1
|
Vaidyanathan S, Wijerathne H, Gamage SST, Shiri F, Zhao Z, Choi J, Park S, Witek MA, McKinney C, Verber M, Hall AR, Childers K, McNickle T, Mog S, Yeh E, Godwin AK, Soper SA. High Sensitivity Extended Nano-Coulter Counter for Detection of Viral Particles and Extracellular Vesicles. Anal Chem 2023; 95:9892-9900. [PMID: 37336762 PMCID: PMC11015478 DOI: 10.1021/acs.analchem.3c00855] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 06/21/2023]
Abstract
We present a chip-based extended nano-Coulter counter (XnCC) that can detect nanoparticles affinity-selected from biological samples with low concentration limit-of-detection that surpasses existing resistive pulse sensors by 2-3 orders of magnitude. The XnCC was engineered to contain 5 in-plane pores each with an effective diameter of 350 nm placed in parallel and can provide high detection efficiency for single particles translocating both hydrodynamically and electrokinetically through these pores. The XnCC was fabricated in cyclic olefin polymer (COP) via nanoinjection molding to allow for high-scale production. The concentration limit-of-detection of the XnCC was 5.5 × 103 particles/mL, which was a 1,100-fold improvement compared to a single in-plane pore device. The application examples of the XnCC included counting affinity selected SARS-CoV-2 viral particles from saliva samples using an aptamer and pillared microchip; the selection/XnCC assay could distinguish the COVID-19(+) saliva samples from those that were COVID-19(-). In the second example, ovarian cancer extracellular vesicles (EVs) were affinity selected using a pillared chip modified with a MUC16 monoclonal antibody. The affinity selection chip coupled with the XnCC was successful in discriminating between patients with high grade serous ovarian cancer and healthy donors using blood plasma as the input sample.
Collapse
Affiliation(s)
- Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Harshani Wijerathne
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Sachindra S T Gamage
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Farhad Shiri
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Zheng Zhao
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Mechanical & Industrial Engineering Department, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Małgorzata A Witek
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Collin McKinney
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Matthew Verber
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27514, United States
| | - Adam R Hall
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- Virginia Tech-Wake Forest University School of Biomedical Engineering and Sciences and Comprehensive Cancer Center, Wake Forest School of Medicine, Winston Salem, North Carolina 27101, United States
| | - Katie Childers
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Taryn McNickle
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Shalee Mog
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Elaine Yeh
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Andrew K Godwin
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Comprehensive Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, Kansas 66045, United States
- Department of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, Kansas 66045, United States
- KU Comprehensive Cancer Center, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
- Department of Mechanical Engineering, The University of Kansas, Lawrence, Kansas 66045, United States
- Kansas Institute for Precision Medicine, University of Kansas Medical Center, Kansas City, Kansas 66160, United States
| |
Collapse
|
2
|
Zhao Z, Vaidyanathan S, Bhanja P, Gamage S, Saha S, McKinney C, Choi J, Park S, Pahattuge T, Wijerathne H, Jackson JM, Huppert ML, Witek MA, Soper SA. In-plane Extended Nano-coulter Counter (XnCC) for the Label-free Electrical Detection of Biological Particles. ELECTROANAL 2022; 34:1961-1975. [PMID: 37539083 PMCID: PMC10399599 DOI: 10.1002/elan.202200091] [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] [Received: 02/24/2022] [Accepted: 06/14/2022] [Indexed: 11/10/2022]
Abstract
We report an in-plane extended nanopore Coulter counter (XnCC) chip fabricated in a thermoplastic via imprinting. The fabrication of the sensor utilized both photolithography and focused ion beam milling to make the microfluidic network and the in-plane pore sensor, respectively, in Si from which UV resin stamps were generated followed by thermal imprinting to produce the final device in the appropriate plastic (cyclic olefin polymer, COP). As an example of the utility of this in-plane extended nanopore sensor, we enumerated SARS-CoV-2 viral particles (VPs) affinity-selected from saliva and extracellular vesicles (EVs) affinity-selected from plasma samples secured from mouse models exposed to different ionizing radiation doses.
