As tissue banking and informatics technologies improve and we gain deeper knowledge of the human genome and its functionality, we will see biomarker identification and target therapies brought about by the research performed on high quality biospecimens. Keywords: biobanking, drug discovery, gene expression, high quality biospecimens, human tissues, molecular profiling, next generation technologies, omics research Expert Opin. Drug Discov. (2014) 9(12):1383-1387
1.
Introduction
Recent omics efforts have accelerated our understanding of the pathogenesis of human diseases, delivering opportunities to identify novel therapeutic targets and develop innovative medicines. High-throughput technologies continue to characterize thousands of biospecimens at a time, providing layers of molecular data in order to distinguish genomic alterations and pathways. This deep profiling allows for the development of a molecular signature for each biospecimen by integrating the high-throughput data including mRNA and microRNA expression, somatic mutations, DNA methylation and copy number variations. These are exciting times for drug discovery as gene expression profiles, combined with the growing data from epigenetics and proteomics, can be leveraged to enhance our knowledge of disease mechanisms. Human tissues are the raw materials from which nucleic acids and proteins are extracted for molecular research. Now, with access to genetic profiling and emerging technologies, human tissues can drive translational efforts more than ever before. The importance of human tissues is recognized throughout the drug discovery process from the discovery phase to on-going clinical trials. In preclinical work, 10.1517/17460441.2014.959926 © 2014 Informa UK, Ltd. ISSN 1746-0441, e-ISSN 1746-045X All rights reserved: reproduction in whole or in part not permitted
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K. A. Tarvin & G. E. Sandusky
genetically profiled human tissue enables researchers to better understand the basis of disease heterogeneity, select and validate new drug targets, find genetic variations contributing to disease and validate animal disease models [1]. Additionally, the integration of this biological data (genomics, transcriptomics, proteomics, etc.) from diseased and normal human tissue samples can be utilized for pharmacodynamic biomarker discovery and stratifying patient populations to predict the success of drug therapy candidates in clinical trials [2].
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2.
Biobanks and biospecimen quality
In the past decade, biobanks have been increasingly recognized as vital investments for biomedical research given their efforts to collect, store and distribute human tissues. The usefulness and reliability of molecular data obtained from the biospecimens depends on the quality of the starting material. The ideal biospecimen is one that is an unaltered representation of the tissue in vivo [3]. In order for biobanks to come as close to this benchmark as possible, several important operational logistics must be considered during the biobank or project design phase. This includes identifying and describing the procedures for tissue acquisition, processing, storage and distribution. The use of standard operating procedures (SOPs) will help ensure that tissue samples are uniformly handled during the collection process, minimizing the chance of preanalytical variability. Preanalytical factors such as ischemia time, type of fixative, fixation time, storage temperature and length of storage are only a few variables that can result in poor quality and low yields of DNA, RNA and protein, affecting gene and protein expression. For example, ischemia and hypoxic conditions prior to freezing or fixation can initiate changes in tissue metabolism such as activation of proteases, leading to apoptotic or necrotic changes [4]. Another important component is the quality of tissue nucleic acids. Fresh and frozen tissue specimens yield better quality DNA and RNA than formalin fixation, if preserving tissue architecture is not an issue [5-7]. Along with adhering to SOPs for daily operations, biobanks are responding to and implementing best practices set forth by professional biobanking organizations such as the International Society of Biological and Environmental Repositories (ISBER) and the National Cancer Institute’s (NCI) Biorepositories and Biospecimen Research Branch. ISBER and NCI best practices for repositories outline recommendations for repository planning and organization, facilities design and management, quality control and quality assurance, safety, data management, ethical, legal and policy issues and cost management to name a few [8,9]. Recognizing the factors that impact biospecimen quality is not only important for biobanks, but for researchers as well. In designing studies and preparing assays, it is beneficial for researchers to prepare their biospecimen request(s) considering three dimensions: specimen type (normal tissue, diseased tissue, blood, serum, urine, etc.), target molecule (DNA, RNA, protein), and analysis platform (immunohistochemistry, 1384
immunoassays, mass spectrometry, quantitative reverse transcription polymerase chain reaction, etc.) [10]. In our experience, we are seeing an increasing trend in the end-users of human tissue requiring that biospecimen and data quality control measures are implemented and documented by the parties responsible for procurement. This control of preanalytical variables benefits early drug development investigations by ensuring the reproducibility of results, controlling for bias and avoiding false discoveries of biomarkers.
Molecular tissue profiling for research and drug development
3.
