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Characteristics and Validation Techniques for PCA-Based Gene-Expression Signatures. Int J Genomics 2017; 2017:2354564. [PMID: 28265563 PMCID: PMC5317117 DOI: 10.1155/2017/2354564] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 12/15/2016] [Accepted: 01/04/2017] [Indexed: 11/30/2022] Open
Abstract
Background. Many gene-expression signatures exist for describing the biological state of profiled tumors. Principal Component Analysis (PCA) can be used to summarize a gene signature into a single score. Our hypothesis is that gene signatures can be validated when applied to new datasets, using inherent properties of PCA. Results. This validation is based on four key concepts. Coherence: elements of a gene signature should be correlated beyond chance. Uniqueness: the general direction of the data being examined can drive most of the observed signal. Robustness: if a gene signature is designed to measure a single biological effect, then this signal should be sufficiently strong and distinct compared to other signals within the signature. Transferability: the derived PCA gene signature score should describe the same biology in the target dataset as it does in the training dataset. Conclusions. The proposed validation procedure ensures that PCA-based gene signatures perform as expected when applied to datasets other than those that the signatures were trained upon. Complex signatures, describing multiple independent biological components, are also easily identified.
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Abstract
Solid tumors are multiscale, open, complex, dynamic systems: complex because they have many interacting components, dynamic because both the components and their interactions can change with time, and open because the tumor freely communicates with surrounding and even distant host tissue. Thus, it is not surprising that striking intratumoral variations are commonly observed in clinical imaging such as MRI and CT and that several recent studies found striking regional variations in the molecular properties of cancer cells from the same tumor. Interestingly, this spatial heterogeneity in molecular properties of tumor cells is typically ascribed to branching clonal evolution due to accumulating mutations while macroscopic variations observed in, for example, clinical MRI scans are usually viewed as functions of blood flow. The clinical significance of spatial heterogeneity has not been fully determined but there is a general consensus that the varying intratumoral landscape along with patient factors such as age, morbidity and lifestyle, contributes significantly to the often unpredictable response of individual patients within a disease cohort treated with the same standard-of-care therapy.Here we investigate the potential link between macroscopic tumor heterogeneity observed by clinical imaging and spatial variations in the observed molecular properties of cancer cells. We build on techniques developed in landscape ecology to link regional variations in the distribution of species with local environmental conditions that define their habitat. That is, we view each region of the tumor as a local ecosystem consisting of environmental conditions such as access to nutrients, oxygen, and means of waste clearance related to blood flow and the local population of tumor cells that both adapt to these conditions and, to some extent, change them through, for example, production of angiogenic factors. Furthermore, interactions among neighboring habitats can produce broader regional dynamics so that the internal diversity of tumors is the net result of complex multiscale somatic Darwinian interactions.Methods in landscape ecology harness Darwinian dynamics to link the environmental properties of a given region to the local populations which are assumed to represent maximally fit phenotypes within those conditions. Consider a common task of a landscape ecologist: defining the spatial distribution of species in a large region, e.g., in a satellite image. Clearly the most accurate approach requires a meter by meter survey of the multiple square kilometers in the region of interest. However, this is both impractical and potentially destructive. Instead, landscape ecology breaks the task into component parts relying on the Darwinian interdependence of environmental properties and fitness of specific species' phenotypic and genotypic properties. First, the satellite map is carefully analyzed to define the number and distribution of habitats. Then the species distribution in a representative sampling of each habitat is empirically determined. Ultimately, this permits sufficient bridging of spatial scales to accurately predict spatial distribution of plant and animal species within large regions.Currently, identifying intratumoral subpopulations requires detailed histological and molecular studies that are expensive and time consuming. Furthermore, this method is subject to sampling bias, is invasive for vital organs such as the brain, and inherently destructive precluding repeated assessments for monitoring post-treatment response and proteogenomic evolution. In contrast, modern cross-sectional imaging can interrogate the entire tumor noninvasively, allowing repeated analysis without disrupting the region of interest. In particular, magnetic resonance imaging (MRI) provides exceptional spatial resolution and generates signals that are unique to the molecular constituents of tissue. Here we propose that MRI scans may be the equivalent of satellite images in landscape ecology and, with appropriate application of Darwinian first principles and sophisticated image analytic methods, can be used to estimate regional variations in the molecular properties of cancer cells.We have initially examined this technique in glioblastoma, a malignant brain neoplasm which is morphologically complex and notorious for a fast progression from diagnosis to recurrence and death, making a suitable subject of noninvasive, rapidly repeated assessment of intratumoral evolution. Quantitative imaging analysis of routine clinical MRIs from glioblastoma has identified macroscopic morphologic characteristics which correlate with proteogenomics and prognosis. The key to the accurate detection and forecasting of intratumoral evolution using quantitative imaging analysis is likely to be in the understanding of the synergistic interactions between observable intratumoral subregions and the resulting tumor behavior.
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Affiliation(s)
- Joo Yeun Kim
- Department of Diagnostic Radiology, H. Lee Moffitt Cancer Center, Tampa, FL, 33612, USA
- Department of Integrative Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Robert A Gatenby
- Department of Diagnostic Radiology, H. Lee Moffitt Cancer Center, Tampa, FL, 33612, USA.
- Department of Integrative Mathematical Oncology, H. Lee Moffitt Cancer Center, Tampa, FL, 33612, USA.
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Thompson JA, Marsit CJ. A METHYLATION-TO-EXPRESSION FEATURE MODEL FOR GENERATING ACCURATE PROGNOSTIC RISK SCORES AND IDENTIFYING DISEASE TARGETS IN CLEAR CELL KIDNEY CANCER. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2017; 22:509-520. [PMID: 27897002 PMCID: PMC5177986 DOI: 10.1142/9789813207813_0047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many researchers now have available multiple high-dimensional molecular and clinical datasets when studying a disease. As we enter this multi-omic era of data analysis, new approaches that combine different levels of data (e.g. at the genomic and epigenomic levels) are required to fully capitalize on this opportunity. In this work, we outline a new approach to multi-omic data integration, which combines molecular and clinical predictors as part of a single analysis to create a prognostic risk score for clear cell renal cell carcinoma. The approach integrates data in multiple ways and yet creates models that are relatively straightforward to interpret and with a high level of performance. Furthermore, the proposed process of data integration captures relationships in the data that represent highly disease-relevant functions.
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Affiliation(s)
- Jeffrey A Thompson
- Program in Quantitative Biomedical Science, Geisel Medical School at Dartmouth College, Lebanon, NH 03756, USA,
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Abstract
Metastases that are resistant to conventional therapy are the major cause of death from cancer. In most patients, metastasis has already occurred by the time of diagnosis. Thus, the prevention of metastasis is unlikely to be of therapeutic benefit. The biological heterogeneity of metastases presents a major obstacle to treatment. However, the growth and survival of metastases depend on interactions between tumor cells and host homeostatic mechanisms. Targeting these interactions, in addition to the tumor cells, can produce synergistic therapeutic effects against existing metastases.
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Affiliation(s)
- Isaiah J Fidler
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 173, Houston, TX, 77030, USA.
| | - Margaret L Kripke
- Department of Immunology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 173, Houston, TX, 77030, USA
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Patel PG, Selvarajah S, Boursalie S, How NE, Ejdelman J, Guerard KP, Bartlett JM, Lapointe J, Park PC, Okello JBA, Berman DM. Preparation of Formalin-fixed Paraffin-embedded Tissue Cores for both RNA and DNA Extraction. J Vis Exp 2016. [PMID: 27583817 PMCID: PMC5091935 DOI: 10.3791/54299] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Formalin-fixed paraffin embedded tissue (FFPET) represents a valuable, well-annotated substrate for molecular investigations. The utility of FFPET in molecular analysis is complicated both by heterogeneous tissue composition and low yields when extracting nucleic acids. A literature search revealed a paucity of protocols addressing these issues, and none that showed a validated method for simultaneous extraction of RNA and DNA from regions of interest in FFPET. This method addresses both issues. Tissue specificity was achieved by mapping cancer areas of interest on microscope slides and transferring annotations onto FFPET blocks. Tissue cores were harvested from areas of interest using 0.6 mm microarray punches. Nucleic acid extraction was performed using a commercial FFPET extraction system, with modifications to homogenization, deparaffinization, and Proteinase K digestion steps to improve tissue digestion and increase nucleic acid yields. The modified protocol yields sufficient quantity and quality of nucleic acids for use in a number of downstream analyses, including a multi-analyte gene expression platform, as well as reverse transcriptase coupled real time PCR analysis of mRNA expression, and methylation-specific PCR (MSP) analysis of DNA methylation.
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Affiliation(s)
- Palak G Patel
- Department of Pathology & Molecular Medicine, Queen's University; Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University
| | - Shamini Selvarajah
- Department of Pathology & Molecular Medicine, Queen's University; Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University
| | - Suzanne Boursalie
- Department of Pathology & Molecular Medicine, Queen's University; Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University
| | - Nathan E How
- Department of Pathology & Molecular Medicine, Queen's University; Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University
| | - Joshua Ejdelman
- Department of Surgery, Division of Urology, McGill University
| | | | - John M Bartlett
- Transformative Pathology Program, Ontario Institute for Cancer Research (OICR)
| | | | - Paul C Park
- Department of Pathology & Molecular Medicine, Queen's University
| | - John B A Okello
- Department of Pathology & Molecular Medicine, Queen's University; Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University
| | - David M Berman
- Department of Pathology & Molecular Medicine, Queen's University; Division of Cancer Biology & Genetics, Queen's Cancer Research Institute, Queen's University;
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Sekula P, Pressler JB, Sauerbrei W, Goebell PJ, Schmitz-Dräger BJ. Assessment of the extent of unpublished studies in prognostic factor research: a systematic review of p53 immunohistochemistry in bladder cancer as an example. BMJ Open 2016; 6:e009972. [PMID: 27531721 PMCID: PMC5013379 DOI: 10.1136/bmjopen-2015-009972] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 06/20/2016] [Accepted: 07/05/2016] [Indexed: 01/05/2023] Open
Abstract
OBJECTIVES When study groups fail to publish their results, a subsequent systematic review may come to incorrect conclusions when combining information only from published studies. p53 expression measured by immunohistochemistry is a potential prognostic factor in bladder cancer. Although numerous studies have been conducted, its role is still under debate. The assumption that unpublished studies too harbour evidence on this research topic leads to the question about the attributable effect when adding this information and comparing it with published data. Thus, the aim was to identify published and unpublished studies and to explore their differences potentially affecting the conclusion on its function as a prognostic biomarker. DESIGN Systematic review of published and unpublished studies assessing p53 in bladder cancer in Germany between 1993 and 2007. RESULTS The systematic search revealed 16 studies of which 11 (69%) have been published and 5 (31%) have not. Key reason for not publishing the results was a loss of interest of the investigators. There were no obviously larger differences between published and unpublished studies. However, a meaningful meta-analysis was not possible mainly due to the poor (ie, incomplete) reporting of study results. CONCLUSIONS Within this well-defined population of studies, we could provide empirical evidence for the failure of study groups to publish their results that was mainly caused by loss of interest. This fact may be coresponsible for the role of p53 as a prognostic factor still being unclear. We consider p53 and the restriction to studies in Germany as a specific example, but the critical issues are probably similar for other prognostic factors and other countries.
