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Paez R, Rowe DJ, Deppen SA, Grogan EL, Kaizer A, Bornhop DJ, Kussrow AK, Barón AE, Maldonado F, Kammer MN. Assessing the clinical utility of biomarkers using the intervention probability curve (IPC). Cancer Biomark 2023:CBM230054. [PMID: 38073376 PMCID: PMC11055936 DOI: 10.3233/cbm-230054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2024]
Abstract
BACKGROUND Assessing the clinical utility of biomarkers is a critical step before clinical implementation. The reclassification of patients across clinically relevant subgroups is considered one of the best methods to estimate clinical utility. However, there are important limitations with this methodology. We recently proposed the intervention probability curve (IPC) which models the likelihood that a provider will choose an intervention as a continuous function of the probability, or risk, of disease. OBJECTIVE To assess the potential impact of a new biomarker for lung cancer using the IPC. METHODS The IPC derived from the National Lung Screening Trial was used to assess the potential clinical utility of a biomarker for suspected lung cancer. The summary statistics of the change in likelihood of intervention over the population can be interpreted as the expected clinical impact of the added biomarker. RESULTS The IPC analysis of the novel biomarker estimated that 8% of the benign nodules could avoid an invasive procedure while the cancer nodules would largely remain unchanged (0.1%). We showed the benefits of this approach compared to traditional reclassification methods based on thresholds. CONCLUSIONS The IPC methodology can be a valuable tool for assessing biomarkers prior to clinical implementation.
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Affiliation(s)
- Rafael Paez
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Multidisciplinary Approach to Stratification of Lung Cancer with Biomarkers, MASLAB, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Dianna J. Rowe
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Multidisciplinary Approach to Stratification of Lung Cancer with Biomarkers, MASLAB, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Stephen A. Deppen
- Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Multidisciplinary Approach to Stratification of Lung Cancer with Biomarkers, MASLAB, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Eric L. Grogan
- Tennessee Valley Healthcare System, Nashville, Tennessee, United States of America
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Multidisciplinary Approach to Stratification of Lung Cancer with Biomarkers, MASLAB, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Alexander Kaizer
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Darryl J. Bornhop
- Department of Chemistry, and The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
| | - Amanda K. Kussrow
- Department of Chemistry, and The Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN
| | - Anna E. Barón
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado, United States of America
| | - Fabien Maldonado
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Multidisciplinary Approach to Stratification of Lung Cancer with Biomarkers, MASLAB, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Michael N. Kammer
- Department of Medicine, Division of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Multidisciplinary Approach to Stratification of Lung Cancer with Biomarkers, MASLAB, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
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Marmor HN, Kammer MN, Deppen SA, Shipe M, Welty VF, Patel K, Godfrey C, Billatos E, Herman JG, Wilson DO, Kussrow AK, Bornhop DJ, Maldonado F, Chen H, Grogan EL. Improving lung cancer diagnosis with cancer, fungal, and imaging biomarkers. J Thorac Cardiovasc Surg 2023; 166:669-678.e4. [PMID: 36792410 PMCID: PMC10287834 DOI: 10.1016/j.jtcvs.2022.12.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 12/09/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
OBJECTIVE Indeterminate pulmonary nodules (IPNs) represent a significant diagnostic burden in health care. We aimed to compare a combination clinical prediction model (Mayo Clinic model), fungal (histoplasmosis serology), imaging (computed tomography [CT] radiomics), and cancer (high-sensitivity cytokeratin fraction 21; hsCYFRA 21-1) biomarker approach to a validated prediction model in diagnosing lung cancer. METHODS A prospective specimen collection, retrospective blinded evaluation study was performed in 3 independent cohorts with 6- to 30-mm IPNs (n = 281). Serum histoplasmosis immunoglobulin G and immunoglobulin M antibodies and hsCYFRA 21-1 levels were measured and a validated CT radiomic score was calculated. Multivariable logistic regression models were estimated with Mayo Clinic model variables, histoplasmosis antibody levels, CT radiomic score, and hsCYFRA 21-1. Diagnostic performance of the combination model was compared with that of the Mayo Clinic model. Bias-corrected clinical net reclassification index (cNRI) was used to estimate the clinical utility of a combination biomarker approach. RESULTS A total of 281 patients were included (111 from a histoplasmosis-endemic region). The combination biomarker model including the Mayo Clinic model score, histoplasmosis antibody levels, radiomics, and hsCYFRA 21-1 level showed improved diagnostic accuracy for IPNs compared with the Mayo Clinic model alone with an area under the receiver operating characteristics curve of 0.80 (95% CI, 0.76-0.84) versus 0.72 (95% CI, 0.66-0.78). Use of this combination model correctly reclassified intermediate risk IPNs into low- or high-risk category (cNRI benign = 0.11 and cNRI malignant = 0.16). CONCLUSIONS The addition of cancer, fungal, and imaging biomarkers improves the diagnostic accuracy for IPNs. Integrating a combination biomarker approach into the diagnostic algorithm of IPNs might decrease unnecessary invasive testing of benign nodules and reduce time to diagnosis for cancer.
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Affiliation(s)
- Hannah N Marmor
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn
| | - Michael N Kammer
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Stephen A Deppen
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn; Section of Thoracic Surgery, Tennessee Valley VA Healthcare System, Nashville, Tenn.
| | - Maren Shipe
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn
| | - Valerie F Welty
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Khushbu Patel
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Caroline Godfrey
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn
| | - Ehab Billatos
- Section of Pulmonary and Critical Care Medicine, Boston Medical Center, Boston, Mass
| | - James G Herman
- Division of Hematology/Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pa
| | - David O Wilson
- Division of Pulmonary, Allergy, and Critical Care Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pa
| | | | | | - Fabien Maldonado
- Department of Allergy, Pulmonary and Critical Care Medicine, Vanderbilt University Medical Center, Nashville, Tenn
| | - Heidi Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tenn
| | - Eric L Grogan
- Department of Thoracic Surgery, Vanderbilt University Medical Center, Nashville, Tenn; Section of Thoracic Surgery, Tennessee Valley VA Healthcare System, Nashville, Tenn
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Kussrow A, Kammer MN, Massion PP, Webster R, Bornhop DJ. Assay Performance of a Label-Free, Solution-Phase CYFRA 21-1 Determination. ACS Omega 2022; 7:31916-31923. [PMID: 36120008 PMCID: PMC9476196 DOI: 10.1021/acsomega.2c02763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
CYFRA 21.1, a cytokeratin fragment of epithelial origin, has long been a valuable blood-based biomarker. As with most biomarkers, the clinical diagnostic value of CYFRA 21.1 is dependent on the quantitative performance of the assay. Looking toward translation, it is shown here that a free-solution assay (FSA) coupled with a compensated interferometric reader (CIR) can be used to provide excellent analytical performance in quantifying CYFRA 21.1 in patient serum samples. This report focuses on the analytical performance of the high-sensitivity (hs)-CYFRA 21.1 assay in the context of quantifying the biomarker in two indeterminate pulmonary nodule (IPN) patient cohorts totaling 179 patients. Each of the ten assay calibrations consisted of 6 concentrations, each run as 7 replicates (e.g., 10 × 6 × 7 data points) and were performed on two different instruments by two different operators. Coefficients of variation (CVs) for the hs-CYFRA 21.1 analytical figures of merit, limit of quantification (LOQ) of ca. 60 pg/mL, B max, initial slope, probe-target binding affinity, and reproducibility of quantifying an unknown were found to range from 2.5 to 8.3%. Our results demonstrate the excellent performance of our FSA-CIR hs-CYFRA 21-1 assay and a proof of concept for potentially redefining the performance characteristics of this existing important candidate biomarker.
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Affiliation(s)
- Amanda
K. Kussrow
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Michael N. Kammer
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Pierre P. Massion
- Division
of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram
Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Rebekah Webster
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department
of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Kammer MN, Lakhani DA, Balar AB, Antic SL, Kussrow AK, Webster RL, Mahapatra S, Barad U, Shah C, Atwater T, Diergaarde B, Qian J, Kaizer A, New M, Hirsch E, Feser WJ, Strong J, Rioth M, Miller YE, Balagurunathan Y, Rowe DJ, Helmey S, Chen SC, Bauza J, Deppen SA, Sandler K, Maldonado F, Spira A, Billatos E, Schabath MB, Gillies RJ, Wilson DO, Walker RC, Landman B, Chen H, Grogan EL, Barón AE, Bornhop DJ, Massion PP. Integrated Biomarkers for the Management of Indeterminate Pulmonary Nodules. Am J Respir Crit Care Med 2021; 204:1306-1316. [PMID: 34464235 PMCID: PMC8786067 DOI: 10.1164/rccm.202012-4438oc] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 08/27/2021] [Indexed: 01/06/2023] Open
Abstract
Rationale: Patients with indeterminate pulmonary nodules (IPNs) at risk of cancer undergo high rates of invasive, costly, and morbid procedures. Objectives: To train and externally validate a risk prediction model that combined clinical, blood, and imaging biomarkers to improve the noninvasive management of IPNs. Methods: In this prospectively collected, retrospective blinded evaluation study, probability of cancer was calculated for 456 patient nodules using the Mayo Clinic model, and patients were categorized into low-, intermediate-, and high-risk groups. A combined biomarker model (CBM) including clinical variables, serum high sensitivity CYFRA 21-1 level, and a radiomic signature was trained in cohort 1 (n = 170) and validated in cohorts 2-4 (total n = 286). All patients were pooled to recalibrate the model for clinical implementation. The clinical utility of the CBM compared with current clinical care was evaluated in 2 cohorts. Measurements and Main Results: The CBM provided improved diagnostic accuracy over the Mayo Clinic model with an improvement in area under the curve of 0.124 (95% bootstrap confidence interval, 0.091-0.156; P < 2 × 10-16). Applying 10% and 70% risk thresholds resulted in a bias-corrected clinical reclassification index for cases and control subjects of 0.15 and 0.12, respectively. A clinical utility analysis of patient medical records estimated that a CBM-guided strategy would have reduced invasive procedures from 62.9% to 50.6% in the intermediate-risk benign population and shortened the median time to diagnosis of cancer from 60 to 21 days in intermediate-risk cancers. Conclusions: Integration of clinical, blood, and image biomarkers improves noninvasive diagnosis of patients with IPNs, potentially reducing the rate of unnecessary invasive procedures while shortening the time to diagnosis.
