1
|
Bao M, Waitkus J, Liu L, Chang Y, Xu Z, Qin P, Chen J, Du K. Micro- and nanosystems for the detection of hemorrhagic fever viruses. LAB ON A CHIP 2023; 23:4173-4200. [PMID: 37675935 DOI: 10.1039/d3lc00482a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Hemorrhagic fever viruses (HFVs) are virulent pathogens that can cause severe and often fatal illnesses in humans. Timely and accurate detection of HFVs is critical for effective disease management and prevention. In recent years, micro- and nano-technologies have emerged as promising approaches for the detection of HFVs. This paper provides an overview of the current state-of-the-art systems for micro- and nano-scale approaches to detect HFVs. It covers various aspects of these technologies, including the principles behind their sensing assays, as well as the different types of diagnostic strategies that have been developed. This paper also explores future possibilities of employing micro- and nano-systems for the development of HFV diagnostic tools that meet the practical demands of clinical settings.
Collapse
Affiliation(s)
- Mengdi Bao
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Jacob Waitkus
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Li Liu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Yu Chang
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| | - Zhiheng Xu
- Department of Industrial Engineering, Rochester Institute of Technology, Rochester, NY, USA
| | - Peiwu Qin
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Juhong Chen
- Department of Biological Systems Engineering, Virginia Tech, Blacksburg, VA, USA
| | - Ke Du
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
| |
Collapse
|
2
|
Park JS, Pisanic T, Zhang Y, Wang TH. Ligation-Enabled Fluorescence-Coding PCR for High-Dimensional Fluorescence-Based Nucleic Acid Detection. Anal Chem 2021; 93:2351-2358. [PMID: 33427441 DOI: 10.1021/acs.analchem.0c04221] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Polymerase chain reaction (PCR) is by far the most commonly used method of nucleic acid amplification and has likewise been employed for a plethora of diagnostic purposes. Nonetheless, multiplexed PCR-based detection schemes have hitherto been largely limited by technical challenges associated with nonspecific interactions and other limitations inherent to traditional fluorescence-based assays. Here, we describe a novel strategy for multiplexed PCR-based analysis called Ligation-eNabled fluorescence-Coding PCR (LiNC PCR) that exponentially enhances the multiplexing capability of standard fluorescence-based PCR assays. The technique relies upon a simple, preliminary ligation reaction in which target DNA sequences are converted to PCR template molecules with distinct endpoint fluorescence signatures. Universal TaqMan probes are used to create target-specific multicolor fluorescence signals that can be readily decoded to identify amplified targets of interest. We demonstrate the LiNC PCR technique by implementing a two-color-based assay for detection of 10 ovarian cancer epigenetic biomarkers at analytical sensitivities as low as 60 template molecules with no detectable target cross-talk. Overall, LiNC PCR provides a simple and inexpensive method for achieving high-dimensional multiplexing that can be implemented in manifold molecular diagnostic applications.
Collapse
Affiliation(s)
- Joon Soo Park
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Thomas Pisanic
- Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ye Zhang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Institute for NanoBioTechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| |
Collapse
|
3
|
Tabe Y, Kawase Y, Miyake K, Satoh N, Aritaka N, Isobe Y, Oshimi K, Komatsu N, Miida T, Ohsaka A. Identification of Bcl-2/IgH fusion sequences using real-time PCR and chip-based microcapillary electrophoresis. Clin Chem Lab Med 2011; 49:809-15. [DOI: 10.1515/cclm.2011.141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
4
|
Kern W, Schoch C, Haferlach T, Schnittger S. Monitoring of minimal residual disease in acute myeloid leukemia. Crit Rev Oncol Hematol 2005; 56:283-309. [PMID: 16213150 DOI: 10.1016/j.critrevonc.2004.06.004] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2004] [Revised: 06/24/2004] [Accepted: 06/24/2004] [Indexed: 11/17/2022] Open
Abstract
Monitoring minimal residual disease (MRD) becomes increasingly important in the risk-adapted management of patients with acute myeloid leukemia (AML). The two most sensitive and quantitative methods for MRD detection are multiparameter flow cytometry (MFC) and real-time polymerase chain reaction (QRT-PCR). Fusion gene-specific PCR in AML is based on the RNA level, and thus in contrast to MFC expression levels rather than cell counts are assessed. For both methods independent prognostic values have been shown. The strong power of MFC has been shown mainly in the assessment of early clearance of the malignant clone. MRD levels in AML with fusion genes have the strongest prognostic power after the end of consolidation therapy. In addition, with QRT-PCR highly predictive initial expression levels can be assessed. With both methods early detection of relapse is possible. So far, validated PCR-based MRD was done with fusion genes that are detectable in only 20-25% of all AML MFC is superior since it is applicable for most AML. However, QRT-PCR is still more sensitive in most cases. Thus, it is desirable to establish new molecular markers for PCR-based studies. Large clinical trials will determine the role and place of immunologic and PCR-based monitoring in the prognostic stratification of patients with AML.