The value of molecular profiled tissue lies in its potential to improve the efficiency of drug discovery and development. The layers of accumulated sequencing and profiling data can be used to identify and validate novel drug targets and provide evidence to support a therapeutic hypothesis. This data will serve as the foundation for developing preclinical models that will better predict the success of late phase clinical trials and, at the same time, terminating others that lack supporting biological evidence. Furthermore, the data from molecular profiled tissues will accelerate progress in the design of clinical trials and targeted patient selection, such as the recently launched Lung Cancer Master Protocol trial for patients with lung squamous cell carcinoma [11]. Familiar successes in translating omics discoveries to targeted therapies include the response of human cancers to inhibitors of EGFR, PARP, BCR-ABL, and BRAF to name a few [12]. There are limitations of target validation based on human genetics and limitations to using a biomarker approach to stratifying patient populations [13,14]. Ultimately, however, the molecular profiling of human tissue enables the identification of biomarkers and druggable targets with greater probability of success, improving the outcomes of pharmaceutical research and development, and thereby yielding significant savings across the drug discovery and development pipeline [2]. For example, Plenge, Scolnick and Altshuler describe the impact human genetics will have in reducing the risk of attrition in Phase II and Phase III clinical trials. “It is estimated that a reduction in Phase II attrition from 66 to 50% would decrease the cost per new molecular entity by ~ $0.5 billion, and a reduction in Phase III attrition from 30 to 20% would decrease costs by ~ $0.3 billion”, according to the authors [13]. 4.
Large scale tissue profiling efforts
To date, advances in genome sequencing technologies have proved incredibly beneficial for oncology research. Large scale research efforts such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium continue to characterize hundreds of human tumor tissues with the common aim to provide cancer researchers comprehensive molecular data sets including, but not limited to, whole genome and exome sequencing and mRNA and microRNA
Expert Opin. Drug Discov. (2014) 9(12)
Downloaded by [University of Nebraska, Lincoln] at 22:02 11 September 2015
Using molecular profiled human tissue to accelerate drug discovery
expression profiling. With the availability of this data, investigators have identified genetic driver abberations and genetically defined tumor subtypes [15,16]. Recently, for example, the TCGA Research Network published their analyses of molecular profiles of 230 untreated, primary lung adenocarcinomas, identifying mutations that affect the RTK/RAS/RAF signaling pathway [17]. Advancements in omics technologies are bringing opportunities to drug development in areas of medicine other than oncology including neurology, cardiology and autoimmune diseases. In February 2014, the Accelerating Medicines Partnership (AMP) was launched to investigate the following diseases: Alzheimer’s disease, type 2 diabetes, rheumatoid arthritis and lupus. AMP joins together the National Institutes of Health (NIH) and 10 pharmaceutical companies in an unlikely public-private partnership where the collaborators have agreed to pool resources (tissue samples, data, expertise and funds) and to make the AMP data publicly accessible [18]. The project’s overall strategy is to provide access to human genetic and phenotype data in order to identify and evaluate the efficacy and safety of potential therapeutic targets, and thereby informing and accelerating the drug development pipeline. Within AMP, program milestones will include the aggregation of several thousand human DNA samples for genome sequence data and the creation of a knowledge portal containing sequence and phenotype data. In meeting these milestones, AMP will provide researchers the tools to test hypotheses related to genetic variation and validate drug targets [19].
Tissue profiling, data acquisition and integration
5.
Despite tremendous gains, the biomedical community has yet to fully capitalize on what high-dimensional molecular data has to offer for drug discovery. This is due to the challenges involving the growth of data, the growing types of data and the integration and analysis of this data. Obtaining gene expression, transcriptome and proteome profiles for millions of human tissue types from millions of individuals requires a high performance computational environment. Next generation technologies continue to make exponential progress in generating and cataloging scales of data from numerous human tissue samples, at which point, the demands are placed on information technology for big data acquisition and organization including data storage, maintenance, access and quality control. Furthermore, the computational architecture must be able to support the integration of large scale, heterogeneous data sets (clinical data, pre-analytical biospecimen variables and omics data) in order to prioritize biologically relevant data and construct predictive models of disease [20]. Moving forward, we will see a focus on the development of interoperable informatics tools, a progressive shift in standardizing data formats and a greater sharing of data [20,21].
6.