Collapse
Affiliation(s)
- Zheng Zhao
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
| | - Swarnagowri Vaidyanathan
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
| | - Payel Bhanja
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160
| | - Sachindra Gamage
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Subhrajit Saha
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, KS 66160
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160
| | - Collin McKinney
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- CRITCL, The University of North Carolina, Chapel Hill, NC
| | - Junseo Choi
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- CRITCL, The University of North Carolina, Chapel Hill, NC
| | - Sunggook Park
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- CRITCL, The University of North Carolina, Chapel Hill, NC
| | - Thilanga Pahattuge
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Harshani Wijerathne
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Joshua M Jackson
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Mateusz L Huppert
- Department of Industrial and Mechanical Engineering, Louisiana State University, Baton Rouge, LA 70803
| | - Małgorzata A Witek
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
| | - Steven A Soper
- Bioengineering Program, The University of Kansas, Lawrence, KS 66045
- Center of BioModular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66045
- University of Kansas Cancer Center, University of Kansas Medical Center, Kansas City, KS 66160
- Department of Chemistry, The University of Kansas, Lawrence, KS 66045
- BioFluidica, Inc., San Diego, CA
- Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66045
| |
Collapse
|
3
|
Kamande JW, Lindell MAM, Witek MA, Voorhees PM, Soper SA. Isolation of circulating plasma cells from blood of patients diagnosed with clonal plasma cell disorders using cell selection microfluidics. Integr Biol (Camb) 2018; 10:82-91. [PMID: 29372735 PMCID: PMC5877822 DOI: 10.1039/c7ib00183e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [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: 11/21/2022]
Abstract
Blood samples from patients with plasma cell disorders were analysed for the presence of circulating plasma cells (CPCs) using a microfluidic device modified with monoclonal anti-CD138 antibodies. CPCs were immuno-phenotyped using a CD38/CD56/CD45 panel and identified in 78% of patients with monoclonal gammopathy of undetermined significance (MGUS), all patients with smouldering and symptomatic multiple myeloma (MM), and none in the controls. The burden of CPCs was higher in patients with symptomatic MM compared with MGUS and smouldering MM (p < 0.05). FISH analysis revealed the presence of chromosome 13 deletions in CPCs that correlated with bone marrow results. Point mutations in KRAS were identified, including different mutations from sub-clones derived from the same patient. The microfluidic assay represents a highly sensitive method for enumerating CPCs and allows for the cytogenetic and molecular characterization of CPCs.
Collapse
Affiliation(s)
- Joyce W Kamande
- Department of Biomedical Engineering, The University of North Carolina at Chapel Hill, NC 27599, USA
| | | | | | | | | |
Collapse
|
4
|
Witek MA, Aufforth RD, Wang H, Kamande JW, Jackson JM, Pullagurla SR, Hupert ML, Usary J, Wysham WZ, Hilliard D, Montgomery S, Bae-Jump V, Carey LA, Gehrig PA, Milowsky MI, Perou CM, Soper JT, Whang YE, Yeh JJ, Martin G, Soper SA. Discrete microfluidics for the isolation of circulating tumor cell subpopulations targeting fibroblast activation protein alpha and epithelial cell adhesion molecule. NPJ Precis Oncol 2017; 1. [PMID: 29657983 PMCID: PMC5871807 DOI: 10.1038/s41698-017-0028-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 12/21/2022] Open
Abstract
Circulating tumor cells consist of phenotypically distinct subpopulations that originate from the tumor microenvironment. We report a circulating tumor cell dual selection assay that uses discrete microfluidics to select circulating tumor cell subpopulations from a single blood sample; circulating tumor cells expressing the established marker epithelial cell adhesion molecule and a new marker, fibroblast activation protein alpha, were evaluated. Both circulating tumor cell subpopulations were detected in metastatic ovarian, colorectal, prostate, breast, and pancreatic cancer patients and 90% of the isolated circulating tumor cells did not co-express both antigens. Clinical sensitivities of 100% showed substantial improvement compared to epithelial cell adhesion molecule selection alone. Owing to high purity (>80%) of the selected circulating tumor cells, molecular analysis of both circulating tumor cell subpopulations was carried out in bulk, including next generation sequencing, mutation analysis, and gene expression. Results suggested fibroblast activation protein alpha and epithelial cell adhesion molecule circulating tumor cells are distinct subpopulations and the use of these in concert can provide information needed to navigate through cancer disease management challenges.
Collapse
Affiliation(s)
- Małgorzata A Witek
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047, USA.,Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Rachel D Aufforth
- Department of Surgery, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Hong Wang
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joyce W Kamande
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Joshua M Jackson
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047, USA
| | - Swathi R Pullagurla
- Department of Chemistry, The University of Kansas, Lawrence, KS 66047, USA.,Center of Biomodular Multiscale Systems for Precision Medicine, The University of Kansas, Lawrence, KS 66047, USA
| | - Mateusz L Hupert
- Department of Biomedical Engineering, The University of North Carolina, Chapel Hill, NC 27599, USA.,BioFluidica, Inc., c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill NC27599, USA
| | - Jerry Usary
- Department of Genetics, The University of North Carolina, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Weiya Z Wysham
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, UNC-Chapel Hill, NC 27599, USA
| | - Dawud Hilliard
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Animal Histopathology Core, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephanie Montgomery
- Animal Histopathology Core, The University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pathology and Laboratory Medicine, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Victoria Bae-Jump
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, UNC-Chapel Hill, NC 27599, USA
| | - Lisa A Carey
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Medicine, Division of Hematology and Oncology, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Paola A Gehrig
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, UNC-Chapel Hill, NC 27599, USA
| | - Matthew I Milowsky
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Charles M Perou
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - John T Soper
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, UNC-Chapel Hill, NC 27599, USA
| | - Young E Whang
- Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA
| | - Jen Jen Yeh
- Department of Surgery, The University of North Carolina, Chapel Hill, NC 27599, USA.,Lineberger Comprehensive Cancer Center, The University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Pharmacology, The University of North Carolina, Chapel Hill, NC 27599, USA
| | | | - Steven A Soper
- BioEngineering Program, The University of Kansas, Lawrence, KS 66047, USA.,Department of Mechanical Engineering, The University of Kansas, Lawrence, KS 66047, USA.,Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| |
Collapse
|
5
|
Jackson JM, Witek MA, Kamande JW, Soper SA. Materials and microfluidics: enabling the efficient isolation and analysis of circulating tumour cells. Chem Soc Rev 2017; 46:4245-4280. [PMID: 28632258 PMCID: PMC5576189 DOI: 10.1039/c7cs00016b] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a critical review of microfluidic technologies and material effects on the analyses of circulating tumour cells (CTCs) selected from the peripheral blood of cancer patients. CTCs are a minimally invasive source of clinical information that can be used to prognose patient outcome, monitor minimal residual disease, assess tumour resistance to therapeutic agents, and potentially screen individuals for the early diagnosis of cancer. The performance of CTC isolation technologies depends on microfluidic architectures, the underlying principles of isolation, and the choice of materials. We present a critical review of the fundamental principles used in these technologies and discuss their performance. We also give context to how CTC isolation technologies enable downstream analysis of selected CTCs in terms of detecting genetic mutations and gene expression that could be used to gain information that may affect patient outcome.
