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Rai SN, Srivastava S, Pan J, Wu X, Rai SP, Mekmaysy CS, DeLeeuw L, Chaires JB, Garbett NC. Multi-group diagnostic classification of high-dimensional data using differential scanning calorimetry plasma thermograms. PLoS One 2019; 14:e0220765. [PMID: 31430304 PMCID: PMC6701772 DOI: 10.1371/journal.pone.0220765] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/23/2019] [Indexed: 11/24/2022] Open
Abstract
The thermoanalytical technique differential scanning calorimetry (DSC) has been applied to characterize protein denaturation patterns (thermograms) in blood plasma samples and relate these to a subject’s health status. The analysis and classification of thermograms is challenging because of the high-dimensionality of the dataset. There are various methods for group classification using high-dimensional data sets; however, the impact of using high-dimensional data sets for cancer classification has been poorly understood. In the present article, we proposed a statistical approach for data reduction and a parametric method (PM) for modeling of high-dimensional data sets for two- and three- group classification using DSC and demographic data. We compared the PM to the non-parametric classification method K-nearest neighbors (KNN) and the semi-parametric classification method KNN with dynamic time warping (DTW). We evaluated the performance of these methods for multiple two-group classifications: (i) normal versus cervical cancer, (ii) normal versus lung cancer, (iii) normal versus cancer (cervical + lung), (iv) lung cancer versus cervical cancer as well as for three-group classification: normal versus cervical cancer versus lung cancer. In general, performance for two-group classification was high whereas three-group classification was more challenging, with all three methods predicting normal samples more accurately than cancer samples. Moreover, specificity of the PM method was mostly higher or the same as KNN and DTW-KNN with lower sensitivity. The performance of KNN and DTW-KNN decreased with the inclusion of demographic data, whereas similar performance was observed for the PM which could be explained by the fact that the PM uses fewer parameters as compared to KNN and DTW-KNN methods and is thus less susceptible to the risk of overfitting. More importantly the accuracy of the PM can be increased by using a greater number of quantile data points and by the inclusion of additional demographic and clinical data, providing a substantial advantage over KNN and DTW-KNN methods.
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Affiliation(s)
- Shesh N. Rai
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (SNR); (NCG)
| | - Sudhir Srivastava
- Department of Bioinformatics and Biostatistics, University of Louisville, Louisville, Kentucky, United States of America
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Jianmin Pan
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Xiaoyong Wu
- Biostatistics and Bioinformatics Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Somesh P. Rai
- School of Public Health and Information Sciences, University of Louisville, Louisville, Kentucky, United States of America
| | - Chongkham S. Mekmaysy
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Lynn DeLeeuw
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
| | - Jonathan B. Chaires
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Biophysical Core Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
| | - Nichola C. Garbett
- Department of Medicine, University of Louisville, Louisville, Kentucky, United States of America
- Biophysical Core Facility, James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky, United States of America
- * E-mail: (SNR); (NCG)
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Garbett NC, Brock GN, Chaires JB, Mekmaysy CS, DeLeeuw L, Sivils KL, Harley JB, Rovin BH, Kulasekera KB, Jarjour WN. Characterization and classification of lupus patients based on plasma thermograms. PLoS One 2017; 12:e0186398. [PMID: 29149219 PMCID: PMC5693473 DOI: 10.1371/journal.pone.0186398] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 09/29/2017] [Indexed: 11/22/2022] Open
Abstract
Objective Plasma thermograms (thermal stability profiles of blood plasma) are being utilized as a new diagnostic approach for clinical assessment. In this study, we investigated the ability of plasma thermograms to classify systemic lupus erythematosus (SLE) patients versus non SLE controls using a sample of 300 SLE and 300 control subjects from the Lupus Family Registry and Repository. Additionally, we evaluated the heterogeneity of thermograms along age, sex, ethnicity, concurrent health conditions and SLE diagnostic criteria. Methods Thermograms were visualized graphically for important differences between covariates and summarized using various measures. A modified linear discriminant analysis was used to segregate SLE versus control subjects on the basis of the thermograms. Classification accuracy was measured based on multiple training/test splits of the data and compared to classification based on SLE serological markers. Results Median sensitivity, specificity, and overall accuracy based on classification using plasma thermograms was 86%, 83%, and 84% compared to 78%, 95%, and 86% based on a combination of five antibody tests. Combining thermogram and serology information together improved sensitivity from 78% to 86% and overall accuracy from 86% to 89% relative to serology alone. Predictive accuracy of thermograms for distinguishing SLE and osteoarthritis / rheumatoid arthritis patients was comparable. Both gender and anemia significantly interacted with disease status for plasma thermograms (p<0.001), with greater separation between SLE and control thermograms for females relative to males and for patients with anemia relative to patients without anemia. Conclusion Plasma thermograms constitute an additional biomarker which may help improve diagnosis of SLE patients, particularly when coupled with standard diagnostic testing. Differences in thermograms according to patient sex, ethnicity, clinical and environmental factors are important considerations for application of thermograms in a clinical setting.
