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Zhang X, Wang X, Shi B, Li J, Fan Y, Li Y, Shi C, Ma C. A biphasic accelerated strand exchange amplification strategy for culture-independent and rapid detection of Salmonella enterica in food samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024. [PMID: 38855899 DOI: 10.1039/d4ay00613e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Salmonella enterica is a common foodborne pathogen that can cause food poisoning in humans. The organism also infects and causes disease in animals. Rapid and sensitive detection of S. enterica is essential to prevent the spread of this pathogen. Traditional technologies for the extraction and detection of this pathogen from complex food matrices are cumbersome and time-consuming. In this study, we introduced a novel strategy of biphasic assay integrated with an accelerated strand exchange amplification (ASEA) method for efficient detection of S. enterica without culture or other extraction procedures. Food samples are rapidly dried, resulting in a physical fluidic network inside the dried food matrix, which allows polymerases and primers to access the target DNA and initiate ASEA. The dried food matrix is defined as the solid phase, while amplification products are enriched in the supernatant (liquid phase) and generate fluorescence signals. The analytical performances demonstrated that this strategy was able to specifically identify S. enterica and did not show any cross-reaction with other common foodborne pathogens. For artificially spiked food samples, the strategy can detect 5.0 × 101 CFU mL-1S. enterica in milk, 1.0 × 102 CFU g-1 in duck, scallop or lettuce, and 1.0 × 103 CFU g-1 in either oyster or cucumber samples without pre-enrichment of the target pathogen. We further validated the strategy using 82 real food samples, and this strategy showed 92% sensitivity. The entire detection process can be finished, sample-to-answer, within 50 min, dramatically decreasing the detection time. Therefore, we believe that the proposed method enables rapid and sensitive detection of S. enterica and holds great promise for the food safety industry.
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Affiliation(s)
- Xiaojun Zhang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Xiujuan Wang
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Binghui Shi
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Junfeng Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Yaofang Fan
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Yong Li
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
| | - Chao Shi
- Qingdao Nucleic Acid Rapid Testing International Science and Technology Cooperation Base, College of Life Sciences, Department of Pathogenic Biology, School of Basic Medicine, Department of Clinical Laboratory, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, PR China
| | - Cuiping Ma
- Shandong Provincial Key Laboratory of Biochemical Engineering, Qingdao Nucleic Acid Rapid Detection Engineering Research Center, College of Marine Science and Biological Engineering, Qingdao University of Science and Technology, Qingdao, 266042, PR China.
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2
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Sen S, Bhowmik P, Tiwari S, Peleg Y, Bandyopadhyay B. Versatility of reverse transcriptase loop-mediated isothermal amplification (RT-LAMP) from diagnosis of early pathological infection to mutation detection in organisms. Mol Biol Rep 2024; 51:211. [PMID: 38270670 DOI: 10.1007/s11033-023-09110-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 12/05/2023] [Indexed: 01/26/2024]
Abstract
Loop-mediated isothermal amplification (LAMP) is a rapid, state-of-the-art DNA amplification technology, used primarily for the quick diagnosis and early identification of microbial infection, caused by pathogens such as virus, bacteria and malaria. A target DNA can be amplified within 30 min using the LAMP reaction, taking place at a steady temperature. The LAMP method uses four or six primers to bind eight regions of a target DNA and has a very high specificity. The devices used for conducting LAMP are usually simple since the LAMP method is an isothermal process. When LAMP is coupled with Reverse Transcription (RT), it allows direct detection of RNA in a sample. This greatly enhances the efficiency of diagnosis of RNA viruses in a sample. Recently, the rampant spread of COVID-19 demanded such a rapid, simple, and cost-effective Point of Care Test (PoCT) for the accurate diagnosis of this pandemic. Loop-mediated isothermal amplification (LAMP) assays are not only used for the detection of microbial pathogens, but there are various other applications such as detection of genetic mutations in food and various organisms. In this review, various implementations of RT-LAMP techniques would be discussed.
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Affiliation(s)
- Srishti Sen
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Priyanka Bhowmik
- Department of Biological Sciences, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Shubhangi Tiwari
- School of Bioscience, Engineering and Technology, VIT Bhopal University, Bhopal, Madhya Pradesh, India
| | - Yoav Peleg
- Structural Proteomics Unit (SPU), Life Sciences Core Facilities (LSCF), Weizmann Institute of Science, Rehovot, Israel
| | - Boudhayan Bandyopadhyay
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India.