Collapse
|
6
|
Nair SV, Witek MA, Jackson JM, Lindell MAM, Hunsucker SA, Sapp T, Perry CE, Hupert ML, Bae-Jump V, Gehrig PA, Wysham WZ, Armistead PM, Voorhees P, Soper SA. Enzymatic cleavage of uracil-containing single-stranded DNA linkers for the efficient release of affinity-selected circulating tumor cells. Chem Commun (Camb) 2016; 51:3266-9. [PMID: 25616078 DOI: 10.1039/c4cc09765c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We report a novel strategy to enzymatically release affinity-selected cells, such as circulating tumor cells (CTCs), from surfaces with high efficiency (∼90%) while maintaining cell viability (>85%). The strategy utilizes single-stranded DNAs that link a capture antibody to the surfaces of a CTC selection device. The DNA linkers contain a uracil residue that can be cleaved.
Collapse
Affiliation(s)
- Soumya V Nair
- Department of Biomedical Engineering, UNC-Chapel Hill, NC, USA.
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
7
|
Jackson JM, Taylor JB, Witek MA, Hunsucker SA, Waugh JP, Fedoriw Y, Shea TC, Soper SA, Armistead PM. Microfluidics for the detection of minimal residual disease in acute myeloid leukemia patients using circulating leukemic cells selected from blood. Analyst 2016; 141:640-51. [PMID: 26523411 PMCID: PMC4701594 DOI: 10.1039/c5an01836f] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 12/23/2022]
Abstract
We report a highly sensitive microfluidic assay to detect minimal residual disease (MRD) in patients with acute myeloid leukemia (AML) that samples peripheral blood to search for circulating leukemic cells (CLCs). Antibodies immobilized within three separate microfluidic devices affinity-selected CLC subpopulations directly from peripheral blood without requiring pre-processing. The microfluidic devices targeted CD33, CD34, and CD117 cell surface antigens commonly expressed by AML leukemic cells so that each subpopulation's CLC numbers could be tracked to determine the onset of relapse. Staining against aberrant markers (e.g. CD7, CD56) identified low levels (11-2684 mL(-1)) of CLCs. The commonly used platforms for the detection of MRD for AML patients are multi-parameter flow cytometry (MFC), typically from highly invasive bone marrow biopsies, or PCR from blood samples, which is limited to <50% of AML patients. In contrast, the microfluidic assay is a highly sensitive blood test that permits frequent sampling for >90% of all AML patients using the markers selected for this study (selection markers CD33, CD34, CD117 and aberrant markers such as CD7 and CD56). We present data from AML patients after stem cell transplant (SCT) therapy using our assay. We observed high agreement of the microfluidic assay with therapeutic treatment and overall outcome. We could detect MRD at an earlier stage compared to both MFC and PCR directly from peripheral blood, obviating the need for a painful bone marrow biopsy. Using the microfluidic assay, we detected MRD 28 days following one patient's SCT and the onset of relapse at day 57, while PCR from a bone marrow biopsy did not detect MRD until day 85 for the same patient. Earlier detection of MRD in AML post-SCT enabled by peripheral blood sampling using the microfluidic assay we report herein can influence curative clinical decisions for AML patients.