Collapse
Affiliation(s)
- Wolfgang Kern
- Laboratory for Leukemia Diagnostics, Ludwig-Maximilians-University, University Hospital Grosshadern, Department of Internal Medicine III, 81366 Muenchen, Germany.
| | | | | | | |
Collapse
|
5
|
Bowman A, Jones D, Medeiros LJ, Luthra R. Quantitative PCR detection of t(14;18) bcl-2/JH fusion sequences in follicular lymphoma patients: comparison of peripheral blood and bone marrow aspirate samples. J Mol Diagn 2005; 6:396-400. [PMID: 15507680 PMCID: PMC1867490 DOI: 10.1016/s1525-1578(10)60537-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
In patients with follicular lymphoma (FL), it is unresolved whether peripheral blood (PB) can replace bone marrow (BM) aspirate samples for detection of bcl-2/JH fusion sequences that result from the t(14;18)(q32;q21). We compare here the results of quantitative polymerase chain reaction (q-PCR) analysis for bcl-2/JH involving the major breakpoint cluster region (mbr) on paired PB and BM aspirate samples from 60 consecutive FL patients. There was a significant correlation between the level of bcl-2/JH fusion sequence obtained from PB and BM aspirate samples (r = 0.886), with 82% of samples showing less than one log of difference. Patients who had histological evidence of FL involving concurrent BM biopsy specimens had moderate to high levels of bcl-2/JH in both PB and BM aspirate samples, allowing unequivocal determination of translocation status (median bcl-2/JH to cyclophilin level was 8.014%). In contrast, patients with no detectable FL in their BM biopsy specimens often showed low levels of bcl-2/JH in both PB and BM aspirate samples (bcl-2/JH to cyclophilin median level = 0.006%), in a range similar to background levels that could be detected in patients without FL (n = 15, median bcl-2 mbr/JH to cyclophilin level = 0.002%). We conclude that PB can be used in place of BM aspirate samples to test for the presence of bcl-2 mbr/JH fusion sequence in FL patients and that either PB or BM aspirate testing yields a rough approximation of the degree of BM involvement by FL. However, in patients with minimal levels of bcl-2/JH in PB or BM aspirate samples, confirmation of this result by testing the primary tumor is recommended to confirm the presence of an identical bcl-2/JH fusion sequence and exclude false-positive results.
Collapse
Affiliation(s)
- Alex Bowman
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77054, USA
| | | | | | | |
Collapse
|
6
|
van der Velden VHJ, Hochhaus A, Cazzaniga G, Szczepanski T, Gabert J, van Dongen JJM. Detection of minimal residual disease in hematologic malignancies by real-time quantitative PCR: principles, approaches, and laboratory aspects. Leukemia 2003; 17:1013-34. [PMID: 12764363 DOI: 10.1038/sj.leu.2402922] [Citation(s) in RCA: 411] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Detection of minimal residual disease (MRD) has prognostic value in many hematologic malignancies, including acute lymphoblastic leukemia, acute myeloid leukemia, chronic myeloid leukemia, non-Hodgkin's lymphoma, and multiple myeloma. Quantitative MRD data can be obtained with real-time quantitative PCR (RQ-PCR) analysis of immunoglobulin and T-cell receptor gene rearrangements, breakpoint fusion regions of chromosome aberrations, fusion-gene transcripts, aberrant genes, or aberrantly expressed genes, their application being dependent on the type of disease. RQ-PCR analysis can be performed with SYBR Green I, hydrolysis (TaqMan) probes, or hybridization (LightCycler) probes, as detection system in several RQ-PCR instruments. Dependent on the type of MRD-PCR target, different types of oligonucleotides can be used for specific detection, such as an allele-specific oligonucleotide (ASO) probe, an ASO forward primer, an ASO reverse primer, or germline probe and primers. To assess the quantity and quality of the RNA/DNA, one or more control genes must be included. Finally, the interpretation of RQ-PCR MRD data needs standardized criteria and reporting of MRD data needs international uniformity. Several European networks have now been established and common guidelines for data analysis and for reporting of MRD data are being developed. These networks also include standardization of technology as well as regular quality control rounds, both being essential for the introduction of RQ-PCR-based MRD detection in multicenter clinical treatment protocols.