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3
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Pandey S, McCoy SS, Stobdan T, Sahoo D. Quantitative mRNA expression measurement at home. Sci Rep 2024; 14:1013. [PMID: 38200031 PMCID: PMC10781964 DOI: 10.1038/s41598-023-49651-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
mRNA measurement is dominated by RT-PCR, which requires expensive laboratory equipment and personnel with advanced degrees. Loop-mediated isothermal amplification (LAMP) is a versatile technique for detecting target DNA and RNA. The sensitivity of LAMP in early reports has been below that of the standard RT-PCR tests. Here, we report the use of a fluorescence-based RT-LAMP protocol to measure CDX2 expression patterns, which match extremely well to the standards of sophisticated RT-PCR techniques (r = 0.99, p < 0.001). The assay works on diverse sample types such as cDNA, mRNA, and direct tissue sample testing in 25 min compared to more than 3 h for RT-PCR. We have developed a new protocol for designing RT-LAMP primers that reduce false positives due to self-amplification and improve quantification. A simple device with a 3D-printed box enables the measurement of mRNA expression at home, outdoors, and point-of-care setting.
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Affiliation(s)
- Sonalisa Pandey
- Shanvi, San Diego, CA, USA
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0703, Leichtag Building 132, La Jolla, CA, 92093-0703, USA
| | - Sara Safa McCoy
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0703, Leichtag Building 132, La Jolla, CA, 92093-0703, USA
- Department of Computer Science and Engineering, Jacob's School of Engineering, University of California San Diego, La Jolla, USA
| | - Tsering Stobdan
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0703, Leichtag Building 132, La Jolla, CA, 92093-0703, USA
| | - Debashis Sahoo
- Shanvi, San Diego, CA, USA.
- Department of Pediatrics, University of California San Diego, 9500 Gilman Drive, MC 0703, Leichtag Building 132, La Jolla, CA, 92093-0703, USA.
- Department of Computer Science and Engineering, Jacob's School of Engineering, University of California San Diego, La Jolla, USA.
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4
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A culture-free biphasic approach for sensitive and rapid detection of pathogens in dried whole-blood matrix. Proc Natl Acad Sci U S A 2022; 119:e2209607119. [PMID: 36161889 DOI: 10.1073/pnas.2209607119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Blood stream infections (BSIs) cause high mortality, and their rapid detection remains a significant diagnostic challenge. Timely and informed administration of antibiotics can significantly improve patient outcomes. However, blood culture, which takes up to 5 d for a negative result, followed by PCR remains the gold standard in diagnosing BSI. Here, we introduce a new approach to blood-based diagnostics where large blood volumes can be rapidly dried, resulting in inactivation of the inhibitory components in blood. Further thermal treatments then generate a physical microscale and nanoscale fluidic network inside the dried matrix to allow access to target nucleic acid. The amplification enzymes and primers initiate the reaction within the dried blood matrix through these networks, precluding any need for conventional nucleic acid purification. High heme background is confined to the solid phase, while amplicons are enriched in the clear supernatant (liquid phase), giving fluorescence change comparable to purified DNA reactions. We demonstrate single-molecule sensitivity using a loop-mediated isothermal amplification reaction in our platform and detect a broad spectrum of pathogens, including gram-positive methicillin-resistant and methicillin-susceptible Staphylococcus aureus bacteria, gram-negative Escherichia coli bacteria, and Candida albicans (fungus) from whole blood with a limit of detection (LOD) of 1.2 colony-forming units (CFU)/mL from 0.8 to 1 mL of starting blood volume. We validated our assay using 63 clinical samples (100% sensitivity and specificity) and significantly reduced sample-to-result time from over 20 h to <2.5 h. The reduction in instrumentation complexity and costs compared to blood culture and alternate molecular diagnostic platforms can have broad applications in healthcare systems in developed world and resource-limited settings.