Collapse
MESH Headings
- Animals
- Hematopoietic Stem Cell Transplantation
- Humans
- Lab-On-A-Chip Devices
- Leukemia, Myeloid, Acute/blood
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/surgery
- Neoplasm, Residual/blood
- Neoplasm, Residual/diagnosis
- Neoplasm, Residual/pathology
- Neoplastic Cells, Circulating/pathology
- Recurrence
- Sensitivity and Specificity
Collapse
Affiliation(s)
- Joshua M Jackson
- Department of Chemistry, UNC-Chapel Hill, USA. and Center for Biomodular Multi-scale Systems for Precision Medicine, UNC-Chapel Hill, USA
| | - James B Taylor
- Department of Chemistry, UNC-Chapel Hill, USA. and Center for Biomodular Multi-scale Systems for Precision Medicine, UNC-Chapel Hill, USA
| | - Małgorzata A Witek
- Center for Biomodular Multi-scale Systems for Precision Medicine, UNC-Chapel Hill, USA and Department of Biomedical Engineering, UNC-Chapel Hill, USA
| | - Sally A Hunsucker
- University of North Carolina Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, USA.
| | | | - Yuri Fedoriw
- University of North Carolina Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, USA. and Department of Medicine, UNC-Chapel Hill, USA
| | | | - Steven A Soper
- Department of Chemistry, UNC-Chapel Hill, USA. and Center for Biomodular Multi-scale Systems for Precision Medicine, UNC-Chapel Hill, USA
| | - Paul M Armistead
- University of North Carolina Lineberger Comprehensive Cancer Center, UNC-Chapel Hill, USA. and Department of Medicine, UNC-Chapel Hill, USA
| |
Collapse
|
8
|
Hupert ML, Jackson JM, Wang H, Witek MA, Kamande J, Milowsky MI, Whang YE, Soper SA. Arrays of High-Aspect Ratio Microchannels for High-Throughput Isolation of Circulating Tumor Cells (CTCs). Microsyst Technol 2014; 20:1815-1825. [PMID: 25349469 PMCID: PMC4207852 DOI: 10.1007/s00542-013-1941-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Microsystem-based technologies are providing new opportunities in the area of in vitro diagnostics due to their ability to provide process automation enabling point-of-care operation. As an example, microsystems used for the isolation and analysis of circulating tumor cells (CTCs) from complex, heterogeneous samples in an automated fashion with improved recoveries and selectivity are providing new opportunities for this important biomarker. Unfortunately, many of the existing microfluidic systems lack the throughput capabilities and/or are too expensive to manufacture to warrant their widespread use in clinical testing scenarios. Here, we describe a disposable, all-polymer, microfluidic system for the high-throughput (HT) isolation of CTCs directly from whole blood inputs. The device employs an array of high aspect ratio (HAR), parallel, sinusoidal microchannels (25 µm × 150 µm; W × D; AR = 6.0) with walls covalently decorated with anti-EpCAM antibodies to provide affinity-based isolation of CTCs. Channel width, which is similar to an average CTC diameter (12-25 µm), plays a critical role in maximizing the probability of cell/wall interactions and allows for achieving high CTC recovery. The extended channel depth allows for increased throughput at the optimized flow velocity (2 mm/s in a microchannel); maximizes cell recovery, and prevents clogging of the microfluidic channels during blood processing. Fluidic addressing of the microchannel array with a minimal device footprint is provided by large cross-sectional area feed and exit channels poised orthogonal to the network of the sinusoidal capillary channels (so-called Z-geometry). Computational modeling was used to confirm uniform addressing of the channels in the isolation bed. Devices with various numbers of parallel microchannels ranging from 50 to 320 have been successfully constructed. Cyclic olefin copolymer (COC) was chosen as the substrate material due to its superior properties during UV-activation of the HAR microchannels surfaces prior to antibody attachment. Operation of the HT-CTC device has been validated by isolation of CTCs directly from blood secured from patients with metastatic prostate cancer. High CTC sample purities (low number of contaminating white blood cells, WBCs) allowed for direct lysis and molecular profiling of isolated CTCs.
Collapse
Affiliation(s)
- Mateusz L. Hupert
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA
- BioFluidica, Inc., Chapel Hill, NC, USA
| | - Joshua M. Jackson
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
| | - Hong Wang
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Małgorzata A. Witek
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA
| | - Joyce Kamande
- Department of Chemistry, Louisiana State University, Baton Rouge, LA, USA
| | - Matthew I. Milowsky
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC, USA
| | - Young E. Whang
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC, USA
| | - Steven A. Soper
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, UNC School of Medicine, Chapel Hill, NC, USA
- BioFluidica, Inc., Chapel Hill, NC, USA
| |
Collapse
|
9
|
Pullagurla SR, Witek MA, Jackson JM, Lindell MAM, Hupert ML, Nesterova IV, Baird AE, Soper SA. Parallel affinity-based isolation of leukocyte subsets using microfluidics: application for stroke diagnosis. Anal Chem 2014; 86:4058-65. [PMID: 24650222 PMCID: PMC4004188 DOI: 10.1021/ac5007766] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 12/02/2022]
Abstract
![]()
We report the design and performance
of a polymer microfluidic
device that can affinity select multiple types of biological cells
simultaneously with sufficient recovery and purity to allow for the
expression profiling of mRNA isolated from these cells. The microfluidic
device consisted of four independent selection beds with curvilinear
channels that were 25 μm wide and 80 μm deep and were
modified with antibodies targeting antigens specifically expressed
by two different cell types. Bifurcated and Z-configured device geometries
were evaluated for cell selection. As an example of the performance
of these devices, CD4+ T-cells and neutrophils were selected from
whole blood as these cells are known to express genes found in stroke-related
expression profiles that can be used for the diagnosis of this disease.
