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Dehghan Banadaki M, Torabi S, Strike WD, Noble A, Keck JW, Berry SM. Improving wastewater-based epidemiology performance through streamlined automation. JOURNAL OF ENVIRONMENTAL CHEMICAL ENGINEERING 2023; 11:109595. [PMID: 36875746 PMCID: PMC9970922 DOI: 10.1016/j.jece.2023.109595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/02/2023] [Accepted: 02/26/2023] [Indexed: 06/18/2023]
Abstract
Wastewater-based epidemiology (WBE) has enabled us to describe Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections in populations. However, implementation of wastewater monitoring of SARS-CoV-2 is limited due to the need for expert staff, expensive equipment, and prolonged processing times. As WBE increases in scope (beyond SARS-CoV-2) and scale (beyond developed regions), there is a need to make WBE processes simpler, cheaper, and faster. We developed an automated workflow based on a simplified method termed exclusion-based sample preparation (ESP). Our automated workflow takes 40 min from raw wastewater to purified RNA, which is several times faster than conventional WBE methods. The total assay cost per sample/replicate is $6.50 which includes consumables and reagents for concentration, extraction, and RT-qPCR quantification. The assay complexity is reduced significantly, as extraction and concentration steps are integrated and automated. The high recovery efficiency of the automated assay (84.5 ± 25.4%) yielded an improved Limit of Detection (LoDAutomated=40 copies/mL) compared to the manual process (LoDManual=206 copies/mL), increasing analytical sensitivity. We validated the performance of the automated workflow by comparing it with the manual method using wastewater samples from several locations. The results from the two methods correlated strongly (r = 0.953), while the automated method was shown to be more precise. In 83% of the samples, the automated method showed lower variation between replicates, which is likely due to higher technical errors in the manual process e.g., pipetting. Our automated wastewater workflow can support the expansion of WBE in the fight against Coronavirus Disease of 2019 (COVID-19) and other epidemics.
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Affiliation(s)
| | - Soroosh Torabi
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - William D Strike
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
| | - Ann Noble
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
| | - James W Keck
- Department of Family and Community Medicine, College of Medicine, University of Kentucky, United States
| | - Scott M Berry
- Department of Mechanical Engineering, College of Engineering, University of Kentucky, United States
- Department of Biomedical Engineering, College of Engineering, University of Kentucky, United States
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2
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Strike W, Amirsoleimani A, Olaleye A, Noble A, Lewis K, Faulkner L, Backus S, Lindeman S, Eterovich K, Fraley M, Banadaki MD, Torabi S, Rockward A, Zeitlow E, Liversedge M, Keck J, Berry S. Development and Validation of a Simplified Method for Analysis of SARS-CoV-2 RNA in University Dormitories. ACS ES&T WATER 2022; 2:1984-1991. [PMID: 37552725 PMCID: PMC9115885 DOI: 10.1021/acsestwater.2c00044] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/26/2022] [Accepted: 05/02/2022] [Indexed: 05/26/2023]
Abstract
Over the course of the COVID-19 pandemic, wastewater surveillance has become a useful tool for describing SARS-CoV-2 prevalence in populations of varying size, from individual facilities (e.g., university residence halls, nursing homes, prisons) to entire municipalities. Wastewater analysis for SARS-CoV-2 RNA requires specialized equipment, expensive consumables, and expert staff, limiting its feasibility and scalability. Further, the extremely labile nature of viral RNA complicates sample transportation, especially in regions with limited access to reliable cold chains. Here, we present a new method for wastewater analysis, termed exclusion-based sample preparation (ESP), that substantially simplifies workflow (at least 70% decrease in time; 40% decrease in consumable usage compared with traditional techniques) by targeting the labor-intensive processing steps of RNA purification and concentration. To optimize and validate this method, we analyzed wastewater samples from residence halls at the University of Kentucky, of which 34% (44/129) contained detectible SARS-CoV-2 RNA. Although concurrent clinical testing was not comprehensive, student infections were identified in the 7 days following a positive wastewater detection in 68% of samples. This pilot study among university residence halls validated the performance and utility of the ESP method, laying the foundation for future studies in regions of the world where wastewater testing is not currently feasible.