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Affiliation(s)
- Michael N. Kammer
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Chemistry, and
| | - Dhairya A. Lakhani
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Aneri B. Balar
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Sanja L. Antic
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Amanda K. Kussrow
- Department of Chemistry, and
- Vanderbilt Institute for Chemical Biology, Nashville, Tennessee
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | | | - Shayan Mahapatra
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | | | | | - Thomas Atwater
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Brenda Diergaarde
- Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh and UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Jun Qian
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Alexander Kaizer
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | | | - Erin Hirsch
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - William J. Feser
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jolene Strong
- Biomedical Informatics and Personalized Medicine, and
| | - Matthew Rioth
- Medical Oncology and Biomedical Informatics and Personalized Medicine, School of Medicine, University of Colorado, Aurora, Colorado
| | | | | | - Dianna J. Rowe
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Sherif Helmey
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Sheau-Chiann Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Joseph Bauza
- American College of Radiology, Philadelphia, Pennsylvania
| | - Stephen A. Deppen
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Kim Sandler
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Fabien Maldonado
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Avrum Spira
- Department of Medicine, Boston University, Boston, Massachusetts
| | - Ehab Billatos
- Department of Medicine, Boston University, Boston, Massachusetts
| | | | | | - David O. Wilson
- Department of Medicine, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania; and
| | | | - Bennett Landman
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee
| | - Heidi Chen
- American College of Radiology, Philadelphia, Pennsylvania
| | - Eric L. Grogan
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
| | - Anna E. Barón
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Darryl J. Bornhop
- Department of Chemistry, and
- Vanderbilt Institute for Chemical Biology, Nashville, Tennessee
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine, Department of Medicine
- Vanderbilt Ingram Cancer Center, Nashville, Tennessee
- Pulmonary Section, Medical Service, Tennessee Valley Healthcare Systems Nashville Campus, Nashville, Tennessee
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5
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Ray M, Kihara Y, Bornhop DJ, Chun J. Lysophosphatidic acid (LPA)-antibody (504B3) engagement detected by interferometry identifies off-target binding. Lipids Health Dis 2021; 20:32. [PMID: 33853612 PMCID: PMC8048308 DOI: 10.1186/s12944-021-01454-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/15/2021] [Indexed: 11/10/2022] Open
Abstract
Background Lysophosphatidic acid (LPA) is a bioactive lysophospholipid that acts through its six cognate G protein-coupled receptors. As a family, lysophospholipids have already produced medicines (e.g., sphingosine 1-phosphate) as is being pursued for LPA through the use of specific antibodies that reduce ligand availability. Methods The binding properties of a commercially available, reportedly specific, monoclonal LPA antibody named 504B3 that is related to the clinical candidate Lpathomab/LT3015 were reexamined using a free solution assay (FSA) measured in a compensated interferometric reader (CIR). Results Measurement of 504B3 binding properties with an FSA-CIR approach revealed similar binding affinities for 504B3 against LPA as well as the non-LPA lipids, phosphatidic acid (PA) and lysophosphatidylcholine (LPC). Conclusions Antibody binding specificity and sensitivity, particularly involving lipid ligands, can be assessed in solution and without labels using FSA-CIR. These findings could affect interpretations of both current and past basic and clinical studies employing 504B3 and related anti-LPA antibodies.
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Affiliation(s)
- Manisha Ray
- Translational Neuroscience Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Yasuyuki Kihara
- Translational Neuroscience Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Nashville, TN, 37235, USA
| | - Jerold Chun
- Translational Neuroscience Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.
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Kammer MN, Kussrow AK, Olmsted IR, Jackson GW, Bornhop DJ. Correction to Free Solution Assay Signal Modulation in Variable-Stem-Length Hairpin Aptamers. ACS Omega 2020; 5:22683. [PMID: 32923829 PMCID: PMC7482408 DOI: 10.1021/acsomega.0c03754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Indexed: 06/11/2023]
Abstract
[This corrects the article DOI: 10.1021/acsomega.9b04341.].
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Ray M, Nagai K, Kihara Y, Kussrow A, Kammer MN, Frantz A, Bornhop DJ, Chun J. Unlabeled lysophosphatidic acid receptor binding in free solution as determined by a compensated interferometric reader. J Lipid Res 2020; 61:1244-1251. [PMID: 32513900 PMCID: PMC7397748 DOI: 10.1194/jlr.d120000880] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 06/01/2020] [Indexed: 12/11/2022] Open
Abstract
Native interactions between lysophospholipids (LPs) and their cognate LP receptors are difficult to measure because of lipophilicity and/or the adhesive properties of lipids, which contribute to high levels of nonspecific binding in cell membrane preparations. Here, we report development of a free-solution assay (FSA) where label-free LPs bind to their cognate G protein-coupled receptors (GPCRs), combined with a recently reported compensated interferometric reader (CIR) to quantify native binding interactions between receptors and ligands. As a test case, the binding parameters between lysophosphatidic acid (LPA) receptor 1 (LPA1; one of six cognate LPA GPCRs) and LPA were determined. FSA-CIR detected specific binding through the simultaneous real-time comparison of bound versus unbound species by measuring the change in the solution dipole moment produced by binding-induced conformational and/or hydration changes. FSA-CIR identified KD values for chemically distinct LPA species binding to human LPA1 and required only a few nanograms of protein: 1-oleoyl (18:1; KD = 2.08 ± 1.32 nM), 1-linoleoyl (18:2; KD = 2.83 ± 1.64 nM), 1-arachidonoyl (20:4; KD = 2.59 ± 0.481 nM), and 1-palmitoyl (16:0; KD = 1.69 ± 0.1 nM) LPA. These KD values compared favorably to those obtained using the previous generation back-scattering interferometry system, a chip-based technique with low-throughput and temperature sensitivity. In conclusion, FSA-CIR offers a new increased-throughput approach to assess quantitatively label-free lipid ligand-receptor binding, including nonactivating antagonist binding, under near-native conditions.
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Affiliation(s)
- Manisha Ray
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Kazufumi Nagai
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Yasuyuki Kihara
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Michael N Kammer
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Aaron Frantz
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92037
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Jerold Chun
- Degenerative Disease Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
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Kammer M, Kussrow AK, Olmsted IR, Jackson GW, Bornhop DJ. Free Solution Assay Signal Modulation in Variable-Stem-Length Hairpin Aptamers. ACS Omega 2020; 5:11308-11313. [PMID: 32478218 PMCID: PMC7254501 DOI: 10.1021/acsomega.9b04341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 04/03/2020] [Indexed: 06/11/2023]
Abstract
Interferometric measurements of free solution assays (FSAs) quantify changes in molecular conformation and hydration upon binding. Here, we demonstrate that aptamer probes designed to undergo varying levels of conformational change upon binding produce corresponding variations in FSA signals. A series of hairpin aptamers were synthesized for the small molecule (tenofovir) with identical loop regions that contain the binding pocket, with between 2 and 10 self-associating base pairings in the stem region. Aptamers selected for tenofovir showed a decrease in the FSA signal and binding affinity (increase in K D) with increasing stem length. Thermodynamic calculations of the Gibbs free energy (ΔG) reported a decrease in ΔG with respect to a corresponding increase in the aptamer stem length. Collectively, these observations provide an expanded understanding of FSA and demonstrate the potential for the rational design of label-free aptamer beacons using FSA as readout.
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Affiliation(s)
- Michael
N. Kammer
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - George W. Jackson
- Base
Pair Biotechnologies, Inc., Pearland, Texas 77584, United States
| | - Darryl J. Bornhop
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt
University Institute of Chemical Biology, Nashville, Tennessee 37232-6304, United States
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Kammer MN, Kussrow A, Gandhi I, Drabek R, Batchelor RH, Jackson GW, Bornhop DJ. Quantification of Opioids in Urine Using an Aptamer-Based Free-Solution Assay. Anal Chem 2019; 91:10582-10588. [PMID: 31314489 DOI: 10.1021/acs.analchem.9b01638] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The opioid epidemic continues in the United States. Many have been impacted by this epidemic, including neonates who exhibit Neonatal Abstinence Syndrome (NAS). Opioid diagnosis and NAS can be negatively impacted by limited testing options outside the hospital, due to poor assay performance, false-negatives, rapid drug clearance rates, and difficulty in obtaining enough specimen for testing. Here we report a small volume urine assay for oxycodone, hydrocodone, fentanyl, noroxycodone, norhydrocodone, and norfentanyl with excellent LODs and LOQs. The free-solution assay (FSA), coupled with high affinity DNA aptamer probes and a compensated interferometric reader (CIR), represents a potential solution for quantifying opioids rapidly, at high sensitivity, and noninvasively on small sample volumes. The mix-and-read test is 5- to 275-fold and 50- to 1250-fold more sensitive than LC-MS/MS and immunoassays, respectively. Using FSA, oxycodone, hydrocodone, fentanyl, and their urinary metabolites were quantified using 10 μL of urine at 28-81 pg/mL, with >95% specificity and excellent accuracy in ∼1 h. The assay sensitivity, small sample size requirement, and speed could enable opioid screening, particularly for neonates, and points to the potential for pharmacokinetic tracking.