CD4+ T-cells and neutrophils were simultaneously isolated with purities
>90% using affinity-based capture in cyclic olefin copolymer (COC)
devices with a processing time of ∼3 min. In addition, sufficient
quantities of the cells could be recovered from a 50 μL whole
blood input to allow for reverse transcription-polymerase chain reaction
(RT-PCR) following cell lysis. The expression of genes from isolated
T-cells and neutrophils, such as S100A9, TCRB, and FPR1, was evaluated using RT-PCR.
The modification and isolation procedures demonstrated here can also
be used to analyze other cell types as well where multiple subsets
must be interrogated.
Collapse
Affiliation(s)
- Swathi R Pullagurla
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | | | | | | | | | | | | | | |
Collapse
|
10
|
Battle KN, Jackson JM, Witek MA, Hupert ML, Hunsucker SA, Armistead PM, Soper SA. Solid-phase extraction and purification of membrane proteins using a UV-modified PMMA microfluidic bioaffinity μSPE device. Analyst 2014; 139:1355-63. [PMID: 24487280 PMCID: PMC3970079 DOI: 10.1039/c3an02400h] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We present a novel microfluidic solid-phase extraction (μSPE) device for the affinity enrichment of biotinylated membrane proteins from whole cell lysates. The device offers features that address challenges currently associated with the extraction and purification of membrane proteins from whole cell lysates, including the ability to release the enriched membrane protein fraction from the extraction surface so that they are available for downstream processing. The extraction bed was fabricated in PMMA using hot embossing and was comprised of 3600 micropillars. Activation of the PMMA micropillars by UV/O3 treatment permitted generation of surface-confined carboxylic acid groups and the covalent attachment of NeutrAvidin onto the μSPE device surfaces, which was used to affinity select biotinylated MCF-7 membrane proteins directly from whole cell lysates. The inclusion of a disulfide linker within the biotin moiety permitted release of the isolated membrane proteins via DTT incubation. Very low levels (∼20 fmol) of membrane proteins could be isolated and recovered with ∼89% efficiency with a bed capacity of 1.7 pmol. Western blotting indicated no traces of cytosolic proteins in the membrane protein fraction as compared to significant contamination using a commercial detergent-based method. We highlight future avenues for enhanced extraction efficiency and increased dynamic range of the μSPE device using computational simulations of different micropillar geometries to guide future device designs.
Collapse
Affiliation(s)
- Katrina N. Battle
- Department of Chemistry, Louisiana State University, 232 Choppin Hall, Baton Rouge, LA 70803-1804, USA
| | - Joshua M. Jackson
- Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
| | - Małgorzata A. Witek
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
| | - Mateusz L. Hupert
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
- BioFluidica, LLC, c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill, NC, 27599
| | - Sally A. Hunsucker
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Paul M. Armistead
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC, USA
| | - Steven A. Soper
- Department of Chemistry, University of North Carolina, Campus Box 3290, Chapel Hill, NC 27599-3290, USA
- Department of Biomedical Engineering, University of North Carolina,152 MacNider Hall Campus Box 7575 Chapel Hill, NC 27599-7575, USA
- BioFluidica, LLC, c/o Carolina Kick-Start, 321 Bondurant Hall, Chapel Hill, NC, 27599
- School of Nano-Bioscience and Chemical Engineering, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
| |
Collapse
|
11
|
Jackson JM, Witek MA, Hupert ML, Brady C, Pullagurla S, Kamande J, Aufforth RD, Tignanelli CJ, Torphy RJ, Yeh JJ, Soper SA. UV activation of polymeric high aspect ratio microstructures: ramifications in antibody surface loading for circulating tumor cell selection. Lab Chip 2014; 14:106-17. [PMID: 23900277 PMCID: PMC4182936 DOI: 10.1039/c3lc50618e] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The need to activate thermoplastic surfaces using robust and efficient methods has been driven by the fact that replication techniques can be used to produce microfluidic devices in a high production mode and at low cost, making polymer microfluidics invaluable for in vitro diagnostics, such as circulating tumor cell (CTC) analysis, where device disposability is critical to mitigate artifacts associated with sample carryover. Modifying the surface chemistry of thermoplastic devices through activation techniques can be used to increase the wettability of the surface or to produce functional scaffolds to allow for the covalent attachment of biologics, such as antibodies for CTC recognition. Extensive surface characterization tools were used to investigate UV activation of various surfaces to produce uniform and high surface coverage of functional groups, such as carboxylic acids in microchannels of different aspect ratios. We found that the efficiency of the UV activation process is highly dependent on the microchannel aspect ratio and the identity of the thermoplastic substrate. Colorimetric assays and fluorescence imaging of UV-activated microchannels following EDC/NHS coupling of Cy3-labeled oligonucleotides indicated that UV-activation of a PMMA microchannel with an aspect ratio of ~3 was significantly less efficient toward the bottom of the channel compared to the upper sections. This effect was a consequence of the bulk polymer's damping of the modifying UV radiation due to absorption artifacts. In contrast, this effect was less pronounced for COC. Moreover, we observed that after thermal fusion bonding of the device's cover plate to the substrate, many of the generated functional groups buried into the bulk rendering them inaccessible. The propensity of this surface reorganization was found to be higher for PMMA compared to COC. As an example of the effects of material and microchannel aspect ratios on device functionality, thermoplastic devices for the selection of CTCs from whole blood were evaluated, which required the immobilization of monoclonal antibodies to channel walls. From our results, we concluded the CTC yield and purity of isolated CTCs were dependent on the substrate material with COC producing the highest clinical yields for CTCs as well as better purities compared to PMMA.