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Affiliation(s)
- William Strike
- Departments of Biomedical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Atena Amirsoleimani
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Abisola Olaleye
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Ann Noble
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Kevin Lewis
- Environmental Quality Management, University of Kentucky, 355 Cooper Drive, Lexington, KY 40508
| | - Lee Faulkner
- Environmental Quality Management, University of Kentucky, 355 Cooper Drive, Lexington, KY 40508
| | - Spencer Backus
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Sierra Lindeman
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Katrina Eterovich
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Melicity Fraley
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Mohammad Dehghan Banadaki
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Soroosh Torabi
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Alexus Rockward
- Departments of Biomedical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
| | - Eli Zeitlow
- Department of Mechanical Engineering, University of Wisconsin-Platteville, 1 University Plaza, Platteville, WI 53818
| | - Matthew Liversedge
- Family and Community Medicine, University of Kentucky 2195 Harrodsburg Rd, Ste 125, Lexington, KY 40504
| | - James Keck
- Family and Community Medicine, University of Kentucky 2195 Harrodsburg Rd, Ste 125, Lexington, KY 40504
| | - Scott Berry
- Departments of Biomedical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
- Mechanical Engineering, University of Kentucky, 151 Ralph G. Anderson Building Lexington, KY 40506-0503
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Rodriguez-Mateos P, Ngamsom B, Iles A, Pamme N. Microscale immiscible phase magnetic processing for bioanalytical applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
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Fakhraldeen SA, Berry SM, Beebe DJ, Roopra A, Bisbach CM, Spiegelman VS, Niemi NM, Alexander CM. Enhanced immunoprecipitation techniques for the identification of RNA-binding protein partners: IGF2BP1 interactions in mammary epithelial cells. J Biol Chem 2022; 298:101649. [PMID: 35104504 PMCID: PMC8891971 DOI: 10.1016/j.jbc.2022.101649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/21/2022] [Accepted: 01/22/2022] [Indexed: 11/24/2022] Open
Abstract
RNA-binding proteins (RBPs) regulate the expression of large cohorts of RNA species to produce programmatic changes in cellular phenotypes. To describe the function of RBPs within a cell, it is key to identify their mRNA-binding partners. This is often done by crosslinking nucleic acids to RBPs, followed by chemical release of the nucleic acid fragments for analysis. However, this methodology is lengthy, which involves complex processing with attendant sample losses, thus large amounts of starting materials and prone to artifacts. To evaluate potential alternative technologies, we tested “exclusion-based” purification of immunoprecipitates (IFAST or SLIDE) and report here that these methods can efficiently, rapidly, and specifically isolate RBP–RNA complexes. The analysis requires less than 1% of the starting material required for techniques that include crosslinking. Depending on the antibody used, 50% to 100% starting protein can be retrieved, facilitating the assay of endogenous levels of RBPs; the isolated ribonucleoproteins are subsequently analyzed using standard techniques, to provide a comprehensive portrait of RBP complexes. Using exclusion-based techniques, we show that the mRNA-binding partners for RBP IGF2BP1 in cultured mammary epithelial cells are enriched in mRNAs important for detoxifying superoxides (specifically glutathione peroxidase [GPX]-1 and GPX-2) and mRNAs encoding mitochondrial proteins. We show that these interactions are functionally significant, as loss of function of IGF2BP1 leads to destabilization of GPX mRNAs and reduces mitochondrial membrane potential and oxygen consumption. We speculate that this underlies a consistent requirement for IGF2BP1 for the expression of clonogenic activity in vitro.
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Affiliation(s)
- Saja A Fakhraldeen
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Scott M Berry
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Avtar Roopra
- Department of Neuroscience, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Celia M Bisbach
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Vladimir S Spiegelman
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, Pennsylvania State University College of Medicine, Hershey, Pennsylvania, USA
| | - Natalie M Niemi
- Department of Biochemistry & Molecular Biophysics, Washington University in St Louis
| | - Caroline M Alexander
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, Wisconsin, USA.