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5
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Zhang KS, Nadkarni AV, Paul R, Martin AM, Tang SKY. Microfluidic Surgery in Single Cells and Multicellular Systems. Chem Rev 2022; 122:7097-7141. [PMID: 35049287 DOI: 10.1021/acs.chemrev.1c00616] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Microscale surgery on single cells and small organisms has enabled major advances in fundamental biology and in engineering biological systems. Examples of applications range from wound healing and regeneration studies to the generation of hybridoma to produce monoclonal antibodies. Even today, these surgical operations are often performed manually, but they are labor intensive and lack reproducibility. Microfluidics has emerged as a powerful technology to control and manipulate cells and multicellular systems at the micro- and nanoscale with high precision. Here, we review the physical and chemical mechanisms of microscale surgery and the corresponding design principles, applications, and implementations in microfluidic systems. We consider four types of surgical operations: (1) sectioning, which splits a biological entity into multiple parts, (2) ablation, which destroys part of an entity, (3) biopsy, which extracts materials from within a living cell, and (4) fusion, which joins multiple entities into one. For each type of surgery, we summarize the motivating applications and the microfluidic devices developed. Throughout this review, we highlight existing challenges and opportunities. We hope that this review will inspire scientists and engineers to continue to explore and improve microfluidic surgical methods.
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Affiliation(s)
- Kevin S Zhang
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Ambika V Nadkarni
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States.,Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California 94158, United States
| | - Rajorshi Paul
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Adrian M Martin
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
| | - Sindy K Y Tang
- Department of Mechanical Engineering, Stanford University, Stanford, California 94305, United States
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6
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Ahmed R, Augustine R, Valera E, Ganguli A, Mesaeli N, Ahmad IS, Bashir R, Hasan A. Spatial mapping of cancer tissues by OMICS technologies. Biochim Biophys Acta Rev Cancer 2021; 1877:188663. [PMID: 34861353 DOI: 10.1016/j.bbcan.2021.188663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 11/15/2021] [Accepted: 11/26/2021] [Indexed: 12/14/2022]
Abstract
Spatial mapping of heterogeneity in gene expression in cancer tissues can improve our understanding of cancers and help in the rapid detection of cancers with high accuracy and reliability. Significant advancements have been made in recent years in OMICS technologies, which possess the strong potential to be applied in the spatial mapping of biopsy tissue samples and their molecular profiling to a single-cell level. The clinical application of OMICS technologies in spatial profiling of cancer tissues is also advancing. The current review presents recent advancements and prospects of applying OMICS technologies to the spatial mapping of various analytes in cancer tissues. We benchmark the current state of the art in the field to advance existing OMICS technologies for high throughput spatial profiling. The factors taken into consideration include spatial resolution, types of biomolecules, number of different biomolecules that can be detected from the same assay, labeled versus label-free approaches, and approximate time required for each assay. Further advancements are still needed for the widespread application of OMICs technologies in performing fast and high throughput spatial mapping of cancer tissues as well as their effective use in research and clinical applications.
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Affiliation(s)
- Rashid Ahmed
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar; Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA
| | - Robin Augustine
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar
| | - Enrique Valera
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
| | - Anurup Ganguli
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA
| | - Nasrin Mesaeli
- Department of Biochemistry, Weill Cornell Medicine in Qatar, Qatar Foundation, Doha, Qatar
| | - Irfan S Ahmad
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA
| | - Rashid Bashir
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana Champaign, IL, USA; Department of Bioengineering, University of Illinois at Urbana Champaign, IL, USA; Carle Illinois College of Medicine, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| | - Anwarul Hasan
- Department of Mechanical and Industrial Engineering, College of Engineering, Qatar University, Doha 2713, Qatar; Biomedical Research Center (BRC), Qatar University, Doha 2713, Qatar.