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Affiliation(s)
- Peggy Sekula
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center – University of Freiburg,Freiburg, Germany
| | - Julia B Pressler
- Department of Urology, Schön-Klinik Nürnberg Fürth, Fürth, Germany
- KUNO University Children's Hospital, Regensburg, Germany
| | - Willi Sauerbrei
- Institute for Medical Biometry and Statistics, Faculty of Medicine and Medical Center – University of Freiburg,Freiburg, Germany
| | - Peter J Goebell
- Department of Urology, University Clinic of Erlangen, Waldkrankenhaus St. Marien, Erlangen, Germany
| | - Bernd J Schmitz-Dräger
- Department of Urology, Schön-Klinik Nürnberg Fürth, Fürth, Germany
- Department of Urology, University Clinic of Erlangen, Waldkrankenhaus St. Marien, Erlangen, Germany
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Alekseenko IV, Pleshkan VV, Monastyrskaya GS, Kuzmich AI, Snezhkov EV, Didych DA, Sverdlov ED. Fundamentally low reproducibility in molecular genetic cancer research. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416070036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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108
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Blanchard A. Mapping ethical and social aspects of cancer biomarkers. N Biotechnol 2016; 33:763-772. [PMID: 27318010 DOI: 10.1016/j.nbt.2016.06.1458] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 06/10/2016] [Indexed: 11/16/2022]
Abstract
Cancer biomarkers represent a revolutionary advance toward personalised cancer treatment, promising therapies that are tailored to subgroups of patients sharing similar generic traits. Notwithstanding the optimism driving this development, biomarkers also present an array of social and ethical questions, as witnessed in sporadic debates across different literatures. This review article seeks to consolidate these debates in a mapping of the complex terrain of ethical and social aspects of cancer biomarker research. This mapping was undertaken from the vantage point offered by a working cancer biomarker research centre called the Centre for Cancer Biomarkers (CCBIO) in Norway, according to a dialectic move between the literature and discussions with researchers and practitioners in the laboratory. Starting in the lab, we found that, with the exception of some classical bioethical dilemmas, researchers regarded many issues relative to the ethos of the biomarker community; how the complexity and uncertainty characterising biomarker research influence their scientific norms of quality. Such challenges to the ethos of cancer research remain largely implicit, outside the scope of formal bioethical enquiry, yet form the basis for other social and ethical issues. Indeed, looking out from the lab we see how questions of complexity, uncertainty and quality contribute to debates around social and global justice; undermining policies for the prioritisation of care, framing the stratification of those patients worthy of treatment, and limiting global access to this highly sophisticated research. We go on to discuss biomarker research within the culturally-constructed 'war on cancer' and highlight an important tension between the expectations of 'magic bullets' and the complexity and uncertainty faced in the lab. We conclude by arguing, with researchers in the CCBIO, for greater reflexivity and humility in cancer biomarker research and policy.
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Affiliation(s)
- Anne Blanchard
- Centre for the Study of the Sciences and the Humanities, University of Bergen, Allegaten 34, 5020 Bergen, Norway; Centre for Cancer Biomarkers, Jonas Lies vei 87, 5021 Bergen, Norway.
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109
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Qin LX, Levine DA. Study design and data analysis considerations for the discovery of prognostic molecular biomarkers: a case study of progression free survival in advanced serous ovarian cancer. BMC Med Genomics 2016; 9:27. [PMID: 27282150 PMCID: PMC4901402 DOI: 10.1186/s12920-016-0187-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 06/01/2016] [Indexed: 12/18/2022] Open
Abstract
Background Accurate discovery of molecular biomarkers that are prognostic of a clinical outcome is an important yet challenging task, partly due to the combination of the typically weak genomic signal for a clinical outcome and the frequently strong noise due to microarray handling effects. Effective strategies to resolve this challenge are in dire need. Methods We set out to assess the use of careful study design and data normalization for the discovery of prognostic molecular biomarkers. Taking progression free survival in advanced serous ovarian cancer as an example, we conducted empirical analysis on two sets of microRNA arrays for the same set of tumor samples: arrays in one set were collected using careful study design (that is, uniform handling and randomized array-to-sample assignment) and arrays in the other set were not. Results We found that (1) handling effects can confound the clinical outcome under study as a result of chance even with randomization, (2) the level of confounding handling effects can be reduced by data normalization, and (3) good study design cannot be replaced by post-hoc normalization. In addition, we provided a practical approach to define positive and negative control markers for detecting handling effects and assessing the performance of a normalization method. Conclusions Our work showcased the difficulty of finding prognostic biomarkers for a clinical outcome of weak genomic signals, illustrated the benefits of careful study design and data normalization, and provided a practical approach to identify handling effects and select a beneficial normalization method. Our work calls for careful study design and data analysis for the discovery of robust and translatable molecular biomarkers. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0187-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Li-Xuan Qin
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Douglas A Levine
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
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110
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Rush A, Byrne JA. Quality and reporting practices in an Australian cancer biobank cohort. Clin Biochem 2016; 49:492-497. [DOI: 10.1016/j.clinbiochem.2015.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/11/2015] [Accepted: 12/15/2015] [Indexed: 12/16/2022]
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111
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Kim S, Lin CW, Tseng GC. MetaKTSP: a meta-analytic top scoring pair method for robust cross-study validation of omics prediction analysis. Bioinformatics 2016; 32:1966-73. [PMID: 27153719 DOI: 10.1093/bioinformatics/btw115] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Accepted: 02/19/2016] [Indexed: 01/08/2023] Open
Abstract
MOTIVATION Supervised machine learning is widely applied to transcriptomic data to predict disease diagnosis, prognosis or survival. Robust and interpretable classifiers with high accuracy are usually favored for their clinical and translational potential. The top scoring pair (TSP) algorithm is an example that applies a simple rank-based algorithm to identify rank-altered gene pairs for classifier construction. Although many classification methods perform well in cross-validation of single expression profile, the performance usually greatly reduces in cross-study validation (i.e. the prediction model is established in the training study and applied to an independent test study) for all machine learning methods, including TSP. The failure of cross-study validation has largely diminished the potential translational and clinical values of the models. The purpose of this article is to develop a meta-analytic top scoring pair (MetaKTSP) framework that combines multiple transcriptomic studies and generates a robust prediction model applicable to independent test studies. RESULTS We proposed two frameworks, by averaging TSP scores or by combining P-values from individual studies, to select the top gene pairs for model construction. We applied the proposed methods in simulated data sets and three large-scale real applications in breast cancer, idiopathic pulmonary fibrosis and pan-cancer methylation. The result showed superior performance of cross-study validation accuracy and biomarker selection for the new meta-analytic framework. In conclusion, combining multiple omics data sets in the public domain increases robustness and accuracy of the classification model that will ultimately improve disease understanding and clinical treatment decisions to benefit patients. AVAILABILITY AND IMPLEMENTATION An R package MetaKTSP is available online. (http://tsenglab.biostat.pitt.edu/software.htm). CONTACT ctseng@pitt.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- SungHwan Kim
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA Department of Statistics, Korea University, Seoul, South Korea
| | - Chien-Wei Lin
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA Department of Computational and Systems Biology Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
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112
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Lechner M, Fenton TR. The Genomics, Epigenomics, and Transcriptomics of HPV-Associated Oropharyngeal Cancer--Understanding the Basis of a Rapidly Evolving Disease. ADVANCES IN GENETICS 2016; 93:1-56. [PMID: 26915269 DOI: 10.1016/bs.adgen.2015.12.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human papillomavirus (HPV) has been shown to represent a major independent risk factor for head and neck squamous cell cancer, in particular for oropharyngeal carcinoma. This type of cancer is rapidly evolving in the Western world, with rising trends particularly in the young, and represents a distinct epidemiological, clinical, and molecular entity. It is the aim of this review to give a detailed description of genomic, epigenomic, transcriptomic, and posttranscriptional changes that underlie the phenotype of this deadly disease. The review will also link these changes and examine what is known about the interactions between the host genome and viral genome, and investigate changes specific for the viral genome. These data are then integrated into an updated model of HPV-induced head and neck carcinogenesis.
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Affiliation(s)
- M Lechner
- Head and Neck Centre, University College London Hospital, London, UK; UCL Cancer Institute, University College London, London, United Kingdom
| | - T R Fenton
- UCL Cancer Institute, University College London, London, United Kingdom
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113
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Diebel KW, Zhou K, Clarke AB, Bemis LT. Beyond the Ribosome: Extra-translational Functions of tRNA Fragments. Biomark Insights 2016; 11:1-8. [PMID: 26843810 PMCID: PMC4734663 DOI: 10.4137/bmi.s35904] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/17/2015] [Accepted: 12/17/2015] [Indexed: 01/05/2023] Open
Abstract
High-throughput sequencing studies of small RNAs reveal a complex milieu of noncoding RNAs in biological samples. Early data analysis was often limited to microRNAs due to their regulatory nature and potential as biomarkers; however, many more classes of noncoding RNAs are now being recognized. A class of fragments initially excluded from analysis were those derived from transfer RNAs (tRNAs) because they were thought to be degradation products. More recently, critical cellular function has been attributed to tRNA fragments (tRFs), and their conservation across all domains of life has propelled them into an emerging area of scientific study. The biogenesis of tRFs is currently being elucidated, and initial studies show that a diverse array of tRFs are generated from all parts of a tRNA molecule. The goal of this review was to present what is currently known about tRFs and their potential as biomarkers for the earlier detection of disease.