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Zeng S, Han M, Jiang M, Liu F, Hu Y, Long Y, Zhu C, Zeng F, Gan Q, Ye W, Fu W, Yang H. Serum complement proteomics reveal biomarkers for hypertension disorder of pregnancy and the potential role of Clusterin. Reprod Biol Endocrinol 2021; 19:56. [PMID: 33874952 PMCID: PMC8054419 DOI: 10.1186/s12958-021-00742-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/07/2021] [Indexed: 01/06/2023] Open
Abstract
INTRODUCTION Hypertension disorder of pregnancy (HDP) is one of the leading causes of maternal and foetal illness. The aim of the current study was to identify and verify novel serum markers for HDP. METHODS A label-free LC-MS/MS method was used to establish the serum proteomic profiles of 12 pre-HDP (before clinical diagnosis of HDP) pregnancies and verify prioritized candidates in the verification set of 48 pre-HDP pregnancies. These biomarkers were revalidated by ELISA in an independent cohort of 88 pre-HDP pregnancies. Subsequently, the candidate biomarkers were histologically analysed by immunohistochemistry, and function was evaluated in TEV-1 cells. RESULTS We identified 33 proteins with significantly increased abundance and 14 with decreased abundance (peptide FDR ≤ 1%, P < 0.05). Complement was one of the top enriched components in the pre-HDP group compared with the control group. Three complement factors (CLU, CFHR5, and CRP) were significantly increased in the three sets, of which CLU was a critical factor for the development of HDP (OR = 1.22, P < 0.001). When these three factors and body weight were combined, the AUC was 0.74, with a sensitivity of 0.67 and specificity of 0.68 for HDP prediction compared with normal pregnancy. In addition, inflammation-induced CLU could inhibit the invasion of TEV-1 cells. CONCLUSIONS Complement proteins may play an essential role in the occurrence of HDP by acting on trophoblast cells. CLU may be a high-risk factor for HDP, and the models combining candidates show reasonable screening efficiency of HDP in the first half of pregnancy.
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Affiliation(s)
- Shanshui Zeng
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Mengru Han
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Min Jiang
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Fei Liu
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Yanwei Hu
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Yan Long
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China
| | - Chunyan Zhu
- School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Fangling Zeng
- Department of Gynaecology and Obstetrics, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, Guangzhou, 510623, China
| | - Qiangsheng Gan
- School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Weitao Ye
- School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Wenjin Fu
- Clinical Laboratory, Houjie Hospital of Guangdong Medical University, HeTian Road, Dongguan, 523945, Guangdong, China.
| | - Hongling Yang
- Department of Laboratory, Guangzhou Women and Children's Medical Centre, Guangzhou Medical University, No.9, Jinsui Road, Guangzhou, 510623, Guangdong, China.
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Jiang L, Hu LG. Serpin peptidase inhibitor clade A member 1-overexpression in gastric cancer promotes tumor progression in vitro and is associated with poor prognosis. Oncol Lett 2020; 20:278. [PMID: 33014156 PMCID: PMC7520747 DOI: 10.3892/ol.2020.12141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/01/2020] [Indexed: 12/14/2022] Open
Abstract
Gastric cancer is the second most common cause of cancer-associated death in Asia. The incidence and mortality rates of gastric cancer have markedly increased in the past few decades. Therefore, the identification of novel gastric cancer biomarkers are needed to determine prognosis. The role of serpin peptidase inhibitor clade A member 1 (SERPINA1) has been studied in several types of cancer; however, little is known about its mechanism in gastric cancer. The present study aimed to evaluate SERPINA1 as a potential prognostic biomarker in gastric cancer and to identify the possible mechanisms underlying its action. The expression levels of SERPINA1 in several gastric cancer datasets were assessed, and it was identified that high expression of SERPINA1 was associated to poor clinical outcomes. Furthermore, using histochemical analysis, western blotting, apoptotic analysis, gap closure and invasion assays in cell lines, it was reported that silencing of SERPINA1 inhibited the formation of cellular pseudopodia and did not affect apoptosis, but promoted cell cycle S-phase entry. In addition, overexpression of SERPINA1 increased the migration and invasion of gastric cancer cells, whereas knockdown of SERPINA1 decreased these functions. Moreover, SERPINA1 overexpression increased the protein levels of SMAD4, which is a key regulator of the transforming growth factor (TGF)-β signaling pathway. Taken together, the present data demonstrated that SERPINA1 promotes gastric cancer progression through TGF-β signaling, and suggested that SERPINA1 may be a novel prognostic biomarker from tumor tissue biopsy in gastric cancer.
