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Jiang Y, Rex DA, Schuster D, Neely BA, Rosano GL, Volkmar N, Momenzadeh A, Peters-Clarke TM, Egbert SB, Kreimer S, Doud EH, Crook OM, Yadav AK, Vanuopadath M, Hegeman AD, Mayta M, Duboff AG, Riley NM, Moritz RL, Meyer JG. Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry. ACS MEASUREMENT SCIENCE AU 2024; 4:338-417. [PMID: 39193565 PMCID: PMC11348894 DOI: 10.1021/acsmeasuresciau.3c00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/03/2024] [Accepted: 05/03/2024] [Indexed: 08/29/2024]
Abstract
Proteomics is the large scale study of protein structure and function from biological systems through protein identification and quantification. "Shotgun proteomics" or "bottom-up proteomics" is the prevailing strategy, in which proteins are hydrolyzed into peptides that are analyzed by mass spectrometry. Proteomics studies can be applied to diverse studies ranging from simple protein identification to studies of proteoforms, protein-protein interactions, protein structural alterations, absolute and relative protein quantification, post-translational modifications, and protein stability. To enable this range of different experiments, there are diverse strategies for proteome analysis. The nuances of how proteomic workflows differ may be challenging to understand for new practitioners. Here, we provide a comprehensive overview of different proteomics methods. We cover from biochemistry basics and protein extraction to biological interpretation and orthogonal validation. We expect this Review will serve as a handbook for researchers who are new to the field of bottom-up proteomics.
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Affiliation(s)
- Yuming Jiang
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Devasahayam Arokia
Balaya Rex
- Center for
Systems Biology and Molecular Medicine, Yenepoya Research Centre, Yenepoya (Deemed to be University), Mangalore 575018, India
| | - Dina Schuster
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
- Department
of Biology, Institute of Molecular Biology
and Biophysics, ETH Zurich, Zurich 8093, Switzerland
- Laboratory
of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen 5232, Switzerland
| | - Benjamin A. Neely
- Chemical
Sciences Division, National Institute of
Standards and Technology, NIST, Charleston, South Carolina 29412, United States
| | - Germán L. Rosano
- Mass
Spectrometry
Unit, Institute of Molecular and Cellular
Biology of Rosario, Rosario, 2000 Argentina
| | - Norbert Volkmar
- Department
of Biology, Institute of Molecular Systems
Biology, ETH Zurich, Zurich 8093, Switzerland
| | - Amanda Momenzadeh
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Trenton M. Peters-Clarke
- Department
of Pharmaceutical Chemistry, University
of California—San Francisco, San Francisco, California, 94158, United States
| | - Susan B. Egbert
- Department
of Chemistry, University of Manitoba, Winnipeg, Manitoba, R3T 2N2 Canada
| | - Simion Kreimer
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
| | - Emma H. Doud
- Center
for Proteome Analysis, Indiana University
School of Medicine, Indianapolis, Indiana, 46202-3082, United States
| | - Oliver M. Crook
- Oxford
Protein Informatics Group, Department of Statistics, University of Oxford, Oxford OX1 3LB, United
Kingdom
| | - Amit Kumar Yadav
- Translational
Health Science and Technology Institute, NCR Biotech Science Cluster 3rd Milestone Faridabad-Gurgaon
Expressway, Faridabad, Haryana 121001, India
| | | | - Adrian D. Hegeman
- Departments
of Horticultural Science and Plant and Microbial Biology, University of Minnesota, Twin Cities, Minnesota 55108, United States
| | - Martín
L. Mayta
- School
of Medicine and Health Sciences, Center for Health Sciences Research, Universidad Adventista del Plata, Libertador San Martin 3103, Argentina
- Molecular
Biology Department, School of Pharmacy and Biochemistry, Universidad Nacional de Rosario, Rosario 2000, Argentina
| | - Anna G. Duboff
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas M. Riley
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Robert L. Moritz
- Institute
for Systems biology, Seattle, Washington 98109, United States
| | - Jesse G. Meyer
- Department
of Computational Biomedicine, Cedars Sinai
Medical Center, Los Angeles, California 90048, United States
- Smidt Heart
Institute, Cedars Sinai Medical Center, Los Angeles, California 90048, United States
- Advanced
Clinical Biosystems Research Institute, Cedars Sinai Medical Center, Los
Angeles, California 90048, United States
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Mishra AK, Chong B, Arunachalam SP, Oberg AL, Majumder S. Machine Learning Models for Pancreatic Cancer Risk Prediction Using Electronic Health Record Data-A Systematic Review and Assessment. Am J Gastroenterol 2024; 119:1466-1482. [PMID: 38752654 PMCID: PMC11296923 DOI: 10.14309/ajg.0000000000002870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 05/06/2024] [Indexed: 06/20/2024]
Abstract
INTRODUCTION Accurate risk prediction can facilitate screening and early detection of pancreatic cancer (PC). We conducted a systematic review to critically evaluate effectiveness of machine learning (ML) and artificial intelligence (AI) techniques applied to electronic health records (EHR) for PC risk prediction. METHODS Ovid MEDLINE(R), Ovid EMBASE, Ovid Cochrane Central Register of Controlled Trials, Ovid Cochrane Database of Systematic Reviews, Scopus, and Web of Science were searched for articles that utilized ML/AI techniques to predict PC, published between January 1, 2012, and February 1, 2024. Study selection and data extraction were conducted by 2 independent reviewers. Critical appraisal and data extraction were performed using the CHecklist for critical Appraisal and data extraction for systematic Reviews of prediction Modelling Studies checklist. Risk of bias and applicability were examined using prediction model risk of bias assessment tool. RESULTS Thirty studies including 169,149 PC cases were identified. Logistic regression was the most frequent modeling method. Twenty studies utilized a curated set of known PC risk predictors or those identified by clinical experts. ML model discrimination performance (C-index) ranged from 0.57 to 1.0. Missing data were underreported, and most studies did not implement explainable-AI techniques or report exclusion time intervals. DISCUSSION AI/ML models for PC risk prediction using known risk factors perform reasonably well and may have near-term applications in identifying cohorts for targeted PC screening if validated in real-world data sets. The combined use of structured and unstructured EHR data using emerging AI models while incorporating explainable-AI techniques has the potential to identify novel PC risk factors, and this approach merits further study.
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Affiliation(s)
- Anup Kumar Mishra
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Bradford Chong
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | | | - Ann L. Oberg
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN, USA
| | - Shounak Majumder
- Department of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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Webster AP, Ecker S, Moghul I, Liu X, Dhami P, Marzi S, Paul DS, Kuxhausen M, Lee SJ, Spellman SR, Wang T, Feber A, Rakyan V, Peggs KS, Beck S. Donor whole blood DNA methylation is not a strong predictor of acute graft versus host disease in unrelated donor allogeneic haematopoietic cell transplantation. Front Genet 2024; 15:1242636. [PMID: 38633407 PMCID: PMC11021570 DOI: 10.3389/fgene.2024.1242636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Allogeneic hematopoietic cell transplantation (HCT) is used to treat many blood-based disorders and malignancies, however it can also result in serious adverse events, such as the development of acute graft-versus-host disease (aGVHD). This study aimed to develop a donor-specific epigenetic classifier to reduce incidence of aGVHD by improving donor selection. Genome-wide DNA methylation was assessed in a discovery cohort of 288 HCT donors selected based on recipient aGVHD outcome; this cohort consisted of 144 cases with aGVHD grades III-IV and 144 controls with no aGVHD. We applied a machine learning algorithm to identify CpG sites predictive of aGVHD. Receiver operating characteristic (ROC) curve analysis of these sites resulted in a classifier with an encouraging area under the ROC curve (AUC) of 0.91. To test this classifier, we used an independent validation cohort (n = 288) selected using the same criteria as the discovery cohort. Attempts to validate the classifier failed with the AUC falling to 0.51. These results indicate that donor DNA methylation may not be a suitable predictor of aGVHD in an HCT setting involving unrelated donors, despite the initial promising results in the discovery cohort. Our work highlights the importance of independent validation of machine learning classifiers, particularly when developing classifiers intended for clinical use.
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Affiliation(s)
- Amy P. Webster
- UCL Cancer Institute, University College London, London, United Kindom
- The University of Exeter Medical School, University of Exeter, Exeter, United Kindom
| | - Simone Ecker
- UCL Cancer Institute, University College London, London, United Kindom
| | - Ismail Moghul
- UCL Cancer Institute, University College London, London, United Kindom
| | - Xiaohong Liu
- UCL Cancer Institute, University College London, London, United Kindom
| | - Pawan Dhami
- UCL Cancer Institute, University College London, London, United Kindom
- NIHR Biomedical Research Centre, Guy’s Hospital London, London, United Kindom
| | - Sarah Marzi
- Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kindom
| | - Dirk S. Paul
- Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, United Kindom
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, NMDP, Minneapolis, United Kindom
| | - Stephanie J. Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, United Kindom
- Fred Hutchinson Cancer Research Center, University of Washington, Seattle, United Kindom
| | - Stephen R. Spellman
- Center for International Blood and Marrow Transplant Research, NMDP, Minneapolis, United Kindom
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, United Kindom
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, United Kindom
| | - Andrew Feber
- UCL Cancer Institute, University College London, London, United Kindom
- The Institute of Cancer Research, London, United Kindom
| | - Vardhman Rakyan
- Blizard Institute, Barts and the London School of Medicine and Dentistry, London, United Kindom
| | - Karl S. Peggs
- UCL Cancer Institute, University College London, London, United Kindom
- Department of Haematology, University College London, London, United Kindom
| | - Stephan Beck
- UCL Cancer Institute, University College London, London, United Kindom
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Surappa S, Multani P, Parlatan U, Sinawang PD, Kaifi J, Akin D, Demirci U. Integrated "lab-on-a-chip" microfluidic systems for isolation, enrichment, and analysis of cancer biomarkers. LAB ON A CHIP 2023; 23:2942-2958. [PMID: 37314731 PMCID: PMC10834032 DOI: 10.1039/d2lc01076c] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The liquid biopsy has garnered considerable attention as a complementary clinical tool for the early detection, molecular characterization and monitoring of cancer over the past decade. In contrast to traditional solid biopsy techniques, liquid biopsy offers a less invasive and safer alternative for routine cancer screening. Recent advances in microfluidic technologies have enabled handling of liquid biopsy-derived biomarkers with high sensitivity, throughput, and convenience. The integration of these multi-functional microfluidic technologies into a 'lab-on-a-chip' offers a powerful solution for processing and analyzing samples on a single platform, thereby reducing the complexity, bio-analyte loss and cross-contamination associated with multiple handling and transfer steps in more conventional benchtop workflows. This review critically addresses recent developments in integrated microfluidic technologies for cancer detection, highlighting isolation, enrichment, and analysis strategies for three important sub-types of cancer biomarkers: circulating tumor cells, circulating tumor DNA and exosomes. We first discuss the unique characteristics and advantages of the various lab-on-a-chip technologies developed to operate on each biomarker subtype. This is then followed by a discussion on the challenges and opportunities in the field of integrated systems for cancer detection. Ultimately, integrated microfluidic platforms form the core of a new class of point-of-care diagnostic tools by virtue of their ease-of-operation, portability and high sensitivity. Widespread availability of such tools could potentially result in more frequent and convenient screening for early signs of cancer at clinical labs or primary care offices.
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Affiliation(s)
- Sushruta Surappa
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Priyanka Multani
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Ugur Parlatan
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
| | - Prima Dewi Sinawang
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Jussuf Kaifi
- Department of Surgery, School of Medicine, University of Missouri, Columbia, MO 65212, USA
- Harry S. Truman Memorial Veterans' Hospital, Columbia, MO 65201, USA
| | - Demir Akin
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
- Center for Cancer Nanotechnology Excellence for Translational Diagnostics (CCNE-TD), School of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Utkan Demirci
- Canary Center at Stanford for Cancer Early Detection, Bio-Acoustic MEMS in Medicine (BAMM) Lab, Department of Radiology, School of Medicine, Stanford University, Palo Alto, CA 94304, USA.
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Squires M, Tao X, Elangovan S, Gururajan R, Zhou X, Acharya UR, Li Y. Deep learning and machine learning in psychiatry: a survey of current progress in depression detection, diagnosis and treatment. Brain Inform 2023; 10:10. [PMID: 37093301 PMCID: PMC10123592 DOI: 10.1186/s40708-023-00188-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/08/2023] [Indexed: 04/25/2023] Open
Abstract
Informatics paradigms for brain and mental health research have seen significant advances in recent years. These developments can largely be attributed to the emergence of new technologies such as machine learning, deep learning, and artificial intelligence. Data-driven methods have the potential to support mental health care by providing more precise and personalised approaches to detection, diagnosis, and treatment of depression. In particular, precision psychiatry is an emerging field that utilises advanced computational techniques to achieve a more individualised approach to mental health care. This survey provides an overview of the ways in which artificial intelligence is currently being used to support precision psychiatry. Advanced algorithms are being used to support all phases of the treatment cycle. These systems have the potential to identify individuals suffering from mental health conditions, allowing them to receive the care they need and tailor treatments to individual patients who are mostly to benefit. Additionally, unsupervised learning techniques are breaking down existing discrete diagnostic categories and highlighting the vast disease heterogeneity observed within depression diagnoses. Artificial intelligence also provides the opportunity to shift towards evidence-based treatment prescription, moving away from existing methods based on group averages. However, our analysis suggests there are several limitations currently inhibiting the progress of data-driven paradigms in care. Significantly, none of the surveyed articles demonstrate empirically improved patient outcomes over existing methods. Furthermore, greater consideration needs to be given to uncertainty quantification, model validation, constructing interdisciplinary teams of researchers, improved access to diverse data and standardised definitions within the field. Empirical validation of computer algorithms via randomised control trials which demonstrate measurable improvement to patient outcomes are the next step in progressing models to clinical implementation.