Future directions
Biorepositories and project-driven procurement initiatives should begin to collect ‘next generation biospecimens’ for comprehensive molecular characterization [21]. We broadly define these next generation biospecimens as fit-for-purpose, collected under controlled preanalytical conditions, with the downstream application in mind. These biospecimens and their associated preanalytical and clinical data will be required for emerging, various sequencing and profiling technologies such as exome sequencing and whole genome sequencing that will provide a deeper characterization of genome exploration. Additionally, future work with genetically profiled human tissue will focus on single cell sequencing and intra-tissue heterogeneity [22]. These efforts will be facilitated by multidisciplinary teams -- patients, clinicians, pathologists, biospecimen scientists, biomedical researchers, statisticians and the life science industry -- with hope that the molecular profiles will lead to biological breakthroughs in disease and translate into clinical applications for improving patient care. 7.
Expert opinion
Due to both academic and NIH/NCI rigor in tissue banking research, the research quality of human tissues has moved from many repositories that contain samples of very poor genomic and proteomic quality to repositories that contain well-annotated, high quality tissue samples. Regardless, many tissue banking operations in the US and abroad still do not collect biospecimens under proper protocols and SOPs for tissue collection. In many repositories the maintenance of proper storage of samples is not adhered to, and the histologic, molecular, and proteomic quality control metrics of the stored tissue samples do not meet the standards set by ISBER and NCI. These weaknesses inherent of so many tissue banks are current limitations for drug discovery researchers who rely on high quality tissue samples for target validation. The potential of improving on the quality metrics set by ISBER and NCI is a daunting task for many tissue banks. Most do not have the funds required to set up a viable business plan and to implement this endeavor into a strong, quality-controlled biorepository. Biospecimen storage solutions, whether basic or automatic, tend to be expensive to set up and maintain. What is known is the variety of storage solutions is expanding with technology improvements and the development of energy-efficient equipment. Continual advancements in nucleic acid and cell stability and quality assessment technologies will also greatly impact the tissue banking arena and lead to cost savings in current specimen storage formats (e.g., freezers and liquid nitrogen [LN2] tanks) and improve the speed of specimen processing and analysis times. Paper cards are one solution for ambient temperature long-term storage that permit the collection and
Expert Opin. Drug Discov. (2014) 9(12)
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K. A. Tarvin & G. E. Sandusky
storage of DNA or RNA without compromising their quality. Paper cards also allow for easy and efficient transport of dry samples without the need for bulky packaging materials and cold chain transportation. The scientific knowledge is quickly being gained by tissue banking scientists to store both processed DNA and RNA in a global fashion at most biorepositories in the next 5 -10 years. Current technologies will need to be continually reassessed for their adequacy to meet improved standards for reducing preanalytical variation. In consequence of this gained biospecimen quality and biostorage knowledge, this should limit the tissue sample size that is maintained in LN2 storage and limit the facility size needed for LN2 and freezer capacity. In the next few years, room temperature preservation and storage formats will move into institutional and private tissue banking operations. Room temperature preservation and storage will reduce the costs of storage and transport. One development we are watching includes the further development and refinement of the stabilization of mammalian cells in a dehydrated state as compared to liquid state [23,24]. The stability of RNA and cells at ambient temperature is still under development and has shorter shelf life as compared to DNA. With more research dollars and public/ private grant support, these technologies will soon be as valuable as the use of ambient DNA storage and be considered a standard practice for preserving RNA and cells. Technology developments for biobanking and biostorage are aimed at improving the quality of tissue samples as research materials, which are required to generate reliable, consistent gene expression data for drug discovery. Advancements in the molecular stabilization, preservation, and analysis of tissue specimens and the applications thereof will help improve the utilization rates of biospecimens. Many, if not all, biobanking operations maintain few to hundreds of tissue samples that are of poor molecular quality and contain little associated data. These unusable tissue samples are expensive to maintain. In our opinion, adherence to biospecimen best practices and SOPs combined with a close collaboration with the end users of the tissue specimens are the best approaches for reducing a biospecimen’s time in storage, making it readily usable for research.
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The ultimate goal of any human tissue biobanking operation is to provide standardized, fit-for-purpose human tissue specimens for translational research to academic institutions, biotechnology firms and the pharmaceutical industries. To this end, collection strategies must be consistent, data-driven and informed by the research priorities of the end-users of the tissue specimens. Biospecimens collected under these conditions can minimize the effect that pre-analytical factors would have on gene expression or protein phosphorylation, for example. However, preanalytical variables alone will not capture a biospecimen’s history. The donor diagnosis, demographics and treatment history must also be considered. These data points along with the molecular profile for each specimen can be added to larger disease data sets. Analysis of this data and across multiple data sets has the potential to answer important biological questions during drug discovery such as identifying biomarkers of disease progression, identifying disease subtypes and understanding which patients will likely respond to the candidate drug. As a result, we could see more effective, less toxic drug candidates in clinical development. Improvements in the drug discovery process start with biobanking and tissue specimens as the raw materials for research. Ultimately, high-quality biobanking can lead to better data, effective clinical trials, decreased research and discovery costs, improved patient outcomes, and increased drug discovery. Personalized medicine brought about by the research performed on high quality human tissue samples from various diseases will greatly change the current standard of care guidelines that are being used today to manage many different types of diseases, including Alzheimer’s disease, many type of cancer, many types of cardiovascular disease, obesity, diabetes and psychiatric diseases.