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7
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Leal-Calvo T, Avanzi C, Mendes MA, Benjak A, Busso P, Pinheiro RO, Sarno EN, Cole ST, Moraes MO. A new paradigm for leprosy diagnosis based on host gene expression. PLoS Pathog 2021; 17:e1009972. [PMID: 34695167 PMCID: PMC8568100 DOI: 10.1371/journal.ppat.1009972] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/04/2021] [Accepted: 09/28/2021] [Indexed: 11/18/2022] Open
Abstract
Transcriptional profiling is a powerful tool to investigate and detect human diseases. In this study, we used bulk RNA-sequencing (RNA-Seq) to compare the transcriptomes in skin lesions of leprosy patients or controls affected by other dermal conditions such as granuloma annulare, a confounder for paucibacillary leprosy. We identified five genes capable of accurately distinguishing multibacillary and paucibacillary leprosy from other skin conditions. Indoleamine 2,3-dioxygenase 1 (IDO1) expression alone was highly discriminatory, followed by TLR10, BLK, CD38, and SLAMF7, whereas the HS3ST2 and CD40LG mRNA separated multi- and paucibacillary leprosy. Finally, from the main differentially expressed genes (DEG) and enriched pathways, we conclude that paucibacillary disease is characterized by epithelioid transformation and granuloma formation, with an exacerbated cellular immune response, while multibacillary leprosy features epithelial-mesenchymal transition with phagocytic and lipid biogenesis patterns in the skin. These findings will help catalyze the development of better diagnostic tools and potential host-based therapeutic interventions. Finally, our data may help elucidate host-pathogen interplay driving disease clinical manifestations.
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Affiliation(s)
- Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Charlotte Avanzi
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Mayara Abud Mendes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Andrej Benjak
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Philippe Busso
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Roberta Olmo Pinheiro
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Euzenir Nunes Sarno
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Stewart Thomas Cole
- Global Health Institute, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
| | - Milton Ozório Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Rio de Janeiro, Brazil
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8
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Berger J, Aydin MY, Stavins R, Heredia J, Mostafa A, Ganguli A, Valera E, Bashir R, King WP. Portable Pathogen Diagnostics Using Microfluidic Cartridges Made from Continuous Liquid Interface Production Additive Manufacturing. Anal Chem 2021; 93:10048-10055. [PMID: 34251790 DOI: 10.1021/acs.analchem.1c00654] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Biomedical diagnostics based on microfluidic devices have the potential to significantly benefit human health; however, the manufacturing of microfluidic devices is a key limitation to their widespread adoption. Outbreaks of infectious disease continue to demonstrate the need for simple, sensitive, and translatable tests for point-of-care use. Additive manufacturing (AM) is an attractive alternative to conventional approaches for microfluidic device manufacturing based on injection molding; however, there is a need for development and validation of new AM process capabilities and materials that are compatible with microfluidic diagnostics. In this paper, we demonstrate the development and characterization of AM cartridges using continuous liquid interface production (CLIP) and investigate process characteristics and capabilities of the AM microfluidic device manufacturing. We find that CLIP accurately produces microfluidic channels as small as 400 μm and that it is possible to routinely produce fluid channels as small as 100 μm with high repeatability. We also developed a loop-mediated isothermal amplification (LAMP) assay for detection of E. coli from whole blood directly on the CLIP-based AM microfluidic cartridges, with a 50 cfu/μL limit of detection, validating the use of CLIP processes and materials for pathogen detection. The portable diagnostic platform presented in this paper could be used to investigate and validate other AM processes for microfluidic diagnostics and could be an important component of scaling up the diagnostics for current and future infectious diseases and pandemics.
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Affiliation(s)
- Jacob Berger
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Mehmet Y Aydin
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Robert Stavins
- Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - John Heredia
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Anurup Ganguli
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
| | - William P King
- Holonyak Micro and Nano Technology Laboratory, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Mechanical Science and Engineering, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States.,Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Ganguli A, Mostafa A, Berger J, Lim J, Araud E, Baek J, Stewart de Ramirez SA, Baltaji A, Roth K, Aamir M, Aedma S, Mady M, Mahajan P, Sathe S, Johnson M, White K, Kumar J, Valera E, Bashir R. Reverse Transcription Loop-Mediated Isothermal Amplification Assay for Ultrasensitive Detection of SARS-CoV-2 in Saliva and Viral Transport Medium Clinical Samples. Anal Chem 2021; 93:7797-7807. [PMID: 34033472 DOI: 10.1021/acs.analchem.0c05170] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The COVID-19 pandemic has underscored the shortcomings in the deployment of state-of-the-art diagnostics platforms. Although several polymerase chain reaction (PCR)-based techniques have been rapidly developed to meet the growing testing needs, such techniques often need samples collected through a swab, the use of RNA extraction kits, and expensive thermocyclers in order to successfully perform the test. Isothermal amplification-based approaches have also been recently demonstrated for rapid severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by minimizing sample preparation while also reducing the instrumentation and reaction complexity. In addition, there are limited reports of saliva as the sample source, and some of these indicate inferior sensitivity when comparing reverse transcription loop-mediated isothermal amplification (RT-LAMP) with PCR-based techniques. In this paper, we demonstrate an improved sensitivity assay from saliva using a two-step RT-LAMP assay, where a short 10 min RT step is performed with only B3 and backward inner primers before the final reaction. We show that while the one-step RT-LAMP demonstrates satisfactory results, the optimized two-step approach allows detection of only few molecules per reaction and performs significantly better than the one-step RT-LAMP and conventional two-step RT-LAMP approaches with all primers included in the RT step. We show control measurements with RT-PCR, and importantly, we demonstrate RNA extraction-free RT-LAMP-based assays for detection of SARS-CoV-2 from viral transport media and saliva clinical samples.