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Affiliation(s)
- Nichola C. Garbett
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, United States of America
- * E-mail:
| | - Guy N. Brock
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, United States of America
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, United States of America
| | - Chongkham S. Mekmaysy
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, United States of America
| | - Lynn DeLeeuw
- James Graham Brown Cancer Center, Department of Medicine, University of Louisville, Louisville, KY, United States of America
| | - Kathy L. Sivils
- Arthritis and Clinical Immunology Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, United States of America
| | - John B. Harley
- U.S. Department of Veterans Affairs Medical Center, Cincinnati, OH, United States of America
- The Center for Autoimmune Genomics and Etiology, Department of Pediatrics, Cincinnati Children’s Hospital Medical Center & University of Cincinnati, Cincinnati, OH, United States of America
| | - Brad H. Rovin
- Nephrology Division, The Ohio State University Wexner Medical Center, Columbus, OH, United States of America
| | - K. B. Kulasekera
- Department of Bioinformatics and Biostatistics, School of Public Health and Information Sciences, University of Louisville, Louisville, KY, United States of America
| | - Wael N. Jarjour
- Division of Rheumatology and Immunology, Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH, United States of America
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Garbett NC, Mekmaysy CS, DeLeeuw L, Chaires JB. Clinical application of plasma thermograms. Utility, practical approaches and considerations. Methods 2014; 76:41-50. [PMID: 25448297 DOI: 10.1016/j.ymeth.2014.10.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 10/11/2014] [Accepted: 10/13/2014] [Indexed: 11/30/2022] Open
Abstract
Differential scanning calorimetry (DSC) studies of blood plasma are part of an emerging area of the clinical application of DSC to biofluid analysis. DSC analysis of plasma from healthy individuals and patients with various diseases has revealed changes in the thermal profiles of the major plasma proteins associated with the clinical status of the patient. The sensitivity of DSC to the concentration of proteins, their interactions with other proteins or ligands, or their covalent modification underlies the potential utility of DSC analysis. A growing body of literature has demonstrated the versatility and performance of clinical DSC analysis across a range of biofluids and in a number of disease settings. The principles, practice and challenges of DSC analysis of plasma are described in this article.
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Affiliation(s)
- Nichola C Garbett
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Medicine, Division of Medical Oncology and Hematology, University of Louisville School of Medicine, Louisville, KY 40202, USA.