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Affiliation(s)
- Michael N Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
| | - Ilavarasi Gandhi
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Rafal Drabek
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Robert H Batchelor
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - George W Jackson
- Base Pair Biotechnologies, Inc. , Pearland , Texas 77584 , United States
| | - Darryl J Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology , Vanderbilt University , Nashville , Tennessee 37235 , United States
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Kammer MN, Kussrow AK, Antic SL, Nguyen R, Chen H, Bornhop DJ, Massion PP. Abstract 4218: Validation of a new blood-based biomarker strategy for the early detection of lung cancer. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4218] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Rationale: The management of indeterminate pulmonary nodules (IPNs) remains a challenging problem. Our new assay methodology, the Free Solution Assay (FSA), measured by the Compensated Interferometric Reader (CIR), consisting of a diode laser, capillary and CCD, provides 40-fold lower limits of quantitation (LOQ) than ELISA for known candidate serum protein biomarkers, while speeding assay development, accuracy, and sensitivity. We hypothesized that lowering the LOQ of previously investigated biomarkers can increase the biomarker discriminatory power, enabling patients in an intermediate risk group (15-80%) to be reclassified into a low (<15) or high (>80) risk group. Methods: In this retrospective case-control study, FSA-CIR was used to measure the serum concentration of CYFRA 21-1 in two patient cohorts, a training cohort (N=274) of patients with IPNs collected at Vanderbilt University Medical Center and an external validation cohort (N=103) collected at the University of Pittsburgh Medical Center. Patient malignancy was determined by tissue biopsy or 2-year follow-up CT scan showing no signs of nodule growth. Baseline risk for cancer was calculated using nodule size. The added value of CYFRA 21-1 was assessed by comparing the difference in risk for lung cancer after incorporating CYFRA 21-1 into the model. Results: The limit of detection (LOD) of 6pg/mL and an average LOQ for standards was determined to be 60pg/mL. Patient samples in the training cohort were found to have CYFRA 21-1 concentrations ranging 100 pg/mL to 10 ng/mL, with a median of 0.79 (0.28-1.22, interquartile range) ng/mL in the control population and 1.90 (1.33-3.35) ng/mL in the case population, providing a ROC-AUC of 0.86 across three histological subtypes (adenocarcinoma, squamous cell carcinoma, and small cell lung cancer). The CYFRA 21-1 + nodule size risk model correctly reclassified 28 (25%) [DB1] of intermediate-risk benign nodules into the low-risk group and 28(24%) of intermediate-risk malignant nodules into the high-risk group. The independent validation cohort’s controls had a median of 0.35 (0.20-0.56) ng/mL, while cases had 0.97(0.66-1.22) ng/mL, providing a ROC-AUC of 0.84 and correct reclassification of 12(34%) of intermediate-risk benign nodules and 6(15%) of intermediate-risk malignant nodules. The CYFRA 21-1 + nodule size risk model correctly classified 90.6% in the low-risk group and 87.0% in the high-risk group. Conclusions: FSA-CIR measurements requiring only a few microliters of serum allowed for reclassification of patients in the intermediate risk group in both the training and validation cohorts. The results suggest that CYFRA 21-1 measured by FSA-CIR represents a strong candidate biomarker for risk stratification of patients with IPNs.
Citation Format: Michael N. Kammer, Amanda K. Kussrow, Sanja L. Antic, Rina Nguyen, Heidi Chen, Darryl J. Bornhop, Pierre P. Massion. Validation of a new blood-based biomarker strategy for the early detection of lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 4218.
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11
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Kammer MN, Kussrow AK, Webster RL, Chen H, Hoeksema M, Christenson R, Massion PP, Bornhop DJ. Compensated Interferometry Measures of CYFRA 21-1 Improve Diagnosis of Lung Cancer. ACS Comb Sci 2019; 21:465-472. [PMID: 31022347 DOI: 10.1021/acscombsci.9b00022] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Diagnosis of lung cancer patients with indeterminate pulmonary nodules (IPNs) presents a significant clinical challenge, with morbidity and management costs of $28 billion/year. We show that a quantitative free-solution assay (FSA), coupled with a compensated interferometric reader (CIR), improves the diagnostic performance of CYFRA 21-1 as a lung cancer biomarker. FSA-CIR is a rapid, mix-and-read, isothermal, label- and enzyme-free, matrix-insensitive, and target and probe-agnostic assay. Operating FSA-CIR at ∼40, 0.75 μL samples/day delivered a serum CYFRA 21-1 limit of quantification (LOQ) of 81 pg/mL with intra-assay and interassay CVs of 4.9% and 9.6% for four-day replicate determinations. Blinded analysis of a 225 patient cohort, consisting of 75 nonmalignant nodules, 45 adenocarcinomas, 44 squamous cell carcinomas, and 61 small cell lung cancers, gave a clear separation of cases and controls, not observed in the Cobas ECL analysis. The area under the curve (AUC) for the Mayo model increased from 0.595 to 0.923 when combined with the FSA-CIR CYFRA 21-1 measurements. In a population with nodules between 6 and 30 mm, the AUC increased from 0.567 to 0.943. In this subgroup, the positive predictive value (PPV) for all tumors by the CYFRA 21-1 assay was 98.7%. Our results demonstrate increased performance of the CYFRA 21-1 assay using FSA-CIR and represents a proof of concept for redefining the performance characteristics of this important candidate biomarker.
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Affiliation(s)
- Michael N. Kammer
- Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Rebekah L. Webster
- Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Heidi Chen
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Megan Hoeksema
- Division of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Robert Christenson
- Department of Pathology, University of Maryland, Baltimore, Maryland 21201, United States
| | - Pierre P. Massion
- Division of Allergy, Pulmonary and Critical Care Medicine and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
| | - Darryl J. Bornhop
- Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Leclercq L, Saetear P, Rolland-Sabaté A, Biron JP, Chamieh J, Cipelletti L, Bornhop DJ, Cottet H. Size-Based Characterization of Polysaccharides by Taylor Dispersion Analysis with Photochemical Oxidation or Backscattering Interferometry Detections. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Laurent Leclercq
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
| | - Phoonthawee Saetear
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
- Department of Chemistry and the Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama 6 Road, Ratchathewi, Bangkok 10400, Thailand
| | - Agnès Rolland-Sabaté
- UR1268 Biopolymères Interactions Assemblages, INRA, F-44300 Nantes, France
- UMR0408 Sécurité et Qualité des Produits d’Origine Végétale, INRA, Université Avignon, F-84000 Avignon, France
| | | | - Joseph Chamieh
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
| | - Luca Cipelletti
- L2C, Université de Montpellier, CNRS, Montpellier 34095, France
| | | | - Hervé Cottet
- IBMM, Université de Montpellier, CNRS, ENSCM, Montpellier 34095, France
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13
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Mizuno H, Kihara Y, Kussrow A, Chen A, Ray M, Rivera R, Bornhop DJ, Chun J. Lysophospholipid G protein-coupled receptor binding parameters as determined by backscattering interferometry. J Lipid Res 2018; 60:212-217. [PMID: 30463988 DOI: 10.1194/jlr.d089938] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [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: 09/17/2018] [Revised: 11/13/2018] [Indexed: 12/23/2022] Open
Abstract
Lysophosphatidic acid (LPA) activates cognate G protein-coupled receptors (GPCRs) to initiate biological signaling cascades. Lysophospholipid (LP) receptor binding properties remain incompletely assessed because of difficulties with ligand lipophilicity and lipid "stickiness." These inherent attributes produce high levels of nonspecific binding within cell-membrane preparations used to assess GPCRs, as has been shown in classical binding assays using radiolabeled ligands, making accurate measurements of lipid binding kinetics difficult to achieve. Backscattering interferometry (BSI) is an optical technology that measures molecular binding interactions by reporting changes in the refractive index of a solution after binding events. Here, we report the use of BSI to assess LPA1 for its ability to bind to naturally occurring lipids and a synthetic LPA1 antagonist (ONO-9780307), under both primary- and competition-binding conditions. Assessment of 12 different lipids demonstrated that the known LP ligand, 1-oleoyl-LPA, as well as an endocannabinoid metabolite, anandamide phosphate, are specific ligands for LPA1, whereas other LPs tested were not. Newly determined dissociation constants (Kd values) for orthosteric lipid ligands approximated 10-9 M, substantially lower (i.e., with higher affinity) than measured Kd values in classical binding or cell-based assays. These results demonstrate that BSI may have particular utility in assessing binding interactions between lipid receptors and their lipid ligands and could provide new screening approaches for lipid receptor identification and drug discovery.
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Affiliation(s)
- Hirotaka Mizuno
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037.,Discovery Technology Research Laboratories, Ono Pharmaceutical Co., Ltd., Osaka 618-8585, Japan
| | - Yasuyuki Kihara
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Amanda Kussrow
- Department of Chemistry Vanderbilt University, Nashville, TN 37235.,Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Allison Chen
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Manisha Ray
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Richard Rivera
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
| | - Darryl J Bornhop
- Department of Chemistry Vanderbilt University, Nashville, TN 37235.,Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN 37235
| | - Jerold Chun
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037
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14
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Abstract
Here we report an improved interferometric sensing approach that facilitates high sensitivity nanovolume refractive index (RI) measurements and molecular interaction assays without a temperature controller. The compensated backscattering interferometer (CBSI) is based on a helium-neon (He-Ne) laser, a microfluidic chip, and a CCD array. The CBSI enables simultaneous differential RI measurements within nanoliter volumes, at a compensation level of ca. 5 × 10-8 RIU in the presence of large thermal perturbations (8 °C). This level of d n/d T compensation is enabled by elongating the laser beam along the central axis of the microfluidic channel and measuring the difference in positional shift of interference patterns from two adjacent regions of the channel. By separating two solutions by an air gap or oil droplet, CBSI can discriminate the difference in RI for the sample and reference at a detection limit of 7 × 10-7 RIU in the absence of electronic filtering. At this level of ΔRI sensitivity, it is possible to perform label-free, free-solution biochemical assays at the 10s of nM level without the typical high-resolution temperature control needed in conventional interferometers. Here we illustrate the effective use of CBSI by quantifying the binding affinities for mannose-concanavalin A and Ca2+-recoverin interactions.
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Affiliation(s)
- Michael N. Kammer
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Amanda K. Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Ian R. Olmsted
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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15
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Kammer MN, Kussrow AK, Bornhop DJ. Longitudinal pixel averaging for improved compensation in backscattering interferometry. Opt Lett 2018; 43:482-485. [PMID: 29400820 DOI: 10.1364/ol.43.000482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 12/19/2017] [Indexed: 06/07/2023]
Abstract
Longitudinal averaging of the interference pattern in a compensated backscattering interferometer provides improved compensation for temperature induced refractive index perturbations. Fringe pattern likeness between two discrete detection regions of an off-the-shelf microfluidic chip illuminated by an inexpensive diode laser scales with interrogation length. Averaging the intensity distribution along a 2.75 mm length of the channel results in a 750-fold reduction in sensitivity to temperature and a baseline noise level of 3×10-8 refractive index units (RIU). These observations enable nanoliter-volume interferometric measurements at a level of 10-7 RIU in the presence of a 2°C temperature variation without the need for temperature control.