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Affiliation(s)
- Kevin W Diebel
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
| | - Kun Zhou
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
| | - Aaron B Clarke
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
| | - Lynne T Bemis
- Department of Biomedical Sciences, University of Minnesota Medical School Duluth campus, Duluth, MN, USA
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114
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Salto-Tellez M, Kennedy RD. Integrated molecular pathology: the Belfast model. Drug Discov Today 2015; 20:1451-4. [PMID: 26499202 DOI: 10.1016/j.drudis.2015.10.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 02/07/2023]
Affiliation(s)
- Manuel Salto-Tellez
- Centre for Cancer Research and Cell Biology, Queen's University Belfast & Belfast Health and Social Care Board, Belfast, Northern Ireland, UK.
| | - Richard D Kennedy
- Centre for Cancer Research and Cell Biology, Queen's University Belfast & Belfast Health and Social Care Board, Belfast, Northern Ireland, UK; Almac Diagnostics, Craigavon, Northern Ireland, UK
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115
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Shah DK. Pharmacokinetic and pharmacodynamic considerations for the next generation protein therapeutics. J Pharmacokinet Pharmacodyn 2015; 42:553-71. [PMID: 26373957 DOI: 10.1007/s10928-015-9447-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 09/10/2015] [Indexed: 12/27/2022]
Abstract
Increasingly sophisticated protein engineering efforts have been undertaken lately to generate protein therapeutics with desired properties. This has resulted in the discovery of the next generation of protein therapeutics, which include: engineered antibodies, immunoconjugates, bi/multi-specific proteins, antibody mimetic novel scaffolds, and engineered ligands/receptors. These novel protein therapeutics possess unique physicochemical properties and act via a unique mechanism-of-action, which collectively makes their pharmacokinetics (PK) and pharmacodynamics (PD) different than other established biological molecules. Consequently, in order to support the discovery and development of these next generation molecules, it becomes important to understand the determinants controlling their PK/PD. This review discusses the determinants that a PK/PD scientist should consider during the design and development of next generation protein therapeutics. In addition, the role of systems PK/PD models in enabling rational development of the next generation protein therapeutics is emphasized.
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Affiliation(s)
- Dhaval K Shah
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, The State University of New York at Buffalo, 455 Kapoor Hall, Buffalo, NY, 14214-8033, USA.
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116
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Cheng C, Varn FS, Marsit CJ. E2F4 Program Is Predictive of Progression and Intravesical Immunotherapy Efficacy in Bladder Cancer. Mol Cancer Res 2015; 13:1316-24. [PMID: 26032289 PMCID: PMC4734892 DOI: 10.1158/1541-7786.mcr-15-0120] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 05/19/2015] [Indexed: 11/16/2022]
Abstract
UNLABELLED Bladder cancer is a common malignant disease, with non-muscle-invasive bladder cancer (NMIBC) representing the majority of tumors. This cancer subtype is typically treated by transurethral resection. In spite of treatment, up to 70% of patients show local recurrences. Intravesical BCG (Bacillus Calmette-Guerin) immunotherapy has been widely used to treat NMIBC, but it fails to suppress recurrence of bladder tumors in up to 40% of patients. Therefore, the development of prognostic markers is needed to predict the progression of bladder cancer and the efficacy of intravesical BCG treatment. This study demonstrates the effectiveness of an E2F4 signature for prognostic prediction of bladder cancer. E2F4 scores for each sample in a bladder cancer expression dataset were calculated by summarizing the relative expression levels of E2F4 target genes identified by ChIP-seq, and then the scores were used to stratify patients into good- and poor-outcome groups. The molecular signature was investigated in a single bladder cancer dataset and then its effectiveness was confirmed in two meta-bladder datasets consisting of specimens from multiple independent studies. These results were consistent in different datasets and demonstrate that the E2F4 score is predictive of clinical outcomes in bladder cancer, with patients whose tumors exhibit an E2F4 score >0 having significantly shorter survival times than those with an E2F4 score <0, in both non-muscle-invasive, and muscle-invasive bladder cancer. Furthermore, although intravesical BCG immunotherapy can significantly improve the clinical outcome of NMIBC patients with positive E2F4 scores (E2F4>0 group), it does not show significant treatment effect for those with negative scores (E2F4<0 group). IMPLICATIONS The E2F4 signature can be applied to predict the progression/recurrence and the responsiveness of patients to intravesical BCG immunotherapy in bladder cancer.
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Affiliation(s)
- Chao Cheng
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire. Institute for Quantitative Biomedical Sciences, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire. Norris Cotton Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire.
| | - Frederick S Varn
- Department of Genetics, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
| | - Carmen J Marsit
- Department of Pharmacology and Toxicology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire
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Nduom EK, Wei J, Yaghi NK, Huang N, Kong LY, Gabrusiewicz K, Ling X, Zhou S, Ivan C, Chen JQ, Burks JK, Fuller GN, Calin GA, Conrad CA, Creasy C, Ritthipichai K, Radvanyi L, Heimberger AB. PD-L1 expression and prognostic impact in glioblastoma. Neuro Oncol 2015; 18:195-205. [PMID: 26323609 DOI: 10.1093/neuonc/nov172] [Citation(s) in RCA: 410] [Impact Index Per Article: 45.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Accepted: 07/25/2015] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Therapeutic targeting of the immune checkpoints cytotoxic T-lymphocyte-associated molecule-4 (CTLA-4) and PD-1/PD-L1 has demonstrated tumor regression in clinical trials, and phase 2 trials are ongoing in glioblastoma (GBM). Previous reports have suggested that responses are more frequent in patients with tumors that express PD-L1; however, this has been disputed. At issue is the validation of PD-L1 biomarker assays and prognostic impact. METHODS Using immunohistochemical analysis, we measured the incidence of PD-L1 expression in 94 patients with GBM. We categorized our results according to the total number of PD-L1-expressing cells within the GBMs and then validated this finding in ex vivo GBM flow cytometry with further analysis of the T cell populations. We then evaluated the association between PD-L1 expression and median survival time using the protein expression datasets and mRNA from The Cancer Genome Atlas. RESULTS The median percentage of PD-L1-expressing cells in GBM by cell surface staining is 2.77% (range: 0%-86.6%; n = 92), which is similar to the percentage found by ex vivo flow cytometry. The majority of GBM patients (61%) had tumors with at least 1% or more PD-L1-positive cells, and 38% had at least 5% or greater PD-L1 expression. PD-L1 is commonly expressed on the GBM-infiltrating T cells. Expression of both PD-L1 and PD-1 are negative prognosticators for GBM outcome. CONCLUSIONS The incidence of PD-L1 expression in GBM patients is frequent but is confined to a minority subpopulation, similar to other malignancies that have been profiled for PD-L1 expression. Higher expression of PD-L1 is correlated with worse outcome.
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Affiliation(s)
- Edjah K Nduom
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Jun Wei
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Nasser K Yaghi
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Neal Huang
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Ling-Yuan Kong
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Konrad Gabrusiewicz
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Xiaoyang Ling
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Shouhao Zhou
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Cristina Ivan
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Jie Qing Chen
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Jared K Burks
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Greg N Fuller
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - George A Calin
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Charles A Conrad
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Caitlin Creasy
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Krit Ritthipichai
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Laszlo Radvanyi
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
| | - Amy B Heimberger
- Departments of Neurosurgery, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (E.K.N., J.W., N.K.Y., N.H., L.-Y.K., K.G., X.L., A.B.H.); Department of Biostatistics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (S.Z.); Center for RNA Interference and Non-Coding RNAs, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.I.); Flow Cytometry and Cell Imaging Core Facility, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (J.K.B.); Neuropathology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.N.F.); Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (G.A.C.); Neuro-Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.A.C.); Melanoma Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas (C.C., K.R.); Lion Biotechnologies, Woodland Hills, California (J.Q.C., L.R.); Dept. of Immunology, H. Lee Moffitt Cancer Center, Tampa, Florida (J.Q.C., L.R.)
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Barker AD, Compton CC, Poste G. The National Biomarker Development Alliance accelerating the translation of biomarkers to the clinic. Biomark Med 2015; 8:873-6. [PMID: 25224942 DOI: 10.2217/bmm.14.52] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
- Anna D Barker
- Complex Adaptive Systems, National Biomarker Development Alliance (NBDA), Arizona State University, SkySong, 1475 N. Scottsdale Rd, Suite 361, Scottsdale, AZ 85257, USA
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Hornick NI, Huan J, Doron B, Goloviznina NA, Lapidus J, Chang BH, Kurre P. Serum Exosome MicroRNA as a Minimally-Invasive Early Biomarker of AML. Sci Rep 2015; 5:11295. [PMID: 26067326 PMCID: PMC4650871 DOI: 10.1038/srep11295] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/21/2015] [Indexed: 12/18/2022] Open
Abstract
Relapse remains the major cause of mortality for patients with Acute Myeloid Leukemia (AML). Improved tracking of minimal residual disease (MRD) holds the promise of timely treatment adjustments to preempt relapse. Current surveillance techniques detect circulating blasts that coincide with advanced disease and poorly reflect MRD during early relapse. Here, we investigate exosomes as a minimally invasive platform for a microRNA (miRNA) biomarker. We identify a set of miRNA enriched in AML exosomes and track levels of circulating exosome miRNA that distinguish leukemic xenografts from both non-engrafted and human CD34+ controls. We develop biostatistical models that reveal circulating exosomal miRNA at low marrow tumor burden and before circulating blasts can be detected. Remarkably, both leukemic blasts and marrow stroma contribute to serum exosome miRNA. We propose development of serum exosome miRNA as a platform for a novel, sensitive compartment biomarker for prospective tracking and early detection of AML recurrence.