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Affiliation(s)
- Longchang Jiang
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
| | - Liangbiao George Hu
- Translational Safety and Bioanalytical Sciences, Amgen Research, Amgen Asia Research and Development Center, Shanghai 201210, P.R. China
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Svirid AV, Ershov PV, Yablokov EO, Kaluzhskiy LA, Mezentsev YV, Florinskaya AV, Sushko TA, Strushkevich NV, Gilep AA, Usanov SA, Medvedev AE, Ivanov AS. Direct Molecular Fishing of New Protein Partners for Human Thromboxane Synthase. Acta Naturae 2017; 9:92-100. [PMID: 29340222 PMCID: PMC5762833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Indexed: 11/17/2022] Open
Abstract
Thromboxane synthase (TBXAS1) catalyzes the isomerization reaction of prostaglandin H2 producing thromboxane A2, the autocrine and paracrine factor in many cell types. A high activity and metastability by these arachidonic acid derivatives suggests the existence of supramolecular structures that are involved in the regulation of the biosynthesis and directed translocation of thromboxane to the receptor. The objective of this study was to identify TBXAS1 protein partners from human liver tissue lysate using a complex approach based on the direct molecular fishing technique, LC-MS/MS protein identification, and protein-protein interaction validation by surface plasmon resonance (SPR). As a result, 12 potential TBXAS1 protein partners were identified, including the components regulating cytoskeleton organization (BBIP1 and ANKMY1), components of the coagulation cascade of human blood (SERPINA1, SERPINA3, APOH, FGA, and FN1), and the enzyme involved in the metabolism of xenobiotics and endogenous bioregulators (CYP2E1). SPR validation on the Biacore 3000 biosensor confirmed the effectiveness of the interaction between CYP2E1 (the enzyme that converts prostaglandin H2 to 12-HHT/thromboxane A2 proantagonist) and TBXAS1 (Kd = (4.3 ± 0.4) × 10-7 M). Importantly, the TBXAS1•CYP2E1 complex formation increases fivefold in the presence of isatin (indole-2,3-dione, a low-molecular nonpeptide endogenous bioregulator, a product of CYP2E1). These results suggest that the interaction between these hemoproteins is important in the regulation of the biosynthesis of eicosanoids.
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Affiliation(s)
- A. V. Svirid
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - P. V. Ershov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - E. O. Yablokov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - L. A. Kaluzhskiy
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - Yu. V. Mezentsev
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - A. V. Florinskaya
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - T. A. Sushko
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
- Department of Bioengineering, School of Engineering, The University of Tokyo, Tokyo, 108-8639, Japan
| | - N. V. Strushkevich
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - A. A. Gilep
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - S. A. Usanov
- Institute of Bioorganic Chemistry, National Academy of Sciences of Belarus, Akad. Kuprevicha Str. 5 /2, Minsk, 220141, Belarus
| | - A. E. Medvedev
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
| | - A. S. Ivanov
- Institute of Biomedical Chemistry, Pogodinskaya Street 10, bldg. 8, Moscow, 119121, Russia
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van der Toom EE, Verdone JE, Jun C, Petrisor D, Lim S, de la Rosette JJMCH, de Reijke TM, Gorin MA, Pienta KJ, Stoianovici D. A surface tension magnetophoretic device for rare cell isolation and characterization. Med Oncol 2017; 34:22. [PMID: 28058627 DOI: 10.1007/s12032-016-0877-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 12/27/2016] [Indexed: 12/18/2022]
Abstract
The cancer community continues to search for an efficient and cost-effective technique to isolate and characterize circulating cells (CTCs) as a 'real-time liquid biopsy'. Existing methods to isolate and analyze CTCs require various transfer, wash, and staining steps that can be time consuming, expensive, and led to the loss of rare cells. To overcome the limitations of existing CTC isolation strategies, we have developed an inexpensive 'lab on a chip' device for the enrichment, staining, and analysis of rare cell populations. This device utilizes immunomagnetic positive selection of antibody-bound cells, isolation of cells through an immiscible interface, and filtration. The isolated cells can then be stained utilizing immunofluorescence or used for other downstream detection methods. We describe the construction and initial preclinical testing of the device. Initial tests suggest that the device may be well suited for the isolation of CTCs and could allow the monitoring of cancer progression and the response to therapy over time.