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Affiliation(s)
- Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Jongwon Lim
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Elbashir Araud
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Janice Baek
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Sarah A Stewart de Ramirez
- Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, Illinois 61603-3200, United States
| | - Ali Baltaji
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Kelly Roth
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Muhammad Aamir
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Surya Aedma
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mohamed Mady
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Pranav Mahajan
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Sanjivani Sathe
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States
| | - Mark Johnson
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Karen White
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - James Kumar
- Carle Foundation Hospital, Urbana, Illinois 61801-2500, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3028, United States.,Carle Illinois College of Medicine, Urbana, Illinois 61820, United States
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10
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Ganguli A, Mostafa A, Saavedra C, Kim Y, Le P, Faramarzi V, Feathers RW, Berger J, Ramos-Cruz KP, Adeniba O, Diaz GJP, Drnevich J, Wright CL, Hernandez AG, Lin W, Smith AM, Kosari F, Vasmatzis G, Anastasiadis PZ, Bashir R. Three-dimensional microscale hanging drop arrays with geometric control for drug screening and live tissue imaging. SCIENCE ADVANCES 2021; 7:7/17/eabc1323. [PMID: 33893093 PMCID: PMC8064630 DOI: 10.1126/sciadv.abc1323] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 03/05/2021] [Indexed: 05/09/2023]
Abstract
Existing three-dimensional (3D) culture techniques are limited by trade-offs between throughput, capacity for high-resolution imaging in living state, and geometric control. Here, we introduce a modular microscale hanging drop culture where simple design elements allow high replicates for drug screening, direct on-chip real-time or high-resolution confocal microscopy, and geometric control in 3D. Thousands of spheroids can be formed on our microchip in a single step and without any selective pressure from specific matrices. Microchip cultures from human LN229 glioblastoma and patient-derived mouse xenograft cells retained genomic alterations of originating tumors based on mate pair sequencing. We measured response to drugs over time with real-time microscopy on-chip. Last, by engineering droplets to form predetermined geometric shapes, we were able to manipulate the geometry of cultured cell masses. These outcomes can enable broad applications in advancing personalized medicine for cancer and drug discovery, tissue engineering, and stem cell research.
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Affiliation(s)
- A Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - A Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - C Saavedra
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Y Kim
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - P Le
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - V Faramarzi
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - R W Feathers
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - J Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - K P Ramos-Cruz
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - O Adeniba
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - G J Pagan Diaz
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - J Drnevich
- High-Performance Biological Computing, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - C L Wright
- DNA Services Lab, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - A G Hernandez
- DNA Services Lab, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - W Lin
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - A M Smith
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61820, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - F Kosari
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - G Vasmatzis
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - P Z Anastasiadis
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA.