Declaration of interest K Tarvin is an employee of Analytical Biological Services, Inc. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
Expert Opin. Drug Discov. (2014) 9(12)
Using molecular profiled human tissue to accelerate drug discovery
Bibliography Papers of special note have been highlighted as either of interest () or of considerable interest () to readers. 1.
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biological and environmental repositories. Biopreserv Biobank 2012;10(2):79-161 International Society of Biological and Environmental Repositories: best practices for repositories. Biorepositories and Biospecimen Research Branch. NCI best practices for biospecimen resources. National Cancer Institute, National Institutes of Health; 2011. Published online at: http:// biospecimens.cancer.gov/practices/ default.asp National Cancer Institute: best practices for biospecimen resources.
com/nature/journal/vaop/ncurrent/full/ nature13385.html [Retrieved 10 July 2014] 18.
Mullard A. Drug makers and NIH team up to find and validate targets. Nat Rev Drug Discov 2014;13(4):241-3
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Accelerating Medicines Partnership TDTDSC. Accelerating medicines partnership type 2 diabetes program executive summary. Foundation for the National Institutes of Health; 2014. Published online at: http://fnih. org/sites/all/files/documents/AMP%20-% 20T2D%20-%20Research%20Plan.pdf
Paul SM, Mytelka DS, Dunwiddie CT, et al. How to improve R&D productivity: the pharmaceutical industry’s grand challenge. Nat Rev Drug Discov 2010;9(3):203-14
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Shankar SK, Mahadevan A. Biobanking for cancer research: preservation of tissue integrity - Some technical considerations. Indian J Neurosurg 2012;1:130-8
Compton C. The revisioning of caHUB as a center for biospecimen science and standards development. BRN Symposium, Bethesda, Maryland; 2011
Schadt EE, Linderman MD, Sorenson J, et al. Computational solutions to largescale data management and analysis. Nat Rev Genet 2010;11(9):647-57
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National Cancer Institute. Lung-MAP launches: first precision medicine trial from National Clinical Trials Network. NCI Press Release, posted June 16 2014. Available from: http://www.cancer. gov/newscenter/newsfromnci/2014/ LungMAPlaunch [Retrieved 19 June 2014]
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Basik M, Aguilar-Mahecha A, Rousseau C, et al. Biopsies: nextgeneration biospecimens for tailoring therapy. Nat Rev Clin Oncol 2013;10(8):437-50 Next-generation biospecimens.
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Spruessel A, Steimann G, Jung M, et al. Tissue ischemia time affects gene and protein expression patterns within minutes following surgical tumor excision. Biotechniques 2004;36(6):1030-7 Huang WY, Sheehy TM, Moore LE, et al. Simultaneous recovery of DNA and RNA from formalin-fixed paraffinembedded tissue and application in epidemiologic studies. Cancer Epidemiol Biomarkers Prev 2010;19(4):973-7 Scicchitano MS, Dalmas DA, Bertiaux MA, et al. Preliminary comparison of quantity, quality, and microarray performance of RNA extracted from formalin-fixed, paraffin-embedded, and unfixed frozen tissue samples. J Histochem Cytochem 2006;54(11):1229-37
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Haber DA, Gray NS, Baselga J. The evolving war on cancer. Cell 2011;145(1):19-24
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Plenge RM, Scolnick EM, Altshuler D. Validating therapeutic targets through human genetics. Nat Rev Drug Discov 2013;12(8):581-94
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Freidlin B, Korn EL. Biomarker enrichment strategies: matching trial design to biomarker credentials. Nat Rev Clin Oncol 2014;11(2):81-90
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Gnanapragasam VJ. Unlocking the molecular archive: the emerging use of formalin-fixed paraffin-embedded tissue for biomarker research in urological cancer. BJU Int 2010;105(2):274-8
Cancer Genome Atlas Research Network. Comprehensive molecular portraits of human breast tumours. Nature 2012;490(7418):61-70
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Campbell LD, Betsou F, Garcia DL, et al. 2012 best practices for repositories collection, storage, retrieval, and distribution of biological materials for research international society for
Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 2014;507(7492):315-22
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Cancer Genome Atlas Research Network. Comprehensive molecular profiling of lung adenocarcinoma. Nature 2014. Available from: http://www.nature.