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Affiliation(s)
- Emma E van der Toom
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA.,Department of Urology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - James E Verdone
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Changhan Jun
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Doru Petrisor
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Sunghwan Lim
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | | | - Theo M de Reijke
- Department of Urology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Michael A Gorin
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Kenneth J Pienta
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA
| | - Dan Stoianovici
- Department of Urology, The James Buchanan Brady Urological Institute, School of Medicine, Johns Hopkins University, Baltimore, MD, 21287, USA.
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Guckenberger DJ, Pezzi HM, Regier MC, Berry SM, Fawcett K, Barrett K, Beebe DJ. Magnetic System for Automated Manipulation of Paramagnetic Particles. Anal Chem 2016; 88:9902-9907. [PMID: 27598856 DOI: 10.1021/acs.analchem.6b02257] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The simple, rapid magnetic manipulation of paramagnetic particles (PMPs) paired with the wide range of available surface chemistries has strongly positioned PMPs in the field of analyte isolation. One recent technology, sliding lid for immobilized droplet extractions (SLIDE), presents a simple, rapid alternative to traditional PMP isolation protocols. Rather than remove fluid from PMP-bound analyte, SLIDE directly removes the PMPs from the fluid. SLIDE collects the PMPs on a hydrophobic, removable surface, which allows PMPs to be captured from one well and then transferred and released into a second well. Despite several key advantages, SLIDE remains limited by its passive magnetic manipulation that only allows for a one-time capture-and-release of PMPs, preventing wash steps and limiting purity. Furthermore, the strategy employed by SLIDE constrains the position of the wells, thereby limiting throughput and integration into automated systems. Here, we introduce a new, mechanically and operationally simplistic magnetic manipulation system for integration with the SLIDE technology to overcome the previously stated limitations. This magnetic system is compatible with nearly any plate design, can be integrated into automated workflows, enables high-throughput formats, simplifies mechanical requirements, and is amenable to a range of analytes. Using this magnetic system, PMPs can be collected, released, and resuspended throughout multiple wells regardless of proximity. We demonstrate this system's capabilities to isolate whole cells, mRNA, and DNA, demonstrating up to a 28-fold improvement of purity via the multiwash protocols enabled by this magnetic technology.
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Affiliation(s)
- David J Guckenberger
- Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison , 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Salus Discovery, LLC , 110 East Main Street, Madison, Wisconsin 53703, United States
| | - Hannah M Pezzi
- Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison , 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Salus Discovery, LLC , 110 East Main Street, Madison, Wisconsin 53703, United States
| | - Mary C Regier
- Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison , 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Gilson, Inc. , 3000 Parmenter Street, Middleton, Wisconsin 53562, United States
| | - Scott M Berry
- Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison , 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Salus Discovery, LLC , 110 East Main Street, Madison, Wisconsin 53703, United States
| | - Kevin Fawcett
- Gilson, Inc. , 3000 Parmenter Street, Middleton, Wisconsin 53562, United States
| | - Kevin Barrett
- Gilson, Inc. , 3000 Parmenter Street, Middleton, Wisconsin 53562, United States
| | - David J Beebe
- Department of Biomedical Engineering, Wisconsin Institutes for Medical Research, University of Wisconsin-Madison , 1111 Highland Avenue, Madison, Wisconsin 53705, United States.,Salus Discovery, LLC , 110 East Main Street, Madison, Wisconsin 53703, United States
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10