- Department of Cancer Biology, Mayo Clinic, Jacksonville, FL 32224, USA
| | - R Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
- Mayo-Illinois Alliance for Technology-Based Healthcare, Urbana, IL, USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61820, USA
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11
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Ganguli A, Mostafa A, Berger J, Aydin MY, Sun F, Ramirez SASD, Valera E, Cunningham BT, King WP, Bashir R. Rapid isothermal amplification and portable detection system for SARS-CoV-2. Proc Natl Acad Sci U S A 2020; 117:22727-22735. [PMID: 32868442 PMCID: PMC7502724 DOI: 10.1073/pnas.2014739117] [Citation(s) in RCA: 246] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay protocols and primer sequences become widely known, many laboratories perform diagnostic tests using methods such as RT-PCR or reverse transcription loop mediated isothermal amplification (RT-LAMP). Here, we report an RT-LAMP isothermal assay for the detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus and demonstrate the assay on clinical samples using a simple and accessible point-of-care (POC) instrument. We characterized the assay by dipping swabs into synthetic nasal fluid spiked with the virus, moving the swab to viral transport medium (VTM), and sampling a volume of the VTM to perform the RT-LAMP assay without an RNA extraction kit. The assay has a limit of detection (LOD) of 50 RNA copies per μL in the VTM solution within 30 min. We further demonstrate our assay by detecting SARS-CoV-2 viruses from 20 clinical samples. Finally, we demonstrate a portable and real-time POC device to detect SARS-CoV-2 from VTM samples using an additively manufactured three-dimensional cartridge and a smartphone-based reader. The POC system was tested using 10 clinical samples, and was able to detect SARS-CoV-2 from these clinical samples by distinguishing positive samples from negative samples after 30 min. The POC tests are in complete agreement with RT-PCR controls. This work demonstrates an alternative pathway for SARS-CoV-2 diagnostics that does not require conventional laboratory infrastructure, in settings where diagnosis is required at the point of sample collection.
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Affiliation(s)
- Anurup Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Ariana Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Jacob Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Mehmet Y Aydin
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Fu Sun
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Sarah A Stewart de Ramirez
- Emergency Medicine, University of Illinois College of Medicine at Peoria & OSF Healthcare, Peoria, IL 61637
| | - Enrique Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Brian T Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - William P King
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801
| | - Rashid Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801;
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, Urbana, IL 61801
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12
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Ganguli A, Mostafa A, Berger J, Aydin M, Sun F, Valera E, Cunningham BT, King WP, Bashir R. Rapid Isothermal Amplification and Portable Detection System for SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.05.21.108381. [PMID: 32511358 PMCID: PMC7263486 DOI: 10.1101/2020.05.21.108381] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
The COVID-19 pandemic provides an urgent example where a gap exists between availability of state-of-the-art diagnostics and current needs. As assay details and primer sequences become widely known, many laboratories could perform diagnostic tests using methods such as RT-PCR or isothermal RT-LAMP amplification. A key advantage of RT-LAMP based approaches compared to RT-PCR is that RT-LAMP is known to be robust in detecting targets from unprocessed samples. In addition, RT-LAMP assays are performed at a constant temperature enabling speed, simplicity, and point-of-use testing. Here, we provide the details of an RT-LAMP isothermal assay for the detection of SARS-CoV-2 virus with performance comparable to currently approved tests using RT-PCR. We characterize the assay by introducing swabs in virus spiked synthetic nasal fluids, moving the swab to viral transport medium (VTM), and using a volume of that VTM for performing the amplification without an RNA extraction kit. The assay has a Limit-of-Detection (LOD) of 50 RNA copies/μL in the VTM solution within 20 minutes, and LOD of 5000 RNA copies/μL in the nasal solution. Additionally, we show the utility of this assay for real-time point-of-use testing by demonstrating detection of SARS-CoV-2 virus in less than 40 minutes using an additively manufactured cartridge and a smartphone-based reader. Finally, we explore the speed and cost advantages by comparing the required resources and workflows with RT-PCR. This work could accelerate the development and availability of SARS-CoV-2 diagnostics by proving alternatives to conventional laboratory benchtop tests.