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Fox EJ, Loeb LA. One cell at a time. Nature 2014;512(7513):143-4
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Oliver AE. Dry state preservation of nucleated cells: progress and challenges. Biopreserv Biobank 2012;10(4):376-85
24.
Diaz P, Muller R, Desharnais J, et al. Development of stabilizers for live cell preservation at room temperature (779.10). FASEB J 2014;28:1 Suppl
Affiliation Katherine A Tarvin1 MPH & George E Sandusky†2 DVM PhD † Author for correspondence 1 Biospecimen Operations Manager, Analytical Biological Services, Inc., 701 Cornell Drive, Wilmington, DE 19801, USA 2 Senior Research Professor, Indiana University School of Medicine, Department of Pathology and Laboratory Medicine, Van Nuys Medical Science Building, 635 Barnhill Drive, Room A128, Indianapolis, IN 46202-5120, USA Tel: +1 317 278 2304; Fax: +1 317 278 2018; E-mail: [email protected]
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ISSN: 1746-0441 (Print) 1746-045X (Online) Journal homepage: http://www.tandfonline.com/loi/iedc20
Using molecular profiled human tissue to accelerate drug discovery Katherine A Tarvin MPH & George E Sandusky DVM PhD To cite this article: Katherine A Tarvin MPH & George E Sandusky DVM PhD (2014) Using molecular profiled human tissue to accelerate drug discovery, Expert Opinion on Drug Discovery, 9:12, 1383-1387 To link to this article: http://dx.doi.org/10.1517/17460441.2014.959926
Published online: 12 Sep 2014.
Submit your article to this journal
Article views: 122
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=iedc20 Download by: [University of Nebraska, Lincoln]
Date: 11 September 2015, At: 22:02
Editorial
Using molecular profiled human tissue to accelerate drug discovery Katherine A Tarvin & George E Sandusky† †
1.
Introduction
2.
Biobanks and biospecimen quality
3.
Molecular tissue profiling for research and drug development
Downloaded by [University of Nebraska, Lincoln] at 22:02 11 September 2015
4.
Large scale tissue profiling efforts
5.
Tissue profiling, data acquisition and integration
6.
Future directions
7.
Expert opinion
Indiana University School of Medicine, Department of Pathology & Laboratory Medicine, Indianapolis, IN, USA
The value of molecular profiled human tissue lies in its potential to improve the efficiency of drug discovery and development. The sequencing and profiling of human biospecimens across multiple omics dimensions provides layers of molecular information that can be used to enhance our knowledge of disease mechanisms to identify and prioritize novel drug targets and provide supportive biological evidence to support a therapeutic hypothesis. It is critical to control pre-analytical variables because the reproducibility and accuracy of molecular data generated by high-throughput technologies is dependent upon biospecimen quality. The scientific knowledge and technology developments gained in tissue banking research are transforming biospecimen collection and biostorage practices. These tissue banking advancements will improve specimen quality and utilization and, at the same time, reduce biobanking costs. Furthermore, well-annotated, high quality biospecimens will provide reliable, consistent gene expression data for target validation for drug discovery. Challenges in understanding the molecular signatures of biospecimens follow the challenges of human tissue acquisition. Sequencing and profiling high-throughput technologies generate heterogeneous, complex data sets that require sophisticated informatics tools for data storage and analysis. As tissue banking and informatics technologies improve and we gain deeper knowledge of the human genome and its functionality, we will see biomarker identification and target therapies brought about by the research performed on high quality biospecimens. Keywords: biobanking, drug discovery, gene expression, high quality biospecimens, human tissues, molecular profiling, next generation technologies, omics research Expert Opin. Drug Discov. (2014) 9(12):1383-1387
1.