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Berry SM, Pezzi HM, LaVanway AJ, Guckenberger D, Anderson M, Beebe DJ. AirJump: Using Interfaces to Instantly Perform Simultaneous Extractions. ACS APPLIED MATERIALS & INTERFACES 2016; 8:15040-5. [PMID: 27249333 PMCID: PMC5058634 DOI: 10.1021/acsami.6b02555] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Analyte isolation is an important process that spans a range of biomedical disciplines, including diagnostics, research, and forensics. While downstream analytical techniques have advanced in terms of both capability and throughput, analyte isolation technology has lagged behind, increasingly becoming the bottleneck in these processes. Thus, there exists a need for simple, fast, and easy to integrate analyte separation protocols to alleviate this bottleneck. Recently, a new class of technologies has emerged that leverages the movement of paramagnetic particle (PMP)-bound analytes through phase barriers to achieve a high efficiency separation in a single or a few steps. Specifically, the passage of a PMP/analyte aggregate through a phase interface (aqueous/air in this case) acts to efficiently "exclude" unbound (contaminant) material from PMP-bound analytes with higher efficiency than traditional washing-based solid-phase extraction (SPE) protocols (i.e., bind, wash several times, elute). Here, we describe for the first time a new type of "exclusion-based" sample preparation, which we term "AirJump". Upon realizing that much of the contaminant carryover stems from interactions with the sample vessel surface (e.g., pipetting residue, wetting), we aim to eliminate the influence of that factor. Thus, AirJump isolates PMP-bound analyte by "jumping" analyte directly out of a free liquid/air interface. Through careful characterization, we have demonstrated the validity of AirJump isolation through comparison to traditional washing-based isolations. Additionally, we have confirmed the suitability of AirJump in three important independent biological isolations, including protein immunoprecipitation, viral RNA isolation, and cell culture gene expression analysis. Taken together, these data sets demonstrate that AirJump performs efficiently, with high analyte yield, high purity, no cross contamination, rapid time-to-isolation, and excellent reproducibility.
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11
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E3 ubiquitin ligase RFWD2 controls lung branching through protein-level regulation of ETV transcription factors. Proc Natl Acad Sci U S A 2016; 113:7557-62. [PMID: 27335464 DOI: 10.1073/pnas.1603310113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The mammalian lung is an elaborate branching organ, and it forms following a highly stereotypical morphogenesis program. It is well established that precise control at the transcript level is a key genetic underpinning of lung branching. In comparison, little is known about how regulation at the protein level may play a role. Ring finger and WD domain 2 (RFWD2, also termed COP1) is an E3 ubiquitin ligase that modifies specific target proteins, priming their degradation via the ubiquitin proteasome system. RFWD2 is known to function in the adult in pathogenic processes such as tumorigenesis. Here, we show that prenatal inactivation of Rfwd2 gene in the lung epithelium led to a striking halt in branching morphogenesis shortly after secondary branch formation. This defect is accompanied by distalization of the lung epithelium while growth and cellular differentiation still occurred. In the mutant lung, two E26 transformation-specific (ETS) transcription factors essential for normal lung branching, ETS translocation variant 4 (ETV4) and ETV5, were up-regulated at the protein level, but not at the transcript level. Introduction of Etv loss-of-function alleles into the Rfwd2 mutant background attenuated the branching phenotype, suggesting that RFWD2 functions, at least in part, through degrading ETV proteins. Because a number of E3 ligases are known to target factors important for lung development, our findings provide a preview of protein-level regulatory network essential for lung branching morphogenesis.
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Abstract
Fibronectin is a large vertebrate glycoprotein that is found in soluble and insoluble forms and involved in diverse processes. Protomeric fibronectin is a dimer of subunits, each of which comprises 29-31 modules - 12 type I, two type II and 15-17 type III. Plasma fibronectin is secreted by hepatocytes and circulates in a compact conformation before it binds to cell surfaces, converts to an extended conformation and is assembled into fibronectin fibrils. Here we review biophysical and structural studies that have shed light on how plasma fibronectin transitions from the compact to the extended conformation. The three types of modules each have a well-organized secondary and tertiary structure as defined by NMR and crystallography and have been likened to "beads on a string". There are flexible sequences in the N-terminal tail, between the fifth and sixth type I modules, between the first two and last two of the type III modules, and at the C-terminus. Several specific module-module interactions have been identified that likely maintain the compact quaternary structure of circulating fibronectin. The quaternary structure is perturbed in response to binding events, including binding of fibronectin to the surface of vertebrate cells for fibril assembly and to bacterial adhesins.