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Affiliation(s)
- A. Ganguli
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
| | - A. Mostafa
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
| | - J. Berger
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
| | - M. Aydin
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
| | - F. Sun
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
| | - E. Valera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
| | - B. T. Cunningham
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
| | - W. P. King
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Carle Illinois College of Medicine, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
| | - R. Bashir
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory, University of Illinois at Urbana-Champaign, Illinois, USA
- Department of Mechanical Science and Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
- Carle Illinois College of Medicine, Urbana, IL, USA
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Illinois, USA
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13
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Infrared Spectroscopic Imaging Visualizes a Prognostic Extracellular Matrix-Related Signature in Breast Cancer. Sci Rep 2020; 10:5442. [PMID: 32214177 PMCID: PMC7096505 DOI: 10.1038/s41598-020-62403-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 02/27/2020] [Indexed: 12/22/2022] Open
Abstract
Molecular analysis techniques such as gene expression analysis and proteomics have contributed greatly to our understanding of cancer heterogeneity. In prior studies, gene expression analysis was shown to stratify patient outcome on the basis of tumor-microenvironment associated genes. A specific gene expression profile, referred to as ECM3 (Extracellular Matrix Cluster 3), indicated poorer survival in patients with grade III tumors. In this work, we aimed to visualize the downstream effects of this gene expression profile onto the tissue, thus providing a spatial context to altered gene expression profiles. Using infrared spectroscopic imaging, we identified spectral patterns specific to the ECM3 gene expression profile, achieving a high spectral classification performance of 0.87 as measured by the area under the curve of the receiver operating characteristic curve. On a patient level, we correctly identified 20 out of 22 ECM3 group patients and 19 out of 20 non-ECM3 group patients by using this spectroscopic imaging-based classifier. By comparing pixels that were identified as ECM3 or non-ECM3 with H&E and IHC images, we were also able to observe an association between tissue morphology and the gene expression clusters, showing the ability of our method to capture broad outcome associated features from infrared images.
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14
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Lin Q, Ye X, Huang Z, Yang B, Fang X, Chen H, Kong J. Graphene Oxide-Based Suppression of Nonspecificity in Loop-Mediated Isothermal Amplification Enabling the Sensitive Detection of Cyclooxygenase-2 mRNA in Colorectal Cancer. Anal Chem 2019; 91:15694-15702. [PMID: 31725282 DOI: 10.1021/acs.analchem.9b03861] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Cyclooxygenase-2 (COX2) mRNA represents a key biomarker for identifying subjects with colorectal cancer (CRC), while there is still no rapid and sensitive detection method for COX2 mRNA. Loop-mediated isothermal amplification (LAMP) is extensively developed for the amplification of nucleic acids; however, its application is frequently hindered by serious nonspecific amplification. Herein, this work reported a graphene oxide (GO)-based LAMP method to enable the one-step detection of COX2 mRNA in cancer cells and serum samples. We found that GO greatly enhanced the specificity of LAMP through decreasing nonspecific hybridization and the fluorescence background signal because of the simultaneous adsorption of single-stranded primers and DNA staining dyes on GO. The detection limit of developed GO-based LAMP was 2 orders of magnitude more sensitive compared to that of classical LAMP. Then a GO-based reverse transcription (RT)-LAMP strategy was further developed and applied to detect COX2 mRNA in CRC cancer cells and serum samples with high specificity. The GO-based LAMP platform with advantages of low cost, simplicity, high specificity, and sensitivity holds considerable potential for real-time fluorescence monitoring of nucleic acid amplification in a wide range of fields.
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Affiliation(s)
- Qiuyuan Lin
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Xin Ye
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Zhipeng Huang
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Bin Yang
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Xueen Fang
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Hui Chen
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
| | - Jilie Kong
- Department of Chemistry , Fudan University , Shanghai 200438 , P. R. China
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15
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Utilizing multiplex fluor LAMPs to illuminate multiple gene expressions in situ. PLoS One 2019; 14:e0223333. [PMID: 31584968 PMCID: PMC6777751 DOI: 10.1371/journal.pone.0223333] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/18/2019] [Indexed: 11/23/2022] Open
Abstract
In situ gene expression detection is the best way to determine temporal and spatial differences in gene expression. However, in situ hybridization procedures are inherently difficult to execute and typically suffer from degradation of sample tissues, limited sensitivity to genes with low expression, high background, and limitation to single gene detections. We propose to utilize an isothermal gene amplification technique, LAMP (Loop-Mediated Isothermal Amplification), to solve these problems in a novel way. LAMP greatly amplifies the signal of expressed genes and can use multiple sets of primers and different fluorescent-labeled probes to produce multiplex gene detection. LAMP is a rapid, isothermal reaction that reduces the handling and degradation of tissue by cutting down on the washing steps required by other methods. Using this technique, we have successfully amplified 3 target genes, have produced positive fluorescent in situ results simultaneously for two genes. We have also demonstrated that LAMP can be used to exploit standard NBT/BCIP (nitro-blue tetrazolium chloride/5-bromo-4-chloro-3'-indolyphosphate p-toluidine salt) detection of single expression. In situ LAMP is a robust and applicable method that can be exploited for detection of gene expression in plant species, as well as in animals and bacteria.