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MESH Headings
- Animals
- Biomarkers, Tumor/blood
- Exosomes/metabolism
- HL-60 Cells
- Humans
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- MicroRNAs/blood
- Neoplasms, Experimental/blood
- Neoplasms, Experimental/pathology
- RNA, Neoplasm/blood
- U937 Cells
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Affiliation(s)
- Noah I. Hornick
- Department of Pediatrics, Oregon Health & Science University, Portland, OR
- Department of Medicine, Oregon Health & Science University, Portland, OR
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR
| | - Jianya Huan
- Department of Pediatrics, Oregon Health & Science University, Portland, OR
- Department of Medicine, Oregon Health & Science University, Portland, OR
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR
| | - Ben Doron
- Department of Pediatrics, Oregon Health & Science University, Portland, OR
- Department of Medicine, Oregon Health & Science University, Portland, OR
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR
| | - Natalya A. Goloviznina
- Department of Pediatrics, Oregon Health & Science University, Portland, OR
- Department of Medicine, Oregon Health & Science University, Portland, OR
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR
| | - Jodi Lapidus
- Department of Public Health, Oregon Health & Science University, Portland, OR
| | - Bill H. Chang
- Department of Pediatrics, Oregon Health & Science University, Portland, OR
- Department of Medicine, Oregon Health & Science University, Portland, OR
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
| | - Peter Kurre
- Department of Pediatrics, Oregon Health & Science University, Portland, OR
- Department of Medicine, Oregon Health & Science University, Portland, OR
- Papé Family Pediatric Research Institute, Oregon Health & Science University, Portland, OR
- Knight Cancer Institute, Oregon Health & Science University, Portland, OR
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Geman D, Ochs M, Price ND, Tomasetti C, Younes L. An argument for mechanism-based statistical inference in cancer. Hum Genet 2015; 134:479-95. [PMID: 25381197 PMCID: PMC4612627 DOI: 10.1007/s00439-014-1501-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 10/14/2014] [Indexed: 01/07/2023]
Abstract
Cancer is perhaps the prototypical systems disease, and as such has been the focus of extensive study in quantitative systems biology. However, translating these programs into personalized clinical care remains elusive and incomplete. In this perspective, we argue that realizing this agenda—in particular, predicting disease phenotypes, progression and treatment response for individuals—requires going well beyond standard computational and bioinformatics tools and algorithms. It entails designing global mathematical models over network-scale configurations of genomic states and molecular concentrations, and learning the model parameters from limited available samples of high-dimensional and integrative omics data. As such, any plausible design should accommodate: biological mechanism, necessary for both feasible learning and interpretable decision making; stochasticity, to deal with uncertainty and observed variation at many scales; and a capacity for statistical inference at the patient level. This program, which requires a close, sustained collaboration between mathematicians and biologists, is illustrated in several contexts, including learning biomarkers, metabolism, cell signaling, network inference and tumorigenesis.
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Affiliation(s)
- Donald Geman
- Department of Applied Mathematics and Statistics, Johns Hopkins University, Baltimore, MD, 21210, USA,
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Modelska A, Quattrone A, Re A. Molecular portraits: the evolution of the concept of transcriptome-based cancer signatures. Brief Bioinform 2015; 16:1000-7. [PMID: 25832647 PMCID: PMC4652618 DOI: 10.1093/bib/bbv013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Indexed: 12/13/2022] Open
Abstract
Cancer results from dysregulation of multiple steps of gene expression programs. We review how transcriptome profiling has been widely explored for cancer classification and biomarker discovery but resulted in limited clinical impact. Therefore, we discuss alternative and complementary omics approaches.
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Tan GW, Khoo ASB, Tan LP. Evaluation of extraction kits and RT-qPCR systems adapted to high-throughput platform for circulating miRNAs. Sci Rep 2015; 5:9430. [PMID: 25800946 PMCID: PMC4371102 DOI: 10.1038/srep09430] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 03/05/2015] [Indexed: 01/14/2023] Open
Abstract
MicroRNAs regulate gene expression at the post-transcriptional level. Differential expression of miRNAs can potentially be used as biomarkers for early diagnosis and prediction for outcomes. Failure in validation of miRNA profiles is often caused by variations in experimental parameters. In this study, the performance of five extraction kits and three RT-qPCR systems were evaluated using BioMark high-throughput platform and the effects of different experimental parameters on circulating miRNA levels were determined. Differences in the performance of extraction kits as well as varying accuracy, sensitivity and reproducibility in qPCR systems were observed. Normalisation of RT-qPCR data to spike-in controls can reduce extraction bias. However, the extent of correlation for different qPCR systems varies in different assays. At different time points, there was no significant fold change in eight of the plasma miRNAs that we evaluated. Higher level of miRNAs was detected in plasma as compared to serum of the same cohort. In summary, we demonstrated that high-throughput RT-qPCR with pre-amplification step had increased sensitivity and can be achieved with accuracy and high reproducibility through stringent experimental controls. The information provided here is useful for planning biomarker validation studies involving circulating miRNAs.
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Affiliation(s)
- Geok Wee Tan
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Alan Soo Beng Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
| | - Lu Ping Tan
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Jalan Pahang, 50588 Kuala Lumpur, Malaysia
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123
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Detecting cancers through tumor-activatable minicircles that lead to a detectable blood biomarker. Proc Natl Acad Sci U S A 2015; 112:3068-73. [PMID: 25713388 DOI: 10.1073/pnas.1414156112] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Earlier detection of cancers can dramatically improve the efficacy of available treatment strategies. However, despite decades of effort on blood-based biomarker cancer detection, many promising endogenous biomarkers have failed clinically because of intractable problems such as highly variable background expression from nonmalignant tissues and tumor heterogeneity. In this work we present a tumor-detection strategy based on systemic administration of tumor-activatable minicircles that use the pan-tumor-specific Survivin promoter to drive expression of a secretable reporter that is detectable in the blood nearly exclusively in tumor-bearing subjects. After systemic administration we demonstrate a robust ability to differentiate mice bearing human melanoma metastases from tumor-free subjects for up to 2 wk simply by measuring blood reporter levels. Cumulative change in reporter levels also identified tumor-bearing subjects, and a receiver operator-characteristic curve analysis highlighted this test's performance with an area of 0.918 ± 0.084. Lung tumor burden additionally correlated (r(2) = 0.714; P < 0.05) with cumulative reporter levels, indicating that determination of disease extent was possible. Continued development of our system could improve tumor detectability dramatically because of the temporally controlled, high reporter expression in tumors and nearly zero background from healthy tissues. Our strategy's highly modular nature also allows it to be iteratively optimized over time to improve the test's sensitivity and specificity. We envision this system could be used first in patients at high risk for tumor recurrence, followed by screening high-risk populations before tumor diagnosis, and, if proven safe and effective, eventually may have potential as a powerful cancer-screening tool for the general population.
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124
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Evaluation of serum-based cancer biomarkers: A brief review from a clinical and computational viewpoint. Crit Rev Oncol Hematol 2015; 93:103-15. [DOI: 10.1016/j.critrevonc.2014.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 08/07/2014] [Accepted: 10/01/2014] [Indexed: 12/26/2022] Open
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Mordente A, Meucci E, Martorana GE, Silvestrini A. Cancer Biomarkers Discovery and Validation: State of the Art, Problems and Future Perspectives. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 867:9-26. [DOI: 10.1007/978-94-017-7215-0_2] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Poste G, Compton CC, Barker AD. The national biomarker development alliance: confronting the poor productivity of biomarker research and development. Expert Rev Mol Diagn 2014; 15:211-8. [PMID: 25420639 DOI: 10.1586/14737159.2015.974561] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Making precision (personalized) medicine a routine clinical reality will require a comprehensive inventory of validated biomarkers and molecular diagnostic tests to stratify disease subtypes and improve accuracy in diagnosis and treatment selection. Realization of this promise has been hindered by the poor productivity of biomarker identification and validation. This situation reflects deficiencies that are pervasive across the entire spectrum of biomarker R&D, from discovery to clinical validation and in the failure of regulatory and reimbursement policies to accommodate new classes of biomarkers. The launch of the National Biomarker Development Alliance is the culmination of a 2-year review and consultation process involving diverse stakeholders to advance standards, best practices and guidelines to enhance biomarker discovery and validation by adoption of systems-based approaches and trans-sector collaboration between academia, clinical medicine and relevant private and public sector stakeholders.
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Affiliation(s)
- George Poste
- NBDA, Arizona State University, SkySong, 1475 N. Scottsdale Rd., Suite 361, Scottsdale, AZ 85257, USA
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Kang H, Kiess A, Chung CH. Emerging biomarkers in head and neck cancer in the era of genomics. Nat Rev Clin Oncol 2014; 12:11-26. [PMID: 25403939 DOI: 10.1038/nrclinonc.2014.192] [Citation(s) in RCA: 201] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Head and neck cancer (HNC) broadly includes carcinomas arising from the mucosal epithelia of the head and neck region as well as various cell types of salivary glands and the thyroid. As reflected by the multiple sites and histologies of HNC, the molecular characteristics and clinical outcomes of this disease vary widely. In this Review, we focus on established and emerging biomarkers that are most relevant to nasopharyngeal carcinoma and head and neck squamous-cell carcinoma (HNSCC), which includes primary sites in the oral cavity, oropharynx, hypopharynx and larynx. Applications and limitations of currently established biomarkers are discussed along with examples of successful biomarker development. For emerging biomarkers, preclinical or retrospective data are also described in the context of recently completed comprehensive molecular analyses of HNSCC, which provide a broad genetic landscape and molecular classification beyond histology and clinical characteristics. We will highlight the ongoing effort that will see a shift from prognostic to predictive biomarker development in HNC with the goal of delivering individualized cancer therapy.