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Retzlaff CL, Kussrow A, Schorkopf T, Saetear P, Bornhop DJ, Hardaway JA, Sturgeon SM, Wright J, Blakely RD. Metallo-β-lactamase Domain-Containing Protein 1 (MBLAC1) Is a Specific, High-Affinity Target for the Glutamate Transporter Inducer Ceftriaxone. ACS Chem Neurosci 2017; 8:2132-2138. [PMID: 28783953 DOI: 10.1021/acschemneuro.7b00232] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Ceftriaxone, a β-lactam antibiotic, has been reported to act independently of its antimicrobial actions to normalize perturbed central nervous system glutamate levels, principally by elevating expression of glial glutamate transporters. Identification of a specific, high-affinity target for ceftriaxone could significantly impact therapeutic development for multiple brain disorders, ranging from neurodegenerative disorders to addiction. Recently, we identified a glial-expressed Caenorhabditis elegans gene, swip-10, that encodes a metallo-β-lactamase domain-containing protein, and limits glutamate-dependent changes in dopamine neuron excitability. Bioinformatic analyses identified MBLAC1 as the likely mammalian orthologue of swip-10. Using cyanogen bromide immobilized ceftriaxone for affinity capture experiments and backscattering interferometry to monitor MBLAC1 binding of unmodified ceftriaxone, we obtained evidence for specific, high affinity (KD = 2.2 μM) binding of ceftriaxone to MBLAC1. We discuss our findings with respect to MBLAC1 as a potentially exclusive, high-affinity binding partner of ceftriaxone in the CNS, and the path forward in the development of novel, MBLAC1-based therapeutics.
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Affiliation(s)
- Cassandra L. Retzlaff
- Department
of Biomedical Science and Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
| | | | | | | | | | | | | | | | - Randy D. Blakely
- Department
of Biomedical Science and Brain Institute, Charles E. Schmidt College of Medicine, Florida Atlantic University, Jupiter, Florida 33458, United States
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Saetear P, Chamieh J, Kammer MN, Manuel TJ, Biron JP, Bornhop DJ, Cottet H. Taylor Dispersion Analysis of Polysaccharides Using Backscattering Interferometry. Anal Chem 2017; 89:6710-6718. [DOI: 10.1021/acs.analchem.7b00946] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
| | - Joseph Chamieh
- IBMM, Univ. Montpellier,
CNRS, ENSCM, Montpellier, France
| | - Michael N. Kammer
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- The
Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Thomas J. Manuel
- Department
of Agricultural and Biological Engineering, Mississippi State University, Starkville, Mississippi 39762, United States
| | | | - Darryl J. Bornhop
- Department
of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- The
Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Hervé Cottet
- IBMM, Univ. Montpellier,
CNRS, ENSCM, Montpellier, France
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18
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Wang M, Kussrow AK, Ocana MF, Chabot JR, Lepsy CS, Bornhop DJ, O'Hara DM. Physiologically relevant binding affinity quantification of monoclonal antibody PF-00547659 to mucosal addressin cell adhesion molecule for in vitro in vivo correlation. Br J Pharmacol 2016; 174:70-81. [PMID: 27760281 PMCID: PMC5221447 DOI: 10.1111/bph.13654] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/30/2016] [Accepted: 10/06/2016] [Indexed: 12/29/2022] Open
Abstract
Background and Purpose A monoclonal antibody (PF‐00547659) against mucosal addressin cell adhesion molecule (MAdCAM), expressed as both soluble (sMAdCAM) and trans‐membrane (mMAdCAM) target forms, showed over 30‐fold difference in antibody‐target KD between in vitro (Biacore) and clinically derived (KD,in‐vivo) values. Back‐scattering interferometry (BSI) was applied to acquire physiologically relevant KD values which were used to establish in vitro and in vivo correlation (IVIVC). Experimental Approach BSI was applied to obtain KD values between PF‐00547659 and recombinant human MAdCAM in buffer or CHO cells and endogenous MAdCAM in human serum or colon tissue. CHO cells and tissue were minimally processed to yield homogenate containing membrane vesicles and soluble proteins. A series of binding affinities in serum with various dilution factors was used to estimate both KD,in‐vivo and target concentrations; MAdCAM concentrations were also measured using LC–MS/MS. Key Results BSI measurements revealed low KD values (higher affinity) for sMAdCAM in buffer and serum, yet a 20‐fold higher KD value (lower affinity) for mMAdCAM in CHO, mMAdCAM and sMAdCAM in tissue. BSI predicted KD,in‐vivo in serum was similar to clinically derived KD,in‐vivo, and the BSI‐estimated serum sMAdCAM concentration also matched the measured concentration by LC–MS/MS. Conclusions and Implications Our results successfully demonstrated that BSI measurements of physiologically relevant KD values can be used to establish IVIVC, for PF‐00547659 to MAdCAM despite the lack of correlation when using Biacore measured KD and accurately estimates endogenous target concentrations. The application of BSI would greatly enhance successful basic pharmacological research and drug development.
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Affiliation(s)
- Mengmeng Wang
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | - Amanda K Kussrow
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | | | - Jeffrey R Chabot
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
| | | | - Darryl J Bornhop
- Department of Chemistry, Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA
| | - Denise M O'Hara
- Pharmacokinetics, Dynamics and Metabolism, Pfizer Inc, Andover, MA, USA
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Kammer MN, Olmsted IR, Kussrow AK, Morris MJ, Jackson GW, Bornhop DJ. Characterizing aptamer small molecule interactions with backscattering interferometry. Analyst 2015; 139:5879-84. [PMID: 25229067 DOI: 10.1039/c4an01227e] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Aptamers are segments of single-strand DNA or RNA used in a wide array of applications, including sensors, therapeutics, and cellular process regulators. Aptamers can bind many target species, including proteins, peptides, and small molecules (SM) with high affinity and specificity. They are advantageous because they can be identified in vitro by SELEX, produced rapidly and relatively economically using oligonucleotide synthesis. The use of aptamers as SM probes has experienced a recent rebirth, and because of their unique properties they represent an attractive alternative to antibodies. Current assay methodology for characterizing small molecule-aptamer binding is limited by either mass sensitivity, as in biolayer interferometry (BLI) and surface plasmon resonance (SPR), or the need for using a fluorophore, as in thermophoresis. Here we report that backscattering interferometry (BSI), a label-free and free-solution sensing technique, can be used to effectively characterize SM-aptamer interactions, providing Kd values on microliter sample quantities and at low nanomolar sensitivity. To demonstrate this capability we measured the aptamer affinity for three previously reported small molecules; bisphenol A, tenofovir, and epirubicin showing BSI provided values consistent with those published previously. We then quantified the Kd values for aptamers to ampicillin, tetracycline and norepinephrine. All measurements produced R(2) values >0.95 and an excellent signal to noise ratio at target concentrations that enable true Kd values to be obtained. No immobilization or labeling chemistry was needed, expediting the assay which is also insensitive to the large relative mass difference between the interacting molecules.
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Affiliation(s)
- Michael N Kammer
- Department of Chemistry, Vanderbilt University, 2201 West End Avenue, Nashville, Tennessee, USA.
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20
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Saetear P, Perrin AJ, Bartholdson SJ, Wanaguru M, Kussrow A, Bornhop DJ, Wright GJ. Quantification of Plasmodium-host protein interactions on intact, unmodified erythrocytes by back-scattering interferometry. Malar J 2015; 14:88. [PMID: 25889240 PMCID: PMC4349660 DOI: 10.1186/s12936-015-0553-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 01/06/2015] [Indexed: 11/17/2022] Open
Abstract
Background Invasion of host erythrocytes by Plasmodium falciparum is central to the pathogenesis of malaria. Invasion involves recognition events between erythrocyte receptors and ligands on the merozoite, the invasive blood form of the parasite. Identifying and characterizing host-parasite interactions is impeded by the biochemical challenges of working with membrane-embedded glycoprotein receptors. For example, the interaction between P. falciparum erythrocyte binding antigen 175 (PfEBA175) and glycophorin A (GYPA) depends on post-translational modifications that are not easily added in recombinant expression systems, and the use of native GYPA is limited by the hydrophobic transmembrane region, making it difficult to biochemically manipulate. It would, therefore, be desirable to perform quantitative binding assays with receptors embedded within the membranes of intact human erythrocytes. Methods The extracellular region of GYPA was over-expressed as a soluble protein in HEK293E cells. This protein was characterized, sialylated and evaluated for binding to the PfEBA175 protein. The label-free and free-solution assay, backscattering interferometry (BSI), was used to perform binding assays of two well-characterized P. falciparum invasion ligands to intact unmodified human erythrocytes. Results Findings indicate that the post-translational modifications present on native GYPA are required for it to bind recombinant PfEBA175 and that these modifications cannot be recapitulated in vitro using mammalian overexpression methods. Here, BSI was used to obtain quantitative, high fidelity interaction determinations on intact, unmodified erythrocytes. Using BSI and purified recombinant proteins constituting the entire ectodomains of the P. falciparum merozoite ligands PfEBA175 and PfRH5, KDs of 1.1 μM and 50 nM were measured for the PfRH5-BSG and PfEBA175-GYPA interactions, respectively, in good agreement with previous biophysical measurements of these interactions. Conclusions These results demonstrate that BSI can be used to detect and quantify the interactions of two merozoite invasion ligands with their receptors on intact human erythrocytes. BSI assays were performed on unlabelled, free-solution proteins in their native environment, requiring only nanomoles of recombinant protein. This study suggests that BSI can be used to investigate host-parasite protein interactions without the limitations of other assay platforms, and therefore represents a valuable new method to investigate the molecular mechanisms involved in erythrocyte invasion by P. falciparum.
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Affiliation(s)
- Phoonthawee Saetear
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok, 10400, Thailand.
| | - Abigail J Perrin
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - S Josefin Bartholdson
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Madushi Wanaguru
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
| | - Amanda Kussrow
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee, 37235, USA.
| | - Darryl J Bornhop
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee, 37235, USA.
| | - Gavin J Wright
- Cell Surface Signalling Laboratory and Malaria Programme, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK.