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16
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Real-time fluorescence loop-mediated isothermal amplification assay for rapid and sensitive detection of Streptococcus gallolyticus subsp. gallolyticus associated with colorectal cancer. Anal Bioanal Chem 2019; 411:6877-6887. [PMID: 31388715 DOI: 10.1007/s00216-019-02059-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/24/2019] [Accepted: 07/31/2019] [Indexed: 12/26/2022]
Abstract
The increasing threat of Streptococcus gallolyticus subsp. gallolyticus (SGG) infections has gained considerable attention for its strong association with colorectal cancer (CRC). Herein, we proposed real-time fluorescence loop-mediated isothermal amplification (LAMP) as a novel, simple, rapid, and highly sensitive assay for identifying SGG for the first time. This assay was capable of detecting SGG with initial DNA concentrations ranging from 102 to 108 copies per microliter, under isothermal conditions within 30 min via real-time fluorescence monitoring. Our method was tested for specific identification of SGG strains without cross-reaction with other Streptococcus gallolyticus subspecies and Escherichia coli. The developed LAMP shows a superior performance with shorter time and higher sensitivity compared with conventional polymerase chain reaction (PCR). Significantly, this proposed approach was successfully applied for detecting SGG in clinical urine samples, which is non-invasive diagnosis, showing excellent accuracy and reliability to discriminate healthy controls and CRC patients. For comparison, these samples were also tested against PCR assay. These results yielded an analytical sensitivity of 100% and a specificity of 100% for SGG testing using LAMP. The findings suggest LAMP can be employed for detecting SGG infections which is useful for diagnosis and screening of CRC.
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17
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Zeng T, Dai H. Single-Cell RNA Sequencing-Based Computational Analysis to Describe Disease Heterogeneity. Front Genet 2019; 10:629. [PMID: 31354786 PMCID: PMC6640157 DOI: 10.3389/fgene.2019.00629] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/17/2019] [Indexed: 12/25/2022] Open
Abstract
The trillions of cells in the human body can be viewed as elementary but essential biological units that achieve different body states, but the low resolution of previous cell isolation and measurement approaches limits our understanding of the cell-specific molecular profiles. The recent establishment and rapid growth of single-cell sequencing technology has facilitated the identification of molecular profiles of heterogeneous cells, especially on the transcription level of single cells [single-cell RNA sequencing (scRNA-seq)]. As a novel method, the robustness of scRNA-seq under changing conditions will determine its practical potential in major research programs and clinical applications. In this review, we first briefly presented the scRNA-seq-related methods from the point of view of experiments and computation. Then, we compared several state-of-the-art scRNA-seq analysis frameworks mainly by analyzing their performance robustness on independent scRNA-seq datasets for the same complex disease. Finally, we elaborated on our hypothesis on consensus scRNA-seq analysis and summarized the potential indicative and predictive roles of individual cells in understanding disease heterogeneity by single-cell technologies.
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Affiliation(s)
- Tao Zeng
- Key Laboratory of Systems Biology, Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
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18
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The Spatial and Genomic Hierarchy of Tumor Ecosystems Revealed by Single-Cell Technologies. Trends Cancer 2019; 5:411-425. [PMID: 31311656 DOI: 10.1016/j.trecan.2019.05.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 05/23/2019] [Accepted: 05/28/2019] [Indexed: 12/23/2022]
Abstract
Many malignancies display heterogeneous features that support cancer progression. Emerging high-resolution methods provide a view of heterogeneity that recognizes the influence of diverse cell types and cell states of the tumor microenvironment. Here we outline a hierarchical organization of tumor heterogeneity from a genomic perspective, summarize the origins of spatially patterned metabolic features, and review recent developments in single-cell and spatially resolved techniques for genome-wide study of multicellular tissues. We also discuss how integrating these approaches can yield new insights into human cancer and emerging immune therapies. Applying these technologies for the analysis of primary tumors, patient-derived xenografts, and in vitro systems holds great promise for understanding the hierarchical structure and environmental influences that underlie tumor ecosystems.
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