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Affiliation(s)
- Matthew Squires
- School of Mathematics, Physics and Computing, University of Southern Queensland, Toowoomba, QLD, Australia.
| | - Xiaohui Tao
- School of Mathematics, Physics and Computing, University of Southern Queensland, Toowoomba, QLD, Australia
| | | | - Raj Gururajan
- School of Business, University of Southern Queensland, Springfield, QLD, Australia
| | - Xujuan Zhou
- School of Business, University of Southern Queensland, Springfield, QLD, Australia
| | - U Rajendra Acharya
- School of Mathematics, Physics and Computing, University of Southern Queensland, Toowoomba, QLD, Australia
| | - Yuefeng Li
- School of Computer Science, Queensland University of Technology, Brisbane, QLD, Australia
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Patterson A, Elbasir A, Tian B, Auslander N. Computational Methods Summarizing Mutational Patterns in Cancer: Promise and Limitations for Clinical Applications. Cancers (Basel) 2023; 15:1958. [PMID: 37046619 PMCID: PMC10093138 DOI: 10.3390/cancers15071958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 02/24/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
Since the rise of next-generation sequencing technologies, the catalogue of mutations in cancer has been continuously expanding. To address the complexity of the cancer-genomic landscape and extract meaningful insights, numerous computational approaches have been developed over the last two decades. In this review, we survey the current leading computational methods to derive intricate mutational patterns in the context of clinical relevance. We begin with mutation signatures, explaining first how mutation signatures were developed and then examining the utility of studies using mutation signatures to correlate environmental effects on the cancer genome. Next, we examine current clinical research that employs mutation signatures and discuss the potential use cases and challenges of mutation signatures in clinical decision-making. We then examine computational studies developing tools to investigate complex patterns of mutations beyond the context of mutational signatures. We survey methods to identify cancer-driver genes, from single-driver studies to pathway and network analyses. In addition, we review methods inferring complex combinations of mutations for clinical tasks and using mutations integrated with multi-omics data to better predict cancer phenotypes. We examine the use of these tools for either discovery or prediction, including prediction of tumor origin, treatment outcomes, prognosis, and cancer typing. We further discuss the main limitations preventing widespread clinical integration of computational tools for the diagnosis and treatment of cancer. We end by proposing solutions to address these challenges using recent advances in machine learning.
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Affiliation(s)
- Andrew Patterson
- Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- The Wistar Institute, Philadelphia, PA 19104, USA
| | | | - Bin Tian
- The Wistar Institute, Philadelphia, PA 19104, USA
| | - Noam Auslander
- The Wistar Institute, Philadelphia, PA 19104, USA
- Department of Cancer Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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Comparative Studies on Resampling Techniques in Machine Learning and Deep Learning Models for Drug-Target Interaction Prediction. Molecules 2023; 28:molecules28041663. [PMID: 36838652 PMCID: PMC9964614 DOI: 10.3390/molecules28041663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 01/23/2023] [Accepted: 01/24/2023] [Indexed: 02/12/2023] Open
Abstract
The prediction of drug-target interactions (DTIs) is a vital step in drug discovery. The success of machine learning and deep learning methods in accurately predicting DTIs plays a huge role in drug discovery. However, when dealing with learning algorithms, the datasets used are usually highly dimensional and extremely imbalanced. To solve this issue, the dataset must be resampled accordingly. In this paper, we have compared several data resampling techniques to overcome class imbalance in machine learning methods as well as to study the effectiveness of deep learning methods in overcoming class imbalance in DTI prediction in terms of binary classification using ten (10) cancer-related activity classes from BindingDB. It is found that the use of Random Undersampling (RUS) in predicting DTIs severely affects the performance of a model, especially when the dataset is highly imbalanced, thus, rendering RUS unreliable. It is also found that SVM-SMOTE can be used as a go-to resampling method when paired with the Random Forest and Gaussian Naïve Bayes classifiers, whereby a high F1 score is recorded for all activity classes that are severely and moderately imbalanced. Additionally, the deep learning method called Multilayer Perceptron recorded high F1 scores for all activity classes even when no resampling method was applied.
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Blood Plasma Metabolome Profiling at Different Stages of Renal Cell Carcinoma. Cancers (Basel) 2022; 15:cancers15010140. [PMID: 36612136 PMCID: PMC9818272 DOI: 10.3390/cancers15010140] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 12/23/2022] [Accepted: 12/24/2022] [Indexed: 12/28/2022] Open
Abstract
Early diagnostics significantly improves the survival of patients with renal cell carcinoma (RCC), which is the prevailing type of adult kidney cancer. However, the absence of clinically obvious symptoms and effective screening strategies at the early stages result to disease progression and survival rate reducing. The study was focused on revealing of potential low molecular biomarkers for early-stage RCC. The untargeted direct injection mass spectrometry-based metabolite profiling of blood plasma samples from 51 non-cancer volunteers (control) and 78 patients with different RCC subtypes and stages (early stages of clear cell RCC (ccRCC), papillary RCC (pRCC), chromophobe RCC (chrRCC) and advanced stages of ccRCC) was performed. Comparative analysis of the blood plasma metabolites between the control and cancer groups provided the detection of metabolites associated with different tumor stages. The designed model based on the revealed metabolites demonstrated high diagnostic power and accuracy. Overall, using the metabolomics approach the study revealed the metabolites demonstrating a high value for design of plasma-based test to improve early ccRCC diagnosis.
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Desaire H, Go EP, Hua D. Advances, obstacles, and opportunities for machine learning in proteomics. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101069. [PMID: 36381226 PMCID: PMC9648337 DOI: 10.1016/j.xcrp.2022.101069] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The fields of proteomics and machine learning are both large disciplines, each producing well over 5,000 publications per year. However, studies combining both fields are still relatively rare, with only about 2% of recent proteomics papers including machine learning. This review, which focuses on the intersection of the fields, is intended to inspire proteomics researchers to develop skills and knowledge in the application of machine learning. A brief tutorial introduction to machine learning is provided, and research advances that rely on both fields, particularly as they relate to proteomics tools development and biomarker discovery, are highlighted. Key knowledge gaps and opportunities for scientific advancement are also enumerated.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - Eden P. Go
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
| | - David Hua
- Department of Chemistry, University of Kansas, Lawrence, KS 66045, USA
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Abstract
This review "teaches" researchers how to make their lackluster proteomics data look really impressive, by applying an inappropriate but pervasive strategy that selects features in a biased manner. The strategy is demonstrated and used to build a classification model with an accuracy of 92% and AUC of 0.98, while relying completely on random numbers for the data set. This "lesson" in data processing is not to be practiced by anyone; on the contrary, it is meant to be a cautionary tale showing that very unreliable results are obtained when a biomarker panel is generated first, using all the available data, and then tested by cross-validation. Data scientists describe the error committed in this scenario as having test data leak into the feature selection step, and it is currently a common mistake in proteomics biomarker studies that rely on machine learning. After the demonstration, advice is provided about how machine learning methods can be applied to proteomics data sets without generating artificially inflated accuracies.
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Affiliation(s)
- Heather Desaire
- Department of Chemistry, University of Kansas, Lawrence, Kansas 66045, United States
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11
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Clinical validation of a next-generation sequencing-based multi-cancer early detection "liquid biopsy" blood test in over 1,000 dogs using an independent testing set: The CANcer Detection in Dogs (CANDiD) study. PLoS One 2022; 17:e0266623. [PMID: 35471999 PMCID: PMC9041869 DOI: 10.1371/journal.pone.0266623] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 03/23/2022] [Indexed: 12/11/2022] Open
Abstract
Cancer is the leading cause of death in dogs, yet there are no established screening paradigms for early detection. Liquid biopsy methods that interrogate cancer-derived genomic alterations in cell-free DNA in blood are being adopted for multi-cancer early detection in human medicine and are now available for veterinary use. The CANcer Detection in Dogs (CANDiD) study is an international, multi-center clinical study designed to validate the performance of a novel multi-cancer early detection “liquid biopsy” test developed for noninvasive detection and characterization of cancer in dogs using next-generation sequencing (NGS) of blood-derived DNA; study results are reported here. In total, 1,358 cancer-diagnosed and presumably cancer-free dogs were enrolled in the study, representing the range of breeds, weights, ages, and cancer types seen in routine clinical practice; 1,100 subjects met inclusion criteria for analysis and were used in the validation of the test. Overall, the liquid biopsy test demonstrated a 54.7% (95% CI: 49.3–60.0%) sensitivity and a 98.5% (95% CI: 97.0–99.3%) specificity. For three of the most aggressive canine cancers (lymphoma, hemangiosarcoma, osteosarcoma), the detection rate was 85.4% (95% CI: 78.4–90.9%); and for eight of the most common canine cancers (lymphoma, hemangiosarcoma, osteosarcoma, soft tissue sarcoma, mast cell tumor, mammary gland carcinoma, anal sac adenocarcinoma, malignant melanoma), the detection rate was 61.9% (95% CI: 55.3–68.1%). The test detected cancer signal in patients representing 30 distinct cancer types and provided a Cancer Signal Origin prediction for a subset of patients with hematological malignancies. Furthermore, the test accurately detected cancer signal in four presumably cancer-free subjects before the onset of clinical signs, further supporting the utility of liquid biopsy as an early detection test. Taken together, these findings demonstrate that NGS-based liquid biopsy can offer a novel option for noninvasive multi-cancer detection in dogs.
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Zhang M, Huang L, Yang J, Xu W, Su H, Cao J, Wang Q, Pu J, Qian K. Ultra-Fast Label-Free Serum Metabolic Diagnosis of Coronary Heart Disease via a Deep Stabilizer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2101333. [PMID: 34323397 PMCID: PMC8456274 DOI: 10.1002/advs.202101333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/19/2021] [Indexed: 05/07/2023]
Abstract
Although mass spectrometry (MS) of metabolites has the potential to provide real-time monitoring of patient status for diagnostic purposes, the diagnostic application of MS is limited due to sample treatment and data quality/reproducibility. Here, the generation of a deep stabilizer for ultra-fast, label-free MS detection and the application of this method for serum metabolic diagnosis of coronary heart disease (CHD) are reported. Nanoparticle-assisted laser desorption/ionization-MS is used to achieve direct metabolic analysis of trace unprocessed serum in seconds. Furthermore, a deep stabilizer is constructed to map native MS results to high-quality results obtained by established methods. Finally, using the newly developed protocol and diagnosis variation characteristic surface to characterize sensitivity/specificity and variation, CHD is diagnosed with advanced accuracy in a high-throughput/speed manner. This work advances design of metabolic analysis tools for disease detection as it provides a direct label-free, ultra-fast, and stabilized platform for future protocol development in clinics.
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Affiliation(s)
- Mengji Zhang
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Lin Huang
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Jing Yang
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Wei Xu
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Haiyang Su
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Jing Cao
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Qian Wang
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringInstitute of Medical Robotics and Med‐X Research InstituteShanghai Jiao Tong UniversityShanghai200030P. R. China
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong UniversityShanghai Cancer Institute160 Pujian RoadShanghai200127P. R. China
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Padoan A, Clerico A, Zaninotto M, Trenti T, Tozzoli R, Aloe R, Alfano A, Rizzardi S, Dittadi R, Migliardi M, Bagnasco M, Plebani M. Percentile transformation and recalibration functions allow harmonization of thyroid-stimulating hormone (TSH) immunoassay results. Clin Chem Lab Med 2021; 58:1663-1672. [PMID: 31927515 DOI: 10.1515/cclm-2019-1167] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 12/09/2019] [Indexed: 01/22/2023]
Abstract
Background The comparability of thyroid-stimulating hormone (TSH) results cannot be easily obtained using SI-traceable reference measurement procedures (RPMs) or reference materials, whilst harmonization is more feasible. The aim of this study was to identify and validate a new approach for the harmonization of TSH results. Methods Percentile normalization was applied to 125,419 TSH results, obtained from seven laboratories using three immunoassays (Access 3rd IS Thyrotropin, Beckman Coulter Diagnostics; Architect System, Abbott Diagnostics and Elecsys, Roche Diagnostics). Recalibration equations (RCAL) were derived by robust regressions using bootstrapped distribution. Two datasets, the first of 119 EQAs, the second of 610, 638 and 639 results from Access, Architect and Elecsys TSH results, respectively, were used to validate RCAL. A dataset of 142,821 TSH values was used to derive reference intervals (RIs) after applying RCAL. Results Access, Abbott and Elecsys TSH distributions were significantly different (p < 0.001). RCAL intercepts and slopes were -0.003 and 0.984 for Access, 0.032 and 1.041 for Architect, -0.031 and 1.003 for Elecsys, respectively. Validation using EQAs showed that before and after RCAL, the coefficients of variation (CVs) or among-assay results decreased from 10.72% to 8.16%. The second validation dataset was used to test RCALs. The median of between-assay differences ranged from -0.0053 to 0.1955 mIU/L of TSH. Elecsys recalibrated to Access (and vice-versa) showed non-significant difference. TSH RI after RCAL resulted in 0.37-5.11 mIU/L overall, 0.49-4.96 mIU/L for females and 0.40-4.92 mIU/L for males. A significant difference across age classes was identified. Conclusions Percentile normalization and robust regression are valuable tools for deriving RCALs and harmonizing TSH values.