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Affiliation(s)
- Hyunseok Kang
- Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA
| | - Ana Kiess
- Department of Radiation Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA
| | - Christine H Chung
- 1] Department of Oncology, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA. [2] Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Johns Hopkins Medical Institutions, 1650 Orleans Street, CRB-1 Room 344, Baltimore, MD 21287-0013, USA
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Bass MB, Yao B, Hei YJ, Ye Y, Davis GJ, Davis MT, Kaesdorf BA, Chan SS, Patterson SD. Challenges in developing a validated biomarker for angiogenesis inhibitors: the motesanib experience. PLoS One 2014; 9:e108048. [PMID: 25314641 PMCID: PMC4196848 DOI: 10.1371/journal.pone.0108048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 08/24/2014] [Indexed: 12/19/2022] Open
Abstract
PURPOSE We sought to develop placental growth factor as a predictive pharmacodynamic biomarker for motesanib efficacy as first-line therapy in patients with advanced nonsquamous non-small-cell lung cancer. EXPERIMENTAL DESIGN Placental growth factor was evaluated at baseline and study week 4 (after 3 weeks treatment) in an exploratory analysis of data from a randomized phase 2 study of motesanib 125 mg once daily plus carboplatin/paclitaxel and in a prespecified analysis of data from a randomized, double-blind phase 3 study of motesanib 125 mg once daily plus carboplatin/paclitaxel vs placebo plus carboplatin/paclitaxel (MONET1). Associations between fold-change from baseline in placental growth factor and overall survival were evaluated using Cox proportional hazards models. RESULTS In the phase 2 study, serum placental growth factor increased from baseline a mean 2.8-fold at study week 4. Patients with ≥2.2-fold change from baseline in placental growth factor (n = 18) had significantly longer overall survival than those with <2.2-fold change (n = 19; 22.9 vs 7.9 months; hazard ratio, 0.30; 95% CI, 0.12-0.74; P = 0.009). Consequently, placental growth factor was investigated as a pharmacodynamic biomarker in the phase 3 MONET1 study. There was no association between log-transformed placental growth factor fold-change from baseline to week 4 (continuous variable) and overall survival (hazard ratio, 0.98; 95% CI, 0.79-1.22; P = 0.868). MONET1 did not meet its primary endpoint of overall survival. Likewise, median overall survival was similar among patients with ≥2.0-fold change in placental growth factor (n = 229) compared with <2.0-fold change (n = 127; 14.8 vs 13.8 months; hazard ratio, 0.88; 95% CI, 0.67-1.15, P = 0.340). CONCLUSIONS Our results illustrate the challenges of successfully translating phase 2 biomarker results into phase 3 studies. TRIAL REGISTRATION ClinicalTrials.gov NCT00460317, NCT00369070.
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Affiliation(s)
- Michael B. Bass
- Molecular Sciences and Computational Biology, Amgen Inc., Thousand Oaks, CA, United States of America
- * E-mail: (MBB); (SSC)
| | - Bin Yao
- Global Biostatistical Science, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Yong-Jiang Hei
- Oncology Development, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Yining Ye
- Global Biostatistical Science, Amgen Inc. South San Francisco, San Francisco, CA, United States of America
| | - Gerard J. Davis
- Diagnostics Division Research and Development, Abbott Laboratories, Abbott Park, IL, United States of America
| | - Michael T. Davis
- Molecular Sciences and Computational Biology, Amgen Inc., Thousand Oaks, CA, United States of America
| | - Barbara A. Kaesdorf
- Diagnostics Division Research and Development, Abbott Laboratories, Abbott Park, IL, United States of America
| | - Sabrina S. Chan
- Diagnostics Division Research and Development, Abbott Laboratories, Abbott Park, IL, United States of America
- * E-mail: (MBB); (SSC)
| | - Scott D. Patterson
- Medical Sciences, Amgen Inc., Thousand Oaks, CA, United States of America
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Abstract
Subclonal cancer populations change spatially and temporally during the disease course. Studies are revealing branched evolutionary cancer growth with low-frequency driver events present in subpopulations of cells, providing escape mechanisms for targeted therapeutic approaches. Despite such complexity, evidence is emerging for parallel evolution of subclones, mediated through distinct somatic events converging on the same gene, signal transduction pathway, or protein complex in different subclones within the same tumor. Tumors may follow gradualist paths (microevolution) as well as major shifts in evolutionary trajectories (macroevolution). Although macroevolution has been subject to considerable controversy in post-Darwinian evolutionary theory, we review evidence that such nongradual, saltatory leaps, driven through chromosomal rearrangements or genome doubling, may be particularly relevant to tumor evolution. Adapting cancer care to the challenges imposed by tumor micro- and macroevolution and developing deeper insight into parallel evolutionary events may prove central to improving outcome and reducing drug development costs.
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Affiliation(s)
- Marco Gerlinger
- Cancer Research UK London Research Institute, London, United Kingdom WC2A 3LY;
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130
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Cao HY, Yuan AH, Chen W, Shi XS, Miao Y. A DNA aptamer with high affinity and specificity for molecular recognition and targeting therapy of gastric cancer. BMC Cancer 2014; 14:699. [PMID: 25248985 PMCID: PMC4242496 DOI: 10.1186/1471-2407-14-699] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 09/10/2014] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Aptamers have emerged as excellent molecular probes for cancer diagnosis and therapy. The aim of the current study was to determine the feasibility of using DNA aptamer cy-apt 20 developed by live cell-SELEX for detecting and targeting gastric cancer. METHODS The specificity, sensitivity and biostability of cy-apt 20 in detecting gastric cancer were assessed by binding assay, cell fluorescence imaging, and in vivo tumor imaging in animal model in comparison with non-gastric cancers. RESULTS Flow cytometric analysis showed that cy-apt 20 had higher than 78% of maximal binding rate to gastric cancer cells, much higher than that of non-gastric cancer cells. Cell fluorescence imaging and in vivo tumor imaging showed that the targeting recognition could be visualized by using minimal dose of fluorochrome labeled cy-apt 20. Meanwhile, strong fluorescence signals were detected and lasted for a period of time longer than 50 min in vitro and 240 min in vivo. The fluorescence intensities of gastric cancer were about seven folds in vitro and five folds of that of non-gastric cancers in vivo. CONCLUSION Our study demonstrated that cy-apt 20 was an excellent molecular probe with high specificity and sensitivity and a certain degree of biostability for molecular recognition and targeting therapy of gastric cancer.
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Affiliation(s)
- Hong-Yong Cao
- />Department of General Surgery, Nanjing Hospital Affiliated to Nanjing Medical University, Nanjing, P. R. China
- />Department of General Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, P. R. China
| | - Ai-Hua Yuan
- />Department of General Surgery, Nanjing Hospital Affiliated to Nanjing Medical University, Nanjing, P. R. China
| | - Wei Chen
- />Department of General Surgery, Nanjing Hospital Affiliated to Nanjing Medical University, Nanjing, P. R. China
| | - Xue-Song Shi
- />Department of General Surgery, Nanjing Hospital Affiliated to Nanjing Medical University, Nanjing, P. R. China
| | - Yi Miao
- />Department of General Surgery, First Affiliated Hospital of Nanjing Medical University, Nanjing, P. R. China
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Li L, Masica D, Ishida M, Tomuleasa C, Umegaki S, Kalloo AN, Georgiades C, Singh VK, Khashab M, Amateau S, Li Z, Okolo P, Lennon AM, Saxena P, Geschwind JF, Schlachter T, Hong K, Pawlik TM, Canto M, Law J, Sharaiha R, Weiss CR, Thuluvath P, Goggins M, Ji Shin E, Peng H, Kumbhari V, Hutfless S, Zhou L, Mezey E, Meltzer SJ, Karchin R, Selaru FM. Human bile contains microRNA-laden extracellular vesicles that can be used for cholangiocarcinoma diagnosis. Hepatology 2014; 60:896-907. [PMID: 24497320 PMCID: PMC4121391 DOI: 10.1002/hep.27050] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Accepted: 01/29/2014] [Indexed: 12/15/2022]
Abstract
UNLABELLED Cholangiocarcinoma (CCA) presents significant diagnostic challenges, resulting in late patient diagnosis and poor survival rates. Primary sclerosing cholangitis (PSC) patients pose a particularly difficult clinical dilemma because they harbor chronic biliary strictures that are difficult to distinguish from CCA. MicroRNAs (miRs) have recently emerged as a valuable class of diagnostic markers; however, thus far, neither extracellular vesicles (EVs) nor miRs within EVs have been investigated in human bile. We aimed to comprehensively characterize human biliary EVs, including their miR content. We have established the presence of extracellular vesicles in human bile. In addition, we have demonstrated that human biliary EVs contain abundant miR species, which are stable and therefore amenable to the development of disease marker panels. Furthermore, we have characterized the protein content, size, numbers, and size distribution of human biliary EVs. Utilizing multivariate organization of combinatorial alterations (MOCA), we defined a novel biliary vesicle miR-based panel for CCA diagnosis that demonstrated a sensitivity of 67% and specificity of 96%. Importantly, our control group contained 13 PSC patients, 16 with biliary obstruction of varying etiologies (including benign biliary stricture, papillary stenosis, choledocholithiasis, extrinsic compression from pancreatic cysts, and cholangitis), and 3 with bile leak syndromes. Clinically, these types of patients present with a biliary obstructive clinical picture that could be confused with CCA. CONCLUSION These findings establish the importance of using extracellular vesicles, rather than whole bile, for developing miR-based disease markers in bile. Finally, we report on the development of a novel bile-based CCA diagnostic panel that is stable, reproducible, and has potential clinical utility.