Introduction
Recent omics efforts have accelerated our understanding of the pathogenesis of human diseases, delivering opportunities to identify novel therapeutic targets and develop innovative medicines. High-throughput technologies continue to characterize thousands of biospecimens at a time, providing layers of molecular data in order to distinguish genomic alterations and pathways. This deep profiling allows for the development of a molecular signature for each biospecimen by integrating the high-throughput data including mRNA and microRNA expression, somatic mutations, DNA methylation and copy number variations. These are exciting times for drug discovery as gene expression profiles, combined with the growing data from epigenetics and proteomics, can be leveraged to enhance our knowledge of disease mechanisms. Human tissues are the raw materials from which nucleic acids and proteins are extracted for molecular research. Now, with access to genetic profiling and emerging technologies, human tissues can drive translational efforts more than ever before. The importance of human tissues is recognized throughout the drug discovery process from the discovery phase to on-going clinical trials. In preclinical work, 10.1517/17460441.2014.959926 © 2014 Informa UK, Ltd. ISSN 1746-0441, e-ISSN 1746-045X All rights reserved: reproduction in whole or in part not permitted
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K. A. Tarvin & G. E. Sandusky
genetically profiled human tissue enables researchers to better understand the basis of disease heterogeneity, select and validate new drug targets, find genetic variations contributing to disease and validate animal disease models [1]. Additionally, the integration of this biological data (genomics, transcriptomics, proteomics, etc.) from diseased and normal human tissue samples can be utilized for pharmacodynamic biomarker discovery and stratifying patient populations to predict the success of drug therapy candidates in clinical trials [2].
Downloaded by [University of Nebraska, Lincoln] at 22:02 11 September 2015
2.
Biobanks and biospecimen quality
In the past decade, biobanks have been increasingly recognized as vital investments for biomedical research given their efforts to collect, store and distribute human tissues. The usefulness and reliability of molecular data obtained from the biospecimens depends on the quality of the starting material. The ideal biospecimen is one that is an unaltered representation of the tissue in vivo [3]. In order for biobanks to come as close to this benchmark as possible, several important operational logistics must be considered during the biobank or project design phase. This includes identifying and describing the procedures for tissue acquisition, processing, storage and distribution. The use of standard operating procedures (SOPs) will help ensure that tissue samples are uniformly handled during the collection process, minimizing the chance of preanalytical variability. Preanalytical factors such as ischemia time, type of fixative, fixation time, storage temperature and length of storage are only a few variables that can result in poor quality and low yields of DNA, RNA and protein, affecting gene and protein expression. For example, ischemia and hypoxic conditions prior to freezing or fixation can initiate changes in tissue metabolism such as activation of proteases, leading to apoptotic or necrotic changes [4]. Another important component is the quality of tissue nucleic acids. Fresh and frozen tissue specimens yield better quality DNA and RNA than formalin fixation, if preserving tissue architecture is not an issue [5-7]. Along with adhering to SOPs for daily operations, biobanks are responding to and implementing best practices set forth by professional biobanking organizations such as the International Society of Biological and Environmental Repositories (ISBER) and the National Cancer Institute’s (NCI) Biorepositories and Biospecimen Research Branch. ISBER and NCI best practices for repositories outline recommendations for repository planning and organization, facilities design and management, quality control and quality assurance, safety, data management, ethical, legal and policy issues and cost management to name a few [8,9]. Recognizing the factors that impact biospecimen quality is not only important for biobanks, but for researchers as well. In designing studies and preparing assays, it is beneficial for researchers to prepare their biospecimen request(s) considering three dimensions: specimen type (normal tissue, diseased tissue, blood, serum, urine, etc.), target molecule (DNA, RNA, protein), and analysis platform (immunohistochemistry, 1384
immunoassays, mass spectrometry, quantitative reverse transcription polymerase chain reaction, etc.) [10]. In our experience, we are seeing an increasing trend in the end-users of human tissue requiring that biospecimen and data quality control measures are implemented and documented by the parties responsible for procurement. This control of preanalytical variables benefits early drug development investigations by ensuring the reproducibility of results, controlling for bias and avoiding false discoveries of biomarkers.
Molecular tissue profiling for research and drug development
3.
The value of molecular profiled tissue lies in its potential to improve the efficiency of drug discovery and development. The layers of accumulated sequencing and profiling data can be used to identify and validate novel drug targets and provide evidence to support a therapeutic hypothesis. This data will serve as the foundation for developing preclinical models that will better predict the success of late phase clinical trials and, at the same time, terminating others that lack supporting biological evidence. Furthermore, the data from molecular profiled tissues will accelerate progress in the design of clinical trials and targeted patient selection, such as the recently launched Lung Cancer Master Protocol trial for patients with lung squamous cell carcinoma [11]. Familiar successes in translating omics discoveries to targeted therapies include the response of human cancers to inhibitors of EGFR, PARP, BCR-ABL, and BRAF to name a few [12]. There are limitations of target validation based on human genetics and limitations to using a biomarker approach to stratifying patient populations [13,14]. Ultimately, however, the molecular profiling of human tissue enables the identification of biomarkers and druggable targets with greater probability of success, improving the outcomes of pharmaceutical research and development, and thereby yielding significant savings across the drug discovery and development pipeline [2]. For example, Plenge, Scolnick and Altshuler describe the impact human genetics will have in reducing the risk of attrition in Phase II and Phase III clinical trials. “It is estimated that a reduction in Phase II attrition from 66 to 50% would decrease the cost per new molecular entity by ~ $0.5 billion, and a reduction in Phase III attrition from 30 to 20% would decrease costs by ~ $0.3 billion”, according to the authors [13]. 4.