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Affiliation(s)
- Andrea Padoan
- Department of Medicine (DIMED), University of Padova, via Giustiniani 2, 35128, Padova, Italy.,Department of Laboratory Medicine, University-Hospital of Padova, via Giustiniani 2, 35128, Padova, Italy
| | - Aldo Clerico
- Laboratory of Cardiovascular Endocrinology and Cell Biology, Department of Laboratory Medicine, Fondazione CNR-Regione Toscana Gabriele Monasterio, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Martina Zaninotto
- Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy
| | - Tommaso Trenti
- Dipartimento di Medicina di Laboratorio e Anatomia Patologica, Azienda Ospedaliera Universitaria e USL di Modena, Modena, Italy
| | - Renato Tozzoli
- Clinical Pathology Laboratory, Department of Laboratory Medicine, Azienda per l'Assistenza Sanitaria n.5, Pordenone Hospital, Pordenone, Italy
| | - Rosalia Aloe
- Dipartimento di Biochimica ad Elevata Automazione, Dipartimento Diagnostico, Azienda Ospedaliero-Universitaria di Parma, Parma, Italy
| | - Antonio Alfano
- Clinical Pathology, Hospital ASL TO4, Ciriè, Turin, Italy
| | - Sara Rizzardi
- Laboratorio Analisi Aziendale (SC), Azienda Socio-Sanitaria Territoriale di Cremona, Istituti Ospitalieri, Cremona, Italy
| | - Ruggero Dittadi
- U.O.C. Laboratorio Analisi, Ospedale dell'Angelo, AULSS3 Serenissima, Mestre, Venezia, Italy
| | - Marco Migliardi
- S.C. Laboratorio Analisi, A.O. Ordine Mauriziano di Torino, Turin, Italy
| | | | - Mario Plebani
- Department of Laboratory Medicine, University-Hospital of Padova, Padova, Italy.,Department of Medicine (DIMED), University of Padova, Padova, Italy
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14
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Ask EH, Tschan-Plessl A, Gjerdingen TJ, Sætersmoen ML, Hoel HJ, Wiiger MT, Olweus J, Wahlin BE, Lingjærde OC, Horowitz A, Cashen AF, Watkins M, Fehniger TA, Holte H, Kolstad A, Malmberg KJ. A Systemic Protein Deviation Score Linked to PD-1+ CD8+ T Cell Expansion That Predicts Overall Survival in Diffuse Large B Cell Lymphoma. MED 2021; 2:180-195.e5. [DOI: 10.1016/j.medj.2020.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 10/01/2020] [Accepted: 10/30/2020] [Indexed: 10/22/2022]
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15
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Chen X, Sun J, Wang X, Yuan Y, Cai L, Xie Y, Fan Z, Liu K, Jiao X. A Meta-Analysis of Proteomic Blood Markers of Colorectal Cancer. Curr Med Chem 2021; 28:1176-1196. [PMID: 32338203 DOI: 10.2174/0929867327666200427094054] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 02/23/2020] [Accepted: 03/24/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Early diagnosis will significantly improve the survival rate of colorectal cancer (CRC); however, the existing methods for CRC screening were either invasive or inefficient. There is an emergency need for novel markers in CRC's early diagnosis. Serum proteomics has gained great potential in discovering novel markers, providing markers that reflect the early stage of cancer and prognosis prediction of CRC. In this paper, the results of proteomics of CRC studies were summarized through a meta-analysis in order to obtain the diagnostic efficiency of novel markers. METHODS A systematic search on bibliographic databases was performed to collect the studies that explore blood-based markers for CRC applying proteomics. The detection and validation methods, as well as the specificity and sensitivity of the biomarkers in these studies, were evaluated. Newcastle- Ottawa Scale (NOS) case-control studies version was used for quality assessment of included studies. RESULTS Thirty-four studies were selected from 751 studies, in which markers detected by proteomics were summarized. In total, fifty-nine proteins were classified according to their biological function. The sensitivity, specificity, or AUC varied among these markers. Among them, Mammalian STE20-like protein kinase 1/ Serine threonine kinase 4 (MST1/STK4), S100 calcium-binding protein A9 (S100A9), and Tissue inhibitor of metalloproteinases 1 (TIMP1) were suitable for effect sizes merging, and their diagnostic efficiencies were recalculated after merging. MST1/STK4 obtained a sensitivity of 68% and a specificity of 78%. S100A9 achieved a sensitivity of 72%, a specificity of 83%, and an AUC of 0.88. TIMP1 obtained a sensitivity of 42%, a specificity of 88%, and an AUC of 0.71. CONCLUSION MST1/STK4, S100A9, and TIMP1 showed excellent performance for CRC detection. Several other markers also presented optimized diagnostic efficacy for CRC early detection, but further verification is still needed before they are suitable for clinical use. The discovering of more efficient markers will benefit CRC treatment.
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Affiliation(s)
- Xiang Chen
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Jiayu Sun
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xue Wang
- Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yumeng Yuan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Leshan Cai
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yanxuan Xie
- The First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhiqiang Fan
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Kaixi Liu
- Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Xiaoyang Jiao
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou, Guangdong 515041, China
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16
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Xu W, Lin J, Gao M, Chen Y, Cao J, Pu J, Huang L, Zhao J, Qian K. Rapid Computer-Aided Diagnosis of Stroke by Serum Metabolic Fingerprint Based Multi-Modal Recognition. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2002021. [PMID: 33173737 PMCID: PMC7610260 DOI: 10.1002/advs.202002021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/30/2020] [Indexed: 05/07/2023]
Abstract
Stroke is a leading cause of mortality and disability worldwide, expected to result in 61 million disability-adjusted life-years in 2020. Rapid diagnostics is the core of stroke management for early prevention and medical treatment. Serum metabolic fingerprints (SMFs) reflect underlying disease progression, predictive of patient phenotypes. Deep learning (DL) encoding SMFs with clinical indexes outperforms single biomarkers, while posing challenges with poor prediction to interpret by feature selection. Herein, rapid computer-aided diagnosis of stroke is performed using SMF based multi-modal recognition by DL, to combine adaptive machine learning with a novel feature selection approach. SMFs are extracted by nano-assisted laser desorption/ionization mass spectrometry (LDI MS), consuming 100 nL of serum in seconds. A multi-modal recognition is constructed by integrating SMFs and clinical indexes with an enhanced area under curve (AUC) up to 0.845 for stroke screening, compared to single-modal diagnosis by only SMFs or clinical indexes. The prediction of DL is addressed by selecting 20 key metabolite features with differential regulation through a saliency map approach, shedding light on the molecular mechanisms in stroke. The approach highlights the emerging role of DL in precision medicine and suggests an expanding utility for computational analysis of SMFs in stroke screening.
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Affiliation(s)
- Wei Xu
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Jixian Lin
- Department of NeurologyMinhang HospitalFudan University170 Xinsong RoadShanghai201199P. R. China
| | - Ming Gao
- School of Management Science and EngineeringDongbei University of Finance and EconomicsDalian116025P. R. China
- Center for Post‐doctoral Studies of Computer ScienceNortheastern UniversityShenyang110819P. R. China
| | - Yuhan Chen
- School of Management Science and EngineeringDongbei University of Finance and EconomicsDalian116025P. R. China
- Center for Post‐doctoral Studies of Computer ScienceNortheastern UniversityShenyang110819P. R. China
| | - Jing Cao
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Jun Pu
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
| | - Lin Huang
- Stem Cell Research CenterRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
| | - Jing Zhao
- Department of NeurologyMinhang HospitalFudan University170 Xinsong RoadShanghai201199P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related GenesDivision of CardiologyRenji HospitalSchool of MedicineShanghai Jiao Tong University160 Pujian RoadShanghai200127P. R. China
- State Key Laboratory for Oncogenes and Related GenesSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai200030P. R. China
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Challenges and Opportunities in Clinical Applications of Blood-Based Proteomics in Cancer. Cancers (Basel) 2020; 12:cancers12092428. [PMID: 32867043 PMCID: PMC7564506 DOI: 10.3390/cancers12092428] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The traditional approach in identifying cancer related protein biomarkers has focused on evaluation of a single peptide/protein in tissue or circulation. At best, this approach has had limited success for clinical applications, since multiple pathological tumor pathways may be involved during initiation or progression of cancer which diminishes the significance of a single candidate protein/peptide. Emerging sensitive proteomic based technologies like liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics can provide a platform for evaluating serial serum or plasma samples to interrogate secreted products of tumor–host interactions, thereby revealing a more “complete” repertoire of biological variables encompassing heterogeneous tumor biology. However, several challenges need to be met for successful application of serum/plasma based proteomics. These include uniform pre-analyte processing of specimens, sensitive and specific proteomic analytical platforms and adequate attention to study design during discovery phase followed by validation of discovery-level signatures for prognostic, predictive, and diagnostic cancer biomarker applications. Abstract Blood is a readily accessible biofluid containing a plethora of important proteins, nucleic acids, and metabolites that can be used as clinical diagnostic tools in diseases, including cancer. Like the on-going efforts for cancer biomarker discovery using the liquid biopsy detection of circulating cell-free and cell-based tumor nucleic acids, the circulatory proteome has been underexplored for clinical cancer biomarker applications. A comprehensive proteome analysis of human serum/plasma with high-quality data and compelling interpretation can potentially provide opportunities for understanding disease mechanisms, although several challenges will have to be met. Serum/plasma proteome biomarkers are present in very low abundance, and there is high complexity involved due to the heterogeneity of cancers, for which there is a compelling need to develop sensitive and specific proteomic technologies and analytical platforms. To date, liquid chromatography mass spectrometry (LC-MS)-based quantitative proteomics has been a dominant analytical workflow to discover new potential cancer biomarkers in serum/plasma. This review will summarize the opportunities of serum proteomics for clinical applications; the challenges in the discovery of novel biomarkers in serum/plasma; and current proteomic strategies in cancer research for the application of serum/plasma proteomics for clinical prognostic, predictive, and diagnostic applications, as well as for monitoring minimal residual disease after treatments. We will highlight some of the recent advances in MS-based proteomics technologies with appropriate sample collection, processing uniformity, study design, and data analysis, focusing on how these integrated workflows can identify novel potential cancer biomarkers for clinical applications.
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Hanas JS, Hocker JRS, Evangeline B, Prabhakaran V, Oommen A, Rajshekhar V, Drevets DA, Carabin H. Distinguishing patients with idiopathic epilepsy from solitary cysticercus granuloma epilepsy and biochemical phenotype assessment using a serum biomolecule profiling platform. PLoS One 2020; 15:e0237064. [PMID: 32823271 PMCID: PMC7527271 DOI: 10.1371/journal.pone.0237064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 06/24/2020] [Indexed: 11/19/2022] Open
Abstract
A major source of epilepsy is Neurocysticercosis (NCC), caused by Taenia solium infection. Solitary cysticercus granuloma (SCG), a sub-group of NCC induced epilepsy, is the most common form of NCC in India. Current diagnostic criteria for SCG epilepsy require brain imaging which may not be available in communities where the disease is endemic. Identification of serum changes and potential biomolecules that could distinguish SCG epilepsy from idiopathic generalized epilepsy (IE), without the initial need for imaging, could assist in disease identification, understanding, and treatment. The objective here was to investigate, using mass spectrometry (MS), sera biomolecule differences between patients with SCG epilepsy or IE to help distinguish these disorders based on physiological differences, to understand underlying phenotypes and mechanisms, and to lay ground work for future therapeutic and biomarker analyses. Sera were obtained from patients with SCG or IE (N = 29 each group). Serum mass peak profiling was performed with electrospray ionization (ESI) MS, and mass peak area means in the two groups were compared using leave one [serum sample] out cross validation (LOOCV). Serum LOOCV analysis identified significant differences between SCG and IE patient groups (p = 10-20), which became non-significant (p = 0.074) when the samples were randomly allocated to the groups and reanalyzed. Tandem MS/MS peptide analysis of serum mass peaks from SCG or IE patients was performed to help identify potential peptide/protein biochemical and phenotypic changes involving these two forms of epilepsy. Bioinformatic analysis of these peptide/protein changes suggested neurological, inflammatory, seizure, blood brain barrier, cognition, ion channel, cell death, and behavior related biochemical systems were being altered in these disease states. This study provides groundwork for aiding in distinguishing SCG and IE patients in minimally invasive, lower-cost manners, for improving understanding of underlying epilepsy mechanisms, and for further identifying discriminatory biomarkers and potential therapeutic targets.