| | - Chongkham S Mekmaysy
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Medicine, Division of Medical Oncology and Hematology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Lynn DeLeeuw
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Medicine, Division of Medical Oncology and Hematology, University of Louisville School of Medicine, Louisville, KY 40202, USA
| | - Jonathan B Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, USA; Department of Medicine, Division of Medical Oncology and Hematology, University of Louisville School of Medicine, Louisville, KY 40202, USA
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Petraccone L, Spink C, Trent JO, Garbett NC, Mekmaysy CS, Giancola C, Chaires JB. Structure and stability of higher-order human telomeric quadruplexes. J Am Chem Soc 2011; 133:20951-61. [PMID: 22082001 PMCID: PMC3244555 DOI: 10.1021/ja209192a] [Citation(s) in RCA: 151] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
G-quadruplex formation in the sequences 5'-(TTAGGG)(n) and 5'(TTAGGG)(n)TT (n = 4, 8, 12) was studied using circular dichroism, sedimentation velocity, differential scanning calorimetry, and molecular dynamics simulations. Sequences containing 8 and 12 repeats formed higher-order structures with two and three contiguous quadruplexes, respectively. Plausible structures for these sequences were determined by molecular dynamics simulations followed by experimental testing of predicted hydrodynamic properties by sedimentation velocity. These structures featured folding of the strand into contiguous quadruplexes with mixed hybrid conformations. Thermodynamic studies showed the strands folded spontaneous to contain the maximum number contiguous quadruplexes. For the sequence 5'(TTAGGG)(12)TT, more than 90% of the strands contained completely folded structures with three quadruplexes. Statistical mechanical-based deconvolution of thermograms for three quadruplex structures showed that each quadruplex melted independently with unique thermodynamic parmameters. Thermodynamic analysis revealed further that quadruplexes in higher-ordered structures were destabilized relative to their monomeric counterparts, with unfavorable coupling free energies. Quadruplex stability thus depends critically on the sequence and structural context.
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Affiliation(s)
- Luigi Petraccone
- Dept. Chimica “P. Corradini”, University of Naples “Federico II”, 80122 Naples, Italy
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Charles Spink
- Department of Chemistry, SUNY-Cortland, Cortland, NY 13045
| | - John O. Trent
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Nichola C. Garbett
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Chongkham S. Mekmaysy
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
| | - Concetta Giancola
- Dept. Chimica “P. Corradini”, University of Naples “Federico II”, 80122 Naples, Italy
| | - Jonathan B. Chaires
- Department of Medicine, James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock St., Louisville, KY 40202
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Abstract
Analytical ultracentrifugation (AUC) is a powerful technique for the characterization of hydrodynamic and thermodynamic properties. The intent of this article is to demonstrate the utility of sedimentation velocity (SV) studies to obtain hydrodynamic information for G-quadruplex (GQ) systems and to provide insights into one part of this process, namely, data analysis of existing SV data. An array of data analysis software is available, mostly written and continually developed by established researchers in the AUC field, with particularly rapid advances in the analysis of SV data. Each program has its own learning curve, and this article is intended as a resource in the data analysis process for beginning researchers in the field. We discuss the application of three of the most commonly used data analysis programs, DCDT+, Sedfit, and SedAnal, to the interpretation of SV data obtained in our laboratory on two GQ systems.
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Affiliation(s)
- Nichola C. Garbett
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, United States
| | - Chongkham S. Mekmaysy
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, United States
| | - Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, KY 40202, United States
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Garbett NC, Mekmaysy CS, Helm CW, Jenson AB, Chaires JB. Differential scanning calorimetry of blood plasma for clinical diagnosis and monitoring. Exp Mol Pathol 2009; 86:186-91. [DOI: 10.1016/j.yexmp.2008.12.001] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2008] [Indexed: 11/29/2022]
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Mekmaysy CS, Petraccone L, Garbett NC, Ragazzon PA, Gray R, Trent JO, Chaires JB. Effect of O6-methylguanine on the stability of G-quadruplex DNA. J Am Chem Soc 2008; 130:6710-1. [PMID: 18447358 DOI: 10.1021/ja801976h] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effects of substitution of O6-methylguanine on the structure and stability of a human telomere quadruplex was studied by circular dichroism, thermal denaturation, analytical ultracentrifugation, and molecular dynamics simulations. The results show that, while quadruplex structures can form containing the modified base, they are much less stable than the normal unmodified structure. The extent of destabilization is critically dependent on the exact position of the modified base within the quadruplex structure.
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Affiliation(s)
- Chongkham S Mekmaysy
- James Graham Brown Cancer Center and University of Louisville, 529 South Jackson Street, Louisville, Kentucky 40202, USA
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