Large scale tissue profiling efforts
To date, advances in genome sequencing technologies have proved incredibly beneficial for oncology research. Large scale research efforts such as The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium continue to characterize hundreds of human tumor tissues with the common aim to provide cancer researchers comprehensive molecular data sets including, but not limited to, whole genome and exome sequencing and mRNA and microRNA
Expert Opin. Drug Discov. (2014) 9(12)
Downloaded by [University of Nebraska, Lincoln] at 22:02 11 September 2015
Using molecular profiled human tissue to accelerate drug discovery
expression profiling. With the availability of this data, investigators have identified genetic driver abberations and genetically defined tumor subtypes [15,16]. Recently, for example, the TCGA Research Network published their analyses of molecular profiles of 230 untreated, primary lung adenocarcinomas, identifying mutations that affect the RTK/RAS/RAF signaling pathway [17]. Advancements in omics technologies are bringing opportunities to drug development in areas of medicine other than oncology including neurology, cardiology and autoimmune diseases. In February 2014, the Accelerating Medicines Partnership (AMP) was launched to investigate the following diseases: Alzheimer’s disease, type 2 diabetes, rheumatoid arthritis and lupus. AMP joins together the National Institutes of Health (NIH) and 10 pharmaceutical companies in an unlikely public-private partnership where the collaborators have agreed to pool resources (tissue samples, data, expertise and funds) and to make the AMP data publicly accessible [18]. The project’s overall strategy is to provide access to human genetic and phenotype data in order to identify and evaluate the efficacy and safety of potential therapeutic targets, and thereby informing and accelerating the drug development pipeline. Within AMP, program milestones will include the aggregation of several thousand human DNA samples for genome sequence data and the creation of a knowledge portal containing sequence and phenotype data. In meeting these milestones, AMP will provide researchers the tools to test hypotheses related to genetic variation and validate drug targets [19].
Tissue profiling, data acquisition and integration
5.
Despite tremendous gains, the biomedical community has yet to fully capitalize on what high-dimensional molecular data has to offer for drug discovery. This is due to the challenges involving the growth of data, the growing types of data and the integration and analysis of this data. Obtaining gene expression, transcriptome and proteome profiles for millions of human tissue types from millions of individuals requires a high performance computational environment. Next generation technologies continue to make exponential progress in generating and cataloging scales of data from numerous human tissue samples, at which point, the demands are placed on information technology for big data acquisition and organization including data storage, maintenance, access and quality control. Furthermore, the computational architecture must be able to support the integration of large scale, heterogeneous data sets (clinical data, pre-analytical biospecimen variables and omics data) in order to prioritize biologically relevant data and construct predictive models of disease [20]. Moving forward, we will see a focus on the development of interoperable informatics tools, a progressive shift in standardizing data formats and a greater sharing of data [20,21].
6.
Future directions
Biorepositories and project-driven procurement initiatives should begin to collect ‘next generation biospecimens’ for comprehensive molecular characterization [21]. We broadly define these next generation biospecimens as fit-for-purpose, collected under controlled preanalytical conditions, with the downstream application in mind. These biospecimens and their associated preanalytical and clinical data will be required for emerging, various sequencing and profiling technologies such as exome sequencing and whole genome sequencing that will provide a deeper characterization of genome exploration. Additionally, future work with genetically profiled human tissue will focus on single cell sequencing and intra-tissue heterogeneity [22]. These efforts will be facilitated by multidisciplinary teams -- patients, clinicians, pathologists, biospecimen scientists, biomedical researchers, statisticians and the life science industry -- with hope that the molecular profiles will lead to biological breakthroughs in disease and translate into clinical applications for improving patient care. 7.