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Affiliation(s)
- Jay S. Hanas
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - James Randolph Sanders Hocker
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
| | - Betcy Evangeline
- Department of Neurological Sciences, Christian Medical College, Vellore, India
| | | | - Anna Oommen
- Department of Neurological Sciences, Christian Medical College, Vellore, India
| | - Vedantam Rajshekhar
- Department of Neurological Sciences, Christian Medical College, Vellore, India
| | - Douglas A. Drevets
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, and the Veterans Administration Medical Center, Oklahoma City, OK, United States of America
| | - Hélène Carabin
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, United States of America
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, Canada
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19
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Hocker JR, Lerner M, Lightfoot SA, Peyton MD, Thompson JL, Deb S, Reinersman M, Hanas RJ, Postier RG, Edil BH, Burkhart HM, Hanas JS. Serum discrimination and phenotype assessment of coronary artery disease patents with and without type 2 diabetes prior to coronary artery bypass graft surgery. PLoS One 2020; 15:e0234539. [PMID: 32756554 PMCID: PMC7527241 DOI: 10.1371/journal.pone.0234539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 05/12/2020] [Indexed: 11/18/2022] Open
Abstract
Diabetes Mellitus (DM) accelerates coronary artery disease (CAD) and atherosclerosis, the causes of most heart attacks. The biomolecules involved in these inter-related disease processes are not well understood. This study analyzes biomolecules in the sera of patients with CAD, with and without type (T) 2DM, who are about to undergo coronary artery bypass graft (CABG) surgery. The goal is to develop methodology to help identify and monitor CAD patients with and without T2DM, in order to better understand these phenotypes and to glean relationships through analysis of serum biomolecules. Aorta, fat, muscle, and vein tissues from CAD T2DM patients display diabetic-related histologic changes (e.g., lipid accumulation, fibrosis, loss of cellularity) when compared to non-diabetic CAD patients. The patient discriminatory methodology utilized is serum biomolecule mass profiling. This mass spectrometry (MS) approach is able to distinguish the sera of a group of CAD patients from controls (p value 10−15), with the CAD group containing both T2DM and non-diabetic patients. This result indicates the T2DM phenotype does not interfere appreciably with the CAD determination versus control individuals. Sera from a group of T2DM CAD patients however are distinguishable from non-T2DM CAD patients (p value 10−8), indicating it may be possible to examine the T2DM phenotype within the CAD disease state with this MS methodology. The same serum samples used in the CAD T2DM versus non-T2DM binary group comparison were subjected to MS/MS peptide structure analysis to help identify potential biochemical and phenotypic changes associated with CAD and T2DM. Such peptide/protein identifications could lead to improved understanding of underlying mechanisms, additional biomarkers for discriminating and monitoring these disease conditions, and potential therapeutic targets. Bioinformatics/systems biology analysis of the peptide/protein changes associated with CAD and T2DM suggested cell pathways/systems affected include atherosclerosis, DM, fibrosis, lipogenesis, loss of cellularity (apoptosis), and inflammation.
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Affiliation(s)
- James R. Hocker
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Megan Lerner
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Stan A. Lightfoot
- Department of Medicine The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Marvin D. Peyton
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Jess L. Thompson
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Subrato Deb
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Mathew Reinersman
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - R. Jane Hanas
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Russel G. Postier
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Barish H. Edil
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Harold M. Burkhart
- Department of Surgery The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
| | - Jay S. Hanas
- Department of Biochemistry and Molecular Biology The University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, United States of America
- * E-mail:
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Hanas JS, Hocker JRS, Vannarath C, Evangeline B, Prabhakaran V, Oommen A, Couch J, Anderson M, Rajshekhar V, Carabin H, Drevets D. Distinguishing and Biochemical Phenotype Analysis of Epilepsy Patients Using a Novel Serum Profiling Platform. Brain Sci 2020; 10:brainsci10080504. [PMID: 32751954 PMCID: PMC7464346 DOI: 10.3390/brainsci10080504] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/19/2020] [Accepted: 07/29/2020] [Indexed: 11/19/2022] Open
Abstract
Diagnosis of non-symptomatic epilepsy includes a history of two or more seizures and brain imaging to rule out structural changes like trauma, tumor, infection. Such analysis can be problematic. It is important to develop capabilities to help identify non-symptomatic epilepsy in order to better monitor and understand the condition. This understanding could lead to improved diagnostics and therapeutics. Serum mass peak profiling was performed using electrospray ionization mass spectrometry (ESI-MS). A comparison of sera mass peaks between epilepsy and control groups was performed via leave one [serum sample] out cross-validation (LOOCV). MS/MS peptide analysis was performed on serum mass peaks to compare epilepsy patient and control groups. LOOCV identified significant differences between the epilepsy patient group and control group (p = 10−22). This value became non-significant (p = 0.10) when the samples were randomly allocated between the groups and reanalyzed by LOOCV. LOOCV was thus able to distinguish a non-symptomatic epilepsy patient group from a control group based on physiological differences and underlying phenotype. MS/MS was able to identify potential peptide/protein changes involved in this epilepsy versus control comparison, with 70% of the top 100 proteins indicating overall neurologic function. Specifically, peptide/protein sera changes suggested neuro-inflammatory, seizure, ion-channel, synapse, and autoimmune pathways changing between epilepsy patients and controls.
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Affiliation(s)
- Jay S. Hanas
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.R.S.H.); (C.V.)
- Correspondence:
| | - James R. S. Hocker
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.R.S.H.); (C.V.)
| | - Christian Vannarath
- Department of Biochemistry, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (J.R.S.H.); (C.V.)
| | - Betcy Evangeline
- Department of Neurological Sciences, Christian Medical College, Vellore 632004, India; (B.E.); (V.P.); (A.O.); (V.R.)
| | - Vasudevan Prabhakaran
- Department of Neurological Sciences, Christian Medical College, Vellore 632004, India; (B.E.); (V.P.); (A.O.); (V.R.)
| | - Anna Oommen
- Department of Neurological Sciences, Christian Medical College, Vellore 632004, India; (B.E.); (V.P.); (A.O.); (V.R.)
| | - James Couch
- Department of Neurology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
| | - Michael Anderson
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.); (H.C.)
| | - Vedantam Rajshekhar
- Department of Neurological Sciences, Christian Medical College, Vellore 632004, India; (B.E.); (V.P.); (A.O.); (V.R.)
| | - Hélène Carabin
- Department of Biostatistics and Epidemiology, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA; (M.A.); (H.C.)
- Department of Pathology and Microbiology, Faculty of Veterinary Medicine, Université de Montréal, Saint-Hyacinthe, QC H3T 1J4, Canada
| | - Douglas Drevets
- Department of Internal Medicine, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104, USA;
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21
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Di Giovanni N, Meuwis MA, Louis E, Focant JF. Untargeted Serum Metabolic Profiling by Comprehensive Two-Dimensional Gas Chromatography–High-Resolution Time-of-Flight Mass Spectrometry. J Proteome Res 2019; 19:1013-1028. [DOI: 10.1021/acs.jproteome.9b00535] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Nicolas Di Giovanni
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
| | - Marie-Alice Meuwis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Edouard Louis
- GIGA institute, Translational Gastroenterology and CHU de Liège, Hepato-Gastroenterology and Digestive Oncology, Quartier Hôpital, University of Liège, Avenue de l’Hôpital 13, B34-35, B-4000 Liège, Belgium
| | - Jean-François Focant
- Department of Chemistry, Organic and Biological Analytical Chemistry Group, Quartier Agora, University of Liège, Allée du Six Août, B6c, B-4000 Liège (Sart Tilman), Belgium
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22
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Hanas JS, Hocker JRS, Lerner MR, Couch JR. Distinguishing and phenotype monitoring of traumatic brain injury and post-concussion syndrome including chronic migraine in serum of Iraq and Afghanistan war veterans. PLoS One 2019; 14:e0215762. [PMID: 31026304 PMCID: PMC6485717 DOI: 10.1371/journal.pone.0215762] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 04/08/2019] [Indexed: 12/31/2022] Open
Abstract
Traumatic Brain Injury (TBI) and persistent post-concussion syndrome (PCS) including chronic migraine (CM) are major health issues for civilians and the military. It is important to understand underlying biochemical mechanisms of these conditions, and be able to monitor them in an accurate and minimally invasive manner. This study describes the initial use of a novel serum analytical platform to help distinguish TBI patients, including those with post-traumatic headache (PTH), and to help identify phenotypes at play in these disorders. The hypothesis is that physiological responses to disease states like TBI and PTH and related bodily stresses are reflected in biomolecules in the blood in disease-specific manner. Leave one out (serum sample) cross validations (LOOCV) and sample randomizations were utilized to distinguished serum samples from the following TBI patient groups: TBI +PTSD + CM + severe depression (TBI "most affected" group) vs healthy controls, TBI "most affected" vs TBI, TBI vs controls, TBI + CM vs controls, and TBI + CM vs TBI. Inter-group discriminatory p values were ≤ 10-10, and sample group randomizations resulted in p non-significant values. Peptide/protein identifications of discriminatory mass peaks from the TBI "most affected" vs controls and from the TBI plus vs TBI minus CM groups yielded information of the cellular/molecular effects of these disorders (immune responses, amyloidosis/Alzheimer's disease/dementia, neuronal development). More specific biochemical disease effects appear to involve blood brain barrier, depression, migraine headache, autoimmunity, and autophagy pathways. This study demonstrated the ability for the first time of a novel, accurate, biomarker platform to monitor these conditions in serum, and help identify biochemical relationships leading to better understanding of these disorders and to potential therapeutic approaches.
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Affiliation(s)
- Jay S. Hanas
- Department of Biochemistry, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, United States of America
- Department of Surgery, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, United States of America
- Veterans Administration Hospital, Oklahoma City, Oklahoma, United States of America
| | - James R. S. Hocker
- Department of Biochemistry, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, United States of America
| | - Megan R. Lerner
- Department of Surgery, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, United States of America
| | - James R. Couch
- Department of Neurology, University of Oklahoma College of Medicine, Oklahoma City, Oklahoma, United States of America
- Department of Neurology, Veterans Administration Hospital, Oklahoma City, Oklahoma, United States of America
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23
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Zhao Z, Fan J, Hsu YMS, Lyon CJ, Ning B, Hu TY. Extracellular vesicles as cancer liquid biopsies: from discovery, validation, to clinical application. LAB ON A CHIP 2019; 19:1114-1140. [PMID: 30882822 PMCID: PMC6469512 DOI: 10.1039/c8lc01123k] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Substantial research has been devoted to elucidate the roles that extracellular vesicles (EVs) play in the regulation of both normal and pathological processes, and multiple studies have demonstrated their potential as a source of cancer biomarkers. However, several factors have slowed the development of liquid biopsy EV biomarkers for cancer diagnosis, including logistical and technical difficulties associated with reproducibly obtaining highly purified EVs suitable for diagnostic analysis. Significant effort has focused on addressing these problems, and multiple groups have now reported EV analysis methods using liquid biopsies that have the potential for clinical translation. However, there are still important issues that must be addressed if these discoveries and technical advances are to be used for clinical translation of EV cancer biomarkers from liquid biopsies. To address these issues, this review focuses on the potential application of EV biomarkers for diagnosis of major cancer types, discussing approaches for EV biomarker discovery and verification, EV clinical assay development, analytical and clinical validation, clinical trials, regulatory submission, and end user utilization for the intended clinical application. This review also discusses key difficulties related to these steps, and recommendations for how to best accomplish steps in order to translate EV-based biomarkers into clinical settings.
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Affiliation(s)
- Zhen Zhao
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
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24
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Vaysse PM, Heeren RMA, Porta T, Balluff B. Mass spectrometry imaging for clinical research - latest developments, applications, and current limitations. Analyst 2018. [PMID: 28642940 DOI: 10.1039/c7an00565b] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mass spectrometry is being used in many clinical research areas ranging from toxicology to personalized medicine. Of all the mass spectrometry techniques, mass spectrometry imaging (MSI), in particular, has continuously grown towards clinical acceptance. Significant technological and methodological improvements have contributed to enhance the performance of MSI recently, pushing the limits of throughput, spatial resolution, and sensitivity. This has stimulated the spread of MSI usage across various biomedical research areas such as oncology, neurological disorders, cardiology, and rheumatology, just to name a few. After highlighting the latest major developments and applications touching all aspects of translational research (i.e. from early pre-clinical to clinical research), we will discuss the present challenges in translational research performed with MSI: data management and analysis, molecular coverage and identification capabilities, and finally, reproducibility across multiple research centers, which is the largest remaining obstacle in moving MSI towards clinical routine.
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Affiliation(s)
- Pierre-Maxence Vaysse
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Ron M A Heeren
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Tiffany Porta
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
| | - Benjamin Balluff
- Maastricht MultiModal Molecular Imaging (M4I) institute, Division of Imaging Mass Spectrometry, Maastricht University, Universiteitssingel 50, 6229 ER, Maastricht, The Netherlands.