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21
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Olmsted IR, Hassanein M, Kussrow A, Hoeksema M, Li M, Massion PP, Bornhop DJ. Toward rapid, high-sensitivity, volume-constrained biomarker quantification and validation using backscattering interferometry. Anal Chem 2014; 86:7566-74. [PMID: 24954171 PMCID: PMC4215853 DOI: 10.1021/ac501355q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [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: 04/14/2014] [Accepted: 06/20/2014] [Indexed: 12/21/2022]
Abstract
Realizing personalized medicine, which promises to enable early disease detection, efficient diagnostic staging, and therapeutic efficacy monitoring, hinges on biomarker quantification in patient samples. Yet, the lack of a sensitive technology and assay methodology to rapidly validate biomarker candidates continues to be a bottleneck for clinical translation. In our first direct and quantitative comparison of backscattering interferometry (BSI) to fluorescence sensing by ELISA, we show that BSI could aid in overcoming this limitation. The analytical validation study was performed against ELISA for two biomarkers for lung cancer detection: Cyfra 21-1 and Galectin-7. Spiked serum was used for calibration and comparison of analytical figures of merit, followed by analysis of blinded patient samples. Using the ELISA antibody as the probe chemistry in a mix-and-read assay, BSI provided significantly lower detection limits for spiked serum samples with each of the biomarkers. The limit of quantification (LOQ) for Cyrfa-21-1 was measured to be 230 pg/mL for BSI versus 4000 pg/mL for ELISA, and for Galectin-7, it was 13 pg/mL versus 500 pg/mL. The coefficient of variation for 5 day, triplicate determinations was <15% for BSI and <10% for ELISA. The two techniques correlated well, ranging from 3-29% difference for Cyfra 21-1 in a blinded patient sample analysis. The label-free and free-solution operation of BSI allowed for a significant improvement in analysis speed, with greater ease, improved LOQ values, and excellent day-to-day reproducibility. In this unoptimized format, BSI required 5.5-fold less sample quantity needed for ELISA (a 10 point calibration curve measured in triplicate required 36 μL of serum for BSI vs 200 μL for ELISA). The results indicate that the BSI platform can enable rapid, sensitive analytical validation of serum biomarkers and should significantly impact the validation bottleneck of biomarkers.
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Affiliation(s)
- Ian R. Olmsted
- Department
of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Mohamed Hassanein
- Division
of Allergy, Pulmonary and Critical Care Medicine, Thoracic Program,
Vanderbilt Ingram Cancer Center, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37235, United States
| | - Amanda Kussrow
- Department
of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Megan Hoeksema
- Division
of Allergy, Pulmonary and Critical Care Medicine, Thoracic Program,
Vanderbilt Ingram Cancer Center, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37235, United States
| | - Ming Li
- Department
of Biostatistics, Vanderbilt Ingram Cancer Center, Vanderbilt University School of Medicine Nashville, Tennessee 37235, United States
| | - Pierre P. Massion
- Division
of Allergy, Pulmonary and Critical Care Medicine, Thoracic Program,
Vanderbilt Ingram Cancer Center, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37235, United States
- Department
of Cancer Biology, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37235, United States
- Veterans Affairs,
Tennessee Valley Healthcare System, Nashville Campus, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department
of Chemistry and the Vanderbilt Institute of Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee 37235, United States
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Samuelson LE, Anderson BM, Bai M, Dukes MJ, Hunt CR, Casey JD, Han Z, Papadopoulos V, Bornhop DJ. A self-internalizing mitochondrial TSPO targeting imaging probe for fluorescence, MRI and EM. RSC Adv 2014; 4:9003-9011. [PMID: 32051760 DOI: 10.1039/c3ra47161f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Advances in probes for cellular imaging have driven discoveries in biology and medicine. Primarily, antibodies and small molecules have been made for contrast enhancement of specific proteins. The development of new dendrimer-based tools offers opportunities to tune cellular internalization and targeting, image multiple modalities in the same molecule and explore therapeutics. The translocator protein (TSPO) offers an ideal target to develop dendrimer tools because it is well characterized and implicated in a number of disease states. The TSPO-targeted dendrimers reported here, primarily ClPhIQ-PAMAM-Gd-Liss, are cell membrane permeable nanoparticles that enable labeling of TSPO and provide contrast in fluorescence, electron microscopy and magnetic resonance imaging. The molecular binding affinity for TSPO was found to be 0.51 μM, 3 times greater than the monomeric agents previously demonstrated in our laboratory. The relaxivity per Gd3+ of the ClPhIQ23-PAMAM-Gd18 dendrimer was 7.7 and 8.0 mM-1 s-1 for r 1 and r 2 respectively, approximately double that of the clinically used monomeric Gd3+ chelates. In vitro studies confirmed molecular selectively for labeling TSPO in the mitochondria of C6 rat glioma and MDA-MB-231 cell lines. Fluorescence co-registration with Mitotracker Green® and increased contrast of osmium-staining in electron microscopy confirmed mitochondrial labeling of these TSPO-targeted agents. Taken collectively these experiments demonstrate the versatility of conjugation of our PAMAM dendrimeric chemistry to allow multi-modality agents to be prepared. These agents target organelles and use complementary imaging modalities in vitro, potentially allowing disease mechanism studies with high sensitivity and high resolution techniques.
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Affiliation(s)
- Lynn E Samuelson
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
| | - Bernard M Anderson
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
| | - Mingfeng Bai
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
| | - Madeline J Dukes
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
| | - Colette R Hunt
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
| | - Jonathon D Casey
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
| | - Zeqiu Han
- Department of Biochemistry &Molecular and Ceilular Biology, Georgetown University Medical Center, BSB Room 315, 3900 Reservoir Road NW, Washington, DC 20057, USA
| | - Vassilios Papadopoulos
- The Research Institute of the McGill University Health Centre, Departments of Medicine, Biochemistry, and Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Darryl J Bornhop
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822, USA
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Abstract
Chemotherapeutics such as doxorubicin (DOX) and paclitaxel (PXL) have dose-limiting systemic toxicities, including cardiotoxicity and peripheral neuropathy. Delivery strategies to minimize these undesirable effects are needed and could improve efficacy, while reducing patient morbidity. Here, DOX and PXL were conjugated to a nanodendron (ND) through an MMP9-cleavable peptide linker, producing two new therapies, ND2(DOX) and ND2(PXL), designed to improve delivery specificity to the tumor microenvironment and reduce systemic toxicity. Comparative cytotoxicity assays were performed between intact ND-drug conjugates and the MMP9 released drug in cell lines with and without MMP9 expression. While ND2(DOX) was found to lose cytotoxicity due to the modification of DOX for conjugation to the ND; ND2(PXL) was determined to have the desired properties for a prodrug delivery system. ND2(PXL) was found to be cytotoxic in MMP9-expressing mouse mammary carcinoma (R221A-luc) (53%) and human breast carcinoma (MDA-MB-231) (66%) at a concentration of 50 nM (in PXL) after 48 h. Treating ND2(PXL) with MMP9 prior to the cytotoxicity assay resulted in a faster response; however, both cleaved and intact versions of the drug reached the same efficacy as the unmodified drug by 96 h in the R221A-luc and MDA-MB-231 cell lines. Further studies in modified Lewis lung carcinoma cells that either do (LLC(MMP9)) or do not (LLC(RSV)) express MMP9 demonstrate the selectivity of ND2(PXL) for MMP9. LLC(MMP9) cells were only 20% viable after 48 h of treatment, while LLC(RSV) were not affected. Inclusion of an MMP inhibitor, GM6001, when treating the LLC(MMP9) cells with ND2(PXL) eliminated the response of the MMP9 expressing cells (LLC(MMP9)). The data presented here suggests that these NDs, specifically ND2(PXL), are nontoxic until activated by MMP9, a protease common in the microenvironment of tumors, indicating that incorporation of chemotherapeutic or cytostatic agents onto the ND platform have potential for tumor-targeted efficacy with reduced in vivo systemic toxicities.
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Affiliation(s)
- Lynn E Samuelson
- Department of Cancer Biology, The Vanderbilt Institute for Chemical Biology, Vanderbilt University , VU Station B 351822, Nashville, Tennessee 37235-1822, United States
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Adams NM, Olmsted IR, Haselton FR, Bornhop DJ, Wright DW. The effect of hybridization-induced secondary structure alterations on RNA detection using backscattering interferometry. Nucleic Acids Res 2013; 41:e103. [PMID: 23519610 PMCID: PMC3643578 DOI: 10.1093/nar/gkt165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Backscattering interferometry (BSI) has been used to successfully monitor molecular interactions without labeling and with high sensitivity. These properties suggest that this approach might be useful for detecting biomarkers of infection. In this report, we identify interactions and characteristics of nucleic acid probes that maximize BSI signal upon binding the respiratory syncytial virus nucleocapsid gene RNA biomarker. The number of base pairs formed upon the addition of oligonucleotide probes to a solution containing the viral RNA target correlated with the BSI signal magnitude. Using RNA folding software mfold, we found that the predicted number of unpaired nucleotides in the targeted regions of the RNA sequence generally correlated with BSI sensitivity. We also demonstrated that locked nucleic acid (LNA) probes improved sensitivity approximately 4-fold compared to DNA probes of the same sequence. We attribute this enhancement in BSI performance to the increased A-form character of the LNA:RNA hybrid. A limit of detection of 624 pM, corresponding to ∼10(5) target molecules, was achieved using nine distinct ∼23-mer DNA probes complementary to regions distributed along the RNA target. Our results indicate that BSI has promise as an effective tool for sensitive RNA detection and provides a road map for further improving detection limits.
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Affiliation(s)
- Nicholas M Adams
- Department of Chemistry, Vanderbilt University, Nashville, TN 37235, USA
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25
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Olmsted IR, Kussrow A, Bornhop DJ. Comparison of free-solution and surface-immobilized molecular interactions using a single platform. Anal Chem 2012; 84:10817-22. [PMID: 23173653 DOI: 10.1021/ac302933h] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
While it is generally accepted that surface immobilization affects the binding properties of proteins, it has been difficult to quantify these effects due to the lack of technology capable of making affinity measurements with species tethered and in free solution on a single platform. Further, quantifying the interaction of binding pairs with widely differing masses has also been challenging, particularly when it is desirable to tether the high molecular weight protein. Here we describe the use of backscattering interferometry (BSI) to quantify the binding affinity of mannose and glucose to concanavalin A (ConA), a 106 KDa homotetramer protein, in free solution using picomoles of the protein. Using the same platform, BSI, we then studied the effect on the binding constants of the ConA-carbohydrate interactions upon chemically immobilizing ConA on the sensor surface. By varying the distances (0, 7.17, and 20.35 nm) of the ConA tether and comparing these results to the free-solution measurements, it has been possible to quantify the effect that protein immobilization has on binding. Our results indicate that the apparent binding affinity of the sugar-lectin pair increases as the distance between ConA and the surface decreases. These observations could lend insight as to why the affinity values reported in the literature sometimes vary significantly from one measurement technique to another.