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Affiliation(s)
- Lisa M Maurer
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , United States
| | - Wenjiang Ma
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , United States
| | - Deane F Mosher
- a Departments of Biomolecular Chemistry and Medicine , University of Wisconsin-Madison , Madison , WI , United States
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Korbolina EE, Ershov NI, Bryzgalov LO, Kolosova NG. Application of quantitative trait locus mapping and transcriptomics to studies of the senescence-accelerated phenotype in rats. BMC Genomics 2014; 15 Suppl 12:S3. [PMID: 25563673 PMCID: PMC4303943 DOI: 10.1186/1471-2164-15-s12-s3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Etiology of complex disorders, such as cataract and neurodegenerative diseases including age-related macular degeneration (AMD), remains poorly understood due to the paucity of animal models, fully replicating the human disease. Previously, two quantitative trait loci (QTLs) associated with early cataract, AMD-like retinopathy, and some behavioral aberrations in senescence-accelerated OXYS rats were uncovered on chromosome 1 in a cross between OXYS and WAG rats. To confirm the findings, we generated interval-specific congenic strains, WAG/OXYS-1.1 and WAG/OXYS-1.2, carrying OXYS-derived loci of chromosome 1 in the WAG strain. Both congenic strains displayed early cataract and retinopathy but differed clinically from OXYS rats. Here we applied a high-throughput RNA sequencing (RNA-Seq) strategy to facilitate nomination of the candidate genes and functional pathways that may be responsible for these differences and can contribute to the development of the senescence-accelerated phenotype of OXYS rats. Results First, the size and map position of QTL-derived congenic segments were determined by comparative analysis of coding single-nucleotide polymorphisms (SNPs), which were identified for OXYS, WAG, and congenic retinal RNAs after sequencing. The transferred locus was not what we expected in WAG/OXYS-1.1 rats. In rat retina, 15442 genes were expressed. Coherent sets of differentially expressed genes were identified when we compared RNA-Seq retinal profiles of 20-day-old WAG/OXYS-1.1, WAG/OXYS-1.2, and OXYS rats. The genes most different in the average expression level between the congenic strains included those generally associated with the Wnt, integrin, and TGF-β signaling pathways, widely involved in neurodegenerative processes. Several candidate genes (including Arhgap33, Cebpg, Gtf3c1, Snurf, Tnfaip3, Yme1l1, Cbs, Car9 and Fn1) were found to be either polymorphic in the congenic loci or differentially expressed between the strains. These genes may contribute to the development of cataract and retinopathy. Conclusions This study is the first RNA-Seq analysis of the rat retinal transcriptome generated with 40 mln sequencing read depth. The integration of QTL and transcriptomic analyses in our study forms the basis of future research into the relationship between the candidate genes within the congenic regions and specific changes in the retinal transcriptome as possible causal mechanisms that underlie age-associated disorders.
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Harris G, Ma W, Maurer LM, Potts JR, Mosher DF. Borrelia burgdorferi protein BBK32 binds to soluble fibronectin via the N-terminal 70-kDa region, causing fibronectin to undergo conformational extension. J Biol Chem 2014; 289:22490-9. [PMID: 24962582 DOI: 10.1074/jbc.m114.578419] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BBK32 is a fibronectin (FN)-binding protein expressed on the cell surface of Borrelia burgdorferi, the causative agent of Lyme disease. There is conflicting information about where and how BBK32 interacts with FN. We have characterized interactions of a recombinant 86-mer polypeptide, "Bbk32," comprising the unstructured FN-binding region of BBK32. Competitive enzyme-linked assays utilizing various FN fragments and epitope-mapped anti-FN monoclonal antibodies showed that Bbk32 binding involves both the fibrin-binding and the gelatin-binding domains of the 70-kDa N-terminal region (FN70K). Crystallographic and NMR analyses of smaller Bbk32 peptides complexed, respectively, with (2-3)FNI and (8-9)FNI, demonstrated that binding occurs by β-strand addition. Isothermal titration calorimetry indicated that Bbk32 binds to isolated FN70K more tightly than to intact FN. In a competitive enzyme-linked binding assay, complex formation with Bbk32 enhanced binding of FN with mAbIII-10 to the (10)FNIII module. Thus, Bbk32 binds to multiple FN type 1 modules of the FN70K region by a tandem β-zipper mechanism, and in doing so increases accessibility of FNIII modules that interact with other ligands. The similarity in the FN-binding mechanism of BBK32 and previously studied streptococcal proteins suggests that the binding and associated conformational change of FN play a role in infection.