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25
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Hanas JS, Hocker JR, Ramajayam G, Prabhakaran V, Rajshekhar V, Oommen A, Manoj JJ, Anderson MP, Drevets DA, Carabin H. Distinguishing neurocysticercosis epilepsy from epilepsy of unknown etiology using a minimal serum mass profiling platform. Exp Parasitol 2018; 192:98-107. [PMID: 30096291 DOI: 10.1016/j.exppara.2018.07.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2018] [Revised: 06/08/2018] [Accepted: 07/20/2018] [Indexed: 11/29/2022]
Abstract
Neurocysticercosis is associated with epilepsy in pig-raising communities with poor sanitation. Current internationally recognized diagnostic guidelines for neurocysticercosis rely on brain imaging, a technology that is frequently not available or not accessible in areas endemic for neurocysticercosis. Minimally invasive and low-cost aids for diagnosing neurocysticercosis epilepsy could improve treatment of neurocysticercosis. The goal of this study was to test the extent to which patients with neurocysticercosis epilepsy, epilepsy of unknown etiology, idiopathic headaches and among different types of neurocysticercosis lesions could be distinguished from each other based on serum mass profiling. For this, we collected sera from patients with neurocysticercosis-associated epilepsy, epilepsy of unknown etiology, recovered neurocysticercosis, and idiopathic headaches then performed binary group comparisons among them using electrospray ionization mass spectrometry. A leave one [serum sample] out cross validation procedure was employed to analyze spectral data. Sera from neurocysticercosis patients was distinguished from epilepsy of unknown etiology patients with a p-value of 10-28. This distinction was lost when samples were randomized to either group (p-value = 0.22). Similarly, binary comparisons of patients with neurocysticercosis who has different types of lesions showed that different forms of this disease were also distinguishable from one another. These results suggest neurocysticercosis epilepsy can be distinguished from epilepsy of unknown etiology based on biomolecular differences in sera detected by mass profiling.
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Affiliation(s)
- Jay S Hanas
- Dept. of Biochemistry, University of Oklahoma Health Sciences Center (HSC), Oklahoma City, 73104, USA
| | - James R Hocker
- Dept. of Biochemistry, University of Oklahoma Health Sciences Center (HSC), Oklahoma City, 73104, USA
| | - Govindan Ramajayam
- Dept. of Neurological Sciences, Christian Medical College, Vellore, 632004, India
| | | | - Vedantam Rajshekhar
- Dept. of Neurological Sciences, Christian Medical College, Vellore, 632004, India
| | - Anna Oommen
- Dept. of Neurological Sciences, Christian Medical College, Vellore, 632004, India
| | - Josephine J Manoj
- Dept. of Neurological Sciences, Christian Medical College, Vellore, 632004, India
| | - Michael P Anderson
- Dept. of Biostatistics and Epidemiology, University of Oklahoma HSC, Oklahoma City, 73104, USA
| | - Douglas A Drevets
- Dept. of Internal Medicine, University of Oklahoma HSC, And the VA Medical Center, Oklahoma City, 73104, USA
| | - Hélène Carabin
- Dept. of Biostatistics and Epidemiology, University of Oklahoma HSC, Oklahoma City, 73104, USA.
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Abstract
Abstract
Both incidence and mortality of colorectal cancer (CRC) in Romania have shown a continuous increase during the last decades. Hereditary Non-Polyposic Colorectal Cancer (HNPCC), also known as Lynch syndrome, is mainly attributable to mismatch repair (MMR) genes MSH2, MSH6, and MLH1. Individuals carrying germ-line mutations of these genes present high lifetime risk of colorectal and other cancers, compared to non-carriers. Oncogenetics is developed worldwide nowadays, for identifying hereditary predisposition to cancer and offering appropriate clinical follow-up to patients and mutation carriers in Lynch families. Molecular oncogenetic diagnosis in Lynch syndrome is based on complete Sanger sequencing of entire MMR genes, which is time and resources consuming, therefore needing an appropriate and adapted optimization. Conventional sequencing requires a sufficient number of available samples to be processed simultaneously, which increases the waiting time for diagnostic results. Complete analysis for only one patient meets difficult technical problems due to the complex co-amplification of all gene regions of interest within the same conditions, therefore increasing the costs and reducing the cost-effectiveness of the test. Here we present an original and robust technical protocol for sequencing the entire MSH2, MSH6, and MLH1 coding sequence for one patient in a single PCR plate. Our optimized and verified system overcomes all technical problems and offers a quick, robust, and cost-effective possibility to personalize molecular oncogenetic diagnosis in Lynch syndrome.
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27
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Biomarker Guidelines for High-Dimensional Genomic Studies in Transplantation: Adding Method to the Madness. Transplantation 2018; 101:457-463. [PMID: 28212255 DOI: 10.1097/tp.0000000000001622] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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28
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Lyons-Weiler J. Standards of Excellence and Open Questions in Cancer Biomarker Research: An Informatics Perspective. Cancer Inform 2017. [DOI: 10.1177/117693510500100105] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Hocker JR, Deb SJ, Li M, Lerner MR, Lightfoot SA, Quillet AA, Hanas RJ, Reinersman M, Thompson JL, Vu NT, Kupiec TC, Brackett DJ, Peyton MD, Dubinett SM, Burkhart HM, Postier RG, Hanas JS. Serum Monitoring and Phenotype Identification of Stage I Non-Small Cell Lung Cancer Patients. Cancer Invest 2017; 35:573-585. [PMID: 28949774 DOI: 10.1080/07357907.2017.1373120] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
A stage I non-small cell lung cancer (NSCLC) serum profiling platform is presented which is highly efficient and accurate. Test sensitivity (0.95) for stage I NSCLC is the highest reported so far. Test metrics are reported for discriminating stage I adenocarcinoma vs squamous cell carcinoma subtypes. Blinded analysis identified 23 out of 24 stage I NSCLC and control serum samples. Group-discriminating mass peaks were targeted for tandem mass spectrometry peptide/protein identification, and yielded a lung cancer phenotype. Bioinformatic analysis revealed a novel lymphocyte adhesion pathway involved with early-stage lung cancer.
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Affiliation(s)
- James R Hocker
- a Department of Biochemistry and Molecular biology, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , 940 Stanton L. Young Blvd., BMSB 853, Oklahoma City , OK , USA
| | - Subrato J Deb
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Min Li
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Megan R Lerner
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA.,c Department of Veterans Affairs , Veterans Affairs Medical Center , 921 NE 13th Street, Oklahoma City , OK , USA
| | - Stan A Lightfoot
- c Department of Veterans Affairs , Veterans Affairs Medical Center , 921 NE 13th Street, Oklahoma City , OK , USA
| | - Aurelien A Quillet
- a Department of Biochemistry and Molecular biology, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , 940 Stanton L. Young Blvd., BMSB 853, Oklahoma City , OK , USA
| | - R Jane Hanas
- a Department of Biochemistry and Molecular biology, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , 940 Stanton L. Young Blvd., BMSB 853, Oklahoma City , OK , USA
| | - Matthew Reinersman
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Jess L Thompson
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Nicole T Vu
- d Analytical Research Laboratories BioPharma , 840 Research Parkway, Ste. 546, Oklahoma City , OK , USA
| | - Thomas C Kupiec
- d Analytical Research Laboratories BioPharma , 840 Research Parkway, Ste. 546, Oklahoma City , OK , USA
| | - Daniel J Brackett
- c Department of Veterans Affairs , Veterans Affairs Medical Center , 921 NE 13th Street, Oklahoma City , OK , USA
| | - Marvin D Peyton
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Stephen M Dubinett
- e David Geffen School of Medicine , University of California , 10833 Le Conte Ave. CHS 37-131, Los Angeles , CA , USA
| | - Harold M Burkhart
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Russell G Postier
- b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA
| | - Jay S Hanas
- a Department of Biochemistry and Molecular biology, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , 940 Stanton L. Young Blvd., BMSB 853, Oklahoma City , OK , USA.,b Department of Surgery, Stephenson Cancer Center , University of Oklahoma Health Sciences Center , P.O. Box Williams Pavilion Room 2140. Oklahoma City , OK , USA.,c Department of Veterans Affairs , Veterans Affairs Medical Center , 921 NE 13th Street, Oklahoma City , OK , USA
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30
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Al-Anni R, Hou J, Abdu-Aljabar RD, Xiang Y. Prediction of NSCLC recurrence from microarray data with GEP. IET Syst Biol 2017; 11:77-85. [PMID: 28518058 DOI: 10.1049/iet-syb.2016.0033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Lung cancer is one of the deadliest diseases in the world. Non-small cell lung cancer (NSCLC) is the most common and dangerous type of lung cancer. Despite the fact that NSCLC is preventable and curable for some cases if diagnosed at early stages, the vast majority of patients are diagnosed very late. Furthermore, NSCLC usually recurs sometime after treatment. Therefore, it is of paramount importance to predict NSCLC recurrence, so that specific and suitable treatments can be sought. Nonetheless, conventional methods of predicting cancer recurrence rely solely on histopathology data and predictions are not reliable in many cases. The microarray gene expression (GE) technology provides a promising and reliable way to predict NSCLC recurrence by analysing the GE of sample cells. This study proposes a new model from GE programming to use microarray datasets for NSCLC recurrence prediction. To this end, the authors also propose a hybrid method to rank and select relevant prognostic genes that are related to NSCLC recurrence prediction. The proposed model was evaluated on real NSCLC microarray datasets and compared with other representational models. The results demonstrated the effectiveness of the proposed model.
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Affiliation(s)
- Russul Al-Anni
- School of Information Technology, Deakin University, Victoria, Australia.
| | - Jingyu Hou
- School of Information Technology, Deakin University, Victoria, Australia
| | | | - Yong Xiang
- School of Information Technology, Deakin University, Victoria, Australia
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31
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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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32
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Saldanha G, Joshi K, Lawes K, Bamford M, Moosa F, Teo KW, Pringle JH. 5-Hydroxymethylcytosine is an independent predictor of survival in malignant melanoma. Mod Pathol 2017; 30:60-68. [PMID: 27713424 PMCID: PMC6176904 DOI: 10.1038/modpathol.2016.159] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 07/30/2016] [Indexed: 12/23/2022]
Abstract
Outcomes for melanoma patients vary within cancer stage. Prognostic biomarkers are potential adjuncts to provide more precise prognostic information. Simple, low-cost biomarker assays, such as those based on immunohistochemistry, have strong translational potential. 5-hydroxymethylcytosine (5 hmC) shows prognostic potential in melanoma but prior studies were small. We, therefore, analysed 5 hmC in a retrospective cohort to provide external validation of its prognostic value. Two hundred primary melanomas were evaluated for 5 hmC expression using immunohistochemistry. The primary objective was to assess the effect on overall survival while controlling for important confounders. Univariable and multivariable analyses were performed. REMARK guidelines were followed. The 5 hmC immunohistochemistry scoring showed very strong inter-observer agreement (ICC 0.88) and expression was significantly related to age, site, Breslow thickness, ulceration, mitotic rate, and stage. Kaplan-Meier analysis showed 5 hmC was associated with metastasis-free, melanoma-specific, and overall survival, P<0.0001 for each. In univariable Cox proportional hazards models, 5 hmC hazard ratios were significant and remained so in a multivariable model. A two-step cox model was created using stage and 5 hmC, as stage is the gold standard for clinical practice. The addition of 5 hmC produced significant improvement in the model and 5 hmC and stage were independent significant predictors. This is the largest study of the prognostic value of 5 hmC immunohistochemistry in melanoma. The 5 hmC scoring was easily and reproducibly performed and it was an independent predictor of metastasis-free survival, melanoma-specific survival, and overall survival. This work supports further development of 5 hmC as a prognostic biomarker and suggests that it could add more precision to American Joint Committee on Cancer staging.
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Affiliation(s)
- Gerald Saldanha
- Department of Cancer Studies, University of Leicester, Leicester Royal Infirmary, Leicester, UK
- EMPATH Department of Cellular Pathology, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Kushal Joshi
- Department of Cancer Studies, University of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Kathryn Lawes
- EMPATH Department of Cellular Pathology, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Mark Bamford
- EMPATH Department of Cellular Pathology, University Hospitals of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Farhaan Moosa
- Department of Cancer Studies, University of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - Kah Wee Teo
- Department of Cancer Studies, University of Leicester, Leicester Royal Infirmary, Leicester, UK
| | - J Howard Pringle
- Department of Cancer Studies, University of Leicester, Leicester Royal Infirmary, Leicester, UK
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Cai H, Stott MA, Ozcelik D, Parks JW, Hawkins AR, Schmidt H. On-chip wavelength multiplexed detection of cancer DNA biomarkers in blood. BIOMICROFLUIDICS 2016; 10:064116. [PMID: 28058082 PMCID: PMC5176344 DOI: 10.1063/1.4968033] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/06/2016] [Indexed: 05/03/2023]
Abstract
We have developed an optofluidic analysis system that processes biomolecular samples starting from whole blood and then analyzes and identifies multiple targets on a silicon-based molecular detection platform. We demonstrate blood filtration, sample extraction, target enrichment, and fluorescent labeling using programmable microfluidic circuits. We detect and identify multiple targets using a spectral multiplexing technique based on wavelength-dependent multi-spot excitation on an antiresonant reflecting optical waveguide chip. Specifically, we extract two types of melanoma biomarkers, mutated cell-free nucleic acids -BRAFV600E and NRAS, from whole blood. We detect and identify these two targets simultaneously using the spectral multiplexing approach with up to a 96% success rate. These results point the way toward a full front-to-back chip-based optofluidic compact system for high-performance analysis of complex biological samples.