Collapse
Affiliation(s)
- V H J van der Velden
- Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Dr Molewaterplein 50, Rotterdam 3015 GE, The Netherlands
| | | | | | | | | | | |
Collapse
|
7
|
Hirt C, Schüler F, Dölken G. Minimal residual disease (MRD) in follicular lymphoma in the era of immunotherapy with rituximab. Semin Cancer Biol 2003; 13:223-31. [PMID: 12959353 DOI: 10.1016/s1044-579x(03)00017-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The t(14;18)-translocation can be detected by PCR analysis in more than 90% of cytogenetically t(14;18)-positive follicular lymphomas (FLs), thus providing an easily accessible marker for molecular disease monitoring. Various technical aspects of the detection of residual lymphoma cells as well as the prognostic and clinical significance of the detection of minimal residual disease (MRD) after radiotherapy, chemotherapy and therapy with the monoclonal antibody rituximab are discussed. Up to now the comparability of the different studies investigating minimal residual disease in follicular lymphoma patients is hampered by the use of a variety of PCR techniques. A more standardized quantitative approach based on the real-time PCR technique will provide a powerful tool for the evaluation and optimization of therapy for each individual patient.
Collapse
Affiliation(s)
- Carsten Hirt
- Department of Hematology and Oncology, University Medical Center, Ernst-Moritz-Arndt-University, Sauerbruchstrasse, D-17487 Greifswald, Germany.
| | | | | |
Collapse
|
8
|
Sanchez-Vega B, Vega F, Hai S, Medeiros LJ, Luthra R. Real-Time t(14;18)(q32;q21) PCR assay combined with high-resolution capillary electrophoresis: a novel and rapid approach that allows accurate quantitation and size determination of bcl-2/JH fusion sequences. Mod Pathol 2002; 15:448-53. [PMID: 11950920 DOI: 10.1038/modpathol.3880545] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Follicular lymphoma is characterized by the presence of the t(14;18)(q32;q21) chromosomal translocation that juxtaposes the bcl-2 gene at 18q21 with the immunoglobulin heavy chain (IgH) locus at 14q32. We have previously shown that accurate quantitation of t(14;18)-carrying cells in follicular lymphoma patients can be achieved by non-gel-based real-time TaqMan polymerase chain reaction (PCR; Applied Biosystems, Foster City, CA). Since our report, several studies have demonstrated that real-time PCR is highly sensitive and a reliable tool for evaluating treatment effectiveness and for following minimal residual disease in follicular lymphoma patients. Unfortunately, currently available real-time PCR methods do not determine the size of the amplification product, which is useful for excluding contamination and is commonly used as presumptive evidence of clonal identity or disparity when multiple samples from the same patient are analyzed. We describe a modified real-time PCR assay that rapidly allows accurate quantitation and precise determination of the size of the t(14;18) fusion sequence without the need for gel electrophoresis. In this assay, a consensus immunoglobulin heavy chain-joining region gene (JH) primer labeled at its 5' end with the fluorescent dye NED (Applied Biosystems) is included in the real-time PCR assay and thus is incorporated into the bcl-2/JH fusion product. The JH-NED primer did not interfere with the TaqMan probe fluorescent signal or target detection and allowed subsequent amplicon size determination by semiautomated high-resolution capillary electrophoresis.
Collapse
MESH Headings
- Chromosomes, Human, Pair 14/genetics
- Chromosomes, Human, Pair 18/genetics
- DNA, Neoplasm/genetics
- Electrophoresis, Capillary/methods
- HL-60 Cells
- Humans
- Immunoglobulin Joining Region/genetics
- Lymphoma, Follicular/genetics
- Lymphoma, Follicular/pathology
- Oncogene Proteins, Fusion/genetics
- Polymerase Chain Reaction/methods
- Proto-Oncogene Proteins c-bcl-2/genetics
- Sensitivity and Specificity
- Translocation, Genetic
Collapse
Affiliation(s)
- Beatriz Sanchez-Vega
- Division of Pathology and Laboratory Medicine, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77054, USA
| | | | | | | | | |
Collapse
|
9
|
Greiner TC. Advances in molecular hematopathology: T-cell receptor gamma and bcl-2 genes. THE AMERICAN JOURNAL OF PATHOLOGY 1999; 154:7-9. [PMID: 9916911 PMCID: PMC1853455 DOI: 10.1016/s0002-9440(10)65243-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- T C Greiner
- University of Nebraska Medical Center, Omaha 68198-3135, USA.