Collapse
|
12
|
Dharmasiri U, Njoroge SK, Witek MA, Adebiyi MG, Kamande JW, Hupert ML, Barany F, Soper SA. High-throughput selection, enumeration, electrokinetic manipulation, and molecular profiling of low-abundance circulating tumor cells using a microfluidic system. Anal Chem 2011; 83:2301-9. [PMID: 21319808 DOI: 10.1021/ac103172y] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A circulating tumor cell (CTC) selection microfluidic device was integrated to an electrokinetic enrichment device for preconcentrating CTCs directly from whole blood to allow for the detection of mutations contained within the genomic DNA of the CTCs. Molecular profiling of CTCs can provide important clinical information that cannot be garnered simply by enumerating the selected CTCs. We evaluated our approach using SW620 and HT29 cells (colorectal cancer cell lines) seeded into whole blood as a model system. Because SW620 and HT29 cells overexpress the integral membrane protein EpCAM, they could be immunospecifically selected using a microfluidic device containing anti-EpCAM antibodies immobilized to the walls of a selection bed. The microfluidic device was operated at an optimized flow rate of 2 mm s(-1), which allowed for the ability to process 1 mL of whole blood in <40 min. The selected CTCs were then enzymatically released from the antibody selection surface and hydrodynamically transported through a pair of Pt electrodes for conductivity-based enumeration. The efficiency of CTC selection was found to be 96% ± 4%. Following enumeration, the CTCs were hydrodynamically transported at a flow rate of 1 μL min(-1) to an on-chip electromanipulation unit, where they were electrophoretically withdrawn from the bulk hydrodynamic flow and directed into a receiving reservoir. Using an electric field of 100 V cm(-1), the negatively charged CTCs were enriched into an anodic receiving reservoir to a final volume of 2 μL, providing an enrichment factor of 500. The collected CTCs could then be searched for point mutations using a PCR/LDR/capillary electrophoresis assay. The DNA extracted from the CTCs was subjected to a primary polymerase chain reaction (PCR) with the amplicons used for a ligase detection reaction (LDR) to probe for KRAS oncogenic point mutations. Point mutations in codon 12 of the KRAS gene were successfully detected in the SW620 CTCs for samples containing <10 CTCs in 1 mL of whole blood. However, the HT29 cells did not contain these mutations, consistent with their known genotype.
Collapse
Affiliation(s)
- Udara Dharmasiri
- Center for Bio-Modular Multi-Scale Systems, Louisiana State University, 8000 GSRI Road, Building 3100, Baton Rouge, Louisiana 70820-7403, United States
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Abstract
Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device integration. In this chapter, we will focus exclusively on the front-end processing microfluidic devices and systems for proteome processing, and not on the interface technology of these platforms to mass spectrometry due to the extensive reviews that already exist on these types of interfaces.
Collapse
Affiliation(s)
- John K Osiri
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70817, USA
| | | | | | | |
Collapse
|
14
|
Dharmasiri U, Witek MA, Adams AA, Osiri JK, Hupert ML, Bianchi TS, Roelke DL, Soper SA. Enrichment and detection of Escherichia coli O157:H7 from water samples using an antibody modified microfluidic chip. Anal Chem 2010; 82:2844-9. [PMID: 20218574 DOI: 10.1021/ac100323k] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Low abundant (<100 cells mL(-1)) E. coli O157:H7 cells were isolated and enriched from environmental water samples using a microfluidic chip. The poly(methylmethacrylate), PMMA, chip contained 8 devices, each equipped with 16 curvilinear high aspect ratio channels that were covalently decorated with polyclonal anti-O157 antibodies (pAb) and could search for rare cells through a pAb mediated process. The chip could process independently 8 different samples or one sample using 8 different parallel inputs to increase volume processing throughput. After cell enrichment, cells were released and enumerated using benchtop real-time quantitative polymerase chain reaction (PCR), targeting genes which effectively discriminated the O157:H7 serotype from other nonpathogenic bacteria. The recovery of target cells from water samples was determined to be approximately 72%, and the limit-of-detection was found to be 6 colony forming units (cfu) using the slt1 gene as a reporter. We subsequently performed analysis of lake and wastewater samples. The simplicity in manufacturing and ease of operation makes this device attractive for the selection of pathogenic species from a variety of water supplies suspected of containing bacterial pathogens at extremely low frequencies.