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Affiliation(s)
- H Cai
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - M A Stott
- Department of Electrical and Computer Engineering, Brigham Young University , 459 Clyde Building, Provo, Utah 84602, USA
| | - D Ozcelik
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - J W Parks
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
| | - A R Hawkins
- Department of Electrical and Computer Engineering, Brigham Young University , 459 Clyde Building, Provo, Utah 84602, USA
| | - H Schmidt
- School of Engineering, University of California , Santa Cruz. 1156 High Street, Santa Cruz, California 95064, USA
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Ma Z, Kim Y, Hu F, Lee JK. Point success rate for patient therapeutic response prediction by continuous biomarker scores. Stat Methods Med Res 2016; 25:1638-47. [DOI: 10.1177/0962280213493161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Various predictive diagnostic tests are highly demanded to guide optimal treatments for individual patients, as individual patients with the same disease such as cancer frequently exhibit dramatically different therapeutic responses to multiple available treatment options. A large number of clinical trials have thus been performed to test the predictive ability and utility of various therapeutic biomarker tests. However, in these trial designs the conventional optimization criteria such as positive predictive value or negative predictive value cannot reflect each patient’s true chance of success associated with continuous predictive biomarker scores. We have developed a novel statistical concept, point success rate (PSR), to overcome deficiencies in these conventional methods for optimizing biomarker-based clinical trials. We demonstrate statistical superiority as well as clinical improvement by a PSR-based treatment selection both with simulated and breast cancer patient data.
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Affiliation(s)
- Zhenjun Ma
- Department of Statistics, University of Virginia, Charlottesville, VA, USA
| | - Youngchul Kim
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Feifang Hu
- Department of Statistics, University of Virginia, Charlottesville, VA, USA
| | - Jae K Lee
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
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35
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Burke HB. Predicting Clinical Outcomes Using Molecular Biomarkers. BIOMARKERS IN CANCER 2016; 8:89-99. [PMID: 27279751 PMCID: PMC4896533 DOI: 10.4137/bic.s33380] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/10/2016] [Accepted: 04/13/2016] [Indexed: 12/11/2022]
Abstract
Over the past 20 years, there has been an exponential increase in the number of biomarkers. At the last count, there were 768,259 papers indexed in PubMed.gov directly related to biomarkers. Although many of these papers claim to report clinically useful molecular biomarkers, embarrassingly few are currently in clinical use. It is suggested that a failure to properly understand, clinically assess, and utilize molecular biomarkers has prevented their widespread adoption in treatment, in comparative benefit analyses, and their integration into individualized patient outcome predictions for clinical decision-making and therapy. A straightforward, general approach to understanding how to predict clinical outcomes using risk, diagnostic, and prognostic molecular biomarkers is presented. In the future, molecular biomarkers will drive advances in risk, diagnosis, and prognosis, they will be the targets of powerful molecular therapies, and they will individualize and optimize therapy. Furthermore, clinical predictions based on molecular biomarkers will be displayed on the clinician’s screen during the physician–patient interaction, they will be an integral part of physician–patient-shared decision-making, and they will improve clinical care and patient outcomes.
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Affiliation(s)
- Harry B Burke
- Professor of Medicine, Department of Medicine, F. Edward Hebert School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
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Trachana SP, Pilalis E, Gavalas NG, Tzannis K, Papadodima O, Liontos M, Rodolakis A, Vlachos G, Thomakos N, Haidopoulos D, Lykka M, Koutsoukos K, Kostouros E, Terpos E, Chatziioannou A, Dimopoulos MA, Bamias A. The Development of an Angiogenic Protein "Signature" in Ovarian Cancer Ascites as a Tool for Biologic and Prognostic Profiling. PLoS One 2016; 11:e0156403. [PMID: 27258020 PMCID: PMC4892506 DOI: 10.1371/journal.pone.0156403] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 05/13/2016] [Indexed: 01/07/2023] Open
Abstract
Advanced ovarian cancer (AOC) is one of the leading lethal gynecological cancers in developed countries. Based on the important role of angiogenesis in ovarian cancer oncogenesis and expansion, we hypothesized that the development of an "angiogenic signature" might be helpful in prediction of prognosis and efficacy of anti-angiogenic therapies in this disease. Sixty-nine samples of ascitic fluid- 35 from platinum sensitive and 34 from platinum resistant patients managed with cytoreductive surgery and 1st-line carboplatin-based chemotherapy- were analyzed using the Proteome ProfilerTM Human Angiogenesis Array Kit, screening for the presence of 55 soluble angiogenesis-related factors. A protein profile based on the expression of a subset of 25 factors could accurately separate resistant from sensitive patients with a success rate of approximately 90%. The protein profile corresponding to the "sensitive" subset was associated with significantly longer PFS (8 [95% Confidence Interval {CI}: 8-9] vs. 20 months [95% CI: 15-28]; Hazard ratio {HR}: 8.3, p<0.001) and OS (20.5 months [95% CI: 13.5-30] vs. 74 months [95% CI: 36-not reached]; HR: 5.6 [95% CI: 2.8-11.2]; p<0.001). This prognostic performance was superior to that of stage, histology and residual disease after cytoreductive surgery and the levels of vascular endothelial growth factor (VEGF) in ascites. In conclusion, we developed an "angiogenic signature" for patients with AOC, which can be used, after appropriate validation, as a prognostic marker and a tool for selection for anti-angiogenic therapies.
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Affiliation(s)
- Sofia-Paraskevi Trachana
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
- * E-mail:
| | - Eleftherios Pilalis
- Metabolic Engineering and Bioinformatics Program Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Nikos G. Gavalas
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Kimon Tzannis
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Olga Papadodima
- Metabolic Engineering and Bioinformatics Program Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Michalis Liontos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Alexandros Rodolakis
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Georgios Vlachos
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Nikolaos Thomakos
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Dimitrios Haidopoulos
- First Department of Obstetrics and Gynecology, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Maria Lykka
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Konstantinos Koutsoukos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Efthimios Kostouros
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Evagelos Terpos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Aristotelis Chatziioannou
- Metabolic Engineering and Bioinformatics Program Institute of Biology, Medicinal Chemistry & Biotechnology, National Hellenic Research Foundation, Athens, Greece
| | - Meletios-Athanasios Dimopoulos
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
| | - Aristotelis Bamias
- Department of Clinical Therapeutics, Medical School, National and Kapodistrian University of Athens, Alexandra General Hospital, Athens, Greece
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Zou M, Zhang PJ, Chen L, Tian YP, Wang Y. Identifying joint biomarker panel from multiple level dataset by an optimization model. Biomark Med 2016; 10:567-75. [PMID: 27172589 DOI: 10.2217/bmm-2015-0022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Joint biomarker panel takes advantage of coherence across multiple level datasets and holds the promise to improve disease diagnosis accuracy. METHODS We collected 101 colorectal cancer and 95 benign samples, measured the molecular concentrations by serum assays and mass spectra, and developed LPGLO (Linear Programming based on Group Lasso Optimization) to identify the joint biomarker panel. RESULTS A joint biomarker panel, with ten serum biomarkers and six mass spectra peaks, achieves LOOCV accuracy 0.8724, which is better than the optimal panels identified from separate datasets (LOOCV = 0.7551 for mass spectra only or 0.8265 for serum assay only) and the simply merged dataset (LOOCV = 0.8622). CONCLUSION LPGLO is useful to identify joint biomarker panel to help tumor diagnosis.
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Affiliation(s)
- Meng Zou
- National Center for Mathematics & Interdisciplinary Sciences, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China
| | - Peng-Jun Zhang
- Core Laboratory of Translational Medicine, State Key Laboratory of Kidney Disease, Chinese PLA General Hospital, Beijing, 100853, China
| | - Luonan Chen
- Key Laboratory of Systems Biology, Innovation Center for Cell Signaling Network, Institute of Biochemistry & Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
| | - Ya-Ping Tian
- Core Laboratory of Translational Medicine, State Key Laboratory of Kidney Disease, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yong Wang
- National Center for Mathematics & Interdisciplinary Sciences, Academy of Mathematics & Systems Science, Chinese Academy of Sciences, Beijing 100080, China
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Sluiter N, de Cuba E, Kwakman R, Kazemier G, Meijer G, Te Velde EA. Adhesion molecules in peritoneal dissemination: function, prognostic relevance and therapeutic options. Clin Exp Metastasis 2016; 33:401-16. [PMID: 27074785 PMCID: PMC4884568 DOI: 10.1007/s10585-016-9791-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 04/07/2016] [Indexed: 12/14/2022]
Abstract
Peritoneal dissemination is diagnosed in 10–25 % of colorectal cancer patients. Selected patients are treated with cytoreductive surgery and hyperthermic intraperitoneal chemotherapy. For these patients, earlier diagnosis, optimised selection criteria and a personalised approach are warranted. Biomarkers could play a crucial role here. However, little is known about possible candidates. Considering tumour cell adhesion as a key step in peritoneal dissemination, we aim to provide an overview of the functional importance of adhesion molecules in peritoneal dissemination and discuss the prognostic, diagnostic and therapeutic options of these candidate biomarkers. A systematic literature search was conducted according to the PRISMA guidelines. In 132 in vitro, ex vivo and in vivo studies published between 1995 and 2013, we identified twelve possibly relevant adhesion molecules in various cancers that disseminate peritoneally. The most studied molecules in tumour cell adhesion are integrin α2β1, CD44 s and MUC16. Furthermore, L1CAM, EpCAM, MUC1, sLex and Lex, chemokine receptors, Betaig-H3 and uPAR might be of clinical importance. ICAM1 was found to be less relevant in tumour cell adhesion in the context of peritoneal metastases. Based on currently available data, sLea and MUC16 are the most promising prognostic biomarkers for colorectal peritoneal metastases that may help improve patient selection. Different adhesion molecules appear expressed in haematogenous and transcoelomic spread, indicating two different attachment processes. However, our extensive assessment of available literature reveals that knowledge on metastasis-specific genes and their possible candidates is far from complete.
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Affiliation(s)
- Nina Sluiter
- Department of Surgery, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Erienne de Cuba
- Department of Surgery, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.,Department of Pathology, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Riom Kwakman
- Department of Surgery, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Geert Kazemier
- Department of Surgery, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - Gerrit Meijer
- Department of Pathology, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.,Department of Pathology, Antoni van Leeuwenhoek Hospital (NKI-AVL), Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Elisabeth Atie Te Velde
- Department of Surgery, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands. .,Department of Surgical Oncology, VU University Medical Centre, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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Dazard JE, Choe M, LeBlanc M, Rao JS. Cross-validation and Peeling Strategies for Survival Bump Hunting using Recursive Peeling Methods. Stat Anal Data Min 2016; 9:12-42. [PMID: 27034730 DOI: 10.1002/sam.11301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We introduce a framework to build a survival/risk bump hunting model with a censored time-to-event response. Our Survival Bump Hunting (SBH) method is based on a recursive peeling procedure that uses a specific survival peeling criterion derived from non/semi-parametric statistics such as the hazards-ratio, the log-rank test or the Nelson--Aalen estimator. To optimize the tuning parameter of the model and validate it, we introduce an objective function based on survival or prediction-error statistics, such as the log-rank test and the concordance error rate. We also describe two alternative cross-validation techniques adapted to the joint task of decision-rule making by recursive peeling and survival estimation. Numerical analyses show the importance of replicated cross-validation and the differences between criteria and techniques in both low and high-dimensional settings. Although several non-parametric survival models exist, none addresses the problem of directly identifying local extrema. We show how SBH efficiently estimates extreme survival/risk subgroups unlike other models. This provides an insight into the behavior of commonly used models and suggests alternatives to be adopted in practice. Finally, our SBH framework was applied to a clinical dataset. In it, we identified subsets of patients characterized by clinical and demographic covariates with a distinct extreme survival outcome, for which tailored medical interventions could be made. An R package PRIMsrc (Patient Rule Induction Method in Survival, Regression and Classification settings) is available on CRAN (Comprehensive R Archive Network) and GitHub.
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Affiliation(s)
- Jean-Eudes Dazard
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michael Choe
- Center for Proteomics and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Michael LeBlanc
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA 98195, USA; Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - J Sunil Rao
- Division of Biostatistics, Department of Epidemiology and Public Health, The University of Miami, Miami, FL 33136, USA
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40
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Young GP, Senore C, Mandel JS, Allison JE, Atkin WS, Benamouzig R, Bossuyt PMM, Silva MD, Guittet L, Halloran SP, Haug U, Hoff G, Itzkowitz SH, Leja M, Levin B, Meijer GA, O'Morain CA, Parry S, Rabeneck L, Rozen P, Saito H, Schoen RE, Seaman HE, Steele RJC, Sung JJY, Winawer SJ. Recommendations for a step-wise comparative approach to the evaluation of new screening tests for colorectal cancer. Cancer 2016; 122:826-39. [PMID: 26828588 PMCID: PMC5066737 DOI: 10.1002/cncr.29865] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/14/2015] [Accepted: 11/30/2015] [Indexed: 12/21/2022]
Abstract
BACKGROUND New screening tests for colorectal cancer continue to emerge, but the evidence needed to justify their adoption in screening programs remains uncertain. METHODS A review of the literature and a consensus approach by experts was undertaken to provide practical guidance on how to compare new screening tests with proven screening tests. RESULTS Findings and recommendations from the review included the following: Adoption of a new screening test requires evidence of effectiveness relative to a proven comparator test. Clinical accuracy supported by programmatic population evaluation in the screening context on an intention-to-screen basis, including acceptability, is essential. Cancer-specific mortality is not essential as an endpoint provided that the mortality benefit of the comparator has been demonstrated and that the biologic basis of detection is similar. Effectiveness of the guaiac-based fecal occult blood test provides the minimum standard to be achieved by a new test. A 4-phase evaluation is recommended. An initial retrospective evaluation in cancer cases and controls (Phase 1) is followed by a prospective evaluation of performance across the continuum of neoplastic lesions (Phase 2). Phase 3 follows the demonstration of adequate accuracy in these 2 prescreening phases and addresses programmatic outcomes at 1 screening round on an intention-to-screen basis. Phase 4 involves more comprehensive evaluation of ongoing screening over multiple rounds. Key information is provided from the following parameters: the test positivity rate in a screening population, the true-positive and false-positive rates, and the number needed to colonoscope to detect a target lesion. CONCLUSIONS New screening tests can be evaluated efficiently by this stepwise comparative approach.