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Affiliation(s)
- Ian R Olmsted
- Department of Chemistry and the Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, Tennessee 37235, USA
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26
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Olmsted IR, Massion PP, Bornhop DJ, Hassanein M, Hoeksema M. Validation of galectin-7 using backscattering interferometry. J Clin Oncol 2012. [DOI: 10.1200/jco.2012.30.30_suppl.15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
15 Background: More than 60% of lung cancer patients are diagnosed with advanced disease due to a lack of early diagnosis tools. These patients are ineligible for surgical resection and have a poor prognosis. This situation could be avoided if we could quantify lung cancer specific biomarkers at sufficiently low concentrations, providing an indication of disease threat. Backscattering Inerferometry (BSI) is a label-free sensor with a simple optical train that is used to quantify biomarkers in complex matrices at picomolar to femtomolar levels. Here we demonstrate that BSI can enable lung cancer biomarker validation in complex, volume constrained samples and at detection limits significantly better than ELISA. Methods: A BSI dose response curve for Galectin-7 was constructed by incubating increasing concentrations (0-20 ng/mL) of recombinant galectin-7 with 100 ng/mL of polyclonal antibody. The samples were mixed at 300 RPM for 2 before being injected into the BSI instrument and measured in triplicate each day. All reagents used were obtained from a commercial ELISA kit. An ELISA dose response curve was similarly constructed using spiked serum and spiked plasma according to the manufacturer’s recommended procedure. Finally, 9 patient serum samples were quantified using BSI and ELISA for direct comparison of the two technologies. Results: BSI was used to quantify galectin-7 in spiked serum and patients samples. The lower limit of detection with standards was determined to be 0.5 ng/mL for ELISA in serum, 10 ng/mL for ELISA in plasma, and 0.04 ng/mL for BSI in serum. In the analysis of 9 patient serum samples, all were quantifiable using BSI, which enjoys low pg/mL detection limits, yet with ELISA only 5 samples contained a galectin-7 concentration high enough to be measured. In this small sample set there was a good correlation between disease state and galectin-7 concentration as measured by BSI. Conclusions: This study demonstrates that BSI is well-suited for biomarker detection and validation, having a greater dynamic operating range and much lower limits of detection than standard commercially available ELISA kits. Future work will focus on detecting other NSCLC biomarkers that are undetectable with currently available technology.
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Haddad GL, Young SC, Heindel ND, Bornhop DJ, Flowers RA. Back-Scattering Interferometry: An Ultrasensitive Method for the Unperturbed Detection of Acetylcholinesterase-Inhibitor Interactions. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Haddad GL, Young SC, Heindel ND, Bornhop DJ, Flowers RA. Back-scattering interferometry: an ultrasensitive method for the unperturbed detection of acetylcholinesterase-inhibitor interactions. Angew Chem Int Ed Engl 2012; 51:11126-30. [PMID: 23037915 DOI: 10.1002/anie.201203640] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/24/2012] [Indexed: 11/12/2022]
Abstract
A series of inhibitors of acetylcholinesterase (AChE) have been screened by back-scattering interferometry (BSI). Enzyme levels as low as 100 pM (22,000 molecules of AChE) can be detected. This method can be used to screen for mixed AChE inhibitors, agents that have shown high efficacy against Alzheimer's disease, by detecting dual-binding interactions. E = enzyme, I = inhibitor, S = substrate.
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29
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Wyatt SK, Manning HC, Bai M, Ehtesham M, Mapara KY, Thompson RC, Bornhop DJ. Preclinical molecular imaging of the translocator protein (TSPO) in a metastases model based on breast cancer xenografts propagated in the murine brain. Curr Mol Med 2012; 12:458-66. [PMID: 22348613 DOI: 10.2174/156652412800163361] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 01/09/2012] [Accepted: 02/02/2012] [Indexed: 01/14/2023]
Abstract
Previous studies have demonstrated the feasibility of translocator protein (TSPO) imaging to visualize and quantify human breast adenocarcinoma (MDA-MB-231) cells in vivo using a TSPO-targeted near-infrared (NIR) probe (NIR-conPK11195). This study aimed to extend the use of the TSPO-targeted probe to a more biologically relevant and clinically important tumor microenvironment as well as to assess our ability to longitudinally detect the presence and progression of breast cancer cells in the brain. The in vivo biodistribution and accumulation of NIR-conPK11195 and free (unconjugated) NIR dye were quantitatively evaluated in intracranial MDA-MB-231-bearing mice and non-tumor-bearing control mice longitudinally once a week from two to five weeks post-inoculation. The in vivo time-activity curves illustrate distinct clearance profiles for NIR-conPK11195 and free NIR dye, resulting in preferential accumulation of the TSPO-targeted probe in the intracranial tumor bearing hemisphere (TBH) with significant tumor contrast over normal muscle tissue (p < 0.005 at five weeks; p < 0.01 at four weeks). In addition, the TSPO-labeled TBHs demonstrated significant contrast over the TBHs of mice injected with free NIR dye (p < 0.001 at four and five weeks) as well as over the TSPO-labeled non-tumor-bearing hemispheres (NTBHs) of control mice (p < 0.005 at four and five weeks). Overall, TSPO-targeted molecular imaging appears useful for visualizing and quantifying breast cancer xenografts propagated in the murine brain and may assist in preclinical detection, diagnosis and monitoring of metastatic disease as well as drug discovery. Furthermore, these results indicate it should be possible to perform TSPO-imaging of breast cancer cells in the brain using radiolabeled TSPO-targeted agents, particularly in light of the fact that [11C]-labeled TSPO probes such as [11C]-PK 11195 have been successfully used to image gliomas in the clinic.
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Affiliation(s)
- Shelby K Wyatt
- Vanderbilt University Institute of Imaging Science, Vanderbilt University Medical Center, Nashville, TN, USA
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Samuelson LE, Scherer RL, Kathy CJ, Dozier EA, Printz S, VanSaun MN, Fan KH, Shyr Y, Matrisian PE, Bornhop DJ, Matrisian LM, McIntyre JO. Abstract 1947: Self-reporting dendritic nanoparticles (nanodendrons) for drug delivery targeted to the tumor microenvironment and with reduced neurotoxicity. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-1947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Proteinases, including matrix metalloproteinases (MMPs), contribute to cancer progression and other pathologies. Selective MMP expression can be used to distinguish benign from malignant tumors and identify aggressive tumors associated with poor outcome. MMP9, a basement membrane-degrading type-IV collagenase/gelatinase, is associated with tumor invasion and metastasis. In this project, we describe a new class of dendritic nanoparticles, nanodendrons (NDs), with MMP molecular recognition and targeting capabilities. These NDs can be studied as individual dendrons tuned for specific functions such as enhanced imaging or targeted drug treatments. Additionally, the NDs can be coupled to facilitate multifunctional purposes such as in NDs that can self-report drug delivery to tumors. The prototypical system presented here describes NDs that are activated by MMP9: 1) ND-PB, a near infrared imaging beacon; 2) ND-PXL, a therapeutic that delivers paclitaxel (PXL) and 3) NDPB-NDPXL, a bi-functional agent. In vivo studies in two orthotopic models of breast cancer demonstrate efficacy of these NDs to image and treat breast cancer. The proteinase-activated prodrug, NDPXL, delivers PXL to breast cancer through release of the drug in the tumor microenvironment and increases therapeutic efficacy while reducing systemic toxicity (including peripheral neuropathy). The delivery of PXL using the proteolytically activated ND-PXL is effective in inhibiting tumor growth in two orthotopic models of breast cancer (PyVT-R221A and MDA-MB231). Daily treatment of MDA-MB231 tumors with 12.5 mg/kg PXL as either ND-PXL or Abraxane® (Abx), showed similar reduction in tumor growth as compared with vehicle-treated animals. Further investigation of the NDPXL in a fully immunocompetent mouse model (PyVT-R221A) with treatments given on alternate days at a dose of 12.5 mg/kg (ND-PXL or Abx) yielded similar results: an average reduction in tumor growth of 58% and 53% in ND-PXL and Abx cohorts, respectively. Peripheral nerve toxicity, a debilitating, long term side effect of Abx therapy, was assessed in both tumor and non-tumor mice through monitoring behavior indicative of peripheral nerve damage before, during and after administration of each drug. Peripheral neurotoxicity is markedly reduced in the ND-PXL-treated versus Abraxane®-treated mice as evident in a number of behavioral assessments. The development of this novel class of NDs expands upon the current capabilities of modern proteinase-based optical beacons and prodrugs and is a step forward in treatment of both primary and metastatic cancer. [Supported in part by Susan G. Komen for the Cure®]
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 1947. doi:1538-7445.AM2012-1947
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Affiliation(s)
| | | | | | | | - Sheree Printz
- 1Vanderbilt University Medical Center, Nashville, TN
| | | | | | - Y Shyr
- 1Vanderbilt University Medical Center, Nashville, TN
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K. Wyatt S, Charles Manning H, Bai M, Ehtesham M, Y. Mapara K, C. Thompson R, J. Bornhop D. Preclinical Molecular Imaging of the Translocator Protein (TSPO) in a Metastases Model Based on Breast Cancer Xenografts Propagated in the Murine Brain. Curr Mol Med 2012. [DOI: 10.2174/1566524011207040458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Affiliation(s)
- Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Carolyn S. Enders
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 7330 Stevenson Center, Nashville, Tennessee 37235, United States
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Olmsted IR, Xiao Y, Cho M, Csordas AT, Sheehan JH, Meiler J, Soh HT, Bornhop DJ. Measurement of aptamer-protein interactions with back-scattering interferometry. Anal Chem 2011; 83:8867-70. [PMID: 22032342 DOI: 10.1021/ac202823m] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report the quantitative measurement of aptamer-protein interactions using backscattering interferometry (BSI) and show that BSI can determine when distinct binding regions are accessed. As a model system, we utilized two DNA aptamers (Tasset and Bock) that bind to distinct sites of a target protein (human α-thrombin). This is the first time BSI has been used to study a multivalent system in free solution wherein more than one ligand binds to a single target. We measured aptamer equilibrum dissociation constants (K(d)) of 3.84 nM (Tasset-thrombin) and 5.96 nM (Bock-thrombin), in close agreement with the literature. Unexpectedly, we observed allosteric effects such that the binding of the first aptamer resulted in a significant change in the binding affinity of the second aptamer. For example, the K(d) of Bock aptamer binding to preformed Tasset-thrombin complexes was 7-fold lower (indicating higher affinity) compared to binding to thrombin alone. Preliminary modeling efforts suggest evidence for allosteric linkage between the two exosites.