Collapse
Affiliation(s)
- Udara Dharmasiri
- Center for Bio-Modular Multi-Scale Systems, Louisiana State University, 8000 G.SRI Road, Bldg. 3100, Baton Rouge, Louisiana 70820-7403, USA
| | | | | | | | | | | | | | | |
Collapse
|
15
|
Njoroge SK, Witek MA, Hupert ML, Soper SA. Microchip electrophoresis of Alu elements for gender determination and inference of human ethnic origin. Electrophoresis 2010; 31:981-90. [PMID: 20309932 DOI: 10.1002/elps.200900641] [Citation(s) in RCA: 9] [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] [Indexed: 01/28/2023]
Abstract
We performed a series of multi-locus PCRs followed by the rapid and efficient microchip electrophoretic sorting of Alu products with LIF detection. Five polymorphic human-specific Alu insertions (RC5, A1, PV92, TPA and ACE) were used for inference of human ethnicity and two monomorphic Alu insertions for sex typing, one fixed on the X chromosome (AluSTXa) and the other on the Y chromosome (AluSTYa). These markers were used to generate unique DNA profiles for five different DNA samples. The PCR-based assays used primers that flank the insertion point to determine genotypes based on the presence or absence of the Alu element. A1, RC5, PV92, TPA and ACE were used for ethnicity determinations and have two alleles, each indicating the presence (+) or absence (-) of the Alu element on the paired chromosomes, which results in three genotypes (+/+, +/- or -/-). RC5 and A1 did not show ethnic heterogeneity resulting in a homozygous (-/-) genotype, which correctly inferred that DNA samples originating from a Caucasian male and an Asian male were not of African ancestry. The results from the five Alu markers indicated that these Alu loci could assist in identifying the individual's ethnicity using microchip electrophoresis in under 15 min of separation time. Using microchip electrophoresis and mixed genotype ratios, male DNA-to-female DNA of 1:9, corresponding to a ratio of Y-to-X chromosomes of 1:19, was also detected for both AluSTXa and AluSTYa to provide gender identification without requiring separation of female from male cells prior to the assay.
Collapse
Affiliation(s)
- Samuel K Njoroge
- Department of Chemistry and Center for BioModular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA, USA.
| | | | | | | |
Collapse
|
16
|
Abstract
Efficient selection and enumeration of low-abundance biological cells are highly important in a variety of applications. For example, the clinical utility of circulating tumor cells (CTCs) in peripheral blood is recognized as a viable biomarker for the management of various cancers, in which the clinically relevant number of CTCs per 7.5 ml of blood is two to five. Although there are several methods for isolating rare cells from a variety of heterogeneous samples, such as immunomagnetic-assisted cell sorting and fluorescence-activated cell sorting, they are fraught with challenges. Microsystem-based technologies are providing new opportunities for selecting and isolating rare cells from complex, heterogeneous samples. Such approaches involve reductions in target-cell loss, process automation, and minimization of contamination issues. In this review, we introduce different application areas requiring rare cell analysis, conventional techniques for their selection, and finally microsystem approaches for low-abundance-cell isolation and enumeration.
Collapse
Affiliation(s)
- Udara Dharmasiri
- Departments of Chemistry, Louisiana State University, Baton Rouge, 70803, USA.
| | | | | | | |
Collapse
|
17
|
Park DSW, Hupert ML, Witek MA, You BH, Datta P, Guy J, Lee JB, Soper SA, Nikitopoulos DE, Murphy MC. A titer plate-based polymer microfluidic platform for high throughput nucleic acid purification. Biomed Microdevices 2008; 10:21-33. [PMID: 17659445 DOI: 10.1007/s10544-007-9106-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
A 96-well solid-phase reversible immobilization (SPRI) reactor plate was designed to demonstrate functional titer plate-based microfluidic platforms. Nickel, large area mold inserts were fabricated using an SU-8 based, UV-LIGA technique on 150 mm diameter silicon substrates. Prior to UV exposure, the prebaked SU-8 resist was flycut to reduce the total thickness variation to less than 5 mum. Excellent UV lithography results, with highly vertical sidewalls, were obtained in the SU-8 by using an UV filter to remove high absorbance wavelengths below 350 nm. Overplating of nickel in the SU-8 patterns produced high quality, high precision, metal mold inserts, which were used to replicate titer plate-based SPRI reactors using hot embossing of polycarbonate (PC). Optimized molding conditions yielded good feature replication fidelity and feature location integrity over the entire surface area. Thermal fusion bonding of the molded PC chips at 150 degrees C resulted in leak-free sealing, which was verified in leakage tests using a fluorescent dye. The assembled SPRI reactor was used for simple, fast purification of genomic DNA from whole cell lysates of several bacterial species, which was verified by PCR amplification of the purified genomic DNA.