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Affiliation(s)
- Graeme P. Young
- Flinders Center for Innovation in CancerFlinders UniversityAdelaideSouth AustraliaAustralia
| | - Carlo Senore
- Reference Center for Epidemiology and Cancer Prevention, Piedmont Regional Center for Preventive OncologyCity Health and Science University Hospital of TurinTurinItaly
| | - Jack S. Mandel
- Environmental and Occupational MedicineUniversity of MinnesotaMinneapolisMinnesota
| | - James E. Allison
- Division of GastroenterologyUniversity of California, San Francisco and Kaiser Division of ResearchOaklandCalifornia
| | - Wendy S. Atkin
- Gastrointestinal EpidemiologyImperial CollegeLondonUnited Kingdom
| | - Robert Benamouzig
- Gastroenterology Department, Avicenne HospitalParis 13 UniversityParisFrance
| | | | - Mahinda De Silva
- Department of GastroenterologyRepatriation General HospitalAdelaideSouth AustraliaAustralia
| | - Lydia Guittet
- Unit 1086, French National Institute for Health and Medical Research, Cancers and Preventions CenterCaen University HospitalCaenFrance
| | - Stephen P. Halloran
- Faculty of Health and Medical Sciences, University of SurreyGuildfordUnited Kingdom
| | - Ulrike Haug
- Department of Clinical EpidemiologyLeibniz Institute for Prevention Research and EpidemiologyBremenGermany
| | - Geir Hoff
- Telemark Hospital, Skein Cancer Registry of NorwayUniversity of OsloOsloNorway
| | - Steven H. Itzkowitz
- Gastrointestinal DivisionIcahn School of Medicine at Mount SinaiNew YorkNew York
| | - Marcis Leja
- Digestive Diseases Center, GASTRO, Faculty of MedicineUniversity of LatviaRigaLatvia
| | - Bernard Levin
- Division of Cancer PreventionThe University of Texas MD Anderson Cancer CenterHoustonTexas
| | | | | | - Susan Parry
- Ministry of Health Bowel Cancer ProgramAuckland HospitalAucklandNew Zealand
| | - Linda Rabeneck
- Prevention and Cancer ControlCancer Care Ontario, and University of TorontoTorontoOntarioCanada
| | - Paul Rozen
- Department of GastroenterologySestopali Fund for Gastrointestinal Cancer PreventionTel AvivIsrael
| | - Hiroshi Saito
- Research Center for Cancer Prevention and ScreeningNational Cancer CenterTokyoJapan
| | - Robert E. Schoen
- Department of Medicine and EpidemiologyUniversity of PittsburghPittsburghPennsylvania
| | - Helen E. Seaman
- National Health Service Bowel Cancer Screening Southern Program HubRoyal Surrey County HospitalGuildfordUnited Kingdom
| | | | - Joseph J. Y. Sung
- Office of the Vice ChancellorThe Chinese University of Hong KongShatinChina
| | - Sidney J. Winawer
- Gastroenterology and Nutrition Service, Department of MedicineMemorial Sloan‐Kettering Cancer CenterNew YorkNew York
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Schubert M, Junker K, Heinzelmann J. Prognostic and predictive miRNA biomarkers in bladder, kidney and prostate cancer: Where do we stand in biomarker development? J Cancer Res Clin Oncol 2015; 142:1673-95. [DOI: 10.1007/s00432-015-2089-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/30/2015] [Indexed: 12/17/2022]
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Molinaro AM, Wrensch MR, Jenkins RB, Eckel-Passow JE. Statistical considerations on prognostic models for glioma. Neuro Oncol 2015; 18:609-23. [PMID: 26657835 DOI: 10.1093/neuonc/nov255] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 09/14/2015] [Indexed: 12/16/2022] Open
Abstract
Given the lack of beneficial treatments in glioma, there is a need for prognostic models for therapeutic decision making and life planning. Recently several studies defining subtypes of glioma have been published. Here, we review the statistical considerations of how to build and validate prognostic models, explain the models presented in the current glioma literature, and discuss advantages and disadvantages of each model. The 3 statistical considerations to establishing clinically useful prognostic models are: study design, model building, and validation. Careful study design helps to ensure that the model is unbiased and generalizable to the population of interest. During model building, a discovery cohort of patients can be used to choose variables, construct models, and estimate prediction performance via internal validation. Via external validation, an independent dataset can assess how well the model performs. It is imperative that published models properly detail the study design and methods for both model building and validation. This provides readers the information necessary to assess the bias in a study, compare other published models, and determine the model's clinical usefulness. As editors, reviewers, and readers of the relevant literature, we should be cognizant of the needed statistical considerations and insist on their use.
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Affiliation(s)
- Annette M Molinaro
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California (A.M.M., M.R.W.); Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California (A.M.M., M.R.W.); Institute of Human Genetics, University of California San Francisco, San Francisco, California (M.R.W.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (R.B.J.); Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota (J.E.E.-P.)
| | - Margaret R Wrensch
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California (A.M.M., M.R.W.); Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California (A.M.M., M.R.W.); Institute of Human Genetics, University of California San Francisco, San Francisco, California (M.R.W.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (R.B.J.); Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota (J.E.E.-P.)
| | - Robert B Jenkins
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California (A.M.M., M.R.W.); Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California (A.M.M., M.R.W.); Institute of Human Genetics, University of California San Francisco, San Francisco, California (M.R.W.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (R.B.J.); Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota (J.E.E.-P.)
| | - Jeanette E Eckel-Passow
- Department of Neurological Surgery, University of California San Francisco (UCSF), San Francisco, California (A.M.M., M.R.W.); Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California (A.M.M., M.R.W.); Institute of Human Genetics, University of California San Francisco, San Francisco, California (M.R.W.); Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota (R.B.J.); Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota (J.E.E.-P.)
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Gerke TA, Martin NE, Ding Z, Nuttall EJ, Stack EC, Giovannucci E, Lis RT, Stampfer MJ, Kantoff PW, Parmigiani G, Loda M, Mucci LA. Evaluating a 4-marker signature of aggressive prostate cancer using time-dependent AUC. Prostate 2015; 75:1926-33. [PMID: 26469352 PMCID: PMC4831584 DOI: 10.1002/pros.23090] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Accepted: 08/25/2015] [Indexed: 11/05/2022]
Abstract
BACKGROUND We previously identified a protein tumor signature of PTEN, SMAD4, SPP1, and CCND1 that, together with clinical features, was associated with lethal outcomes among prostate cancer patients. In the current study, we sought to validate the molecular model using time-dependent measures of AUC and predictive values for discriminating lethal from non-lethal prostate cancer. METHODS Using data from the initial study, we fit survival models for men with prostate cancer who were participants in the Physicians' Health Study (PHS; n = 276). Based on these models, we generated prognostic risk scores in an independent population, the Health Professionals Follow-up Study (HPFS; n = 347) to evaluate external validity. In each cohort, men were followed prospectively from cancer diagnosis through 2011 for development of distant metastasis or cancer mortality. We measured protein tumor expression of PTEN, SMAD4, SPP1, and CCND1 on tissue microarrays. RESULTS During a median of 11.9 and 14.3 years follow-up in the PHS and HPFS cohorts, 24 and 32 men (9%) developed lethal disease. When used as a prognostic factor in a new population, addition of the four markers to clinical variables did not improve discriminatory accuracy through 15 years of follow-up. CONCLUSIONS Although the four markers have been identified as key biological mediators in metastatic progression, they do not provide independent, long-term prognostic information beyond clinical factors when measured at diagnosis. This finding may underscore the broad heterogeneity in aggressive prostate tumors and highlight the challenges that may result from overfitting in discovery-based research.
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Affiliation(s)
- Travis A. Gerke
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Epidemiology, University of Florida, Gainesville, FL, USA
| | - Neil E. Martin
- Department of Radiation Oncology, Brigham and Women’s Hospital/Dana-Farber Cancer Institute, Boston, MA, USA
| | - Zhihu Ding
- Belfer Center for Applied Cancer Science, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Elizabeth J. Nuttall
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Edward C. Stack
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
| | - Edward Giovannucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Rosina T. Lis
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Meir J. Stampfer
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard School of Public Health, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Phillip W. Kantoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Giovanni Parmigiani
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Massimo Loda
- Center for Molecular Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lorelei A. Mucci
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, USA
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Development of triple-negative breast cancer radiosensitive gene signature and validation based on transcriptome analysis. Breast Cancer Res Treat 2015; 154:57-62. [DOI: 10.1007/s10549-015-3611-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/14/2015] [Indexed: 01/21/2023]
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45
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High Resolution Discovery Proteomics Reveals Candidate Disease Progression Markers of Alzheimer's Disease in Human Cerebrospinal Fluid. PLoS One 2015; 10:e0135365. [PMID: 26270474 PMCID: PMC4535975 DOI: 10.1371/journal.pone.0135365] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 07/21/2015] [Indexed: 11/21/2022] Open
Abstract
Disease modifying treatments for Alzheimer’s disease (AD) constitute a major goal in medicine. Current trends suggest that biomarkers reflective of AD neuropathology and modifiable by treatment would provide supportive evidence for disease modification. Nevertheless, a lack of quantitative tools to assess disease modifying treatment effects remains a major hurdle. Cerebrospinal fluid (CSF) biochemical markers such as total tau, p-tau and Ab42 are well established markers of AD; however, global quantitative biochemical changes in CSF in AD disease progression remain largely uncharacterized. Here we applied a high resolution open discovery platform, dMS, to profile a cross-sectional cohort of lumbar CSF from post-mortem diagnosed AD patients versus those from non-AD/non-demented (control) patients. Multiple markers were identified to be statistically significant in the cohort tested. We selected two markers SME-1 (p<0.0001) and SME-2 (p = 0.0004) for evaluation in a second independent longitudinal cohort of human CSF from post-mortem diagnosed AD patients and age-matched and case-matched control patients. In cohort-2, SME-1, identified as neuronal secretory protein VGF, and SME-2, identified as neuronal pentraxin receptor-1 (NPTXR), in AD were 21% (p = 0.039) and 17% (p = 0.026) lower, at baseline, respectively, than in controls. Linear mixed model analysis in the longitudinal cohort estimate a decrease in the levels of VGF and NPTXR at the rate of 10.9% and 6.9% per year in the AD patients, whereas both markers increased in controls. Because these markers are detected by mass spectrometry without the need for antibody reagents, targeted MS based assays provide a clear translation path for evaluating selected AD disease-progression markers with high analytical precision in the clinic.
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Gentles AJ, Newman AM, Liu CL, Bratman SV, Feng W, Kim D, Nair VS, Xu Y, Khuong A, Hoang CD, Diehn M, West RB, Plevritis SK, Alizadeh AA. The prognostic landscape of genes and infiltrating immune cells across human cancers. Nat Med 2015; 21:938-945. [PMID: 26193342 PMCID: PMC4852857 DOI: 10.1038/nm.3909] [Citation(s) in RCA: 2159] [Impact Index Per Article: 239.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 06/19/2015] [Indexed: 12/12/2022]
Abstract
Molecular profiles of tumors and tumor-associated cells hold great promise as biomarkers of clinical outcomes. However, existing data sets are fragmented and difficult to analyze systematically. Here we present a pan-cancer resource and meta-analysis of expression signatures from ∼18,000 human tumors with overall survival outcomes across 39 malignancies. By using this resource, we identified a forkhead box MI (FOXM1) regulatory network as a major predictor of adverse outcomes, and we found that expression of favorably prognostic genes, including KLRB1 (encoding CD161), largely reflect tumor-associated leukocytes. By applying CIBERSORT, a computational approach for inferring leukocyte representation in bulk tumor transcriptomes, we identified complex associations between 22 distinct leukocyte subsets and cancer survival. For example, tumor-associated neutrophil and plasma cell signatures emerged as significant but opposite predictors of survival for diverse solid tumors, including breast and lung adenocarcinomas. This resource and associated analytical tools (http://precog.stanford.edu) may help delineate prognostic genes and leukocyte subsets within and across cancers, shed light on the impact of tumor heterogeneity on cancer outcomes, and facilitate the discovery of biomarkers and therapeutic targets.