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Affiliation(s)
- Ling Li
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA,Division of Gastroenterology, Third hospital of Peking University Health Science Center, Beijing, China
| | - David Masica
- Department of Biomedical Engineering and Institute for Computational Medicine Johns Hopkins University, Baltimore, Maryland, USA
| | - Masaharu Ishida
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Ciprian Tomuleasa
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA,Center for Genomics and Translational Medicine, Iuliu Hatieganu University of Medicine and Pharmacy, and Department of Hematology, Ion Chiricuta Comprehensive Cancer Center, Cluj Napoca, Romania
| | - Sho Umegaki
- Tohoku University School of Medicine, Sendai, Miyagi, Japan
| | - Anthony N. Kalloo
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Christos Georgiades
- Division of Gastroenterology and Hepatology, Department of Radiology, Johns Hopkins Hospital, Baltimore, Maryland, USA,Vascular & Interventional Radiology, American Medical Center, Nicosia, Cyprus
| | - Vikesh K. Singh
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Mouen Khashab
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Stuart Amateau
- Division of Gastroenterology and Hepatology, University of Colorado, Denver, Colorado, USA
| | - Zhiping Li
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Patrick Okolo
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Anne-Marie Lennon
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Payal Saxena
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Jean-Francois Geschwind
- Division of Gastroenterology and Hepatology, Department of Radiology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Todd Schlachter
- Division of Gastroenterology and Hepatology, Department of Radiology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Kelvin Hong
- Division of Gastroenterology and Hepatology, Department of Radiology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Timothy M. Pawlik
- Division of Gastroenterology and Hepatology, Department of Surgery, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Marcia Canto
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Joanna Law
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Reem Sharaiha
- Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, USA
| | - Clifford R. Weiss
- Division of Gastroenterology and Hepatology, Department of Radiology, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Paul Thuluvath
- The Institute for Digestive Health & Liver Disease at Mercy, Baltimore, USA
| | - Michael Goggins
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Eun Ji Shin
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Haoran Peng
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Vivek Kumbhari
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Susan Hutfless
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Liya Zhou
- Division of Gastroenterology, Third hospital of Peking University Health Science Center, Beijing, China
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA
| | - Rachel Karchin
- Department of Biomedical Engineering and Institute for Computational Medicine Johns Hopkins University, Baltimore, Maryland, USA
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland, USA,Sidney Kimmel Cancer Center, Johns Hopkins Hospital, Baltimore, Maryland, USA,Correspondence: Florin M. Selaru, MD, Johns Hopkins University, 720 Rutland Ave, Suite 950, Tel: (410) 614-3369, Fax: (410) 614-9612,
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132
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Su YH, Lin SY, Song W, Jain S. DNA markers in molecular diagnostics for hepatocellular carcinoma. Expert Rev Mol Diagn 2014; 14:803-17. [PMID: 25098554 DOI: 10.1586/14737159.2014.946908] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Hepatocellular carcinoma (HCC) is the one of the leading causes of cancer mortality in the world, mainly due to the difficulty of early detection and limited therapeutic options. The implementation of HCC surveillance programs in well-defined, high-risk populations were only able to detect about 40-50% of HCC at curative stages (Barcelona Clinic Liver Cancer stages 0 & 1) due to the low sensitivities of the current screening methods. The advance of sequencing technologies has identified numerous modifications as potential candidate DNA markers for diagnosis/surveillance. Here we aim to provide an overview of the DNA alterations that result in activation of cancer pathways known to potentially drive HCC carcinogenesis and to summarize performance characteristics of each DNA marker in the periphery (blood or urine) for HCC screening.
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Affiliation(s)
- Ying-Hsiu Su
- Department of Microbiology and Immunology, Drexel University College of Medicine, 3805 Old Easton Road, Philadelphia, PA 18902, USA
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Gardeux V, Achour I, Li J, Maienschein-Cline M, Li H, Pesce L, Parinandi G, Bahroos N, Winn R, Foster I, Garcia JGN, Lussier YA. 'N-of-1-pathways' unveils personal deregulated mechanisms from a single pair of RNA-Seq samples: towards precision medicine. J Am Med Inform Assoc 2014; 21:1015-25. [PMID: 25301808 PMCID: PMC4215042 DOI: 10.1136/amiajnl-2013-002519] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Background The emergence of precision medicine allowed the incorporation of individual molecular data into patient care. Indeed, DNA sequencing predicts somatic mutations in individual patients. However, these genetic features overlook dynamic epigenetic and phenotypic response to therapy. Meanwhile, accurate personal transcriptome interpretation remains an unmet challenge. Further, N-of-1 (single-subject) efficacy trials are increasingly pursued, but are underpowered for molecular marker discovery. Method ‘N-of-1-pathways’ is a global framework relying on three principles: (i) the statistical universe is a single patient; (ii) significance is derived from geneset/biomodules powered by paired samples from the same patient; and (iii) similarity between genesets/biomodules assesses commonality and differences, within-study and cross-studies. Thus, patient gene-level profiles are transformed into deregulated pathways. From RNA-Seq of 55 lung adenocarcinoma patients, N-of-1-pathways predicts the deregulated pathways of each patient. Results Cross-patient N-of-1-pathways obtains comparable results with conventional genesets enrichment analysis (GSEA) and differentially expressed gene (DEG) enrichment, validated in three external evaluations. Moreover, heatmap and star plots highlight both individual and shared mechanisms ranging from molecular to organ-systems levels (eg, DNA repair, signaling, immune response). Patients were ranked based on the similarity of their deregulated mechanisms to those of an independent gold standard, generating unsupervised clusters of diametric extreme survival phenotypes (p=0.03). Conclusions The N-of-1-pathways framework provides a robust statistical and relevant biological interpretation of individual disease-free survival that is often overlooked in conventional cross-patient studies. It enables mechanism-level classifiers with smaller cohorts as well as N-of-1 studies. Software http://lussierlab.org/publications/N-of-1-pathways
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Affiliation(s)
- Vincent Gardeux
- Department of Medicine, Bio5 Institute, UA Cancer Center, University of Arizona, Tucson, Arizona, USA Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA Department of Informatics, School of Engineering, EISTI (École Internationale des Sciences du Traitement de l'Information), Cergy-Pontoise, France Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Ikbel Achour
- Department of Medicine, Bio5 Institute, UA Cancer Center, University of Arizona, Tucson, Arizona, USA Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Jianrong Li
- Department of Medicine, Bio5 Institute, UA Cancer Center, University of Arizona, Tucson, Arizona, USA Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Mark Maienschein-Cline
- Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Haiquan Li
- Department of Medicine, Bio5 Institute, UA Cancer Center, University of Arizona, Tucson, Arizona, USA Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Lorenzo Pesce
- Computation Institute, Argonne National Laboratory & University of Chicago, Chicago, Illinois, USA
| | - Gurunadh Parinandi
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Neil Bahroos
- Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Robert Winn
- Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA University of Illinois Cancer Center, Chicago, Illinois, USA
| | - Ian Foster
- Computation Institute, Argonne National Laboratory & University of Chicago, Chicago, Illinois, USA Department of Computer Science, University of Chicago, Chicago, Illinois, USA Mathematics and Computer Science Division, Argonne National Laboratory, Chicago, Illinois, USA
| | - Joe G N Garcia
- Department of Medicine, Bio5 Institute, UA Cancer Center, University of Arizona, Tucson, Arizona, USA
| | - Yves A Lussier
- Department of Medicine, Bio5 Institute, UA Cancer Center, University of Arizona, Tucson, Arizona, USA Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA Institute for Translational Health Informatics, University of Illinois at Chicago, Chicago, Illinois, USA Computation Institute, Argonne National Laboratory & University of Chicago, Chicago, Illinois, USA University of Illinois Cancer Center, Chicago, Illinois, USA Department of Bioengineering, University of Illinois at Chicago, Chicago, Illinois, USA Department of Biopharmaceutical Science, College of Pharmacy, University of Illinois at Chicago, Illinois, USA Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA Department of Pharmacology, University of Illinois at Chicago, Chicago, Illinois, USA
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Khunger M, Kumar U, Roy HK, Tiwari AK. Dysplasia and cancer screening in 21st century. APMIS 2014; 122:674-82. [DOI: 10.1111/apm.12283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 03/24/2014] [Indexed: 12/16/2022]
Affiliation(s)
- Monica Khunger
- Department of Internal Medicine; All India Institute of Medical Sciences; New Delhi India
| | - Ujjwal Kumar
- Department of Internal Medicine; Michigan State University; East Lansing MI USA
| | - Hemant K. Roy
- Division of Gastroenterology, Department of Internal Medicine; Boston Medical Center; Boston MA USA
| | - Ashish K. Tiwari
- Department of Internal Medicine; Michigan State University; East Lansing MI USA
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135
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Fox NS, Starmans MHW, Haider S, Lambin P, Boutros PC. Ensemble analyses improve signatures of tumour hypoxia and reveal inter-platform differences. BMC Bioinformatics 2014; 15:170. [PMID: 24902696 PMCID: PMC4061774 DOI: 10.1186/1471-2105-15-170] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Accepted: 05/27/2014] [Indexed: 12/24/2022] Open
Abstract
Background The reproducibility of transcriptomic biomarkers across datasets remains poor, limiting clinical application. We and others have suggested that this is in-part caused by differential error-structure between datasets, and their incomplete removal by pre-processing algorithms. Methods To test this hypothesis, we systematically assessed the effects of pre-processing on biomarker classification using 24 different pre-processing methods and 15 distinct signatures of tumour hypoxia in 10 datasets (2,143 patients). Results We confirm strong pre-processing effects for all datasets and signatures, and find that these differ between microarray versions. Importantly, exploiting different pre-processing techniques in an ensemble technique improved classification for a majority of signatures. Conclusions Assessing biomarkers using an ensemble of pre-processing techniques shows clear value across multiple diseases, datasets and biomarkers. Importantly, ensemble classification improves biomarkers with initially good results but does not result in spuriously improved performance for poor biomarkers. While further research is required, this approach has the potential to become a standard for transcriptomic biomarkers.
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Affiliation(s)
| | | | | | | | - Paul C Boutros
- Informatics and Bio-computing Platform, Ontario Institute for Cancer Research, Toronto, Canada.
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136
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Aerts HJWL, Velazquez ER, Leijenaar RTH, Parmar C, Grossmann P, Carvalho S, Cavalho S, Bussink J, Monshouwer R, Haibe-Kains B, Rietveld D, Hoebers F, Rietbergen MM, Leemans CR, Dekker A, Quackenbush J, Gillies RJ, Lambin P. Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach. Nat Commun 2014; 5:4006. [PMID: 24892406 PMCID: PMC4059926 DOI: 10.1038/ncomms5006] [Citation(s) in RCA: 2902] [Impact Index Per Article: 290.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 04/29/2014] [Indexed: 11/09/2022] Open
Abstract
Human cancers exhibit strong phenotypic differences that can be visualized noninvasively by medical imaging. Radiomics refers to the comprehensive quantification of tumour phenotypes by applying a large number of quantitative image features. Here we present a radiomic analysis of 440 features quantifying tumour image intensity, shape and texture, which are extracted from computed tomography data of 1,019 patients with lung or head-and-neck cancer. We find that a large number of radiomic features have prognostic power in independent data sets of lung and head-and-neck cancer patients, many of which were not identified as significant before. Radiogenomics analysis reveals that a prognostic radiomic signature, capturing intratumour heterogeneity, is associated with underlying gene-expression patterns. These data suggest that radiomics identifies a general prognostic phenotype existing in both lung and head-and-neck cancer. This may have a clinical impact as imaging is routinely used in clinical practice, providing an unprecedented opportunity to improve decision-support in cancer treatment at low cost. An individual tumour is often heterogeneous and its various features can be visualised noninvasively using medical imaging. Here, the authors analyse large computed tomography data sets using radiomic algorithms to identify heterogeneity, and find that some of these tumour features have prognostic value across cancer types.