Collapse
Affiliation(s)
- D S-W Park
- Center for Bio-Modular Multi-Scale Systems, Louisiana State University, Baton Rouge, LA 70803, USA
| | | | | | | | | | | | | | | | | | | |
Collapse
|
18
|
Witek MA, Hupert ML, Park DSW, Fears K, Murphy MC, Soper SA. 96-well polycarbonate-based microfluidic titer plate for high-throughput purification of DNA and RNA. Anal Chem 2008; 80:3483-91. [PMID: 18355091 DOI: 10.1021/ac8002352] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report a simple and effective method for the high-throughput purification of a variety of nucleic acids (NAs) from whole cell lysates or whole blood using a photactivated polycarbonate solid-phase reversible immobilization (PPC-SPRI) microfluidic chip. High-throughput operation was achieved by placing 96 purification beds, each containing an array of 3800 20 microm diameter posts, on a single 3" x 5" polycarbonate (PC) wafer fabricated by hot embossing. All beds were interconnected through a common microfluidic network that permitted parallel access through the use of a vacuum and syringe pump for delivery of immobilization buffer (IB) and effluent. The PPC-SPRI purification was accomplished by condensation of NAs onto a UV-modified PC surface in the presence of the IB comprised of polyethylene glycol, NaCl, and ethanol with a composition dependent on the length of the NAs to be isolated and the identity of the sample matrix. The performance of the device was validated by quantification of the recovered material following PCR (for DNA) or RT-PCR (for RNA). The extraction bed load capacity of NAs was 206 +/- 93 ng for gDNA and 165 +/- 81 ng for TRNA from Escherichia coli. Plate-to-plate variability was found to be 35 +/- 10%. The purification process was fast (<30 min) and easy to automate, and the low cost of wafer fabrication makes it appropriate for single-use applications.
Collapse
Affiliation(s)
- Małgorzata A Witek
- Center for Bio-Modular Multi-Scale Systems, Louisiana State University and Agricultural and Mechanical College, 8000 GSRI Road, Baton Rouge, Louisiana 70820, USA
| | | | | | | | | | | |
Collapse
|
19
|
Witek MA, Llopis SD, Wheatley A, McCarley RL, Soper SA. Purification and preconcentration of genomic DNA from whole cell lysates using photoactivated polycarbonate (PPC) microfluidic chips. Nucleic Acids Res 2006; 34:e74. [PMID: 16757572 PMCID: PMC1475748 DOI: 10.1093/nar/gkl146] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We discuss the use of a photoactivated polycarbonate (PPC) microfluidic chip for the solid-phase, reversible immobilization (SPRI) and purification of genomic DNA (gDNA) from whole cell lysates. The surface of polycarbonate was activated by UV radiation resulting in a photo-oxidation reaction, which produced a channel surface containing carboxylate groups. The gDNA was selectively captured on this photoactivated surface in an immobilization buffer, which consisted of 3% polyethylene glycol, 0.4 M NaCl and 70% ethanol. The methodology reported herein is similar to conventional SPRI in that surface-confined carboxylate groups are used for the selective immobilization of DNA; however, no magnetic beads or a magnetic field are required. As observed by UV spectroscopy, a load of ∼7.6 ± 1.6 µg/ml of gDNA was immobilized onto the PPC bed. The recovery of DNA following purification was estimated to be 85 ± 5%. The immobilization and purification assay using this PPC microchip could be performed within ∼25 min as follows: (i) DNA immobilization ∼6 min, (ii) chip washout with ethanol 10 min, and (iii) drying and gDNA desorption ∼6 min. The PPC microchip could also be used for subsequent assays with no substantial loss in recovery, no observable carryover and no need for ‘reactivation’ of the PC surface with UV light.
Collapse
Affiliation(s)
- Małgorzata A. Witek
- Center for Biomodular Multi-Scale Systems, Louisiana State UniversityBaton Rouge, LA 70803, USA
- Department of Chemistry, Louisiana State University232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Shawn D. Llopis
- Center for Biomodular Multi-Scale Systems, Louisiana State UniversityBaton Rouge, LA 70803, USA
- Department of Chemistry, Louisiana State University232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Abigail Wheatley
- Department of Chemistry, Louisiana State University232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Robin L. McCarley
- Center for Biomodular Multi-Scale Systems, Louisiana State UniversityBaton Rouge, LA 70803, USA
- Department of Chemistry, Louisiana State University232 Choppin Hall, Baton Rouge, LA 70803, USA
| | - Steven A. Soper
- Center for Biomodular Multi-Scale Systems, Louisiana State UniversityBaton Rouge, LA 70803, USA
- Department of Chemistry, Louisiana State University232 Choppin Hall, Baton Rouge, LA 70803, USA
- To whom correspondence should be addressed. Tel: 1 225 578 1527; Fax: 1 225 578 3458;
| |
Collapse
|
20
|
Witek MA, Swain GM. Aliphatic polyamine oxidation response variability and stability at boron-doped diamond thin-film electrodes as studied by flow-injection analysis. Anal Chim Acta 2001. [DOI: 10.1016/s0003-2670(01)01055-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
|