Expert opinion
Due to both academic and NIH/NCI rigor in tissue banking research, the research quality of human tissues has moved from many repositories that contain samples of very poor genomic and proteomic quality to repositories that contain well-annotated, high quality tissue samples. Regardless, many tissue banking operations in the US and abroad still do not collect biospecimens under proper protocols and SOPs for tissue collection. In many repositories the maintenance of proper storage of samples is not adhered to, and the histologic, molecular, and proteomic quality control metrics of the stored tissue samples do not meet the standards set by ISBER and NCI. These weaknesses inherent of so many tissue banks are current limitations for drug discovery researchers who rely on high quality tissue samples for target validation. The potential of improving on the quality metrics set by ISBER and NCI is a daunting task for many tissue banks. Most do not have the funds required to set up a viable business plan and to implement this endeavor into a strong, quality-controlled biorepository. Biospecimen storage solutions, whether basic or automatic, tend to be expensive to set up and maintain. What is known is the variety of storage solutions is expanding with technology improvements and the development of energy-efficient equipment. Continual advancements in nucleic acid and cell stability and quality assessment technologies will also greatly impact the tissue banking arena and lead to cost savings in current specimen storage formats (e.g., freezers and liquid nitrogen [LN2] tanks) and improve the speed of specimen processing and analysis times. Paper cards are one solution for ambient temperature long-term storage that permit the collection and
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storage of DNA or RNA without compromising their quality. Paper cards also allow for easy and efficient transport of dry samples without the need for bulky packaging materials and cold chain transportation. The scientific knowledge is quickly being gained by tissue banking scientists to store both processed DNA and RNA in a global fashion at most biorepositories in the next 5 -10 years. Current technologies will need to be continually reassessed for their adequacy to meet improved standards for reducing preanalytical variation. In consequence of this gained biospecimen quality and biostorage knowledge, this should limit the tissue sample size that is maintained in LN2 storage and limit the facility size needed for LN2 and freezer capacity. In the next few years, room temperature preservation and storage formats will move into institutional and private tissue banking operations. Room temperature preservation and storage will reduce the costs of storage and transport. One development we are watching includes the further development and refinement of the stabilization of mammalian cells in a dehydrated state as compared to liquid state [23,24]. The stability of RNA and cells at ambient temperature is still under development and has shorter shelf life as compared to DNA. With more research dollars and public/ private grant support, these technologies will soon be as valuable as the use of ambient DNA storage and be considered a standard practice for preserving RNA and cells. Technology developments for biobanking and biostorage are aimed at improving the quality of tissue samples as research materials, which are required to generate reliable, consistent gene expression data for drug discovery. Advancements in the molecular stabilization, preservation, and analysis of tissue specimens and the applications thereof will help improve the utilization rates of biospecimens. Many, if not all, biobanking operations maintain few to hundreds of tissue samples that are of poor molecular quality and contain little associated data. These unusable tissue samples are expensive to maintain. In our opinion, adherence to biospecimen best practices and SOPs combined with a close collaboration with the end users of the tissue specimens are the best approaches for reducing a biospecimen’s time in storage, making it readily usable for research.
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The ultimate goal of any human tissue biobanking operation is to provide standardized, fit-for-purpose human tissue specimens for translational research to academic institutions, biotechnology firms and the pharmaceutical industries. To this end, collection strategies must be consistent, data-driven and informed by the research priorities of the end-users of the tissue specimens. Biospecimens collected under these conditions can minimize the effect that pre-analytical factors would have on gene expression or protein phosphorylation, for example. However, preanalytical variables alone will not capture a biospecimen’s history. The donor diagnosis, demographics and treatment history must also be considered. These data points along with the molecular profile for each specimen can be added to larger disease data sets. Analysis of this data and across multiple data sets has the potential to answer important biological questions during drug discovery such as identifying biomarkers of disease progression, identifying disease subtypes and understanding which patients will likely respond to the candidate drug. As a result, we could see more effective, less toxic drug candidates in clinical development. Improvements in the drug discovery process start with biobanking and tissue specimens as the raw materials for research. Ultimately, high-quality biobanking can lead to better data, effective clinical trials, decreased research and discovery costs, improved patient outcomes, and increased drug discovery. Personalized medicine brought about by the research performed on high quality human tissue samples from various diseases will greatly change the current standard of care guidelines that are being used today to manage many different types of diseases, including Alzheimer’s disease, many type of cancer, many types of cardiovascular disease, obesity, diabetes and psychiatric diseases.
Declaration of interest K Tarvin is an employee of Analytical Biological Services, Inc. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.
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Using molecular profiled human tissue to accelerate drug discovery
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Affiliation Katherine A Tarvin1 MPH & George E Sandusky†2 DVM PhD † Author for correspondence 1 Biospecimen Operations Manager, Analytical Biological Services, Inc., 701 Cornell Drive, Wilmington, DE 19801, USA 2 Senior Research Professor, Indiana University School of Medicine, Department of Pathology and Laboratory Medicine, Van Nuys Medical Science Building, 635 Barnhill Drive, Room A128, Indianapolis, IN 46202-5120, USA Tel: +1 317 278 2304; Fax: +1 317 278 2018; E-mail: [email protected]
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