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Affiliation(s)
- Hugo J W L Aerts
- 1] Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands [2] Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA [3] Department of Radiology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA [4] Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA [5]
| | - Emmanuel Rios Velazquez
- 1] Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands [2] Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA [3]
| | - Ralph T H Leijenaar
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands
| | - Chintan Parmar
- 1] Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands [2] Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA
| | - Patrick Grossmann
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02215-5450, USA
| | | | - Sara Cavalho
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands
| | - Johan Bussink
- Department of Radiation Oncology, Radboud University Medical Center Nijmegen, PB 9101, 6500HB Nijmegen, The Netherlands
| | - René Monshouwer
- Department of Radiation Oncology, Radboud University Medical Center Nijmegen, PB 9101, 6500HB Nijmegen, The Netherlands
| | - Benjamin Haibe-Kains
- Princess Margaret Cancer Centre, University Health Network and Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada M5G 1L7
| | - Derek Rietveld
- Department of Radiation Oncology, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands
| | - Frank Hoebers
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands
| | - Michelle M Rietbergen
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands
| | - C René Leemans
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, 1081 HZ Amsterdam, The Netherlands
| | - Andre Dekker
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands
| | - John Quackenbush
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA
| | - Robert J Gillies
- Department of Cancer Imaging and Metabolism, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida 33612, USA
| | - Philippe Lambin
- Department of Radiation Oncology (MAASTRO), Research Institute GROW, Maastricht University, 6229ET Maastricht, The Netherlands
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137
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Tumor protein D52 (TPD52) and cancer-oncogene understudy or understudied oncogene? Tumour Biol 2014; 35:7369-82. [PMID: 24798974 DOI: 10.1007/s13277-014-2006-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 04/22/2014] [Indexed: 12/16/2022] Open
Abstract
The Tumor protein D52 (TPD52) gene was identified nearly 20 years ago through its overexpression in human cancer, and a substantial body of data now strongly supports TPD52 representing a gene amplification target at chromosome 8q21.13. This review updates progress toward understanding the significance of TPD52 overexpression and targeting, both in tumors known to be characterized by TPD52 overexpression/amplification, and those where TPD52 overexpression/amplification has been recently or variably reported. We highlight recent findings supporting microRNA regulation of TPD52 expression in experimental systems and describe progress toward deciphering TPD52's cellular functions, particularly in cancer cells. Finally, we provide an overview of TPD52's potential as a cancer biomarker and immunotherapeutic target. These combined studies highlight the potential value of genes such as TPD52, which are overexpressed in many cancer types, but have been relatively understudied.
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138
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Acosta-Martin AE, Lane L. Combining bioinformatics and MS-based proteomics: clinical implications. Expert Rev Proteomics 2014; 11:269-84. [PMID: 24720436 DOI: 10.1586/14789450.2014.900446] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research.
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139
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Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst 2014; 106:dju049. [PMID: 24700801 DOI: 10.1093/jnci/dju049] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Ovarian cancer is the fifth most common cause of cancer deaths in women in the United States. Numerous gene signatures of patient prognosis have been proposed, but diverse data and methods make these difficult to compare or use in a clinically meaningful way. We sought to identify successful published prognostic gene signatures through systematic validation using public data. METHODS A systematic review identified 14 prognostic models for late-stage ovarian cancer. For each, we evaluated its 1) reimplementation as described by the original study, 2) performance for prognosis of overall survival in independent data, and 3) performance compared with random gene signatures. We compared and ranked models by validation in 10 published datasets comprising 1251 primarily high-grade, late-stage serous ovarian cancer patients. All tests of statistical significance were two-sided. RESULTS Twelve published models had 95% confidence intervals of the C-index that did not include the null value of 0.5; eight outperformed 97.5% of signatures including the same number of randomly selected genes and trained on the same data. The four top-ranked models achieved overall validation C-indices of 0.56 to 0.60 and shared anticorrelation with expression of immune response pathways. Most models demonstrated lower accuracy in new datasets than in validation sets presented in their publication. CONCLUSIONS This analysis provides definitive support for a handful of prognostic models but also confirms that these require improvement to be of clinical value. This work addresses outstanding controversies in the ovarian cancer literature and provides a reproducible framework for meta-analytic evaluation of gene signatures.
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Affiliation(s)
- Levi Waldron
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Benjamin Haibe-Kains
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Aedín C Culhane
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Markus Riester
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Jie Ding
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Xin Victoria Wang
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Mahnaz Ahmadifar
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Svitlana Tyekucheva
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Christoph Bernau
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Thomas Risch
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Benjamin Frederick Ganzfried
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Curtis Huttenhower
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Michael Birrer
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Giovanni Parmigiani
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB).
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Waldron L, Haibe-Kains B, Culhane AC, Riester M, Ding J, Wang XV, Ahmadifar M, Tyekucheva S, Bernau C, Risch T, Ganzfried BF, Huttenhower C, Birrer M, Parmigiani G. Comparative meta-analysis of prognostic gene signatures for late-stage ovarian cancer. J Natl Cancer Inst 2014. [PMID: 24700801 DOI: 10.1093/jnci/dju049.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Ovarian cancer is the fifth most common cause of cancer deaths in women in the United States. Numerous gene signatures of patient prognosis have been proposed, but diverse data and methods make these difficult to compare or use in a clinically meaningful way. We sought to identify successful published prognostic gene signatures through systematic validation using public data. METHODS A systematic review identified 14 prognostic models for late-stage ovarian cancer. For each, we evaluated its 1) reimplementation as described by the original study, 2) performance for prognosis of overall survival in independent data, and 3) performance compared with random gene signatures. We compared and ranked models by validation in 10 published datasets comprising 1251 primarily high-grade, late-stage serous ovarian cancer patients. All tests of statistical significance were two-sided. RESULTS Twelve published models had 95% confidence intervals of the C-index that did not include the null value of 0.5; eight outperformed 97.5% of signatures including the same number of randomly selected genes and trained on the same data. The four top-ranked models achieved overall validation C-indices of 0.56 to 0.60 and shared anticorrelation with expression of immune response pathways. Most models demonstrated lower accuracy in new datasets than in validation sets presented in their publication. CONCLUSIONS This analysis provides definitive support for a handful of prognostic models but also confirms that these require improvement to be of clinical value. This work addresses outstanding controversies in the ovarian cancer literature and provides a reproducible framework for meta-analytic evaluation of gene signatures.
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Affiliation(s)
- Levi Waldron
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Benjamin Haibe-Kains
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Aedín C Culhane
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Markus Riester
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Jie Ding
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Xin Victoria Wang
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Mahnaz Ahmadifar
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Svitlana Tyekucheva
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Christoph Bernau
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Thomas Risch
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Benjamin Frederick Ganzfried
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Curtis Huttenhower
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Michael Birrer
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB)
| | - Giovanni Parmigiani
- Affiliations of authors: City University of New York School of Public Health, Hunter College, New York, NY (LW); Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA (LW, AC, MR, JD, XVW, ST, TR, BG, GP); Department of Biostatistics, Harvard School of Public Health, Boston, MA (LW, AC, CH, GP); Center for Cancer Research, Massachusetts General Hospital, Boston, MA (MB); Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada (BH); Medical Biophysics Department, University of Toronto, Toronto, Ontario, Canada (BH);Institute for Medical Information Sciences, Biometry, and Epidemiology, LMU Munich, Munich, Germany (CB).
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141
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Yang Z, Sweedler JV. Application of capillary electrophoresis for the early diagnosis of cancer. Anal Bioanal Chem 2014; 406:4013-31. [DOI: 10.1007/s00216-014-7722-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2013] [Revised: 02/18/2014] [Accepted: 02/21/2014] [Indexed: 02/07/2023]
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142
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Lin K, Lloyd-Jones DM, Li D, Carr JC. Quantitative imaging biomarkers for the evaluation of cardiovascular complications in type 2 diabetes mellitus. J Diabetes Complications 2014; 28:234-42. [PMID: 24309215 DOI: 10.1016/j.jdiacomp.2013.09.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 09/19/2013] [Accepted: 09/19/2013] [Indexed: 01/24/2023]
Abstract
Type 2 diabetes mellitus (T2DM) is a prevalent condition in aged populations. Cardiovascular diseases are leading causes of death and disability in patients with T2DM. Traditional strategies for controlling the cardiovascular complications of diabetes primarily target a cluster of well-defined risk factors, such as hyperglycemia, lipid disorders and hypertension. However, there is controversy over some recent clinical trials aimed at evaluating efficacy of intensive treatments for T2DM. As a powerful tool for quantitative cardiovascular risk estimation, multi-disciplinary cardiovascular imaging have been applied to detect and quantify morphological and functional abnormalities in the cardiovascular system. Quantitative imaging biomarkers acquired with advanced imaging procedures are expected to provide new insights to stratify absolute cardiovascular risks and reduce the overall costs of health care for people with T2DM by facilitating the selection of optimal therapies. This review discusses principles of state-of-the-art cardiovascular imaging techniques and compares applications of those techniques in various clinical circumstances. Individuals measurements of cardiovascular disease burdens from multiple aspects, which are closely related to existing biomarkers and clinical outcomes, are recommended as promising candidates for quantitative imaging biomarkers to assess the responses of the cardiovascular system during diabetic regimens.
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Affiliation(s)
- Kai Lin
- Department of Radiology, Northwestern University Feinberg School of Medicine, 737N Michigan Avenue, Suite 1600, Chicago, IL 60611, USA
| | - Donald M Lloyd-Jones
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680N Lake shore drive, Suite 1400, Chicago, IL 60611, USA
| | - Debiao Li
- Department of Radiology, Northwestern University Feinberg School of Medicine, 737N Michigan Avenue, Suite 1600, Chicago, IL 60611, USA
| | - James C Carr
- Department of Radiology, Northwestern University Feinberg School of Medicine, 737N Michigan Avenue, Suite 1600, Chicago, IL 60611, USA.