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Affiliation(s)
- Gemma Harris
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - Wenjiang Ma
- the Departments of Biomolecular Chemistry and Medicine, University of Wisconsin, Madison, Wisconsin 53706
| | - Lisa M Maurer
- the Departments of Biomolecular Chemistry and Medicine, University of Wisconsin, Madison, Wisconsin 53706
| | - Jennifer R Potts
- From the Department of Biology, University of York, York YO10 5DD, United Kingdom and
| | - Deane F Mosher
- the Departments of Biomolecular Chemistry and Medicine, University of Wisconsin, Madison, Wisconsin 53706
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Berry SM, Chin EN, Jackson SS, Strotman LN, Goel M, Thompson NE, Alexander CM, Miyamoto S, Burgess RR, Beebe DJ. Weak protein-protein interactions revealed by immiscible filtration assisted by surface tension. Anal Biochem 2013; 447:133-40. [PMID: 24215910 DOI: 10.1016/j.ab.2013.10.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 10/24/2013] [Accepted: 10/30/2013] [Indexed: 11/25/2022]
Abstract
Biological mechanisms are often mediated by transient interactions between multiple proteins. The isolation of intact protein complexes is essential to understanding biochemical processes and an important prerequisite for identifying new drug targets and biomarkers. However, low-affinity interactions are often difficult to detect. Here, we use a newly described method called immiscible filtration assisted by surface tension (IFAST) to isolate proteins under defined binding conditions. This method, which gives a near-instantaneous isolation, enables significantly higher recovery of transient complexes compared to current wash-based protocols, which require reequilibration at each of several wash steps, resulting in protein loss. The method moves proteins, or protein complexes, captured on a solid phase through one or more immiscible-phase barriers that efficiently exclude the passage of nonspecific material in a single operation. We use a previously described polyol-responsive monoclonal antibody to investigate the potential of this new method to study protein binding. In addition, difficult-to-isolate complexes involving the biologically and clinically important Wnt signaling pathway were isolated. We anticipate that this simple, rapid method to isolate intact, transient complexes will enable the discoveries of new signaling pathways, biomarkers, and drug targets.
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Affiliation(s)
- Scott M Berry
- Department of Biomedical Engineering, University of Wisconsin at Madison, Madison, WI 53705, USA.
| | - Emily N Chin
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Shawn S Jackson
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Lindsay N Strotman
- Department of Biomedical Engineering, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Mohit Goel
- Department of Biotechnology, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Nancy E Thompson
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Caroline M Alexander
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Shigeki Miyamoto
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - Richard R Burgess
- Department of Oncology, University of Wisconsin at Madison, Madison, WI 53705, USA
| | - David J Beebe
- Department of Biomedical Engineering, University of Wisconsin at Madison, Madison, WI 53705, USA
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Howard AL, Pezzi HM, Beebe DJ, Berry SM. Exclusion-Based Capture and Enumeration of CD4+ T Cells from Whole Blood for Low-Resource Settings. ACTA ACUST UNITED AC 2013; 19:313-21. [PMID: 24142472 DOI: 10.1177/2211068213509248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2013] [Indexed: 11/17/2022]
Abstract
In developing countries, demand exists for a cost-effective method to evaluate human immunodeficiency virus patients' CD4(+) T-helper cell count. The TH (CD4) cell count is the current marker used to identify when an HIV patient has progressed to acquired immunodeficiency syndrome, which results when the immune system can no longer prevent certain opportunistic infections. A system to perform TH count that obviates the use of costly flow cytometry will enable physicians to more closely follow patients' disease progression and response to therapy in areas where such advanced equipment is unavailable. Our system of two serially-operated immiscible phase exclusion-based cell isolations coupled with a rapid fluorescent readout enables exclusion-based isolation and accurate counting of T-helper cells at lower cost and from a smaller volume of blood than previous methods. TH cell isolation via immiscible filtration assisted by surface tension (IFAST) compares well against the established Dynal T4 Quant Kit and is sensitive at CD4 counts representative of immunocompromised patients (less than 200 TH cells per microliter of blood). Our technique retains use of open, simple-to-operate devices that enable IFAST as a high-throughput, automatable sample preparation method, improving throughput over previous low-resource methods.
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