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Lau JL, Baksh MM, Fiedler JD, Brown SD, Kussrow A, Bornhop DJ, Ordoukhanian P, Finn M. Evolution and protein packaging of small-molecule RNA aptamers. ACS Nano 2011; 5:7722-9. [PMID: 21899290 PMCID: PMC3209476 DOI: 10.1021/nn2006927] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
A high-affinity RNA aptamer (K(d) = 50 nM) was efficiently identified by SELEX against a heteroaryldihydropyrimidine structure, chosen as a representative drug-like molecule with no cross reactivity with mammalian or bacterial cells. This aptamer, its weaker-binding variants, and a known aptamer against theophylline were each embedded in a longer RNA sequence that was encapsidated inside a virus-like particle by a convenient expression technique. These nucleoprotein particles were shown by backscattering interferometry to bind to the small-molecule ligands with affinities similar to those of the free (nonencapsidated) aptamers. The system therefore comprises a general approach to the production and sequestration of functional RNA molecules, characterized by a convenient label-free analytical technique.
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Affiliation(s)
- Jolene L. Lau
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael M. Baksh
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jason D. Fiedler
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Steven D. Brown
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Amanda Kussrow
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Darryl J. Bornhop
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, TN 37235, USA
| | - Phillip Ordoukhanian
- Center for Protein and Nucleic Acid Research, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - M.G. Finn
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Sexton M, Woodruff G, Horne EA, Lin YH, Muccioli GG, Bai M, Stern E, Bornhop DJ, Stella N. NIR-mbc94, a fluorescent ligand that binds to endogenous CB(2) receptors and is amenable to high-throughput screening. ACTA ACUST UNITED AC 2011; 18:563-8. [PMID: 21609837 DOI: 10.1016/j.chembiol.2011.02.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [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] [Received: 07/29/2010] [Revised: 12/29/2010] [Accepted: 02/03/2011] [Indexed: 11/17/2022]
Abstract
High-throughput screening (HTS) of chemical libraries is often used for the unbiased identification of compounds interacting with G protein-coupled receptors (GPCRs), the largest family of therapeutic targets. However, current HTS methods require removing GPCRs from their native environment, which modifies their pharmacodynamic properties and biases the screen toward false positive hits. Here, we developed and validated a molecular imaging (MI) agent, NIR-mbc94, which emits near infrared (NIR) light and selectively binds to endogenously expressed cannabinoid CB(2) receptors, a recognized target for treating autoimmune diseases, chronic pain and cancer. The precision and ease of this assay allows for the HTS of compounds interacting with CB(2) receptors expressed in their native environment.
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Affiliation(s)
- Michelle Sexton
- Department of Pharmacology, University of Washington, Seattle, WA 98195-7280, USA
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Abstract
Methylation of lysine residues in histones has been known to serve a regulatory role in gene expression. Although enzymatic removal of the methyl groups was discovered as early as 1973, the enzymes responsible for their removal were isolated and their mechanism of action was described only recently. The first enzyme to show such activity was LSD1, a flavin-containing enzyme that removes the methyl groups from lysines 4 and 9 of histone 3 with the generation of formaldehyde from the methyl group. This reaction is similar to the previously described demethylation reactions conducted by the enzymes dimethylglycine dehydrogenase and sarcosine dehydrogenase, in which protein-bound tetrahydrofolate serves as an accepter of the formaldehyde that is generated. We now show that nuclear extracts of HeLa cells contain LSD1 that is associated with folate. Using the method of back-scattering interferometry, we have measured the binding of various forms of folate to both full-length LSD1 and a truncated form of LSD1 in free solution. The 6R,S form of the natural pentaglutamate form of tetrahydrofolate bound with the highest affinity (K(d) = 2.8 μM) to full-length LSD1. The fact that folate participates in the enzymatic demethylation of histones provides an opportunity for this micronutrient to play a role in the epigenetic control of gene expression.
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Affiliation(s)
- Zigmund Luka
- Department of Biochemistry, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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Pesciotta EN, Bornhop DJ, Flowers RA. Backscattering Interferometry: An Alternative Approach for the Study of Hydrogen Bonding Interactions in Organic Solvents. Org Lett 2011; 13:2654-7. [DOI: 10.1021/ol200757a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Esther N. Pesciotta
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States, and Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Darryl J. Bornhop
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States, and Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Robert A. Flowers
- Department of Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States, and Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
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Pesciotta EN, Bornhop DJ, Flowers RA. Back-scattering interferometry: a versatile platform for the study of free-solution versus surface-immobilized hybridization. Chem Asian J 2011; 6:70-3. [PMID: 21082726 DOI: 10.1002/asia.201000614] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Baksh MM, Kussrow AK, Mileni M, Finn MG, Bornhop DJ. Label-free quantification of membrane-ligand interactions using backscattering interferometry. Nat Biotechnol 2011; 29:357-60. [PMID: 21399645 DOI: 10.1038/nbt.1790] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2010] [Accepted: 01/26/2011] [Indexed: 11/09/2022]
Abstract
Although membrane proteins are ubiquitous within all living organisms and represent the majority of drug targets, a general method for direct, label-free measurement of ligand binding to native membranes has not been reported. Here we show that backscattering interferometry (BSI) can accurately quantify ligand-receptor binding affinities in a variety of membrane environments. By detecting minute changes in the refractive index of a solution, BSI allows binding interactions of proteins with their ligands to be measured at picomolar concentrations. Equilibrium binding constants in the micromolar to picomolar range were obtained for small- and large-molecule interactions in both synthetic and cell-derived membranes without the use of labels or supporting substrates. The simple and low-cost hardware, high sensitivity and label-free nature of BSI should make it readily applicable to the study of many membrane-associated proteins of biochemical and pharmacological interest.
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Affiliation(s)
- Michael M Baksh
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, USA
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Kussrow A, Baksh MM, Bornhop DJ, Finn MG. Universal sensing by transduction of antibody binding with backscattering interferometry. Chembiochem 2010; 12:367-70. [PMID: 21290534 DOI: 10.1002/cbic.201000671] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2010] [Indexed: 11/05/2022]
Affiliation(s)
- Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute for Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, TN 37235, USA
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Kussrow A, Enders CS, Castro AR, Cox DL, Ballard RC, Bornhop DJ. The potential of backscattering interferometry as an in vitro clinical diagnostic tool for the serological diagnosis of infectious disease. Analyst 2010; 135:1535-7. [PMID: 20414494 DOI: 10.1039/c0an00098a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Backscattering interferometry enables the detection of syphilis antibody-antigen interactions in the presence of human serum, showing promise as a diagnostic tool for the serological diagnosis of infectious disease with potentially quantitative capabilities.
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Affiliation(s)
- Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee, USA
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Samuelson LE, Dukes MJ, Hunt CR, Casey JD, Bornhop DJ. TSPO targeted dendrimer imaging agent: synthesis, characterization, and cellular internalization. Bioconjug Chem 2009; 20:2082-9. [PMID: 19863077 PMCID: PMC3038571 DOI: 10.1021/bc9002053] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [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: 11/29/2022]
Abstract
While it has become common practice for dendrimers to deliver imaging and therapeutic agents, there are few reported examples of cellular internalization of dendrimers. Moreover, targeting of dendrimers to the mitochondria in cells has not yet been reported. Previously, we have delivered small molecule imaging agents into glioma and breast cancer cells by targeting the translocator protein (TSPO; formerly known as the peripheral benzodiazepine receptor or PBR) with a family of high-affinity conjugable ligands. The 18 kDa multimeric TSPO is expressed in steroid-producing cells, primarily on the outer mitochondrial membrane. This protein is a prime candidate for molecular targeting because tumors and other disease-related cells contain high densities of TSPO. Here, we present the synthesis, characterization, and cellular internalization into C6 rat glioma cells of a TSPO targeted dendrimer imaging agent.
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Affiliation(s)
- Lynn E. Samuelson
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822
| | - Madeline J. Dukes
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822
| | - Colette R. Hunt
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822
| | - Jonathan D. Casey
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822
| | - Darryl J. Bornhop
- Department of Chemistry, The Vanderbilt Institute for Chemical Biology and Vanderbilt-Ingram Cancer Center, Vanderbilt University, VU Station B 351822 Nashville, Tennessee 37235-1822
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Kussrow A, Kaltgrad E, Wolfenden ML, Cloninger MJ, Finn M, Bornhop DJ. Measurement of monovalent and polyvalent carbohydrate-lectin binding by back-scattering interferometry. Anal Chem 2009; 81:4889-97. [PMID: 19462965 PMCID: PMC2713007 DOI: 10.1021/ac900569c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Carbohydrate-protein binding is important to many areas of biochemistry. Here, backscattering interferometry (BSI) has been shown to be a convenient and sensitive method for obtaining quantitative information about the strengths and selectivities of such interactions. The surfaces of glass microfluidic channels were covalently modified with extravidin, to which biotinylated lectins were subsequently attached by incubation and washing. The binding of unmodified carbohydrates to the resulting avidin-immobilized lectins was monitored by BSI. Dose-response curves that were generated within several minutes and were highly reproducible in multiple wash/measure cycles provided adsorption coefficients that showed mannose to bind to concanavalin A (conA) with 3.7 times greater affinity than glucose consistent with literature values. Galactose was observed to bind selectively and with similar affinity to the lectin BS-1. The avidities of polyvalent sugar-coated virus particles for immobilized conA were much higher than monovalent glycans, with increases of 60-200 fold per glycan when arrayed on the exterior surface of cowpea mosaic virus or bacteriophage Qbeta. Sugar-functionalized PAMAM dendrimers showed size-dependent adsorption, which was consistent with the expected density of lectins on the surface. The sensitivity of BSI matches or exceeds that of surface plasmon resonance and quartz crystal microbalance techniques, and is sensitive to the number of binding events, rather than changes in mass. The operational simplicity and generality of BSI, along with the near-native conditions under which the target binding proteins are immobilized, make BSI an attractive method for the quantitative characterization of the binding functions of lectins and other proteins.