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Affiliation(s)
- Andrew J Gentles
- Center for Cancer Systems Biology (CCSB), Stanford University, Stanford, California, USA
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Chih Long Liu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Scott V Bratman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
| | - Weiguo Feng
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
| | - Dongkyoon Kim
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
| | - Viswam S Nair
- Department of Medicine, Division of Pulmonary and Critical Care Medicine, Stanford University, Stanford, California, USA
| | - Yue Xu
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery, Stanford University, Stanford, California, USA
| | - Amanda Khuong
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery, Stanford University, Stanford, California, USA
| | - Chuong D Hoang
- Department of Cardiothoracic Surgery, Division of Thoracic Surgery, Stanford University, Stanford, California, USA
| | - Maximilian Diehn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Department of Radiation Oncology, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
| | - Robert B West
- Department of Pathology, Stanford University, Stanford, California, USA
| | - Sylvia K Plevritis
- Center for Cancer Systems Biology (CCSB), Stanford University, Stanford, California, USA
- Department of Radiology, Stanford University, Stanford, California, USA
| | - Ash A Alizadeh
- Center for Cancer Systems Biology (CCSB), Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA
- Department of Medicine, Division of Oncology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
- Stanford Cancer Institute, Stanford University, Stanford, California, USA
- Department of Medicine, Division of Hematology, Stanford Cancer Institute, Stanford University, Stanford, California, USA
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47
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Locascio JJ, Eberly S, Liao Z, Liu G, Hoesing AN, Duong K, Trisini-Lipsanopoulos A, Dhima K, Hung AY, Flaherty AW, Schwarzschild MA, Hayes MT, Wills AM, Shivraj Sohur U, Mejia NI, Selkoe DJ, Oakes D, Shoulson I, Dong X, Marek K, Zheng B, Ivinson A, Hyman BT, Growdon JH, Sudarsky LR, Schlossmacher MG, Ravina B, Scherzer CR. Association between α-synuclein blood transcripts and early, neuroimaging-supported Parkinson's disease. Brain 2015. [PMID: 26220939 DOI: 10.1093/brain/awv202] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
There are no cures for neurodegenerative diseases and this is partially due to the difficulty of monitoring pathogenic molecules in patients during life. The Parkinson's disease gene α-synuclein (SNCA) is selectively expressed in blood cells and neurons. Here we show that SNCA transcripts in circulating blood cells are paradoxically reduced in early stage, untreated and dopamine transporter neuroimaging-supported Parkinson's disease in three independent regional, national, and international populations representing 500 cases and 363 controls and on three analogue and digital platforms with P < 0.0001 in meta-analysis. Individuals with SNCA transcripts in the lowest quartile of counts had an odds ratio for Parkinson's disease of 2.45 compared to individuals in the highest quartile. Disease-relevant transcript isoforms were low even near disease onset. Importantly, low SNCA transcript abundance predicted cognitive decline in patients with Parkinson's disease during up to 5 years of longitudinal follow-up. This study reveals a consistent association of reduced SNCA transcripts in accessible peripheral blood and early-stage Parkinson's disease in 863 participants and suggests a clinical role as potential predictor of cognitive decline. Moreover, the three independent biobank cohorts provide a generally useful platform for rapidly validating any biological marker of this common disease.
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Affiliation(s)
- Joseph J Locascio
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Shirley Eberly
- 3 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Zhixiang Liao
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ganqiang Liu
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ashley N Hoesing
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Karen Duong
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Ana Trisini-Lipsanopoulos
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Kaltra Dhima
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Albert Y Hung
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Alice W Flaherty
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 6 Department of Psychiatry, Massachusetts General Hospital, Boston, MA 02114, USA
| | | | - Michael T Hayes
- 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Anne-Marie Wills
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - U Shivraj Sohur
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Nicte I Mejia
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Dennis J Selkoe
- 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - David Oakes
- 3 Department of Biostatistics and Computational Biology, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Ira Shoulson
- 8 Program for Regulatory Science and Medicine, Department of Neurology, Georgetown University, Washington, DC 20007, USA
| | - Xianjun Dong
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Ken Marek
- 8 Program for Regulatory Science and Medicine, Department of Neurology, Georgetown University, Washington, DC 20007, USA
| | - Bin Zheng
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Adrian Ivinson
- 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - Bradley T Hyman
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA
| | - John H Growdon
- 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lewis R Sudarsky
- 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | | | - Bernard Ravina
- 10 Program in Neuroscience, Ottawa Hospital Research Institute, University of Ottawa, Ottawa, Ontario K1H8M5, Canada
| | - Clemens R Scherzer
- 1 Neurogenomics Lab and Parkinson Personalized Medicine Program, Harvard Medical School and Brigham and Women's Hospital, Cambridge, MA 02139, USA 2 Department of Neurology, Massachusetts General Hospital, Boston, MA 02114, USA 4 Ann Romney Centre for Neurologic Diseases, Brigham and Women's Hospital, Boston, MA 02115, USA 5 Biomarkers Program, Harvard NeuroDiscovery Center, Boston, MA 02115, USA 7 Department of Neurology, Brigham and Women's Hospital, Boston, MA 02115, USA
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48
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Deng BC, Yun YH, Liang YZ, Cao DS, Xu QS, Yi LZ, Huang X. A new strategy to prevent over-fitting in partial least squares models based on model population analysis. Anal Chim Acta 2015; 880:32-41. [PMID: 26092335 DOI: 10.1016/j.aca.2015.04.045] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 04/11/2015] [Accepted: 04/23/2015] [Indexed: 11/28/2022]
Abstract
Partial least squares (PLS) is one of the most widely used methods for chemical modeling. However, like many other parameter tunable methods, it has strong tendency of over-fitting. Thus, a crucial step in PLS model building is to select the optimal number of latent variables (nLVs). Cross-validation (CV) is the most popular method for PLS model selection because it selects a model from the perspective of prediction ability. However, a clear minimum of prediction errors may not be obtained in CV which makes the model selection difficult. To solve the problem, we proposed a new strategy for PLS model selection which combines the cross-validated coefficient of determination (Qcv(2)) and model stability (S). S is defined as the stability of PLS regression vectors which is obtained using model population analysis (MPA). The results show that, when a clear maximum of Qcv(2) is not obtained, S can provide additional information of over-fitting and it helps in finding the optimal nLVs. Compared with other regression vector based indictors such as the Euclidean 2-norm (B2), the Durbin Watson statistic (DW) and the jaggedness (J), S is more sensitive to over-fitting. The model selected by our method has both good prediction ability and stability.
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Affiliation(s)
- Bai-Chuan Deng
- Department of Chemistry, University of Bergen, Bergen N-5007, Norway; School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Yong-Huan Yun
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
| | - Yi-Zeng Liang
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China.
| | - Dong-Sheng Cao
- School of Pharmaceutical Sciences, Central South University, Changsha 410083, PR China.
| | - Qing-Song Xu
- School of Mathematics and Statistics, Central South University, Changsha 410083, PR China
| | - Lun-Zhao Yi
- Yunnan Food Safety Research Institute, Kunming University of Science and Technology, Kunming 650500, PR China
| | - Xin Huang
- School of Chemistry and Chemical Engineering, Central South University, Changsha 410083, PR China
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49
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Fu G, Hu M, Chu L, Zhang M. The Difference Quantity of Urinary Peptides between Two Groups of Type 2 Diabetic Patients with or without Coronary Artery Disease. Int J Endocrinol 2015; 2015:758402. [PMID: 26089891 PMCID: PMC4451558 DOI: 10.1155/2015/758402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 12/10/2014] [Accepted: 12/10/2014] [Indexed: 01/08/2023] Open
Abstract
Objectives. We aim to explore urinary biomarkers that could monitor CAD in type 2 diabetic patients. Materials and Methods. Urine samples from two groups, twenty-eight type 2 diabetic patients with coexisting CAD and thirty type 2 diabetic patients without CAD, were purified by MB-WCX and then analyzed by MALDI-TOF-MS. Subsequently, we compared the urinary peptide signatures of the two groups by use of ClinProTools2.1 and evaluated the potential ability of the differently expressed peptides to distinguish type 2 diabetic patients with coexisting CAD from type 2 diabetic patients without CAD by ROC analysis. Finally, the differently expressed peptides were identified by nanoliquid chromatography-tandem mass spectrometry. Results. There were six differently expressed peptides (m/z 1305.2, 1743.9, 2184.9, 2756.1, 3223.2, and 6196.1) between the two groups of subjects, and they were identified as fragments of isoform 1 of fibrinogen alpha chain precursor, prothrombin precursor, and interalpha-trypsin inhibitor heavy chain H4. The diagnostic efficacy of m/z 2756.1 and m/z 3223.2 was better than the other peptides. Area under ROC of the m/z 2756.1, and m/z 3223.2 was 0.98 and 0.93, respectively. Conclusions. These urinary peptides are potential urinary biomarkers for monitoring of type 2 diabetic patients with CAD.
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Affiliation(s)
- Guangzhen Fu
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing 100038, China
| | - Mei Hu
- Department of Clinical Laboratory, Capital Medical University, Beijing Shijitan Hospital, Beijing 100038, China
| | - Lina Chu
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing 100038, China
| | - Man Zhang
- Department of Clinical Laboratory, Peking University Ninth School of Clinical Medicine, Beijing Shijitan Hospital, Beijing 100038, China
- Department of Clinical Laboratory, Capital Medical University, Beijing Shijitan Hospital, Beijing 100038, China
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50
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Lehmann BD, Ding Y, Viox DJ, Jiang M, Zheng Y, Liao W, Chen X, Xiang W, Yi Y. Evaluation of public cancer datasets and signatures identifies TP53 mutant signatures with robust prognostic and predictive value. BMC Cancer 2015; 15:179. [PMID: 25886164 PMCID: PMC4404582 DOI: 10.1186/s12885-015-1102-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 02/20/2015] [Indexed: 12/21/2022] Open
Abstract
Background Systematic analysis of cancer gene-expression patterns using high-throughput transcriptional profiling technologies has led to the discovery and publication of hundreds of gene-expression signatures. However, few public signature values have been cross-validated over multiple studies for the prediction of cancer prognosis and chemosensitivity in the neoadjuvant setting. Methods To analyze the prognostic and predictive values of publicly available signatures, we have implemented a systematic method for high-throughput and efficient validation of a large number of datasets and gene-expression signatures. Using this method, we performed a meta-analysis including 351 publicly available signatures, 37,000 random signatures, and 31 breast cancer datasets. Survival analyses and pathologic responses were used to assess prediction of prognosis, chemoresponsiveness, and chemo-drug sensitivity. Results Among 31 breast cancer datasets and 351 public signatures, we identified 22 validation datasets, two robust prognostic signatures (BRmet50 and PMID18271932Sig33) in breast cancer and one signature (PMID20813035Sig137) specific for prognosis prediction in patients with ER-negative tumors. The 22 validation datasets demonstrated enhanced ability to distinguish cancer gene profiles from random gene profiles. Both prognostic signatures are composed of genes associated with TP53 mutations and were able to stratify the good and poor prognostic groups successfully in 82%and 68% of the 22 validation datasets, respectively. We then assessed the abilities of the two signatures to predict treatment responses of breast cancer patients treated with commonly used chemotherapeutic regimens. Both BRmet50 and PMID18271932Sig33 retrospectively identified those patients with an insensitive response to neoadjuvant chemotherapy (mean positive predictive values 85%-88%). Among those patients predicted to be treatment sensitive, distant relapse-free survival (DRFS) was improved (negative predictive values 87%-88%). BRmet50 was further shown to prospectively predict taxane-anthracycline sensitivity in patients with HER2-negative (HER2-) breast cancer. Conclusions We have developed and applied a high-throughput screening method for public cancer signature validation. Using this method, we identified appropriate datasets for cross-validation and two robust signatures that differentiate TP53 mutation status and have prognostic and predictive value for breast cancer patients. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1102-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Brian David Lehmann
- Department of Biochemistry, Vanderbilt University, Nashville, TN, USA. .,Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA.
| | - Yan Ding
- Department of Dermatology, Hainan General Hospital, Haikou, Hainan, China.
| | | | - Ming Jiang
- Division of Epidemiology, Vanderbilt University, Nashville, TN, USA. .,Vanderbilt Ingram Cancer Center, Vanderbilt University, Nashville, TN, USA. .,Laboratory of Nuclear Receptors and Cancer Research, Center for Basic Medical Research, Nantong University School of Medicine, Nantong, Jiangsu, China.
| | - Yi Zheng
- Pediatric Surgery Department, Qilu Hospital of Shandong University, Jinan, Shangdong, China.
| | - Wang Liao
- Department of Cardiovascular Disease, Hainan General Hospital, Haikou, Hainan, China.
| | - Xi Chen
- Department of Biostatistics, Vanderbilt University, Nashville, TN, USA.
| | - Wei Xiang
- Department of Pediatrics, Maternal and Child Health Care Hospital of Hainan Province, Haikou, China.
| | - Yajun Yi
- Department of Medicine, Vanderbilt University, Nashville, TN, USA. .,Division of Genetic Medicine, 536A Light Hall, Vanderbilt University, 2215 Garland Avenue, Nashville, TN, 37232-0275, USA.
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