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143
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Gerlinger M, Horswell S, Larkin J, Rowan AJ, Salm MP, Varela I, Fisher R, McGranahan N, Matthews N, Santos CR, Martinez P, Phillimore B, Begum S, Rabinowitz A, Spencer-Dene B, Gulati S, Bates PA, Stamp G, Pickering L, Gore M, Nicol DL, Hazell S, Futreal PA, Stewart A, Swanton C. Genomic architecture and evolution of clear cell renal cell carcinomas defined by multiregion sequencing. Nat Genet 2014; 46:225-233. [PMID: 24487277 PMCID: PMC4636053 DOI: 10.1038/ng.2891] [Citation(s) in RCA: 948] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 01/13/2014] [Indexed: 02/08/2023]
Abstract
Clear cell renal carcinomas (ccRCCs) can display intratumor heterogeneity (ITH). We applied multiregion exome sequencing (M-seq) to resolve the genetic architecture and evolutionary histories of ten ccRCCs. Ultra-deep sequencing identified ITH in all cases. We found that 73-75% of identified ccRCC driver aberrations were subclonal, confounding estimates of driver mutation prevalence. ITH increased with the number of biopsies analyzed, without evidence of saturation in most tumors. Chromosome 3p loss and VHL aberrations were the only ubiquitous events. The proportion of C>T transitions at CpG sites increased during tumor progression. M-seq permits the temporal resolution of ccRCC evolution and refines mutational signatures occurring during tumor development.
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Affiliation(s)
- Marco Gerlinger
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK
| | - James Larkin
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Andrew J Rowan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Max P Salm
- Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK
| | - Ignacio Varela
- Instituto de Biomedicina y Biotecnología de Cantabria (CSIC-UC-Sodercan), Departamento de Biología Molecular, Universidad de Cantabria, Santander, Spain
| | - Rosalie Fisher
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Nicholas McGranahan
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Nicholas Matthews
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Claudio R Santos
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Pierre Martinez
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
| | - Benjamin Phillimore
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Sharmin Begum
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Adam Rabinowitz
- Advanced Sequencing Facility, Cancer Research UK London Research Institute, London, UK
| | - Bradley Spencer-Dene
- Experimental Histopathology, Cancer Research UK London Research Institute, London, UK
| | - Sakshi Gulati
- Biomolecular Modelling, Cancer Research UK London Research Institute, London, UK
| | - Paul A Bates
- Biomolecular Modelling, Cancer Research UK London Research Institute, London, UK
| | - Gordon Stamp
- Experimental Histopathology, Cancer Research UK London Research Institute, London, UK
| | - Lisa Pickering
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - Martin Gore
- Department of Medicine, Royal Marsden Hospital, London, UK
| | - David L Nicol
- Department of Urology, Royal Marsden Hospital, London, UK
| | - Steven Hazell
- Department of Pathology, Royal Marsden Hospital, London, UK
| | - P Andrew Futreal
- Department of Genomic Medicine, MD Anderson Cancer Center, Houston, Texas, USA
| | - Aengus Stewart
- Bioinformatics and Biostatistics, Cancer Research UK London Research Institute, London, UK
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, London, UK
- University College London Cancer Institute, University College London, London, UK
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144
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Aguirre-Gamboa R, Trevino V. SurvMicro: assessment of miRNA-based prognostic signatures for cancer clinical outcomes by multivariate survival analysis. Bioinformatics 2014; 30:1630-2. [DOI: 10.1093/bioinformatics/btu087] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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145
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Zhou M, Hall L, Goldgof D, Russo R, Balagurunathan Y, Gillies R, Gatenby R. Radiologically defined ecological dynamics and clinical outcomes in glioblastoma multiforme: preliminary results. Transl Oncol 2014; 7:5-13. [PMID: 24772202 PMCID: PMC3998688 DOI: 10.1593/tlo.13730] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 12/24/2013] [Accepted: 01/06/2014] [Indexed: 12/14/2022] Open
Abstract
MATERIALS AND METHODS We examined pretreatment magnetic resonance imaging (MRI) examinations from 32 patients with glioblastoma multiforme (GBM) enrolled in The Cancer Genome Atlas (TCGA). Spatial variations in T1 post-gadolinium and either T2-weighted or fluid attenuated inversion recovery sequences from each tumor MRI study were used to characterize each small region of the tumor by its local contrast enhancement and edema/cellularity ("habitat"). The patient cohort was divided into group 1 (survival < 400 days, n = 16) and group 2 (survival > 400 days, n = 16). RESULTS Histograms of relative values in each sequence demonstrated that the tumor regions were consistently divided into high and low blood contrast enhancement, each of which could be subdivided into regions of high, low, and intermediate cell density/interstitial edema. Group 1 tumors contained greater volumes of habitats with low contrast enhancement but intermediate and high cell density (not fully necrotic) than group 2. Both leave-one-out and 10-fold cross-validation schemes demonstrated that individual patients could be correctly assigned to the short or long survival group with 81.25% accuracy. CONCLUSION We demonstrate that novel image analytic techniques can characterize regional habitat variations in GBMs using combinations of MRI sequences. A preliminary study of 32 patients from the TCGA database found that the distribution of MRI-defined habitats varied significantly among the different survival groups. Radiologically defined ecological tumor analysis may provide valuable prognostic and predictive biomarkers in GBM and other tumors.
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Affiliation(s)
- Mu Zhou
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL
| | - Lawrence Hall
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL
| | - Dmitry Goldgof
- Department of Computer Science and Engineering, University of South Florida, Tampa, FL
| | - Robin Russo
- Departments of Radiology and Experimental Imaging, Moffitt Cancer Center, Tampa, FL
| | | | - Robert Gillies
- Departments of Radiology and Experimental Imaging, Moffitt Cancer Center, Tampa, FL
| | - Robert Gatenby
- Departments of Radiology and Experimental Imaging, Moffitt Cancer Center, Tampa, FL
- Cancer Biology and Evolution Program, Moffitt Cancer Center, Tampa, FL
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146
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Fleischhacker M, Dietrich D, Liebenberg V, Field JK, Schmidt B. The role of DNA methylation as biomarkers in the clinical management of lung cancer. Expert Rev Respir Med 2014; 7:363-83. [DOI: 10.1586/17476348.2013.814397] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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147
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Biobanking 3.0: evidence based and customer focused biobanking. Clin Biochem 2014; 47:300-8. [PMID: 24406300 DOI: 10.1016/j.clinbiochem.2013.12.018] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2013] [Revised: 12/08/2013] [Accepted: 12/13/2013] [Indexed: 01/19/2023]
Abstract
Biobanking is a new and very dynamic field. To achieve long term financial sustainability of biobank infrastructures we propose that a new focus is needed on activities, products and services provided by the biobank that relate to the external stakeholder: biobanking 3.0. Earlier stages of biobanking are biobanking 1.0 (primary focus on the number of biospecimens and data) and biobanking 2.0 (primary focus on the quality of biospecimens and data). Both stages 1.0 and 2.0 are predominantly product oriented areas and have required a mostly internal focus on operational development within the biobank itself. In this paper we will introduce our concept of biobanking 3.0 which capitalizes on the earlier stages but dictates a shift in focus to enhancing the value and impact for the three major sets of external stakeholders (people/patients, funders, and research customers) and creating a path to balanced and planned investment in biobank infrastructure and the sustainability of biobanking. Biobanking 3.0 will improve real understanding as well as perceptions of value across different stakeholders. Patients and donors will appreciate seeing how their biospecimens and data are effectively used for research. Funders will value the ability to plan efficient targeting of funding and to monitor the impact of their support. Researchers will capitalize on the ability to translate their ideas into effective knowledge. Ultimately adoption of biobanking 3.0 will impact on the sustainability in the three main dimensions relevant to biobanking: social sustainability (acceptability), operational sustainability (efficiency), and financial sustainability (accomplishment).
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148
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Anderson D, Kodukula K. Biomarkers in pharmacology and drug discovery. Biochem Pharmacol 2014; 87:172-88. [DOI: 10.1016/j.bcp.2013.08.026] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 08/19/2013] [Indexed: 12/21/2022]
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149
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Luo F, Gu J, Chen L, Xu X. Systems pharmacology strategies for anticancer drug discovery based on natural products. MOLECULAR BIOSYSTEMS 2014; 10:1912-7. [DOI: 10.1039/c4mb00105b] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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150
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Abstract
Cancer therapy, even when highly targeted, typically fails because of the remarkable capacity of malignant cells to evolve effective adaptations. These evolutionary dynamics are both a cause and a consequence of cancer system heterogeneity at many scales, ranging from genetic properties of individual cells to large-scale imaging features. Tumors of the same organ and cell type can have remarkably diverse appearances in different patients. Furthermore, even within a single tumor, marked variations in imaging features, such as necrosis or contrast enhancement, are common. Similar spatial variations recently have been reported in genetic profiles. Radiologic heterogeneity within tumors is usually governed by variations in blood flow, whereas genetic heterogeneity is typically ascribed to random mutations. However, evolution within tumors, as in all living systems, is subject to Darwinian principles; thus, it is governed by predictable and reproducible interactions between environmental selection forces and cell phenotype (not genotype). This link between regional variations in environmental properties and cellular adaptive strategies may permit clinical imaging to be used to assess and monitor intratumoral evolution in individual patients. This approach is enabled by new methods that extract, report, and analyze quantitative, reproducible, and mineable clinical imaging data. However, most current quantitative metrics lack spatialness, expressing quantitative radiologic features as a single value for a region of interest encompassing the whole tumor. In contrast, spatially explicit image analysis recognizes that tumors are heterogeneous but not well mixed and defines regionally distinct habitats, some of which appear to harbor tumor populations that are more aggressive and less treatable than others. By identifying regional variations in key environmental selection forces and evidence of cellular adaptation, clinical imaging can enable us to define intratumoral Darwinian dynamics before and during therapy. Advances in image analysis will place clinical imaging in an increasingly central role in the development of evolution-based patient-specific cancer therapy.
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Affiliation(s)
- Robert A Gatenby
- Departments of Radiology and Cancer Imaging and Metabolism, Moffitt Cancer Center, 12902 Magnolia Dr, Tampa, FL 33612
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