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Affiliation(s)
- Amanda Kussrow
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, TN 37235 USA
| | - Eiton Kaltgrad
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - Mark L. Wolfenden
- Department of Chemistry and Biochemistry and Center for Bioinspired Nanomaterials, Montana State University, 103 Chemistry and Biochemistry Building, Bozeman, MT 59717 USA
| | - Mary J. Cloninger
- Department of Chemistry and Biochemistry and Center for Bioinspired Nanomaterials, Montana State University, 103 Chemistry and Biochemistry Building, Bozeman, MT 59717 USA
| | - M.G. Finn
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla, CA 92037 USA
| | - Darryl J. Bornhop
- Department of Chemistry and Vanderbilt Institute of Chemical Biology, Vanderbilt University, 4226 Stevenson Center, Nashville, TN 37235 USA
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Latham JC, Stein R, Bornhop DJ, Mchaourab HS. Free-solution label-free detection of alpha-crystallin chaperone interactions by back-scattering interferometry. Anal Chem 2009; 81:1865-71. [PMID: 19178288 PMCID: PMC2787765 DOI: 10.1021/ac802327h] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [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: 11/29/2022]
Abstract
We report the quantitative, label-free analysis of protein-protein interactions in free solution within picoliter volumes using backscatter interferometry (BSI). Changes in the refractive index are measured for solutions introduced on a PDMS microchip allowing determination of forward and reverse rate constants for two-mode binding. Time-dependent BSI traces are directly fit using a global analysis approach to characterize the interaction of the small heat-shock protein alpha-Crystallin with two substrates: destabilized mutants of T4 lysozyme and the in vivo target betaB1-Crystallin. The results recapitulate the selectivity of alphaB-Crystallin differentially binding T4L mutants according to their free energies of unfolding. Furthermore, we demonstrate that an alphaA-Crystallin mutant linked to hereditary cataract has activated binding to betaB1-Crystallin. Binding isotherms obtained from steady-state values of the BSI signal yielded meaningful dissociation constants and establishes BSI as a novel tool for the rapid identification of molecular partners using exceedingly small sample quantities under physiological conditions. This work demonstrates that BSI can be extended to screen libraries of disease-related mutants to quantify changes in affinity and/or kinetics of binding.
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Affiliation(s)
- Joey C. Latham
- Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, VU Station B 351822 Nashville, TN 37235-1822, , fax (615) 343-1234
| | - Richard Stein
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 2215 Garland Ave., 741 Light Hall, Nashville, TN 37232, , fax (615) 343-1234
| | - Darryl J. Bornhop
- Department of Chemistry and The Vanderbilt Institute for Chemical Biology, Vanderbilt University, VU Station B 351822 Nashville, TN 37235-1822, , fax (615) 343-1234
| | - Hassane S. Mchaourab
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, 2215 Garland Ave., 741 Light Hall, Nashville, TN 37232, , fax (615) 343-1234
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Manning HC, Merchant NB, Foutch AC, Virostko JM, Wyatt SK, Shah C, McKinley ET, Xie J, Mutic NJ, Washington MK, LaFleur B, Tantawy MN, Peterson TE, Ansari MS, Baldwin RM, Rothenberg ML, Bornhop DJ, Gore JC, Coffey RJ. Molecular imaging of therapeutic response to epidermal growth factor receptor blockade in colorectal cancer. Clin Cancer Res 2009; 14:7413-22. [PMID: 19010858 DOI: 10.1158/1078-0432.ccr-08-0239] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
PURPOSE To evaluate noninvasive molecular imaging methods as correlative biomarkers of therapeutic efficacy of cetuximab in human colorectal cancer cell line xenografts grown in athymic nude mice. The correlation between molecular imaging and immunohistochemical analysis to quantify epidermal growth factor (EGF) binding, apoptosis, and proliferation was evaluated in treated and untreated tumor-bearing cohorts. EXPERIMENTAL DESIGN Optical imaging probes targeting EGF receptor (EGFR) expression (NIR800-EGF) and apoptosis (NIR700-Annexin V) were synthesized and evaluated in vitro and in vivo. Proliferation was assessed by 3'-[18F]fluoro-3'-deoxythymidine ([18F]FLT) positron emission tomography. Assessment of inhibition of EGFR signaling by cetuximab was accomplished by concomitant imaging of NIR800-EGF, NIR700-Annexin V, and [18F]FLT in cetuximab-sensitive (DiFi) and insensitive (HCT-116) human colorectal cancer cell line xenografts. Imaging results were validated by measurement of tumor size and immunohistochemical analysis of total and phosphorylated EGFR, caspase-3, and Ki-67 immediately following in vivo imaging. RESULTS NIR800-EGF accumulation in tumors reflected relative EGFR expression and EGFR occupancy by cetuximab. NIR700-Annexin V accumulation correlated with cetuximab-induced apoptosis as assessed by immunohistochemical staining of caspase-3. No significant difference in tumor proliferation was noted between treated and untreated animals by [18F]FLT positron emission tomography or Ki-67 immunohistochemistry. CONCLUSIONS Molecular imaging can accurately assess EGF binding, proliferation, and apoptosis in human colorectal cancer xenografts. These imaging approaches may prove useful for serial, noninvasive monitoring of the biological effects of EGFR inhibition in preclinical studies. It is anticipated that these assays can be adapted for clinical use.
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Affiliation(s)
- H Charles Manning
- Vanderbilt Institute of Imaging Science, Department of Radiology and Radiological Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
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Abstract
Cannabinoid CB 2 receptor is a particularly attractive target for noninvasive imaging of neuroinflammation and monitoring of therapeutic efficacy. Its expression is low to undetectable in healthy brain and induced in resident microglial cells (the macrophage of the brain) after cerebral ischemia, injury, and in neuroinflammatory disease. Additionally, immune cells migrating across the blood-brain barrier typically express CB 2 receptors, which adds to the expression pool of this target and provides a reliable indicator of inflammation in the brain. Here, we synthesized a novel conjugable CB 2 receptor ligand, mbc94, which has a terminal amino group that allows for facile conjugation to imaging moieties. A near-infrared (NIR) dye labeled mbc94, NIRmbc94, was developed for CB 2 targeted imaging. Preliminary evidence, including in vitro fluorescence imaging and a competition study, showed that NIRmbc94 specifically labeled CB 2-expressing cells.
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Affiliation(s)
- Mingfeng Bai
- Department of Chemistry, Vanderbilt University, VU Station B 351822, Nashville, Tennessee 37235-1822, USA
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Manning HC, Merchant NB, Foutch AC, Viostko J, Wyatt SK, Washington MK, Lafleur B, Baldwin R, Bornhop DJ, Gore JC, Coffey RJ. QS107. Non-Invasive Molecular Imaging Biomarkers of Therapeutic Response in Colorectal Cancer. J Surg Res 2008. [DOI: 10.1016/j.jss.2007.12.347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Abstract
The translocator protein (TSPO) is an attractive target for tumor imaging due to its up-regulation in numerous cancer cell types. Here, we report a series of functional TSPO ligands, n-TSPOmbb732, which can be conjugated to a variety of signaling moieties and are widely applicable in TSPO-targeted molecular imaging. Two fluorescent dye-labeled 6-TSPOmbb732 displayed nanomolar binding affinities to TSPO and were successfully imaged in vitro.
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Affiliation(s)
- Mingfeng Bai
- Department of Chemistry, Vanderbilt University, VU Station B 351822, Nashville, TN 37235-1822, USA
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Bornhop DJ, Latham JC, Kussrow A, Markov DA, Jones RD, Sørensen HS. Free-Solution, Label-Free Molecular Interactions Studied by Back-Scattering Interferometry. Science 2007; 317:1732-6. [PMID: 17885132 DOI: 10.1126/science.1146559] [Citation(s) in RCA: 173] [Impact Index Per Article: 10.2] [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: 11/02/2022]
Abstract
Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules and protein, were determined with high dynamic range dissociation constants (Kd spanning six decades) and unmatched sensitivity (picomolar Kd's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G, interleukin-2 with its monoclonal antibody, and calmodulin with calcium ion Ca2+, a small molecule inhibitor, the protein calcineurin, and the M13 peptide. The high sensitivity of back-scattering interferometry and small volumes of microfluidics allowed the entire calmodulin assay to be performed with 200 picomoles of solute.
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Affiliation(s)
- Darryl J Bornhop
- Department of Chemistry, Vanderbilt Institute of Chemical Biology, Vanderbilt University, VU Station B 351822, Nashville, TN 37235-1822, USA.
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Deane NG, Manning HC, Foutch AC, Washington MK, Aronow BJ, Aronow BA, Bornhop DJ, Coffey RJ. Targeted imaging of colonic tumors in smad3-/- mice discriminates cancer and inflammation. Mol Cancer Res 2007; 5:341-9. [PMID: 17426249 DOI: 10.1158/1541-7786.mcr-06-0225] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [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: 11/16/2022]
Abstract
The peripheral benzodiazepine receptor (PBR) is a trans-mitochondrial membrane protein that modulates steroid biosynthesis. Recently, up-regulation and nuclear localization of PBR has been shown to be associated with colon, prostate, and breast cancer. PBR has been targeted by the exogenous synthetic ligand, PK11195, for various purposes including imaging. To capitalize on these observations, we developed a high-throughput, noninvasive, in vivo imaging approach to detect spontaneously arising colonic tumors in mice using a novel PBR-targeted molecular imaging agent (NIR-conPK11195). NIR-conPK11195 localized and was retained in colonic adenomas and carcinomas in Smad3(-/-) mice but not in non-neoplastic hamartomas or chronically inflamed colonic tissue. Using a fluorescence signal-to-noise ratio of > or =4-fold 13 h after injection of the agent, we detected colonic tumors with a sensitivity of 67% and a specificity of 86% in a cohort of 37 Smad3(-/-) mice and control littermates. Furthermore, using oral administration of dextran sulfate to induce colonic inflammation, we showed that the clearance profile of NIR-conPK11195 distinguished transient uptake in inflammatory tissue from longer term retention in tumors. Taken together, these results indicate that NIR-conPK11195 is a promising optical molecular imaging tool to rapidly screen for colonic tumors in mice and to discriminate inflammation from cancer.
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Affiliation(s)
- Natasha G Deane
- Department of Surgery and Division of Surgical Oncology, Vanderbilt University, Nashville, TN 37235, USA
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