| |
Collapse
|
10
|
Bohling SD, King TC, Wittwer CT, Elenitoba-Johnson KS. Rapid simultaneous amplification and detection of the MBR/JH chromosomal translocation by fluorescence melting curve analysis. THE AMERICAN JOURNAL OF PATHOLOGY 1999; 154:97-103. [PMID: 9916923 PMCID: PMC1853425 DOI: 10.1016/s0002-9440(10)65255-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Polymerase chain reaction (PCR) amplification and product analysis for the detection of chromosomal translocations, such as the t(14;18), has traditionally been a two-step process. PCR product detection has generally entailed gel electrophoresis and/or hybridization or sequencing for confirmation of assay specificity. Using a microvolume fluorimeter integrated with a thermal cycler and a PCR-compatible double-stranded DNA (dsDNA) binding fluorescent dye (SYBR Green I), we investigated the feasibility of simultaneous thermal amplification and detection of MBR/JH translocation products by fluorescence melting curve analysis. We analyzed DNA from 30 cases of lymphoproliferative disorders comprising 19 cases of previously documented MBR/JH-positive follicle center lymphoma and 11 reactive lymphadenopathies. The samples were coded and analyzed blindly for the presence of MBR/JH translocations by fluorescence melting curve analysis. We also performed dilutional assays using the MBR/JH-positive cell line SUDHL-6. Multiplex PCR for MBR/JH and beta-globin was used to simultaneously assess sample adequacy. All (100%) of the 19 cases previously determined to be MBR/JH positive by conventional PCR analysis showed a characteristic sharp decrease in fluorescence at approximately 90 degrees C by melting curve analysis after amplification. Fluorescence melting peaks obtained by plotting the negative derivative of fluorescence over temperature (-dF/dT) versus temperature (T) showed melting temperatures (Tm) at 88.85+/-1.15 degrees C. In addition, multiplex assays using both MBR/JH and beta-globin primers yielded easily distinguishable fluorescence melting peaks at approximately 90 degrees C and 81.2 degrees C, respectively. Dilutional assays revealed that fluorescence melting curve analysis was more sensitive than conventional PCR and agarose gel electrophoresis with ultraviolet transillumination by as much as 100-fold. Simultaneous amplification and fluorescence melting curve analysis is a simple, reliable, and sensitive method for the detection of MBR/JH translocations. The feasibility of specific PCR product detection without electrophoresis or utilization of expensive fluorescently labeled probes makes this method attractive for routine molecular diagnostics.
Collapse
Affiliation(s)
- S D Bohling
- Department of Pathology, University of Utah Health Sciences Center and ARUP Institute for Clinical and Experimental Pathology, Salt Lake City 84132, USA
| | | | | | | |
Collapse
|
11
|
Luthra R, McBride JA, Cabanillas F, Sarris A. Novel 5' exonuclease-based real-time PCR assay for the detection of t(14;18)(q32;q21) in patients with follicular lymphoma. THE AMERICAN JOURNAL OF PATHOLOGY 1998; 153:63-8. [PMID: 9665466 PMCID: PMC1852934 DOI: 10.1016/s0002-9440(10)65546-0] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The exonuclease-based real-time polymerase chain reaction (PCR) exploits 5'-->3' exonuclease activity of Taq polymerase and measures PCR product accumulation as the reaction proceeds through a dual-labeled fluorogenic probe. The utility of this exonuclease-based PCR assay as a rapid alternative to conventional PCR for follicular lymphoma-associated t(14;18)(q32;q21) was evaluated in this study. The specificity of the assay for t(14;18) involving bcl-2 and immunoglobulin heavy-chain joining region (JH) genes was assessed by analyzing DNA from 53 patients (38 B-cell non-Hodgkin's lymphomas and 15 nonneoplastic proliferations) and correlating the exonuclease PCR data with conventional PCR results. bcl-2/JH fusion sequences were detected by exonuclease-based PCR in 24 of 25 cases shown to be bcl-2 rearranged by conventional PCR. Fusion sequences were not detected in patients who were negative by conventional PCR. The overall concordance between the two assays was 98% (52 of 53 cases concordant positive or negative). In a serial dilution study using t(14;18)-positive cell line DNA, exonuclease-based PCR detected fusion sequences at DNA concentrations of 5 pg, equivalent to 0.6 to 0.8 genomes per reaction. Thus, this study demonstrated that exonuclease-based PCR for t(14;18) is both specific and highly sensitive. The elimination of the post-PCR amplicon detection steps and the ability to quantitate the input target DNA sequences make this assay ideal for routine diagnostics and monitoring minimal residual disease.
Collapse
Affiliation(s)
- R Luthra
- Department of Pathology, The University of Texas M.D. Anderson Cancer Center, Houston 77030, USA
| | | | | | | |
Collapse
|